From 2785caf1882324ffaeced04f6ec2aede2b57cda6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 27 May 2022 09:25:13 -0600
Subject: [PATCH 0001/1248] Seperate out nrepr loops into ones for matrixcn off
 and on

---
 src/biogeochem/CNCStateUpdate1Mod.F90 | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90
index 717b524383..8c6fc11602 100644
--- a/src/biogeochem/CNCStateUpdate1Mod.F90
+++ b/src/biogeochem/CNCStateUpdate1Mod.F90
@@ -430,18 +430,18 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
             end if
             cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_livestemc_patch(p)*dt
             cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_livestemc_storage_patch(p)*dt
-            cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_reproductivec_patch(p,1)*dt
-            cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_reproductivec_storage_patch(p,1)*dt
+            do k = 1, nrepr
+                cs_veg%cpool_patch(p)          = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_reproductivec_patch(p,k)*dt
+                cs_veg%cpool_patch(p)          = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt
+            end do
             if(.not. use_matrixcn)then
                cs_veg%livestemc_patch(p)          = cs_veg%livestemc_patch(p)          + cf_veg%cpool_to_livestemc_patch(p)*dt
                cs_veg%livestemc_storage_patch(p)  = cs_veg%livestemc_storage_patch(p)  + cf_veg%cpool_to_livestemc_storage_patch(p)*dt
                do k = 1, nrepr
-                  cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_patch(p,k)*dt
-                  cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) &
-                       + cf_veg%cpool_to_reproductivec_patch(p,k)*dt
-                  cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt
+                  cs_veg%reproductivec_patch(p,k)         = cs_veg%reproductivec_patch(p,k) &
+                                                          + cf_veg%cpool_to_reproductivec_patch(p,k)*dt
                   cs_veg%reproductivec_storage_patch(p,k) = cs_veg%reproductivec_storage_patch(p,k) &
-                       + cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt
+                                                          + cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt
                end do
             else
                ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)

From 266cc6212e1f8bbdd303575b32bfffd4da5bff46 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 22 Aug 2022 12:06:43 -0600
Subject: [PATCH 0002/1248] Apply dust branch based off of release-clm5.0.34 to
 dev branch

Do a diff of the dmleung DUSTEMIS branch based off of release-clm5.0.34
to ctsm5.1.dev106 and apply the diff after updating the paths for
namelist_definition and lnd_import_export.F90 in the diff.

git apply -3 dust.diff

Diffs with conflicts:
	modified:   src/biogeochem/DUSTMod.F90
	modified:   src/biogeophys/SoilStateInitTimeConstMod.F90
	modified:   src/main/controlMod.F90
	modified:   src/cpl/mct/lnd_import_export.F90

The changes in lnd_import_export were to change a check for negative
LW that seems to be removed in the latest version.
---
 .../namelist_definition_ctsm.xml              |   9 +
 src/biogeochem/DUSTMod.F90                    | 466 ++++++++++++++++--
 src/biogeophys/SoilStateInitTimeConstMod.F90  |  24 +-
 src/biogeophys/SoilStateType.F90              |   8 +-
 src/main/clm_varctl.F90                       |   1 +
 src/main/controlMod.F90                       |  13 +
 src/main/lnd2atmMod.F90                       |   8 +
 7 files changed, 496 insertions(+), 33 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index a08795dd1f..ddc5d8372c 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -2796,4 +2796,13 @@ use case.)
 
 </entry>
 
+<!-- added by dmleung to CLM5, 17 Dec 2021 -->
+<!-- roughness factor f_eff   -dmleung, 22 Apr 2020 -->
+<entry id="rough_fct" type="char*256" input_pathname="abs" category="datasets"
+       group="clm_inparm" valid_values="" >
+Full pathname of time-invariant roughness factor dataset for calculating drag partition of dust emission.
+</entry>
+
+
+
 </namelist_definition>
diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index a86531ba62..7f7c92722c 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -15,7 +15,8 @@ module DUSTMod
   use shr_kind_mod         , only : r8 => shr_kind_r8 
   use shr_log_mod          , only : errMsg => shr_log_errMsg
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
-  use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr
+  use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr, &
+                                    natpft_lb, natpft_ub, natpft_size     ! -dmleung added 24 Jul 2022
   use clm_varcon           , only : grav, spval
   use landunit_varcon      , only : istcrop, istsoil
   use clm_varctl           , only : iulog
@@ -30,6 +31,9 @@ module DUSTMod
   use LandunitType         , only : lun
   use ColumnType           , only : col
   use PatchType            , only : patch
+  use clm_instur           , only : wt_lunit, wt_nat_patch  ! dmleung added 24 Jul 2022
+  use landunit_varcon      , only : istsoil, istcrop        ! dmleung added 24 Jul 2022 (refering to main/landunit_varcon.F90, for wt_lunit, istsoil=1 is nat veg, istcrop=2 is crop)
+  use pftconMod            , only : noveg              ! dmleung added 24 Jul 2022
   !  
   ! !PUBLIC TYPES
   implicit none
@@ -60,7 +64,32 @@ module DUSTMod
      real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
      real(r8), pointer, private :: vlc_trb_4_patch           (:)   ! turbulent deposition velocity 4(m/s)
      real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! basin factor
-
+     !########### added by dmleung 27 Nov 2021 ########################################################################
+     real(r8), pointer, private :: dst_emiss_coeff_patch     (:)   ! dust emission coefficient (unitless)
+     real(r8), pointer, private :: wnd_frc_thr_patch         (:)   ! wet fluid threshold (m/s)
+     real(r8), pointer, private :: wnd_frc_thr_dry_patch     (:)   ! dry fluid threshold (m/s)
+     real(r8), pointer, private :: lnd_frc_mble_patch        (:)   ! land mobile fraction -dmleung
+     real(r8), pointer, private :: liq_frac_patch            (:)   ! liquid fraction of total water
+     real(r8), pointer, private :: wnd_frc_soil_patch        (:)   ! soil wind friction velocity (m/s)
+     real(r8), pointer, private :: gwc_patch                 (:)   ! gravimetric water content (kg/kg)
+     !########### added by dmleung 2 Dec 2021 #########################################################################
+     real(r8), pointer, private :: intrmtncy_fct_patch       (:)   ! intermittency factor, accounting for turbulence shutting down dust emissions (unitless)
+     real(r8), pointer, private :: stblty_patch              (:)   ! stability parameter for checking stability condition (stblty < 0 is unstable atmosphere)
+     real(r8), pointer, private :: u_mean_slt_patch          (:)   ! wind speed 0.1 m level of dust saltation (m/s)
+     real(r8), pointer, private :: u_sd_slt_patch            (:)   ! sd of wind speed 0.1 m level of dust saltation (m/s)
+     real(r8), pointer, private :: u_fld_thr_patch           (:)   ! fluid threshold wind speed 0.1 m level of dust saltation (m/s)
+     real(r8), pointer, private :: u_impct_thr_patch         (:)   ! impact threshold wind speed at 0.1 m level of dust saltation (m/s)
+     real(r8), pointer, private :: thr_crs_rate_patch        (:)   ! threshold crossing rate (unitless)
+     real(r8), pointer, private :: prb_crs_fld_thr_patch     (:)   ! probability of wind speed crossing fluid threshold
+     real(r8), pointer, private :: prb_crs_impct_thr_patch   (:)   ! probability of wind speed crossing impact threshold
+     !########### added by dmleung 17 Dec 2021 ########################################################################
+     real(r8), pointer, private :: ustar_patch               (:)   ! output friction velocity for SP mode (m/s)
+     !########### added by dmleung 20 Dec 2021 ########################################################################
+     real(r8), pointer, private :: ssr_patch                 (:)   ! [dimless] integrated shear stress ratiio, defined by Okin (2008) and then integrated by Caroline Pierre et al. (2014)
+     real(r8), pointer, private :: lai_patch                 (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin's drag partition, averaged to landunit level
+     real(r8), pointer, private :: frc_thr_rghn_fct_patch    (:)   ! [dimless] hybrid drag partition (or called roughness) factor
+     !########### added by dmleung 28 Jul 2022 ########################################################################
+     real(r8), pointer, private :: wnd_frc_thr_std_patch     (:)   ! standardized fluid threshold friction velocity (m/s)
    contains
 
      procedure , public  :: Init
@@ -113,7 +142,32 @@ subroutine InitAllocate(this, bounds)
     allocate(this%vlc_trb_3_patch           (begp:endp))        ; this%vlc_trb_3_patch           (:)   = nan
     allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
     allocate(this%mbl_bsn_fct_col           (begc:endc))        ; this%mbl_bsn_fct_col     (:)   = nan
-
+    !#### added by dmleung 27 Nov 2021 #####################################
+    allocate(this%dst_emiss_coeff_patch     (begp:endp))        ; this%dst_emiss_coeff_patch     (:)   = nan
+    allocate(this%wnd_frc_thr_patch         (begp:endp))        ; this%wnd_frc_thr_patch         (:)   = nan
+    allocate(this%wnd_frc_thr_dry_patch     (begp:endp))        ; this%wnd_frc_thr_dry_patch     (:)   = nan
+    allocate(this%lnd_frc_mble_patch        (begp:endp))        ; this%lnd_frc_mble_patch        (:)   = nan
+    allocate(this%wnd_frc_soil_patch        (begp:endp))        ; this%wnd_frc_soil_patch        (:)   = nan
+    allocate(this%gwc_patch                 (begp:endp))        ; this%gwc_patch                 (:)   = nan
+    allocate(this%liq_frac_patch            (begp:endp))        ; this%liq_frac_patch            (:)   = nan
+    !#### added by dmleung 2 Dec 2021 ######################################
+    allocate(this%intrmtncy_fct_patch       (begp:endp))        ; this%intrmtncy_fct_patch       (:)   = nan
+    allocate(this%stblty_patch              (begp:endp))        ; this%stblty_patch              (:)   = nan
+    allocate(this%u_mean_slt_patch          (begp:endp))        ; this%u_mean_slt_patch          (:)   = nan
+    allocate(this%u_sd_slt_patch            (begp:endp))        ; this%u_sd_slt_patch            (:)   = nan
+    allocate(this%u_fld_thr_patch           (begp:endp))        ; this%u_fld_thr_patch           (:)   = nan
+    allocate(this%u_impct_thr_patch         (begp:endp))        ; this%u_impct_thr_patch         (:)   = nan
+    allocate(this%thr_crs_rate_patch        (begp:endp))        ; this%thr_crs_rate_patch        (:)   = nan
+    allocate(this%prb_crs_fld_thr_patch     (begp:endp))        ; this%prb_crs_fld_thr_patch     (:)   = nan
+    allocate(this%prb_crs_impct_thr_patch   (begp:endp))        ; this%prb_crs_impct_thr_patch   (:)   = nan
+    !#### added by dmleung 17 Dec 2021 ######################################
+    allocate(this%ustar_patch               (begp:endp))        ; this%ustar_patch               (:)   = nan
+    !#### added by dmleung 17 Dec 2021 ######################################
+    allocate(this%ssr_patch                 (begp:endp))        ; this%ssr_patch                 (:)   = nan
+    allocate(this%lai_patch                 (begp:endp))        ; this%lai_patch                 (:)   = nan
+    allocate(this%frc_thr_rghn_fct_patch    (begp:endp))        ; this%frc_thr_rghn_fct_patch    (:)   = nan
+    !#### added by dmleung 28 Jul 2022 ######################################
+    allocate(this%wnd_frc_thr_std_patch     (begp:endp))        ; this%wnd_frc_thr_std_patch     (:)   = nan
   end subroutine InitAllocate
 
   !------------------------------------------------------------------------
@@ -158,6 +212,97 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='turbulent deposition velocity 4', &
          ptr_patch=this%vlc_trb_4_patch, default='inactive')
 
+    !#####added by dmleung 27 Nov 2021#########################################
+    this%dst_emiss_coeff_patch(begp:endp) = spval
+    call hist_addfld1d (fname='C_d', units='dimensionless',  &
+         avgflag='A', long_name='dust emission coefficient', &
+         ptr_patch=this%dst_emiss_coeff_patch, set_lake=0._r8, set_urb=0._r8)
+    this%wnd_frc_thr_patch(begp:endp) = spval
+    call hist_addfld1d (fname='WND_FRC_FT', units='m/s',  &
+         avgflag='A', long_name='fluid threshold friction velocity', &
+         ptr_patch=this%wnd_frc_thr_patch, set_lake=0._r8, set_urb=0._r8)
+    this%wnd_frc_thr_dry_patch(begp:endp) = spval
+    call hist_addfld1d (fname='WND_FRC_FT_DRY', units='m/s',  &
+         avgflag='A', long_name='dry fluid threshold friction velocity', &
+         ptr_patch=this%wnd_frc_thr_dry_patch, set_lake=0._r8, set_urb=0._r8)
+    this%wnd_frc_soil_patch(begp:endp) = spval
+    call hist_addfld1d (fname='WND_FRC_SOIL', units='m/s',  &
+         avgflag='A', long_name='soil surface wind friction velocity', &
+         ptr_patch=this%wnd_frc_soil_patch, set_lake=0._r8, set_urb=0._r8)
+    this%lnd_frc_mble_patch(begp:endp) = spval
+    call hist_addfld1d (fname='LND_FRC_MBLE', units='dimensionless',  &
+         avgflag='A', long_name='land mobile fraction', &
+         ptr_patch=this%lnd_frc_mble_patch, set_lake=0._r8, set_urb=0._r8)
+    this%gwc_patch(begp:endp) = spval
+    call hist_addfld1d (fname='GWC', units='kg/kg',  &
+         avgflag='A', long_name='gravimetric water content', &
+         ptr_patch=this%gwc_patch, set_lake=0._r8, set_urb=0._r8)
+    this%liq_frac_patch(begp:endp) = spval
+    call hist_addfld1d (fname='LIQ_FRAC', units='dimensionless',  &
+         avgflag='A', long_name='fraction of total water that is liquid', &
+         ptr_patch=this%liq_frac_patch, set_lake=0._r8, set_urb=0._r8)
+    !#####added by dmleung 2 Dec 2021 #########################################
+    this%u_mean_slt_patch(begp:endp) = spval
+    call hist_addfld1d (fname='U_S_MEAN', units='m/s',  &
+         avgflag='A', long_name='mean wind velocity at saltation level', &
+         ptr_patch=this%u_mean_slt_patch, set_lake=0._r8, set_urb=0._r8)
+    this%u_sd_slt_patch(begp:endp) = spval
+    call hist_addfld1d (fname='U_S_SIGMA', units='m/s',  &
+         avgflag='A', long_name='sd of wind velocity at saltation level', &
+         ptr_patch=this%u_sd_slt_patch, set_lake=0._r8, set_urb=0._r8)
+    this%stblty_patch(begp:endp) = spval
+    call hist_addfld1d (fname='ZETA', units='',  &
+         avgflag='A', long_name='stability parameter', &
+         ptr_patch=this%stblty_patch, set_lake=0._r8, set_urb=0._r8)
+    this%u_fld_thr_patch(begp:endp) = spval
+    call hist_addfld1d (fname='U_FT', units='m/s',  &
+         avgflag='A', long_name='fluid threshold velocity at saltation level', &
+         ptr_patch=this%u_fld_thr_patch, set_lake=0._r8, set_urb=0._r8)
+    this%u_impct_thr_patch(begp:endp) = spval
+    call hist_addfld1d (fname='U_IT', units='m/s',  &
+         avgflag='A', long_name='impact threshold velocity at saltation level', &
+         ptr_patch=this%u_impct_thr_patch, set_lake=0._r8, set_urb=0._r8)
+    this%thr_crs_rate_patch(begp:endp) = spval
+    call hist_addfld1d (fname='ALPHA', units='',  &
+         avgflag='A', long_name='threshold crossing rate', &
+         ptr_patch=this%thr_crs_rate_patch, set_lake=0._r8, set_urb=0._r8)
+    this%prb_crs_fld_thr_patch(begp:endp) = spval
+    call hist_addfld1d (fname='P_FT', units='',  &
+         avgflag='A', long_name='probability of crossing fluid threshold', &
+         ptr_patch=this%prb_crs_fld_thr_patch, set_lake=0._r8, set_urb=0._r8)
+    this%prb_crs_impct_thr_patch(begp:endp) = spval
+    call hist_addfld1d (fname='P_IT', units='',  &
+         avgflag='A', long_name='probability of crossing impact threshold', &
+         ptr_patch=this%prb_crs_impct_thr_patch, set_lake=0._r8, set_urb=0._r8)
+    this%intrmtncy_fct_patch(begp:endp) = spval
+    call hist_addfld1d (fname='ETA', units='',  &
+         avgflag='A', long_name='intermittency factor', &
+         ptr_patch=this%intrmtncy_fct_patch, set_lake=0._r8, set_urb=0._r8)
+    !#####added by dmleung 2 Dec 2021 #########################################
+    this%ustar_patch(begp:endp) = spval
+    call hist_addfld1d (fname='USTAR', units='m/s',  &
+         avgflag='A', long_name='friction velocity', &
+         ptr_patch=this%ustar_patch, set_lake=0._r8, set_urb=0._r8)
+    !#####added by dmleung 20 Dec 2021 ########################################
+    this%ssr_patch(begp:endp) = spval
+    call hist_addfld1d (fname='SSR', units='m/s',  &
+         avgflag='A', long_name='Okin-Pierre shear stress ratio', &
+         ptr_patch=this%ssr_patch, set_lake=0._r8, set_urb=0._r8)
+    this%lai_patch(begp:endp) = spval
+    call hist_addfld1d (fname='LAI', units='m/s',  &
+         avgflag='A', long_name='landunit-mean LAI for Okin-Pierre scheme', &
+         ptr_patch=this%lai_patch, set_lake=0._r8, set_urb=0._r8)
+    this%frc_thr_rghn_fct_patch(begp:endp) = spval
+    call hist_addfld1d (fname='FRC_THR_RGHN_FCT', units='dimensionless',  &
+         avgflag='A', long_name='hybrid drag partition (or roughness) factor', &
+         ptr_patch=this%frc_thr_rghn_fct_patch, set_lake=0._r8, set_urb=0._r8)
+    !#####added by dmleung 28 Jul 2022 ########################################
+    this%wnd_frc_thr_std_patch(begp:endp) = spval
+    call hist_addfld1d (fname='WND_FRC_FT_STD', units='m/s',  &
+         avgflag='A', long_name='standardized fluid threshold friction velocity', &
+         ptr_patch=this%wnd_frc_thr_std_patch, set_lake=0._r8, set_urb=0._r8)
+    !##########################################################################
+
   end subroutine InitHistory
 
   !-----------------------------------------------------------------------
@@ -224,7 +369,7 @@ subroutine DustEmission (bounds, &
     real(r8) :: flx_mss_vrt_dst_ttl(bounds%begp:bounds%endp)
     real(r8) :: frc_thr_wet_fct
     real(r8) :: frc_thr_rgh_fct
-    real(r8) :: wnd_frc_thr_slt
+    !real(r8) :: wnd_frc_thr_slt    ! dmleung commented and put below 2 Dec 2021
     real(r8) :: wnd_rfr_thr_slt
     real(r8) :: wnd_frc_slt
     real(r8) :: lnd_frc_mbl(bounds%begp:bounds%endp)
@@ -235,13 +380,43 @@ subroutine DustEmission (bounds, &
     real(r8) :: sumwt(bounds%begl:bounds%endl) ! sum of weights
     logical  :: found                          ! temporary for error check
     integer  :: index
+    !########### added by dmleung 27 Nov 2021 #########################################
+    real(r8) :: tmp2   ! calculates the dry fluid threshold using Shao and Lu (2000) scheme; replace the tmp1 (Iversen and White, 1982) that was passed from Dustini to DustEmission; tmp2 will be calculated here  23 May 2020 -dmleung
+    real(r8) :: wnd_frc_thr_slt_std ! [m/s] The soil threshold friction speed at standard air density (1.2250 kg/m3) -jfk
+    real(r8) :: frag_expt           ! fragmentation exponent, -dmleung 22 Jun 2021
+    !########### added by dmleung 2 Dec 2021 for intermittency scheme #################
+    real(r8) :: wnd_frc_thr_slt_it  ! [m/s] created for impact threshold friction velocity, dmleung 9 Jun 2021
+    real(r8) :: wnd_frc_thr_slt     ! [m/s] used for wet fluid threshold friction velocity, dmleung 9 Jun 2021
+    !########### added by dmleung 20 Dec 2021 for drag partition effect #################
+    real(r8) :: K_length            ! [dimless] normalized mean interobstacle distance, or called gap length (Okin, 2008)
+    !########### added by dmleung 22 Jul 2022 for LUH2 land cover ####################
+    real(r8) :: bare_frc            ! LUH2 bare soil land cover fraction
+    real(r8) :: veg_frc             ! LUH2 natural vegetation + crop land cover fraction
     !    
     ! constants
     !
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
-    real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
+    !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
+    !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
+    !####### added by dmleung 27 Nov 2021 ###########################################################################
     character(len=*),parameter :: subname = 'DUSTEmission'
+    real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; dmleung suggests 1 or 0.5, and the default 0.3 seems a bit too small -dmleung 27 Nov 2021
+    real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient -jfk
+    real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent -jfk
+    real(r8), parameter :: Ce = 2.0_r8                 ! [dimless] proportionality constant scaling exponential dependence of dust emission coefficient on standardized soil threshold friction speed -jfk
+    real(r8), parameter :: C_tune = 0.05_r8             ! [dimless] global tuning constant for vertical dust flux; set to produce ~same global dust flux in control sim (I_2000) as old parameterization -jfk
+    real(r8), parameter :: wnd_frc_thr_slt_std_min = 0.16_r8 ! [m/s] minimum standardized soil threshold friction speed -jfk
+    real(r8), parameter :: forc_rho_std = 1.2250_r8    ! [kg/m3] density of air at standard pressure (101325) and temperature (293 K) -jfk
+    real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles, dml 23 May 2020
+    !####### added by dmleung 2 Dec 2021 for intermittency ##########################################################
+    real(r8), parameter :: B_it = 0.82_r8              ! [dimless] ratio = u_star_it / u_star_ft0 (may need to change into a fn of moisture later on) -dml
+    real(r8), parameter :: k = 0.4_r8                  ! [dimless] von Karman constant -dml
+    !####### added by dmleung 2 Dec 2021 for Okin (2008) drag partition for plants ##########################################################
+    real(r8), parameter :: f_0 = 0.32_r8               ! [dimless] SSR in the immediate lee of a plant, dimensionless
+    real(r8), parameter :: c_e = 4.8_r8                  ! [dimless] e-folding distance velocity recovery, dimensionless
+    !################################################################################################################
+    !################################################################################################################
     !------------------------------------------------------------------------
 
     associate(                                                         & 
@@ -264,7 +439,34 @@ subroutine DustEmission (bounds, &
          
          mbl_bsn_fct         => dust_inst%mbl_bsn_fct_col            , & ! Input:  [real(r8) (:)   ]  basin factor                                      
          flx_mss_vrt_dst     => dust_inst%flx_mss_vrt_dst_patch      , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
-         flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch    & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
+         flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch  , & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
+         ! the following are added by dmleung 27 Nov 2021
+         dst_emiss_coeff     => dust_inst%dst_emiss_coeff_patch      , & ! Output dust emission coefficient
+         wnd_frc_thr         => dust_inst%wnd_frc_thr_patch          , & ! output impact threshold -dmleung
+         wnd_frc_thr_dry     => dust_inst%wnd_frc_thr_dry_patch      , & ! output dry threshold
+         lnd_frc_mble        => dust_inst%lnd_frc_mble_patch         , & ! -dmleung, 3 Feb 2020
+         wnd_frc_soil        => dust_inst%wnd_frc_soil_patch         , & ! soil friction velocity u_*s = (u_*)(f_eff)
+         gwc                 => dust_inst%gwc_patch                  , & ! output gravimetric water content
+         liq_frac            => dust_inst%liq_frac_patch             , &
+         ! added by dmleung 8 Jul 2019, recoded 2 Dec 2021
+         intrmtncy_fct       => dust_inst%intrmtncy_fct_patch        , &
+         stblty              => dust_inst%stblty_patch               , &
+         u_mean_slt          => dust_inst%u_mean_slt_patch           , &
+         u_sd_slt            => dust_inst%u_sd_slt_patch             , &
+         u_fld_thr           => dust_inst%u_fld_thr_patch            , &
+         u_impct_thr         => dust_inst%u_impct_thr_patch          , &
+         thr_crs_rate        => dust_inst%thr_crs_rate_patch         , &
+         prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , &
+         prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , &
+         ! added by dmleung 17 Dec 2021
+         roughfct            => soilstate_inst%roughfct_patch        , &
+         ustar               => dust_inst%ustar_patch                , & ! Output friction velocity for SP mode
+         ! added by dmleung 20 Dec 2021
+         ssr                 => dust_inst%ssr_patch                  , &
+         lai                 => dust_inst%lai_patch                  , &
+         frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , &
+         ! added by dmleung 28 Jul 2022
+         wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch       &
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -342,6 +544,32 @@ subroutine DustEmission (bounds, &
       do fp = 1,num_nolakep
          p = filter_nolakep(fp)
          flx_mss_vrt_dst_tot(p) = 0.0_r8
+         ! the following are added by dmleung 27 Nov 2021
+         dst_emiss_coeff(p) = 0.0_r8
+         wnd_frc_thr(p) = 0.0_r8
+         wnd_frc_thr_dry(p) = 0.0_r8
+         lnd_frc_mble(p) = 0.0_r8
+         wnd_frc_soil(p) = 0.0_r8
+         gwc(p) = 0.0_r8
+         liq_frac(p) = 0.0_r8
+         ! dmleung's edit, 8 Jul 2019; added by dmleung 2 Dec 2021
+         u_mean_slt(p) = 0.0_r8
+         u_sd_slt(p) = 0.0_r8
+         stblty(p)   = 0.0_r8
+         u_fld_thr(p) = 0.0_r8
+         u_impct_thr(p) = 0.0_r8
+         thr_crs_rate(p) = 0.0_r8
+         prb_crs_fld_thr(p) = 0.0_r8
+         prb_crs_impct_thr(p) = 0.0_r8
+         intrmtncy_fct(p) = 0.0_r8
+         ! dmleung's edit for including friction velcoity for SP mode output, 17 Dec 2021
+         ustar(p) = 0.0_r8
+         ! dmleung's edit, 20 Dec 2021
+         ssr(p) = 0.0_r8
+         lai(p) = 0.0_r8
+         frc_thr_rghn_fct(p) = 0.0_r8
+         ! dmleung added 28 Jul 2022
+         wnd_frc_thr_std(p) = 0.0_r8
       end do
       do n = 1, ndst
          do fp = 1,num_nolakep
@@ -356,6 +584,109 @@ subroutine DustEmission (bounds, &
          l = patch%landunit(p)
          g = patch%gridcell(p)
 
+         !################################################################################################
+         ! put dust emission calculation here to output threshold friction velocity for the whole globe,
+         ! not just when lnd_frc_mbl = 0. Edited by dmleung 27 Nov 2021
+         bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
+         gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
+         if (gwc_sfc > gwc_thr(c)) then
+            frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)
+         else
+            frc_thr_wet_fct = 1.0_r8
+         end if
+
+         ! output moisture variables -dmleung, coded Jul 2020, recoded 18 Mar 2021, added to CLM5 27 Nov 2021
+         gwc(p) = gwc_sfc     ! output surface gravimetric water content
+
+         ! slevis: adding liqfrac here, because related to effects from soil water
+         liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) ) !-dmleung 27 Nov 2021
+         ! output liquid fraction -dmleung 27 Nov 2021
+         liq_frac(p) = liqfrac
+
+         !#######################################################################################################
+         ! calculate Shao & Lu (2000) dust emission threshold scheme here
+         ! use tmp1 from DUSTini for Iversen and White I&W (1982) (75 um is optimal); use tmp2 for S&L (2000) (107 um is optimal)
+         ! recoded to CLM5 27 Nov 2021
+         !#######################################################################################################
+
+         tmp2 = 1.0_r8*sqrt(0.0123_r8 * (dns_slt*grav*130.0e-6_r8 + 1.65e-4_r8/130.0e-6_r8)) ! calculate S&L (2000) scheme here for threshold; gamma = 1.65e-4 following S&L00, D_p = 127 um ~ 130 um following dmleung's dust paper. As this is a global constant, this line can be put outside the loop to save computational power.
+         wnd_frc_thr_dry(p) = tmp2 / sqrt(forc_rho(c))    ! output dry fluid threshold
+         wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! use as threshold in this module
+         wnd_frc_thr_slt_it = B_it * tmp2 / sqrt(forc_rho(c)) ! define impact threshold -dml 9 Jun 2021, recoded to CLM5 27 Nov 2021
+
+         !wnd_frc_thr_dry(p) = tmp1 / sqrt(forc_rho(c))    ! output dry fluid threshold         
+         !wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! use as threshold in this module
+         !wnd_frc_thr_slt_it = B_it * tmp1 / sqrt(forc_rho(c)) ! define impact threshold -dmleung 9 Jun 2021, recoded to CLM5 27 Nov 2021
+         ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme -dmleung, 23 Feb 2020, added to CLM5 27 Nov 2021
+         wnd_frc_thr(p) = wnd_frc_thr_slt          ! output fluid threshold -dmleung
+
+         ! use emission threshold to calculate standardized threshold and dust emission coefficient dmleung 27 Nov 2021
+         wnd_frc_thr_slt_std = wnd_frc_thr_slt * sqrt(forc_rho(c) / forc_rho_std) ! standardized soil threshold friction speed -jfk (defined using fluid threshold
+         wnd_frc_thr_std(p) = wnd_frc_thr_slt_std          ! output standardized fluid threshold -dmleung added 28 Jul 2022
+         dst_emiss_coeff(p) = Cd0 * exp(-Ce * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min) ! save dust emission coefficient here for all grids, -dml, 1 Mar 2021 
+
+         ! framentation exponent dmleung 27 Nov 2021; moved to this block 23 Dec 2021
+         frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a) -dmleung 27 Nov 2021
+         if (frag_expt > 3_r8) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
+            frag_expt = 3_r8
+         end if
+
+         !################ drag partition effect, and soil friction velocity############################
+         ! subsection on computing vegetation drag partition and hybrid drag partition factors 
+         ! in our scheme, drag partition effect is applied on the wind instead of the threshold
+         !  -dmleung, 7 Jul 2021 , coded to CLM5 27 Nov 2021
+         !##############################################################################################
+         ! the following comes from subr. frc_thr_rgh_fct_get
+         ! purpose: compute factor by which surface roughness increases threshold
+         !          friction velocity (currently a constant)
+
+         if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
+            ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014), dmleung 20 Dec 2021
+            lai(p) = tlai_lu(l)       ! LAI+SAI averaged to landunit level; saved for output
+            if (lai(p) < 0.1_r8) then
+               lai(p)  = 0.1_r8   ! setting LAI ~ 0.1 to be a threshold value as computing K involves 1 / LAI
+            end if
+            ! calculate Okin's shear stress ratio (which is drag partition factor) using Pierre's equation   
+            K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup
+            ssr(p) = (K_length+f_0*c_e)/(K_length+c_e)
+
+            !frc_thr_rgh_fct = (rockfrc(p)*(roughfct(p))**3_r8 + (vegefrc(p)+sparfrc(p))*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using static GLCNMo bare land fraction LC0, dmleung 20 Dec 2021i; dmleung commented 24 Jul 2022
+
+            ! dmleung added calculation of LUH2 bare vs veg fraction within a grid 24 Jul 2022
+            bare_frc = wt_lunit(g,istsoil) * wt_nat_patch(g,noveg) 
+            veg_frc = wt_lunit(g,istsoil) * sum(wt_nat_patch(g,(noveg+1):natpft_ub)) + wt_lunit(g,istcrop)
+
+            frc_thr_rgh_fct = (bare_frc*(roughfct(p))**3_r8 + veg_frc*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using LUH2 land cover, dmleung 24 Jul 2022
+
+
+            wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt will be used in the dust emission equation  -dmleung
+
+            frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save hybrid drag partition factor, dmleung 20 Dec 2021
+         else
+            wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
+            frc_thr_rghn_fct(p) = 0.0_r8            ! save hybrid drag partition factor, dmleung 20 Dec 2021
+         end if
+
+         !##########end of drag partition effect #######################################################
+
+         !############ Add Owen effect; if not, comment out this block !-dmleung, 27 Nov 2021 ###########
+         ! the following if-block comes from subr. wnd_frc_slt_get 
+         ! purpose: compute the saltating friction velocity
+         ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
+
+         !if (u10(p) >= wnd_rfr_thr_slt) then
+         !   wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
+         !   wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
+         !   wnd_frc_slt = wnd_frc_slt + wnd_frc_slt_dlt   ! careful that RHS is now wnd_frc_slt instead of fv(p)
+         ! ! because wnd_frc_slt takes drag partition effect into account, but fv(p) doesn't. dmleung 27 Nov 2021
+         !end if
+         !########## end of Owen effect ################################################################
+
+         ! save soil friction velocity and roughness effect before the if-statement, -dml, 1 Mar 2021, coded to CLM5 27 Nov 2021
+         wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect  -dml
+         ustar(p)        = fv(p)        ! save friction velocity for SP mode (use_cn=0) since only CN/BGC mode (use_cn=1) has FV output -dmleung 17 Dec 2021
+         ! save land mobile fraction
+         lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement, -dml, 1 Mar 2021
          ! only perform the following calculations if lnd_frc_mbl is non-zero 
 
          if (lnd_frc_mbl(p) > 0.0_r8) then
@@ -364,7 +695,7 @@ subroutine DustEmission (bounds, &
             ! purpose: compute factor by which surface roughness increases threshold
             !          friction velocity (currently a constant)
 
-            frc_thr_rgh_fct = 1.0_r8
+            !frc_thr_rgh_fct = 1.0_r8
 
             ! the following comes from subr. frc_thr_wet_fct_get
             ! purpose: compute factor by which soil moisture increases threshold friction velocity
@@ -372,17 +703,17 @@ subroutine DustEmission (bounds, &
             ! modified 4/5/2002 (slevis) to use gravimetric instead of volumetric
             ! water content
 
-            bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
-            gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
-            if (gwc_sfc > gwc_thr(c)) then
-               frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)
-            else
-               frc_thr_wet_fct = 1.0_r8
-            end if
+            !bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
+            !gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
+            !if (gwc_sfc > gwc_thr(c)) then
+            !   frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)
+            !else
+            !   frc_thr_wet_fct = 1.0_r8
+            !end if
 
             ! slevis: adding liqfrac here, because related to effects from soil water
 
-            liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
+            !liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
 
             ! the following lines come from subr. dst_mbl
             ! purpose: adjust threshold friction velocity to acct for moisture and
@@ -390,52 +721,125 @@ subroutine DustEmission (bounds, &
             !          subr. wnd_frc_thr_slt_get which computes dry threshold
             !          friction velocity for saltation
 
-            wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
+            !wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
 
             ! reset these variables which will be updated in the following if-block
 
-            wnd_frc_slt = fv(p)
+            !wnd_frc_slt = fv(p)
             flx_mss_hrz_slt_ttl = 0.0_r8
             flx_mss_vrt_dst_ttl(p) = 0.0_r8
 
             ! the following line comes from subr. dst_mbl
             ! purpose: threshold saltation wind speed
 
-            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)
+            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)     ! keep and use if I want Z03 scheme -dmleung
 
             ! the following if-block comes from subr. wnd_frc_slt_get 
             ! purpose: compute the saltating friction velocity
             ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
 
-            if (u10(p) >= wnd_rfr_thr_slt) then
-               wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
-               wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
-               wnd_frc_slt = fv(p) + wnd_frc_slt_dlt
-            end if
+            !if (u10(p) >= wnd_rfr_thr_slt) then
+            !   wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
+            !   wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
+            !   wnd_frc_slt = fv(p) + wnd_frc_slt_dlt
+            !end if
 
             ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
             ! purpose: compute vertically integrated streamwise mass flux of particles
 
-            if (wnd_frc_slt > wnd_frc_thr_slt) then
-               wnd_frc_rat = wnd_frc_thr_slt / wnd_frc_slt
-               flx_mss_hrz_slt_ttl = cst_slt * forc_rho(c) * (wnd_frc_slt**3.0_r8) * &
-                    (1.0_r8 - wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) / grav
+            !if (wnd_frc_slt > wnd_frc_thr_slt) then! if want to use fluid threshold for dust emission, uncomment this one,  -dmleung 2 Dec 2021
+            if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if want to use impact threshold for dust emission, uncomment this one, -dmleung 2 Dec 2021
+
+               !################### for Zender et al. (2003) scheme -dmleung ###########################
+               !################ uncomment the below block if want to use Z03 scheme ###################
+               !wnd_frc_rat = wnd_frc_thr_slt / wnd_frc_slt
+               !flx_mss_hrz_slt_ttl = cst_slt * forc_rho(c) * (wnd_frc_slt**3.0_r8) * &
+               !     (1.0_r8 - wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) / grav
 
                ! the following loop originates from subr. dst_mbl
                ! purpose: apply land sfc and veg limitations and global tuning factor
                ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect 
                ! of frozen soil
 
-               flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * mbl_bsn_fct(c) * &
-                    flx_mss_fdg_fct * liqfrac
+               !flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * mbl_bsn_fct(c) * &
+               !     flx_mss_fdg_fct * liqfrac
+
+               ! dmleung moved to this block
+               !dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )
+               !flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
+               !########################################################################################
+
+               !################### for Kok et al. (2014) scheme -dmleung ##############################
+               !################ uncomment the below block if want to use K14 scheme ###################
+
+               ! if want to use fluid threshold for dust emission, uncomment this one, -dmleung 27 Nov 2021
+               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt)**frag_expt  ! change forc_rho(g) to forc_rho(c) to avoid passing Nan values to the coupler -Longlei ! if want to use fluid threshold for dust emission, uncomment this one, -dml 27 Nov 2021
+
+               ! if want to use impact threshold for dust emission, uncomment this one, -dmleung 2 Dec 2021
+               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! if want to use impact threshold for dust emission, uncomment this one, -dml 2 Dec 2021
+
+               ! account for bare soil fraction, frozen soil fraction, and apply global tuning parameter (Kok et al. 2014)
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * lnd_frc_mbl(p) * C_tune * liqfrac
+               !########################################################################################
             end if
 
             ! the following comes from subr. flx_mss_vrt_dst_ttl_MaB95_get
             ! purpose: diagnose total vertical mass flux of dust from vertically
             !          integrated streamwise mass flux
 
-            dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )
-            flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
+            !dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )  ! dmleung commented and moved to the previous block
+            !flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
+
+            !############## added by dmleung 2 Dec 2021 #############################################
+            ! subsection for intermittency factor calculation
+            ! need to use with impact threshold and cannot be used with fluid threshold
+            ! Danny M. Leung, 24 Jun 2019, readded into CLM5 by dmleung 2 Dec 2021
+            ! 2 Dec 2021 note: assume no buoyancy contribution to the wind fluctuation (u_sd_slt), so no obul(p) is needed. It is shown to be important for the wind fluctuations contribute little to the intermittency factor. We might add this back in the future revisions.
+
+            ! mean lowpass-filtered wind speed at 0.1 m saltation height (assuming aerodynamic roughness length = 1e-4 m globally for ease; also assuming neutral condition)
+            u_mean_slt(p) = (wnd_frc_slt/k) * log(0.1_r8 / 1e-4_r8)
+
+            ! sd of lowpass-filtered wind speed
+            !if (obul(p)==0) then
+            !   zetaobu = 0
+            !else 
+               !zetaobu = zii(p) / obul(p)   ! For now zii is a constant of 1000 m in CLM -dml, 24 Aug 2021
+            !   zetaobu = 1000_r8 / obul(p)   ! For now zii is a constant of 1000 m in CLM -dml, 24 Aug 2021
+            !end if
+            !stblty(p) = zetaobu    ! zetaobu get outputted as the Obukhov stability parameter
+            stblty(p) = 0   ! -dmleung 2 Dec 2021: use 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
+            if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then
+               u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
+            else
+               u_sd_slt(p) = 0.001_r8   ! should have used 0 theoretically; used 0.001 here to avoid undefined values
+            end if
+
+            ! threshold velocities
+            ! Here wnd_frc_thr_slt is the fluid threshold; wnd_frc_thr_dry(p) is the dry fluid threshold; B_it*wnd_frc_thr_dry(p) is the impact threshold, -dml, 1 Mar 2021
+            ! fluid threshold wind at 0.1 m saltation height
+            u_fld_thr(p) = (wnd_frc_thr_slt/k) * log(0.1_r8 / 1e-4_r8)
+            ! impact threshold wind at 0.1 m saltation height
+            u_impct_thr(p) = (wnd_frc_thr_slt_it/k) * log(0.1_r8 / 1e-4_r8)  ! to avoid model error
+
+            ! threshold crossing rate
+            thr_crs_rate(p) = (exp((u_fld_thr(p)**2_r8 - u_impct_thr(p)**2_r8 - 2_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2_r8 * u_sd_slt(p)**2_r8)) + 1_r8)**(-1_r8)
+
+            ! probability that lowpass-filtered wind speed does not exceed u_ft
+            prb_crs_fld_thr(p) = 0.5_r8 * (1_r8 + erf((u_fld_thr(p) - u_mean_slt(p)) / (1.414_r8 * u_sd_slt(p))))
+            ! probability that lowpass-filtered wind speed does not exceed u_it
+            prb_crs_impct_thr(p) = 0.5_r8 * (1_r8 + erf((u_impct_thr(p) - u_mean_slt(p)) / (1.414_r8 * u_sd_slt(p))))
+
+            ! intermittency factor (from 0 to 1)
+            intrmtncy_fct(p) = 1_r8 - prb_crs_fld_thr(p) + thr_crs_rate(p) * (prb_crs_fld_thr(p) - prb_crs_impct_thr(p))
+
+            ! multiply dust emission flux by intermittency factor
+            if (intrmtncy_fct(p) /= intrmtncy_fct(p)) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted, dmleung 9 Jun 2021
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p)  !  -dmleung
+            else
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * intrmtncy_fct(p)  ! multiply dust flux by intermittency -dmleung
+            end if
+
+            !############### end my subsection here -dmleung ########################################
 
          end if   ! lnd_frc_mbl > 0.0
 
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 9122b56890..2c1b00a8f6 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -172,6 +172,7 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     use clm_varcon          , only : secspday, denh2o, denice, grlnd
     use clm_varctl          , only : use_cn, use_lch4, use_fates
     use clm_varctl          , only : iulog, fsurdat, paramfile, soil_layerstruct_predefined
+    use clm_varctl          , only : rough_fct    ! -dmleung added to CESM2/CLM5 17 Dec 2021
     use landunit_varcon     , only : istdlak, istwet, istsoil, istcrop, istice
     use column_varcon       , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv 
     use fileutils           , only : getfil
@@ -220,6 +221,7 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     real(r8) ,pointer  :: sand3d (:,:)                  ! read in - soil texture: percent sand (needs to be a pointer for use in ncdio)
     real(r8) ,pointer  :: clay3d (:,:)                  ! read in - soil texture: percent clay (needs to be a pointer for use in ncdio)
     real(r8) ,pointer  :: organic3d (:,:)               ! read in - organic matter: kg/m3 (needs to be a pointer for use in ncdio)
+    real(r8) ,pointer  :: roughfct2d(:)                 ! read in - time-invariant roughness factor,   dmleung added 17 Dec 2021
     character(len=256) :: locfn                         ! local filename
     integer            :: ipedof  
     integer            :: begp, endp
@@ -369,6 +371,25 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
 
     call ncd_pio_closefile(ncid)
 
+    !############ subsection for input data for new dust emission scheme ##############
+
+    ! dmleung added to CESM2/CLM5 17 Dec 2021
+    allocate(roughfct2d(begg:endg))                                   ! dmleung, 16 Jul 2020
+    ! here to read roughness factor file, 16 Jul 2020
+    !write(iulog,*) 'Attempting to read roughness factor data, by dmleung .....'
+    call getfil (rough_fct, locfn, 0)
+    call ncd_pio_openfile (ncid, locfn, 0)
+    call ncd_io(ncid=ncid, varname='F_eff', flag='read', data=roughfct2d, dim1name=grlnd, readvar=readvar)
+    !write(iulog,*) 'initialize pft level roughness factor from roughfct2d(g) to roughfct(p)'  
+
+    do p = begp,endp
+       g = patch%gridcell(p)
+       soilstate_inst%roughfct_patch(p) = roughfct2d(g)
+    end do
+
+    call ncd_pio_closefile(ncid)
+    !##################################################################################
+
     ! --------------------------------------------------------------------
     ! get original soil depths to be used in interpolation of sand and clay
     ! --------------------------------------------------------------------
@@ -702,7 +723,8 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     do c = begc,endc
        g = col%gridcell(c)
 
-       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8
+       soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  !Fecan et al. (1999) -jfk, dmleung coded 27 Nov 2021 for CLM clay fraction
+       !soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 -dmleung commented 27 Nov 2021
        soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
     end do
 
diff --git a/src/biogeophys/SoilStateType.F90 b/src/biogeophys/SoilStateType.F90
index e301cc27b9..fa3d5a6aaf 100644
--- a/src/biogeophys/SoilStateType.F90
+++ b/src/biogeophys/SoilStateType.F90
@@ -24,12 +24,15 @@ module SoilStateType
 
      ! sand/ clay/ organic matter
      real(r8), pointer :: sandfrac_patch       (:)   ! patch sand fraction
-     real(r8), pointer :: clayfrac_patch       (:)   ! patch clay fraction
+     real(r8), pointer :: clayfrac_patch       (:)   ! patch clay fraction 
      real(r8), pointer :: mss_frc_cly_vld_col  (:)   ! col mass fraction clay limited to 0.20
      real(r8), pointer :: cellorg_col          (:,:) ! col organic matter for gridcell containing column (1:nlevsoi)
      real(r8), pointer :: cellsand_col         (:,:) ! sand value for gridcell containing column (1:nlevsoi)
      real(r8), pointer :: cellclay_col         (:,:) ! clay value for gridcell containing column (1:nlevsoi)
      real(r8), pointer :: bd_col               (:,:) ! col bulk density of dry soil material [kg/m^3] (CN)
+     !####################### for new dust emission scheme  -dmleung ############################
+     real(r8), pointer :: roughfct_patch       (:)   ! roughness factor, 17 dec 2021
+     !###########################################################################################
 
      ! hydraulic properties
      real(r8), pointer :: hksat_col            (:,:) ! col hydraulic conductivity at saturation (mm H2O /s) 
@@ -131,6 +134,9 @@ subroutine InitAllocate(this, bounds)
     allocate(this%cellclay_col         (begc:endc,nlevsoi))             ; this%cellclay_col         (:,:) = nan 
     allocate(this%bd_col               (begc:endc,nlevgrnd))            ; this%bd_col               (:,:) = nan
 
+    !################ dmleung added 14 Dec 2021 ########################
+    allocate(this%roughfct_patch       (begp:endp))                     ; this%roughfct_patch       (:)   = nan
+    !###################################################################
     allocate(this%hksat_col            (begc:endc,nlevgrnd))            ; this%hksat_col            (:,:) = spval
     allocate(this%hksat_min_col        (begc:endc,nlevgrnd))            ; this%hksat_min_col        (:,:) = spval
     allocate(this%hk_l_col             (begc:endc,nlevgrnd))            ; this%hk_l_col             (:,:) = nan   
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 9be9af2f73..3b7b1321ea 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -113,6 +113,7 @@ module clm_varctl
   character(len=fname_len), public :: nrevsn     = ' '        ! restart data file name for branch run
   character(len=fname_len), public :: fsnowoptics  = ' '      ! snow optical properties file name
   character(len=fname_len), public :: fsnowaging   = ' '      ! snow aging parameters file name
+  character(len=fname_len), public :: rough_fct   = ' '       ! roughness factor, dmleung, added 17 Dec 2021
 
   character(len=fname_len), public :: fatmlndfrc = ' '        ! lnd frac file on atm grid
                                                               ! only needed for LILAC and MCT drivers
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index a7bca1aa87..5645c8a0ca 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -282,6 +282,9 @@ subroutine control_init(dtime)
          use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, &
          use_nguardrail
 
+    ! dust emission, dmleung 14 Dec 2021
+    namelist /clm_inparm/  &
+         rough_fct    !-dmleung 17 Dec 2021
 
     ! ----------------------------------------------------------------------
     ! Default values
@@ -653,6 +656,9 @@ subroutine control_spmd()
     call mpi_bcast (fsnowoptics, len(fsnowoptics),  MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fsnowaging,  len(fsnowaging),   MPI_CHARACTER, 0, mpicom, ier)
 
+    ! initialize input data for new dust emission module dmleung 14 Dec 2021
+    call mpi_bcast (rough_fct, len(rough_fct), MPI_CHARACTER, 0, mpicom, ier)! added by dmleung, 17 Dec 2021
+
     ! Irrigation
     call mpi_bcast(irrigate, 1, MPI_LOGICAL, 0, mpicom, ier)
 
@@ -904,6 +910,13 @@ subroutine control_print ()
     write(iulog,*) '   Threshold above which the model keeps the lake landunit =', toosmall_lake
     write(iulog,*) '   Threshold above which the model keeps the wetland landunit =', toosmall_wetland
     write(iulog,*) '   Threshold above which the model keeps the urban landunits =', toosmall_urban
+    !##### for dmleung's input data for new dust emission module #####
+    if (rough_fct == ' ') then    ! -dmleung, 17 Dec 2021
+       write(iulog,*) '   rough_fct surface dataset not set'
+    else
+       write(iulog,*) '   surface data   = ',trim(rough_fct)
+    end if
+    !#################################################################
     if (use_cn) then
        if (suplnitro /= suplnNon)then
           write(iulog,*) '   Supplemental Nitrogen mode is set to run over Patches: ', &
diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90
index ff7324e428..2638aa5f46 100644
--- a/src/main/lnd2atmMod.F90
+++ b/src/main/lnd2atmMod.F90
@@ -140,6 +140,14 @@ subroutine lnd2atm_minimal(bounds, &
          p2c_scale_type='unity', c2l_scale_type= 'urbanf', l2g_scale_type='unity')
 
     do g = bounds%begg,bounds%endg
+       !#####added by dmleung to avoid negative eflx_lwrad_out_grc(g) 11 Dec 2021 ###################
+       if (lnd2atm_inst%eflx_lwrad_out_grc(g) < 0) then
+          write(iulog,*) 'FIRE = ', lnd2atm_inst%eflx_lwrad_out_grc(g)
+          write(iulog,*) 'gridcell index = ', g
+          !write(iulog,*) 'sb constant = ', sb
+          lnd2atm_inst%eflx_lwrad_out_grc(g) = 100_r8
+       end if
+       !##### should not be here but I am not sure why sometimes LW radiation is negative yet #######
        lnd2atm_inst%t_rad_grc(g) = sqrt(sqrt(lnd2atm_inst%eflx_lwrad_out_grc(g)/sb))
     end do
 

From 33dcd9feed81a07177bc57b48d0ab2723614c374 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 22 Aug 2022 18:04:20 -0600
Subject: [PATCH 0003/1248] Set roughfct2d to 1.0 if rough_fct dataset is not
 being used

---
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 33 ++++++++++++--------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 2c1b00a8f6..c5e2a72977 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -374,20 +374,27 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     !############ subsection for input data for new dust emission scheme ##############
 
     ! dmleung added to CESM2/CLM5 17 Dec 2021
-    allocate(roughfct2d(begg:endg))                                   ! dmleung, 16 Jul 2020
-    ! here to read roughness factor file, 16 Jul 2020
-    !write(iulog,*) 'Attempting to read roughness factor data, by dmleung .....'
-    call getfil (rough_fct, locfn, 0)
-    call ncd_pio_openfile (ncid, locfn, 0)
-    call ncd_io(ncid=ncid, varname='F_eff', flag='read', data=roughfct2d, dim1name=grlnd, readvar=readvar)
-    !write(iulog,*) 'initialize pft level roughness factor from roughfct2d(g) to roughfct(p)'  
+    if (rough_fct /= ' ') then
+       allocate(roughfct2d(begg:endg))                                   ! dmleung, 16 Jul 2020
+       ! here to read roughness factor file, 16 Jul 2020
+       !write(iulog,*) 'Attempting to read roughness factor data, by dmleung .....'
+       call getfil (rough_fct, locfn, 0)
+       call ncd_pio_openfile (ncid, locfn, 0)
+       call ncd_io(ncid=ncid, varname='F_eff', flag='read', data=roughfct2d, dim1name=grlnd, readvar=readvar)
+       !write(iulog,*) 'initialize pft level roughness factor from roughfct2d(g) to roughfct(p)'  
+   
+       do p = begp,endp
+          g = patch%gridcell(p)
+          soilstate_inst%roughfct_patch(p) = roughfct2d(g)
+       end do
+
+       call ncd_pio_closefile(ncid)
+    else
+       do p = begp,endp
+          soilstate_inst%roughfct_patch(p) = 1.0_r8
+       end do
 
-    do p = begp,endp
-       g = patch%gridcell(p)
-       soilstate_inst%roughfct_patch(p) = roughfct2d(g)
-    end do
-
-    call ncd_pio_closefile(ncid)
+    end if
     !##################################################################################
 
     ! --------------------------------------------------------------------

From c8c885ae4e6a1f06296ac9803b183f08234174c4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 22 Aug 2022 18:05:01 -0600
Subject: [PATCH 0004/1248] Distinguish between normal fsurdat surface dataset
 and the rough_fct dataset

---
 src/main/controlMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 5645c8a0ca..49788b351c 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -912,9 +912,9 @@ subroutine control_print ()
     write(iulog,*) '   Threshold above which the model keeps the urban landunits =', toosmall_urban
     !##### for dmleung's input data for new dust emission module #####
     if (rough_fct == ' ') then    ! -dmleung, 17 Dec 2021
-       write(iulog,*) '   rough_fct surface dataset not set'
+       write(iulog,*) '   rough_fct surface roughness dataset not set'
     else
-       write(iulog,*) '   surface data   = ',trim(rough_fct)
+       write(iulog,*) '   surface roughness data   = ',trim(rough_fct)
     end if
     !#################################################################
     if (use_cn) then

From 564875ed626419bd3867669786eb9083c212a473 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 22 Aug 2022 18:05:23 -0600
Subject: [PATCH 0005/1248] Always output FV

---
 src/biogeophys/FrictionVelocityMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90
index 21a09fbc13..43f82495b7 100644
--- a/src/biogeophys/FrictionVelocityMod.F90
+++ b/src/biogeophys/FrictionVelocityMod.F90
@@ -231,12 +231,12 @@ subroutine InitHistory(this, bounds)
             ptr_patch=this%ram1_patch, default='inactive')
     end if
 
-    if (use_cn) then
+    !if (use_cn) then
        this%fv_patch(begp:endp) = spval
        call hist_addfld1d (fname='FV', units='m/s', &
             avgflag='A', long_name='friction velocity', &
             ptr_patch=this%fv_patch)
-    end if
+    !end if
 
        call hist_addfld1d (fname='RAH1', units='s/m', &
             avgflag='A', long_name='aerodynamical resistance ', &

From f71bb054eaaaa0fbdb7bb760604edb55583cee3b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 22 Aug 2022 18:06:27 -0600
Subject: [PATCH 0006/1248] Make sure to distinquish history variable names as
 it will otherwise abort, don't output USTAR as FV is already output in
 FrictionVelocity

---
 src/biogeochem/DUSTMod.F90 | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 7f7c92722c..b51468a62f 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -251,7 +251,7 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='sd of wind velocity at saltation level', &
          ptr_patch=this%u_sd_slt_patch, set_lake=0._r8, set_urb=0._r8)
     this%stblty_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ZETA', units='',  &
+    call hist_addfld1d (fname='ZETAOBU', units='',  &
          avgflag='A', long_name='stability parameter', &
          ptr_patch=this%stblty_patch, set_lake=0._r8, set_urb=0._r8)
     this%u_fld_thr_patch(begp:endp) = spval
@@ -263,7 +263,7 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='impact threshold velocity at saltation level', &
          ptr_patch=this%u_impct_thr_patch, set_lake=0._r8, set_urb=0._r8)
     this%thr_crs_rate_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ALPHA', units='',  &
+    call hist_addfld1d (fname='ALPHA_TC_RATE', units='',  &
          avgflag='A', long_name='threshold crossing rate', &
          ptr_patch=this%thr_crs_rate_patch, set_lake=0._r8, set_urb=0._r8)
     this%prb_crs_fld_thr_patch(begp:endp) = spval
@@ -279,10 +279,11 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='intermittency factor', &
          ptr_patch=this%intrmtncy_fct_patch, set_lake=0._r8, set_urb=0._r8)
     !#####added by dmleung 2 Dec 2021 #########################################
-    this%ustar_patch(begp:endp) = spval
-    call hist_addfld1d (fname='USTAR', units='m/s',  &
-         avgflag='A', long_name='friction velocity', &
-         ptr_patch=this%ustar_patch, set_lake=0._r8, set_urb=0._r8)
+    ! This is already output as FV in FrictionVelocityMod
+    !this%ustar_patch(begp:endp) = spval
+    !call hist_addfld1d (fname='USTAR', units='m/s',  &
+         !avgflag='A', long_name='friction velocity', &
+         !ptr_patch=this%ustar_patch, set_lake=0._r8, set_urb=0._r8)
     !#####added by dmleung 20 Dec 2021 ########################################
     this%ssr_patch(begp:endp) = spval
     call hist_addfld1d (fname='SSR', units='m/s',  &

From 9a4ec5702f84db07d18b9dbbba7366ca684fa95c Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Mon, 3 Oct 2022 17:51:53 -0500
Subject: [PATCH 0007/1248] Modify Urban Time Varying data

1. `src\cpl\share_esmf\UrbanTimeVarType.F90`: Modify `stream_varnames` dimensions so that it becomes independent of urban density type indices (7-9), to prepare for future time varying data input for `p_ac` (and `p_h`, possibly);
2.  `src\biogeophys\UrbBuildTempOleson2015Mod.F90`: Add `p_ac` to the equation of `eflx_urban_ac`; not being implemented yet.
---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 |  4 +
 src/cpl/share_esmf/UrbanTimeVarType.F90      | 82 +++++++++++++++-----
 2 files changed, 66 insertions(+), 20 deletions(-)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index bf8b68c7eb..e13f7e1b47 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -924,8 +924,12 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
 
             if (t_building_bef_hac(l) > t_building_max(l)) then
               t_building(l) = t_building_max(l)
+              ! [Cathy] orig: 
               eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
                                  - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
+              ! [Cathy] dev:
+              ! eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
+              !                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
             else if (t_building_bef_hac(l) < t_building_min(l)) then
               t_building(l) = t_building_min(l)
               eflx_urban_heat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index cc48bf4833..a76c176f1c 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -12,7 +12,7 @@ module UrbanTimeVarType
   use abortutils      , only : endrun
   use decompMod       , only : bounds_type, subgrid_level_landunit
   use clm_varctl      , only : iulog
-  use landunit_varcon , only : isturb_MIN, isturb_MAX
+  use landunit_varcon , only : isturb_MIN, isturb_MAX ! Cathy: min and max types urban; equals 7 and 9, resp.
   use clm_varcon      , only : spval
   use LandunitType    , only : lun
   use GridcellType    , only : grc
@@ -24,6 +24,8 @@ module UrbanTimeVarType
   type, public :: urbantv_type
      !
      real(r8), public, pointer :: t_building_max(:)    ! lun maximum internal building air temperature (K)
+     ! ! Cathy [dev]
+     ! real(r8), public, pointer :: p_ac(:)              ! lun air-conditioning ownership rate (unitless, between 0 and 1)
      type(shr_strdata_type)    :: sdat_urbantv         ! urban time varying input data stream
    contains
      ! !PUBLIC MEMBER FUNCTIONS:
@@ -31,8 +33,11 @@ module UrbanTimeVarType
      procedure, public :: urbantv_init      ! Initialize urban time varying stream
      procedure, public :: urbantv_interp    ! Interpolate urban time varying stream
   end type urbantv_type
-
-  character(15), private :: stream_varnames(isturb_MIN:isturb_MAX)
+  
+  ! Cathy [orig]
+  ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX)
+  ! Cathy [dev]
+  character(15), private :: stream_varnames(1:3)
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -63,6 +68,8 @@ subroutine Init(this, bounds, NLFilename)
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
+    ! ! Cathy [dev]
+    ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
 
     call this%urbantv_init(bounds, NLFilename)
     call this%urbantv_interp(bounds)
@@ -72,6 +79,11 @@ subroutine Init(this, bounds, NLFilename)
           avgflag='A', long_name='prescribed maximum interior building temperature',   &
           ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
+    ! ! Cathy [dev]
+    ! call hist_addfld1d (fname='P_AC', units='unitless',      &
+          avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)',   &
+          ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
+          l2g_scale_type='unity')
 
   end subroutine Init
 
@@ -85,7 +97,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
     use clm_nlUtilsMod   , only : find_nlgroup_name
     use spmdMod          , only : masterproc, mpicom, iam
     use shr_mpi_mod      , only : shr_mpi_bcast
-    use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md
+    use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md ! Cathy: equals 7, 8 and 9
     use dshr_strdata_mod , only : shr_strdata_init_from_inline
     use lnd_comp_shr     , only : mesh, model_clock
     !
@@ -93,22 +105,23 @@ subroutine urbantv_init(this, bounds, NLFilename)
     implicit none
     class(urbantv_type)           :: this
     type(bounds_type), intent(in) :: bounds
-    character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+    character(len=*),  intent(in) :: NLFilename   ! Namelist filename ???is this the netCDF file name?
     !
     ! !LOCAL VARIABLES:
     integer            :: n
     integer            :: stream_year_first_urbantv         ! first year in urban tv stream to use
     integer            :: stream_year_last_urbantv          ! last year in urban tv stream to use
     integer            :: model_year_align_urbantv          ! align stream_year_first_urbantv with this model year
-    integer            :: nu_nml                            ! unit for namelist file
+    integer            :: nu_nml                            ! unit for namelist file ???
     integer            :: nml_error                         ! namelist i/o error flag
-    character(len=CL)  :: stream_fldFileName_urbantv        ! urban tv streams filename
-    character(len=CL)  :: stream_meshfile_urbantv           ! urban tv streams filename
-    character(len=CL)  :: urbantvmapalgo = 'nn'             ! mapping alogrithm for urban ac
+    character(len=CL)  :: stream_fldFileName_urbantv        ! urban tv streams filename ???
+    character(len=CL)  :: stream_meshfile_urbantv           ! urban tv streams filename ???
+    character(len=CL)  :: urbantvmapalgo = 'nn'             ! mapping alogrithm for urban ac ???
     character(len=CL)  :: urbantv_tintalgo = 'linear'       ! time interpolation alogrithm
     integer            :: rc                                ! error code
-    character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string
-    character(*), parameter :: subName = "('urbantv_init')"
+    ! Cathy [orig]
+    ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string ???
+    character(*), parameter :: subName = "('urbantv_init')" ! ???
     !-----------------------------------------------------------------------
 
     namelist /urbantv_streams/       &
@@ -126,9 +139,14 @@ subroutine urbantv_init(this, bounds, NLFilename)
     model_year_align_urbantv   = 1       ! align stream_year_first_urbantv with this model year
     stream_fldFileName_urbantv = ' '
     stream_meshfile_urbantv    = ' '
-    stream_varnames(isturb_tbd) = urbantvString//"TBD"
-    stream_varnames(isturb_hd)  = urbantvString//"HD"
-    stream_varnames(isturb_md)  = urbantvString//"MD"
+    ! Cathy [orig]
+    ! stream_varnames(isturb_tbd) = urbantvString//"TBD"
+    ! stream_varnames(isturb_hd)  = urbantvString//"HD"
+    ! stream_varnames(isturb_md)  = urbantvString//"MD"
+    ! Cathy [dev]
+    stream_varnames(1) = "tbuildmax_TBD"
+    stream_varnames(2) = "tbuildmax_HD"
+    stream_varnames(3) = "tbuildmax_MD"
 
     ! Read urbantv_streams namelist
     if (masterproc) then
@@ -159,7 +177,10 @@ subroutine urbantv_init(this, bounds, NLFilename)
        write(iulog,'(a,a)' ) '  stream_fldFileName_urbantv = ',stream_fldFileName_urbantv
        write(iulog,'(a,a)' ) '  stream_meshfile_urbantv    = ',stream_meshfile_urbantv
        write(iulog,'(a,a)' ) '  urbantv_tintalgo           = ',urbantv_tintalgo
-       do n = isturb_tbd,isturb_md
+       ! Cathy [orig]
+       ! do n = isturb_tbd,isturb_md
+       ! Cathy [dev]
+       do n = 1,3
           write(iulog,'(a,a)' ) '  stream_varname         = ',trim(stream_varnames(n))
        end do
        write(iulog,*) ' '
@@ -176,8 +197,12 @@ subroutine urbantv_init(this, bounds, NLFilename)
          stream_lev_dimname  = 'null',                               &
          stream_mapalgo      = trim(urbantvmapalgo),                 &
          stream_filenames    = (/trim(stream_fldfilename_urbantv)/), &
-         stream_fldlistFile  = stream_varnames(isturb_tbd:isturb_md),&
-         stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),&
+         ! Cathy [orig]
+         ! stream_fldlistFile  = stream_varnames(isturb_tbd:isturb_md),&
+         ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),&
+         ! Cathy [dev]
+         stream_fldlistFile  = stream_varnames(1:3),                 &
+         stream_fldListModel = stream_varnames(1:3),                 &
          stream_yearFirst    = stream_year_first_urbantv,            &
          stream_yearLast     = stream_year_last_urbantv,             &
          stream_yearAlign    = model_year_align_urbantv,             &
@@ -235,8 +260,12 @@ subroutine urbantv_interp(this, bounds)
 
     ! Create 2d array for all stream variable data
     lsize = bounds%endg - bounds%begg + 1
-    allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX))
-    do n = isturb_MIN,isturb_MAX
+    ! Cathy [orig]
+    ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX))
+    ! do n = isturb_MIN,isturb_MAX
+    ! Cathy [dev]
+    allocate(dataptr2d(lsize, 1:3))
+    do n = 1,3
        call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), &
             fldptr1=dataptr1d, rc=rc)
        if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
@@ -257,13 +286,20 @@ subroutine urbantv_interp(this, bounds)
              ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
-          do n = isturb_MIN,isturb_MAX
+          ! Cathy [orig]
+          ! do n = isturb_MIN,isturb_MAX
+          ! Cathy [dev]
+          do n = 1,3
              if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
                 this%t_building_max(l) = dataptr2d(ig,n)
+                ! ! Cathy [dev]
+                ! this%p_ac(l) = dataptr2d(ig,n) ! ???
              end if
           end do
        else
           this%t_building_max(l) = spval
+          ! ! Cathy [dev]
+          ! this%p_ac(l) = spval
        end if
     end do
     deallocate(dataptr2d)
@@ -277,7 +313,11 @@ subroutine urbantv_interp(this, bounds)
              ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
+          ! Cathy [orig]
           if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
+          ! Cathy [dev]
+          ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)
+          !  & .or. (this%p_ac(l) <= 0._r8) .or. (this%p_ac(l) >= 1._r8)) then
              found = .true.
              gindx = g
              lindx = l
@@ -290,6 +330,8 @@ subroutine urbantv_interp(this, bounds)
        write(iulog,*)'landunit type:   ',lun%itype(lindx)
        write(iulog,*)'urban_valid:     ',urban_valid(gindx)
        write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
+       ! ! Cathy [dev]
+       ! write(iulog,*)'p_ac:            ',this%p_ac(lindx)
        call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, &
             msg=errmsg(sourcefile, __LINE__))
     end if

From eb160f2827f14666e06e38ac390802138620cb04 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 5 Oct 2022 17:07:24 -0500
Subject: [PATCH 0008/1248] Update UrbanTimeVarType.F90

Add missing comment signs
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index a76c176f1c..cf379801ce 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -81,9 +81,9 @@ subroutine Init(this, bounds, NLFilename)
           l2g_scale_type='unity')
     ! ! Cathy [dev]
     ! call hist_addfld1d (fname='P_AC', units='unitless',      &
-          avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)',   &
-          ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
-          l2g_scale_type='unity')
+    !     avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)',   &
+    !     ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
+    !     l2g_scale_type='unity')
 
   end subroutine Init
 

From 8cec89cefeec0f5ac5a523ec260430be7258b489 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 6 Oct 2022 16:44:51 -0500
Subject: [PATCH 0009/1248] Update UrbanTimeVarType.F90

[dev.01] Debugging after first test run.

Problem:
First test run (job 6762983) returned all URBAN_AC results as 0. Suspect a mismatch between the indices of `stream_varnames` and `t_building_max`, which may have resulted in all `t_building_max` being set to nan/very large number.

Solution:
Modify subroutine `urbantv_interp` by hard-coding *land unit type - 6* to ensure the if statement criterion returns true.
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index cf379801ce..1bed4e2967 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -60,7 +60,7 @@ subroutine Init(this, bounds, NLFilename)
     character(len=*)  , intent(in) :: NLFilename   ! Namelist filename
     !
     ! !LOCAL VARIABLES:
-    integer		:: begl, endl
+    integer		:: begl, endl                       ! Cathy: beginning and ending landunit index, from src/main/decompMod
     !---------------------------------------------------------------------
 
     begl = bounds%begl; endl = bounds%endl
@@ -75,6 +75,7 @@ subroutine Init(this, bounds, NLFilename)
     call this%urbantv_interp(bounds)
 
     ! Add history fields
+    ! Cathy: the subroutine is in scr/main/histFileMod.F90
     call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
           avgflag='A', long_name='prescribed maximum interior building temperature',   &
           ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
@@ -290,14 +291,17 @@ subroutine urbantv_interp(this, bounds)
           ! do n = isturb_MIN,isturb_MAX
           ! Cathy [dev]
           do n = 1,3
-             if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
+             ! Cathy [orig]
+             ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
+             ! Cathy [dev.01]
+             if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then
                 this%t_building_max(l) = dataptr2d(ig,n)
                 ! ! Cathy [dev]
                 ! this%p_ac(l) = dataptr2d(ig,n) ! ???
              end if
           end do
        else
-          this%t_building_max(l) = spval
+          this%t_building_max(l) = spval ! Cathy: special value for real data, set to 1.e36 in src/main/clm_varcon
           ! ! Cathy [dev]
           ! this%p_ac(l) = spval
        end if

From fd7e5e0e12f326de981fe75761e25d9b46aa77ce Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Fri, 14 Oct 2022 12:46:03 -0600
Subject: [PATCH 0010/1248] 14 Oct 2022: dmleung edited DUSTMod to properly use
 LUH2 to compute hybrid drag partitioning. (previous use of wt_lunit in
 DUSTMod was not working because wt_lunit was deallocated after CTSM
 initialization.)

---
 src/biogeochem/DUSTMod.F90 | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index b51468a62f..56721e2536 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -31,8 +31,8 @@ module DUSTMod
   use LandunitType         , only : lun
   use ColumnType           , only : col
   use PatchType            , only : patch
-  use clm_instur           , only : wt_lunit, wt_nat_patch  ! dmleung added 24 Jul 2022
-  use landunit_varcon      , only : istsoil, istcrop        ! dmleung added 24 Jul 2022 (refering to main/landunit_varcon.F90, for wt_lunit, istsoil=1 is nat veg, istcrop=2 is crop)
+  !use clm_instur           , only : wt_lunit, wt_nat_patch  ! dmleung added 24 Jul 2022
+  !use landunit_varcon      , only : istsoil, istcrop        ! dmleung added 24 Jul 2022 (refering to main/landunit_varcon.F90, for wt_lunit, istsoil=1 is nat veg, istcrop=2 is crop)
   use pftconMod            , only : noveg              ! dmleung added 24 Jul 2022
   !  
   ! !PUBLIC TYPES
@@ -345,6 +345,9 @@ subroutine DustEmission (bounds, &
     ! !USES
     use shr_const_mod, only : SHR_CONST_RHOFW
     use subgridaveMod, only : p2g
+    !use clm_instur           , only : wt_lunit, wt_nat_patch  ! dmleung added 24 Jul 2022
+    !use landunit_varcon      , only : istsoil, istcrop        ! dmleung added 24 Jul 2022 (refering to main/landunit_varcon.F90, for wt_lunit, istsoil=1 is nat veg, istcrop=2 is crop)
+    use pftconMod            , only : noveg              ! dmleung added 24 Jul 2022
     !
     ! !ARGUMENTS:
     type(bounds_type)      , intent(in)    :: bounds                      
@@ -540,6 +543,8 @@ subroutine DustEmission (bounds, &
          end if
       end do
 
+      ! dmleung add output for bare_frc and veg_frc here if wanted !!!!!!!!!----------------------
+
       ! reset history output variables before next if-statement to avoid output = inf
 
       do fp = 1,num_nolakep
@@ -654,11 +659,21 @@ subroutine DustEmission (bounds, &
             !frc_thr_rgh_fct = (rockfrc(p)*(roughfct(p))**3_r8 + (vegefrc(p)+sparfrc(p))*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using static GLCNMo bare land fraction LC0, dmleung 20 Dec 2021i; dmleung commented 24 Jul 2022
 
             ! dmleung added calculation of LUH2 bare vs veg fraction within a grid 24 Jul 2022
-            bare_frc = wt_lunit(g,istsoil) * wt_nat_patch(g,noveg) 
-            veg_frc = wt_lunit(g,istsoil) * sum(wt_nat_patch(g,(noveg+1):natpft_ub)) + wt_lunit(g,istcrop)
+            !bare_frc = wt_lunit(g,istsoil) * wt_nat_patch(g,noveg) 
+            !veg_frc = wt_lunit(g,istsoil) * sum(wt_nat_patch(g,(noveg+1):natpft_ub)) + wt_lunit(g,istcrop)
 
-            frc_thr_rgh_fct = (bare_frc*(roughfct(p))**3_r8 + veg_frc*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using LUH2 land cover, dmleung 24 Jul 2022
+            !frc_thr_rgh_fct = (bare_frc*(roughfct(p))**3_r8 + veg_frc*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using LUH2 land cover, dmleung 24 Jul 2022
 
+            ! dmleung added calculation of LUH2 bare vs veg fraction within a grid 6 Oct 2022
+            if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
+               if (patch%itype(p) == noveg) then
+                  frc_thr_rgh_fct = roughfct(p)
+               else 
+                  frc_thr_rgh_fct = ssr(p)
+               end if
+            else 
+               frc_thr_rgh_fct = 1.0_r8
+            end if
 
             wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt will be used in the dust emission equation  -dmleung
 

From c7e0cf8d001fee1772cadad518c2b7e4929e0f2c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 21 Oct 2022 14:54:10 -0600
Subject: [PATCH 0011/1248] Add in externals to run a FHIST compset with CAM,
 CICE, and CICE5 from the cesm2_3_beta09 tag

---
 Externals.cfg | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/Externals.cfg b/Externals.cfg
index ff9882d574..a020acc12d 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -33,6 +33,29 @@ repo_url = https://github.com/nmizukami/mizuRoute
 hash = 34723c2
 required = True
 
+[cice5]
+tag = cice5_20220204
+protocol = git
+repo_url = https://github.com/ESCOMP/CESM_CICE5
+local_path = components/cice5
+required = True
+
+[cice6]
+tag = cesm_cice6_2_0_22
+protocol = git
+repo_url = https://github.com/ESCOMP/CESM_CICE
+local_path = components/cice
+externals = Externals.cfg
+required = True
+
+[cam6]
+tag = cam6_3_058
+protocol = git
+repo_url = https://github.com/ESCOMP/CAM
+local_path = components/cam
+externals = Externals_CAM.cfg
+required = True
+
 [ccs_config]
 tag = ccs_config_cesm0.0.38
 protocol = git

From 5b6d00e9c8a6397ffbba7e51f80ef1b6bff24abf Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Fri, 11 Nov 2022 12:53:49 -0700
Subject: [PATCH 0012/1248] dmleung 11 Nov 2022: removed the added lines in
 lnd2atmMod.F90 that force the outgoing longwave radiation to be non-negative.

---
 src/main/lnd2atmMod.F90 | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90
index 2638aa5f46..ff7324e428 100644
--- a/src/main/lnd2atmMod.F90
+++ b/src/main/lnd2atmMod.F90
@@ -140,14 +140,6 @@ subroutine lnd2atm_minimal(bounds, &
          p2c_scale_type='unity', c2l_scale_type= 'urbanf', l2g_scale_type='unity')
 
     do g = bounds%begg,bounds%endg
-       !#####added by dmleung to avoid negative eflx_lwrad_out_grc(g) 11 Dec 2021 ###################
-       if (lnd2atm_inst%eflx_lwrad_out_grc(g) < 0) then
-          write(iulog,*) 'FIRE = ', lnd2atm_inst%eflx_lwrad_out_grc(g)
-          write(iulog,*) 'gridcell index = ', g
-          !write(iulog,*) 'sb constant = ', sb
-          lnd2atm_inst%eflx_lwrad_out_grc(g) = 100_r8
-       end if
-       !##### should not be here but I am not sure why sometimes LW radiation is negative yet #######
        lnd2atm_inst%t_rad_grc(g) = sqrt(sqrt(lnd2atm_inst%eflx_lwrad_out_grc(g)/sb))
     end do
 

From 1592ebbf154782c3eac16f6ca2fa3843b2c57f6b Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 14 Nov 2022 16:37:39 -0700
Subject: [PATCH 0013/1248] dmleung changed the upper limit of the
 gragmentation exponent from 3 to 5. (14 Nov 2022)

---
 src/biogeochem/DUSTMod.F90 | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 56721e2536..421b046030 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -268,11 +268,11 @@ subroutine InitHistory(this, bounds)
          ptr_patch=this%thr_crs_rate_patch, set_lake=0._r8, set_urb=0._r8)
     this%prb_crs_fld_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='P_FT', units='',  &
-         avgflag='A', long_name='probability of crossing fluid threshold', &
+         avgflag='A', long_name='probability of winds crossing fluid threshold', &
          ptr_patch=this%prb_crs_fld_thr_patch, set_lake=0._r8, set_urb=0._r8)
     this%prb_crs_impct_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='P_IT', units='',  &
-         avgflag='A', long_name='probability of crossing impact threshold', &
+         avgflag='A', long_name='probability of winds crossing impact threshold', &
          ptr_patch=this%prb_crs_impct_thr_patch, set_lake=0._r8, set_urb=0._r8)
     this%intrmtncy_fct_patch(begp:endp) = spval
     call hist_addfld1d (fname='ETA', units='',  &
@@ -287,7 +287,7 @@ subroutine InitHistory(this, bounds)
     !#####added by dmleung 20 Dec 2021 ########################################
     this%ssr_patch(begp:endp) = spval
     call hist_addfld1d (fname='SSR', units='m/s',  &
-         avgflag='A', long_name='Okin-Pierre shear stress ratio', &
+         avgflag='A', long_name='Okin-Pierre vegetation shear stress ratio (drag partition factor)', &
          ptr_patch=this%ssr_patch, set_lake=0._r8, set_urb=0._r8)
     this%lai_patch(begp:endp) = spval
     call hist_addfld1d (fname='LAI', units='m/s',  &
@@ -611,7 +611,7 @@ subroutine DustEmission (bounds, &
 
          !#######################################################################################################
          ! calculate Shao & Lu (2000) dust emission threshold scheme here
-         ! use tmp1 from DUSTini for Iversen and White I&W (1982) (75 um is optimal); use tmp2 for S&L (2000) (107 um is optimal)
+         ! use tmp1 from DUSTini for Iversen and White I&W (1982) (75 um is optimal); use tmp2 for S&L (2000) (80 um is optimal)
          ! recoded to CLM5 27 Nov 2021
          !#######################################################################################################
 
@@ -633,8 +633,8 @@ subroutine DustEmission (bounds, &
 
          ! framentation exponent dmleung 27 Nov 2021; moved to this block 23 Dec 2021
          frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a) -dmleung 27 Nov 2021
-         if (frag_expt > 3_r8) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
-            frag_expt = 3_r8
+         if (frag_expt > 5_r8) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
+            frag_expt = 5_r8
          end if
 
          !################ drag partition effect, and soil friction velocity############################

From 571dc5edb82fc3b12ed0cdb6f3543ca2f863c92c Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 14 Nov 2022 16:44:42 -0700
Subject: [PATCH 0014/1248] dmleung changed the upper limit of the
 fragmentation exponent from 3 to 5. (14 Nov 2022)

---
 src/biogeochem/DUSTMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 421b046030..0374d9e645 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -633,8 +633,8 @@ subroutine DustEmission (bounds, &
 
          ! framentation exponent dmleung 27 Nov 2021; moved to this block 23 Dec 2021
          frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a) -dmleung 27 Nov 2021
-         if (frag_expt > 5_r8) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
-            frag_expt = 5_r8
+         if (frag_expt > 5.0_r8) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
+            frag_expt = 5.0_r8
          end if
 
          !################ drag partition effect, and soil friction velocity############################

From db585020d6c3742ba11115be4f367012030f0864 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 14 Nov 2022 16:56:34 -0700
Subject: [PATCH 0015/1248] set 0.1 as the minimum LAI for the Okin-Pierre drag
 partioning equation; code cleanup dmleung 14 Nov 2022

---
 src/biogeochem/DUSTMod.F90 | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 0374d9e645..8935c50585 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -648,10 +648,11 @@ subroutine DustEmission (bounds, &
 
          if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
             ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014), dmleung 20 Dec 2021
-            lai(p) = tlai_lu(l)       ! LAI+SAI averaged to landunit level; saved for output
-            if (lai(p) < 0.1_r8) then
-               lai(p)  = 0.1_r8   ! setting LAI ~ 0.1 to be a threshold value as computing K involves 1 / LAI
-            end if
+            lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; saved for output
+            if (lai(p) > 1_r8) then
+               lai(p)  = 1_r8   ! setting LAI ~ 0.1 to be a min value (since the value goes to infinity when LAI=0)
+            end if              ! and 1 to be a max value as computing K involves 1 / LAI
+
             ! calculate Okin's shear stress ratio (which is drag partition factor) using Pierre's equation   
             K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup
             ssr(p) = (K_length+f_0*c_e)/(K_length+c_e)
@@ -677,13 +678,13 @@ subroutine DustEmission (bounds, &
 
             wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt will be used in the dust emission equation  -dmleung
 
-            frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save hybrid drag partition factor, dmleung 20 Dec 2021
+            frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor, dmleung 20 Dec 2021
          else
             wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
-            frc_thr_rghn_fct(p) = 0.0_r8            ! save hybrid drag partition factor, dmleung 20 Dec 2021
+            frc_thr_rghn_fct(p) = 0.0_r8            ! save and output hybrid drag partition factor, dmleung 20 Dec 2021
          end if
 
-         !##########end of drag partition effect #######################################################
+         !########## end of drag partition effect #######################################################
 
          !############ Add Owen effect; if not, comment out this block !-dmleung, 27 Nov 2021 ###########
          ! the following if-block comes from subr. wnd_frc_slt_get 
@@ -855,7 +856,7 @@ subroutine DustEmission (bounds, &
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * intrmtncy_fct(p)  ! multiply dust flux by intermittency -dmleung
             end if
 
-            !############### end my subsection here -dmleung ########################################
+            !############### end my intermittency subsection here -dmleung ########################################
 
          end if   ! lnd_frc_mbl > 0.0
 

From 5830686b1dbf5541a96648b6bc834b3c52ef29ec Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 14 Nov 2022 18:53:27 -0700
Subject: [PATCH 0016/1248] dmleung removed outputting ustar (USTAR) in the
 DustMod.F90 since Erik enabled outputting fv (FV) in FrictionVelocityMod.F90
 14 Nov 2022

---
 src/biogeochem/DUSTMod.F90 | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 8935c50585..5ec021a01d 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -82,8 +82,6 @@ module DUSTMod
      real(r8), pointer, private :: thr_crs_rate_patch        (:)   ! threshold crossing rate (unitless)
      real(r8), pointer, private :: prb_crs_fld_thr_patch     (:)   ! probability of wind speed crossing fluid threshold
      real(r8), pointer, private :: prb_crs_impct_thr_patch   (:)   ! probability of wind speed crossing impact threshold
-     !########### added by dmleung 17 Dec 2021 ########################################################################
-     real(r8), pointer, private :: ustar_patch               (:)   ! output friction velocity for SP mode (m/s)
      !########### added by dmleung 20 Dec 2021 ########################################################################
      real(r8), pointer, private :: ssr_patch                 (:)   ! [dimless] integrated shear stress ratiio, defined by Okin (2008) and then integrated by Caroline Pierre et al. (2014)
      real(r8), pointer, private :: lai_patch                 (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin's drag partition, averaged to landunit level
@@ -161,8 +159,6 @@ subroutine InitAllocate(this, bounds)
     allocate(this%prb_crs_fld_thr_patch     (begp:endp))        ; this%prb_crs_fld_thr_patch     (:)   = nan
     allocate(this%prb_crs_impct_thr_patch   (begp:endp))        ; this%prb_crs_impct_thr_patch   (:)   = nan
     !#### added by dmleung 17 Dec 2021 ######################################
-    allocate(this%ustar_patch               (begp:endp))        ; this%ustar_patch               (:)   = nan
-    !#### added by dmleung 17 Dec 2021 ######################################
     allocate(this%ssr_patch                 (begp:endp))        ; this%ssr_patch                 (:)   = nan
     allocate(this%lai_patch                 (begp:endp))        ; this%lai_patch                 (:)   = nan
     allocate(this%frc_thr_rghn_fct_patch    (begp:endp))        ; this%frc_thr_rghn_fct_patch    (:)   = nan
@@ -278,12 +274,6 @@ subroutine InitHistory(this, bounds)
     call hist_addfld1d (fname='ETA', units='',  &
          avgflag='A', long_name='intermittency factor', &
          ptr_patch=this%intrmtncy_fct_patch, set_lake=0._r8, set_urb=0._r8)
-    !#####added by dmleung 2 Dec 2021 #########################################
-    ! This is already output as FV in FrictionVelocityMod
-    !this%ustar_patch(begp:endp) = spval
-    !call hist_addfld1d (fname='USTAR', units='m/s',  &
-         !avgflag='A', long_name='friction velocity', &
-         !ptr_patch=this%ustar_patch, set_lake=0._r8, set_urb=0._r8)
     !#####added by dmleung 20 Dec 2021 ########################################
     this%ssr_patch(begp:endp) = spval
     call hist_addfld1d (fname='SSR', units='m/s',  &
@@ -402,7 +392,6 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
     !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
-    !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
     !####### added by dmleung 27 Nov 2021 ###########################################################################
     character(len=*),parameter :: subname = 'DUSTEmission'
     real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; dmleung suggests 1 or 0.5, and the default 0.3 seems a bit too small -dmleung 27 Nov 2021
@@ -464,7 +453,6 @@ subroutine DustEmission (bounds, &
          prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , &
          ! added by dmleung 17 Dec 2021
          roughfct            => soilstate_inst%roughfct_patch        , &
-         ustar               => dust_inst%ustar_patch                , & ! Output friction velocity for SP mode
          ! added by dmleung 20 Dec 2021
          ssr                 => dust_inst%ssr_patch                  , &
          lai                 => dust_inst%lai_patch                  , &
@@ -568,8 +556,6 @@ subroutine DustEmission (bounds, &
          prb_crs_fld_thr(p) = 0.0_r8
          prb_crs_impct_thr(p) = 0.0_r8
          intrmtncy_fct(p) = 0.0_r8
-         ! dmleung's edit for including friction velcoity for SP mode output, 17 Dec 2021
-         ustar(p) = 0.0_r8
          ! dmleung's edit, 20 Dec 2021
          ssr(p) = 0.0_r8
          lai(p) = 0.0_r8
@@ -701,7 +687,6 @@ subroutine DustEmission (bounds, &
 
          ! save soil friction velocity and roughness effect before the if-statement, -dml, 1 Mar 2021, coded to CLM5 27 Nov 2021
          wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect  -dml
-         ustar(p)        = fv(p)        ! save friction velocity for SP mode (use_cn=0) since only CN/BGC mode (use_cn=1) has FV output -dmleung 17 Dec 2021
          ! save land mobile fraction
          lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement, -dml, 1 Mar 2021
          ! only perform the following calculations if lnd_frc_mbl is non-zero 

From 07b787382cf4fcce7a445a1c196373aa816eb081 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Tue, 24 Jan 2023 18:22:03 -0600
Subject: [PATCH 0017/1248] Add p_ac to urban time varying data

1. `src\cpl\share_esmf\UrbanTimeVarType.F90`: Add 3 more dimensions to `stream_varnames` (4,5,6) for `p_ac`;
2.  `src\biogeophys\UrbBuildTempOleson2015Mod.F90`: Use `p_ac` in the equation of `eflx_urban_ac`.
---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 |  6 +-
 src/cpl/share_esmf/UrbanTimeVarType.F90      | 64 ++++++++++----------
 2 files changed, 36 insertions(+), 34 deletions(-)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index e13f7e1b47..260c6658af 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -925,11 +925,11 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
             if (t_building_bef_hac(l) > t_building_max(l)) then
               t_building(l) = t_building_max(l)
               ! [Cathy] orig: 
-              eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
+              ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
                                  - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
               ! [Cathy] dev:
-              ! eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
-              !                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
+              eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
+                                 - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
             else if (t_building_bef_hac(l) < t_building_min(l)) then
               t_building(l) = t_building_min(l)
               eflx_urban_heat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 01f924935e..d96cc11157 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -24,8 +24,8 @@ module UrbanTimeVarType
   type, public :: urbantv_type
      !
      real(r8), public, pointer :: t_building_max(:)    ! lun maximum internal building air temperature (K)
-     ! ! Cathy [dev]
-     ! real(r8), public, pointer :: p_ac(:)              ! lun air-conditioning ownership rate (unitless, between 0 and 1)
+     ! Cathy [dev]
+     real(r8), public, pointer :: p_ac(:)              ! lun air-conditioning ownership rate (unitless, between 0 and 1)
      type(shr_strdata_type)    :: sdat_urbantv         ! urban time varying input data stream
    contains
      ! !PUBLIC MEMBER FUNCTIONS:
@@ -36,8 +36,8 @@ module UrbanTimeVarType
   
   ! Cathy [orig]
   ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX)
-  ! Cathy [dev]
-  character(15), private :: stream_varnames(1:3)
+  ! Cathy [dev]: 
+  character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -68,23 +68,22 @@ subroutine Init(this, bounds, NLFilename)
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
-    ! ! Cathy [dev]
-    ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
+    ! Cathy [dev]
+    allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
 
     call this%urbantv_init(bounds, NLFilename)
     call this%urbantv_interp(bounds)
 
-    ! Add history fields
-    ! Cathy: the subroutine is in scr/main/histFileMod.F90
+    ! Add history fields     ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90
     call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
           avgflag='A', long_name='prescribed maximum interior building temperature',   &
           ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
-    ! ! Cathy [dev]
-    ! call hist_addfld1d (fname='P_AC', units='unitless',      &
-    !     avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)',   &
-    !     ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
-    !     l2g_scale_type='unity')
+    ! Cathy [dev] 
+    call hist_addfld1d (fname='P_AC', units='unitless',      &
+          avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)',   &
+          ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
+          l2g_scale_type='unity')
 
   end subroutine Init
 
@@ -120,8 +119,8 @@ subroutine urbantv_init(this, bounds, NLFilename)
     character(len=CL)  :: urbantvmapalgo = 'nn'             ! mapping alogrithm for urban ac ???
     character(len=CL)  :: urbantv_tintalgo = 'linear'       ! time interpolation alogrithm
     integer            :: rc                                ! error code
-    ! Cathy [orig]
-    ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string ???
+    ! Cathy [orig]: this is taken out because field strings are now hard coded in
+    ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string
     character(*), parameter :: subName = "('urbantv_init')" ! ???
     !-----------------------------------------------------------------------
 
@@ -148,6 +147,9 @@ subroutine urbantv_init(this, bounds, NLFilename)
     stream_varnames(1) = "tbuildmax_TBD"
     stream_varnames(2) = "tbuildmax_HD"
     stream_varnames(3) = "tbuildmax_MD"
+    stream_varnames(4) = "p_ac_TBD"
+    stream_varnames(5) = "p_ac_HD"
+    stream_varnames(6) = "p_ac_MD"
 
     ! Read urbantv_streams namelist
     if (masterproc) then
@@ -181,7 +183,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
        ! Cathy [orig]
        ! do n = isturb_tbd,isturb_md
        ! Cathy [dev]
-       do n = 1,3
+       do n = 1,6
           write(iulog,'(a,a)' ) '  stream_varname         = ',trim(stream_varnames(n))
        end do
        write(iulog,*) ' '
@@ -202,8 +204,8 @@ subroutine urbantv_init(this, bounds, NLFilename)
          ! stream_fldlistFile  = stream_varnames(isturb_tbd:isturb_md),&
          ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),&
          ! Cathy [dev]
-         stream_fldlistFile  = stream_varnames(1:3),                 &
-         stream_fldListModel = stream_varnames(1:3),                 &
+         stream_fldlistFile  = stream_varnames(1:6),                 &
+         stream_fldListModel = stream_varnames(1:6),                 &
          stream_yearFirst    = stream_year_first_urbantv,            &
          stream_yearLast     = stream_year_last_urbantv,             &
          stream_yearAlign    = model_year_align_urbantv,             &
@@ -265,8 +267,8 @@ subroutine urbantv_interp(this, bounds)
     ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX))
     ! do n = isturb_MIN,isturb_MAX
     ! Cathy [dev]
-    allocate(dataptr2d(lsize, 1:3))
-    do n = 1,3
+    allocate(dataptr2d(lsize, 1:6))
+    do n = 1,6
        call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), &
             fldptr1=dataptr1d, rc=rc)
        if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
@@ -290,20 +292,20 @@ subroutine urbantv_interp(this, bounds)
           ! Cathy [orig]
           ! do n = isturb_MIN,isturb_MAX
           ! Cathy [dev]
-          do n = 1,3
+          do n = 1,6
              ! Cathy [orig]
              ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
-             ! Cathy [dev.01]
+             ! Cathy [dev.02]
              if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then
                 this%t_building_max(l) = dataptr2d(ig,n)
-                ! ! Cathy [dev]
-                ! this%p_ac(l) = dataptr2d(ig,n) ! ???
+             if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then
+                this%p_ac(l) = dataptr2d(ig,n)
              end if
           end do
        else
           this%t_building_max(l) = spval ! Cathy: special value for real data, set to 1.e36 in src/main/clm_varcon
-          ! ! Cathy [dev]
-          ! this%p_ac(l) = spval
+          ! Cathy [dev]
+          this%p_ac(l) = 0._r8 ! Cathy: set to 0 for non-urban landunit
        end if
     end do
     deallocate(dataptr2d)
@@ -318,10 +320,10 @@ subroutine urbantv_interp(this, bounds)
              if (g == lun%gridcell(l)) exit
           end do
           ! Cathy [orig]
-          if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
+          ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
           ! Cathy [dev]
-          ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)
-          !  & .or. (this%p_ac(l) <= 0._r8) .or. (this%p_ac(l) >= 1._r8)) then
+          if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) &
+             .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then
              found = .true.
              gindx = g
              lindx = l
@@ -334,8 +336,8 @@ subroutine urbantv_interp(this, bounds)
        write(iulog,*)'landunit type:   ',lun%itype(lindx)
        write(iulog,*)'urban_valid:     ',urban_valid(gindx)
        write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
-       ! ! Cathy [dev]
-       ! write(iulog,*)'p_ac:            ',this%p_ac(lindx)
+       ! Cathy [dev]
+       write(iulog,*)'p_ac:            ',this%p_ac(lindx)
        call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, &
             msg=errmsg(sourcefile, __LINE__))
     end if

From e621628352f457bfadb118ca67b7b4c4634d668a Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 25 Jan 2023 00:13:28 -0600
Subject: [PATCH 0018/1248] Update UrbanTimeVarType.F90

Bug fix: added missing "end if"
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index d96cc11157..bc0c82af6a 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -298,6 +298,7 @@ subroutine urbantv_interp(this, bounds)
              ! Cathy [dev.02]
              if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then
                 this%t_building_max(l) = dataptr2d(ig,n)
+             end if
              if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then
                 this%p_ac(l) = dataptr2d(ig,n)
              end if

From eabe116800f8cf40c1a17755205e2d72b80df033 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 25 Jan 2023 10:58:24 -0600
Subject: [PATCH 0019/1248] Update UrbBuildTempOleson2015Mod.F90

Bug fix: declare p_ac type; comment out original code
---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index 260c6658af..d54d3ff86d 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -324,6 +324,8 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     t_floor           => temperature_inst%t_floor_lun      , & ! InOut:  [real(r8) (:)]  floor temperature (K)
     t_building        => temperature_inst%t_building_lun   , & ! InOut:  [real(r8) (:)]  internal building air temperature (K)
 
+    ! Cathy [dev]
+    p_ac              => urbantv_inst%p_ac                 , & ! Input:  [real(r8) (:)]  air-conditioning penetration rate (-)
     t_building_max    => urbantv_inst%t_building_max       , & ! Input:  [real(r8) (:)]  maximum internal building air temperature (K)
     t_building_min    => urbanparams_inst%t_building_min   , & ! Input:  [real(r8) (:)]  minimum internal building air temperature (K)
 
@@ -926,7 +928,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
               t_building(l) = t_building_max(l)
               ! [Cathy] orig: 
               ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
-                                 - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
+              !                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
               ! [Cathy] dev:
               eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
                                  - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )

From ed26fd3a2b66429204b47a043a43ca5051786659 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 26 Jan 2023 12:22:47 -0600
Subject: [PATCH 0020/1248] Debug dev.02

---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 27 +++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index bc0c82af6a..d542d2440e 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -72,6 +72,10 @@ subroutine Init(this, bounds, NLFilename)
     allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
 
     call this%urbantv_init(bounds, NLFilename)
+
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: urbantv_init done.'
+
     call this%urbantv_interp(bounds)
 
     ! Add history fields     ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90
@@ -188,6 +192,9 @@ subroutine urbantv_init(this, bounds, NLFilename)
        end do
        write(iulog,*) ' '
     endif
+    
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: before shr_strdata_init_from_inline'
 
     ! Initialize the cdeps data type this%sdat_urbantv
     call shr_strdata_init_from_inline(this%sdat_urbantv,             &
@@ -215,6 +222,10 @@ subroutine urbantv_init(this, bounds, NLFilename)
          stream_tintalgo     = urbantv_tintalgo,                     &
          stream_name         = 'Urban time varying data',            &
          rc                  = rc)
+
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: before shr_strdata_init_from_inline'
+
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
     end if
@@ -253,14 +264,24 @@ subroutine urbantv_interp(this, bounds)
     real(r8), pointer :: dataptr2d(:,:)
     !-----------------------------------------------------------------------
 
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: before get_curr_date'
+
     ! Advance sdat stream
     call get_curr_date(year, mon, day, sec)
     mcdate = year*10000 + mon*100 + day
+
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: after get_curr_date, before shr_strdata_advance'
+
     call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
     end if
 
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: before creating 2d array'    
+
     ! Create 2d array for all stream variable data
     lsize = bounds%endg - bounds%begg + 1
     ! Cathy [orig]
@@ -281,6 +302,9 @@ subroutine urbantv_interp(this, bounds)
        end do
     end do
 
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits'
+
     ! Determine this%tbuilding_max for all landunits
     do l = bounds%begl,bounds%endl
        if (lun%urbpoi(l)) then
@@ -311,6 +335,9 @@ subroutine urbantv_interp(this, bounds)
     end do
     deallocate(dataptr2d)
 
+    ! Cathy [dev.02]
+    write(*,*) 'Cathy: after determining t_building_max and p_ac for all landunits'
+
     ! Error check
     found = .false.
     do l = bounds%begl,bounds%endl

From e10e338f2b165a2c8dbe122598e5caf5efd620c4 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 26 Jan 2023 13:41:40 -0600
Subject: [PATCH 0021/1248] Update UrbanTimeVarType.F90

---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index d542d2440e..1f679b88a3 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -74,7 +74,7 @@ subroutine Init(this, bounds, NLFilename)
     call this%urbantv_init(bounds, NLFilename)
 
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: urbantv_init done.'
+    write(iulog,*) 'Cathy: urbantv_init done.'
 
     call this%urbantv_interp(bounds)
 
@@ -190,11 +190,14 @@ subroutine urbantv_init(this, bounds, NLFilename)
        do n = 1,6
           write(iulog,'(a,a)' ) '  stream_varname         = ',trim(stream_varnames(n))
        end do
-       write(iulog,*) ' '
+       ! Cathy [orig]
+       ! write(iulog,*) ' '
+       ! Cathy [dev.02]
+       write(iulog,*) 'Cathy: does write statements have to be inside if?'
     endif
     
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: before shr_strdata_init_from_inline'
+    write(iulog,*) 'Cathy: before shr_strdata_init_from_inline'
 
     ! Initialize the cdeps data type this%sdat_urbantv
     call shr_strdata_init_from_inline(this%sdat_urbantv,             &
@@ -224,7 +227,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
          rc                  = rc)
 
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: before shr_strdata_init_from_inline'
+    write(iulog,*) 'Cathy: before shr_strdata_init_from_inline'
 
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
@@ -265,14 +268,14 @@ subroutine urbantv_interp(this, bounds)
     !-----------------------------------------------------------------------
 
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: before get_curr_date'
+    write(iulog,*) 'Cathy: before get_curr_date'
 
     ! Advance sdat stream
     call get_curr_date(year, mon, day, sec)
     mcdate = year*10000 + mon*100 + day
 
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: after get_curr_date, before shr_strdata_advance'
+    write(iulog,*) 'Cathy: after get_curr_date, before shr_strdata_advance'
 
     call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
@@ -280,7 +283,7 @@ subroutine urbantv_interp(this, bounds)
     end if
 
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: before creating 2d array'    
+    write(iulog,*) 'Cathy: before creating 2d array'    
 
     ! Create 2d array for all stream variable data
     lsize = bounds%endg - bounds%begg + 1
@@ -303,7 +306,7 @@ subroutine urbantv_interp(this, bounds)
     end do
 
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits'
+    write(iulog,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits'
 
     ! Determine this%tbuilding_max for all landunits
     do l = bounds%begl,bounds%endl
@@ -336,7 +339,7 @@ subroutine urbantv_interp(this, bounds)
     deallocate(dataptr2d)
 
     ! Cathy [dev.02]
-    write(*,*) 'Cathy: after determining t_building_max and p_ac for all landunits'
+    write(iulog,*) 'Cathy: after determining t_building_max and p_ac for all landunits'
 
     ! Error check
     found = .false.

From 36d1feec1da582f8c4280ee5ea1393aa8ca5c8de Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 31 Jan 2023 01:29:30 -0700
Subject: [PATCH 0022/1248] 31 Jan 2023: dmleung added capabilities of reading
 stream files for Prigent's roughness data

---
 bld/CLMBuildNamelist.pm                       |  10 +
 bld/namelist_files/namelist_defaults_ctsm.xml |  11 +
 .../namelist_definition_ctsm.xml              |  15 +
 src/biogeochem/DUSTMod.F90                    |  42 +-
 .../share_esmf/PrigentRoughnessStreamType.F90 | 397 ++++++++++++++++++
 5 files changed, 469 insertions(+), 6 deletions(-)
 create mode 100644 src/cpl/share_esmf/PrigentRoughnessStreamType.F90

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index cbd5e3ce44..d078b3869c 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1560,6 +1560,7 @@ sub process_namelist_inline_logic {
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_fates($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl);
+  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl); # dmleung added 31 Dec 2022
 
   #########################################
   # namelist group: atm2lnd_inparm
@@ -4178,6 +4179,15 @@ sub setup_logic_misc {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_prigent_roughness {
+  # dmleung added on 31 Dec 2022 for reading Prigent's roughness stream file
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_prigentroughness' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_prigentroughness' );
+}
+
+#-------------------------------------------------------------------------------
+
 sub write_output_files {
   my ($opts, $nl_flags, $defaults, $nl) = @_;
 
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 2686d62b9a..3d0f5ef5e1 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2524,6 +2524,17 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <stream_meshfile_ch4finundated finundation_method="ZWT_inversion"
 >lnd/clm2/paramdata/finundated_inversiondata_0.9x1_ESMFmesh_cdf5_130621.nc</stream_meshfile_ch4finundated>
 
+<!-- =========================================  -->
+<!-- Defaults for Prigent's roughness data      -->
+<!-- dmleung only specified def resolution      -->
+<!-- 31 Dec 2022                                -->
+<!-- =========================================  -->
+
+<stream_fldfilename_prigentroughness
+>/glade/u/home/dleung/CESM2/ctsm_dustemis_dev/cdf5_Z0a_Prigent-Globe-025x025-01242023.nc</stream_fldfilename_prigentroughness>
+<stream_meshfile_prigentroughness
+>/glade/u/home/dleung/CESM2/ctsm_dustemis_dev/lnd_mesh.nc</stream_meshfile_prigentroughness>
+
 <!-- =========================================  -->
 <!-- Defaults for different BGC/decomp modes    -->
 <!-- =========================================  -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index ddc5d8372c..6cdf4e3ce5 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1693,6 +1693,21 @@ Mapping method from Nitrogen deposition input file to the model resolution
     copy     = copy using the same indices
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- Prigent roughness stream -->
+<!-- dmleung added 31 Dec 2022 -->
+<!-- ========================================================================================  -->
+
+<entry id="stream_fldfilename_prigentroughness" type="char*256" category="datasets"
+       input_pathname="abs" group="prigentroughness" valid_values="" >
+Filename of input stream data for aeolian roughness length (from Prigent's roughness dataset)
+</entry>
+
+<entry id="stream_meshfile_prigentroughness" type="char*256" category="datasets"
+       input_pathname="abs" group="prigentroughness" valid_values="" >
+mesh filename of input stream data for aeolian roughness length (from Prigent's roughness dataset)
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- finundated stream -->
 <!-- ========================================================================================  -->
diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 5ec021a01d..381ecfe41d 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -88,6 +88,9 @@ module DUSTMod
      real(r8), pointer, private :: frc_thr_rghn_fct_patch    (:)   ! [dimless] hybrid drag partition (or called roughness) factor
      !########### added by dmleung 28 Jul 2022 ########################################################################
      real(r8), pointer, private :: wnd_frc_thr_std_patch     (:)   ! standardized fluid threshold friction velocity (m/s)
+     !########### added by dmleung 31 Dec 2022 ########################################################################
+     type(prigentroughnessstream_type), private :: prigentroughnessstream      ! Prigent roughness stream data
+     real(r8), pointer, private :: dpfct_rock_patch          (:)   ! [fraction] rock drag partition factor, time-constant
    contains
 
      procedure , public  :: Init
@@ -105,13 +108,15 @@ module DUSTMod
 contains
 
   !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
+  !##### dmleung edited for initializing stream files 31 Dec 2022  ########
+  subroutine Init(this, bounds, NLFilename)
 
     class(dust_type) :: this
     type(bounds_type), intent(in) :: bounds  
 
     call this%InitAllocate (bounds)
     call this%InitHistory  (bounds)
+    call this%prigentroughnessstream%Init( bounds, NLFilename )  ! dmleung added 31 Dec 2022
     call this%InitCold     (bounds)
     call this%InitDustVars (bounds)
 
@@ -164,6 +169,8 @@ subroutine InitAllocate(this, bounds)
     allocate(this%frc_thr_rghn_fct_patch    (begp:endp))        ; this%frc_thr_rghn_fct_patch    (:)   = nan
     !#### added by dmleung 28 Jul 2022 ######################################
     allocate(this%wnd_frc_thr_std_patch     (begp:endp))        ; this%wnd_frc_thr_std_patch     (:)   = nan
+    !#### added by dmleung 31 Dec 2022 ######################################
+    allocate(this%dpfct_rock_patch          (begp:endp))        ; this%dpfct_rock_patch          (:)   = nan
   end subroutine InitAllocate
 
   !------------------------------------------------------------------------
@@ -292,16 +299,23 @@ subroutine InitHistory(this, bounds)
     call hist_addfld1d (fname='WND_FRC_FT_STD', units='m/s',  &
          avgflag='A', long_name='standardized fluid threshold friction velocity', &
          ptr_patch=this%wnd_frc_thr_std_patch, set_lake=0._r8, set_urb=0._r8)
+    !#####added by dmleung 31 Dec 2022 ########################################
+    this%dpfct_rock_patch(begp:endp) = spval
+    call hist_addfld1d (fname='DPFCT_ROCK', units='m/s',  &
+         avgflag='A', long_name='rock drag partition factor', &
+         ptr_patch=this%dpfct_rock_patch, set_lake=0._r8, set_urb=0._r8)
     !##########################################################################
 
   end subroutine InitHistory
 
   !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
+  subroutine InitCold(this, bounds)   !dmleung commented 31 Dec 2022
+  !subroutine InitCold(this, bounds)
     !
     ! !ARGUMENTS:
-    class (dust_type) :: this
+    class(dust_type), intent(inout) :: this  ! dmleung used class instead of type, 31 Dec 2022
     type(bounds_type), intent(in) :: bounds  
+    !type(dust_type), intent(inout) :: dust_inst
     !
     ! !LOCAL VARIABLES:
     integer :: c,l
@@ -317,6 +331,19 @@ subroutine InitCold(this, bounds)
        end if
     end do
 
+    !associate(                                                                 &
+    !     dpfct_rock                 =>   this%dpfct_rock_patch                 &
+    !     )
+      ! Caulculate Drag Partition factor, dmleung added 31 Dec 2022
+      if ( this%prigentroughnessstream%useStreams() )then !if usestreams == true, and it should be always true
+         call this%prigentroughnessstream%CalcDragPartition( bounds, &
+                               num_nolakep, filter_nolakep, this%dpfct_rock_patch(bounds%begp:bounds%endp) )
+      else
+
+         call endrun( "ERROR:: Drag partitioning MUST now use a streams file of aeolian roughness length to calculate, it can no longer read from the fsurdat file" )
+      end if
+    !end associate
+
   end subroutine InitCold
 
   !------------------------------------------------------------------------
@@ -452,13 +479,15 @@ subroutine DustEmission (bounds, &
          prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , &
          prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , &
          ! added by dmleung 17 Dec 2021
-         roughfct            => soilstate_inst%roughfct_patch        , &
+         roughfct            => soilstate_inst%roughfct_patch        , &  ! dmleung replaced it by dpfct_rock below, 31 Dec 2022
          ! added by dmleung 20 Dec 2021
          ssr                 => dust_inst%ssr_patch                  , &
          lai                 => dust_inst%lai_patch                  , &
          frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , &
          ! added by dmleung 28 Jul 2022
-         wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch       &
+         wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch      , &
+         ! added by dmleung 31 Dec 2022
+         dpfct_rock          => dust_inst%dpfct_rock_patch            &  ! dmleung used roughfct (roughness factor) instead of dpfct_rock (rock drag partition factor) here. Could change it back to dpfct_rock here and below later, 31 Dec 2022
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -654,7 +683,8 @@ subroutine DustEmission (bounds, &
             ! dmleung added calculation of LUH2 bare vs veg fraction within a grid 6 Oct 2022
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then
-                  frc_thr_rgh_fct = roughfct(p)
+                  !frc_thr_rgh_fct = roughfct(p)  ! dmleung commented out 13 Dec 2022 and added next line
+                  frc_thr_rgh_fct = dpfct_rock(p)
                else 
                   frc_thr_rgh_fct = ssr(p)
                end if
diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
new file mode 100644
index 0000000000..7da0e7bf50
--- /dev/null
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -0,0 +1,397 @@
+module PrigentRoughnessStreamType
+!dmleung modified based on ch4FInundatedStreamType on 17 Nov 2022
+#include "shr_assert.h"             ! What is this? In many modules but not dust module
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Contains methods for reading in the Prigent et al. (1997) roughness length streams file. dmleung 22 Nov 2022
+  !
+  ! !USES
+  use ESMF                         
+  use dshr_strdata_mod , only : shr_strdata_type
+  use shr_kind_mod     , only : r8 => shr_kind_r8, CL => shr_kind_cl
+  use shr_log_mod      , only : errMsg => shr_log_errMsg
+  use spmdMod          , only : mpicom, masterproc
+  use clm_varctl       , only : iulog
+  use abortutils       , only : endrun
+  use decompMod        , only : bounds_type
+  !use ch4varcon        , only : finundation_mtd   ! dmleung commented out. need to replace anything here?
+
+  ! !PUBLIC TYPES:
+  implicit none
+  private
+
+  type, public :: prigentroughnessstream_type
+     ! dmleung commented the next five lines. Does it need any replacement here?
+     real(r8), pointer, private :: prigent_rghn  (:)         ! Prigent et al. (1997) roughness length (m)
+     !real(r8), pointer, private :: zwt0_gdc  (:)         ! col coefficient for determining finundated (m)
+     !real(r8), pointer, private :: f0_gdc    (:)         ! col maximum inundated fraction for a gridcell (for methane code)
+     !real(r8), pointer, private :: p3_gdc    (:)         ! col coefficient for determining finundated (m)
+     !real(r8), pointer, private :: fws_slope_gdc     (:) ! col slope in fws = slope * tws + intercept (A coefficient)
+     !real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient)
+  contains
+
+      ! !PUBLIC MEMBER FUNCTIONS:
+      procedure, public :: Init            ! Initialize and read data in
+      !procedure, public :: CalcFinundated  ! Calculate finundated based on input streams
+      procedure, public :: CalcDragPartition ! Calculate drag partitioning based on input streams
+      procedure, public :: UseStreams      ! If streams will be used -- dmleung set default as yes
+
+      ! !PRIVATE MEMBER FUNCTIONS:
+      procedure, private :: InitAllocate   ! Allocate data
+
+  end type prigentroughnessstream_type
+
+  ! ! PRIVATE DATA:
+  type, private :: streamcontrol_type
+     character(len=CL)  :: stream_fldFileName_prigentroughness   ! data Filename
+     character(len=CL)  :: stream_meshfile_prigentroughness      ! mesh Filename
+     character(len=CL)  :: prigentroughnessmapalgo               ! map algo
+  contains
+     procedure, private :: ReadNML     ! Read in namelist
+  end type streamcontrol_type
+
+  type(streamcontrol_type), private :: control        ! Stream control data
+
+  character(len=*), parameter, private :: sourcefile = &  
+       __FILE__
+
+!==============================================================================
+contains
+!==============================================================================
+
+  subroutine Init(this, bounds, NLFilename)
+   !
+   ! Initialize the prigent roughness stream object
+   !
+   ! Uses:
+   use spmdMod          , only : iam                !what is this and do I need this
+   !use ch4varcon        , only : finundation_mtd_h2osfc
+   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+   use lnd_comp_shr     , only : mesh, model_clock
+   use dshr_strdata_mod , only : shr_strdata_init_from_inline, shr_strdata_print
+   use dshr_strdata_mod , only : shr_strdata_advance
+   use dshr_methods_mod , only : dshr_fldbun_getfldptr                !what is this and do I need this (read ncdata?)
+   !
+   ! arguments
+   implicit none
+   class(prigentroughnessstream_type) :: this
+   type(bounds_type), intent(in)   :: bounds
+   character(len=*),  intent(in)   :: NLFilename   ! Namelist filename
+   !
+   ! local variables
+   integer                        :: ig, g, n           ! Indices
+   integer                        :: year               ! year (0, ...) for nstep+1
+   integer                        :: mon                ! month (1, ..., 12) for nstep+1
+   integer                        :: day                ! day of month (1, ..., 31) for nstep+1
+   integer                        :: sec                ! seconds into current date for nstep+1
+   integer                        :: mcdate             ! Current model date (yyyymmdd)
+   type(shr_strdata_type)         :: sdat_rghn      ! input data stream
+   character(len=16), allocatable :: stream_varnames(:) ! array of stream field names
+   integer                        :: rc                 ! error code
+   real(r8), pointer              :: dataptr1d(:)       ! temporary pointer
+   !character(len=*), parameter    :: stream_name = 'prigentroughness'
+   !-----------------------------------------------------------------------
+
+   !if ( finundation_mtd /= finundation_mtd_h2osfc )then     ! how should I change this? comment out for now
+      call this%InitAllocate( bounds )
+      call control%ReadNML( bounds, NLFileName )
+
+      if ( this%useStreams() )then     ! is this a namelist input and is it set in namelist default
+
+         !if (finundation_mtd == finundation_mtd_ZWT_inversion  )then
+         !   allocate(stream_varnames(3))
+         !   stream_varnames = (/"ZWT0","F0  ","P3  "/)
+         !else if ( finundation_mtd == finundation_mtd_TWS_inversion  )then
+            allocate(stream_varnames(1))
+            stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
+         !else
+         !   call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// &
+         !        errMsg(sourcefile, __LINE__))
+         !end if
+
+         if (masterproc) then
+            write(iulog,*) '  stream_varnames                  = ',stream_varnames
+      end if
+
+      ! Initialize the cdeps data type sdat_rghn
+      call shr_strdata_init_from_inline(sdat_rghn,                                  &     ! what is this function and where does it come from?
+              my_task             = iam,                                                &
+              logunit             = iulog,                                              &
+              compname            = 'LND',                                              &
+              model_clock         = model_clock,                                        &
+              model_mesh          = mesh,                                               &
+              stream_meshfile     = control%stream_meshfile_prigentroughness,              &
+              stream_lev_dimname  = 'null',                                             &
+              stream_mapalgo      = control%prigentroughnessmapalgo,                       &
+              stream_filenames    = (/trim(control%stream_fldFileName_prigentroughness)/), &
+              stream_fldlistFile  = stream_varnames,                                    &
+              stream_fldListModel = stream_varnames,                                    &
+              stream_yearFirst    = 1997,                                               &
+              stream_yearLast     = 1997,                                               &
+              stream_yearAlign    = 1,                                                  &
+              stream_offset       = 0,                                                  &
+              stream_taxmode      = 'extend',                                           &
+              stream_dtlimit      = 1.0e30_r8,                                          &
+              stream_tintalgo     = 'linear',                                           &
+              stream_name         = 'Prigent roughness',                                 &
+              rc                  = rc)
+         if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+            call ESMF_Finalize(endflag=ESMF_END_ABORT)
+         end if
+
+         ! Explicitly set current date to a hardcoded constant value. Otherwise
+         ! using the real date can cause roundoff differences that are
+         ! detrected as issues with exact restart.  EBK M05/20/2017
+         ! call get_curr_date(year, mon, day, sec)
+         year = 1997
+         mon  = 12
+         day  = 31
+         sec  = 0
+         mcdate = year*10000 + mon*100 + day
+
+         call shr_strdata_advance(sdat_rghn, ymd=mcdate, tod=sec, logunit=iulog, istr='prigentrghn', rc=rc)   ! what is istr and do I need to change elsewhere because the change of istr here
+         if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+            call ESMF_Finalize(endflag=ESMF_END_ABORT)
+         end if
+
+         ! Get pointer for stream data that is time and spatially interpolate to model time and grid
+         do n = 1,size(stream_varnames) 
+            call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)   ! is the ncdf datasets read here, looping across all available variables in the files? Also, not sure about pstrm and fldbun_model
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+               call ESMF_Finalize(endflag=ESMF_END_ABORT)
+            end if
+            if (trim(stream_varnames(n)) == 'Z0a') then
+               ig = 0
+               do g = bounds%begg,bounds%endg
+                  ig = ig+1                   ! not sure why +1 is needed but it's okay
+                  this%prigent_rghn(g) = dataptr1d(ig)
+               end do
+
+            end if
+
+         end do
+      end if
+   !end if         !comment out for now
+
+  end subroutine Init
+
+  !==============================================================================
+  logical function UseStreams(this)
+    !
+    ! !DESCRIPTION:
+    ! Return true if
+    !
+    ! !USES:
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(prigentroughnessstream_type) :: this
+    !
+    ! !LOCAL VARIABLES:
+    if ( trim(control%stream_fldFileName_prigentroughness) == '' )then
+       UseStreams = .false.  ! dmleung: this won't happen and UseStreams will always be true
+    else
+       UseStreams = .true.
+    end if
+  end function UseStreams
+
+  !==============================================================================
+  subroutine InitAllocate(this, bounds)
+    !
+    ! !DESCRIPTION:
+    ! Allocate module variables and data structures
+    !
+    ! !USES:
+    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
+    !use ch4varcon     , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(prigentroughnessstream_type) :: this
+    type(bounds_type), intent(in) :: bounds
+    !
+    ! !LOCAL VARIABLES:
+    !integer  :: begc, endc
+    integer  :: begg, endg
+    !---------------------------------------------------------------------
+
+    !begc = bounds%begc; endc = bounds%endc
+    begg = bounds%begg; endg = bounds%endg
+
+    !if( finundation_mtd == finundation_mtd_ZWT_inversion )then
+       allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
+    !   allocate(this%zwt0_gdc         (begg:endg))            ;  this%zwt0_gdc         (:)   = nan
+    !   allocate(this%f0_gdc           (begg:endg))            ;  this%f0_gdc           (:)   = nan
+    !   allocate(this%p3_gdc           (begg:endg))            ;  this%p3_gdc           (:)   = nan
+    !else if( finundation_mtd == finundation_mtd_TWS_inversion )then
+    !   allocate(this%fws_slope_gdc    (begg:endg))            ;  this%fws_slope_gdc    (:)   = nan
+    !   allocate(this%fws_intercept_gdc(begg:endg))            ;  this%fws_intercept_gdc(:)   = nan
+    !end if
+
+  end subroutine InitAllocate
+
+  !==============================================================================
+  !subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, &
+  !                          waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated )
+  subroutine CalcDragPartition(this, bounds, num_nolakep, filter_nolakep, dpfct_rock)
+    !
+    ! !DESCRIPTION:
+    ! Commented below by dmleung 31 Dec 2022
+    ! Calculate the drag partition effect of friction velocity due to surface roughness following 
+    ! Leung et al. (2022).  This module is used in the dust emission module DUSTMod.F90 for 
+    ! calculating drag partitioning. The drag partition equation comes from Marticorena and 
+    ! Bergametti (1995) with constants modified by Darmenova et al. (2009). Here it is assumed 
+    ! that this equation is used only over arid/desertic regions, such that Catherine Prigent's
+    ! roughness measurements represents mostly rocks. For more vegetated areas, the vegetation
+    ! roughness and drag partitioning are calculated in the DustEmission subroutine. This 
+    ! subroutine is used in the InitCold subroutine of DUSTMod.F90.
+    !
+    ! !USES:
+    !use ColumnType              , only : col
+    use PatchType               , only : patch
+    !use ch4varcon               , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion
+    !use ch4varcon               , only : finundation_mtd_TWS_inversion
+    !use clm_varpar              , only : nlevsoi
+    !use SoilHydrologyType       , only : soilhydrology_type
+    !use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(prigentroughnessstream_type)             :: this
+    type(bounds_type)              , intent(in)    :: bounds
+    !integer                        , intent(in)    :: num_soilc                       ! number of column soil points in column filter
+    !integer                        , intent(in)    :: filter_soilc(:)                 ! column filter for soil points
+    integer                        , intent(in)    :: num_nolakep                      !
+    integer                        , intent(in)    :: filter_nolakep(num_nolakep)      !
+    !type(soilhydrology_type)       , intent(in)    :: soilhydrology_inst
+    !type(waterdiagnosticbulk_type) , intent(in)    :: waterdiagnosticbulk_inst
+    !real(r8)                       , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
+    !real(r8)                       , intent(inout) :: finundated(bounds%begc:)        ! fractional inundated area in soil column (excluding dedicated wetland columns)
+    real(r8)                       , intent(inout) :: dpfct_rock(bounds%begp:)      ! [fraction] rock drag partition factor (roughness effect)
+    !
+    ! !LOCAL VARIABLES:
+    !integer  :: g, c, fc    ! Indices
+    integer  :: g, p, fp    ! Indices
+    real(r8) :: z0s         ! smooth roughness length (m)
+    !real(r8) :: zwt_actual  ! Total water storage (ZWT) to use either perched or total depending on conditions
+    
+    ! constants
+    real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2022)
+    real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume estimating roughness effect at a distance of 10 m following Leung et al. (2022)
+    !---------------------------------------------------------------------
+
+    !SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__)    ! not sure what this is
+    !SHR_ASSERT_ALL_FL((ubound(finundated)        == (/bounds%endc/)), sourcefile, __LINE__)
+    SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__) !what's the use of this
+
+    !associate(                                                     &
+         !z           =>   col%z                                   & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
+         !zwt         =>   soilhydrology_inst%zwt_col         ,     & ! Input:  [real(r8) (:)   ]  water table depth (m)
+         !zwt_perched =>   soilhydrology_inst%zwt_perched_col ,     & ! Input:  [real(r8) (:)   ]  perched water table depth (m)
+         !tws         =>   waterdiagnosticbulk_inst%tws_grc   ,     & ! Input:  [real(r8) (:)   ]  total water storage (kg m-2)
+         !frac_h2osfc =>   waterdiagnosticbulk_inst%frac_h2osfc_col & ! Input:  [real(r8) (:)   ]  fraction of ground covered by surface water (0 to 1)
+    !)
+
+    ! Calculate finundated
+    !do fc = 1, num_soilc
+    !   c = filter_soilc(fc)
+    !   g = col%gridcell(c)
+    !   select case( finundation_mtd )
+    !      case ( finundation_mtd_h2osfc )
+    !         finundated(c) = frac_h2osfc(c)
+    !      case ( finundation_mtd_ZWT_inversion )
+    !         if (this%zwt0_gdc(g) > 0._r8) then
+    !            if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then
+    !               zwt_actual = zwt_perched(c)
+    !            else
+    !               zwt_actual = zwt(c)
+    !            end if
+    !            finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c)
+    !         else
+    !            finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c)
+    !         end if
+    !      case ( finundation_mtd_TWS_inversion )
+    !         finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g)
+    !   end select
+    !   finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) )
+    !end do
+
+    ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks. We save the drag partition factor as a patch level quantity.
+    z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006). Here we assume soil medium size is a global constant, and so is smooth roughness length.
+    do fp = 1,num_nolakep
+       p = filter_nolakep(fp)
+       g = patch%gridcell(p)
+
+       dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)^0.8_r8) ) ! Calculating rock drag partition factor using Marticorena and Bergametti (1995). 0.01 is used to convert Z0a from centimeter to meter.
+    end do
+
+    !end associate
+
+  end subroutine CalcDragPartition
+
+  !==============================================================================
+  subroutine ReadNML(this, bounds, NLFilename)
+   !
+   ! Read the namelist data stream information.
+   !
+   ! Uses:
+   use shr_nl_mod       , only : shr_nl_find_group_name
+   use shr_log_mod      , only : errMsg => shr_log_errMsg
+   use shr_mpi_mod      , only : shr_mpi_bcast
+   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+   !
+   ! arguments
+   implicit none
+   class(streamcontrol_type)     :: this
+   type(bounds_type), intent(in) :: bounds
+   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+   !
+   ! local variables
+   integer            :: nu_nml    ! unit for namelist file
+   integer            :: nml_error ! namelist i/o error flag
+   character(len=CL)  :: stream_fldFileName_prigentroughness = ' '
+   character(len=CL)  :: stream_meshfile_prigentroughness = ' '
+   character(len=CL)  :: prigentroughnessmapalgo = 'bilinear'
+   character(len=*), parameter :: namelist_name = 'prigentroughness'    ! MUST agree with group name in namelist definition to read. dmleung commented
+   !character(len=*), parameter :: subName = "('prigentroughness::ReadNML')"
+   !-----------------------------------------------------------------------
+
+   namelist /prigentroughness/ &               ! MUST agree with namelist_name above
+        prigentroughnessmapalgo,  stream_fldFileName_prigentroughness, stream_meshfile_prigentroughness
+
+   ! Default values for namelist
+
+   ! Read prigentroughness namelist
+   if (masterproc) then
+      open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+      call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error)
+      if (nml_error == 0) then
+         read(nu_nml, nml=prigentroughness,iostat=nml_error)   ! MUST agree with namelist_name above
+         if (nml_error /= 0) then
+            call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
+         end if
+      else
+         call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
+      end if
+      close(nu_nml)
+   endif
+
+   call shr_mpi_bcast(prigentroughnessmapalgo             , mpicom)
+   call shr_mpi_bcast(stream_fldFileName_prigentroughness , mpicom)
+   call shr_mpi_bcast(stream_meshfile_prigentroughness    , mpicom)
+
+   if (masterproc) then
+      write(iulog,*) ' '
+      write(iulog,*) namelist_name, ' stream settings:'
+      write(iulog,*) '  stream_fldFileName_prigentroughness = ',stream_fldFileName_prigentroughness
+      write(iulog,*) '  stream_meshfile_prigentroughness    = ',stream_meshfile_prigentroughness
+      write(iulog,*) '  prigentroughnessmapalgo             = ',prigentroughnessmapalgo
+   endif
+   this%stream_fldFileName_prigentroughness = stream_fldFileName_prigentroughness
+   this%stream_meshfile_prigentroughness    = stream_meshfile_prigentroughness
+   this%prigentroughnessmapalgo             = prigentroughnessmapalgo
+
+ end subroutine ReadNML
+
+end module PrigentRoughnessStreamType

From 512c7027e86e18ee7826f0eaa9903c817d2e22ff Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 31 Jan 2023 16:36:45 -0700
Subject: [PATCH 0023/1248] dmleung fixed some bugs for the streams capability
 and further modified clm_instMod.F90. Now CTSM can compile successfully. 31
 Jan 2023

---
 src/biogeochem/DUSTMod.F90                    | 20 ++++++++++++++-----
 .../share_esmf/PrigentRoughnessStreamType.F90 | 14 +++++++------
 src/main/clm_instMod.F90                      |  2 +-
 3 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 381ecfe41d..8425a413c5 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -34,6 +34,7 @@ module DUSTMod
   !use clm_instur           , only : wt_lunit, wt_nat_patch  ! dmleung added 24 Jul 2022
   !use landunit_varcon      , only : istsoil, istcrop        ! dmleung added 24 Jul 2022 (refering to main/landunit_varcon.F90, for wt_lunit, istsoil=1 is nat veg, istcrop=2 is crop)
   use pftconMod            , only : noveg              ! dmleung added 24 Jul 2022
+  use PrigentRoughnessStreamType    , only : prigentroughnessstream_type
   !  
   ! !PUBLIC TYPES
   implicit none
@@ -109,14 +110,19 @@ module DUSTMod
 
   !------------------------------------------------------------------------
   !##### dmleung edited for initializing stream files 31 Dec 2022  ########
+  !subroutine Init(this, bounds, NLFilename, num_nolakep, filter_nolakep)
   subroutine Init(this, bounds, NLFilename)
 
     class(dust_type) :: this
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds 
+    character(len=*),  intent(in) :: NLFilename   ! dmleung added 31 Dec 2022
+    !integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
+    !integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points  
 
     call this%InitAllocate (bounds)
     call this%InitHistory  (bounds)
     call this%prigentroughnessstream%Init( bounds, NLFilename )  ! dmleung added 31 Dec 2022
+    !call this%InitCold     (bounds, num_nolakep, filter_nolakep)
     call this%InitCold     (bounds)
     call this%InitDustVars (bounds)
 
@@ -309,12 +315,15 @@ subroutine InitHistory(this, bounds)
   end subroutine InitHistory
 
   !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)   !dmleung commented 31 Dec 2022
-  !subroutine InitCold(this, bounds)
+  !subroutine InitCold(this, bounds, num_nolakep, filter_nolakep)   !dmleung commented 31 Dec 2022
+  subroutine InitCold(this, bounds)
     !
     ! !ARGUMENTS:
     class(dust_type), intent(inout) :: this  ! dmleung used class instead of type, 31 Dec 2022
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds 
+    ! dmleung also added the below no-lake filter 31 Dec 2022
+    !integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
+    !integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points 
     !type(dust_type), intent(inout) :: dust_inst
     !
     ! !LOCAL VARIABLES:
@@ -337,7 +346,8 @@ subroutine InitCold(this, bounds)   !dmleung commented 31 Dec 2022
       ! Caulculate Drag Partition factor, dmleung added 31 Dec 2022
       if ( this%prigentroughnessstream%useStreams() )then !if usestreams == true, and it should be always true
          call this%prigentroughnessstream%CalcDragPartition( bounds, &
-                               num_nolakep, filter_nolakep, this%dpfct_rock_patch(bounds%begp:bounds%endp) )
+    !                           num_nolakep, filter_nolakep, this%dpfct_rock_patch(bounds%begp:bounds%endp) )
+                                this%dpfct_rock_patch(bounds%begp:bounds%endp) )
       else
 
          call endrun( "ERROR:: Drag partitioning MUST now use a streams file of aeolian roughness length to calculate, it can no longer read from the fsurdat file" )
diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 7da0e7bf50..246d25aee0 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -234,7 +234,8 @@ end subroutine InitAllocate
   !==============================================================================
   !subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, &
   !                          waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated )
-  subroutine CalcDragPartition(this, bounds, num_nolakep, filter_nolakep, dpfct_rock)
+  !subroutine CalcDragPartition(this, bounds, num_nolakep, filter_nolakep, dpfct_rock)
+  subroutine CalcDragPartition(this, bounds, dpfct_rock)
     !
     ! !DESCRIPTION:
     ! Commented below by dmleung 31 Dec 2022
@@ -262,8 +263,8 @@ subroutine CalcDragPartition(this, bounds, num_nolakep, filter_nolakep, dpfct_ro
     type(bounds_type)              , intent(in)    :: bounds
     !integer                        , intent(in)    :: num_soilc                       ! number of column soil points in column filter
     !integer                        , intent(in)    :: filter_soilc(:)                 ! column filter for soil points
-    integer                        , intent(in)    :: num_nolakep                      !
-    integer                        , intent(in)    :: filter_nolakep(num_nolakep)      !
+    !integer                        , intent(in)    :: num_nolakep                      !
+    !integer                        , intent(in)    :: filter_nolakep(num_nolakep)      !
     !type(soilhydrology_type)       , intent(in)    :: soilhydrology_inst
     !type(waterdiagnosticbulk_type) , intent(in)    :: waterdiagnosticbulk_inst
     !real(r8)                       , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
@@ -319,11 +320,12 @@ subroutine CalcDragPartition(this, bounds, num_nolakep, filter_nolakep, dpfct_ro
 
     ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks. We save the drag partition factor as a patch level quantity.
     z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006). Here we assume soil medium size is a global constant, and so is smooth roughness length.
-    do fp = 1,num_nolakep
-       p = filter_nolakep(fp)
+    !do fp = 1,num_nolakep
+    !   p = filter_nolakep(fp)
+    do p = bounds%begp,bounds%endp
        g = patch%gridcell(p)
 
-       dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)^0.8_r8) ) ! Calculating rock drag partition factor using Marticorena and Bergametti (1995). 0.01 is used to convert Z0a from centimeter to meter.
+       dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)**0.8_r8) ) ! Calculating rock drag partition factor using Marticorena and Bergametti (1995). 0.01 is used to convert Z0a from centimeter to meter.
     end do
 
     !end associate
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index 7924c2111e..13390d3417 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -340,7 +340,7 @@ subroutine clm_instInit(bounds)
 
     call surfrad_inst%Init(bounds)
 
-    call dust_inst%Init(bounds)
+    call dust_inst%Init(bounds, NLFilename)   ! dmleung added NLFilename 31 Dec 2022
 
     allocate(scf_method, source = CreateAndInitSnowCoverFraction( &
          snow_cover_fraction_method = snow_cover_fraction_method, &

From 059597c896e8c2593ff1b740f32df163208bc159 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 6 Feb 2023 13:05:05 -0700
Subject: [PATCH 0024/1248] code cleanup by dmleung; 6 Feb 2023

---
 bld/CLMBuildNamelist.pm                       |  1 +
 .../share_esmf/PrigentRoughnessStreamType.F90 | 88 ++-----------------
 2 files changed, 10 insertions(+), 79 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index d078b3869c..0a548a857f 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4236,6 +4236,7 @@ sub write_output_files {
   push @groups, "ch4finundated";
   push @groups, "soilbgc_decomp";
   push @groups, "clm_canopy_inparm";
+  push @groups, "prigentroughness";
   if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') {
      push @groups, "scf_swenson_lawrence_2012_inparm";
   }
diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 246d25aee0..e3f8b68014 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -4,7 +4,7 @@ module PrigentRoughnessStreamType
 
   !-----------------------------------------------------------------------
   ! !DESCRIPTION:
-  ! Contains methods for reading in the Prigent et al. (1997) roughness length streams file. dmleung 22 Nov 2022
+  ! Contains methods for reading in the Prigent et al. (2005) roughness length streams file. dmleung 22 Nov 2022
   !
   ! !USES
   use ESMF                         
@@ -15,25 +15,17 @@ module PrigentRoughnessStreamType
   use clm_varctl       , only : iulog
   use abortutils       , only : endrun
   use decompMod        , only : bounds_type
-  !use ch4varcon        , only : finundation_mtd   ! dmleung commented out. need to replace anything here?
 
   ! !PUBLIC TYPES:
   implicit none
   private
 
   type, public :: prigentroughnessstream_type
-     ! dmleung commented the next five lines. Does it need any replacement here?
      real(r8), pointer, private :: prigent_rghn  (:)         ! Prigent et al. (1997) roughness length (m)
-     !real(r8), pointer, private :: zwt0_gdc  (:)         ! col coefficient for determining finundated (m)
-     !real(r8), pointer, private :: f0_gdc    (:)         ! col maximum inundated fraction for a gridcell (for methane code)
-     !real(r8), pointer, private :: p3_gdc    (:)         ! col coefficient for determining finundated (m)
-     !real(r8), pointer, private :: fws_slope_gdc     (:) ! col slope in fws = slope * tws + intercept (A coefficient)
-     !real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient)
   contains
 
       ! !PUBLIC MEMBER FUNCTIONS:
       procedure, public :: Init            ! Initialize and read data in
-      !procedure, public :: CalcFinundated  ! Calculate finundated based on input streams
       procedure, public :: CalcDragPartition ! Calculate drag partitioning based on input streams
       procedure, public :: UseStreams      ! If streams will be used -- dmleung set default as yes
 
@@ -65,13 +57,11 @@ subroutine Init(this, bounds, NLFilename)
    ! Initialize the prigent roughness stream object
    !
    ! Uses:
-   use spmdMod          , only : iam                !what is this and do I need this
-   !use ch4varcon        , only : finundation_mtd_h2osfc
-   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+   use spmdMod          , only : iam                
    use lnd_comp_shr     , only : mesh, model_clock
    use dshr_strdata_mod , only : shr_strdata_init_from_inline, shr_strdata_print
    use dshr_strdata_mod , only : shr_strdata_advance
-   use dshr_methods_mod , only : dshr_fldbun_getfldptr                !what is this and do I need this (read ncdata?)
+   use dshr_methods_mod , only : dshr_fldbun_getfldptr                
    !
    ! arguments
    implicit none
@@ -90,7 +80,7 @@ subroutine Init(this, bounds, NLFilename)
    character(len=16), allocatable :: stream_varnames(:) ! array of stream field names
    integer                        :: rc                 ! error code
    real(r8), pointer              :: dataptr1d(:)       ! temporary pointer
-   !character(len=*), parameter    :: stream_name = 'prigentroughness'
+   character(len=*), parameter    :: stream_name = 'prigentroughness'
    !-----------------------------------------------------------------------
 
    !if ( finundation_mtd /= finundation_mtd_h2osfc )then     ! how should I change this? comment out for now
@@ -99,16 +89,8 @@ subroutine Init(this, bounds, NLFilename)
 
       if ( this%useStreams() )then     ! is this a namelist input and is it set in namelist default
 
-         !if (finundation_mtd == finundation_mtd_ZWT_inversion  )then
-         !   allocate(stream_varnames(3))
-         !   stream_varnames = (/"ZWT0","F0  ","P3  "/)
-         !else if ( finundation_mtd == finundation_mtd_TWS_inversion  )then
-            allocate(stream_varnames(1))
-            stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
-         !else
-         !   call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// &
-         !        errMsg(sourcefile, __LINE__))
-         !end if
+         allocate(stream_varnames(1))
+         stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
 
          if (masterproc) then
             write(iulog,*) '  stream_varnames                  = ',stream_varnames
@@ -157,7 +139,7 @@ subroutine Init(this, bounds, NLFilename)
 
          ! Get pointer for stream data that is time and spatially interpolate to model time and grid
          do n = 1,size(stream_varnames) 
-            call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)   ! is the ncdf datasets read here, looping across all available variables in the files? Also, not sure about pstrm and fldbun_model
+            call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)
             if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
                call ESMF_Finalize(endflag=ESMF_END_ABORT)
             end if
@@ -204,7 +186,6 @@ subroutine InitAllocate(this, bounds)
     !
     ! !USES:
     use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    !use ch4varcon     , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
     !
     ! !ARGUMENTS:
     implicit none
@@ -219,15 +200,7 @@ subroutine InitAllocate(this, bounds)
     !begc = bounds%begc; endc = bounds%endc
     begg = bounds%begg; endg = bounds%endg
 
-    !if( finundation_mtd == finundation_mtd_ZWT_inversion )then
-       allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
-    !   allocate(this%zwt0_gdc         (begg:endg))            ;  this%zwt0_gdc         (:)   = nan
-    !   allocate(this%f0_gdc           (begg:endg))            ;  this%f0_gdc           (:)   = nan
-    !   allocate(this%p3_gdc           (begg:endg))            ;  this%p3_gdc           (:)   = nan
-    !else if( finundation_mtd == finundation_mtd_TWS_inversion )then
-    !   allocate(this%fws_slope_gdc    (begg:endg))            ;  this%fws_slope_gdc    (:)   = nan
-    !   allocate(this%fws_intercept_gdc(begg:endg))            ;  this%fws_intercept_gdc(:)   = nan
-    !end if
+    allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
 
   end subroutine InitAllocate
 
@@ -251,73 +224,31 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     ! !USES:
     !use ColumnType              , only : col
     use PatchType               , only : patch
-    !use ch4varcon               , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion
-    !use ch4varcon               , only : finundation_mtd_TWS_inversion
-    !use clm_varpar              , only : nlevsoi
-    !use SoilHydrologyType       , only : soilhydrology_type
-    !use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type
     !
     ! !ARGUMENTS:
     implicit none
     class(prigentroughnessstream_type)             :: this
     type(bounds_type)              , intent(in)    :: bounds
-    !integer                        , intent(in)    :: num_soilc                       ! number of column soil points in column filter
-    !integer                        , intent(in)    :: filter_soilc(:)                 ! column filter for soil points
     !integer                        , intent(in)    :: num_nolakep                      !
     !integer                        , intent(in)    :: filter_nolakep(num_nolakep)      !
-    !type(soilhydrology_type)       , intent(in)    :: soilhydrology_inst
-    !type(waterdiagnosticbulk_type) , intent(in)    :: waterdiagnosticbulk_inst
-    !real(r8)                       , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
-    !real(r8)                       , intent(inout) :: finundated(bounds%begc:)        ! fractional inundated area in soil column (excluding dedicated wetland columns)
     real(r8)                       , intent(inout) :: dpfct_rock(bounds%begp:)      ! [fraction] rock drag partition factor (roughness effect)
     !
     ! !LOCAL VARIABLES:
     !integer  :: g, c, fc    ! Indices
     integer  :: g, p, fp    ! Indices
     real(r8) :: z0s         ! smooth roughness length (m)
-    !real(r8) :: zwt_actual  ! Total water storage (ZWT) to use either perched or total depending on conditions
     
     ! constants
     real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2022)
     real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume estimating roughness effect at a distance of 10 m following Leung et al. (2022)
     !---------------------------------------------------------------------
 
-    !SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__)    ! not sure what this is
-    !SHR_ASSERT_ALL_FL((ubound(finundated)        == (/bounds%endc/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__) !what's the use of this
 
     !associate(                                                     &
          !z           =>   col%z                                   & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
-         !zwt         =>   soilhydrology_inst%zwt_col         ,     & ! Input:  [real(r8) (:)   ]  water table depth (m)
-         !zwt_perched =>   soilhydrology_inst%zwt_perched_col ,     & ! Input:  [real(r8) (:)   ]  perched water table depth (m)
-         !tws         =>   waterdiagnosticbulk_inst%tws_grc   ,     & ! Input:  [real(r8) (:)   ]  total water storage (kg m-2)
-         !frac_h2osfc =>   waterdiagnosticbulk_inst%frac_h2osfc_col & ! Input:  [real(r8) (:)   ]  fraction of ground covered by surface water (0 to 1)
     !)
 
-    ! Calculate finundated
-    !do fc = 1, num_soilc
-    !   c = filter_soilc(fc)
-    !   g = col%gridcell(c)
-    !   select case( finundation_mtd )
-    !      case ( finundation_mtd_h2osfc )
-    !         finundated(c) = frac_h2osfc(c)
-    !      case ( finundation_mtd_ZWT_inversion )
-    !         if (this%zwt0_gdc(g) > 0._r8) then
-    !            if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then
-    !               zwt_actual = zwt_perched(c)
-    !            else
-    !               zwt_actual = zwt(c)
-    !            end if
-    !            finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c)
-    !         else
-    !            finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c)
-    !         end if
-    !      case ( finundation_mtd_TWS_inversion )
-    !         finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g)
-    !   end select
-    !   finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) )
-    !end do
-
     ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks. We save the drag partition factor as a patch level quantity.
     z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006). Here we assume soil medium size is a global constant, and so is smooth roughness length.
     !do fp = 1,num_nolakep
@@ -341,7 +272,6 @@ subroutine ReadNML(this, bounds, NLFilename)
    use shr_nl_mod       , only : shr_nl_find_group_name
    use shr_log_mod      , only : errMsg => shr_log_errMsg
    use shr_mpi_mod      , only : shr_mpi_bcast
-   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
    !
    ! arguments
    implicit none
@@ -356,7 +286,7 @@ subroutine ReadNML(this, bounds, NLFilename)
    character(len=CL)  :: stream_meshfile_prigentroughness = ' '
    character(len=CL)  :: prigentroughnessmapalgo = 'bilinear'
    character(len=*), parameter :: namelist_name = 'prigentroughness'    ! MUST agree with group name in namelist definition to read. dmleung commented
-   !character(len=*), parameter :: subName = "('prigentroughness::ReadNML')"
+   character(len=*), parameter :: subName = "('prigentroughness::ReadNML')"
    !-----------------------------------------------------------------------
 
    namelist /prigentroughness/ &               ! MUST agree with namelist_name above

From 436329500392af185d640b1200e4a72c46200141 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 8 Feb 2023 12:43:44 -0600
Subject: [PATCH 0025/1248] [dev.03] Fix interior building temperature update

1. changed how interior building temperature is updated based on proposed scheme, by adding back the heat not removed by AC;
2. added an intermediate local variable `efllx_urban_ac_sat`;
3. `t_building_max` now indicates the saturation setpoints.
---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index d54d3ff86d..024922348a 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -236,6 +236,8 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     real(r8) :: t_floor_bef(bounds%begl:bounds%endl)       ! floor temperature at previous time step (K)              
     real(r8) :: t_building_bef(bounds%begl:bounds%endl)    ! internal building air temperature at previous time step [K]
     real(r8) :: t_building_bef_hac(bounds%begl:bounds%endl)! internal building air temperature before applying HAC [K]
+    ! Cathy [dev.03]
+    real(r8) :: eflx_urban_ac_sat(bounds%begl:bounds%endl) ! urban air conditioning flux under AC adoption saturation (W/m**2)
     real(r8) :: hcv_roofi(bounds%begl:bounds%endl)         ! roof convective heat transfer coefficient (W m-2 K-1)
     real(r8) :: hcv_sunwi(bounds%begl:bounds%endl)         ! sunwall convective heat transfer coefficient (W m-2 K-1)
     real(r8) :: hcv_shdwi(bounds%begl:bounds%endl)         ! shadewall convective heat transfer coefficient (W m-2 K-1)
@@ -925,13 +927,17 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
 !           rho_dair(l) = pstd / (rair*t_building(l))
 
             if (t_building_bef_hac(l) > t_building_max(l)) then
-              t_building(l) = t_building_max(l)
-              ! [Cathy] orig: 
+              ! Cathy [orig] 
+              ! t_building(l) = t_building_max(l)
               ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
               !                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
-              ! [Cathy] dev:
-              eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
-                                 - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
+              ! Cathy [dev.03]      ! after the change, t_building_max is saturation setpoint
+              eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) &
+                                     - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
+              t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urbann_ac_sat(l) &
+                              * dtime / (ht_roof(l) * rho_dair(l) * cpair)
+              eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l)
+
             else if (t_building_bef_hac(l) < t_building_min(l)) then
               t_building(l) = t_building_min(l)
               eflx_urban_heat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &

From ab0f8e15a64b8391a49b02d9a1f789a3cbbeaa4b Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 8 Feb 2023 16:47:07 -0600
Subject: [PATCH 0026/1248] [dev03] Fix typo

---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index 024922348a..e5626cb65c 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -934,7 +934,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
               ! Cathy [dev.03]      ! after the change, t_building_max is saturation setpoint
               eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) &
                                      - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
-              t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urbann_ac_sat(l) &
+              t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) &
                               * dtime / (ht_roof(l) * rho_dair(l) * cpair)
               eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l)
 

From aa68753b6a7339808350ba8c23b83e6d494131ac Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 22 Feb 2023 23:56:54 -0600
Subject: [PATCH 0027/1248] [dev.03] Remove write statements

Remove 8 write to log statements (added in as part of dev.02 for debugging) to fix the timing issues
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 32 ++-----------------------
 1 file changed, 2 insertions(+), 30 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 1f679b88a3..ae34449c1e 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -72,10 +72,6 @@ subroutine Init(this, bounds, NLFilename)
     allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
 
     call this%urbantv_init(bounds, NLFilename)
-
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: urbantv_init done.'
-
     call this%urbantv_interp(bounds)
 
     ! Add history fields     ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90
@@ -190,14 +186,8 @@ subroutine urbantv_init(this, bounds, NLFilename)
        do n = 1,6
           write(iulog,'(a,a)' ) '  stream_varname         = ',trim(stream_varnames(n))
        end do
-       ! Cathy [orig]
-       ! write(iulog,*) ' '
-       ! Cathy [dev.02]
-       write(iulog,*) 'Cathy: does write statements have to be inside if?'
+       write(iulog,*) ' '
     endif
-    
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: before shr_strdata_init_from_inline'
 
     ! Initialize the cdeps data type this%sdat_urbantv
     call shr_strdata_init_from_inline(this%sdat_urbantv,             &
@@ -226,9 +216,6 @@ subroutine urbantv_init(this, bounds, NLFilename)
          stream_name         = 'Urban time varying data',            &
          rc                  = rc)
 
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: before shr_strdata_init_from_inline'
-
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
     end if
@@ -267,23 +254,14 @@ subroutine urbantv_interp(this, bounds)
     real(r8), pointer :: dataptr2d(:,:)
     !-----------------------------------------------------------------------
 
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: before get_curr_date'
-
     ! Advance sdat stream
     call get_curr_date(year, mon, day, sec)
     mcdate = year*10000 + mon*100 + day
 
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: after get_curr_date, before shr_strdata_advance'
-
     call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
-    end if
-
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: before creating 2d array'    
+    end if 
 
     ! Create 2d array for all stream variable data
     lsize = bounds%endg - bounds%begg + 1
@@ -305,9 +283,6 @@ subroutine urbantv_interp(this, bounds)
        end do
     end do
 
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits'
-
     ! Determine this%tbuilding_max for all landunits
     do l = bounds%begl,bounds%endl
        if (lun%urbpoi(l)) then
@@ -338,9 +313,6 @@ subroutine urbantv_interp(this, bounds)
     end do
     deallocate(dataptr2d)
 
-    ! Cathy [dev.02]
-    write(iulog,*) 'Cathy: after determining t_building_max and p_ac for all landunits'
-
     ! Error check
     found = .false.
     do l = bounds%begl,bounds%endl

From cc7696eb8c6f4fca96020e0679df0fc9c486d5eb Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Sat, 25 Feb 2023 21:47:12 -0700
Subject: [PATCH 0028/1248]  dmleung added a nolake filter in calculating the
 drag partition effect (25 Feb 2023).

---
 src/biogeochem/DUSTMod.F90                    | 10 +-
 .../share_esmf/PrigentRoughnessStreamType.F90 | 97 ++++++++++++++++---
 2 files changed, 93 insertions(+), 14 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 8425a413c5..8488fdf682 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -123,7 +123,7 @@ subroutine Init(this, bounds, NLFilename)
     call this%InitHistory  (bounds)
     call this%prigentroughnessstream%Init( bounds, NLFilename )  ! dmleung added 31 Dec 2022
     !call this%InitCold     (bounds, num_nolakep, filter_nolakep)
-    call this%InitCold     (bounds)
+    call this%InitCold     (bounds)                             ! dmleung commented 31 Dec 2022
     call this%InitDustVars (bounds)
 
   end subroutine Init
@@ -309,7 +309,7 @@ subroutine InitHistory(this, bounds)
     this%dpfct_rock_patch(begp:endp) = spval
     call hist_addfld1d (fname='DPFCT_ROCK', units='m/s',  &
          avgflag='A', long_name='rock drag partition factor', &
-         ptr_patch=this%dpfct_rock_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%dpfct_rock_patch)
     !##########################################################################
 
   end subroutine InitHistory
@@ -317,6 +317,10 @@ end subroutine InitHistory
   !-----------------------------------------------------------------------
   !subroutine InitCold(this, bounds, num_nolakep, filter_nolakep)   !dmleung commented 31 Dec 2022
   subroutine InitCold(this, bounds)
+    !
+    !USES dmleung added 31 Dec 2022
+    !use landunit_varcon      , only : istdlak
+    !use LandunitType         , only : lun
     !
     ! !ARGUMENTS:
     class(dust_type), intent(inout) :: this  ! dmleung used class instead of type, 31 Dec 2022
@@ -346,7 +350,7 @@ subroutine InitCold(this, bounds)
       ! Caulculate Drag Partition factor, dmleung added 31 Dec 2022
       if ( this%prigentroughnessstream%useStreams() )then !if usestreams == true, and it should be always true
          call this%prigentroughnessstream%CalcDragPartition( bounds, &
-    !                           num_nolakep, filter_nolakep, this%dpfct_rock_patch(bounds%begp:bounds%endp) )
+         !                       num_nolakep, filter_nolakep, this%dpfct_rock_patch(bounds%begp:bounds%endp) )
                                 this%dpfct_rock_patch(bounds%begp:bounds%endp) )
       else
 
diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index e3f8b68014..ad8843b706 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -4,7 +4,7 @@ module PrigentRoughnessStreamType
 
   !-----------------------------------------------------------------------
   ! !DESCRIPTION:
-  ! Contains methods for reading in the Prigent et al. (2005) roughness length streams file. dmleung 22 Nov 2022
+  ! Contains methods for reading in the Prigent et al. (1997) roughness length streams file. dmleung 22 Nov 2022
   !
   ! !USES
   use ESMF                         
@@ -15,17 +15,25 @@ module PrigentRoughnessStreamType
   use clm_varctl       , only : iulog
   use abortutils       , only : endrun
   use decompMod        , only : bounds_type
+  !use ch4varcon        , only : finundation_mtd   ! dmleung commented out. need to replace anything here?
 
   ! !PUBLIC TYPES:
   implicit none
   private
 
   type, public :: prigentroughnessstream_type
+     ! dmleung commented the next five lines. Does it need any replacement here?
      real(r8), pointer, private :: prigent_rghn  (:)         ! Prigent et al. (1997) roughness length (m)
+     !real(r8), pointer, private :: zwt0_gdc  (:)         ! col coefficient for determining finundated (m)
+     !real(r8), pointer, private :: f0_gdc    (:)         ! col maximum inundated fraction for a gridcell (for methane code)
+     !real(r8), pointer, private :: p3_gdc    (:)         ! col coefficient for determining finundated (m)
+     !real(r8), pointer, private :: fws_slope_gdc     (:) ! col slope in fws = slope * tws + intercept (A coefficient)
+     !real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient)
   contains
 
       ! !PUBLIC MEMBER FUNCTIONS:
       procedure, public :: Init            ! Initialize and read data in
+      !procedure, public :: CalcFinundated  ! Calculate finundated based on input streams
       procedure, public :: CalcDragPartition ! Calculate drag partitioning based on input streams
       procedure, public :: UseStreams      ! If streams will be used -- dmleung set default as yes
 
@@ -57,11 +65,13 @@ subroutine Init(this, bounds, NLFilename)
    ! Initialize the prigent roughness stream object
    !
    ! Uses:
-   use spmdMod          , only : iam                
+   use spmdMod          , only : iam                !what is this and do I need this
+   !use ch4varcon        , only : finundation_mtd_h2osfc
+   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
    use lnd_comp_shr     , only : mesh, model_clock
    use dshr_strdata_mod , only : shr_strdata_init_from_inline, shr_strdata_print
    use dshr_strdata_mod , only : shr_strdata_advance
-   use dshr_methods_mod , only : dshr_fldbun_getfldptr                
+   use dshr_methods_mod , only : dshr_fldbun_getfldptr                !what is this and do I need this (read ncdata?)
    !
    ! arguments
    implicit none
@@ -89,8 +99,16 @@ subroutine Init(this, bounds, NLFilename)
 
       if ( this%useStreams() )then     ! is this a namelist input and is it set in namelist default
 
-         allocate(stream_varnames(1))
-         stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
+         !if (finundation_mtd == finundation_mtd_ZWT_inversion  )then
+         !   allocate(stream_varnames(3))
+         !   stream_varnames = (/"ZWT0","F0  ","P3  "/)
+         !else if ( finundation_mtd == finundation_mtd_TWS_inversion  )then
+            allocate(stream_varnames(1))
+            stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
+         !else
+         !   call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// &
+         !        errMsg(sourcefile, __LINE__))
+         !end if
 
          if (masterproc) then
             write(iulog,*) '  stream_varnames                  = ',stream_varnames
@@ -139,7 +157,7 @@ subroutine Init(this, bounds, NLFilename)
 
          ! Get pointer for stream data that is time and spatially interpolate to model time and grid
          do n = 1,size(stream_varnames) 
-            call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)
+            call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)   ! is the ncdf datasets read here, looping across all available variables in the files? Also, not sure about pstrm and fldbun_model
             if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
                call ESMF_Finalize(endflag=ESMF_END_ABORT)
             end if
@@ -186,6 +204,7 @@ subroutine InitAllocate(this, bounds)
     !
     ! !USES:
     use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
+    !use ch4varcon     , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
     !
     ! !ARGUMENTS:
     implicit none
@@ -200,7 +219,15 @@ subroutine InitAllocate(this, bounds)
     !begc = bounds%begc; endc = bounds%endc
     begg = bounds%begg; endg = bounds%endg
 
-    allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
+    !if( finundation_mtd == finundation_mtd_ZWT_inversion )then
+       allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
+    !   allocate(this%zwt0_gdc         (begg:endg))            ;  this%zwt0_gdc         (:)   = nan
+    !   allocate(this%f0_gdc           (begg:endg))            ;  this%f0_gdc           (:)   = nan
+    !   allocate(this%p3_gdc           (begg:endg))            ;  this%p3_gdc           (:)   = nan
+    !else if( finundation_mtd == finundation_mtd_TWS_inversion )then
+    !   allocate(this%fws_slope_gdc    (begg:endg))            ;  this%fws_slope_gdc    (:)   = nan
+    !   allocate(this%fws_intercept_gdc(begg:endg))            ;  this%fws_intercept_gdc(:)   = nan
+    !end if
 
   end subroutine InitAllocate
 
@@ -224,39 +251,86 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     ! !USES:
     !use ColumnType              , only : col
     use PatchType               , only : patch
+    !USES dmleung added 31 Dec 2022
+    use landunit_varcon         , only : istdlak
+    use LandunitType            , only : lun
+    !use ch4varcon               , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion
+    !use ch4varcon               , only : finundation_mtd_TWS_inversion
+    !use clm_varpar              , only : nlevsoi
+    !use SoilHydrologyType       , only : soilhydrology_type
+    !use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type
     !
     ! !ARGUMENTS:
     implicit none
     class(prigentroughnessstream_type)             :: this
     type(bounds_type)              , intent(in)    :: bounds
+    !integer                        , intent(in)    :: num_soilc                       ! number of column soil points in column filter
+    !integer                        , intent(in)    :: filter_soilc(:)                 ! column filter for soil points
     !integer                        , intent(in)    :: num_nolakep                      !
     !integer                        , intent(in)    :: filter_nolakep(num_nolakep)      !
+    !type(soilhydrology_type)       , intent(in)    :: soilhydrology_inst
+    !type(waterdiagnosticbulk_type) , intent(in)    :: waterdiagnosticbulk_inst
+    !real(r8)                       , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
+    !real(r8)                       , intent(inout) :: finundated(bounds%begc:)        ! fractional inundated area in soil column (excluding dedicated wetland columns)
     real(r8)                       , intent(inout) :: dpfct_rock(bounds%begp:)      ! [fraction] rock drag partition factor (roughness effect)
     !
     ! !LOCAL VARIABLES:
     !integer  :: g, c, fc    ! Indices
-    integer  :: g, p, fp    ! Indices
+    integer  :: g, p, fp, l    ! Indices
     real(r8) :: z0s         ! smooth roughness length (m)
+    !real(r8) :: zwt_actual  ! Total water storage (ZWT) to use either perched or total depending on conditions
     
     ! constants
     real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2022)
     real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume estimating roughness effect at a distance of 10 m following Leung et al. (2022)
     !---------------------------------------------------------------------
 
+    !SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__)    ! not sure what this is
+    !SHR_ASSERT_ALL_FL((ubound(finundated)        == (/bounds%endc/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__) !what's the use of this
 
     !associate(                                                     &
          !z           =>   col%z                                   & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
+         !zwt         =>   soilhydrology_inst%zwt_col         ,     & ! Input:  [real(r8) (:)   ]  water table depth (m)
+         !zwt_perched =>   soilhydrology_inst%zwt_perched_col ,     & ! Input:  [real(r8) (:)   ]  perched water table depth (m)
+         !tws         =>   waterdiagnosticbulk_inst%tws_grc   ,     & ! Input:  [real(r8) (:)   ]  total water storage (kg m-2)
+         !frac_h2osfc =>   waterdiagnosticbulk_inst%frac_h2osfc_col & ! Input:  [real(r8) (:)   ]  fraction of ground covered by surface water (0 to 1)
     !)
 
+    ! Calculate finundated
+    !do fc = 1, num_soilc
+    !   c = filter_soilc(fc)
+    !   g = col%gridcell(c)
+    !   select case( finundation_mtd )
+    !      case ( finundation_mtd_h2osfc )
+    !         finundated(c) = frac_h2osfc(c)
+    !      case ( finundation_mtd_ZWT_inversion )
+    !         if (this%zwt0_gdc(g) > 0._r8) then
+    !            if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then
+    !               zwt_actual = zwt_perched(c)
+    !            else
+    !               zwt_actual = zwt(c)
+    !            end if
+    !            finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c)
+    !         else
+    !            finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c)
+    !         end if
+    !      case ( finundation_mtd_TWS_inversion )
+    !         finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g)
+    !   end select
+    !   finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) )
+    !end do
+
     ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks. We save the drag partition factor as a patch level quantity.
     z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006). Here we assume soil medium size is a global constant, and so is smooth roughness length.
     !do fp = 1,num_nolakep
-    !   p = filter_nolakep(fp)
+       !p = filter_nolakep(fp)
     do p = bounds%begp,bounds%endp
        g = patch%gridcell(p)
-
-       dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)**0.8_r8) ) ! Calculating rock drag partition factor using Marticorena and Bergametti (1995). 0.01 is used to convert Z0a from centimeter to meter.
+       l = patch%landunit(p)
+       if (lun%itype(l) /= istdlak) then
+          dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)**0.8_r8) ) ! Calculating rock drag partition factor using Marticorena and Bergametti (1995). 0.01 is used to convert Z0a from centimeter to meter.
+       end if
     end do
 
     !end associate
@@ -272,6 +346,7 @@ subroutine ReadNML(this, bounds, NLFilename)
    use shr_nl_mod       , only : shr_nl_find_group_name
    use shr_log_mod      , only : errMsg => shr_log_errMsg
    use shr_mpi_mod      , only : shr_mpi_bcast
+   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
    !
    ! arguments
    implicit none

From 53ea16556f8de0c99e2bd1e9573a104ccc3c0ce0 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Sat, 25 Feb 2023 22:10:07 -0700
Subject: [PATCH 0029/1248] code cleanup by dmleung 25 Feb 2023

---
 .../share_esmf/PrigentRoughnessStreamType.F90 | 85 ++-----------------
 1 file changed, 7 insertions(+), 78 deletions(-)

diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index ad8843b706..19ab3cb573 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -15,25 +15,17 @@ module PrigentRoughnessStreamType
   use clm_varctl       , only : iulog
   use abortutils       , only : endrun
   use decompMod        , only : bounds_type
-  !use ch4varcon        , only : finundation_mtd   ! dmleung commented out. need to replace anything here?
 
   ! !PUBLIC TYPES:
   implicit none
   private
 
   type, public :: prigentroughnessstream_type
-     ! dmleung commented the next five lines. Does it need any replacement here?
      real(r8), pointer, private :: prigent_rghn  (:)         ! Prigent et al. (1997) roughness length (m)
-     !real(r8), pointer, private :: zwt0_gdc  (:)         ! col coefficient for determining finundated (m)
-     !real(r8), pointer, private :: f0_gdc    (:)         ! col maximum inundated fraction for a gridcell (for methane code)
-     !real(r8), pointer, private :: p3_gdc    (:)         ! col coefficient for determining finundated (m)
-     !real(r8), pointer, private :: fws_slope_gdc     (:) ! col slope in fws = slope * tws + intercept (A coefficient)
-     !real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient)
   contains
 
       ! !PUBLIC MEMBER FUNCTIONS:
       procedure, public :: Init            ! Initialize and read data in
-      !procedure, public :: CalcFinundated  ! Calculate finundated based on input streams
       procedure, public :: CalcDragPartition ! Calculate drag partitioning based on input streams
       procedure, public :: UseStreams      ! If streams will be used -- dmleung set default as yes
 
@@ -65,13 +57,11 @@ subroutine Init(this, bounds, NLFilename)
    ! Initialize the prigent roughness stream object
    !
    ! Uses:
-   use spmdMod          , only : iam                !what is this and do I need this
-   !use ch4varcon        , only : finundation_mtd_h2osfc
-   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+   use spmdMod          , only : iam
    use lnd_comp_shr     , only : mesh, model_clock
    use dshr_strdata_mod , only : shr_strdata_init_from_inline, shr_strdata_print
    use dshr_strdata_mod , only : shr_strdata_advance
-   use dshr_methods_mod , only : dshr_fldbun_getfldptr                !what is this and do I need this (read ncdata?)
+   use dshr_methods_mod , only : dshr_fldbun_getfldptr
    !
    ! arguments
    implicit none
@@ -99,23 +89,15 @@ subroutine Init(this, bounds, NLFilename)
 
       if ( this%useStreams() )then     ! is this a namelist input and is it set in namelist default
 
-         !if (finundation_mtd == finundation_mtd_ZWT_inversion  )then
-         !   allocate(stream_varnames(3))
-         !   stream_varnames = (/"ZWT0","F0  ","P3  "/)
-         !else if ( finundation_mtd == finundation_mtd_TWS_inversion  )then
             allocate(stream_varnames(1))
             stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
-         !else
-         !   call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// &
-         !        errMsg(sourcefile, __LINE__))
-         !end if
 
          if (masterproc) then
             write(iulog,*) '  stream_varnames                  = ',stream_varnames
-      end if
+         end if
 
-      ! Initialize the cdeps data type sdat_rghn
-      call shr_strdata_init_from_inline(sdat_rghn,                                  &     ! what is this function and where does it come from?
+         ! Initialize the cdeps data type sdat_rghn
+         call shr_strdata_init_from_inline(sdat_rghn,                                  &     ! what is this function and where does it come from?
               my_task             = iam,                                                &
               logunit             = iulog,                                              &
               compname            = 'LND',                                              &
@@ -157,7 +139,7 @@ subroutine Init(this, bounds, NLFilename)
 
          ! Get pointer for stream data that is time and spatially interpolate to model time and grid
          do n = 1,size(stream_varnames) 
-            call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)   ! is the ncdf datasets read here, looping across all available variables in the files? Also, not sure about pstrm and fldbun_model
+            call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)
             if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
                call ESMF_Finalize(endflag=ESMF_END_ABORT)
             end if
@@ -204,7 +186,6 @@ subroutine InitAllocate(this, bounds)
     !
     ! !USES:
     use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    !use ch4varcon     , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
     !
     ! !ARGUMENTS:
     implicit none
@@ -219,15 +200,7 @@ subroutine InitAllocate(this, bounds)
     !begc = bounds%begc; endc = bounds%endc
     begg = bounds%begg; endg = bounds%endg
 
-    !if( finundation_mtd == finundation_mtd_ZWT_inversion )then
-       allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
-    !   allocate(this%zwt0_gdc         (begg:endg))            ;  this%zwt0_gdc         (:)   = nan
-    !   allocate(this%f0_gdc           (begg:endg))            ;  this%f0_gdc           (:)   = nan
-    !   allocate(this%p3_gdc           (begg:endg))            ;  this%p3_gdc           (:)   = nan
-    !else if( finundation_mtd == finundation_mtd_TWS_inversion )then
-    !   allocate(this%fws_slope_gdc    (begg:endg))            ;  this%fws_slope_gdc    (:)   = nan
-    !   allocate(this%fws_intercept_gdc(begg:endg))            ;  this%fws_intercept_gdc(:)   = nan
-    !end if
+    allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
 
   end subroutine InitAllocate
 
@@ -254,72 +227,29 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     !USES dmleung added 31 Dec 2022
     use landunit_varcon         , only : istdlak
     use LandunitType            , only : lun
-    !use ch4varcon               , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion
-    !use ch4varcon               , only : finundation_mtd_TWS_inversion
-    !use clm_varpar              , only : nlevsoi
-    !use SoilHydrologyType       , only : soilhydrology_type
-    !use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type
     !
     ! !ARGUMENTS:
     implicit none
     class(prigentroughnessstream_type)             :: this
     type(bounds_type)              , intent(in)    :: bounds
-    !integer                        , intent(in)    :: num_soilc                       ! number of column soil points in column filter
-    !integer                        , intent(in)    :: filter_soilc(:)                 ! column filter for soil points
-    !integer                        , intent(in)    :: num_nolakep                      !
-    !integer                        , intent(in)    :: filter_nolakep(num_nolakep)      !
-    !type(soilhydrology_type)       , intent(in)    :: soilhydrology_inst
-    !type(waterdiagnosticbulk_type) , intent(in)    :: waterdiagnosticbulk_inst
-    !real(r8)                       , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
-    !real(r8)                       , intent(inout) :: finundated(bounds%begc:)        ! fractional inundated area in soil column (excluding dedicated wetland columns)
     real(r8)                       , intent(inout) :: dpfct_rock(bounds%begp:)      ! [fraction] rock drag partition factor (roughness effect)
     !
     ! !LOCAL VARIABLES:
     !integer  :: g, c, fc    ! Indices
     integer  :: g, p, fp, l    ! Indices
     real(r8) :: z0s         ! smooth roughness length (m)
-    !real(r8) :: zwt_actual  ! Total water storage (ZWT) to use either perched or total depending on conditions
     
     ! constants
     real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2022)
     real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume estimating roughness effect at a distance of 10 m following Leung et al. (2022)
     !---------------------------------------------------------------------
 
-    !SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__)    ! not sure what this is
-    !SHR_ASSERT_ALL_FL((ubound(finundated)        == (/bounds%endc/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__) !what's the use of this
 
     !associate(                                                     &
          !z           =>   col%z                                   & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
-         !zwt         =>   soilhydrology_inst%zwt_col         ,     & ! Input:  [real(r8) (:)   ]  water table depth (m)
-         !zwt_perched =>   soilhydrology_inst%zwt_perched_col ,     & ! Input:  [real(r8) (:)   ]  perched water table depth (m)
-         !tws         =>   waterdiagnosticbulk_inst%tws_grc   ,     & ! Input:  [real(r8) (:)   ]  total water storage (kg m-2)
-         !frac_h2osfc =>   waterdiagnosticbulk_inst%frac_h2osfc_col & ! Input:  [real(r8) (:)   ]  fraction of ground covered by surface water (0 to 1)
     !)
 
-    ! Calculate finundated
-    !do fc = 1, num_soilc
-    !   c = filter_soilc(fc)
-    !   g = col%gridcell(c)
-    !   select case( finundation_mtd )
-    !      case ( finundation_mtd_h2osfc )
-    !         finundated(c) = frac_h2osfc(c)
-    !      case ( finundation_mtd_ZWT_inversion )
-    !         if (this%zwt0_gdc(g) > 0._r8) then
-    !            if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then
-    !               zwt_actual = zwt_perched(c)
-    !            else
-    !               zwt_actual = zwt(c)
-    !            end if
-    !            finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c)
-    !         else
-    !            finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c)
-    !         end if
-    !      case ( finundation_mtd_TWS_inversion )
-    !         finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g)
-    !   end select
-    !   finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) )
-    !end do
 
     ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks. We save the drag partition factor as a patch level quantity.
     z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006). Here we assume soil medium size is a global constant, and so is smooth roughness length.
@@ -346,7 +276,6 @@ subroutine ReadNML(this, bounds, NLFilename)
    use shr_nl_mod       , only : shr_nl_find_group_name
    use shr_log_mod      , only : errMsg => shr_log_errMsg
    use shr_mpi_mod      , only : shr_mpi_bcast
-   !use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
    !
    ! arguments
    implicit none

From e6b80df3c8d37f7d262123e2ac5f82227bd04a45 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 1 Mar 2023 17:41:22 -0600
Subject: [PATCH 0030/1248] [dev.04] Add toggle `urban_explicit_ac`

1. Add a new logical variable `urban_explicit_ac` (default true) in __UrbanParamsType.F90__;
2. Add if-else block to building interior building temperature and AC flux calculation in __UrbBuildTempOleson2015Mod.F90__: use p_ac if `urban_explicit_ac` is set to true, otherwise use the original way of calculation;
3. Add `urban_explicit_ac` to __namelist_definition_ctsm.xml__; and
4. Add `urban_explicit_ac` default value (.true.) to __namelist_defaults_ctsm.xml__.
---
 bld/namelist_files/namelist_defaults_ctsm.xml |  6 +++++
 .../namelist_definition_ctsm.xml              |  8 +++++++
 src/biogeophys/UrbBuildTempOleson2015Mod.F90  | 24 ++++++++++++-------
 src/biogeophys/UrbanParamsType.F90            | 11 ++++++++-
 4 files changed, 39 insertions(+), 10 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 69643041a4..5be2604c36 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -166,6 +166,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <calc_human_stress_indices phys="clm5_0" >FAST</calc_human_stress_indices>
 <calc_human_stress_indices phys="clm4_5" >NONE</calc_human_stress_indices>
 
+<!--                                                                              -->
+<!-- Cathy [dev.04]                                                               -->
+<!-- Default urban air conditioning flux and building interior temperature scheme -->
+<urban_explicit_ac phys="clm5_1" >.true.</urban_explicit_ac>
+<urban_explicit_ac phys="clm5_0" >.true.</urban_explicit_ac>
+
 <!-- Default urban traffic flux -->
 <urban_traffic>.false.</urban_traffic>
 
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index bc1dd034aa..aae38a5cec 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -947,6 +947,14 @@ Turn urban air conditioning/heating ON or OFF and add wasteheat:
     ON_WASTEHEAT = Air conditioning/heating is ON and waste-heat sent to urban canyon
 </entry>
 
+<!--                          -->
+<!-- Cathy [dev.04]           -->
+<!--                          -->
+<entry id="urban_explicit_ac" type="logical" category="clm_physics"
+       group="clmu_inparm" valid_values="" >
+If TRUE, use explicit, time-varying AC adoption rate for air-conditioning flux and interior building temperature calculations.
+</entry>
+
 <entry id="urban_traffic" type="logical" category="clm_physics"
        group="clmu_inparm" valid_values="" >
 If TRUE, urban traffic flux will be activated (Currently NOT implemented).
diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index e5626cb65c..0ab72ac0a6 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -210,7 +210,10 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     use clm_varctl      , only : iulog
     use abortutils      , only : endrun
     use clm_varpar      , only : nlevurb, nlevsno, nlevmaxurbgrnd
-    use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on
+    ! Cathy [orig]:
+    ! use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on
+    ! Cathy [dev.04]:
+    use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on, urban_explicit_ac
 !
 ! !ARGUMENTS:
     implicit none
@@ -927,16 +930,19 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
 !           rho_dair(l) = pstd / (rair*t_building(l))
 
             if (t_building_bef_hac(l) > t_building_max(l)) then
-              ! Cathy [orig] 
-              ! t_building(l) = t_building_max(l)
-              ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
-              !                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
-              ! Cathy [dev.03]      ! after the change, t_building_max is saturation setpoint
-              eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) &
+              ! Cathy [dev.04]
+              if (urban_explicit_ac) then   ! use explicit ac adoption rate:
+                ! Cathy [dev.03]            ! after the change, t_building_max is saturation setpoint
+                eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) &
                                      - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
-              t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) &
+                t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) &
                               * dtime / (ht_roof(l) * rho_dair(l) * cpair)
-              eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l)
+                eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l)
+              else
+                ! Cathy [orig] 
+                t_building(l) = t_building_max(l)
+                eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
+                                   - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
 
             else if (t_building_bef_hac(l) < t_building_min(l)) then
               t_building(l) = t_building_min(l)
diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90
index c490ad27cc..c674aac2db 100644
--- a/src/biogeophys/UrbanParamsType.F90
+++ b/src/biogeophys/UrbanParamsType.F90
@@ -101,6 +101,8 @@ module UrbanParamsType
   character(len= *), parameter, public :: urban_hac_on =  'ON'                 
   character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT'  
   character(len= 16), public           :: urban_hac = urban_hac_off
+  ! Cathy [dev.04]
+  logical, public                      :: urban_explicit_ac = .true.  ! whether to use explicit, time-varying AC adoption rate
   logical, public                      :: urban_traffic = .false.     ! urban traffic fluxes
 
   ! !PRIVATE MEMBER DATA:
@@ -847,7 +849,10 @@ subroutine UrbanReadNML ( NLFilename )
     integer :: unitn                ! unit for namelist file
     character(len=32) :: subname = 'UrbanReadNML'  ! subroutine name
 
-    namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method
+    ! Cathy [orig]:
+    ! namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method
+    ! Cathy [dev.04]:
+    namelist / clmu_inparm / urban_hac, urban_explicit_ac, urban_traffic, building_temp_method
     !EOP
     !-----------------------------------------------------------------------
 
@@ -875,6 +880,8 @@ subroutine UrbanReadNML ( NLFilename )
 
     ! Broadcast namelist variables read in
     call shr_mpi_bcast(urban_hac,             mpicom)
+    ! Cathy [dev.04]:
+    call shr_mpi_bcast(urban_explicit_ac,     mpicom)
     call shr_mpi_bcast(urban_traffic,         mpicom)
     call shr_mpi_bcast(building_temp_method,  mpicom)
 
@@ -886,6 +893,8 @@ subroutine UrbanReadNML ( NLFilename )
     !
     if ( masterproc )then
        write(iulog,*) '   urban air conditioning/heating and wasteheat   = ', urban_hac
+       ! Cathy [dev.04]:
+       write(iulog,*) '   urban explicit air-conditioning adoption rate   = ', urban_explicit_ac
        write(iulog,*) '   urban traffic flux   = ', urban_traffic
     end if
 

From 30af382df1b3bb0b00ba7c9cfb3b115fa751eee4 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 1 Mar 2023 17:51:09 -0600
Subject: [PATCH 0031/1248] [dev. 04] Add toggle `urban_explicit_ac` (cont'd)

5. Add `urban_explicit_ac` to __CLMBuildNamelist.pm__.
---
 bld/CLMBuildNamelist.pm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index c2a32da4ac..a56e5b12b7 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2111,6 +2111,8 @@ sub setup_logic_urban {
 
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac');
+  # Cathy [dev.04]
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac')
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic');
 }
 

From 4726cede9bb015acdcf8090440eda62d252314b8 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 1 Mar 2023 18:01:23 -0600
Subject: [PATCH 0032/1248] [dev.04] debug

Add missing ";"
---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index a56e5b12b7..7c185ff6a0 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2112,7 +2112,7 @@ sub setup_logic_urban {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac');
   # Cathy [dev.04]
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac')
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic');
 }
 

From ab2e87aa8fd6e591c7721011ecc14788fb9d87b9 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 1 Mar 2023 18:13:04 -0600
Subject: [PATCH 0033/1248] [dev.04] debug

Add "`end if`"
---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index 0ab72ac0a6..2a5440e324 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -943,6 +943,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
                 t_building(l) = t_building_max(l)
                 eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
                                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
+              end if
 
             else if (t_building_bef_hac(l) < t_building_min(l)) then
               t_building(l) = t_building_min(l)

From 23f44daea7cb26b21fcf0d357389be5aecf86a28 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Fri, 31 Mar 2023 15:00:22 -0600
Subject: [PATCH 0034/1248]  remove the older methods of reading in prigent's
 roughenss data (rough_fct) since the stream methods is here (dmleung 31 Mar
 2023)

---
 bld/CLMBuildNamelist.pm                       |  7 ++++-
 .../namelist_definition_ctsm.xml              |  8 +-----
 src/biogeochem/DUSTMod.F90                    |  2 --
 src/biogeophys/SoilStateInitTimeConstMod.F90  | 27 -------------------
 src/biogeophys/SoilStateType.F90              |  6 -----
 src/main/clm_varctl.F90                       |  1 -
 src/main/controlMod.F90                       | 13 ---------
 7 files changed, 7 insertions(+), 57 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 0a548a857f..3b0c79d000 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1663,6 +1663,11 @@ sub process_namelist_inline_logic {
   ##################################
   setup_logic_lai_streams($opts,  $nl_flags, $definition, $defaults, $nl);
 
+  ##################################
+  # namelist group: dust_emis_streams  #
+  ##################################
+  #setup_logic_dustemis_streams($opts,  $nl_flags, $definition, $defaults, $nl);
+
   ##########################################
   # namelist group: soil_moisture_streams  #
   ##########################################
@@ -4236,7 +4241,7 @@ sub write_output_files {
   push @groups, "ch4finundated";
   push @groups, "soilbgc_decomp";
   push @groups, "clm_canopy_inparm";
-  push @groups, "prigentroughness";
+  push @groups, "prigentroughness"; # dmleung 31 Dec 2022
   if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') {
      push @groups, "scf_swenson_lawrence_2012_inparm";
   }
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 6cdf4e3ce5..ec29018081 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1768,6 +1768,7 @@ If true, will ignore the prescribed soilm data for that point and let the model
 prescribed data.
 </entry>
 
+
 <!-- ========================================================================================  -->
 <!-- lai_streams streams Namelist (when phys = CLM4_5)                              -->
 <!-- ========================================================================================  -->
@@ -2811,13 +2812,6 @@ use case.)
 
 </entry>
 
-<!-- added by dmleung to CLM5, 17 Dec 2021 -->
-<!-- roughness factor f_eff   -dmleung, 22 Apr 2020 -->
-<entry id="rough_fct" type="char*256" input_pathname="abs" category="datasets"
-       group="clm_inparm" valid_values="" >
-Full pathname of time-invariant roughness factor dataset for calculating drag partition of dust emission.
-</entry>
-
 
 
 </namelist_definition>
diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 8488fdf682..f1de13902a 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -492,8 +492,6 @@ subroutine DustEmission (bounds, &
          thr_crs_rate        => dust_inst%thr_crs_rate_patch         , &
          prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , &
          prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , &
-         ! added by dmleung 17 Dec 2021
-         roughfct            => soilstate_inst%roughfct_patch        , &  ! dmleung replaced it by dpfct_rock below, 31 Dec 2022
          ! added by dmleung 20 Dec 2021
          ssr                 => dust_inst%ssr_patch                  , &
          lai                 => dust_inst%lai_patch                  , &
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index c5e2a72977..fc96a878bc 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -172,7 +172,6 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     use clm_varcon          , only : secspday, denh2o, denice, grlnd
     use clm_varctl          , only : use_cn, use_lch4, use_fates
     use clm_varctl          , only : iulog, fsurdat, paramfile, soil_layerstruct_predefined
-    use clm_varctl          , only : rough_fct    ! -dmleung added to CESM2/CLM5 17 Dec 2021
     use landunit_varcon     , only : istdlak, istwet, istsoil, istcrop, istice
     use column_varcon       , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv 
     use fileutils           , only : getfil
@@ -221,7 +220,6 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     real(r8) ,pointer  :: sand3d (:,:)                  ! read in - soil texture: percent sand (needs to be a pointer for use in ncdio)
     real(r8) ,pointer  :: clay3d (:,:)                  ! read in - soil texture: percent clay (needs to be a pointer for use in ncdio)
     real(r8) ,pointer  :: organic3d (:,:)               ! read in - organic matter: kg/m3 (needs to be a pointer for use in ncdio)
-    real(r8) ,pointer  :: roughfct2d(:)                 ! read in - time-invariant roughness factor,   dmleung added 17 Dec 2021
     character(len=256) :: locfn                         ! local filename
     integer            :: ipedof  
     integer            :: begp, endp
@@ -371,31 +369,6 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
 
     call ncd_pio_closefile(ncid)
 
-    !############ subsection for input data for new dust emission scheme ##############
-
-    ! dmleung added to CESM2/CLM5 17 Dec 2021
-    if (rough_fct /= ' ') then
-       allocate(roughfct2d(begg:endg))                                   ! dmleung, 16 Jul 2020
-       ! here to read roughness factor file, 16 Jul 2020
-       !write(iulog,*) 'Attempting to read roughness factor data, by dmleung .....'
-       call getfil (rough_fct, locfn, 0)
-       call ncd_pio_openfile (ncid, locfn, 0)
-       call ncd_io(ncid=ncid, varname='F_eff', flag='read', data=roughfct2d, dim1name=grlnd, readvar=readvar)
-       !write(iulog,*) 'initialize pft level roughness factor from roughfct2d(g) to roughfct(p)'  
-   
-       do p = begp,endp
-          g = patch%gridcell(p)
-          soilstate_inst%roughfct_patch(p) = roughfct2d(g)
-       end do
-
-       call ncd_pio_closefile(ncid)
-    else
-       do p = begp,endp
-          soilstate_inst%roughfct_patch(p) = 1.0_r8
-       end do
-
-    end if
-    !##################################################################################
 
     ! --------------------------------------------------------------------
     ! get original soil depths to be used in interpolation of sand and clay
diff --git a/src/biogeophys/SoilStateType.F90 b/src/biogeophys/SoilStateType.F90
index fa3d5a6aaf..2ee4894ece 100644
--- a/src/biogeophys/SoilStateType.F90
+++ b/src/biogeophys/SoilStateType.F90
@@ -30,9 +30,6 @@ module SoilStateType
      real(r8), pointer :: cellsand_col         (:,:) ! sand value for gridcell containing column (1:nlevsoi)
      real(r8), pointer :: cellclay_col         (:,:) ! clay value for gridcell containing column (1:nlevsoi)
      real(r8), pointer :: bd_col               (:,:) ! col bulk density of dry soil material [kg/m^3] (CN)
-     !####################### for new dust emission scheme  -dmleung ############################
-     real(r8), pointer :: roughfct_patch       (:)   ! roughness factor, 17 dec 2021
-     !###########################################################################################
 
      ! hydraulic properties
      real(r8), pointer :: hksat_col            (:,:) ! col hydraulic conductivity at saturation (mm H2O /s) 
@@ -134,9 +131,6 @@ subroutine InitAllocate(this, bounds)
     allocate(this%cellclay_col         (begc:endc,nlevsoi))             ; this%cellclay_col         (:,:) = nan 
     allocate(this%bd_col               (begc:endc,nlevgrnd))            ; this%bd_col               (:,:) = nan
 
-    !################ dmleung added 14 Dec 2021 ########################
-    allocate(this%roughfct_patch       (begp:endp))                     ; this%roughfct_patch       (:)   = nan
-    !###################################################################
     allocate(this%hksat_col            (begc:endc,nlevgrnd))            ; this%hksat_col            (:,:) = spval
     allocate(this%hksat_min_col        (begc:endc,nlevgrnd))            ; this%hksat_min_col        (:,:) = spval
     allocate(this%hk_l_col             (begc:endc,nlevgrnd))            ; this%hk_l_col             (:,:) = nan   
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 3b7b1321ea..9be9af2f73 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -113,7 +113,6 @@ module clm_varctl
   character(len=fname_len), public :: nrevsn     = ' '        ! restart data file name for branch run
   character(len=fname_len), public :: fsnowoptics  = ' '      ! snow optical properties file name
   character(len=fname_len), public :: fsnowaging   = ' '      ! snow aging parameters file name
-  character(len=fname_len), public :: rough_fct   = ' '       ! roughness factor, dmleung, added 17 Dec 2021
 
   character(len=fname_len), public :: fatmlndfrc = ' '        ! lnd frac file on atm grid
                                                               ! only needed for LILAC and MCT drivers
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 49788b351c..a7bca1aa87 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -282,9 +282,6 @@ subroutine control_init(dtime)
          use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, &
          use_nguardrail
 
-    ! dust emission, dmleung 14 Dec 2021
-    namelist /clm_inparm/  &
-         rough_fct    !-dmleung 17 Dec 2021
 
     ! ----------------------------------------------------------------------
     ! Default values
@@ -656,9 +653,6 @@ subroutine control_spmd()
     call mpi_bcast (fsnowoptics, len(fsnowoptics),  MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fsnowaging,  len(fsnowaging),   MPI_CHARACTER, 0, mpicom, ier)
 
-    ! initialize input data for new dust emission module dmleung 14 Dec 2021
-    call mpi_bcast (rough_fct, len(rough_fct), MPI_CHARACTER, 0, mpicom, ier)! added by dmleung, 17 Dec 2021
-
     ! Irrigation
     call mpi_bcast(irrigate, 1, MPI_LOGICAL, 0, mpicom, ier)
 
@@ -910,13 +904,6 @@ subroutine control_print ()
     write(iulog,*) '   Threshold above which the model keeps the lake landunit =', toosmall_lake
     write(iulog,*) '   Threshold above which the model keeps the wetland landunit =', toosmall_wetland
     write(iulog,*) '   Threshold above which the model keeps the urban landunits =', toosmall_urban
-    !##### for dmleung's input data for new dust emission module #####
-    if (rough_fct == ' ') then    ! -dmleung, 17 Dec 2021
-       write(iulog,*) '   rough_fct surface roughness dataset not set'
-    else
-       write(iulog,*) '   surface roughness data   = ',trim(rough_fct)
-    end if
-    !#################################################################
     if (use_cn) then
        if (suplnitro /= suplnNon)then
           write(iulog,*) '   Supplemental Nitrogen mode is set to run over Patches: ', &

From 70125066da34fb3aa6a90cea491b3b99e9429db3 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Mon, 24 Apr 2023 16:30:53 -0500
Subject: [PATCH 0035/1248] Update clm_varpar.F90

Changed nlevurb to 10 (line 207) to conform to the new surfdata file.
---
 src/main/clm_varpar.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90
index f54b750181..7c7c1681b7 100644
--- a/src/main/clm_varpar.F90
+++ b/src/main/clm_varpar.F90
@@ -203,7 +203,8 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft)
     max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb)
 
     nlevsoifl   =  10
-    nlevurb     =  5
+    [Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10]
+    nlevurb     =  10 ! originally 5
 
     if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined
     if ( masterproc ) write(iulog, *) 'soil_layerstruct_userdefined varpar ', soil_layerstruct_userdefined

From 23876810d4f7eefd81dbe9d442edaf01b83b58de Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Mon, 24 Apr 2023 16:38:52 -0500
Subject: [PATCH 0036/1248] Update clm_varpar.F90

Fix syntax error
---
 src/main/clm_varpar.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90
index 7c7c1681b7..e1179e43b3 100644
--- a/src/main/clm_varpar.F90
+++ b/src/main/clm_varpar.F90
@@ -203,7 +203,7 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft)
     max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb)
 
     nlevsoifl   =  10
-    [Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10]
+    ![Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10]
     nlevurb     =  10 ! originally 5
 
     if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined

From 2bcfc13acde7b2b42b1a316fb3d6ea1c5770be38 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Fri, 26 May 2023 13:57:31 -0600
Subject: [PATCH 0037/1248] 26 May 2023: dmleung removed the markers from the
 codes. Comments stay.

---
 bld/CLMBuildNamelist.pm                       |   5 +-
 bld/namelist_files/namelist_defaults_ctsm.xml |   2 -
 .../namelist_definition_ctsm.xml              |   1 -
 src/biogeochem/DUSTMod.F90                    | 300 ++++++------------
 src/biogeophys/SoilStateInitTimeConstMod.F90  |   4 +-
 .../share_esmf/PrigentRoughnessStreamType.F90 |  43 +--
 src/main/clm_instMod.F90                      |   2 +-
 7 files changed, 112 insertions(+), 245 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 3b0c79d000..ab1b6ac579 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1560,7 +1560,7 @@ sub process_namelist_inline_logic {
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_fates($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl);
-  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl); # dmleung added 31 Dec 2022
+  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);
 
   #########################################
   # namelist group: atm2lnd_inparm
@@ -4185,7 +4185,6 @@ sub setup_logic_misc {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_prigent_roughness {
-  # dmleung added on 31 Dec 2022 for reading Prigent's roughness stream file
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_prigentroughness' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_prigentroughness' );
@@ -4241,7 +4240,7 @@ sub write_output_files {
   push @groups, "ch4finundated";
   push @groups, "soilbgc_decomp";
   push @groups, "clm_canopy_inparm";
-  push @groups, "prigentroughness"; # dmleung 31 Dec 2022
+  push @groups, "prigentroughness";
   if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') {
      push @groups, "scf_swenson_lawrence_2012_inparm";
   }
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 3d0f5ef5e1..36719a55b7 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2526,8 +2526,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 
 <!-- =========================================  -->
 <!-- Defaults for Prigent's roughness data      -->
-<!-- dmleung only specified def resolution      -->
-<!-- 31 Dec 2022                                -->
 <!-- =========================================  -->
 
 <stream_fldfilename_prigentroughness
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index ec29018081..1405605bf9 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1695,7 +1695,6 @@ Mapping method from Nitrogen deposition input file to the model resolution
 
 <!-- ========================================================================================  -->
 <!-- Prigent roughness stream -->
-<!-- dmleung added 31 Dec 2022 -->
 <!-- ========================================================================================  -->
 
 <entry id="stream_fldfilename_prigentroughness" type="char*256" category="datasets"
diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index f1de13902a..bcf3ae3db5 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -16,7 +16,7 @@ module DUSTMod
   use shr_log_mod          , only : errMsg => shr_log_errMsg
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
   use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr, &
-                                    natpft_lb, natpft_ub, natpft_size     ! -dmleung added 24 Jul 2022
+                                    natpft_lb, natpft_ub, natpft_size  
   use clm_varcon           , only : grav, spval
   use landunit_varcon      , only : istcrop, istsoil
   use clm_varctl           , only : iulog
@@ -31,9 +31,7 @@ module DUSTMod
   use LandunitType         , only : lun
   use ColumnType           , only : col
   use PatchType            , only : patch
-  !use clm_instur           , only : wt_lunit, wt_nat_patch  ! dmleung added 24 Jul 2022
-  !use landunit_varcon      , only : istsoil, istcrop        ! dmleung added 24 Jul 2022 (refering to main/landunit_varcon.F90, for wt_lunit, istsoil=1 is nat veg, istcrop=2 is crop)
-  use pftconMod            , only : noveg              ! dmleung added 24 Jul 2022
+  use pftconMod            , only : noveg    
   use PrigentRoughnessStreamType    , only : prigentroughnessstream_type
   !  
   ! !PUBLIC TYPES
@@ -65,15 +63,13 @@ module DUSTMod
      real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
      real(r8), pointer, private :: vlc_trb_4_patch           (:)   ! turbulent deposition velocity 4(m/s)
      real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! basin factor
-     !########### added by dmleung 27 Nov 2021 ########################################################################
      real(r8), pointer, private :: dst_emiss_coeff_patch     (:)   ! dust emission coefficient (unitless)
      real(r8), pointer, private :: wnd_frc_thr_patch         (:)   ! wet fluid threshold (m/s)
      real(r8), pointer, private :: wnd_frc_thr_dry_patch     (:)   ! dry fluid threshold (m/s)
-     real(r8), pointer, private :: lnd_frc_mble_patch        (:)   ! land mobile fraction -dmleung
+     real(r8), pointer, private :: lnd_frc_mble_patch        (:)   ! land mobile fraction
      real(r8), pointer, private :: liq_frac_patch            (:)   ! liquid fraction of total water
      real(r8), pointer, private :: wnd_frc_soil_patch        (:)   ! soil wind friction velocity (m/s)
      real(r8), pointer, private :: gwc_patch                 (:)   ! gravimetric water content (kg/kg)
-     !########### added by dmleung 2 Dec 2021 #########################################################################
      real(r8), pointer, private :: intrmtncy_fct_patch       (:)   ! intermittency factor, accounting for turbulence shutting down dust emissions (unitless)
      real(r8), pointer, private :: stblty_patch              (:)   ! stability parameter for checking stability condition (stblty < 0 is unstable atmosphere)
      real(r8), pointer, private :: u_mean_slt_patch          (:)   ! wind speed 0.1 m level of dust saltation (m/s)
@@ -83,13 +79,10 @@ module DUSTMod
      real(r8), pointer, private :: thr_crs_rate_patch        (:)   ! threshold crossing rate (unitless)
      real(r8), pointer, private :: prb_crs_fld_thr_patch     (:)   ! probability of wind speed crossing fluid threshold
      real(r8), pointer, private :: prb_crs_impct_thr_patch   (:)   ! probability of wind speed crossing impact threshold
-     !########### added by dmleung 20 Dec 2021 ########################################################################
      real(r8), pointer, private :: ssr_patch                 (:)   ! [dimless] integrated shear stress ratiio, defined by Okin (2008) and then integrated by Caroline Pierre et al. (2014)
      real(r8), pointer, private :: lai_patch                 (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin's drag partition, averaged to landunit level
      real(r8), pointer, private :: frc_thr_rghn_fct_patch    (:)   ! [dimless] hybrid drag partition (or called roughness) factor
-     !########### added by dmleung 28 Jul 2022 ########################################################################
      real(r8), pointer, private :: wnd_frc_thr_std_patch     (:)   ! standardized fluid threshold friction velocity (m/s)
-     !########### added by dmleung 31 Dec 2022 ########################################################################
      type(prigentroughnessstream_type), private :: prigentroughnessstream      ! Prigent roughness stream data
      real(r8), pointer, private :: dpfct_rock_patch          (:)   ! [fraction] rock drag partition factor, time-constant
    contains
@@ -109,21 +102,16 @@ module DUSTMod
 contains
 
   !------------------------------------------------------------------------
-  !##### dmleung edited for initializing stream files 31 Dec 2022  ########
-  !subroutine Init(this, bounds, NLFilename, num_nolakep, filter_nolakep)
   subroutine Init(this, bounds, NLFilename)
 
     class(dust_type) :: this
     type(bounds_type), intent(in) :: bounds 
-    character(len=*),  intent(in) :: NLFilename   ! dmleung added 31 Dec 2022
-    !integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
-    !integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points  
+    character(len=*),  intent(in) :: NLFilename
 
     call this%InitAllocate (bounds)
     call this%InitHistory  (bounds)
-    call this%prigentroughnessstream%Init( bounds, NLFilename )  ! dmleung added 31 Dec 2022
-    !call this%InitCold     (bounds, num_nolakep, filter_nolakep)
-    call this%InitCold     (bounds)                             ! dmleung commented 31 Dec 2022
+    call this%prigentroughnessstream%Init( bounds, NLFilename )
+    call this%InitCold     (bounds)
     call this%InitDustVars (bounds)
 
   end subroutine Init
@@ -151,7 +139,6 @@ subroutine InitAllocate(this, bounds)
     allocate(this%vlc_trb_3_patch           (begp:endp))        ; this%vlc_trb_3_patch           (:)   = nan
     allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
     allocate(this%mbl_bsn_fct_col           (begc:endc))        ; this%mbl_bsn_fct_col     (:)   = nan
-    !#### added by dmleung 27 Nov 2021 #####################################
     allocate(this%dst_emiss_coeff_patch     (begp:endp))        ; this%dst_emiss_coeff_patch     (:)   = nan
     allocate(this%wnd_frc_thr_patch         (begp:endp))        ; this%wnd_frc_thr_patch         (:)   = nan
     allocate(this%wnd_frc_thr_dry_patch     (begp:endp))        ; this%wnd_frc_thr_dry_patch     (:)   = nan
@@ -159,7 +146,6 @@ subroutine InitAllocate(this, bounds)
     allocate(this%wnd_frc_soil_patch        (begp:endp))        ; this%wnd_frc_soil_patch        (:)   = nan
     allocate(this%gwc_patch                 (begp:endp))        ; this%gwc_patch                 (:)   = nan
     allocate(this%liq_frac_patch            (begp:endp))        ; this%liq_frac_patch            (:)   = nan
-    !#### added by dmleung 2 Dec 2021 ######################################
     allocate(this%intrmtncy_fct_patch       (begp:endp))        ; this%intrmtncy_fct_patch       (:)   = nan
     allocate(this%stblty_patch              (begp:endp))        ; this%stblty_patch              (:)   = nan
     allocate(this%u_mean_slt_patch          (begp:endp))        ; this%u_mean_slt_patch          (:)   = nan
@@ -169,13 +155,10 @@ subroutine InitAllocate(this, bounds)
     allocate(this%thr_crs_rate_patch        (begp:endp))        ; this%thr_crs_rate_patch        (:)   = nan
     allocate(this%prb_crs_fld_thr_patch     (begp:endp))        ; this%prb_crs_fld_thr_patch     (:)   = nan
     allocate(this%prb_crs_impct_thr_patch   (begp:endp))        ; this%prb_crs_impct_thr_patch   (:)   = nan
-    !#### added by dmleung 17 Dec 2021 ######################################
     allocate(this%ssr_patch                 (begp:endp))        ; this%ssr_patch                 (:)   = nan
     allocate(this%lai_patch                 (begp:endp))        ; this%lai_patch                 (:)   = nan
     allocate(this%frc_thr_rghn_fct_patch    (begp:endp))        ; this%frc_thr_rghn_fct_patch    (:)   = nan
-    !#### added by dmleung 28 Jul 2022 ######################################
     allocate(this%wnd_frc_thr_std_patch     (begp:endp))        ; this%wnd_frc_thr_std_patch     (:)   = nan
-    !#### added by dmleung 31 Dec 2022 ######################################
     allocate(this%dpfct_rock_patch          (begp:endp))        ; this%dpfct_rock_patch          (:)   = nan
   end subroutine InitAllocate
 
@@ -221,7 +204,6 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='turbulent deposition velocity 4', &
          ptr_patch=this%vlc_trb_4_patch, default='inactive')
 
-    !#####added by dmleung 27 Nov 2021#########################################
     this%dst_emiss_coeff_patch(begp:endp) = spval
     call hist_addfld1d (fname='C_d', units='dimensionless',  &
          avgflag='A', long_name='dust emission coefficient', &
@@ -250,7 +232,6 @@ subroutine InitHistory(this, bounds)
     call hist_addfld1d (fname='LIQ_FRAC', units='dimensionless',  &
          avgflag='A', long_name='fraction of total water that is liquid', &
          ptr_patch=this%liq_frac_patch, set_lake=0._r8, set_urb=0._r8)
-    !#####added by dmleung 2 Dec 2021 #########################################
     this%u_mean_slt_patch(begp:endp) = spval
     call hist_addfld1d (fname='U_S_MEAN', units='m/s',  &
          avgflag='A', long_name='mean wind velocity at saltation level', &
@@ -287,7 +268,6 @@ subroutine InitHistory(this, bounds)
     call hist_addfld1d (fname='ETA', units='',  &
          avgflag='A', long_name='intermittency factor', &
          ptr_patch=this%intrmtncy_fct_patch, set_lake=0._r8, set_urb=0._r8)
-    !#####added by dmleung 20 Dec 2021 ########################################
     this%ssr_patch(begp:endp) = spval
     call hist_addfld1d (fname='SSR', units='m/s',  &
          avgflag='A', long_name='Okin-Pierre vegetation shear stress ratio (drag partition factor)', &
@@ -300,35 +280,24 @@ subroutine InitHistory(this, bounds)
     call hist_addfld1d (fname='FRC_THR_RGHN_FCT', units='dimensionless',  &
          avgflag='A', long_name='hybrid drag partition (or roughness) factor', &
          ptr_patch=this%frc_thr_rghn_fct_patch, set_lake=0._r8, set_urb=0._r8)
-    !#####added by dmleung 28 Jul 2022 ########################################
     this%wnd_frc_thr_std_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_FT_STD', units='m/s',  &
          avgflag='A', long_name='standardized fluid threshold friction velocity', &
          ptr_patch=this%wnd_frc_thr_std_patch, set_lake=0._r8, set_urb=0._r8)
-    !#####added by dmleung 31 Dec 2022 ########################################
     this%dpfct_rock_patch(begp:endp) = spval
     call hist_addfld1d (fname='DPFCT_ROCK', units='m/s',  &
          avgflag='A', long_name='rock drag partition factor', &
          ptr_patch=this%dpfct_rock_patch)
-    !##########################################################################
 
   end subroutine InitHistory
 
   !-----------------------------------------------------------------------
-  !subroutine InitCold(this, bounds, num_nolakep, filter_nolakep)   !dmleung commented 31 Dec 2022
   subroutine InitCold(this, bounds)
     !
-    !USES dmleung added 31 Dec 2022
-    !use landunit_varcon      , only : istdlak
-    !use LandunitType         , only : lun
     !
     ! !ARGUMENTS:
-    class(dust_type), intent(inout) :: this  ! dmleung used class instead of type, 31 Dec 2022
+    class(dust_type), intent(inout) :: this  ! Danny M. Leung used class instead of type
     type(bounds_type), intent(in) :: bounds 
-    ! dmleung also added the below no-lake filter 31 Dec 2022
-    !integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
-    !integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points 
-    !type(dust_type), intent(inout) :: dust_inst
     !
     ! !LOCAL VARIABLES:
     integer :: c,l
@@ -344,19 +313,14 @@ subroutine InitCold(this, bounds)
        end if
     end do
 
-    !associate(                                                                 &
-    !     dpfct_rock                 =>   this%dpfct_rock_patch                 &
-    !     )
-      ! Caulculate Drag Partition factor, dmleung added 31 Dec 2022
+      ! Caulculate Drag Partition factor
       if ( this%prigentroughnessstream%useStreams() )then !if usestreams == true, and it should be always true
          call this%prigentroughnessstream%CalcDragPartition( bounds, &
-         !                       num_nolakep, filter_nolakep, this%dpfct_rock_patch(bounds%begp:bounds%endp) )
                                 this%dpfct_rock_patch(bounds%begp:bounds%endp) )
       else
 
          call endrun( "ERROR:: Drag partitioning MUST now use a streams file of aeolian roughness length to calculate, it can no longer read from the fsurdat file" )
       end if
-    !end associate
 
   end subroutine InitCold
 
@@ -376,9 +340,7 @@ subroutine DustEmission (bounds, &
     ! !USES
     use shr_const_mod, only : SHR_CONST_RHOFW
     use subgridaveMod, only : p2g
-    !use clm_instur           , only : wt_lunit, wt_nat_patch  ! dmleung added 24 Jul 2022
-    !use landunit_varcon      , only : istsoil, istcrop        ! dmleung added 24 Jul 2022 (refering to main/landunit_varcon.F90, for wt_lunit, istsoil=1 is nat veg, istcrop=2 is crop)
-    use pftconMod            , only : noveg              ! dmleung added 24 Jul 2022
+    use pftconMod            , only : noveg     
     !
     ! !ARGUMENTS:
     type(bounds_type)      , intent(in)    :: bounds                      
@@ -404,7 +366,7 @@ subroutine DustEmission (bounds, &
     real(r8) :: flx_mss_vrt_dst_ttl(bounds%begp:bounds%endp)
     real(r8) :: frc_thr_wet_fct
     real(r8) :: frc_thr_rgh_fct
-    !real(r8) :: wnd_frc_thr_slt    ! dmleung commented and put below 2 Dec 2021
+    !real(r8) :: wnd_frc_thr_slt    ! Danny M. Leung commented and put below
     real(r8) :: wnd_rfr_thr_slt
     real(r8) :: wnd_frc_slt
     real(r8) :: lnd_frc_mbl(bounds%begp:bounds%endp)
@@ -415,16 +377,13 @@ subroutine DustEmission (bounds, &
     real(r8) :: sumwt(bounds%begl:bounds%endl) ! sum of weights
     logical  :: found                          ! temporary for error check
     integer  :: index
-    !########### added by dmleung 27 Nov 2021 #########################################
-    real(r8) :: tmp2   ! calculates the dry fluid threshold using Shao and Lu (2000) scheme; replace the tmp1 (Iversen and White, 1982) that was passed from Dustini to DustEmission; tmp2 will be calculated here  23 May 2020 -dmleung
-    real(r8) :: wnd_frc_thr_slt_std ! [m/s] The soil threshold friction speed at standard air density (1.2250 kg/m3) -jfk
-    real(r8) :: frag_expt           ! fragmentation exponent, -dmleung 22 Jun 2021
-    !########### added by dmleung 2 Dec 2021 for intermittency scheme #################
-    real(r8) :: wnd_frc_thr_slt_it  ! [m/s] created for impact threshold friction velocity, dmleung 9 Jun 2021
-    real(r8) :: wnd_frc_thr_slt     ! [m/s] used for wet fluid threshold friction velocity, dmleung 9 Jun 2021
-    !########### added by dmleung 20 Dec 2021 for drag partition effect #################
+    
+    real(r8) :: tmp2   ! calculates the dry fluid threshold using Shao and Lu (2000) scheme; replace the tmp1 (Iversen and White, 1982) that was passed from Dustini to DustEmission; tmp2 will be calculated here
+    real(r8) :: wnd_frc_thr_slt_std ! [m/s] The soil threshold friction speed at standard air density (1.2250 kg/m3)
+    real(r8) :: frag_expt           ! fragmentation exponent
+    real(r8) :: wnd_frc_thr_slt_it  ! [m/s] created for impact threshold friction velocity
+    real(r8) :: wnd_frc_thr_slt     ! [m/s] used for wet fluid threshold friction velocity
     real(r8) :: K_length            ! [dimless] normalized mean interobstacle distance, or called gap length (Okin, 2008)
-    !########### added by dmleung 22 Jul 2022 for LUH2 land cover ####################
     real(r8) :: bare_frc            ! LUH2 bare soil land cover fraction
     real(r8) :: veg_frc             ! LUH2 natural vegetation + crop land cover fraction
     !    
@@ -433,24 +392,19 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
     !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
-    !####### added by dmleung 27 Nov 2021 ###########################################################################
     character(len=*),parameter :: subname = 'DUSTEmission'
-    real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; dmleung suggests 1 or 0.5, and the default 0.3 seems a bit too small -dmleung 27 Nov 2021
-    real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient -jfk
-    real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent -jfk
-    real(r8), parameter :: Ce = 2.0_r8                 ! [dimless] proportionality constant scaling exponential dependence of dust emission coefficient on standardized soil threshold friction speed -jfk
-    real(r8), parameter :: C_tune = 0.05_r8             ! [dimless] global tuning constant for vertical dust flux; set to produce ~same global dust flux in control sim (I_2000) as old parameterization -jfk
-    real(r8), parameter :: wnd_frc_thr_slt_std_min = 0.16_r8 ! [m/s] minimum standardized soil threshold friction speed -jfk
-    real(r8), parameter :: forc_rho_std = 1.2250_r8    ! [kg/m3] density of air at standard pressure (101325) and temperature (293 K) -jfk
-    real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles, dml 23 May 2020
-    !####### added by dmleung 2 Dec 2021 for intermittency ##########################################################
-    real(r8), parameter :: B_it = 0.82_r8              ! [dimless] ratio = u_star_it / u_star_ft0 (may need to change into a fn of moisture later on) -dml
-    real(r8), parameter :: k = 0.4_r8                  ! [dimless] von Karman constant -dml
-    !####### added by dmleung 2 Dec 2021 for Okin (2008) drag partition for plants ##########################################################
-    real(r8), parameter :: f_0 = 0.32_r8               ! [dimless] SSR in the immediate lee of a plant, dimensionless
-    real(r8), parameter :: c_e = 4.8_r8                  ! [dimless] e-folding distance velocity recovery, dimensionless
-    !################################################################################################################
-    !################################################################################################################
+    real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests 1, and the old 0.3 seems a bit too small
+    real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient
+    real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent
+    real(r8), parameter :: Ce = 2.0_r8                 ! [dimless] proportionality constant scaling exponential dependence of dust emission coefficient on standardized soil threshold friction speed
+    real(r8), parameter :: C_tune = 0.05_r8             ! [dimless] global tuning constant for vertical dust flux; set to produce ~same global dust flux in control sim (I_2000) as old parameterization
+    real(r8), parameter :: wnd_frc_thr_slt_std_min = 0.16_r8 ! [m/s] minimum standardized soil threshold friction speed
+    real(r8), parameter :: forc_rho_std = 1.2250_r8    ! [kg/m3] density of air at standard pressure (101325) and temperature (293 K)
+    real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles
+    real(r8), parameter :: B_it = 0.82_r8              ! [dimless] ratio = u_star_it / u_star_ft0
+    real(r8), parameter :: k = 0.4_r8                  ! [dimless] von Karman constant
+    real(r8), parameter :: f_0 = 0.32_r8               ! [dimless] SSR in the immediate lee of a plant
+    real(r8), parameter :: c_e = 4.8_r8                  ! [dimless] e-folding distance velocity recovery
     !------------------------------------------------------------------------
 
     associate(                                                         & 
@@ -474,15 +428,14 @@ subroutine DustEmission (bounds, &
          mbl_bsn_fct         => dust_inst%mbl_bsn_fct_col            , & ! Input:  [real(r8) (:)   ]  basin factor                                      
          flx_mss_vrt_dst     => dust_inst%flx_mss_vrt_dst_patch      , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
          flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch  , & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
-         ! the following are added by dmleung 27 Nov 2021
+         
          dst_emiss_coeff     => dust_inst%dst_emiss_coeff_patch      , & ! Output dust emission coefficient
-         wnd_frc_thr         => dust_inst%wnd_frc_thr_patch          , & ! output impact threshold -dmleung
+         wnd_frc_thr         => dust_inst%wnd_frc_thr_patch          , & ! output impact threshold
          wnd_frc_thr_dry     => dust_inst%wnd_frc_thr_dry_patch      , & ! output dry threshold
-         lnd_frc_mble        => dust_inst%lnd_frc_mble_patch         , & ! -dmleung, 3 Feb 2020
+         lnd_frc_mble        => dust_inst%lnd_frc_mble_patch         , & ! output bare land fraction
          wnd_frc_soil        => dust_inst%wnd_frc_soil_patch         , & ! soil friction velocity u_*s = (u_*)(f_eff)
          gwc                 => dust_inst%gwc_patch                  , & ! output gravimetric water content
          liq_frac            => dust_inst%liq_frac_patch             , &
-         ! added by dmleung 8 Jul 2019, recoded 2 Dec 2021
          intrmtncy_fct       => dust_inst%intrmtncy_fct_patch        , &
          stblty              => dust_inst%stblty_patch               , &
          u_mean_slt          => dust_inst%u_mean_slt_patch           , &
@@ -492,14 +445,11 @@ subroutine DustEmission (bounds, &
          thr_crs_rate        => dust_inst%thr_crs_rate_patch         , &
          prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , &
          prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , &
-         ! added by dmleung 20 Dec 2021
          ssr                 => dust_inst%ssr_patch                  , &
          lai                 => dust_inst%lai_patch                  , &
          frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , &
-         ! added by dmleung 28 Jul 2022
          wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch      , &
-         ! added by dmleung 31 Dec 2022
-         dpfct_rock          => dust_inst%dpfct_rock_patch            &  ! dmleung used roughfct (roughness factor) instead of dpfct_rock (rock drag partition factor) here. Could change it back to dpfct_rock here and below later, 31 Dec 2022
+         dpfct_rock          => dust_inst%dpfct_rock_patch            &
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -572,14 +522,13 @@ subroutine DustEmission (bounds, &
          end if
       end do
 
-      ! dmleung add output for bare_frc and veg_frc here if wanted !!!!!!!!!----------------------
+      ! dmleung add output for bare_frc and veg_frc here if wanted !!!!----------------------
 
       ! reset history output variables before next if-statement to avoid output = inf
 
       do fp = 1,num_nolakep
          p = filter_nolakep(fp)
          flx_mss_vrt_dst_tot(p) = 0.0_r8
-         ! the following are added by dmleung 27 Nov 2021
          dst_emiss_coeff(p) = 0.0_r8
          wnd_frc_thr(p) = 0.0_r8
          wnd_frc_thr_dry(p) = 0.0_r8
@@ -587,7 +536,6 @@ subroutine DustEmission (bounds, &
          wnd_frc_soil(p) = 0.0_r8
          gwc(p) = 0.0_r8
          liq_frac(p) = 0.0_r8
-         ! dmleung's edit, 8 Jul 2019; added by dmleung 2 Dec 2021
          u_mean_slt(p) = 0.0_r8
          u_sd_slt(p) = 0.0_r8
          stblty(p)   = 0.0_r8
@@ -597,11 +545,9 @@ subroutine DustEmission (bounds, &
          prb_crs_fld_thr(p) = 0.0_r8
          prb_crs_impct_thr(p) = 0.0_r8
          intrmtncy_fct(p) = 0.0_r8
-         ! dmleung's edit, 20 Dec 2021
          ssr(p) = 0.0_r8
          lai(p) = 0.0_r8
          frc_thr_rghn_fct(p) = 0.0_r8
-         ! dmleung added 28 Jul 2022
          wnd_frc_thr_std(p) = 0.0_r8
       end do
       do n = 1, ndst
@@ -617,9 +563,9 @@ subroutine DustEmission (bounds, &
          l = patch%landunit(p)
          g = patch%gridcell(p)
 
-         !################################################################################################
+         !--------------------------------------------------------------------------------------------------
          ! put dust emission calculation here to output threshold friction velocity for the whole globe,
-         ! not just when lnd_frc_mbl = 0. Edited by dmleung 27 Nov 2021
+         ! not just when lnd_frc_mbl = 0. Danny M. Leung 27 Nov 2021
          bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
          gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
          if (gwc_sfc > gwc_thr(c)) then
@@ -628,54 +574,52 @@ subroutine DustEmission (bounds, &
             frc_thr_wet_fct = 1.0_r8
          end if
 
-         ! output moisture variables -dmleung, coded Jul 2020, recoded 18 Mar 2021, added to CLM5 27 Nov 2021
+         ! output moisture variables
          gwc(p) = gwc_sfc     ! output surface gravimetric water content
 
          ! slevis: adding liqfrac here, because related to effects from soil water
-         liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) ) !-dmleung 27 Nov 2021
-         ! output liquid fraction -dmleung 27 Nov 2021
+         liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
+         ! output liquid fraction
          liq_frac(p) = liqfrac
 
          !#######################################################################################################
          ! calculate Shao & Lu (2000) dust emission threshold scheme here
-         ! use tmp1 from DUSTini for Iversen and White I&W (1982) (75 um is optimal); use tmp2 for S&L (2000) (80 um is optimal)
-         ! recoded to CLM5 27 Nov 2021
+         ! use tmp1 from DUSTini for Iversen and White I&W (1982) (~75 um is optimal); use tmp2 for S&L (2000) (~80 um is optimal)
          !#######################################################################################################
 
-         tmp2 = 1.0_r8*sqrt(0.0123_r8 * (dns_slt*grav*130.0e-6_r8 + 1.65e-4_r8/130.0e-6_r8)) ! calculate S&L (2000) scheme here for threshold; gamma = 1.65e-4 following S&L00, D_p = 127 um ~ 130 um following dmleung's dust paper. As this is a global constant, this line can be put outside the loop to save computational power.
+         tmp2 = 1.0_r8*sqrt(0.0123_r8 * (dns_slt*grav*130.0e-6_r8 + 1.65e-4_r8/130.0e-6_r8)) ! calculate S&L (2000) scheme here for threshold; gamma = 1.65e-4 following S&L00, D_p = 127 um ~ 130 um following Leung et al. (2022). As this is a global constant, this line can be put outside the loop to save computational power.
          wnd_frc_thr_dry(p) = tmp2 / sqrt(forc_rho(c))    ! output dry fluid threshold
-         wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! use as threshold in this module
-         wnd_frc_thr_slt_it = B_it * tmp2 / sqrt(forc_rho(c)) ! define impact threshold -dml 9 Jun 2021, recoded to CLM5 27 Nov 2021
-
-         !wnd_frc_thr_dry(p) = tmp1 / sqrt(forc_rho(c))    ! output dry fluid threshold         
-         !wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! use as threshold in this module
-         !wnd_frc_thr_slt_it = B_it * tmp1 / sqrt(forc_rho(c)) ! define impact threshold -dmleung 9 Jun 2021, recoded to CLM5 27 Nov 2021
-         ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme -dmleung, 23 Feb 2020, added to CLM5 27 Nov 2021
-         wnd_frc_thr(p) = wnd_frc_thr_slt          ! output fluid threshold -dmleung
-
-         ! use emission threshold to calculate standardized threshold and dust emission coefficient dmleung 27 Nov 2021
-         wnd_frc_thr_slt_std = wnd_frc_thr_slt * sqrt(forc_rho(c) / forc_rho_std) ! standardized soil threshold friction speed -jfk (defined using fluid threshold
-         wnd_frc_thr_std(p) = wnd_frc_thr_slt_std          ! output standardized fluid threshold -dmleung added 28 Jul 2022
-         dst_emiss_coeff(p) = Cd0 * exp(-Ce * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min) ! save dust emission coefficient here for all grids, -dml, 1 Mar 2021 
-
-         ! framentation exponent dmleung 27 Nov 2021; moved to this block 23 Dec 2021
-         frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a) -dmleung 27 Nov 2021
+         wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold
+         wnd_frc_thr_slt_it = B_it * tmp2 / sqrt(forc_rho(c)) ! define impact threshold
+
+         !wnd_frc_thr_dry(p) = tmp1 / sqrt(forc_rho(c))    ! output dry fluid threshold; tmp1 uses I&W 1982         
+         !wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold
+         !wnd_frc_thr_slt_it = B_it * tmp1 / sqrt(forc_rho(c)) ! define impact threshold
+         ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme
+         wnd_frc_thr(p) = wnd_frc_thr_slt          ! output fluid threshold
+
+         ! use emission threshold to calculate standardized threshold and dust emission coefficient
+         wnd_frc_thr_slt_std = wnd_frc_thr_slt * sqrt(forc_rho(c) / forc_rho_std) ! standardized soil threshold friction speed (defined using fluid threshold)
+         wnd_frc_thr_std(p) = wnd_frc_thr_slt_std          ! output standardized fluid threshold
+         dst_emiss_coeff(p) = Cd0 * exp(-Ce * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min) ! save dust emission coefficient here for all grids
+
+         ! framentation exponent
+         frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a)
          if (frag_expt > 5.0_r8) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
             frag_expt = 5.0_r8
          end if
 
-         !################ drag partition effect, and soil friction velocity############################
+         !################ drag partition effect, and soil friction velocity ###########################
          ! subsection on computing vegetation drag partition and hybrid drag partition factors 
-         ! in our scheme, drag partition effect is applied on the wind instead of the threshold
-         !  -dmleung, 7 Jul 2021 , coded to CLM5 27 Nov 2021
+         ! in Leung et al. (2022), drag partition effect is applied on the wind instead of the threshold
          !##############################################################################################
          ! the following comes from subr. frc_thr_rgh_fct_get
          ! purpose: compute factor by which surface roughness increases threshold
          !          friction velocity (currently a constant)
 
          if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
-            ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014), dmleung 20 Dec 2021
-            lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; saved for output
+            ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
+            lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0 so we add in a small number. Then lai is saved for output
             if (lai(p) > 1_r8) then
                lai(p)  = 1_r8   ! setting LAI ~ 0.1 to be a min value (since the value goes to infinity when LAI=0)
             end if              ! and 1 to be a max value as computing K involves 1 / LAI
@@ -684,18 +628,15 @@ subroutine DustEmission (bounds, &
             K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup
             ssr(p) = (K_length+f_0*c_e)/(K_length+c_e)
 
-            !frc_thr_rgh_fct = (rockfrc(p)*(roughfct(p))**3_r8 + (vegefrc(p)+sparfrc(p))*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using static GLCNMo bare land fraction LC0, dmleung 20 Dec 2021i; dmleung commented 24 Jul 2022
-
-            ! dmleung added calculation of LUH2 bare vs veg fraction within a grid 24 Jul 2022
+            ! dmleung added calculation of LUH2 bare vs veg fraction within a grid
             !bare_frc = wt_lunit(g,istsoil) * wt_nat_patch(g,noveg) 
             !veg_frc = wt_lunit(g,istsoil) * sum(wt_nat_patch(g,(noveg+1):natpft_ub)) + wt_lunit(g,istcrop)
 
-            !frc_thr_rgh_fct = (bare_frc*(roughfct(p))**3_r8 + veg_frc*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using LUH2 land cover, dmleung 24 Jul 2022
+            !frc_thr_rgh_fct = (bare_frc*(roughfct(p))**3_r8 + veg_frc*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using LUH2 land cover
 
-            ! dmleung added calculation of LUH2 bare vs veg fraction within a grid 6 Oct 2022
+            ! calculation of drag partition effect using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then
-                  !frc_thr_rgh_fct = roughfct(p)  ! dmleung commented out 13 Dec 2022 and added next line
                   frc_thr_rgh_fct = dpfct_rock(p)
                else 
                   frc_thr_rgh_fct = ssr(p)
@@ -704,17 +645,18 @@ subroutine DustEmission (bounds, &
                frc_thr_rgh_fct = 1.0_r8
             end if
 
-            wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt will be used in the dust emission equation  -dmleung
+            wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt will be used in the dust emission equation
+
+            frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor
 
-            frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor, dmleung 20 Dec 2021
          else
             wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
-            frc_thr_rghn_fct(p) = 0.0_r8            ! save and output hybrid drag partition factor, dmleung 20 Dec 2021
+            frc_thr_rghn_fct(p) = 0.0_r8            ! save and output hybrid drag partition factor
          end if
 
          !########## end of drag partition effect #######################################################
 
-         !############ Add Owen effect; if not, comment out this block !-dmleung, 27 Nov 2021 ###########
+         !############ comment out Owen's offect this block; dust emission does not need to consider it  ###########
          ! the following if-block comes from subr. wnd_frc_slt_get 
          ! purpose: compute the saltating friction velocity
          ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
@@ -723,82 +665,41 @@ subroutine DustEmission (bounds, &
          !   wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
          !   wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
          !   wnd_frc_slt = wnd_frc_slt + wnd_frc_slt_dlt   ! careful that RHS is now wnd_frc_slt instead of fv(p)
-         ! ! because wnd_frc_slt takes drag partition effect into account, but fv(p) doesn't. dmleung 27 Nov 2021
+         ! ! because wnd_frc_slt takes drag partition effect into account, but fv(p) doesn't. 
          !end if
          !########## end of Owen effect ################################################################
 
-         ! save soil friction velocity and roughness effect before the if-statement, -dml, 1 Mar 2021, coded to CLM5 27 Nov 2021
-         wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect  -dml
+         ! save soil friction velocity and roughness effect before the if-statement
+         wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect
          ! save land mobile fraction
-         lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement, -dml, 1 Mar 2021
+         lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement
          ! only perform the following calculations if lnd_frc_mbl is non-zero 
 
-         if (lnd_frc_mbl(p) > 0.0_r8) then
-
-            ! the following comes from subr. frc_thr_rgh_fct_get
-            ! purpose: compute factor by which surface roughness increases threshold
-            !          friction velocity (currently a constant)
-
-            !frc_thr_rgh_fct = 1.0_r8
-
-            ! the following comes from subr. frc_thr_wet_fct_get
-            ! purpose: compute factor by which soil moisture increases threshold friction velocity
-            ! adjust threshold velocity for inhibition by moisture
-            ! modified 4/5/2002 (slevis) to use gravimetric instead of volumetric
-            ! water content
-
-            !bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
-            !gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
-            !if (gwc_sfc > gwc_thr(c)) then
-            !   frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)
-            !else
-            !   frc_thr_wet_fct = 1.0_r8
-            !end if
-
-            ! slevis: adding liqfrac here, because related to effects from soil water
-
-            !liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
-
-            ! the following lines come from subr. dst_mbl
-            ! purpose: adjust threshold friction velocity to acct for moisture and
-            !          roughness. The ratio tmp1 / sqrt(forc_rho) comes from
-            !          subr. wnd_frc_thr_slt_get which computes dry threshold
-            !          friction velocity for saltation
-
-            !wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
+         if (lnd_frc_mbl(p) > 0.0_r8) then  ! if bare land fraction is larger than 0 then calculate the dust emission equation
 
             ! reset these variables which will be updated in the following if-block
 
-            !wnd_frc_slt = fv(p)
+            !wnd_frc_slt = fv(p)  ! we don't need this line because its calculation is moved upward
             flx_mss_hrz_slt_ttl = 0.0_r8
             flx_mss_vrt_dst_ttl(p) = 0.0_r8
 
             ! the following line comes from subr. dst_mbl
             ! purpose: threshold saltation wind speed
 
-            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)     ! keep and use if I want Z03 scheme -dmleung
-
-            ! the following if-block comes from subr. wnd_frc_slt_get 
-            ! purpose: compute the saltating friction velocity
-            ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
-
-            !if (u10(p) >= wnd_rfr_thr_slt) then
-            !   wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
-            !   wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
-            !   wnd_frc_slt = fv(p) + wnd_frc_slt_dlt
-            !end if
+            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)     ! keep and use if we want the default Z03 scheme
 
+            
             ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
             ! purpose: compute vertically integrated streamwise mass flux of particles
 
-            !if (wnd_frc_slt > wnd_frc_thr_slt) then! if want to use fluid threshold for dust emission, uncomment this one,  -dmleung 2 Dec 2021
-            if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if want to use impact threshold for dust emission, uncomment this one, -dmleung 2 Dec 2021
+            !if (wnd_frc_slt > wnd_frc_thr_slt) then! if using Zender's scheme, use fluid threshold for dust emission equation below
+            if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if using Leung's scheme, use impact threshold for dust emission equation
 
                !################### for Zender et al. (2003) scheme -dmleung ###########################
                !################ uncomment the below block if want to use Z03 scheme ###################
                !wnd_frc_rat = wnd_frc_thr_slt / wnd_frc_slt
                !flx_mss_hrz_slt_ttl = cst_slt * forc_rho(c) * (wnd_frc_slt**3.0_r8) * &
-               !     (1.0_r8 - wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) / grav
+               !     (1.0_r8 - wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) / grav  ! Zender dust emission equation for emission flux
 
                ! the following loop originates from subr. dst_mbl
                ! purpose: apply land sfc and veg limitations and global tuning factor
@@ -808,40 +709,27 @@ subroutine DustEmission (bounds, &
                !flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * mbl_bsn_fct(c) * &
                !     flx_mss_fdg_fct * liqfrac
 
-               ! dmleung moved to this block
+               !
                !dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )
                !flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
                !########################################################################################
 
-               !################### for Kok et al. (2014) scheme -dmleung ##############################
-               !################ uncomment the below block if want to use K14 scheme ###################
-
-               ! if want to use fluid threshold for dust emission, uncomment this one, -dmleung 27 Nov 2021
-               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt)**frag_expt  ! change forc_rho(g) to forc_rho(c) to avoid passing Nan values to the coupler -Longlei ! if want to use fluid threshold for dust emission, uncomment this one, -dml 27 Nov 2021
+               !################### for Leung et al. (2022) ################################################
+               !################ uncomment the below block if want to use Leung's scheme ###################
 
-               ! if want to use impact threshold for dust emission, uncomment this one, -dmleung 2 Dec 2021
-               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! if want to use impact threshold for dust emission, uncomment this one, -dml 2 Dec 2021
+               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
 
                ! account for bare soil fraction, frozen soil fraction, and apply global tuning parameter (Kok et al. 2014)
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * lnd_frc_mbl(p) * C_tune * liqfrac
                !########################################################################################
             end if
 
-            ! the following comes from subr. flx_mss_vrt_dst_ttl_MaB95_get
-            ! purpose: diagnose total vertical mass flux of dust from vertically
-            !          integrated streamwise mass flux
-
-            !dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )  ! dmleung commented and moved to the previous block
-            !flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
-
-            !############## added by dmleung 2 Dec 2021 #############################################
-            ! subsection for intermittency factor calculation
-            ! need to use with impact threshold and cannot be used with fluid threshold
-            ! Danny M. Leung, 24 Jun 2019, readded into CLM5 by dmleung 2 Dec 2021
-            ! 2 Dec 2021 note: assume no buoyancy contribution to the wind fluctuation (u_sd_slt), so no obul(p) is needed. It is shown to be important for the wind fluctuations contribute little to the intermittency factor. We might add this back in the future revisions.
+            !############## Danny M. Leung added the intermittency calculation #################################
+            ! subsection for intermittency factor calculation (only used by Leung's scheme, not Zender's scheme)
+            ! 2 Dec 2021: assume no buoyancy contribution to the wind fluctuation (u_sd_slt), so no obul(p) is needed. It is shown to be important for the wind fluctuations contribute little to the intermittency factor. We might add this back in the future revisions.
 
             ! mean lowpass-filtered wind speed at 0.1 m saltation height (assuming aerodynamic roughness length = 1e-4 m globally for ease; also assuming neutral condition)
-            u_mean_slt(p) = (wnd_frc_slt/k) * log(0.1_r8 / 1e-4_r8)
+            u_mean_slt(p) = (wnd_frc_slt/k) * log(0.1_r8 / 1e-4_r8)  ! translating from ustar (velocity scale) to actual wind
 
             ! sd of lowpass-filtered wind speed
             !if (obul(p)==0) then
@@ -851,15 +739,15 @@ subroutine DustEmission (bounds, &
             !   zetaobu = 1000_r8 / obul(p)   ! For now zii is a constant of 1000 m in CLM -dml, 24 Aug 2021
             !end if
             !stblty(p) = zetaobu    ! zetaobu get outputted as the Obukhov stability parameter
-            stblty(p) = 0   ! -dmleung 2 Dec 2021: use 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
-            if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then
+            stblty(p) = 0   ! -dmleung 2 Dec 2021: use stability = 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
+            if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
                u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
             else
                u_sd_slt(p) = 0.001_r8   ! should have used 0 theoretically; used 0.001 here to avoid undefined values
             end if
 
             ! threshold velocities
-            ! Here wnd_frc_thr_slt is the fluid threshold; wnd_frc_thr_dry(p) is the dry fluid threshold; B_it*wnd_frc_thr_dry(p) is the impact threshold, -dml, 1 Mar 2021
+            ! Here wnd_frc_thr_slt is the fluid threshold; wnd_frc_thr_dry(p) is the dry fluid threshold; B_it*wnd_frc_thr_dry(p) is the impact threshold
             ! fluid threshold wind at 0.1 m saltation height
             u_fld_thr(p) = (wnd_frc_thr_slt/k) * log(0.1_r8 / 1e-4_r8)
             ! impact threshold wind at 0.1 m saltation height
@@ -877,13 +765,13 @@ subroutine DustEmission (bounds, &
             intrmtncy_fct(p) = 1_r8 - prb_crs_fld_thr(p) + thr_crs_rate(p) * (prb_crs_fld_thr(p) - prb_crs_impct_thr(p))
 
             ! multiply dust emission flux by intermittency factor
-            if (intrmtncy_fct(p) /= intrmtncy_fct(p)) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted, dmleung 9 Jun 2021
-               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p)  !  -dmleung
+            if (intrmtncy_fct(p) /= intrmtncy_fct(p)) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) 
             else
-               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * intrmtncy_fct(p)  ! multiply dust flux by intermittency -dmleung
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * intrmtncy_fct(p)  ! multiply dust flux by intermittency
             end if
 
-            !############### end my intermittency subsection here -dmleung ########################################
+            !############ end the intermittency subsection here; only use for Leung's scheme  ##########################
 
          end if   ! lnd_frc_mbl > 0.0
 
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index fc96a878bc..0e31cc2c53 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -703,8 +703,8 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     do c = begc,endc
        g = col%gridcell(c)
 
-       soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  !Fecan et al. (1999) -jfk, dmleung coded 27 Nov 2021 for CLM clay fraction
-       !soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 -dmleung commented 27 Nov 2021
+       soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Danny M. Leung modified the equation of soil moisture effect for dust emissions using a scale factor of 1. 0.01 is to convert from % to fraction.
+       !soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with 1 / (clay fraction) being the scaling factor.
        soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
     end do
 
diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 19ab3cb573..cef34682c9 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -1,11 +1,10 @@
 module PrigentRoughnessStreamType
-!dmleung modified based on ch4FInundatedStreamType on 17 Nov 2022
-#include "shr_assert.h"             ! What is this? In many modules but not dust module
+#include "shr_assert.h"
 
   !-----------------------------------------------------------------------
   ! !DESCRIPTION:
-  ! Contains methods for reading in the Prigent et al. (1997) roughness length streams file. dmleung 22 Nov 2022
-  !
+  ! Contains methods for reading in the Prigent et al. (1997) roughness length streams file
+  ! Created by Danny M. Leung 22 Nov 2022
   ! !USES
   use ESMF                         
   use dshr_strdata_mod , only : shr_strdata_type
@@ -83,11 +82,11 @@ subroutine Init(this, bounds, NLFilename)
    character(len=*), parameter    :: stream_name = 'prigentroughness'
    !-----------------------------------------------------------------------
 
-   !if ( finundation_mtd /= finundation_mtd_h2osfc )then     ! how should I change this? comment out for now
+   !if ( finundation_mtd /= finundation_mtd_h2osfc )then
       call this%InitAllocate( bounds )
       call control%ReadNML( bounds, NLFileName )
 
-      if ( this%useStreams() )then     ! is this a namelist input and is it set in namelist default
+      if ( this%useStreams() )then
 
             allocate(stream_varnames(1))
             stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
@@ -97,7 +96,7 @@ subroutine Init(this, bounds, NLFilename)
          end if
 
          ! Initialize the cdeps data type sdat_rghn
-         call shr_strdata_init_from_inline(sdat_rghn,                                  &     ! what is this function and where does it come from?
+         call shr_strdata_init_from_inline(sdat_rghn,                                  &
               my_task             = iam,                                                &
               logunit             = iulog,                                              &
               compname            = 'LND',                                              &
@@ -132,7 +131,7 @@ subroutine Init(this, bounds, NLFilename)
          sec  = 0
          mcdate = year*10000 + mon*100 + day
 
-         call shr_strdata_advance(sdat_rghn, ymd=mcdate, tod=sec, logunit=iulog, istr='prigentrghn', rc=rc)   ! what is istr and do I need to change elsewhere because the change of istr here
+         call shr_strdata_advance(sdat_rghn, ymd=mcdate, tod=sec, logunit=iulog, istr='prigentrghn', rc=rc)
          if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
             call ESMF_Finalize(endflag=ESMF_END_ABORT)
          end if
@@ -146,7 +145,7 @@ subroutine Init(this, bounds, NLFilename)
             if (trim(stream_varnames(n)) == 'Z0a') then
                ig = 0
                do g = bounds%begg,bounds%endg
-                  ig = ig+1                   ! not sure why +1 is needed but it's okay
+                  ig = ig+1
                   this%prigent_rghn(g) = dataptr1d(ig)
                end do
 
@@ -154,7 +153,7 @@ subroutine Init(this, bounds, NLFilename)
 
          end do
       end if
-   !end if         !comment out for now
+   !end if         !commented out
 
   end subroutine Init
 
@@ -172,7 +171,7 @@ logical function UseStreams(this)
     !
     ! !LOCAL VARIABLES:
     if ( trim(control%stream_fldFileName_prigentroughness) == '' )then
-       UseStreams = .false.  ! dmleung: this won't happen and UseStreams will always be true
+       UseStreams = .false.  ! this won't happen and UseStreams will always be true
     else
        UseStreams = .true.
     end if
@@ -193,11 +192,9 @@ subroutine InitAllocate(this, bounds)
     type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
-    !integer  :: begc, endc
     integer  :: begg, endg
     !---------------------------------------------------------------------
 
-    !begc = bounds%begc; endc = bounds%endc
     begg = bounds%begg; endg = bounds%endg
 
     allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
@@ -205,13 +202,10 @@ subroutine InitAllocate(this, bounds)
   end subroutine InitAllocate
 
   !==============================================================================
-  !subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, &
-  !                          waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated )
-  !subroutine CalcDragPartition(this, bounds, num_nolakep, filter_nolakep, dpfct_rock)
   subroutine CalcDragPartition(this, bounds, dpfct_rock)
     !
     ! !DESCRIPTION:
-    ! Commented below by dmleung 31 Dec 2022
+    ! Commented below by Danny M. Leung 31 Dec 2022
     ! Calculate the drag partition effect of friction velocity due to surface roughness following 
     ! Leung et al. (2022).  This module is used in the dust emission module DUSTMod.F90 for 
     ! calculating drag partitioning. The drag partition equation comes from Marticorena and 
@@ -222,9 +216,7 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     ! subroutine is used in the InitCold subroutine of DUSTMod.F90.
     !
     ! !USES:
-    !use ColumnType              , only : col
     use PatchType               , only : patch
-    !USES dmleung added 31 Dec 2022
     use landunit_varcon         , only : istdlak
     use LandunitType            , only : lun
     !
@@ -235,7 +227,6 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     real(r8)                       , intent(inout) :: dpfct_rock(bounds%begp:)      ! [fraction] rock drag partition factor (roughness effect)
     !
     ! !LOCAL VARIABLES:
-    !integer  :: g, c, fc    ! Indices
     integer  :: g, p, fp, l    ! Indices
     real(r8) :: z0s         ! smooth roughness length (m)
     
@@ -244,17 +235,11 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume estimating roughness effect at a distance of 10 m following Leung et al. (2022)
     !---------------------------------------------------------------------
 
-    SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__) !what's the use of this
-
-    !associate(                                                     &
-         !z           =>   col%z                                   & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
-    !)
+    SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__)
 
 
     ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks. We save the drag partition factor as a patch level quantity.
     z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006). Here we assume soil medium size is a global constant, and so is smooth roughness length.
-    !do fp = 1,num_nolakep
-       !p = filter_nolakep(fp)
     do p = bounds%begp,bounds%endp
        g = patch%gridcell(p)
        l = patch%landunit(p)
@@ -263,8 +248,6 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
        end if
     end do
 
-    !end associate
-
   end subroutine CalcDragPartition
 
   !==============================================================================
@@ -289,7 +272,7 @@ subroutine ReadNML(this, bounds, NLFilename)
    character(len=CL)  :: stream_fldFileName_prigentroughness = ' '
    character(len=CL)  :: stream_meshfile_prigentroughness = ' '
    character(len=CL)  :: prigentroughnessmapalgo = 'bilinear'
-   character(len=*), parameter :: namelist_name = 'prigentroughness'    ! MUST agree with group name in namelist definition to read. dmleung commented
+   character(len=*), parameter :: namelist_name = 'prigentroughness'    ! MUST agree with group name in namelist definition to read.
    character(len=*), parameter :: subName = "('prigentroughness::ReadNML')"
    !-----------------------------------------------------------------------
 
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index 13390d3417..099959581f 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -340,7 +340,7 @@ subroutine clm_instInit(bounds)
 
     call surfrad_inst%Init(bounds)
 
-    call dust_inst%Init(bounds, NLFilename)   ! dmleung added NLFilename 31 Dec 2022
+    call dust_inst%Init(bounds, NLFilename)
 
     allocate(scf_method, source = CreateAndInitSnowCoverFraction( &
          snow_cover_fraction_method = snow_cover_fraction_method, &

From 62b7bcd6f8f8d72b209accb1bff0daff992826c3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Jun 2023 16:52:23 -0600
Subject: [PATCH 0038/1248] Truncate threshold crossing rate to zero, if the
 term going into the exp is going to be large and thus end up with a very
 small term

---
 src/biogeochem/DUSTMod.F90 | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index f1de13902a..496553dd24 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -432,14 +432,14 @@ subroutine DustEmission (bounds, &
     !
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
-    !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
+    !real(r8), parameter :: vai_mbl_thr = 0.3_r8       ! [m2 m-2] VAI threshold quenching dust mobilization
     !####### added by dmleung 27 Nov 2021 ###########################################################################
     character(len=*),parameter :: subname = 'DUSTEmission'
     real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; dmleung suggests 1 or 0.5, and the default 0.3 seems a bit too small -dmleung 27 Nov 2021
     real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient -jfk
     real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent -jfk
     real(r8), parameter :: Ce = 2.0_r8                 ! [dimless] proportionality constant scaling exponential dependence of dust emission coefficient on standardized soil threshold friction speed -jfk
-    real(r8), parameter :: C_tune = 0.05_r8             ! [dimless] global tuning constant for vertical dust flux; set to produce ~same global dust flux in control sim (I_2000) as old parameterization -jfk
+    real(r8), parameter :: C_tune = 0.05_r8            ! [dimless] global tuning constant for vertical dust flux; set to produce ~same global dust flux in control sim (I_2000) as old parameterization -jfk
     real(r8), parameter :: wnd_frc_thr_slt_std_min = 0.16_r8 ! [m/s] minimum standardized soil threshold friction speed -jfk
     real(r8), parameter :: forc_rho_std = 1.2250_r8    ! [kg/m3] density of air at standard pressure (101325) and temperature (293 K) -jfk
     real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles, dml 23 May 2020
@@ -448,7 +448,9 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: k = 0.4_r8                  ! [dimless] von Karman constant -dml
     !####### added by dmleung 2 Dec 2021 for Okin (2008) drag partition for plants ##########################################################
     real(r8), parameter :: f_0 = 0.32_r8               ! [dimless] SSR in the immediate lee of a plant, dimensionless
-    real(r8), parameter :: c_e = 4.8_r8                  ! [dimless] e-folding distance velocity recovery, dimensionless
+    real(r8), parameter :: c_e = 4.8_r8                ! [dimless] e-folding distance velocity recovery, dimensionless
+    real(r8) :: numer                                  ! Numerator term for threshold crossing rate
+    real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     !################################################################################################################
     !################################################################################################################
     !------------------------------------------------------------------------
@@ -866,7 +868,14 @@ subroutine DustEmission (bounds, &
             u_impct_thr(p) = (wnd_frc_thr_slt_it/k) * log(0.1_r8 / 1e-4_r8)  ! to avoid model error
 
             ! threshold crossing rate
-            thr_crs_rate(p) = (exp((u_fld_thr(p)**2_r8 - u_impct_thr(p)**2_r8 - 2_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2_r8 * u_sd_slt(p)**2_r8)) + 1_r8)**(-1_r8)
+            numer = (u_fld_thr(p)**2_r8 - u_impct_thr(p)**2_r8 - 2_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p)))
+            denom = (2_r8 * u_sd_slt(p)**2_r8)
+            ! Truncate to zero if the expression inside exp is becoming too large
+            if ( numer/denom < 30._r8 )then
+               thr_crs_rate(p) = (exp((u_fld_thr(p)**2_r8 - u_impct_thr(p)**2_r8 - 2_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2_r8 * u_sd_slt(p)**2_r8)) + 1_r8)**(-1_r8)
+            else
+               thr_crs_rate(p) = 0.0_r8
+            end if
 
             ! probability that lowpass-filtered wind speed does not exceed u_ft
             prb_crs_fld_thr(p) = 0.5_r8 * (1_r8 + erf((u_fld_thr(p) - u_mean_slt(p)) / (1.414_r8 * u_sd_slt(p))))

From 3868bdccb30c8d85042c8f0869cbbabf8e62d4c1 Mon Sep 17 00:00:00 2001
From: John Alex <jpalex@gmail.com>
Date: Wed, 21 Jun 2023 11:16:14 -0600
Subject: [PATCH 0039/1248] Document that fincl1 maps to 'h0' history file. And
 fexcl1.

---
 src/main/histFileMod.F90 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
index 2497a14667..b6bda0cea6 100644
--- a/src/main/histFileMod.F90
+++ b/src/main/histFileMod.F90
@@ -90,6 +90,7 @@ module histFileMod
 
   character(len=max_namlen+2), public :: &
        hist_fincl1(max_flds) = ' '       ! namelist: list of fields to include in history tape 1
+                                         !            aka 'h0' history file.
   character(len=max_namlen+2), public :: &
        hist_fincl2(max_flds) = ' '       ! namelist: list of fields to include in history tape 2
   character(len=max_namlen+2), public :: &
@@ -115,6 +116,7 @@ module histFileMod
 
   character(len=max_namlen+2), public :: &
        hist_fexcl1(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 1
+                                   !           aka 'h0' history file.
   character(len=max_namlen+2), public :: &
        hist_fexcl2(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2
   character(len=max_namlen+2), public :: &

From 302556635395e7d30c58ef097219a1b242ff4dbf Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 13 Jul 2023 12:49:08 +0800
Subject: [PATCH 0040/1248] Update UrbBuildTempOleson2015Mod.F90

Bug fix: t_building calculation
---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index 2a5440e324..e8f7555e0e 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -936,7 +936,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
                 eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) &
                                      - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
                 t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) &
-                              * dtime / (ht_roof(l) * rho_dair(l) * cpair)
+                              * dtime / (ht_roof(l) * rho_dair(l) * cpair * wtlunit_roof(l))
                 eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l)
               else
                 ! Cathy [orig] 

From af82c41c4ec51f471552295475e63d5d2b31bde5 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 11 Oct 2023 15:51:57 -0500
Subject: [PATCH 0041/1248] Bug fix

Bug fix on view factor and radiative energy balance check
---
 src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index e8f7555e0e..f6330ec10b 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -432,7 +432,10 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
          vf_wf(l)  = 0.5_r8*(1._r8 - vf_rf(l))
 
          ! This view factor implicitly converts from per unit floor area to per unit wall area
-         vf_fw(l) = vf_wf(l) / building_hwr(l)
+         ! Cathy [orig]
+         ! vf_fw(l) = vf_wf(l) / building_hwr(l)
+         ! Cathy [bugfix]
+         vf_fw(l) = vf_wf(l)
 
          ! This view factor implicitly converts from per unit roof area to per unit wall area
          vf_rw(l)  = vf_fw(l)
@@ -838,7 +841,10 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
                         + em_floori(l)*sb*t_floor_bef(l)**4._r8 &
                         + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l))
 
-         qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l)
+         ! Cathy [orig]
+         ! qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l)
+         ! Cathy [bugfix]
+         qrd_building(l) = qrd_roof(l) + qrd_sunw(l) + qrd_shdw(l) + qrd_floor(l)
 
          if (abs(qrd_building(l)) > .10_r8 ) then
            write (iulog,*) 'urban inside building net longwave radiation balance error ',qrd_building(l)

From effacf2b1db196c7bf4c4fa87d45628fd25e9e00 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 28 Nov 2023 14:27:07 -0700
Subject: [PATCH 0042/1248] Corrections for cheyenne test-suite to pass

---
 src/biogeochem/CNCStateUpdate1Mod.F90 |  6 ------
 src/biogeochem/CNNStateUpdate1Mod.F90 | 14 ++++++++------
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90
index 8c6fc11602..76b14585b4 100644
--- a/src/biogeochem/CNCStateUpdate1Mod.F90
+++ b/src/biogeochem/CNCStateUpdate1Mod.F90
@@ -325,15 +325,9 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
               cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
                    - cf_veg%crop_seedc_to_leaf_patch(p) * dt
               do k = repr_grain_min, repr_grain_max
-                 cs_veg%reproductivec_patch(p,k)   = cs_veg%reproductivec_patch(p,k) &
-                      - (cf_veg%repr_grainc_to_food_patch(p,k) + cf_veg%repr_grainc_to_seed_patch(p,k))*dt
                  cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
                       + cf_veg%repr_grainc_to_seed_patch(p,k) * dt
               end do
-              do k = repr_structure_min, repr_structure_max
-                 cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) &
-                      - (cf_veg%repr_structurec_to_cropprod_patch(p,k) + cf_veg%repr_structurec_to_litter_patch(p,k))*dt
-              end do
            end if
         end if !not use_matrixcn
 
diff --git a/src/biogeochem/CNNStateUpdate1Mod.F90 b/src/biogeochem/CNNStateUpdate1Mod.F90
index 8aa24e3aa3..4a9e081583 100644
--- a/src/biogeochem/CNNStateUpdate1Mod.F90
+++ b/src/biogeochem/CNNStateUpdate1Mod.F90
@@ -226,21 +226,23 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
                ns_veg%leafn_patch(p)        = ns_veg%leafn_patch(p)      - nf_veg%leafn_to_biofueln_patch(p)*dt
                ns_veg%livestemn_patch(p)    = ns_veg%livestemn_patch(p)  - nf_veg%livestemn_to_retransn_patch(p)*dt
                ns_veg%retransn_patch(p)     = ns_veg%retransn_patch(p)   + nf_veg%livestemn_to_retransn_patch(p)*dt
+               do k = repr_grain_min, repr_grain_max
+                  ns_veg%reproductiven_patch(p,k)   = ns_veg%reproductiven_patch(p,k) &
+                       - (nf_veg%repr_grainn_to_food_patch(p,k) + nf_veg%repr_grainn_to_seed_patch(p,k))*dt
+               end do
+               do k = repr_structure_min, repr_structure_max
+                  ns_veg%reproductiven_patch(p,k) = ns_veg%reproductiven_patch(p,k) &
+                       - (nf_veg%repr_structuren_to_cropprod_patch(p,k) + nf_veg%repr_structuren_to_litter_patch(p,k))*dt
+               end do
             else
                ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
             end if !not use_matrixcn
             ns_veg%cropseedn_deficit_patch(p) = ns_veg%cropseedn_deficit_patch(p) &
                     - nf_veg%crop_seedn_to_leaf_patch(p) * dt
             do k = repr_grain_min, repr_grain_max
-               ns_veg%reproductiven_patch(p,k)   = ns_veg%reproductiven_patch(p,k) &
-                    - (nf_veg%repr_grainn_to_food_patch(p,k) + nf_veg%repr_grainn_to_seed_patch(p,k))*dt
                ns_veg%cropseedn_deficit_patch(p) = ns_veg%cropseedn_deficit_patch(p) &
                     + nf_veg%repr_grainn_to_seed_patch(p,k) * dt
             end do
-            do k = repr_structure_min, repr_structure_max
-               ns_veg%reproductiven_patch(p,k) = ns_veg%reproductiven_patch(p,k) &
-                    - (nf_veg%repr_structuren_to_cropprod_patch(p,k) + nf_veg%repr_structuren_to_litter_patch(p,k))*dt
-            end do
          end if
 
          ! uptake from soil mineral N pool

From ffc6acc0184df317314d5d2cdd36076627d854a1 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Wed, 29 Nov 2023 17:47:40 -0700
Subject: [PATCH 0043/1248] Upd. expected fails, test list, and relevant error
 checks

---
 bld/CLMBuildNamelist.pm                    |  7 ++++
 cime_config/testdefs/ExpectedTestFails.xml | 28 +++++++++++++++
 cime_config/testdefs/testlist_clm.xml      | 40 ++++++++++++++++++++++
 src/biogeochem/CropReprPoolsMod.F90        | 11 ++++++
 4 files changed, 86 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b0d533ebde..b92acc34c7 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4222,6 +4222,13 @@ sub setup_logic_cnmatrix {
        }
     # Otherwise for CN or BGC mode
     } else {
+      # If matrixcn is on, for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool must be off
+      if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_second_grain_pool"}) ) {
+         $log->fatal_error("for_testing_use_second_grain_pool can NOT be on when use_matrixcn is on" );
+      }
+      if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_repr_structure_pool"}) ) {
+         $log->fatal_error("for_testing_use_repr_structure_pool can NOT be on when use_matrixcn is on" );
+      }
       # If both matrixcn and soil_matrix are off outmatrix can't be on
       if ( ! &value_is_true($nl->get_value("use_matrixcn")) && ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) {
          my $var = "is_outmatrix";
diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 2656079bf7..a55ce73634 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -44,6 +44,34 @@
     </phase>
   </test>
 
+  <test name="LGRAIN2_Ly1_P72x1.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
+    </phase>
+  </test>
+
+  <test name="LGRAIN2_Ly2_P72x1.f10_f10_mg37.I1850Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
+    </phase>
+  </test>
+
+  <test name="LREPRSTRUCT_Ly1_P72x1.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
+    </phase>
+  </test>
+
+  <test name="LREPRSTRUCT_Ly2_P72x1.f10_f10_mg37.I1850Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdDefHydro">
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index e570603ff7..100067f90d 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2599,6 +2599,46 @@
     </machines>
   </test>
 
+  <test name="LGRAIN2_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm">
+        <options>
+          <option name="wallclock">02:00:00</option>
+          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). This and other tests with the ciso_soil_matrixcn_only testmods become redundant when default use_matrixcn = .false.. There are 2 more LGRAIN and two more LREPR tests with the same names but ciso testmods for when default use_matrixcn = .true..</option>
+        </options>
+      </machine>
+    </machines>
+  </test>
+  <test name="LGRAIN2_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm">
+        <options>
+          <option name="wallclock">02:00:00</option>
+          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
+        </options>
+      </machine>
+    </machines>
+  </test>
+  <test name="LREPRSTRUCT_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm">
+        <options>
+          <option name="wallclock">02:00:00</option>
+          <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
+        </options>
+      </machine>
+    </machines>
+  </test>
+  <test name="LREPRSTRUCT_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm">
+        <options>
+          <option name="wallclock">02:00:00</option>
+          <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
+        </options>
+      </machine>
+    </machines>
+  </test>
   <test name="LGRAIN2_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
diff --git a/src/biogeochem/CropReprPoolsMod.F90 b/src/biogeochem/CropReprPoolsMod.F90
index 780b9f2d52..82469b074f 100644
--- a/src/biogeochem/CropReprPoolsMod.F90
+++ b/src/biogeochem/CropReprPoolsMod.F90
@@ -57,6 +57,11 @@ subroutine crop_repr_pools_init()
     ! !DESCRIPTION:
     ! Initialize module-level data
     !
+    ! !USES:
+    use clm_varctl, only: use_matrixcn
+    use abortutils, only: endrun
+    use shr_log_mod, only: errmsg => shr_log_errMsg
+    !
     ! !ARGUMENTS:
     !
     ! !LOCAL VARIABLES:
@@ -77,11 +82,17 @@ subroutine crop_repr_pools_init()
     ! repr_hist_fnames(1) = 'GRAIN_MEAL', grain_hist_fnames(2) = 'GRAIN_OIL', etc.
     if (for_testing_use_second_grain_pool) then
        nrepr_grain = 2
+       if (use_matrixcn) then
+          call endrun(msg="ERROR: for_testing_use_second_grain_pool should be .false. when use_matrixcn = .true."//errmsg(sourcefile, __LINE__))
+       end if
     else
        nrepr_grain = 1
     end if
     if (for_testing_use_repr_structure_pool) then
        nrepr_structure = 2
+       if (use_matrixcn) then
+          call endrun(msg="ERROR: for_testing_use_repr_structure_pool should be .false. when use_matrixcn = .true."//errMsg(sourcefile, __LINE__))
+       end if
     else
        nrepr_structure = 0
     end if

From 040111314eb439f6815b4519174d179882650c42 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Fri, 1 Dec 2023 15:50:14 -0700
Subject: [PATCH 0044/1248] Update expected fails and testlist files

---
 bld/CLMBuildNamelist.pm                    |  5 +++++
 cime_config/testdefs/ExpectedTestFails.xml | 13 +++----------
 cime_config/testdefs/testlist_clm.xml      | 12 ------------
 3 files changed, 8 insertions(+), 22 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b92acc34c7..f02be0c91a 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4222,6 +4222,11 @@ sub setup_logic_cnmatrix {
        }
     # Otherwise for CN or BGC mode
     } else {
+      # TODO (slevis 2023/12/1) The next two if statements do nothing. Erik K and Sam L found that
+      #      for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool
+      #      are empty rather than .true. or .false., but we did not get to the bottom
+      #      of why, yet. The same error-check in the code does get triggered at run-time,
+      #      so we will not pursue fixing this right now.
       # If matrixcn is on, for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool must be off
       if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_second_grain_pool"}) ) {
          $log->fatal_error("for_testing_use_second_grain_pool can NOT be on when use_matrixcn is on" );
diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index a55ce73634..18619818fa 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -30,17 +30,10 @@
 
   <!-- aux_clm test suite failures -->
 
-  <test name="SMS.f10_f10_mg37.I2000Clm50BgcCrop.izumi_pgi.clm-crop">
-    <phase name="MODEL_BUILD">
+  <test name="SMS_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-default--clm-NEON-NIWO">
+    <phase name="SETUP">
       <status>FAIL</status>
-      <issue>PGI problems with the nuopc driver</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_D.f10_f10_mg37.I2000Clm51BgcCrop.izumi_pgi.clm-crop">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>PGI problems with the nuopc driver</issue>
+      <issue>Accessing incorrect url for neon data; will resolve itself when we update cnmatrix to some newer tag</issue>
     </phase>
   </test>
 
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 100067f90d..ede4f6d278 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1177,7 +1177,6 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="izumi"  compiler="intel" category="prebeta"/>
-      <machine name="izumi"  compiler="pgi" category="prebeta"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1431,7 +1430,6 @@
   <test name="SMS" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/crop">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
-      <machine name="izumi" compiler="pgi" category="aux_clm"/>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -1446,15 +1444,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Vmct" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/crop">
-    <machines>
-      <machine name="izumi" compiler="pgi" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >pgi test for MCT driver since nuopc is not passing</option>
-    </options>
-  </test>
   <test name="SMS_Vmct_D_Ld1" grid="f09_g17" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -1548,7 +1537,6 @@
   <test name="SMS_D" grid="f10_f10_mg37" compset="I2000Clm51BgcCrop" testmods="clm/crop">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
-      <machine name="izumi" compiler="pgi" category="aux_clm"/>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>

From 529bd1593064060ef5234089ccaa43fba379775b Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Fri, 1 Dec 2023 17:26:58 -0600
Subject: [PATCH 0045/1248] preparing for PR

Formalized comments in the code
---
 bld/CLMBuildNamelist.pm                       |  2 +-
 bld/namelist_files/namelist_defaults_ctsm.xml |  2 +-
 .../namelist_definition_ctsm.xml              |  2 +-
 src/biogeophys/UrbBuildTempOleson2015Mod.F90  | 22 ++++----
 src/biogeophys/UrbanParamsType.F90            | 10 ++--
 src/cpl/share_esmf/UrbanTimeVarType.F90       | 56 +++++++++----------
 src/main/clm_varpar.F90                       |  2 +-
 7 files changed, 48 insertions(+), 48 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 7c185ff6a0..0895a89ebb 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2111,7 +2111,7 @@ sub setup_logic_urban {
 
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac');
-  # Cathy [dev.04]
+  # X. Li [dev.04]
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic');
 }
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 5be2604c36..a3f488b8f9 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -167,7 +167,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <calc_human_stress_indices phys="clm4_5" >NONE</calc_human_stress_indices>
 
 <!--                                                                              -->
-<!-- Cathy [dev.04]                                                               -->
+<!-- X. Li [dev.04]                                                               -->
 <!-- Default urban air conditioning flux and building interior temperature scheme -->
 <urban_explicit_ac phys="clm5_1" >.true.</urban_explicit_ac>
 <urban_explicit_ac phys="clm5_0" >.true.</urban_explicit_ac>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index aae38a5cec..5f89da9d29 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -948,7 +948,7 @@ Turn urban air conditioning/heating ON or OFF and add wasteheat:
 </entry>
 
 <!--                          -->
-<!-- Cathy [dev.04]           -->
+<!-- X. Li [dev.04]           -->
 <!--                          -->
 <entry id="urban_explicit_ac" type="logical" category="clm_physics"
        group="clmu_inparm" valid_values="" >
diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index f6330ec10b..c07b1ad0e3 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -210,9 +210,9 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     use clm_varctl      , only : iulog
     use abortutils      , only : endrun
     use clm_varpar      , only : nlevurb, nlevsno, nlevmaxurbgrnd
-    ! Cathy [orig]:
+    ! X. Li [orig]:
     ! use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on
-    ! Cathy [dev.04]:
+    ! X. Li [dev.04]:
     use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on, urban_explicit_ac
 !
 ! !ARGUMENTS:
@@ -239,7 +239,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     real(r8) :: t_floor_bef(bounds%begl:bounds%endl)       ! floor temperature at previous time step (K)              
     real(r8) :: t_building_bef(bounds%begl:bounds%endl)    ! internal building air temperature at previous time step [K]
     real(r8) :: t_building_bef_hac(bounds%begl:bounds%endl)! internal building air temperature before applying HAC [K]
-    ! Cathy [dev.03]
+    ! X. Li [dev.03]
     real(r8) :: eflx_urban_ac_sat(bounds%begl:bounds%endl) ! urban air conditioning flux under AC adoption saturation (W/m**2)
     real(r8) :: hcv_roofi(bounds%begl:bounds%endl)         ! roof convective heat transfer coefficient (W m-2 K-1)
     real(r8) :: hcv_sunwi(bounds%begl:bounds%endl)         ! sunwall convective heat transfer coefficient (W m-2 K-1)
@@ -329,7 +329,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     t_floor           => temperature_inst%t_floor_lun      , & ! InOut:  [real(r8) (:)]  floor temperature (K)
     t_building        => temperature_inst%t_building_lun   , & ! InOut:  [real(r8) (:)]  internal building air temperature (K)
 
-    ! Cathy [dev]
+    ! X. Li [dev]
     p_ac              => urbantv_inst%p_ac                 , & ! Input:  [real(r8) (:)]  air-conditioning penetration rate (-)
     t_building_max    => urbantv_inst%t_building_max       , & ! Input:  [real(r8) (:)]  maximum internal building air temperature (K)
     t_building_min    => urbanparams_inst%t_building_min   , & ! Input:  [real(r8) (:)]  minimum internal building air temperature (K)
@@ -432,9 +432,9 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
          vf_wf(l)  = 0.5_r8*(1._r8 - vf_rf(l))
 
          ! This view factor implicitly converts from per unit floor area to per unit wall area
-         ! Cathy [orig]
+         ! X. Li [orig]
          ! vf_fw(l) = vf_wf(l) / building_hwr(l)
-         ! Cathy [bugfix]
+         ! X. Li [bugfix]
          vf_fw(l) = vf_wf(l)
 
          ! This view factor implicitly converts from per unit roof area to per unit wall area
@@ -841,9 +841,9 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
                         + em_floori(l)*sb*t_floor_bef(l)**4._r8 &
                         + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l))
 
-         ! Cathy [orig]
+         ! X. Li [orig]
          ! qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l)
-         ! Cathy [bugfix]
+         ! X. Li [bugfix]
          qrd_building(l) = qrd_roof(l) + qrd_sunw(l) + qrd_shdw(l) + qrd_floor(l)
 
          if (abs(qrd_building(l)) > .10_r8 ) then
@@ -936,16 +936,16 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
 !           rho_dair(l) = pstd / (rair*t_building(l))
 
             if (t_building_bef_hac(l) > t_building_max(l)) then
-              ! Cathy [dev.04]
+              ! X. Li [dev.04]
               if (urban_explicit_ac) then   ! use explicit ac adoption rate:
-                ! Cathy [dev.03]            ! after the change, t_building_max is saturation setpoint
+                ! X. Li [dev.03]            ! after the change, t_building_max is saturation setpoint
                 eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) &
                                      - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
                 t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) &
                               * dtime / (ht_roof(l) * rho_dair(l) * cpair * wtlunit_roof(l))
                 eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l)
               else
-                ! Cathy [orig] 
+                ! X. Li [orig] 
                 t_building(l) = t_building_max(l)
                 eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
                                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90
index c674aac2db..16da4b3ad0 100644
--- a/src/biogeophys/UrbanParamsType.F90
+++ b/src/biogeophys/UrbanParamsType.F90
@@ -101,7 +101,7 @@ module UrbanParamsType
   character(len= *), parameter, public :: urban_hac_on =  'ON'                 
   character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT'  
   character(len= 16), public           :: urban_hac = urban_hac_off
-  ! Cathy [dev.04]
+  ! X. Li [dev.04]
   logical, public                      :: urban_explicit_ac = .true.  ! whether to use explicit, time-varying AC adoption rate
   logical, public                      :: urban_traffic = .false.     ! urban traffic fluxes
 
@@ -849,9 +849,9 @@ subroutine UrbanReadNML ( NLFilename )
     integer :: unitn                ! unit for namelist file
     character(len=32) :: subname = 'UrbanReadNML'  ! subroutine name
 
-    ! Cathy [orig]:
+    ! X. Li [orig]:
     ! namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method
-    ! Cathy [dev.04]:
+    ! X. Li [dev.04]:
     namelist / clmu_inparm / urban_hac, urban_explicit_ac, urban_traffic, building_temp_method
     !EOP
     !-----------------------------------------------------------------------
@@ -880,7 +880,7 @@ subroutine UrbanReadNML ( NLFilename )
 
     ! Broadcast namelist variables read in
     call shr_mpi_bcast(urban_hac,             mpicom)
-    ! Cathy [dev.04]:
+    ! X. Li [dev.04]:
     call shr_mpi_bcast(urban_explicit_ac,     mpicom)
     call shr_mpi_bcast(urban_traffic,         mpicom)
     call shr_mpi_bcast(building_temp_method,  mpicom)
@@ -893,7 +893,7 @@ subroutine UrbanReadNML ( NLFilename )
     !
     if ( masterproc )then
        write(iulog,*) '   urban air conditioning/heating and wasteheat   = ', urban_hac
-       ! Cathy [dev.04]:
+       ! X. Li [dev.04]:
        write(iulog,*) '   urban explicit air-conditioning adoption rate   = ', urban_explicit_ac
        write(iulog,*) '   urban traffic flux   = ', urban_traffic
     end if
diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index ae34449c1e..23dbf54086 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -12,7 +12,7 @@ module UrbanTimeVarType
   use abortutils      , only : endrun
   use decompMod       , only : bounds_type, subgrid_level_landunit
   use clm_varctl      , only : iulog
-  use landunit_varcon , only : isturb_MIN, isturb_MAX ! Cathy: min and max types urban; equals 7 and 9, resp.
+  use landunit_varcon , only : isturb_MIN, isturb_MAX ! X. Li: min and max types urban; equals 7 and 9, resp.
   use clm_varcon      , only : spval
   use LandunitType    , only : lun
   use GridcellType    , only : grc
@@ -24,7 +24,7 @@ module UrbanTimeVarType
   type, public :: urbantv_type
      !
      real(r8), public, pointer :: t_building_max(:)    ! lun maximum internal building air temperature (K)
-     ! Cathy [dev]
+     ! X. Li [dev]
      real(r8), public, pointer :: p_ac(:)              ! lun air-conditioning ownership rate (unitless, between 0 and 1)
      type(shr_strdata_type)    :: sdat_urbantv         ! urban time varying input data stream
    contains
@@ -34,9 +34,9 @@ module UrbanTimeVarType
      procedure, public :: urbantv_interp    ! Interpolate urban time varying stream
   end type urbantv_type
   
-  ! Cathy [orig]
+  ! X. Li [orig]
   ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX)
-  ! Cathy [dev]: 
+  ! X. Li [dev]: 
   character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
 
   character(len=*), parameter, private :: sourcefile = &
@@ -60,7 +60,7 @@ subroutine Init(this, bounds, NLFilename)
     character(len=*)  , intent(in) :: NLFilename   ! Namelist filename
     !
     ! !LOCAL VARIABLES:
-    integer		:: begl, endl                       ! Cathy: beginning and ending landunit index, from src/main/decompMod
+    integer		:: begl, endl                       ! X. Li: beginning and ending landunit index, from src/main/decompMod
     !---------------------------------------------------------------------
 
     begl = bounds%begl; endl = bounds%endl
@@ -68,18 +68,18 @@ subroutine Init(this, bounds, NLFilename)
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
-    ! Cathy [dev]
+    ! X. Li [dev]
     allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
 
     call this%urbantv_init(bounds, NLFilename)
     call this%urbantv_interp(bounds)
 
-    ! Add history fields     ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90
+    ! Add history fields     ! X. Li: this adds an output field. the subroutine is in scr/main/histFileMod.F90
     call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
           avgflag='A', long_name='prescribed maximum interior building temperature',   &
           ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
-    ! Cathy [dev] 
+    ! X. Li [dev] 
     call hist_addfld1d (fname='P_AC', units='unitless',      &
           avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)',   &
           ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
@@ -97,7 +97,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
     use clm_nlUtilsMod   , only : find_nlgroup_name
     use spmdMod          , only : masterproc, mpicom, iam
     use shr_mpi_mod      , only : shr_mpi_bcast
-    use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md ! Cathy: equals 7, 8 and 9
+    use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md ! X. Li: equals 7, 8 and 9
     use dshr_strdata_mod , only : shr_strdata_init_from_inline
     use lnd_comp_shr     , only : mesh, model_clock
     !
@@ -119,7 +119,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
     character(len=CL)  :: urbantvmapalgo = 'nn'             ! mapping alogrithm for urban ac ???
     character(len=CL)  :: urbantv_tintalgo = 'linear'       ! time interpolation alogrithm
     integer            :: rc                                ! error code
-    ! Cathy [orig]: this is taken out because field strings are now hard coded in
+    ! X. Li [orig]: this is taken out because field strings are now hard coded in
     ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string
     character(*), parameter :: subName = "('urbantv_init')" ! ???
     !-----------------------------------------------------------------------
@@ -139,11 +139,11 @@ subroutine urbantv_init(this, bounds, NLFilename)
     model_year_align_urbantv   = 1       ! align stream_year_first_urbantv with this model year
     stream_fldFileName_urbantv = ' '
     stream_meshfile_urbantv    = ' '
-    ! Cathy [orig]
+    ! X. Li [orig]
     ! stream_varnames(isturb_tbd) = urbantvString//"TBD"
     ! stream_varnames(isturb_hd)  = urbantvString//"HD"
     ! stream_varnames(isturb_md)  = urbantvString//"MD"
-    ! Cathy [dev]
+    ! X. Li [dev]
     stream_varnames(1) = "tbuildmax_TBD"
     stream_varnames(2) = "tbuildmax_HD"
     stream_varnames(3) = "tbuildmax_MD"
@@ -180,9 +180,9 @@ subroutine urbantv_init(this, bounds, NLFilename)
        write(iulog,'(a,a)' ) '  stream_fldFileName_urbantv = ',stream_fldFileName_urbantv
        write(iulog,'(a,a)' ) '  stream_meshfile_urbantv    = ',stream_meshfile_urbantv
        write(iulog,'(a,a)' ) '  urbantv_tintalgo           = ',urbantv_tintalgo
-       ! Cathy [orig]
+       ! X. Li [orig]
        ! do n = isturb_tbd,isturb_md
-       ! Cathy [dev]
+       ! X. Li [dev]
        do n = 1,6
           write(iulog,'(a,a)' ) '  stream_varname         = ',trim(stream_varnames(n))
        end do
@@ -200,10 +200,10 @@ subroutine urbantv_init(this, bounds, NLFilename)
          stream_lev_dimname  = 'null',                               &
          stream_mapalgo      = trim(urbantvmapalgo),                 &
          stream_filenames    = (/trim(stream_fldfilename_urbantv)/), &
-         ! Cathy [orig]
+         ! X. Li [orig]
          ! stream_fldlistFile  = stream_varnames(isturb_tbd:isturb_md),&
          ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),&
-         ! Cathy [dev]
+         ! X. Li [dev]
          stream_fldlistFile  = stream_varnames(1:6),                 &
          stream_fldListModel = stream_varnames(1:6),                 &
          stream_yearFirst    = stream_year_first_urbantv,            &
@@ -265,10 +265,10 @@ subroutine urbantv_interp(this, bounds)
 
     ! Create 2d array for all stream variable data
     lsize = bounds%endg - bounds%begg + 1
-    ! Cathy [orig]
+    ! X. Li [orig]
     ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX))
     ! do n = isturb_MIN,isturb_MAX
-    ! Cathy [dev]
+    ! X. Li [dev]
     allocate(dataptr2d(lsize, 1:6))
     do n = 1,6
        call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), &
@@ -291,13 +291,13 @@ subroutine urbantv_interp(this, bounds)
              ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
-          ! Cathy [orig]
+          ! X. Li [orig]
           ! do n = isturb_MIN,isturb_MAX
-          ! Cathy [dev]
+          ! X. Li [dev]
           do n = 1,6
-             ! Cathy [orig]
+             ! X. Li [orig]
              ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
-             ! Cathy [dev.02]
+             ! X. Li [dev.02]
              if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then
                 this%t_building_max(l) = dataptr2d(ig,n)
              end if
@@ -306,9 +306,9 @@ subroutine urbantv_interp(this, bounds)
              end if
           end do
        else
-          this%t_building_max(l) = spval ! Cathy: special value for real data, set to 1.e36 in src/main/clm_varcon
-          ! Cathy [dev]
-          this%p_ac(l) = 0._r8 ! Cathy: set to 0 for non-urban landunit
+          this%t_building_max(l) = spval ! X. Li: special value for real data, set to 1.e36 in src/main/clm_varcon
+          ! X. Li [dev]
+          this%p_ac(l) = 0._r8 ! X. Li: set to 0 for non-urban landunit
        end if
     end do
     deallocate(dataptr2d)
@@ -322,9 +322,9 @@ subroutine urbantv_interp(this, bounds)
              ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
-          ! Cathy [orig]
+          ! X. Li [orig]
           ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
-          ! Cathy [dev]
+          ! X. Li [dev]
           if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) &
              .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then
              found = .true.
@@ -339,7 +339,7 @@ subroutine urbantv_interp(this, bounds)
        write(iulog,*)'landunit type:   ',lun%itype(lindx)
        write(iulog,*)'urban_valid:     ',urban_valid(gindx)
        write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
-       ! Cathy [dev]
+       ! X. Li [dev]
        write(iulog,*)'p_ac:            ',this%p_ac(lindx)
        call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, &
             msg=errmsg(sourcefile, __LINE__))
diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90
index e1179e43b3..3ef9cf48a2 100644
--- a/src/main/clm_varpar.F90
+++ b/src/main/clm_varpar.F90
@@ -203,7 +203,7 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft)
     max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb)
 
     nlevsoifl   =  10
-    ![Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10]
+    ! X. Li: changed below from 5 to 10 to match new surface data
     nlevurb     =  10 ! originally 5
 
     if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined

From def2f7506284508182898bc0d1edeb2c12812572 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 12 Dec 2023 12:16:39 -0700
Subject: [PATCH 0046/1248] Change failing SMS_Ln9_P72x2 test to passing
 SMS_Ln9_P360x2

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 81ad8bced4..52ccfbf2db 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -322,7 +322,7 @@
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="SMS_Ln9_P72x2" grid="C96_C96_mg17" compset="IHistClm50BgcCrop" testmods="clm/clm50cam6LndTuningMode">
+  <test name="SMS_Ln9_P360x2" grid="C96_C96_mg17" compset="IHistClm50BgcCrop" testmods="clm/clm50cam6LndTuningMode">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>

From 08768f9b877caed6efd3c8fbb38f1ac3bbf29991 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Mon, 18 Dec 2023 15:25:38 -0700
Subject: [PATCH 0047/1248] To pass test, add use_matrixcn=.false. to luna
 testmod

---
 cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm
index cbfbb9f525..fb796ebfaf 100644
--- a/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm
@@ -1,3 +1,3 @@
  use_luna    = .true.
  use_flexibleCN = .false.
-
+ use_matrixcn = .false.

From 8b2cb728ac99a2e6c8a7be5738f8b709b5e336b5 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 19 Dec 2023 12:46:43 -0700
Subject: [PATCH 0048/1248] Remove two clm45 tests from ExpectedTestFails

---
 cime_config/testdefs/ExpectedTestFails.xml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 18619818fa..8a43eb0acc 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -44,13 +44,6 @@
     </phase>
   </test>
 
-  <test name="LGRAIN2_Ly2_P72x1.f10_f10_mg37.I1850Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
-    </phase>
-  </test>
-
   <test name="LREPRSTRUCT_Ly1_P72x1.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
     <phase name="RUN">
       <status>FAIL</status>
@@ -58,13 +51,6 @@
     </phase>
   </test>
 
-  <test name="LREPRSTRUCT_Ly2_P72x1.f10_f10_mg37.I1850Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
-    </phase>
-  </test>
-
   <!-- fates test suite failures -->
 
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdDefHydro">

From ddfac7b299d8143fdf2c2d7438cf2729fe1a047d Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Fri, 22 Dec 2023 15:35:13 -0700
Subject: [PATCH 0049/1248] Backed dev100 mods out of 3 more files for
 1x1_brazil test to pass

---
 src/biogeochem/CNCStateUpdate1Mod.F90         | 232 ++----
 src/biogeochem/CNPhenologyMod.F90             | 680 +++++++++---------
 .../SoilBiogeochemNStateUpdate1Mod.F90        |  70 +-
 3 files changed, 429 insertions(+), 553 deletions(-)

diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90
index 8cac85824e..f73453476e 100644
--- a/src/biogeochem/CNCStateUpdate1Mod.F90
+++ b/src/biogeochem/CNCStateUpdate1Mod.F90
@@ -2,9 +2,6 @@ module CNCStateUpdate1Mod
 
   !-----------------------------------------------------------------------
   ! Module for carbon state variable update, non-mortality fluxes.
-  ! When the matrix solution is being used (use_matrixcn and use_soil_matrixcn)
-  ! only some state updates are done here, the other state updates happen
-  ! after the matrix is solved in VegMatrix and SoilMatrix.
   !
   ! !USES:
   use shr_kind_mod                       , only : r8 => shr_kind_r8
@@ -19,7 +16,8 @@ module CNCStateUpdate1Mod
   use CNVegCarbonFluxType                , only : cnveg_carbonflux_type
   use CropType                           , only : crop_type
   use CropReprPoolsMod                   , only : nrepr, repr_grain_min, repr_grain_max, repr_structure_min, repr_structure_max
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn
+  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
+  use SoilBiogeochemDecompCascadeConType , only : use_soil_matrixcn
   use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
   use SoilBiogeochemCarbonStateType      , only : soilbiogeochem_carbonstate_type
   use PatchType                          , only : patch
@@ -193,9 +191,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
          do j = 1,nlevdecomp
             do fc = 1,num_soilc
                c = filter_soilc(fc)
-               !
-               ! State update without the matrix solution
-               !
                if (.not. use_soil_matrixcn) then
                   ! phenology and dynamic land cover fluxes
                   do i = i_litr_min, i_litr_max
@@ -207,12 +202,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                   ! terms have been moved to CStateUpdateDynPatch. I think this is zeroed every
                   ! time step, but to be safe, I'm explicitly setting it to zero here.
                   cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8
-               !
-               ! For the matrix solution the actual state update comes after the matrix
-               ! multiply in SoilMatrix, but the matrix needs to be setup with
-               ! the equivalent of above. Those changes can be here or in the
-               ! native subroutines dealing with that field
-               !
                else
                   ! phenology and dynamic land cover fluxes
                   do i = i_litr_min, i_litr_max
@@ -243,15 +232,11 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
             do j = 1,nlevdecomp
                do fc = 1,num_soilc
                   c = filter_soilc(fc)
-                  !
-                  ! State update without the matrix solution
-                  !
                   if (.not. use_soil_matrixcn) then
                      cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
-                       cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
-                       - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt
-                  ! else  ! not needed here?
-                  end if !not use_soil_matrixcn
+                          cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
+                          - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt
+                  end if !not use_soil_matrixcn 
                end do
             end do
          end do
@@ -260,14 +245,10 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                do j = 1,nlevdecomp
                   do fc = 1,num_soilc
                      c = filter_soilc(fc)
-                     !
-                     ! State update without the matrix solution
-                     !
                      if (.not. use_soil_matrixcn) then
                         cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
-                          cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
-                          + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt
-                     ! else  ! not needed here?
+                             cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
+                             + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt
                      end if !not use_soil_matrixcn
                   end do
                end do
@@ -275,17 +256,13 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
          end do
       end if
 
-    if (.not. use_fates) then
+    if (.not. use_fates) then    
 ptch: do fp = 1,num_soilp
          p = filter_soilp(fp)
          c = patch%column(p)
 
          ! phenology: transfer growth fluxes
-
-         !
-         ! State update without the matrix solution
-         !
-         if(.not. use_matrixcn)then
+        if(.not. use_matrixcn)then
            ! NOTE: Any changes that go here MUST be applied to the matrix
            ! version as well
            cs_veg%leafc_patch(p)           = cs_veg%leafc_patch(p)       + cf_veg%leafc_xfer_to_leafc_patch(p)*dt
@@ -314,11 +291,11 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
               end do
            end if
 
-           ! phenology: litterfall fluxes
+         ! phenology: litterfall fluxes
            cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) - cf_veg%leafc_to_litter_patch(p)*dt
            cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p) - cf_veg%frootc_to_litter_patch(p)*dt
-
-           ! livewood turnover fluxes
+         
+         ! livewood turnover fluxes
            if (woody(ivt(p)) == 1._r8) then
               cs_veg%livestemc_patch(p)  = cs_veg%livestemc_patch(p)  - cf_veg%livestemc_to_deadstemc_patch(p)*dt
               cs_veg%deadstemc_patch(p)  = cs_veg%deadstemc_patch(p)  + cf_veg%livestemc_to_deadstemc_patch(p)*dt
@@ -342,81 +319,57 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                       - (cf_veg%repr_structurec_to_cropprod_patch(p,k) + cf_veg%repr_structurec_to_litter_patch(p,k))*dt
               end do
            end if
-         !
-         ! For the matrix solution the actual state update comes after the matrix
-         ! multiply in VegMatrix, but the matrix needs to be setup with
-         ! the equivalent of above. Those changes can be here or in the
-         ! native subroutines dealing with that field
-         !
-         else
-            ! NOTE: Changes for above that apply for matrix code are in CNPhenology EBK (11/26/2019)
-
-            ! This part below MUST match exactly the code for the non-matrix part
-            ! above!
-            if (ivt(p) >= npcropmin) then
-               cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
-                    - cf_veg%crop_seedc_to_leaf_patch(p) * dt
-               do k = repr_grain_min, repr_grain_max
-                  cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
-                       + cf_veg%repr_grainc_to_seed_patch(p,k) * dt
-               end do
-!        else  ! slevis: I think I rejected this alternative due to a balance error
-!           ! NOTE: Changes for above that apply for matrix code are in CNPhenology EBK (11/26/2019)
-
-!           ! This part below MUST match exactly the code for the non-matrix part
-!           ! above!
-!           if (ivt(p) >= npcropmin) then
-!              cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
-!                   - cf_veg%crop_seedc_to_leaf_patch(p) * dt
-!              do k = repr_grain_min, repr_grain_max
-!                 cs_veg%reproductivec_patch(p,k)   = cs_veg%reproductivec_patch(p,k) &
-!                      - (cf_veg%repr_grainc_to_food_patch(p,k) + cf_veg%repr_grainc_to_seed_patch(p,k))*dt
-!                 cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
-!                      + cf_veg%repr_grainc_to_seed_patch(p,k) * dt
-!              end do
-!              do k = repr_structure_min, repr_structure_max
-!                 cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) &
-!                      - (cf_veg%repr_structurec_to_cropprod_patch(p,k) + cf_veg%repr_structurec_to_litter_patch(p,k))*dt
-!              end do
-            end if
-         end if !not use_matrixcn
+        else
+           ! NOTE: Changes for above that apply for matrix code are in CNPhenology EBK (11/26/2019)
+
+           ! This part below MUST match exactly the code for the non-matrix part
+           ! above!
+           if (ivt(p) >= npcropmin) then
+              cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
+                   - cf_veg%crop_seedc_to_leaf_patch(p) * dt
+              do k = repr_grain_min, repr_grain_max
+                 cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
+                      + cf_veg%repr_grainc_to_seed_patch(p,k) * dt
+              end do
+           end if
+        end if !not use_matrixcn
 
-         check_cpool = cs_veg%cpool_patch(p)- cf_veg%psnsun_to_cpool_patch(p)*dt-cf_veg%psnshade_to_cpool_patch(p)*dt
-         cpool_delta  =  cs_veg%cpool_patch(p)
+        check_cpool = cs_veg%cpool_patch(p)- cf_veg%psnsun_to_cpool_patch(p)*dt-cf_veg%psnshade_to_cpool_patch(p)*dt
+        cpool_delta  =  cs_veg%cpool_patch(p) 
 
-         ! maintenance respiration fluxes from cpool
+           ! maintenance respiration fluxes from cpool
 
-         cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_xsmrpool_patch(p)*dt
-         cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%leaf_curmr_patch(p)*dt
-         cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%froot_curmr_patch(p)*dt
-         If (woody(ivt(p)) == 1._r8) then
+           cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_xsmrpool_patch(p)*dt
+           cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%leaf_curmr_patch(p)*dt
+           cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%froot_curmr_patch(p)*dt
+           If (woody(ivt(p)) == 1._r8) then
               cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%livestem_curmr_patch(p)*dt
               cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%livecroot_curmr_patch(p)*dt
-         end if
-         if (ivt(p) >= npcropmin) then ! skip 2 generic crops
+           end if
+           if (ivt(p) >= npcropmin) then ! skip 2 generic crops
               cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%livestem_curmr_patch(p)*dt
               do k = 1, nrepr
                  cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%reproductive_curmr_patch(p,k)*dt
               end do
-         end if
+           end if
          
          
-         cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) -  cf_veg%cpool_to_resp_patch(p)*dt
+           cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) -  cf_veg%cpool_to_resp_patch(p)*dt
 
-         !RF Add in the carbon spent on uptake respiration
-         cs_veg%cpool_patch(p)= cs_veg%cpool_patch(p) - cf_veg%soilc_change_patch(p)*dt
+           !RF Add in the carbon spent on uptake respiration. 
+           cs_veg%cpool_patch(p)= cs_veg%cpool_patch(p) - cf_veg%soilc_change_patch(p)*dt
            
-         ! maintenance respiration fluxes from xsmrpool
-         cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) + cf_veg%cpool_to_xsmrpool_patch(p)*dt
-         cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%leaf_xsmr_patch(p)*dt
-         cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%froot_xsmr_patch(p)*dt
-         if (woody(ivt(p)) == 1._r8) then
+           ! maintenance respiration fluxes from xsmrpool
+           cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) + cf_veg%cpool_to_xsmrpool_patch(p)*dt
+           cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%leaf_xsmr_patch(p)*dt
+           cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%froot_xsmr_patch(p)*dt
+           if (woody(ivt(p)) == 1._r8) then
               cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%livestem_xsmr_patch(p)*dt
               cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%livecroot_xsmr_patch(p)*dt
-         end if
+           end if
 
-         ! allocation fluxes
-         if (carbon_resp_opt == 1) then
+           ! allocation fluxes
+           if (carbon_resp_opt == 1) then
               cf_veg%cpool_to_leafc_patch(p) = cf_veg%cpool_to_leafc_patch(p) - cf_veg%cpool_to_leafc_resp_patch(p)
               cf_veg%cpool_to_leafc_storage_patch(p) = cf_veg%cpool_to_leafc_storage_patch(p) - &
                    cf_veg%cpool_to_leafc_storage_resp_patch(p)
@@ -427,21 +380,12 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
          cs_veg%cpool_patch(p)             = cs_veg%cpool_patch(p)          - cf_veg%cpool_to_leafc_patch(p)*dt
          cs_veg%cpool_patch(p)             = cs_veg%cpool_patch(p)          - cf_veg%cpool_to_leafc_storage_patch(p)*dt
          cs_veg%cpool_patch(p)             = cs_veg%cpool_patch(p)          - cf_veg%cpool_to_frootc_patch(p)*dt
-         cs_veg%cpool_patch(p)             = cs_veg%cpool_patch(p)          - cf_veg%cpool_to_frootc_storage_patch(p)*dt
-         !
-         ! State update without the matrix solution
-         !
-         if(.not. use_matrixcn) then
+         cs_veg%cpool_patch(p)             = cs_veg%cpool_patch(p)          - cf_veg%cpool_to_frootc_storage_patch(p)*dt 
+        if(.not. use_matrixcn) then
            cs_veg%leafc_patch(p)           = cs_veg%leafc_patch(p)          + cf_veg%cpool_to_leafc_patch(p)*dt
            cs_veg%leafc_storage_patch(p)   = cs_veg%leafc_storage_patch(p)  + cf_veg%cpool_to_leafc_storage_patch(p)*dt
            cs_veg%frootc_patch(p)          = cs_veg%frootc_patch(p)         + cf_veg%cpool_to_frootc_patch(p)*dt
            cs_veg%frootc_storage_patch(p)  = cs_veg%frootc_storage_patch(p) + cf_veg%cpool_to_frootc_storage_patch(p)*dt
-           !
-           ! For the matrix solution the actual state update comes after the matrix
-           ! multiply in VegMatrix, but the matrix needs to be setup with
-           ! the equivalent of above. Those changes can be here or in the
-           ! native subroutines dealing with that field
-           !
          else
            ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
          end if !not use_matrixcn
@@ -461,10 +405,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
             cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_livecrootc_patch(p)*dt
             cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_livecrootc_storage_patch(p)*dt
             cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_deadcrootc_patch(p)*dt
-            cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_deadcrootc_storage_patch(p)*dt
-            !
-            ! State update without the matrix solution
-            !
+            cs_veg%cpool_patch(p)              = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_deadcrootc_storage_patch(p)*dt 
             if(.not. use_matrixcn)then
                cs_veg%livestemc_patch(p)          = cs_veg%livestemc_patch(p)          + cf_veg%cpool_to_livestemc_patch(p)*dt
                cs_veg%livestemc_storage_patch(p)  = cs_veg%livestemc_storage_patch(p)  + cf_veg%cpool_to_livestemc_storage_patch(p)*dt
@@ -474,12 +415,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                cs_veg%livecrootc_storage_patch(p) = cs_veg%livecrootc_storage_patch(p) + cf_veg%cpool_to_livecrootc_storage_patch(p)*dt
                cs_veg%deadcrootc_patch(p)         = cs_veg%deadcrootc_patch(p)         + cf_veg%cpool_to_deadcrootc_patch(p)*dt
                cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) + cf_veg%cpool_to_deadcrootc_storage_patch(p)*dt
-            !
-            ! For the matrix solution the actual state update comes after the matrix
-            ! multiply in VegMatrix, but the matrix needs to be setup with
-            ! the equivalent of above. Those changes can be here or in the
-            ! native subroutines dealing with that field
-            !
             else
                ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
             end if !not use_matrixcn
@@ -496,9 +431,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                 cs_veg%cpool_patch(p)          = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_reproductivec_patch(p,k)*dt
                 cs_veg%cpool_patch(p)          = cs_veg%cpool_patch(p)              - cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt
             end do
-            !
-            ! State update without the matrix solution
-            !
             if(.not. use_matrixcn)then
                cs_veg%livestemc_patch(p)          = cs_veg%livestemc_patch(p)          + cf_veg%cpool_to_livestemc_patch(p)*dt
                cs_veg%livestemc_storage_patch(p)  = cs_veg%livestemc_storage_patch(p)  + cf_veg%cpool_to_livestemc_storage_patch(p)*dt
@@ -508,12 +440,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                   cs_veg%reproductivec_storage_patch(p,k) = cs_veg%reproductivec_storage_patch(p,k) &
                                                           + cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt
                end do
-            !
-            ! For the matrix solution the actual state update comes after the matrix
-            ! multiply in VegMatrix, but the matrix needs to be setup with
-            ! the equivalent of above. Those changes can be here or in the
-            ! native subroutines dealing with that field
-            !
             else
                ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
             end if  !not use_matrixcn
@@ -576,30 +502,17 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
          cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) + cf_veg%cpool_to_gresp_storage_patch(p)*dt
 
          ! move storage pools into transfer pools
-
-         !
-         ! State update without the matrix solution
-         !
-         if(.not. use_matrixcn)then
-            cs_veg%leafc_storage_patch(p)  = cs_veg%leafc_storage_patch(p)  - cf_veg%leafc_storage_to_xfer_patch(p)*dt
-            cs_veg%leafc_xfer_patch(p)     = cs_veg%leafc_xfer_patch(p)     + cf_veg%leafc_storage_to_xfer_patch(p)*dt
-            cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) - cf_veg%frootc_storage_to_xfer_patch(p)*dt
-            cs_veg%frootc_xfer_patch(p)    = cs_veg%frootc_xfer_patch(p)    + cf_veg%frootc_storage_to_xfer_patch(p)*dt
-         !
-         ! For the matrix solution the actual state update comes after the matrix
-         ! multiply in VegMatrix, but the matrix needs to be setup with
-         ! the equivalent of above. Those changes can be here or in the
-         ! native subroutines dealing with that field
-         !
+        if(.not. use_matrixcn)then
+          cs_veg%leafc_storage_patch(p)  = cs_veg%leafc_storage_patch(p)  - cf_veg%leafc_storage_to_xfer_patch(p)*dt
+          cs_veg%leafc_xfer_patch(p)     = cs_veg%leafc_xfer_patch(p)     + cf_veg%leafc_storage_to_xfer_patch(p)*dt
+          cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) - cf_veg%frootc_storage_to_xfer_patch(p)*dt
+          cs_veg%frootc_xfer_patch(p)    = cs_veg%frootc_xfer_patch(p)    + cf_veg%frootc_storage_to_xfer_patch(p)*dt
          else
-            ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
+           ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
          end if !not use_matrixcn
          if (woody(ivt(p)) == 1._r8) then
             cs_veg%gresp_storage_patch(p)      = cs_veg%gresp_storage_patch(p)     - cf_veg%gresp_storage_to_xfer_patch(p)*dt
             cs_veg%gresp_xfer_patch(p)         = cs_veg%gresp_xfer_patch(p)        + cf_veg%gresp_storage_to_xfer_patch(p)*dt
-            !
-            ! State update without the matrix solution
-            !
             if(.not. use_matrixcn)then
                cs_veg%livestemc_storage_patch(p)  = cs_veg%livestemc_storage_patch(p) - cf_veg%livestemc_storage_to_xfer_patch(p)*dt
                cs_veg%livestemc_xfer_patch(p)     = cs_veg%livestemc_xfer_patch(p)    + cf_veg%livestemc_storage_to_xfer_patch(p)*dt
@@ -609,21 +522,12 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                cs_veg%livecrootc_xfer_patch(p)    = cs_veg%livecrootc_xfer_patch(p)   + cf_veg%livecrootc_storage_to_xfer_patch(p)*dt
                cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p)- cf_veg%deadcrootc_storage_to_xfer_patch(p)*dt
                cs_veg%deadcrootc_xfer_patch(p)    = cs_veg%deadcrootc_xfer_patch(p)   + cf_veg%deadcrootc_storage_to_xfer_patch(p)*dt
-            !
-            ! For the matrix solution the actual state update comes after the matrix
-            ! multiply in VegMatrix, but the matrix needs to be setup with
-            ! the equivalent of above. Those changes can be here or in the
-            ! native subroutines dealing with that field
-            !
             else
                ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
             end if !not use_matrixcn
          end if
          if (ivt(p) >= npcropmin) then ! skip 2 generic crops
             ! lines here for consistency; the transfer terms are zero
-            !
-            ! State update without the matrix solution
-            !
             if(.not. use_matrixcn)then
                ! lines here for consistency; the transfer terms are zero
                cs_veg%livestemc_storage_patch(p)  = cs_veg%livestemc_storage_patch(p) - cf_veg%livestemc_storage_to_xfer_patch(p)*dt
@@ -634,12 +538,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                   cs_veg%reproductivec_xfer_patch(p,k) = cs_veg%reproductivec_xfer_patch(p,k) &
                        + cf_veg%reproductivec_storage_to_xfer_patch(p,k)*dt
                end do
-            !
-            ! For the matrix solution the actual state update comes after the matrix
-            ! multiply in VegMatrix, but the matrix needs to be setup with
-            ! the equivalent of above. Those changes can be here or in the
-            ! native subroutines dealing with that field
-            !
             else
                ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019)
             end if !not use_matrixcn
@@ -655,20 +553,16 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                ! an intent(inout)
                ! fluxes should not be updated in this module - not sure where
                ! this belongs
-               ! DML (06-20-2017) While debugging crop isotope code, found that cpool_patch and frootc_patch
-               ! could occasionally be very small but nonzero numbers after crop harvest, which persists
+               ! DML (06-20-2017) While debugging crop isotope code, found that cpool_patch and frootc_patch 
+               ! could occasionally be very small but nonzero numbers after crop harvest, which persists 
                ! through to next planting and for reasons that could not 100%
                ! isolate, caused C12/C13 ratios to occasionally go out of
                ! bounds. Zeroing out these small pools and putting them into the flux to the
                ! atmosphere solved many of the crop isotope problems
 
-               ! Instantly release XSMRPOOL to atmosphere
                if ( .not. dribble_crophrv_xsmrpool_2atm ) then
                   cf_veg%xsmrpool_to_atm_patch(p) = cf_veg%xsmrpool_to_atm_patch(p) + cs_veg%xsmrpool_patch(p)/dt
                   cf_veg%xsmrpool_to_atm_patch(p) = cf_veg%xsmrpool_to_atm_patch(p) + cs_veg%cpool_patch(p)/dt
-                  !
-                  ! State update without the matrix solution
-                  !
                   if(.not. use_matrixcn)then
                      cf_veg%xsmrpool_to_atm_patch(p) = cf_veg%xsmrpool_to_atm_patch(p) + cs_veg%frootc_patch(p)/dt
                   else
@@ -684,9 +578,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                   cs_veg%xsmrpool_loss_patch(p) = cs_veg%xsmrpool_loss_patch(p) + &
                                                   cs_veg%xsmrpool_patch(p) + &
                                                   cs_veg%cpool_patch(p)
-                  !
-                  ! State update without the matrix solution
-                  !
                   if(.not. use_matrixcn)then
                      cs_veg%xsmrpool_loss_patch(p) = cs_veg%xsmrpool_loss_patch(p) + cs_veg%frootc_patch(p)
                   else
@@ -694,9 +585,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                        + cs_veg%frootc_patch(p) * matrix_update_phc(p,cf_veg%ifroot_to_iout_ph,1._r8/dt,dt,cnveg_carbonflux_inst,.true.,.true.)
                   end if
                end if
-               !
-               ! State update without the matrix solution
-               !
                if (.not. use_matrixcn) then
                   cs_veg%frootc_patch(p)          = 0._r8
                end if
@@ -713,8 +601,8 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
             end if
          end if
          
-      end do ptch ! end of patch loop
-    end if   ! end of NOT fates
+        end do ptch ! end of patch loop
+      end if   ! end of NOT fates
     
     end associate
   
diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 5d666c0ffb..e804c0658b 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -136,10 +136,8 @@ module CNPhenologyMod
   integer, allocatable :: maxplantjday(:,:) ! maximum planting julian day
   integer              :: jdayyrstart(inSH) ! julian day of start of year
 
-  ! Two matrix check parameters that will be invoked when the matrix solution
-  ! comes in (use_matrixcn)
-  logical,parameter :: matrixcheck_ph = .True.                   ! Matrix solution check
-  logical,parameter :: acc_ph = .False.                          ! Another matrix solution check
+  logical,parameter :: matrixcheck_ph = .True.                   ! Matrix check
+  logical,parameter :: acc_ph = .False.                          ! Another matrix check
 
   real(r8), private :: initial_seed_at_planting        = 3._r8   ! Initial seed at planting
 
@@ -641,114 +639,115 @@ subroutine CNEvergreenPhenology (num_soilp, filter_soilp , &
     integer :: p                          ! indices
     integer :: fp                         ! lake filter patch index
     
-    real(r8):: tranr
+    real(r8):: tranr 				      
     real(r8):: t1                         ! temporary variable 
     !-----------------------------------------------------------------------
 
     associate(                                        & 
-    ivt        => patch%itype                    , & ! Input:  [integer  (:) ]  patch vegetation type                                
+         ivt        => patch%itype                    , & ! Input:  [integer  (:) ]  patch vegetation type                                
 
-    evergreen  => pftcon%evergreen             , & ! Input:  binary flag for evergreen leaf habit (0 or 1)     
-    leaf_long  => pftcon%leaf_long             , & ! Input:  leaf longevity (yrs)  
+         evergreen  => pftcon%evergreen             , & ! Input:  binary flag for evergreen leaf habit (0 or 1)     
+         leaf_long  => pftcon%leaf_long             , & ! Input:  leaf longevity (yrs)  
          
-    woody                               =>    pftcon%woody                                                         , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)     
+         woody                               =>    pftcon%woody                                                         , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)     
          
-    leafc_storage                       =>    cnveg_carbonstate_inst%leafc_storage_patch                           , & ! Input:  [real(r8) (:)]  (gC/m2) leaf C storage                             
-    frootc_storage                      =>    cnveg_carbonstate_inst%frootc_storage_patch                          , & ! Input:  [real(r8) (:)]  (gC/m2) fine root C storage                         
-    livestemc_storage                   =>    cnveg_carbonstate_inst%livestemc_storage_patch                       , & ! Input:  [real(r8) (:)]  (gC/m2) live stem C storage                         
-    deadstemc_storage                   =>    cnveg_carbonstate_inst%deadstemc_storage_patch                       , & ! Input:  [real(r8) (:)]  (gC/m2) dead stem C storage                         
-    livecrootc_storage                  =>    cnveg_carbonstate_inst%livecrootc_storage_patch                      , & ! Input:  [real(r8) (:)]  (gC/m2) live coarse root C storage                  
-    deadcrootc_storage                  =>    cnveg_carbonstate_inst%deadcrootc_storage_patch                      , & ! Input:  [real(r8) (:)]  (gC/m2) dead coarse root C storage                  
-    gresp_storage                       =>    cnveg_carbonstate_inst%gresp_storage_patch                           , & ! Input:  [real(r8) (:)]  (gC/m2) growth respiration storage   
-    leafc_xfer                          =>    cnveg_carbonstate_inst%leafc_xfer_patch                              , & ! InOut:  [real(r8) (:)]  (gC/m2) leaf C transfer                            
-    frootc_xfer                         =>    cnveg_carbonstate_inst%frootc_xfer_patch                             , & ! InOut:  [real(r8) (:)]  (gC/m2) fine root C transfer                       
-    livestemc_xfer                      =>    cnveg_carbonstate_inst%livestemc_xfer_patch                          , & ! InOut:  [real(r8) (:)]  (gC/m2) live stem C transfer                       
-    deadstemc_xfer                      =>    cnveg_carbonstate_inst%deadstemc_xfer_patch                          , & ! InOut:  [real(r8) (:)]  (gC/m2) dead stem C transfer                       
-    livecrootc_xfer                     =>    cnveg_carbonstate_inst%livecrootc_xfer_patch                         , & ! InOut:  [real(r8) (:)]  (gC/m2) live coarse root C transfer                
-    deadcrootc_xfer                     =>    cnveg_carbonstate_inst%deadcrootc_xfer_patch                         , & ! InOut:  [real(r8) (:)]  (gC/m2) dead coarse root C transfer   
-                   
-    leafn_storage                       =>    cnveg_nitrogenstate_inst%leafn_storage_patch                         , & ! Input:  [real(r8) (:)]  (gN/m2) leaf N storage                              
-    frootn_storage                      =>    cnveg_nitrogenstate_inst%frootn_storage_patch                        , & ! Input:  [real(r8) (:)]  (gN/m2) fine root N storage                         
-    livestemn_storage                   =>    cnveg_nitrogenstate_inst%livestemn_storage_patch                     , & ! Input:  [real(r8) (:)]  (gN/m2) live stem N storage                         
-    deadstemn_storage                   =>    cnveg_nitrogenstate_inst%deadstemn_storage_patch                     , & ! Input:  [real(r8) (:)]  (gN/m2) dead stem N storage                         
-    livecrootn_storage                  =>    cnveg_nitrogenstate_inst%livecrootn_storage_patch                    , & ! Input:  [real(r8) (:)]  (gN/m2) live coarse root N storage                  
-    deadcrootn_storage                  =>    cnveg_nitrogenstate_inst%deadcrootn_storage_patch                    , & ! Input:  [real(r8) (:)]  (gN/m2) dead coarse root N storage               
-    leafn_xfer                          =>    cnveg_nitrogenstate_inst%leafn_xfer_patch                            , & ! InOut:  [real(r8) (:)]  (gN/m2) leaf N transfer                            
-    frootn_xfer                         =>    cnveg_nitrogenstate_inst%frootn_xfer_patch                           , & ! InOut:  [real(r8) (:)]  (gN/m2) fine root N transfer                       
-    livestemn_xfer                      =>    cnveg_nitrogenstate_inst%livestemn_xfer_patch                        , & ! InOut:  [real(r8) (:)]  (gN/m2) live stem N transfer                       
-    deadstemn_xfer                      =>    cnveg_nitrogenstate_inst%deadstemn_xfer_patch                        , & ! InOut:  [real(r8) (:)]  (gN/m2) dead stem N transfer                       
-    livecrootn_xfer                     =>    cnveg_nitrogenstate_inst%livecrootn_xfer_patch                       , & ! InOut:  [real(r8) (:)]  (gN/m2) live coarse root N transfer                
-    deadcrootn_xfer                     =>    cnveg_nitrogenstate_inst%deadcrootn_xfer_patch                       , & ! InOut:  [real(r8) (:)]  (gN/m2) dead coarse root N transfer     
-                    
-    leafc_storage_to_xfer               =>    cnveg_carbonflux_inst%leafc_storage_to_xfer_patch                    , & ! InOut:  [real(r8) (:)]                                                     
-    frootc_storage_to_xfer              =>    cnveg_carbonflux_inst%frootc_storage_to_xfer_patch                   , & ! InOut:  [real(r8) (:)]                                                     
-    livestemc_storage_to_xfer           =>    cnveg_carbonflux_inst%livestemc_storage_to_xfer_patch                , & ! InOut:  [real(r8) (:)]                                                     
-    deadstemc_storage_to_xfer           =>    cnveg_carbonflux_inst%deadstemc_storage_to_xfer_patch                , & ! InOut:  [real(r8) (:)]                                                     
-    livecrootc_storage_to_xfer          =>    cnveg_carbonflux_inst%livecrootc_storage_to_xfer_patch               , & ! InOut:  [real(r8) (:)]                                                     
-    deadcrootc_storage_to_xfer          =>    cnveg_carbonflux_inst%deadcrootc_storage_to_xfer_patch               , & ! InOut:  [real(r8) (:)]                                                     
-    gresp_storage_to_xfer               =>    cnveg_carbonflux_inst%gresp_storage_to_xfer_patch                    , & ! InOut:  [real(r8) (:)]  
-    leafc_xfer_to_leafc                 =>    cnveg_carbonflux_inst%leafc_xfer_to_leafc_patch                      , & ! InOut:  [real(r8) (:)]                                                    
-    frootc_xfer_to_frootc               =>    cnveg_carbonflux_inst%frootc_xfer_to_frootc_patch                    , & ! InOut:  [real(r8) (:)]                                                    
-    livestemc_xfer_to_livestemc         =>    cnveg_carbonflux_inst%livestemc_xfer_to_livestemc_patch              , & ! InOut:  [real(r8) (:)]                                                    
-    deadstemc_xfer_to_deadstemc         =>    cnveg_carbonflux_inst%deadstemc_xfer_to_deadstemc_patch              , & ! InOut:  [real(r8) (:)]                                                    
-    livecrootc_xfer_to_livecrootc       =>    cnveg_carbonflux_inst%livecrootc_xfer_to_livecrootc_patch            , & ! InOut:  [real(r8) (:)]                                                    
-    deadcrootc_xfer_to_deadcrootc       =>    cnveg_carbonflux_inst%deadcrootc_xfer_to_deadcrootc_patch            , & ! InOut:  [real(r8) (:)]   
-                                                       
-    leafn_storage_to_xfer               =>    cnveg_nitrogenflux_inst%leafn_storage_to_xfer_patch                  , & ! InOut:  [real(r8) (:)]                                                     
-    frootn_storage_to_xfer              =>    cnveg_nitrogenflux_inst%frootn_storage_to_xfer_patch                 , & ! InOut:  [real(r8) (:)]                                                     
-    livestemn_storage_to_xfer           =>    cnveg_nitrogenflux_inst%livestemn_storage_to_xfer_patch              , & ! InOut:  [real(r8) (:)]                                                     
-    deadstemn_storage_to_xfer           =>    cnveg_nitrogenflux_inst%deadstemn_storage_to_xfer_patch              , & ! InOut:  [real(r8) (:)]                                                     
-    livecrootn_storage_to_xfer          =>    cnveg_nitrogenflux_inst%livecrootn_storage_to_xfer_patch             , & ! InOut:  [real(r8) (:)]   
-    deadcrootn_storage_to_xfer          =>    cnveg_nitrogenflux_inst%deadcrootn_storage_to_xfer_patch             , & ! InOut:  [real(r8) (:)]                                                     
-    leafn_xfer_to_leafn                 =>    cnveg_nitrogenflux_inst%leafn_xfer_to_leafn_patch                    , & ! InOut:  [real(r8) (:)]                                                    
-    frootn_xfer_to_frootn               =>    cnveg_nitrogenflux_inst%frootn_xfer_to_frootn_patch                  , & ! InOut:  [real(r8) (:)]                                                    
-    livestemn_xfer_to_livestemn         =>    cnveg_nitrogenflux_inst%livestemn_xfer_to_livestemn_patch            , & ! InOut:  [real(r8) (:)]                                                    
-    deadstemn_xfer_to_deadstemn         =>    cnveg_nitrogenflux_inst%deadstemn_xfer_to_deadstemn_patch            , & ! InOut:  [real(r8) (:)]                                                    
-    livecrootn_xfer_to_livecrootn       =>    cnveg_nitrogenflux_inst%livecrootn_xfer_to_livecrootn_patch          , & ! InOut:  [real(r8) (:)]                                                    
-    deadcrootn_xfer_to_deadcrootn       =>    cnveg_nitrogenflux_inst%deadcrootn_xfer_to_deadcrootn_patch          , & ! InOut:  [real(r8) (:)]     
-              
-    bglfr                               => cnveg_state_inst%bglfr_patch , & ! Output: [real(r8) (:) ]  background litterfall rate (1/s)                  
-    bgtr                                => cnveg_state_inst%bgtr_patch  , & ! Output: [real(r8) (:) ]  background transfer growth rate (1/s)             
-    lgsf                                => cnveg_state_inst%lgsf_patch  , & ! Output: [real(r8) (:) ]  long growing season factor [0-1]                  
-    ileafst_to_ileafxf_phc              =>    cnveg_carbonflux_inst%ileafst_to_ileafxf_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool
-    ileafxf_to_ileaf_phc                =>    cnveg_carbonflux_inst%ileafxf_to_ileaf_ph                   , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool
-    ifrootst_to_ifrootxf_phc            =>    cnveg_carbonflux_inst%ifrootst_to_ifrootxf_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool
-    ifrootxf_to_ifroot_phc              =>    cnveg_carbonflux_inst%ifrootxf_to_ifroot_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool
-    ilivestemst_to_ilivestemxf_phc      =>    cnveg_carbonflux_inst%ilivestemst_to_ilivestemxf_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool
-    ilivestemxf_to_ilivestem_phc        =>    cnveg_carbonflux_inst%ilivestemxf_to_ilivestem_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool
-    ideadstemst_to_ideadstemxf_phc      =>    cnveg_carbonflux_inst%ideadstemst_to_ideadstemxf_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool
-    ideadstemxf_to_ideadstem_phc        =>    cnveg_carbonflux_inst%ideadstemxf_to_ideadstem_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool
-    ilivecrootst_to_ilivecrootxf_phc    =>    cnveg_carbonflux_inst%ilivecrootst_to_ilivecrootxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool
-    ilivecrootxf_to_ilivecroot_phc      =>    cnveg_carbonflux_inst%ilivecrootxf_to_ilivecroot_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool
-    ideadcrootst_to_ideadcrootxf_phc    =>    cnveg_carbonflux_inst%ideadcrootst_to_ideadcrootxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool
-    ideadcrootxf_to_ideadcroot_phc      =>    cnveg_carbonflux_inst%ideadcrootxf_to_ideadcroot_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool
-    ilivestem_to_ideadstem_phc          =>    cnveg_carbonflux_inst%ilivestem_to_ideadstem_ph             , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool
-    ilivecroot_to_ideadcroot_phc        =>    cnveg_carbonflux_inst%ilivecroot_to_ideadcroot_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool
-    ileaf_to_iout_phc                   =>    cnveg_carbonflux_inst%ileaf_to_iout_ph                      , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools
-    ifroot_to_iout_phc                  =>    cnveg_carbonflux_inst%ifroot_to_iout_ph                     , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools
-    ilivestem_to_iout_phc               =>    cnveg_carbonflux_inst%ilivestem_to_iout_ph                  , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools
-    igrain_to_iout_phc                  =>    cnveg_carbonflux_inst%igrain_to_iout_ph                     , & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools
-    ileafst_to_ileafxf_phn              =>    cnveg_nitrogenflux_inst%ileafst_to_ileafxf_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool
-    ileafxf_to_ileaf_phn                =>    cnveg_nitrogenflux_inst%ileafxf_to_ileaf_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool
-    ifrootst_to_ifrootxf_phn            =>    cnveg_nitrogenflux_inst%ifrootst_to_ifrootxf_ph             , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool
-    ifrootxf_to_ifroot_phn              =>    cnveg_nitrogenflux_inst%ifrootxf_to_ifroot_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool
-    ilivestemst_to_ilivestemxf_phn      =>    cnveg_nitrogenflux_inst%ilivestemst_to_ilivestemxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool
-    ilivestemxf_to_ilivestem_phn        =>    cnveg_nitrogenflux_inst%ilivestemxf_to_ilivestem_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool
-    ideadstemst_to_ideadstemxf_phn      =>    cnveg_nitrogenflux_inst%ideadstemst_to_ideadstemxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool
-    ideadstemxf_to_ideadstem_phn        =>    cnveg_nitrogenflux_inst%ideadstemxf_to_ideadstem_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool
-    ilivecrootst_to_ilivecrootxf_phn    =>    cnveg_nitrogenflux_inst%ilivecrootst_to_ilivecrootxf_ph     , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool
-    ilivecrootxf_to_ilivecroot_phn      =>    cnveg_nitrogenflux_inst%ilivecrootxf_to_ilivecroot_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool
-    ideadcrootst_to_ideadcrootxf_phn    =>    cnveg_nitrogenflux_inst%ideadcrootst_to_ideadcrootxf_ph     , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool
-    ideadcrootxf_to_ideadcroot_phn      =>    cnveg_nitrogenflux_inst%ideadcrootxf_to_ideadcroot_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool
-    ilivestem_to_ideadstem_phn          =>    cnveg_nitrogenflux_inst%ilivestem_to_ideadstem_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool
-    ilivecroot_to_ideadcroot_phn        =>    cnveg_nitrogenflux_inst%ilivecroot_to_ideadcroot_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool
-    ileaf_to_iout_phn                   =>    cnveg_nitrogenflux_inst%ileaf_to_iout_ph                    , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools
-    ifroot_to_iout_phn                  =>    cnveg_nitrogenflux_inst%ifroot_to_iout_ph                   , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools
-    ilivestem_to_iout_phn               =>    cnveg_nitrogenflux_inst%ilivestem_to_iout_ph                , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools
-    ileaf_to_iretransn_phn              =>    cnveg_nitrogenflux_inst%ileaf_to_iretransn_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to retranslocation pool
-    ilivestem_to_iretransn_phn          =>    cnveg_nitrogenflux_inst%ilivestem_to_iretransn_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to retranslocation pool
-    ilivecroot_to_iretransn_phn         =>    cnveg_nitrogenflux_inst%ilivecroot_to_iretransn_ph          , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root pool to retranslocation pool
-    igrain_to_iout_phn                  =>    cnveg_nitrogenflux_inst%igrain_to_iout_ph                     & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools
+   		 leafc_storage                       =>    cnveg_carbonstate_inst%leafc_storage_patch                           , & ! Input:  [real(r8) (:)]  (gC/m2) leaf C storage                             
+   		 frootc_storage                      =>    cnveg_carbonstate_inst%frootc_storage_patch                          , & ! Input:  [real(r8) (:)]  (gC/m2) fine root C storage                         
+   		 livestemc_storage                   =>    cnveg_carbonstate_inst%livestemc_storage_patch                       , & ! Input:  [real(r8) (:)]  (gC/m2) live stem C storage                         
+   		 deadstemc_storage                   =>    cnveg_carbonstate_inst%deadstemc_storage_patch                       , & ! Input:  [real(r8) (:)]  (gC/m2) dead stem C storage                         
+   		 livecrootc_storage                  =>    cnveg_carbonstate_inst%livecrootc_storage_patch                      , & ! Input:  [real(r8) (:)]  (gC/m2) live coarse root C storage                  
+   		 deadcrootc_storage                  =>    cnveg_carbonstate_inst%deadcrootc_storage_patch                      , & ! Input:  [real(r8) (:)]  (gC/m2) dead coarse root C storage                  
+   		 gresp_storage                       =>    cnveg_carbonstate_inst%gresp_storage_patch                           , & ! Input:  [real(r8) (:)]  (gC/m2) growth respiration storage   
+   		 leafc_xfer                          =>    cnveg_carbonstate_inst%leafc_xfer_patch                              , & ! InOut:  [real(r8) (:)]  (gC/m2) leaf C transfer                            
+   		 frootc_xfer                         =>    cnveg_carbonstate_inst%frootc_xfer_patch                             , & ! InOut:  [real(r8) (:)]  (gC/m2) fine root C transfer                       
+   		 livestemc_xfer                      =>    cnveg_carbonstate_inst%livestemc_xfer_patch                          , & ! InOut:  [real(r8) (:)]  (gC/m2) live stem C transfer                       
+   		 deadstemc_xfer                      =>    cnveg_carbonstate_inst%deadstemc_xfer_patch                          , & ! InOut:  [real(r8) (:)]  (gC/m2) dead stem C transfer                       
+   		 livecrootc_xfer                     =>    cnveg_carbonstate_inst%livecrootc_xfer_patch                         , & ! InOut:  [real(r8) (:)]  (gC/m2) live coarse root C transfer                
+   		 deadcrootc_xfer                     =>    cnveg_carbonstate_inst%deadcrootc_xfer_patch                         , & ! InOut:  [real(r8) (:)]  (gC/m2) dead coarse root C transfer   
+   		                
+   		 leafn_storage                       =>    cnveg_nitrogenstate_inst%leafn_storage_patch                         , & ! Input:  [real(r8) (:)]  (gN/m2) leaf N storage                              
+   		 frootn_storage                      =>    cnveg_nitrogenstate_inst%frootn_storage_patch                        , & ! Input:  [real(r8) (:)]  (gN/m2) fine root N storage                         
+   		 livestemn_storage                   =>    cnveg_nitrogenstate_inst%livestemn_storage_patch                     , & ! Input:  [real(r8) (:)]  (gN/m2) live stem N storage                         
+   		 deadstemn_storage                   =>    cnveg_nitrogenstate_inst%deadstemn_storage_patch                     , & ! Input:  [real(r8) (:)]  (gN/m2) dead stem N storage                         
+   		 livecrootn_storage                  =>    cnveg_nitrogenstate_inst%livecrootn_storage_patch                    , & ! Input:  [real(r8) (:)]  (gN/m2) live coarse root N storage                  
+   		 deadcrootn_storage                  =>    cnveg_nitrogenstate_inst%deadcrootn_storage_patch                    , & ! Input:  [real(r8) (:)]  (gN/m2) dead coarse root N storage               
+   		 leafn_xfer                          =>    cnveg_nitrogenstate_inst%leafn_xfer_patch                            , & ! InOut:  [real(r8) (:)]  (gN/m2) leaf N transfer                            
+   		 frootn_xfer                         =>    cnveg_nitrogenstate_inst%frootn_xfer_patch                           , & ! InOut:  [real(r8) (:)]  (gN/m2) fine root N transfer                       
+   		 livestemn_xfer                      =>    cnveg_nitrogenstate_inst%livestemn_xfer_patch                        , & ! InOut:  [real(r8) (:)]  (gN/m2) live stem N transfer                       
+   		 deadstemn_xfer                      =>    cnveg_nitrogenstate_inst%deadstemn_xfer_patch                        , & ! InOut:  [real(r8) (:)]  (gN/m2) dead stem N transfer                       
+   		 livecrootn_xfer                     =>    cnveg_nitrogenstate_inst%livecrootn_xfer_patch                       , & ! InOut:  [real(r8) (:)]  (gN/m2) live coarse root N transfer                
+   		 deadcrootn_xfer                     =>    cnveg_nitrogenstate_inst%deadcrootn_xfer_patch                       , & ! InOut:  [real(r8) (:)]  (gN/m2) dead coarse root N transfer     
+   		                 
+   		 leafc_storage_to_xfer               =>    cnveg_carbonflux_inst%leafc_storage_to_xfer_patch                    , & ! InOut:  [real(r8) (:)]                                                     
+   		 frootc_storage_to_xfer              =>    cnveg_carbonflux_inst%frootc_storage_to_xfer_patch                   , & ! InOut:  [real(r8) (:)]                                                     
+   		 livestemc_storage_to_xfer           =>    cnveg_carbonflux_inst%livestemc_storage_to_xfer_patch                , & ! InOut:  [real(r8) (:)]                                                     
+   		 deadstemc_storage_to_xfer           =>    cnveg_carbonflux_inst%deadstemc_storage_to_xfer_patch                , & ! InOut:  [real(r8) (:)]                                                     
+   		 livecrootc_storage_to_xfer          =>    cnveg_carbonflux_inst%livecrootc_storage_to_xfer_patch               , & ! InOut:  [real(r8) (:)]                                                     
+   		 deadcrootc_storage_to_xfer          =>    cnveg_carbonflux_inst%deadcrootc_storage_to_xfer_patch               , & ! InOut:  [real(r8) (:)]                                                     
+   		 gresp_storage_to_xfer               =>    cnveg_carbonflux_inst%gresp_storage_to_xfer_patch                    , & ! InOut:  [real(r8) (:)]  
+   		 leafc_xfer_to_leafc                 =>    cnveg_carbonflux_inst%leafc_xfer_to_leafc_patch                      , & ! InOut:  [real(r8) (:)]                                                    
+   		 frootc_xfer_to_frootc               =>    cnveg_carbonflux_inst%frootc_xfer_to_frootc_patch                    , & ! InOut:  [real(r8) (:)]                                                    
+   		 livestemc_xfer_to_livestemc         =>    cnveg_carbonflux_inst%livestemc_xfer_to_livestemc_patch              , & ! InOut:  [real(r8) (:)]                                                    
+   		 deadstemc_xfer_to_deadstemc         =>    cnveg_carbonflux_inst%deadstemc_xfer_to_deadstemc_patch              , & ! InOut:  [real(r8) (:)]                                                    
+   		 livecrootc_xfer_to_livecrootc       =>    cnveg_carbonflux_inst%livecrootc_xfer_to_livecrootc_patch            , & ! InOut:  [real(r8) (:)]                                                    
+   		 deadcrootc_xfer_to_deadcrootc       =>    cnveg_carbonflux_inst%deadcrootc_xfer_to_deadcrootc_patch            , & ! InOut:  [real(r8) (:)]   
+   		                                                    
+   		 leafn_storage_to_xfer               =>    cnveg_nitrogenflux_inst%leafn_storage_to_xfer_patch                  , & ! InOut:  [real(r8) (:)]                                                     
+   		 frootn_storage_to_xfer              =>    cnveg_nitrogenflux_inst%frootn_storage_to_xfer_patch                 , & ! InOut:  [real(r8) (:)]                                                     
+   		 livestemn_storage_to_xfer           =>    cnveg_nitrogenflux_inst%livestemn_storage_to_xfer_patch              , & ! InOut:  [real(r8) (:)]                                                     
+   		 deadstemn_storage_to_xfer           =>    cnveg_nitrogenflux_inst%deadstemn_storage_to_xfer_patch              , & ! InOut:  [real(r8) (:)]                                                     
+   		 livecrootn_storage_to_xfer          =>    cnveg_nitrogenflux_inst%livecrootn_storage_to_xfer_patch             , & ! InOut:  [real(r8) (:)]   
+   		 deadcrootn_storage_to_xfer          =>    cnveg_nitrogenflux_inst%deadcrootn_storage_to_xfer_patch             , & ! InOut:  [real(r8) (:)]                                                     
+   		 leafn_xfer_to_leafn                 =>    cnveg_nitrogenflux_inst%leafn_xfer_to_leafn_patch                    , & ! InOut:  [real(r8) (:)]                                                    
+   		 frootn_xfer_to_frootn               =>    cnveg_nitrogenflux_inst%frootn_xfer_to_frootn_patch                  , & ! InOut:  [real(r8) (:)]                                                    
+   		 livestemn_xfer_to_livestemn         =>    cnveg_nitrogenflux_inst%livestemn_xfer_to_livestemn_patch            , & ! InOut:  [real(r8) (:)]                                                    
+   		 deadstemn_xfer_to_deadstemn         =>    cnveg_nitrogenflux_inst%deadstemn_xfer_to_deadstemn_patch            , & ! InOut:  [real(r8) (:)]                                                    
+   		 livecrootn_xfer_to_livecrootn       =>    cnveg_nitrogenflux_inst%livecrootn_xfer_to_livecrootn_patch          , & ! InOut:  [real(r8) (:)]                                                    
+   		 deadcrootn_xfer_to_deadcrootn       =>    cnveg_nitrogenflux_inst%deadcrootn_xfer_to_deadcrootn_patch          , & ! InOut:  [real(r8) (:)]     
+   		           
+   		 bglfr                               => cnveg_state_inst%bglfr_patch , & ! Output: [real(r8) (:) ]  background litterfall rate (1/s)                  
+   		 bgtr                                => cnveg_state_inst%bgtr_patch  , & ! Output: [real(r8) (:) ]  background transfer growth rate (1/s)             
+   		 lgsf                                => cnveg_state_inst%lgsf_patch  , & ! Output: [real(r8) (:) ]  long growing season factor [0-1]                  
+
+   		 ileafst_to_ileafxf_phc              =>    cnveg_carbonflux_inst%ileafst_to_ileafxf_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool
+   		 ileafxf_to_ileaf_phc                =>    cnveg_carbonflux_inst%ileafxf_to_ileaf_ph                   , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool
+   		 ifrootst_to_ifrootxf_phc            =>    cnveg_carbonflux_inst%ifrootst_to_ifrootxf_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool
+   		 ifrootxf_to_ifroot_phc              =>    cnveg_carbonflux_inst%ifrootxf_to_ifroot_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool
+   		 ilivestemst_to_ilivestemxf_phc      =>    cnveg_carbonflux_inst%ilivestemst_to_ilivestemxf_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool
+   		 ilivestemxf_to_ilivestem_phc        =>    cnveg_carbonflux_inst%ilivestemxf_to_ilivestem_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool
+   		 ideadstemst_to_ideadstemxf_phc      =>    cnveg_carbonflux_inst%ideadstemst_to_ideadstemxf_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool
+   		 ideadstemxf_to_ideadstem_phc        =>    cnveg_carbonflux_inst%ideadstemxf_to_ideadstem_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool
+   		 ilivecrootst_to_ilivecrootxf_phc    =>    cnveg_carbonflux_inst%ilivecrootst_to_ilivecrootxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool
+   		 ilivecrootxf_to_ilivecroot_phc      =>    cnveg_carbonflux_inst%ilivecrootxf_to_ilivecroot_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool
+   		 ideadcrootst_to_ideadcrootxf_phc    =>    cnveg_carbonflux_inst%ideadcrootst_to_ideadcrootxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool
+   		 ideadcrootxf_to_ideadcroot_phc      =>    cnveg_carbonflux_inst%ideadcrootxf_to_ideadcroot_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool
+   		 ilivestem_to_ideadstem_phc          =>    cnveg_carbonflux_inst%ilivestem_to_ideadstem_ph             , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool
+   		 ilivecroot_to_ideadcroot_phc        =>    cnveg_carbonflux_inst%ilivecroot_to_ideadcroot_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool
+   		 ileaf_to_iout_phc                   =>    cnveg_carbonflux_inst%ileaf_to_iout_ph                      , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools
+   		 ifroot_to_iout_phc                  =>    cnveg_carbonflux_inst%ifroot_to_iout_ph                     , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools
+   		 ilivestem_to_iout_phc               =>    cnveg_carbonflux_inst%ilivestem_to_iout_ph                  , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools
+   		 igrain_to_iout_phc                  =>    cnveg_carbonflux_inst%igrain_to_iout_ph                     , & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools
+   		 ileafst_to_ileafxf_phn              =>    cnveg_nitrogenflux_inst%ileafst_to_ileafxf_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool
+   		 ileafxf_to_ileaf_phn                =>    cnveg_nitrogenflux_inst%ileafxf_to_ileaf_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool
+   		 ifrootst_to_ifrootxf_phn            =>    cnveg_nitrogenflux_inst%ifrootst_to_ifrootxf_ph             , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool
+   		 ifrootxf_to_ifroot_phn              =>    cnveg_nitrogenflux_inst%ifrootxf_to_ifroot_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool
+   		 ilivestemst_to_ilivestemxf_phn      =>    cnveg_nitrogenflux_inst%ilivestemst_to_ilivestemxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool
+   		 ilivestemxf_to_ilivestem_phn        =>    cnveg_nitrogenflux_inst%ilivestemxf_to_ilivestem_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool
+   		 ideadstemst_to_ideadstemxf_phn      =>    cnveg_nitrogenflux_inst%ideadstemst_to_ideadstemxf_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool
+   		 ideadstemxf_to_ideadstem_phn        =>    cnveg_nitrogenflux_inst%ideadstemxf_to_ideadstem_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool
+   		 ilivecrootst_to_ilivecrootxf_phn    =>    cnveg_nitrogenflux_inst%ilivecrootst_to_ilivecrootxf_ph     , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool
+   		 ilivecrootxf_to_ilivecroot_phn      =>    cnveg_nitrogenflux_inst%ilivecrootxf_to_ilivecroot_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool
+   		 ideadcrootst_to_ideadcrootxf_phn    =>    cnveg_nitrogenflux_inst%ideadcrootst_to_ideadcrootxf_ph     , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool
+   		 ideadcrootxf_to_ideadcroot_phn      =>    cnveg_nitrogenflux_inst%ideadcrootxf_to_ideadcroot_ph       , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool
+   		 ilivestem_to_ideadstem_phn          =>    cnveg_nitrogenflux_inst%ilivestem_to_ideadstem_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool
+   		 ilivecroot_to_ideadcroot_phn        =>    cnveg_nitrogenflux_inst%ilivecroot_to_ideadcroot_ph         , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool
+   		 ileaf_to_iout_phn                   =>    cnveg_nitrogenflux_inst%ileaf_to_iout_ph                    , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools
+   		 ifroot_to_iout_phn                  =>    cnveg_nitrogenflux_inst%ifroot_to_iout_ph                   , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools
+   		 ilivestem_to_iout_phn               =>    cnveg_nitrogenflux_inst%ilivestem_to_iout_ph                , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools
+   		 ileaf_to_iretransn_phn              =>    cnveg_nitrogenflux_inst%ileaf_to_iretransn_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to retranslocation pool
+   		 ilivestem_to_iretransn_phn          =>    cnveg_nitrogenflux_inst%ilivestem_to_iretransn_ph           , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to retranslocation pool
+   		 ilivecroot_to_iretransn_phn         =>    cnveg_nitrogenflux_inst%ilivecroot_to_iretransn_ph          , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root pool to retranslocation pool
+   		 igrain_to_iout_phn                  =>    cnveg_nitrogenflux_inst%igrain_to_iout_ph                     & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools
          )
 
       avg_dayspyr = get_average_days_per_year()
@@ -770,17 +769,7 @@ subroutine CNEvergreenPhenology (num_soilp, filter_soilp , &
    
          tranr=0.0002_r8   
          ! set carbon fluxes for shifting storage pools to transfer pools    
-         if (.not. use_matrixcn) then
-            leafc_storage_to_xfer(p)  = tranr * leafc_storage(p)/dt
-            frootc_storage_to_xfer(p) = tranr * frootc_storage(p)/dt
-            if (woody(ivt(p)) == 1.0_r8) then
-               livestemc_storage_to_xfer(p)  = tranr * livestemc_storage(p)/dt
-               deadstemc_storage_to_xfer(p)  = tranr * deadstemc_storage(p)/dt
-               livecrootc_storage_to_xfer(p) = tranr * livecrootc_storage(p)/dt
-               deadcrootc_storage_to_xfer(p) = tranr * deadcrootc_storage(p)/dt
-               gresp_storage_to_xfer(p)      = tranr * gresp_storage(p)/dt
-            end if
-         else
+         if (use_matrixcn) then    
             leafc_storage_to_xfer(p)  = leafc_storage(p)  * matrix_update_phc(p,ileafst_to_ileafxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
             frootc_storage_to_xfer(p) = frootc_storage(p) * matrix_update_phc(p,ifrootst_to_ifrootxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
             if (woody(ivt(p)) == 1.0_r8) then   
@@ -789,7 +778,18 @@ subroutine CNEvergreenPhenology (num_soilp, filter_soilp , &
                livecrootc_storage_to_xfer(p)  = livecrootc_storage(p) * matrix_update_phc(p,ilivecrootst_to_ilivecrootxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                deadcrootc_storage_to_xfer(p)  = deadcrootc_storage(p) * matrix_update_phc(p,ideadcrootst_to_ideadcrootxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
             end if
-         end if !not use_matrixcn
+         else
+            ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
+            leafc_storage_to_xfer(p)  = tranr * leafc_storage(p)/dt    
+            frootc_storage_to_xfer(p) = tranr * frootc_storage(p)/dt
+            if (woody(ivt(p)) == 1.0_r8) then    
+               livestemc_storage_to_xfer(p)  = tranr * livestemc_storage(p)/dt    
+               deadstemc_storage_to_xfer(p)  = tranr * deadstemc_storage(p)/dt    
+               livecrootc_storage_to_xfer(p) = tranr * livecrootc_storage(p)/dt   
+               deadcrootc_storage_to_xfer(p) = tranr * deadcrootc_storage(p)/dt   
+               gresp_storage_to_xfer(p)      = tranr * gresp_storage(p)/dt        
+            end if    
+         end if !use_matrixcn
 
         ! set nitrogen fluxes for shifting storage pools to transfer pools    
         if (use_matrixcn) then    
@@ -1849,37 +1849,36 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
                ! between leafc and leafc_store in the flux. RosieF, Nov5 2015. 
                leafc_storage_to_xfer(p)  = max(0.0_r8,(leafc_storage(p)-leafc(p))) * bgtr(p)
                frootc_storage_to_xfer(p) = max(0.0_r8,(frootc_storage(p)-frootc(p))) * bgtr(p)
-
                if (use_matrixcn) then
-                  if(leafc_storage(p) > 0._r8)then
+                  if(leafc_storage(p) .gt. 0)then
                      leafc_storage_to_xfer(p) = leafc_storage(p) * matrix_update_phc(p,ileafst_to_ileafxf_phc,&
                                                 leafc_storage_to_xfer(p) / leafc_storage(p), dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     leafc_storage_to_xfer(p) = 0._r8
+                     leafc_storage_to_xfer(p) = 0
                   end if
-                  if(frootc_storage(p) > 0._r8)then
+                  if(frootc_storage(p) .gt. 0)then
                      frootc_storage_to_xfer(p) = frootc_storage(p) * matrix_update_phc(p,ifrootst_to_ifrootxf_phc,&
                                                  frootc_storage_to_xfer(p) / frootc_storage(p), dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     frootc_storage_to_xfer(p) = 0._r8
+                     frootc_storage_to_xfer(p) = 0   
                   end if
-                  if (woody(ivt(p)) == 1.0_r8) then
+                if (woody(ivt(p)) == 1.0_r8) then
                      livestemc_storage_to_xfer(p)  = livestemc_storage(p)  * matrix_update_phc(p,ilivestemst_to_ilivestemxf_phc ,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      deadstemc_storage_to_xfer(p)  = deadstemc_storage(p)  * matrix_update_phc(p,ideadstemst_to_ideadstemxf_phc ,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      livecrootc_storage_to_xfer(p) = livecrootc_storage(p) * matrix_update_phc(p,ilivecrootst_to_ilivecrootxf_phc,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      deadcrootc_storage_to_xfer(p) = deadcrootc_storage(p) * matrix_update_phc(p,ideadcrootst_to_ideadcrootxf_phc,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
-                  end if
-               else
-                  ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
-                  !                                        and CNNStateUpdate1::NStateUpdate1
-                  if (woody(ivt(p)) == 1.0_r8) then
-                     livestemc_storage_to_xfer(p)  = livestemc_storage(p) * bgtr(p)
-                     deadstemc_storage_to_xfer(p)  = deadstemc_storage(p) * bgtr(p)
-                     livecrootc_storage_to_xfer(p) = livecrootc_storage(p) * bgtr(p)
-                     deadcrootc_storage_to_xfer(p) = deadcrootc_storage(p) * bgtr(p)
-                     gresp_storage_to_xfer(p)      = gresp_storage(p) * bgtr(p)
-                  end if
-               end if !use_matrixcn
+                 end if
+              else
+                 ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
+                 !                                        and CNNStateUpdate1::NStateUpdate1
+                 if (woody(ivt(p)) == 1.0_r8) then
+                    livestemc_storage_to_xfer(p)  = livestemc_storage(p) * bgtr(p)
+                    deadstemc_storage_to_xfer(p)  = deadstemc_storage(p) * bgtr(p)
+                    livecrootc_storage_to_xfer(p) = livecrootc_storage(p) * bgtr(p)
+                    deadcrootc_storage_to_xfer(p) = deadcrootc_storage(p) * bgtr(p)
+                    gresp_storage_to_xfer(p)      = gresp_storage(p) * bgtr(p)
+                 end if
+              end if !use_matrixcn
 
                ! set nitrogen fluxes for shifting storage pools to transfer pools
                if (use_matrixcn) then 
@@ -2920,22 +2919,7 @@ subroutine CNOnsetGrowth (num_soilp, filter_soilp, &
          ! pools should be moved to displayed growth in each timestep.
 
          if (bgtr(p) > 0._r8) then
-            if(.not. use_matrixcn)then
-               leafc_xfer_to_leafc(p)   = leafc_xfer(p) / dt
-               frootc_xfer_to_frootc(p) = frootc_xfer(p) / dt
-               leafn_xfer_to_leafn(p)   = leafn_xfer(p) / dt
-               frootn_xfer_to_frootn(p) = frootn_xfer(p) / dt
-               if (woody(ivt(p)) == 1.0_r8) then
-                  livestemc_xfer_to_livestemc(p)   = livestemc_xfer(p) / dt
-                  deadstemc_xfer_to_deadstemc(p)   = deadstemc_xfer(p) / dt
-                  livecrootc_xfer_to_livecrootc(p) = livecrootc_xfer(p) / dt
-                  deadcrootc_xfer_to_deadcrootc(p) = deadcrootc_xfer(p) / dt
-                  livestemn_xfer_to_livestemn(p)   = livestemn_xfer(p) / dt
-                  deadstemn_xfer_to_deadstemn(p)   = deadstemn_xfer(p) / dt
-                  livecrootn_xfer_to_livecrootn(p) = livecrootn_xfer(p) / dt
-                  deadcrootn_xfer_to_deadcrootn(p) = deadcrootn_xfer(p) / dt
-               end if
-            else
+            if(use_matrixcn)then
                leafc_xfer_to_leafc(p)   = leafc_xfer(p)  * matrix_update_phc(p,ileafxf_to_ileaf_phc,1._r8 / dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                frootc_xfer_to_frootc(p) = frootc_xfer(p) * matrix_update_phc(p,ifrootxf_to_ifroot_phc,1._r8 / dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                leafn_xfer_to_leafn(p)   = leafn_xfer(p)  * matrix_update_phn(p,ileafxf_to_ileaf_phn,1._r8 / dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
@@ -2952,7 +2936,24 @@ subroutine CNOnsetGrowth (num_soilp, filter_soilp, &
                   livecrootn_xfer_to_livecrootn(p) = livecrootn_xfer(p)  * matrix_update_phn(p,ilivecrootxf_to_ilivecroot_phn,1._r8 / dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   deadcrootn_xfer_to_deadcrootn(p) = deadcrootn_xfer(p)  * matrix_update_phn(p,ideadcrootxf_to_ideadcroot_phn,1._r8 / dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                end if
-            end if !not use_matrixcn
+            else
+               ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
+               !                                        and CNNStateUpdate1::NStateUpdate1
+               leafc_xfer_to_leafc(p)   = leafc_xfer(p) / dt
+               frootc_xfer_to_frootc(p) = frootc_xfer(p) / dt
+               leafn_xfer_to_leafn(p)   = leafn_xfer(p) / dt
+               frootn_xfer_to_frootn(p) = frootn_xfer(p) / dt
+               if (woody(ivt(p)) == 1.0_r8) then
+                  livestemc_xfer_to_livestemc(p)   = livestemc_xfer(p) / dt
+                  deadstemc_xfer_to_deadstemc(p)   = deadstemc_xfer(p) / dt
+                  livecrootc_xfer_to_livecrootc(p) = livecrootc_xfer(p) / dt
+                  deadcrootc_xfer_to_deadcrootc(p) = deadcrootc_xfer(p) / dt
+                  livestemn_xfer_to_livestemn(p)   = livestemn_xfer(p) / dt
+                  deadstemn_xfer_to_deadstemn(p)   = deadstemn_xfer(p) / dt
+                  livecrootn_xfer_to_livecrootn(p) = livecrootn_xfer(p) / dt
+                  deadcrootn_xfer_to_deadcrootn(p) = deadcrootn_xfer(p) / dt
+               end if
+            end if !use_matrixcn
          end if ! end if bgtr
 
       end do ! end patch loop
@@ -3113,26 +3114,26 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
 
             if (abs(offset_counter(p) - dt) <= dt/2._r8) then
                t1 = 1.0_r8 / dt
+               frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p)
+               
+               ! biofuel_harvfrac is only non-zero for prognostic crops.
+               leafc_to_litter(p)  = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p)))  + cpool_to_leafc(p)
 
-               ! leafc_litter and frootc_to_litter for matrix
                if (use_matrixcn) then
-                  if(leafc(p) > 0._r8)then
+                  if(leafc(p) .gt. 0)then
                      leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     leafc_to_litter(p) = 0._r8
+                     leafc_to_litter(p) = 0
                   end if
-                  if(frootc(p) > 0._r8)then
+                  if(frootc(p) .gt. 0)then
                      frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     frootc_to_litter(p) = 0._r8
+                     frootc_to_litter(p) = 0
                   end if
                else
-                  frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p)
-               
-                  ! biofuel_harvfrac is only non-zero for prognostic crops.
-                  leafc_to_litter(p)  = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p)))  + cpool_to_leafc(p)
+                  ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
+                  !                                        and CNNStateUpdate1::NStateUpdate1
                end if ! use_matrixcn
-
                ! this assumes that offset_counter == dt for crops
                ! if this were ever changed, we'd need to add code to the "else"
                if (ivt(p) >= npcropmin) then
@@ -3176,101 +3177,105 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                           * (1._r8 - repr_structure_harvfrac(ivt(p), k))
                   end do
                   
-                  ! Matrix for grain, livestem to litter and biofuel
+                  ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of leaf C
+                  ! and move this fration of leaf C to biofuel C, rather than move it to litter
+                  leafc_to_biofuelc(p) = t1 * leafc(p) * biofuel_harvfrac(ivt(p))
+                  leafn_to_biofueln(p) = t1 * leafn(p) * biofuel_harvfrac(ivt(p))
+
+                  ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of livestem C
+                  ! and move this fration of leaf C to biofuel C, rather than move it to litter
+                  livestemc_to_litter(p)   = t1 * livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p)))  + cpool_to_livestemc(p)
+                  livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p))
+                  livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p))
+
                   if(use_matrixcn)then
-                     if(reproductivec(p,1) > 0._r8)then
+                     if(reproductivec(p,1) .gt. 0)then
                         grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        repr_grainc_to_seed(p,1) = 0._r8
-                        repr_grainc_to_food(p,1) = 0._r8
+                        repr_grainc_to_seed(p,1) = 0
+                        repr_grainc_to_food(p,1) = 0
                      end if
-                     if(reproductiven(p,1) > 0._r8)then
+                     if(reproductiven(p,1) .gt. 0)then
                         grainn_to_out = reproductiven(p,1) * matrix_update_phn(p,igrain_to_iout_phn,(repr_grainn_to_seed(p,1) + repr_grainn_to_food(p,1)) / reproductiven(p,1),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        repr_grainn_to_seed(p,1) = 0._r8
-                        repr_grainn_to_food(p,1) = 0._r8
+                        repr_grainn_to_seed(p,1) = 0
+                        repr_grainn_to_food(p,1) = 0
                      end if
-                     if(livestemc(p) > 0._r8)then
+                     if(livestemc(p) .gt. 0)then
                         livestemc_to_litter(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_iout_phc,livestemc_to_litter(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        livestemc_to_litter(p) = 0._r8
+                        livestemc_to_litter(p) = 0
                      end if
-                     if(livestemn(p) > 0._r8)then
+                     if(livestemn(p) .gt. 0)then
                         livestemn_to_biofueln(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_biofueln(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
                      else
-                        livestemn_to_biofueln(p) = 0._r8
+                        livestemn_to_biofueln(p) = 0
                      end if
-                     if(leafn(p) > 0._r8)then
+                     if(leafn(p) > 0)then
                         leafn_to_biofueln(p) =  leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_biofueln(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
                      else
-                        leafn_to_biofueln(p) = 0._r8
+                        leafn_to_biofueln(p) = 0
                      end if
-                     if (leafc(p) > 0._r8)then
+                     if (leafc(p) > 0)then
                        leafc_to_biofuelc(p) =  leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
                      else
-                       leafc_to_biofuelc(p) = 0._r8
+                       leafc_to_biofuelc(p) = 0
                      end if
-                     if(livestemc(p) > 0._r8)then
+                     if(livestemc(p) .gt. 0)then
                         livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
                      else
-                        livestemc_to_biofuelc(p) = 0._r8
+                        livestemc_to_biofuelc(p) = 0
                      end if
                   else
-                     ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of leaf C
-                     ! and move this fration of leaf C to biofuel C, rather than move it to litter
-                     leafc_to_biofuelc(p) = t1 * leafc(p) * biofuel_harvfrac(ivt(p))
-                     leafn_to_biofueln(p) = t1 * leafn(p) * biofuel_harvfrac(ivt(p))
-
-                     ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of livestem C
-                     ! and move this fration of leaf C to biofuel C, rather than move it to litter
-                     livestemc_to_litter(p)   = t1 * livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p)))  + cpool_to_livestemc(p)
-                     livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p))
-                     livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p))
+                     ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
+                     !                                        and CNNStateUpdate1::NStateUpdate1
                   end if ! use_matrixcn
                end if
             else
-               ! Matrix for leafc and frootc to litter
+               t1 = dt * 2.0_r8 / (offset_counter(p) * offset_counter(p))
+               leafc_to_litter(p)  = prev_leafc_to_litter(p)  + t1*(leafc(p)  - prev_leafc_to_litter(p)*offset_counter(p))
+               frootc_to_litter(p) = prev_frootc_to_litter(p) + t1*(frootc(p) - prev_frootc_to_litter(p)*offset_counter(p))
+
                if (use_matrixcn) then
-                  if(leafc(p) > 0._r8)then
+                  if(leafc(p) .gt. 0)then
                      leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     leafc_to_litter(p) = 0._r8
+                     leafc_to_litter(p) = 0
                   end if
-                  if(frootc(p) > 0._r8)then
+                  if(frootc(p) .gt. 0)then
                      frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     frootc_to_litter(p) = 0._r8
+                     frootc_to_litter(p) = 0
                   end if
                else
-                  t1 = dt * 2.0_r8 / (offset_counter(p) * offset_counter(p))
-                  leafc_to_litter(p)  = prev_leafc_to_litter(p)  + t1*(leafc(p)  - prev_leafc_to_litter(p)*offset_counter(p))
-                  frootc_to_litter(p) = prev_frootc_to_litter(p) + t1*(frootc(p) - prev_frootc_to_litter(p)*offset_counter(p))
+                  ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
+                  !                                        and CNNStateUpdate1::NStateUpdate1
                end if !use_matrixcn
             end if
             
             if ( use_fun ) then
                if(leafc_to_litter(p)*dt.gt.leafc(p))then
-                   ! Matrix for leafc to litter
-                   if (use_matrixcn) then
-                     if(leafc(p) > 0._r8)then
+                   leafc_to_litter(p) = leafc(p)/dt + cpool_to_leafc(p)
+                  if (use_matrixcn) then
+                     if(leafc(p) .gt. 0)then
                         leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        leafc_to_litter(p) = 0._r8
+                        leafc_to_litter(p) = 0
                      end if
-                   else
-                      leafc_to_litter(p) = leafc(p)/dt + cpool_to_leafc(p)
-                   end if !use_matrixcn 
+                  else
+                     ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
+                  end if !use_matrixcn 
                endif
                if(frootc_to_litter(p)*dt.gt.frootc(p))then
-                  ! Matrix update for frootc to litter
+                   frootc_to_litter(p) = frootc(p)/dt + cpool_to_frootc(p)
                   if (use_matrixcn) then
-                     if(frootc(p) > 0._r8)then
+                     if(frootc(p) .gt. 0)then
                         frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        frootc_to_litter(p) = 0._r8
+                        frootc_to_litter(p) = 0
                      end if
                   else
-                     frootc_to_litter(p) = frootc(p)/dt + cpool_to_frootc(p)
+                     ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
                   end if !use_matrixcn
                endif
             end if
@@ -3279,8 +3284,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
             if ( use_fun ) then
                leafc_to_litter_fun(p)      =  leafc_to_litter(p)
                leafn_to_retransn(p)        =  paid_retransn_to_npool(p) + free_retransn_to_npool(p)
-               if (leafn(p) > 0._r8) then
-                  if (leafn(p)-leafn_to_retransn(p)*dt > 0._r8) then
+               if (leafn(p).gt.0._r8) then
+                  if (leafn(p)-leafn_to_retransn(p)*dt.gt.0._r8) then
                       leafcn_offset(p)     =  leafc(p)/(leafn(p)-leafn_to_retransn(p)*dt)
                   else
                       leafcn_offset(p)     =  leafc(p)/leafn(p)
@@ -3290,15 +3295,13 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                end if
                leafn_to_litter(p)          =  leafc_to_litter(p)/leafcn_offset(p) - leafn_to_retransn(p)
                leafn_to_litter(p)          =  max(leafn_to_litter(p),0._r8)
-
-               ! Matrix update for leafn to litter and retrans
                if (use_matrixcn) then   
-                  if(leafn(p) > 0._r8)then
+                  if(leafn(p) .gt. 0)then
                       leafn_to_litter(p)   = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                       leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   else
-                      leafn_to_litter(p)   = 0._r8
-                      leafn_to_retransn(p) = 0._r8
+                      leafn_to_litter(p)   = 0
+                      leafn_to_retransn(p) = 0
                   end if
                else
                   ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
@@ -3315,21 +3318,20 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                end if
 
             else
-               if (CNratio_floating) then    
+               if (CNratio_floating .eqv. .true.) then    
                   fr_leafn_to_litter = 0.5_r8    ! assuming 50% of nitrogen turnover goes to litter
                end if
                ! calculate the leaf N litterfall and retranslocation
                leafn_to_litter(p)   = leafc_to_litter(p)  / lflitcn(ivt(p))
                leafn_to_retransn(p) = (leafc_to_litter(p) / leafcn(ivt(p))) - leafn_to_litter(p)
 
-               ! Matrix update for leafn to litter and retrans
                if (use_matrixcn) then   
-                  if(leafn(p) > 0._r8)then
+                  if(leafn(p) .gt. 0)then
                       leafn_to_litter(p)   = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                       leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   else
-                      leafn_to_litter(p)   = 0._r8
-                      leafn_to_retransn(p) = 0._r8
+                      leafn_to_litter(p)   = 0
+                      leafn_to_retransn(p) = 0
                   end if
                else
                   ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
@@ -3338,49 +3340,44 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
 
             ! calculate fine root N litterfall (no retranslocation of fine root N)
             frootn_to_litter(p) = frootc_to_litter(p) / frootcn(ivt(p))
-
-            ! Matrix update for frootn to litter
             if (use_matrixcn) then   
-               if(frootn(p) > 0._r8)then
+               if(frootn(p) .gt. 0)then
                   frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,frootn_to_litter(p) / frootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                else
-                  frootn_to_litter(p) = 0._r8
+                  frootn_to_litter(p) = 0
                end if
             else
                ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
             end if !use_matrixcn
             
-            if (CNratio_floating) then    
-               if (.not. use_matrixcn) then   
-                  if (leafc(p) == 0.0_r8) then    
-                     ntovr_leaf = 0.0_r8    
-                  else    
-                     ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p))   
-                  end if   
+            if (CNratio_floating .eqv. .true.) then    
+               if (leafc(p) == 0.0_r8) then    
+                  ntovr_leaf = 0.0_r8    
+               else    
+                  ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p))   
+               end if   
            
-                  leafn_to_litter(p)   = fr_leafn_to_litter * ntovr_leaf
-                  leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p)
-               else  ! Matrix update for leafn to litter and retrans
-                  if(leafn(p) > 0._r8)then
+               leafn_to_litter(p)   = fr_leafn_to_litter * ntovr_leaf
+               leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p)
+               if (use_matrixcn) then   
+                  if(leafn(p) .gt. 0)then
                       leafn_to_litter(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                       leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   else
-                      leafn_to_litter(p)   = 0._r8
-                      leafn_to_retransn(p) = 0._r8
+                      leafn_to_litter(p)   = 0
+                      leafn_to_retransn(p) = 0
                   end if
-               end if ! .not. use_matrixcn
+               end if !use_matrixcn
                if (frootc(p) == 0.0_r8) then    
                    frootn_to_litter(p) = 0.0_r8    
-               else    
+                else    
                    frootn_to_litter(p) = frootc_to_litter(p) * (frootn(p) / frootc(p))   
-               end if   
-
-               ! Matrix update for frootn to litter
+                end if   
                if (use_matrixcn) then   
-                  if(frootn(p) > 0._r8)then
+                  if(frootn(p) .gt. 0)then
                      frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,frootn_to_litter(p) / frootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     frootn_to_litter(p) = 0._r8
+                     frootn_to_litter(p) = 0
                   end if
                else
                   ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
@@ -3389,26 +3386,21 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
             
             if ( use_fun ) then
                if(frootn_to_litter(p)*dt.gt.frootn(p))then
-
-                  ! Send all frootn to litter
                   if (.not. use_matrixcn) then   
                      frootn_to_litter(p) = frootn(p)/dt
                   else
-                     ! Matrix update for frootn to litter
                      frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,1._r8/dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   end if
                endif    
             end if
 
             if (ivt(p) >= npcropmin) then
-               ! Matrix update for livestemn to litter
+               ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn
+               !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p))
+               ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead
+               livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p)))
                if(use_matrixcn)then
                   livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
-               else
-                  ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn
-                  !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p))
-                  ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead
-                  livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p)))
                end if
             end if
 
@@ -3477,7 +3469,7 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, &
          leafc_to_litter_fun   => cnveg_carbonflux_inst%leafc_to_litter_fun_patch, & ! Output:  [real(r8) (:) ] leaf C litterfall used by FUN (gC/m2/s)
          leafcn_offset         => cnveg_state_inst%leafcn_offset_patch           , & ! Output:  [real(r8) (:) ] Leaf C:N used by FUN
          free_retransn_to_npool=>    cnveg_nitrogenflux_inst%free_retransn_to_npool_patch  , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s)          
-         paid_retransn_to_npool=>    cnveg_nitrogenflux_inst%retransn_to_npool_patch       , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s)
+         paid_retransn_to_npool=>    cnveg_nitrogenflux_inst%retransn_to_npool_patch   , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s)
 
          ileafst_to_ileafxf_phc              =>    cnveg_carbonflux_inst%ileafst_to_ileafxf_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool
          ileafxf_to_ileaf_phc                =>    cnveg_carbonflux_inst%ileafxf_to_ileaf_ph                   , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool
@@ -3526,36 +3518,35 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, &
 
          ! only calculate these fluxes if the background litterfall rate is non-zero
          if (bglfr(p) > 0._r8) then
-            ! Matrix update for leafc and frootc to litter
+            ! units for bglfr are already 1/s
+            leafc_to_litter(p)  = bglfr(p) * leafc(p)
+            frootc_to_litter(p) = bglfr(p) * frootc(p)
             if (use_matrixcn) then
                leafc_to_litter(p)  = leafc(p)  * matrix_update_phc(p,ileaf_to_iout_phc,bglfr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,bglfr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
-            else
-               ! units for bglfr are already 1/s
-               leafc_to_litter(p)  = bglfr(p) * leafc(p)
-               frootc_to_litter(p) = bglfr(p) * frootc(p)
             end if
             if ( use_fun ) then
-               if(.not. use_matrixcn)then
-                  leafc_to_litter_fun(p)     = leafc_to_litter(p)
-                  leafn_to_retransn(p)       = paid_retransn_to_npool(p) + free_retransn_to_npool(p)
-                  if (leafn(p).gt.0._r8) then
-                     if (leafn(p)-leafn_to_retransn(p)*dt.gt.0._r8) then
-                        leafcn_offset(p)     = leafc(p)/(leafn(p)-leafn_to_retransn(p)*dt)
-                     else
-                        leafcn_offset(p)     = leafc(p)/leafn(p)
-                     end if
+               leafc_to_litter_fun(p)     = leafc_to_litter(p)
+               leafn_to_retransn(p)       = paid_retransn_to_npool(p) + free_retransn_to_npool(p)
+               if (leafn(p).gt.0._r8) then
+                  if (leafn(p)-leafn_to_retransn(p)*dt.gt.0._r8) then
+                     leafcn_offset(p)     = leafc(p)/(leafn(p)-leafn_to_retransn(p)*dt)
                   else
-                     leafcn_offset(p)        = leafcn(ivt(p))
+                     leafcn_offset(p)     = leafc(p)/leafn(p)
                   end if
-                  leafn_to_litter(p)         = leafc_to_litter(p)/leafcn_offset(p) - leafn_to_retransn(p)
-                  leafn_to_litter(p)         = max(leafn_to_litter(p),0._r8)
-               else ! Matrix update for leafn to litter and retrans
+               else
+                  leafcn_offset(p)        = leafcn(ivt(p))
+               end if
+               leafn_to_litter(p)         = leafc_to_litter(p)/leafcn_offset(p) - leafn_to_retransn(p)
+               leafn_to_litter(p)         = max(leafn_to_litter(p),0._r8)
+               if(use_matrixcn)then
                   if(leafn(p) .ne. 0._r8)then
                      leafn_to_litter(p)   = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p)        / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                      leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   end if
-               end if ! .not. use_matrixcn
+               else
+                  ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
+               end if !use_matrixcn
 
                denom = ( leafn_to_retransn(p) + leafn_to_litter(p) )
                if ( denom /= 0.0_r8 ) then
@@ -3568,45 +3559,46 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, &
 
 
             else
-               if (CNratio_floating) then    
+               if (CNratio_floating .eqv. .true.) then    
                   fr_leafn_to_litter = 0.5_r8    ! assuming 50% of nitrogen turnover goes to litter
                end if
-               ! Matrix update for leafn to litter and retrans
+               ! calculate the leaf N litterfall and retranslocation
+               leafn_to_litter(p)   = leafc_to_litter(p)  / lflitcn(ivt(p))
+               leafn_to_retransn(p) = (leafc_to_litter(p) / leafcn(ivt(p))) - leafn_to_litter(p)
+
                if (use_matrixcn) then   
-                  if(leafn(p) .ne. 0._r8)then
+                  if(leafn(p) .ne. 0)then
                      leafn_to_litter(p)   = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p)        / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                      leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   end if
                else
                   ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
-                  ! calculate the leaf N litterfall and retranslocation
-                  leafn_to_litter(p)   = leafc_to_litter(p)  / lflitcn(ivt(p))
-                  leafn_to_retransn(p) = (leafc_to_litter(p) / leafcn(ivt(p))) - leafn_to_litter(p)
                end if !use_matrixcn
             end if    
 
             ! calculate fine root N litterfall (no retranslocation of fine root N)
             frootn_to_litter(p) = frootc_to_litter(p) / frootcn(ivt(p))
             
-            if (CNratio_floating) then    
-               if (.not. use_matrixcn) then   
-                  if (leafc(p) == 0.0_r8) then    
-                     ntovr_leaf = 0.0_r8    
-                  else    
-                     ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p))   
-                  end if   
+            if (CNratio_floating .eqv. .true.) then    
+               if (leafc(p) == 0.0_r8) then    
+                  ntovr_leaf = 0.0_r8    
+               else    
+                  ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p))   
+               end if   
            
-                  leafn_to_litter(p)   = fr_leafn_to_litter * ntovr_leaf
-                  leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p)
-               else  ! Matrix update for leafn to litter and retrans
-                  if(leafn(p) > 0._r8)then
+               leafn_to_litter(p)   = fr_leafn_to_litter * ntovr_leaf
+               leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p)
+               if (use_matrixcn) then   
+                  if(leafn(p) .gt. 0)then
                      leafn_to_litter(p)   = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p)        / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                      leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     leafn_to_litter(p)   = 0._r8
-                     leafn_to_retransn(p) = 0._r8
+                     leafn_to_litter(p)   = 0
+                     leafn_to_retransn(p) = 0
                   end if
-               end if ! .not. use_matrixcn
+               else
+                  ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
+               end if !use_matrixcn
                if (frootc(p) == 0.0_r8) then    
                    frootn_to_litter(p) = 0.0_r8    
                 else    
@@ -3620,9 +3612,8 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, &
                endif
             end if
 
-            ! Matrix update for frootn to litter
             if (use_matrixcn) then   
-               if(frootn(p) /= 0._r8)then
+               if(frootn(p) .ne. 0)then
                   frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,frootn_to_litter(p) / frootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                end if
             else
@@ -3682,7 +3673,7 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
          livestemn_to_retransn    =>    cnveg_nitrogenflux_inst%livestemn_to_retransn_patch    , & ! Output: [real(r8) (:) ]                                                    
          livecrootn_to_deadcrootn =>    cnveg_nitrogenflux_inst%livecrootn_to_deadcrootn_patch , & ! Output: [real(r8) (:) ]                                                    
          livecrootn_to_retransn   =>    cnveg_nitrogenflux_inst%livecrootn_to_retransn_patch   , & ! Output: [real(r8) (:) ] 
-         free_retransn_to_npool   =>    cnveg_nitrogenflux_inst%free_retransn_to_npool_patch   , & ! Input:  [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s)
+         free_retransn_to_npool   =>    cnveg_nitrogenflux_inst%free_retransn_to_npool_patch   , & ! Input:  [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s)          
          ileafst_to_ileafxf_phc              =>    cnveg_carbonflux_inst%ileafst_to_ileafxf_ph                 , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool
          ileafxf_to_ileaf_phc                =>    cnveg_carbonflux_inst%ileafxf_to_ileaf_ph                   , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool
          ifrootst_to_ifrootxf_phc            =>    cnveg_carbonflux_inst%ifrootst_to_ifrootxf_ph               , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool
@@ -3736,38 +3727,40 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
 
             ! live stem to dead stem turnover
 
-            ! Matrix update for livestemc to deadstem
+            ctovr = livestemc(p) * lwtop
+            ntovr = ctovr / livewdcn(ivt(p))
+            livestemc_to_deadstemc(p) = ctovr
+            livestemn_to_deadstemn(p) = ctovr / deadwdcn(ivt(p))
             if( use_matrixcn)then
                livestemc_to_deadstemc(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_ideadstem_phc,lwtop,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                if (livestemn(p) .gt. 0.0_r8) then
                   livestemn_to_deadstemn(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_ideadstem_phn,livestemn_to_deadstemn(p)/livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                else
-                  livestemn_to_deadstemn(p) = 0._r8
+                  livestemn_to_deadstemn(p) = 0
                end if
             else
                ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
                !                                        and CNNStateUpdate1::NStateUpdate1
-               ctovr = livestemc(p) * lwtop
-               ntovr = ctovr / livewdcn(ivt(p))
-               livestemc_to_deadstemc(p) = ctovr
-               livestemn_to_deadstemn(p) = ctovr / deadwdcn(ivt(p))
             end if
-            if (CNratio_floating) then    
+            if (CNratio_floating .eqv. .true.) then    
                if (livestemc(p) == 0.0_r8) then    
                    ntovr = 0.0_r8    
                    livestemn_to_deadstemn(p) = 0.0_r8 
-               else    
+                else    
                    ntovr = ctovr * (livestemn(p) / livestemc(p))   
                    livestemn_to_deadstemn(p) = ctovr / deadwdcn(ivt(p)) 
-               end if   
-               if (use_matrixcn)then  ! Matrix update for livestemn to deadstem 
+                end if   
+
+               if (use_matrixcn)then 
                   if (livestemn(p) .gt. 0.0_r8) then
                      livestemn_to_deadstemn(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_ideadstem_phn,&
                                                  livestemn_to_deadstemn(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                   else
                      livestemn_to_deadstemn(p) = 0
                   end if
-               end if  ! use_matrixcn
+               else
+                  ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
+               end if
             end if
             
             livestemn_to_retransn(p)  = ntovr - livestemn_to_deadstemn(p)
@@ -3777,19 +3770,17 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
 
             ctovr = livecrootc(p) * lwtop
             ntovr = ctovr / livewdcn(ivt(p))
-
             if(.not. use_matrixcn)then
                ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
                !                                        and CNNStateUpdate1::NStateUpdate1
                livecrootc_to_deadcrootc(p) = ctovr
                livecrootn_to_deadcrootn(p) = ctovr / deadwdcn(ivt(p))
             else
-               ! Matrix update for livecroot to deadcroot
                livecrootc_to_deadcrootc(p) = livecrootc(p) * matrix_update_phc(p,ilivecroot_to_ideadcroot_phc,lwtop,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                livecrootn_to_deadcrootn(p) = livecrootn(p) * matrix_update_phn(p,ilivecroot_to_ideadcroot_phn,lwtop/deadwdcn(ivt(p)),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
             end if !use_matrixcn
             
-            if (CNratio_floating) then    
+            if (CNratio_floating .eqv. .true.) then    
                if (livecrootc(p) == 0.0_r8) then    
                   ntovr = 0.0_r8    
                   livecrootn_to_deadcrootn(p) = 0.0_r8 
@@ -3797,50 +3788,49 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
                   ntovr = ctovr * (livecrootn(p) / livecrootc(p))   
                   livecrootn_to_deadcrootn(p) = ctovr / deadwdcn(ivt(p)) 
                end if   
-               if (use_matrixcn)then  ! Matrix update for livecroot to deadcroot
+
+               if (use_matrixcn)then 
                   if (livecrootn(p) .ne.0.0_r8 )then
                      livecrootn_to_deadcrootn(p) = matrix_update_phn(p,ilivecroot_to_ideadcroot_phn,&
                                                    livecrootn_to_deadcrootn(p) / livecrootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livecrootn(p)
                   end if
-               end if  ! use_matrixcn
+               else
+                  ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019)
+               end if !use_matrixcn
             end if
 
             livecrootn_to_retransn(p)  = ntovr - livecrootn_to_deadcrootn(p)
-
-            ! Matrix update for livecrootn and livestemn to retrans as well as free retransn to npool with FUN
-            if(use_matrixcn)then
-               if(livecrootn(p) .gt. 0.0_r8) then
-                  livecrootn_to_retransn(p) = matrix_update_phn(p,ilivecroot_to_iretransn_phn,&
-                                              livecrootn_to_retransn(p) / livecrootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livecrootn(p)
-               else
-                  livecrootn_to_retransn(p) = 0
-               end if
-               if(livestemn(p) .gt. 0.0_r8) then
-                  livestemn_to_retransn(p) = matrix_update_phn(p,ilivestem_to_iretransn_phn,&
-                                             livestemn_to_retransn(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livestemn(p)
-               else
-                  livestemn_to_retransn(p)  = 0
-               end if
-               ! WW change logic so livestem_retrans goes to npool (via
-               ! free_retrans flux)
-               ! this should likely be done more cleanly if it works, i.e. not
-               ! update fluxes w/ states
-               ! additional considerations for crop?
-               ! The non-matrix version of this is in NStateUpdate1
-               if (use_fun) then
-                  if (retransn(p) .gt. 0._r8) then
-                     ! The acc matrix check MUST be turned on, or this will
-                     ! fail with Nitrogen balance error EBK 03/11/2021
-                     free_retransn_to_npool(p) = free_retransn_to_npool(p) + retransn(p) * matrix_update_phn(p,iretransn_to_iout, &
-                                                 (livestemn_to_retransn(p) + livecrootn_to_retransn(p)) / retransn(p),dt,         &
-                                                 cnveg_nitrogenflux_inst, matrixcheck_ph, acc=.true.)
+               if(use_matrixcn)then
+                  if(livecrootn(p) .gt. 0.0_r8) then
+                     livecrootn_to_retransn(p) = matrix_update_phn(p,ilivecroot_to_iretransn_phn,&
+                                                 livecrootn_to_retransn(p) / livecrootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livecrootn(p)
                   else
-                     free_retransn_to_npool(p) = 0._r8
+                     livecrootn_to_retransn(p) = 0
                   end if
-               end if
-            else
-               ! The non-matrix version of this is in NStateUpdate1
-            end if !use_matrixcn
+                  if(livestemn(p) .gt. 0.0_r8) then
+                     livestemn_to_retransn(p) = matrix_update_phn(p,ilivestem_to_iretransn_phn,&
+                                                livestemn_to_retransn(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livestemn(p)
+                  else
+                     livestemn_to_retransn(p)  = 0
+                  end if
+                  ! WW change logic so livestem_retrans goes to npool (via
+                  ! free_retrans flux)
+                  ! this should likely be done more cleanly if it works, i.e. not
+                  ! update fluxes w/ states
+                  ! additional considerations for crop?
+                  ! The non-matrix version of this is in NStateUpdate1
+                  if (use_fun) then
+                     if (retransn(p) .gt. 0._r8) then
+                        ! The acc matrix check MUST be turned on, or this will
+                        ! fail with Nitrogen balance error EBK 03/11/2021
+                        free_retransn_to_npool(p) = free_retransn_to_npool(p) + retransn(p) * matrix_update_phn(p,iretransn_to_iout, &
+                                                    (livestemn_to_retransn(p) + livecrootn_to_retransn(p)) / retransn(p),dt,         &
+                                                    cnveg_nitrogenflux_inst, matrixcheck_ph, acc=.true.)
+                     else
+                        free_retransn_to_npool(p) = 0._r8
+                     end if
+                  end if
+               end if !use_matrixcn
 
          end if
 
diff --git a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90
index d7b3c01fc1..4f221c6910 100644
--- a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90
+++ b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90
@@ -9,11 +9,12 @@ module SoilBiogeochemNStateUpdate1Mod
   use clm_time_manager                   , only : get_step_size_real
   use clm_varpar                         , only : nlevdecomp, ndecomp_cascade_transitions
   use clm_varctl                         , only : iulog, use_nitrif_denitrif, use_crop
+  use SoilBiogeochemDecompCascadeConType , only : use_soil_matrixcn
   use clm_varcon                         , only : nitrif_n2o_loss_frac
   use SoilBiogeochemStateType            , only : soilbiogeochem_state_type
   use SoilBiogeochemNitrogenStateType    , only : soilbiogeochem_nitrogenstate_type
   use SoilBiogeochemNitrogenfluxType     , only : soilbiogeochem_nitrogenflux_type
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn
+  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
   use CNSharedParamsMod                  , only : use_fun
   use ColumnType                         , only : col 
   !
@@ -118,50 +119,47 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc,  &
       end if
 
       ! decomposition fluxes
-      if (.not. use_soil_matrixcn) then
-         do k = 1, ndecomp_cascade_transitions
+   if (.not. use_soil_matrixcn) then
+      do k = 1, ndecomp_cascade_transitions
+         do j = 1, nlevdecomp
+            ! column loop
+            do fc = 1,num_soilc
+               c = filter_soilc(fc)
+
+               nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
+                    nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - &
+                    nf%decomp_cascade_ntransfer_vr_col(c,j,k) * dt
+            end do
+         end do
+      end do
+
+
+      do k = 1, ndecomp_cascade_transitions
+         if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
             do j = 1, nlevdecomp
                ! column loop
                do fc = 1,num_soilc
                   c = filter_soilc(fc)
 
+                  nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
+                       nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) + &
+                       (nf%decomp_cascade_ntransfer_vr_col(c,j,k) + &
+                        nf%decomp_cascade_sminn_flux_vr_col(c,j,k)) * dt
+               end do
+            end do
+         else  ! terminal transitions
+            do j = 1, nlevdecomp
+               ! column loop
+               do fc = 1,num_soilc
+                  c = filter_soilc(fc)
                   nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
                        nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - &
-                       nf%decomp_cascade_ntransfer_vr_col(c,j,k) * dt
+                       nf%decomp_cascade_sminn_flux_vr_col(c,j,k) * dt
                end do
             end do
-         end do
-
-
-         do k = 1, ndecomp_cascade_transitions
-            if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
-               do j = 1, nlevdecomp
-                  ! column loop
-                  do fc = 1,num_soilc
-                     c = filter_soilc(fc)
-
-                     nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
-                          nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) + &
-                          (nf%decomp_cascade_ntransfer_vr_col(c,j,k) + &
-                           nf%decomp_cascade_sminn_flux_vr_col(c,j,k)) * dt
-                  end do
-               end do
-            else  ! terminal transitions
-               do j = 1, nlevdecomp
-                  ! column loop
-                  do fc = 1,num_soilc
-                     c = filter_soilc(fc)
-                     nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
-                          nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - &
-                          nf%decomp_cascade_sminn_flux_vr_col(c,j,k) * dt
-                  end do
-               end do
-            end if
-         end do
-      else
-         ! Matrix solution equvalent to above is in CNSoilMatrixMod.F90?
-         ! TODO check on this
-      end if  ! 
+         end if
+      end do
+   end if  ! 
 
       if (.not. use_nitrif_denitrif) then
 

From 42af57b7f6584610e5127874f55044fe16da2ccb Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 28 Dec 2023 13:18:15 -0700
Subject: [PATCH 0050/1248] Matrixcn updates pertaining to GULU (gross unrep.
 landuse chg)

---
 src/biogeochem/CNBalanceCheckMod.F90  |   1 -
 src/biogeochem/CNCStateUpdate2Mod.F90 | 132 ++++++++++-------
 src/biogeochem/CNNStateUpdate2Mod.F90 | 129 +++++++++-------
 src/biogeochem/dynGrossUnrepMod.F90   | 205 +++++++++++++++++++-------
 src/dyn_subgrid/dynHarvestMod.F90     |  19 +--
 5 files changed, 313 insertions(+), 173 deletions(-)

diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90
index fbf30e9549..5b253fdd00 100644
--- a/src/biogeochem/CNBalanceCheckMod.F90
+++ b/src/biogeochem/CNBalanceCheckMod.F90
@@ -60,7 +60,6 @@ module CNBalanceCheckMod
 
   !-----------------------------------------------------------------------
   subroutine Init(this, bounds)
-    use CNSharedParamsMod, only : use_matrixcn
     class(cn_balance_type)         :: this
     type(bounds_type) , intent(in) :: bounds  
 
diff --git a/src/biogeochem/CNCStateUpdate2Mod.F90 b/src/biogeochem/CNCStateUpdate2Mod.F90
index 76fcc340b6..2890c7d1fd 100644
--- a/src/biogeochem/CNCStateUpdate2Mod.F90
+++ b/src/biogeochem/CNCStateUpdate2Mod.F90
@@ -370,15 +370,27 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
          do fc = 1,num_soilc
             c = filter_soilc(fc)
 
-            ! column gross unrepresented landcover change fluxes
-            do i = i_litr_min, i_litr_max
-               cs_soil%decomp_cpools_vr_col(c,j,i) = &
-                  cs_soil%decomp_cpools_vr_col(c,j,i) + cf_veg%gru_c_to_litr_c_col(c,j,i) * dt
-            end do
-            cs_soil%decomp_cpools_vr_col(c,j,i_cwd) = &
-                 cs_soil%decomp_cpools_vr_col(c,j,i_cwd) + cf_veg%gru_c_to_cwdc_col(c,j)  * dt
+            if (.not. use_soil_matrixcn)then
+               ! column gross unrepresented landcover change fluxes
+               do i = i_litr_min, i_litr_max
+                  cs_soil%decomp_cpools_vr_col(c,j,i) = &
+                     cs_soil%decomp_cpools_vr_col(c,j,i) + cf_veg%gru_c_to_litr_c_col(c,j,i) * dt
+               end do
+               cs_soil%decomp_cpools_vr_col(c,j,i_cwd) = &
+                    cs_soil%decomp_cpools_vr_col(c,j,i_cwd) + cf_veg%gru_c_to_cwdc_col(c,j) * dt
 
-            ! wood to product pools - states updated in CNProducts
+               ! wood to product pools - states updated in CNProducts
+            else
+              ! Match above for soil-matrix
+               do i = i_litr_min, i_litr_max
+                  cf_soil%matrix_Cinput%V(c,j+(i-1)*nlevdecomp) = &
+                    cf_soil%matrix_Cinput%V(c,j+(i-1)*nlevdecomp) + cf_veg%gru_c_to_litr_c_col(c,j,i) * dt
+               end do
+               ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and
+               !           i_cwd = 0 if fates, so not including in the i-loop
+               cf_soil%matrix_Cinput%V(c,j+(i_cwd-1)*nlevdecomp) =     &
+                 cf_soil%matrix_Cinput%V(c,j+(i_cwd-1)*nlevdecomp) + cf_veg%gru_c_to_cwdc_col(c,j) * dt
+            end if !soil_matrix
          end do
       end do
 
@@ -387,58 +399,66 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
          p = filter_soilp(fp)
 
          ! patch-level carbon fluxes from gross unrepresented landcover change mortality
-         ! displayed pools
-         cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p)                           &
-              - cf_veg%gru_leafc_to_litter_patch(p) * dt
-         cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p)                         &
-              - cf_veg%gru_frootc_to_litter_patch(p) * dt
-         cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p)                   &
-              - cf_veg%gru_livestemc_to_atm_patch(p) * dt
-         cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p)                   &
-              - cf_veg%gru_deadstemc_to_atm_patch(p) * dt
-         cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p)                   &
-              - cf_veg%gru_wood_productc_gain_patch(p) * dt
-         cs_veg%livecrootc_patch(p) = cs_veg%livecrootc_patch(p)                 &
-              - cf_veg%gru_livecrootc_to_litter_patch(p) * dt
-         cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p)                 &
-              - cf_veg%gru_deadcrootc_to_litter_patch(p) * dt
+         !
+         ! State update without the matrix solution
+         !
+         if(.not. use_matrixcn)then
+            ! displayed pools
+            cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p)                           &
+                 - cf_veg%gru_leafc_to_litter_patch(p) * dt
+            cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p)                         &
+                 - cf_veg%gru_frootc_to_litter_patch(p) * dt
+            cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p)                   &
+                 - cf_veg%gru_livestemc_to_atm_patch(p) * dt
+            cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p)                   &
+                 - cf_veg%gru_deadstemc_to_atm_patch(p) * dt
+            cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p)                   &
+                 - cf_veg%gru_wood_productc_gain_patch(p) * dt
+            cs_veg%livecrootc_patch(p) = cs_veg%livecrootc_patch(p)                 &
+                 - cf_veg%gru_livecrootc_to_litter_patch(p) * dt
+            cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p)                 &
+                 - cf_veg%gru_deadcrootc_to_litter_patch(p) * dt
 
-         ! xsmrpool
-         cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p)                     &
-              - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt
+            ! xsmrpool
+            cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p)                     &
+                 - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt
 
-         ! storage pools
-         cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p)           &
-              - cf_veg%gru_leafc_storage_to_atm_patch(p) * dt
-         cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p)         &
-              - cf_veg%gru_frootc_storage_to_atm_patch(p) * dt
-         cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p)   &
-              - cf_veg%gru_livestemc_storage_to_atm_patch(p) * dt
-         cs_veg%deadstemc_storage_patch(p) = cs_veg%deadstemc_storage_patch(p)   &
-              - cf_veg%gru_deadstemc_storage_to_atm_patch(p) * dt
-         cs_veg%livecrootc_storage_patch(p) = cs_veg%livecrootc_storage_patch(p) &
-              - cf_veg%gru_livecrootc_storage_to_atm_patch(p) * dt
-         cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) &
-              - cf_veg%gru_deadcrootc_storage_to_atm_patch(p) * dt
-         cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p)           &
-              - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt
+            ! storage pools
+            cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p)           &
+                 - cf_veg%gru_leafc_storage_to_atm_patch(p) * dt
+            cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p)         &
+                 - cf_veg%gru_frootc_storage_to_atm_patch(p) * dt
+            cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p)   &
+                 - cf_veg%gru_livestemc_storage_to_atm_patch(p) * dt
+            cs_veg%deadstemc_storage_patch(p) = cs_veg%deadstemc_storage_patch(p)   &
+                 - cf_veg%gru_deadstemc_storage_to_atm_patch(p) * dt
+            cs_veg%livecrootc_storage_patch(p) = cs_veg%livecrootc_storage_patch(p) &
+                 - cf_veg%gru_livecrootc_storage_to_atm_patch(p) * dt
+            cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) &
+                 - cf_veg%gru_deadcrootc_storage_to_atm_patch(p) * dt
+            cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p)           &
+                 - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt
 
-         ! transfer pools
-         cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p)                 &
-              - cf_veg%gru_leafc_xfer_to_atm_patch(p) * dt
-         cs_veg%frootc_xfer_patch(p) = cs_veg%frootc_xfer_patch(p)               &
-              - cf_veg%gru_frootc_xfer_to_atm_patch(p) * dt
-         cs_veg%livestemc_xfer_patch(p) = cs_veg%livestemc_xfer_patch(p)         &
-              - cf_veg%gru_livestemc_xfer_to_atm_patch(p) * dt
-         cs_veg%deadstemc_xfer_patch(p) = cs_veg%deadstemc_xfer_patch(p)         &
-              - cf_veg%gru_deadstemc_xfer_to_atm_patch(p) * dt
-         cs_veg%livecrootc_xfer_patch(p) = cs_veg%livecrootc_xfer_patch(p)       &
-              - cf_veg%gru_livecrootc_xfer_to_atm_patch(p) * dt
-         cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p)       &
-              - cf_veg%gru_deadcrootc_xfer_to_atm_patch(p) * dt
-         cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p)                 &
-              - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt
+            ! transfer pools
+            cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p)                 &
+                 - cf_veg%gru_leafc_xfer_to_atm_patch(p) * dt
+            cs_veg%frootc_xfer_patch(p) = cs_veg%frootc_xfer_patch(p)               &
+                 - cf_veg%gru_frootc_xfer_to_atm_patch(p) * dt
+            cs_veg%livestemc_xfer_patch(p) = cs_veg%livestemc_xfer_patch(p)         &
+                 - cf_veg%gru_livestemc_xfer_to_atm_patch(p) * dt
+            cs_veg%deadstemc_xfer_patch(p) = cs_veg%deadstemc_xfer_patch(p)         &
+                 - cf_veg%gru_deadstemc_xfer_to_atm_patch(p) * dt
+            cs_veg%livecrootc_xfer_patch(p) = cs_veg%livecrootc_xfer_patch(p)       &
+                 - cf_veg%gru_livecrootc_xfer_to_atm_patch(p) * dt
+            cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p)       &
+                 - cf_veg%gru_deadcrootc_xfer_to_atm_patch(p) * dt
+            cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p)                 &
+                 - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt
 
+         else
+            ! NB (slevis) The matrix equivalent of the above is in
+            ! dynGrossUnrepMod::CNGrossUnrep*
+         end if
       end do ! end of patch loop
 
     end associate
diff --git a/src/biogeochem/CNNStateUpdate2Mod.F90 b/src/biogeochem/CNNStateUpdate2Mod.F90
index 2702b80de5..2dbba68b82 100644
--- a/src/biogeochem/CNNStateUpdate2Mod.F90
+++ b/src/biogeochem/CNNStateUpdate2Mod.F90
@@ -358,14 +358,29 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
       do j = 1,nlevdecomp
          do fc = 1,num_soilc
             c = filter_soilc(fc)
-            do i = i_litr_min, i_litr_max
-               ns_soil%decomp_npools_vr_col(c,j,i) = &
-                  ns_soil%decomp_npools_vr_col(c,j,i) + nf_veg%gru_n_to_litr_n_col(c,j,i) * dt
-            end do
-            ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and
-            !           i_cwd = 0 if fates, so not including in the i-loop
-            ns_soil%decomp_npools_vr_col(c,j,i_cwd)     = &
-                 ns_soil%decomp_npools_vr_col(c,j,i_cwd)     + nf_veg%gru_n_to_cwdn_col(c,j)       * dt
+            !
+            ! State update without the matrix solution
+            !
+            if (.not. use_soil_matrixcn)then
+               do i = i_litr_min, i_litr_max
+                  ns_soil%decomp_npools_vr_col(c,j,i) = &
+                     ns_soil%decomp_npools_vr_col(c,j,i) + nf_veg%gru_n_to_litr_n_col(c,j,i) * dt
+               end do
+               ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and
+               !           i_cwd = 0 if fates, so not including in the i-loop
+               ns_soil%decomp_npools_vr_col(c,j,i_cwd) = &
+                    ns_soil%decomp_npools_vr_col(c,j,i_cwd) + nf_veg%gru_n_to_cwdn_col(c,j) * dt
+            else
+               ! Do above for the matrix solution
+               do i = i_litr_min, i_litr_max
+                  nf_soil%matrix_Ninput%V(c,j+(i-1)*nlevdecomp) = &
+                    nf_soil%matrix_Ninput%V(c,j+(i-1)*nlevdecomp) + nf_veg%gru_n_to_litr_n_col(c,j,i) * dt
+               end do
+               ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and
+               !           i_cwd = 0 if fates, so not including in the i-loop
+               nf_soil%matrix_Ninput%V(c,j+(i_cwd-1)*nlevdecomp) = &
+                 nf_soil%matrix_Ninput%V(c,j+(i_cwd-1)*nlevdecomp) + nf_veg%gru_n_to_cwdn_col(c,j) * dt
+            end if !not use_soil_matrixcn
          end do
       end do
 
@@ -374,51 +389,59 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
       do fp = 1,num_soilp
          p = filter_soilp(fp)
 
-         ! displayed pools
-         ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p)                           &
-              - nf_veg%gru_leafn_to_litter_patch(p) * dt
-         ns_veg%frootn_patch(p) = ns_veg%frootn_patch(p)                         &
-              - nf_veg%gru_frootn_to_litter_patch(p) * dt
-         ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p)                   &
-              - nf_veg%gru_livestemn_to_atm_patch(p) * dt
-         ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p)                   &
-              - nf_veg%gru_deadstemn_to_atm_patch(p) * dt
-         ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p)                   &
-              - nf_veg%gru_wood_productn_gain_patch(p) * dt
-         ns_veg%livecrootn_patch(p) = ns_veg%livecrootn_patch(p)                 &
-              - nf_veg%gru_livecrootn_to_litter_patch(p) * dt
-         ns_veg%deadcrootn_patch(p) = ns_veg%deadcrootn_patch(p)                 &
-              - nf_veg%gru_deadcrootn_to_litter_patch(p) * dt
-         ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p)                     &
-              - nf_veg%gru_retransn_to_litter_patch(p) * dt
-
-         ! storage pools
-         ns_veg%leafn_storage_patch(p) = ns_veg%leafn_storage_patch(p)           &
-              - nf_veg%gru_leafn_storage_to_atm_patch(p) * dt
-         ns_veg%frootn_storage_patch(p) = ns_veg%frootn_storage_patch(p)         &
-              - nf_veg%gru_frootn_storage_to_atm_patch(p) * dt
-         ns_veg%livestemn_storage_patch(p) = ns_veg%livestemn_storage_patch(p)   &
-              - nf_veg%gru_livestemn_storage_to_atm_patch(p) * dt
-         ns_veg%deadstemn_storage_patch(p) = ns_veg%deadstemn_storage_patch(p)   &
-              - nf_veg%gru_deadstemn_storage_to_atm_patch(p) * dt
-         ns_veg%livecrootn_storage_patch(p) = ns_veg%livecrootn_storage_patch(p) &
-              - nf_veg%gru_livecrootn_storage_to_atm_patch(p) * dt
-         ns_veg%deadcrootn_storage_patch(p) = ns_veg%deadcrootn_storage_patch(p) &
-              - nf_veg%gru_deadcrootn_storage_to_atm_patch(p) * dt
-
-         ! transfer pools
-         ns_veg%leafn_xfer_patch(p) = ns_veg%leafn_xfer_patch(p)                 &
-              - nf_veg%gru_leafn_xfer_to_atm_patch(p) *dt
-         ns_veg%frootn_xfer_patch(p) = ns_veg%frootn_xfer_patch(p)               &
-              - nf_veg%gru_frootn_xfer_to_atm_patch(p) *dt
-         ns_veg%livestemn_xfer_patch(p) = ns_veg%livestemn_xfer_patch(p)         &
-              - nf_veg%gru_livestemn_xfer_to_atm_patch(p) *dt
-         ns_veg%deadstemn_xfer_patch(p) = ns_veg%deadstemn_xfer_patch(p)         &
-              - nf_veg%gru_deadstemn_xfer_to_atm_patch(p) *dt
-         ns_veg%livecrootn_xfer_patch(p) = ns_veg%livecrootn_xfer_patch(p)       &
-              - nf_veg%gru_livecrootn_xfer_to_atm_patch(p) *dt
-         ns_veg%deadcrootn_xfer_patch(p) = ns_veg%deadcrootn_xfer_patch(p)       &
-              - nf_veg%gru_deadcrootn_xfer_to_atm_patch(p) *dt
+         !
+         ! State update without the matrix solution
+         !
+         if(.not. use_matrixcn)then
+            ! displayed pools
+            ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p)                           &
+                 - nf_veg%gru_leafn_to_litter_patch(p) * dt
+            ns_veg%frootn_patch(p) = ns_veg%frootn_patch(p)                         &
+                 - nf_veg%gru_frootn_to_litter_patch(p) * dt
+            ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p)                   &
+                 - nf_veg%gru_livestemn_to_atm_patch(p) * dt
+            ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p)                   &
+                 - nf_veg%gru_deadstemn_to_atm_patch(p) * dt
+            ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p)                   &
+                 - nf_veg%gru_wood_productn_gain_patch(p) * dt
+            ns_veg%livecrootn_patch(p) = ns_veg%livecrootn_patch(p)                 &
+                 - nf_veg%gru_livecrootn_to_litter_patch(p) * dt
+            ns_veg%deadcrootn_patch(p) = ns_veg%deadcrootn_patch(p)                 &
+                 - nf_veg%gru_deadcrootn_to_litter_patch(p) * dt
+            ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p)                     &
+                 - nf_veg%gru_retransn_to_litter_patch(p) * dt
+
+            ! storage pools
+            ns_veg%leafn_storage_patch(p) = ns_veg%leafn_storage_patch(p)           &
+                 - nf_veg%gru_leafn_storage_to_atm_patch(p) * dt
+            ns_veg%frootn_storage_patch(p) = ns_veg%frootn_storage_patch(p)         &
+                 - nf_veg%gru_frootn_storage_to_atm_patch(p) * dt
+            ns_veg%livestemn_storage_patch(p) = ns_veg%livestemn_storage_patch(p)   &
+                 - nf_veg%gru_livestemn_storage_to_atm_patch(p) * dt
+            ns_veg%deadstemn_storage_patch(p) = ns_veg%deadstemn_storage_patch(p)   &
+                 - nf_veg%gru_deadstemn_storage_to_atm_patch(p) * dt
+            ns_veg%livecrootn_storage_patch(p) = ns_veg%livecrootn_storage_patch(p) &
+                 - nf_veg%gru_livecrootn_storage_to_atm_patch(p) * dt
+            ns_veg%deadcrootn_storage_patch(p) = ns_veg%deadcrootn_storage_patch(p) &
+                 - nf_veg%gru_deadcrootn_storage_to_atm_patch(p) * dt
+
+            ! transfer pools
+            ns_veg%leafn_xfer_patch(p) = ns_veg%leafn_xfer_patch(p)                 &
+                 - nf_veg%gru_leafn_xfer_to_atm_patch(p) *dt
+            ns_veg%frootn_xfer_patch(p) = ns_veg%frootn_xfer_patch(p)               &
+                 - nf_veg%gru_frootn_xfer_to_atm_patch(p) *dt
+            ns_veg%livestemn_xfer_patch(p) = ns_veg%livestemn_xfer_patch(p)         &
+                 - nf_veg%gru_livestemn_xfer_to_atm_patch(p) *dt
+            ns_veg%deadstemn_xfer_patch(p) = ns_veg%deadstemn_xfer_patch(p)         &
+                 - nf_veg%gru_deadstemn_xfer_to_atm_patch(p) *dt
+            ns_veg%livecrootn_xfer_patch(p) = ns_veg%livecrootn_xfer_patch(p)       &
+                 - nf_veg%gru_livecrootn_xfer_to_atm_patch(p) *dt
+            ns_veg%deadcrootn_xfer_patch(p) = ns_veg%deadcrootn_xfer_patch(p)       &
+                 - nf_veg%gru_deadcrootn_xfer_to_atm_patch(p) *dt
+         else
+            ! NB (slevis) The equivalent changes for matrix code are in
+            ! dynGrossUnrepMod::CNGrossUnrep*
+         end if !not use_matrixcn
 
       end do
 
diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90
index bc49e72f4c..b354744b61 100644
--- a/src/biogeochem/dynGrossUnrepMod.F90
+++ b/src/biogeochem/dynGrossUnrepMod.F90
@@ -24,6 +24,7 @@ module dynGrossUnrepMod
   use clm_varpar              , only : natpft_size, i_litr_min, i_litr_max, i_met_lit
   use ColumnType              , only : col                
   use PatchType               , only : patch                
+  use CNSharedParamsMod       , only : use_matrixcn
   !
   ! !PUBLIC MEMBER FUNCTIONS:
   implicit none
@@ -296,61 +297,157 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                m = 0._r8
             end if
 
-            ! patch-level gross unrepresented landcover change carbon fluxes
-            ! displayed pools
-            gru_leafc_to_litter(p)               = leafc(p)               * m
-            gru_frootc_to_litter(p)              = frootc(p)              * m
-            gru_livestemc_to_atm(p)              = livestemc(p)           * m
-            gru_deadstemc_to_atm(p)              = deadstemc(p)           * m * convfrac(ivt(p))
-            gru_wood_productc_gain(p)            = deadstemc(p)           * m * (1._r8 - convfrac(ivt(p)))
-            gru_livecrootc_to_litter(p)          = livecrootc(p)          * m
-            gru_deadcrootc_to_litter(p)          = deadcrootc(p)          * m
-            gru_xsmrpool_to_atm(p)               = xsmrpool(p)            * m
-
-            ! storage pools
-            gru_leafc_storage_to_atm(p)          = leafc_storage(p)       * m
-            gru_frootc_storage_to_atm(p)         = frootc_storage(p)      * m
-            gru_livestemc_storage_to_atm(p)      = livestemc_storage(p)   * m
-            gru_deadstemc_storage_to_atm(p)      = deadstemc_storage(p)   * m
-            gru_livecrootc_storage_to_atm(p)     = livecrootc_storage(p)  * m
-            gru_deadcrootc_storage_to_atm(p)     = deadcrootc_storage(p)  * m
-            gru_gresp_storage_to_atm(p)          = gresp_storage(p)       * m
-
-            ! transfer pools
-            gru_leafc_xfer_to_atm(p)             = leafc_xfer(p)          * m
-            gru_frootc_xfer_to_atm(p)            = frootc_xfer(p)         * m
-            gru_livestemc_xfer_to_atm(p)         = livestemc_xfer(p)      * m
-            gru_deadstemc_xfer_to_atm(p)         = deadstemc_xfer(p)      * m
-            gru_livecrootc_xfer_to_atm(p)        = livecrootc_xfer(p)     * m
-            gru_deadcrootc_xfer_to_atm(p)        = deadcrootc_xfer(p)     * m
-            gru_gresp_xfer_to_atm(p)             = gresp_xfer(p)          * m
+            if(.not. use_matrixcn)then
+               ! patch-level gross unrepresented landcover change carbon fluxes
+               ! displayed pools
+               gru_leafc_to_litter(p)               = leafc(p)               * m
+               gru_frootc_to_litter(p)              = frootc(p)              * m
+               gru_livestemc_to_atm(p)              = livestemc(p)           * m
+               gru_deadstemc_to_atm(p)              = deadstemc(p)           * m * convfrac(ivt(p))
+               gru_wood_productc_gain(p)            = deadstemc(p)           * m * (1._r8 - convfrac(ivt(p)))
+               gru_livecrootc_to_litter(p)          = livecrootc(p)          * m
+               gru_deadcrootc_to_litter(p)          = deadcrootc(p)          * m
+               gru_xsmrpool_to_atm(p)               = xsmrpool(p)            * m
+
+               ! storage pools
+               gru_leafc_storage_to_atm(p)          = leafc_storage(p)       * m
+               gru_frootc_storage_to_atm(p)         = frootc_storage(p)      * m
+               gru_livestemc_storage_to_atm(p)      = livestemc_storage(p)   * m
+               gru_deadstemc_storage_to_atm(p)      = deadstemc_storage(p)   * m
+               gru_livecrootc_storage_to_atm(p)     = livecrootc_storage(p)  * m
+               gru_deadcrootc_storage_to_atm(p)     = deadcrootc_storage(p)  * m
+               gru_gresp_storage_to_atm(p)          = gresp_storage(p)       * m
+
+               ! transfer pools
+               gru_leafc_xfer_to_atm(p)             = leafc_xfer(p)          * m
+               gru_frootc_xfer_to_atm(p)            = frootc_xfer(p)         * m
+               gru_livestemc_xfer_to_atm(p)         = livestemc_xfer(p)      * m
+               gru_deadstemc_xfer_to_atm(p)         = deadstemc_xfer(p)      * m
+               gru_livecrootc_xfer_to_atm(p)        = livecrootc_xfer(p)     * m
+               gru_deadcrootc_xfer_to_atm(p)        = deadcrootc_xfer(p)     * m
+               gru_gresp_xfer_to_atm(p)             = gresp_xfer(p)          * m
 	    
-            ! patch-level gross unrepresented landcover change mortality nitrogen fluxes
-            ! displayed pools
-            gru_leafn_to_litter(p)               = leafn(p)               * m
-            gru_frootn_to_litter(p)              = frootn(p)              * m
-            gru_livestemn_to_atm(p)              = livestemn(p)           * m
-            gru_deadstemn_to_atm(p)              = deadstemn(p)           * m * convfrac(ivt(p))
-            gru_wood_productn_gain(p)            = deadstemn(p)           * m * (1._r8 - convfrac(ivt(p)))
-            gru_livecrootn_to_litter(p)          = livecrootn(p)          * m
-            gru_deadcrootn_to_litter(p)          = deadcrootn(p)          * m
-            gru_retransn_to_litter(p)            = retransn(p)            * m
-
-            ! storage pools
-            gru_leafn_storage_to_atm(p)          = leafn_storage(p)       * m
-            gru_frootn_storage_to_atm(p)         = frootn_storage(p)      * m
-            gru_livestemn_storage_to_atm(p)      = livestemn_storage(p)   * m
-            gru_deadstemn_storage_to_atm(p)      = deadstemn_storage(p)   * m
-            gru_livecrootn_storage_to_atm(p)     = livecrootn_storage(p)  * m
-            gru_deadcrootn_storage_to_atm(p)     = deadcrootn_storage(p)  * m
-
-            ! transfer pools
-            gru_leafn_xfer_to_atm(p)             = leafn_xfer(p)          * m
-            gru_frootn_xfer_to_atm(p)            = frootn_xfer(p)         * m
-            gru_livestemn_xfer_to_atm(p)         = livestemn_xfer(p)      * m
-            gru_deadstemn_xfer_to_atm(p)         = deadstemn_xfer(p)      * m
-            gru_livecrootn_xfer_to_atm(p)        = livecrootn_xfer(p)     * m
-            gru_deadcrootn_xfer_to_atm(p)        = deadcrootn_xfer(p)     * m
+               ! patch-level gross unrepresented landcover change mortality nitrogen fluxes
+               ! displayed pools
+               gru_leafn_to_litter(p)               = leafn(p)               * m
+               gru_frootn_to_litter(p)              = frootn(p)              * m
+               gru_livestemn_to_atm(p)              = livestemn(p)           * m
+               gru_deadstemn_to_atm(p)              = deadstemn(p)           * m * convfrac(ivt(p))
+               gru_wood_productn_gain(p)            = deadstemn(p)           * m * (1._r8 - convfrac(ivt(p)))
+               gru_livecrootn_to_litter(p)          = livecrootn(p)          * m
+               gru_deadcrootn_to_litter(p)          = deadcrootn(p)          * m
+               gru_retransn_to_litter(p)            = retransn(p)            * m
+
+               ! storage pools
+               gru_leafn_storage_to_atm(p)          = leafn_storage(p)       * m
+               gru_frootn_storage_to_atm(p)         = frootn_storage(p)      * m
+               gru_livestemn_storage_to_atm(p)      = livestemn_storage(p)   * m
+               gru_deadstemn_storage_to_atm(p)      = deadstemn_storage(p)   * m
+               gru_livecrootn_storage_to_atm(p)     = livecrootn_storage(p)  * m
+               gru_deadcrootn_storage_to_atm(p)     = deadcrootn_storage(p)  * m
+
+               ! transfer pools
+               gru_leafn_xfer_to_atm(p)             = leafn_xfer(p)          * m
+               gru_frootn_xfer_to_atm(p)            = frootn_xfer(p)         * m
+               gru_livestemn_xfer_to_atm(p)         = livestemn_xfer(p)      * m
+               gru_deadstemn_xfer_to_atm(p)         = deadstemn_xfer(p)      * m
+               gru_livecrootn_xfer_to_atm(p)        = livecrootn_xfer(p)     * m
+               gru_deadcrootn_xfer_to_atm(p)        = deadcrootn_xfer(p)     * m
+            else  ! matrixcn solution
+               ! patch-level gross unrepresented landcover change carbon fluxes
+               ! displayed pools
+               gru_leafc_to_litter(p) = matrix_update_gmc(p,ileaf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             leafc(p)
+               gru_frootc_to_litter(p) = matrix_update_gmc(p,ifroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             frootc(p)
+               gru_livestemc_to_atm(p) = matrix_update_gmc(p,ilivestem_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             livestemc(p)
+               gru_deadstemc_to_atm(p) = matrix_update_gmc(p,ideadstem_to_iout_gmc,m * convfrac(ivt(p)),dtime,cnveg_carbonflux_inst,.True.,.True.)  * &
+                                             deadstemc(p)
+               gru_wood_productc_gain(p) = matrix_update_gmc(p,ideadstem_to_iout_gmc,m * (1._r8 - convfrac(ivt(p))),dtime,cnveg_carbonflux_inst,.True.,.True.)  * &
+                                             deadstemc(p)
+               gru_livecrootc_to_litter(p) = matrix_update_gmc(p,ilivecroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             livecrootc(p)
+               gru_deadcrootc_to_litter(p) = matrix_update_gmc(p,ideadcroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             deadcrootc(p)
+               gru_xsmrpool_to_atm(p) = xsmrpool(p) * m
+
+               ! storage pools
+               gru_leafc_storage_to_atm(p) = matrix_update_gmc(p,ileafst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             leafc_storage(p)
+               gru_frootc_storage_to_atm(p) = matrix_update_gmc(p,ifrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             frootc_storage(p)
+               gru_livestemc_storage_to_atm(p) = matrix_update_gmc(p,ilivestemst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             livestemc_storage(p)
+               gru_deadstemc_storage_to_atm(p) = matrix_update_gmc(p,ideadstemst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             deadstemc_storage(p)
+               gru_livecrootc_storage_to_atm(p) = matrix_update_gmc(p,ilivecrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             livecrootc_storage(p)
+               gru_deadcrootc_storage_to_atm(p) = matrix_update_gmc(p,ideadcrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             deadcrootc_storage(p)
+               gru_gresp_storage_to_atm(p) = gresp_storage(p) * m
+
+               ! transfer pools
+               gru_leafc_xfer_to_atm(p) = matrix_update_gmc(p,ileafxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             leafc_xfer(p)
+               gru_frootc_xfer_to_atm(p) = matrix_update_gmc(p,ifrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             frootc_xfer(p)
+               gru_livestemc_xfer_to_atm(p) = matrix_update_gmc(p,ilivestemxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             livestemc_xfer(p)
+               gru_deadstemc_xfer_to_atm(p) = matrix_update_gmc(p,ideadstemxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             deadstemc_xfer(p)
+               gru_livecrootc_xfer_to_atm(p) = matrix_update_gmc(p,ilivecrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             livecrootc_xfer(p)
+               gru_deadcrootc_xfer_to_atm(p) = matrix_update_gmc(p,ideadcrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * &
+                                             deadcrootc_xfer(p)
+               gru_gresp_xfer_to_atm(p) = gresp_xfer(p) * m
+
+               ! patch-level gross unrepresented landcover change mortality nitrogen fluxes
+               ! displayed pools
+               gru_leafn_to_litter(p) = matrix_update_gmn(p,ileaf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             leafn(p)
+               gru_frootn_to_litter(p) = matrix_update_gmn(p,ifroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             frootn(p)
+               gru_livestemn_to_atm(p) = matrix_update_gmn(p,ilivestem_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             livestemn(p)
+               gru_deadstemn_to_atm(p) = matrix_update_gmn(p,ideadstem_to_iout_gmn,m * convfrac(ivt(p)),dtime,cnveg_nitrogenflux_inst,.True.,.True.)  * &
+                                             deadstemn(p)
+               gru_wood_productn_gain(p) = matrix_update_gmn(p,ideadstem_to_iout_gmn,m * (1._r8 - convfrac(ivt(p))),dtime,cnveg_nitrogenflux_inst,.True.,.True.)  * &
+                                             deadstemn(p)
+               gru_livecrootn_to_litter(p) = matrix_update_gmn(p,ilivecroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             livecrootn(p)
+               gru_deadcrootn_to_litter(p) = matrix_update_gmn(p,ideadcroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             deadcrootn(p)
+               gru_retransn_to_litter(p)   = matrix_update_gmn(p,iretransn_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             retransn(p)
+
+               ! storage pools
+               gru_leafn_storage_to_atm(p) = matrix_update_gmn(p,ileafst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             leafn_storage(p)
+               gru_frootn_storage_to_atm(p) = matrix_update_gmn(p,ifrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             frootn_storage(p)
+               gru_livestemn_storage_to_atm(p) = matrix_update_gmn(p,ilivestemst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             livestemn_storage(p)
+               gru_deadstemn_storage_to_atm(p) = matrix_update_gmn(p,ideadstemst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             deadstemn_storage(p)
+               gru_livecrootn_storage_to_atm(p) = matrix_update_gmn(p,ilivecrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)* &
+                                             livecrootn_storage(p)
+               gru_deadcrootn_storage_to_atm(p) = matrix_update_gmn(p,ideadcrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)* &
+                                             deadcrootn_storage(p)
+               ! transfer pools
+               gru_leafn_xfer_to_atm(p) = matrix_update_gmn(p,ileafxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             leafn_xfer(p)
+               gru_frootn_xfer_to_atm(p) = matrix_update_gmn(p,ifrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             frootn_xfer(p)
+               gru_livestemn_xfer_to_atm(p) = matrix_update_gmn(p,ilivestemxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             livestemn_xfer(p)
+               gru_deadstemn_xfer_to_atm(p) = matrix_update_gmn(p,ideadstemxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             deadstemn_xfer(p)
+               gru_livecrootn_xfer_to_atm(p) = matrix_update_gmn(p,ilivecrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             livecrootn_xfer(p)
+               gru_deadcrootn_xfer_to_atm(p) = matrix_update_gmn(p,ideadcrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
+                                             deadcrootn_xfer(p)
+            end if
 
          end if  ! end tree block
 
diff --git a/src/dyn_subgrid/dynHarvestMod.F90 b/src/dyn_subgrid/dynHarvestMod.F90
index b662d67d73..609ba6679b 100644
--- a/src/dyn_subgrid/dynHarvestMod.F90
+++ b/src/dyn_subgrid/dynHarvestMod.F90
@@ -434,9 +434,9 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                m = 0._r8
             end if
 
-            ! patch-level harvest carbon fluxes
-            ! displayed pools
             if(.not. use_matrixcn)then
+               ! patch-level harvest carbon fluxes
+               ! displayed pools
                hrv_leafc_to_litter(p)               = leafc(p)               * m
                hrv_frootc_to_litter(p)              = frootc(p)              * m
                hrv_livestemc_to_litter(p)           = livestemc(p)           * m
@@ -492,6 +492,8 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
             ! NOTE: The non-matrix part of this update is in CNCStatUpdate2 CStateUpdate2h (EBK 11/25/2019)
             !   and for Nitrogen The non-matrix part of this update is in CNNStatUpdate2 NStateUpdate2h (EBK 11/25/2019)
             else
+               ! patch-level harvest carbon fluxes
+               ! displayed pools
                hrv_leafc_to_litter(p)      = matrix_update_gmc(p,ileaf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.)      * &
                                              leafc(p)
                hrv_frootc_to_litter(p)     = matrix_update_gmc(p,ifroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.)     * &
@@ -506,7 +508,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                                              deadcrootc(p)
                hrv_xsmrpool_to_atm(p)      = xsmrpool(p)            * m
 
-         ! storage pools
+               ! storage pools
                hrv_leafc_storage_to_litter(p)      = matrix_update_gmc(p,ileafst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.)      * &
                                                      leafc_storage(p)
                hrv_frootc_storage_to_litter(p)     = matrix_update_gmc(p,ifrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.)     * &
@@ -521,8 +523,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                                                      deadcrootc_storage(p)
                hrv_gresp_storage_to_litter(p)      = gresp_storage(p)       * m
 
-
-         ! transfer pools
+               ! transfer pools
                hrv_leafc_xfer_to_litter(p)      = matrix_update_gmc(p,ileafxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.)      * &
                                                   leafc_xfer(p)
                hrv_frootc_xfer_to_litter(p)     = matrix_update_gmc(p,ifrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.)     * &
@@ -537,6 +538,8 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                                                   deadcrootc_xfer(p)
                hrv_gresp_xfer_to_litter(p)      = gresp_xfer(p)          * m
 
+               ! patch-level harvest mortality nitrogen fluxes
+               ! displayed pools
                hrv_leafn_to_litter(p)      = matrix_update_gmn(p,ileaf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)      * &
                                              leafn(p)
                hrv_frootn_to_litter(p)     = matrix_update_gmn(p,ifroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)     * &
@@ -552,7 +555,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                hrv_retransn_to_litter(p)   = matrix_update_gmn(p,iretransn_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
                                              retransn(p)
 
-         ! storage pools
+               ! storage pools
                hrv_leafn_storage_to_litter(p)      = matrix_update_gmn(p,ileafst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)     *&
                                                      leafn_storage(p)
                hrv_frootn_storage_to_litter(p)     = matrix_update_gmn(p,ifrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)    *&
@@ -565,7 +568,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                                                      livecrootn_storage(p)
                hrv_deadcrootn_storage_to_litter(p) = matrix_update_gmn(p,ideadcrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)*&
                                                      deadcrootn_storage(p)
-         ! transfer pools
+               ! transfer pools
                hrv_leafn_xfer_to_litter(p)      = matrix_update_gmn(p,ileafxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)      * &
                                                   leafn_xfer(p)
                hrv_frootn_xfer_to_litter(p)     = matrix_update_gmn(p,ifrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)     * &
@@ -578,9 +581,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                                                   livecrootn_xfer(p)
                hrv_deadcrootn_xfer_to_litter(p) = matrix_update_gmn(p,ideadcrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * &
                                                   deadcrootn_xfer(p)
-
             end if
-               
          end if  ! end tree block
       end do ! end of pft loop
 

From 57aa176ae3f28dbea9a9a20c3953fe4c6c1bae12 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 28 Dec 2023 15:55:12 -0700
Subject: [PATCH 0051/1248] Additional updates for matrixcn to work with GULU

---
 src/biogeochem/CNCStateUpdate2Mod.F90 |  5 +++-
 src/biogeochem/CNDriverMod.F90        | 12 +++++---
 src/biogeochem/CNNStateUpdate2Mod.F90 |  5 +++-
 src/biogeochem/dynGrossUnrepMod.F90   | 40 ++++++++++++++++++++++++++-
 4 files changed, 55 insertions(+), 7 deletions(-)

diff --git a/src/biogeochem/CNCStateUpdate2Mod.F90 b/src/biogeochem/CNCStateUpdate2Mod.F90
index 2890c7d1fd..c59d7d47f1 100644
--- a/src/biogeochem/CNCStateUpdate2Mod.F90
+++ b/src/biogeochem/CNCStateUpdate2Mod.F90
@@ -335,7 +335,8 @@ end subroutine CStateUpdate2h
 
   !-----------------------------------------------------------------------
   subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst)
+       cnveg_carbonflux_inst, cnveg_carbonstate_inst, &
+       soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst)
     !
     ! !DESCRIPTION:
     ! Update all the prognostic carbon state
@@ -348,6 +349,7 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
     integer                                , intent(in)    :: filter_soilp(:) ! filter for soil patches
     type(cnveg_carbonflux_type)            , intent(in)    :: cnveg_carbonflux_inst
     type(cnveg_carbonstate_type)           , intent(inout) :: cnveg_carbonstate_inst
+    type(soilbiogeochem_carbonflux_type)   , intent(inout) :: soilbiogeochem_carbonflux_inst
     type(soilbiogeochem_carbonstate_type)  , intent(inout) :: soilbiogeochem_carbonstate_inst
     !
     ! !LOCAL VARIABLES:
@@ -359,6 +361,7 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
     associate(                                     & 
          cf_veg => cnveg_carbonflux_inst         , &
          cs_veg => cnveg_carbonstate_inst        , &
+         cf_soil => soilbiogeochem_carbonflux_inst, &
          cs_soil => soilbiogeochem_carbonstate_inst &
          )
      
diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90
index 3d75ee51f0..d7eb964f1d 100644
--- a/src/biogeochem/CNDriverMod.F90
+++ b/src/biogeochem/CNDriverMod.F90
@@ -799,18 +799,22 @@ subroutine CNDriverNoLeaching(bounds,
     end if
 
     call CStateUpdate2g( num_soilc, filter_soilc,  num_soilp, filter_soilp, &
-         cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst)
+         cnveg_carbonflux_inst, cnveg_carbonstate_inst, &
+         soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst)
     if ( use_c13 ) then
        call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
-            c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst)
+            c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, &
+            c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst)
     end if
     if ( use_c14 ) then
        call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
-            c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst)
+            c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, &
+            c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst)
     end if
 
     call NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
-         cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst)
+         cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, &
+         soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
 
     call t_stopf('CNUpdate2')
 
diff --git a/src/biogeochem/CNNStateUpdate2Mod.F90 b/src/biogeochem/CNNStateUpdate2Mod.F90
index 2dbba68b82..4b6174195e 100644
--- a/src/biogeochem/CNNStateUpdate2Mod.F90
+++ b/src/biogeochem/CNNStateUpdate2Mod.F90
@@ -321,7 +321,8 @@ end subroutine NStateUpdate2h
 
   !-----------------------------------------------------------------------
   subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst)
+       cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, &
+       soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
     !
     ! !DESCRIPTION:
     ! Update all the prognostic nitrogen state
@@ -337,6 +338,7 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
     type(cnveg_nitrogenflux_type)           , intent(in)    :: cnveg_nitrogenflux_inst
     type(cnveg_nitrogenstate_type)          , intent(inout) :: cnveg_nitrogenstate_inst
     type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst
+    type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst
     !
     ! !LOCAL VARIABLES:
     integer :: c,p,j,l,i  ! indices
@@ -347,6 +349,7 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
     associate(                                 & 
          nf_veg  => cnveg_nitrogenflux_inst  , &
          ns_veg  => cnveg_nitrogenstate_inst , &
+         nf_soil => soilbiogeochem_nitrogenflux_inst, &
          ns_soil => soilbiogeochem_nitrogenstate_inst   &
          )
 
diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90
index b354744b61..0c9b1e2c53 100644
--- a/src/biogeochem/dynGrossUnrepMod.F90
+++ b/src/biogeochem/dynGrossUnrepMod.F90
@@ -158,6 +158,7 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, &
     use pftconMod       , only : noveg, nbrdlf_evr_shrub, nc4_grass
     use clm_varcon      , only : secspday
     use clm_time_manager, only : get_step_size_real, is_beg_curr_year
+    use CNVegMatrixMod  , only : matrix_update_gmc, matrix_update_gmn
     !
     ! !ARGUMENTS:
     integer                         , intent(in)    :: num_soilc       ! number of soil columns in filter
@@ -269,7 +270,44 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, &
          gru_livestemn_xfer_to_atm           =>    cnveg_nitrogenflux_inst%gru_livestemn_xfer_to_atm_patch        , & ! Output: [real(r8) (:)]                                                    
          gru_deadstemn_xfer_to_atm           =>    cnveg_nitrogenflux_inst%gru_deadstemn_xfer_to_atm_patch        , & ! Output: [real(r8) (:)]                                                    
          gru_livecrootn_xfer_to_atm          =>    cnveg_nitrogenflux_inst%gru_livecrootn_xfer_to_atm_patch       , & ! Output: [real(r8) (:)]                                                    
-         gru_deadcrootn_xfer_to_atm          =>    cnveg_nitrogenflux_inst%gru_deadcrootn_xfer_to_atm_patch         & ! Output: [real(r8) (:)]                                                    
+         gru_deadcrootn_xfer_to_atm          =>    cnveg_nitrogenflux_inst%gru_deadcrootn_xfer_to_atm_patch       , & ! Output: [real(r8) (:)]
+         ileaf_to_iout_gmc                   =>    cnveg_carbonflux_inst%ileaf_to_iout_gm                         , &
+         ileafst_to_iout_gmc                 =>    cnveg_carbonflux_inst%ileafst_to_iout_gm                       , &
+         ileafxf_to_iout_gmc                 =>    cnveg_carbonflux_inst%ileafxf_to_iout_gm                       , &
+         ifroot_to_iout_gmc                  =>    cnveg_carbonflux_inst%ifroot_to_iout_gm                        , &
+         ifrootst_to_iout_gmc                =>    cnveg_carbonflux_inst%ifrootst_to_iout_gm                      , &
+         ifrootxf_to_iout_gmc                =>    cnveg_carbonflux_inst%ifrootxf_to_iout_gm                      , &
+         ilivestem_to_iout_gmc               =>    cnveg_carbonflux_inst%ilivestem_to_iout_gm                     , &
+         ilivestemst_to_iout_gmc             =>    cnveg_carbonflux_inst%ilivestemst_to_iout_gm                   , &
+         ilivestemxf_to_iout_gmc             =>    cnveg_carbonflux_inst%ilivestemxf_to_iout_gm                   , &
+         ideadstem_to_iout_gmc               =>    cnveg_carbonflux_inst%ideadstem_to_iout_gm                     , &
+         ideadstemst_to_iout_gmc             =>    cnveg_carbonflux_inst%ideadstemst_to_iout_gm                   , &
+         ideadstemxf_to_iout_gmc             =>    cnveg_carbonflux_inst%ideadstemxf_to_iout_gm                   , &
+         ilivecroot_to_iout_gmc              =>    cnveg_carbonflux_inst%ilivecroot_to_iout_gm                    , &
+         ilivecrootst_to_iout_gmc            =>    cnveg_carbonflux_inst%ilivecrootst_to_iout_gm                  , &
+         ilivecrootxf_to_iout_gmc            =>    cnveg_carbonflux_inst%ilivecrootxf_to_iout_gm                  , &
+         ideadcroot_to_iout_gmc              =>    cnveg_carbonflux_inst%ideadcroot_to_iout_gm                    , &
+         ideadcrootst_to_iout_gmc            =>    cnveg_carbonflux_inst%ideadcrootst_to_iout_gm                  , &
+         ideadcrootxf_to_iout_gmc            =>    cnveg_carbonflux_inst%ideadcrootxf_to_iout_gm                  , &
+         ileaf_to_iout_gmn                   =>    cnveg_nitrogenflux_inst%ileaf_to_iout_gm                       , &
+         ileafst_to_iout_gmn                 =>    cnveg_nitrogenflux_inst%ileafst_to_iout_gm                     , &
+         ileafxf_to_iout_gmn                 =>    cnveg_nitrogenflux_inst%ileafxf_to_iout_gm                     , &
+         ifroot_to_iout_gmn                  =>    cnveg_nitrogenflux_inst%ifroot_to_iout_gm                      , &
+         ifrootst_to_iout_gmn                =>    cnveg_nitrogenflux_inst%ifrootst_to_iout_gm                    , &
+         ifrootxf_to_iout_gmn                =>    cnveg_nitrogenflux_inst%ifrootxf_to_iout_gm                    , &
+         ilivestem_to_iout_gmn               =>    cnveg_nitrogenflux_inst%ilivestem_to_iout_gm                   , &
+         ilivestemst_to_iout_gmn             =>    cnveg_nitrogenflux_inst%ilivestemst_to_iout_gm                 , &
+         ilivestemxf_to_iout_gmn             =>    cnveg_nitrogenflux_inst%ilivestemxf_to_iout_gm                 , &
+         ideadstem_to_iout_gmn               =>    cnveg_nitrogenflux_inst%ideadstem_to_iout_gm                   , &
+         ideadstemst_to_iout_gmn             =>    cnveg_nitrogenflux_inst%ideadstemst_to_iout_gm                 , &
+         ideadstemxf_to_iout_gmn             =>    cnveg_nitrogenflux_inst%ideadstemxf_to_iout_gm                 , &
+         ilivecroot_to_iout_gmn              =>    cnveg_nitrogenflux_inst%ilivecroot_to_iout_gm                  , &
+         ilivecrootst_to_iout_gmn            =>    cnveg_nitrogenflux_inst%ilivecrootst_to_iout_gm                , &
+         ilivecrootxf_to_iout_gmn            =>    cnveg_nitrogenflux_inst%ilivecrootxf_to_iout_gm                , &
+         ideadcroot_to_iout_gmn              =>    cnveg_nitrogenflux_inst%ideadcroot_to_iout_gm                  , &
+         ideadcrootst_to_iout_gmn            =>    cnveg_nitrogenflux_inst%ideadcrootst_to_iout_gm                , &
+         ideadcrootxf_to_iout_gmn            =>    cnveg_nitrogenflux_inst%ideadcrootxf_to_iout_gm                , &
+         iretransn_to_iout_gmn               =>    cnveg_nitrogenflux_inst%iretransn_to_iout_gm                     &
          )
 
       dtime = get_step_size_real()

From 1242be2f5b74d65729682322c4c8228a0b6e07aa Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 28 Dec 2023 20:44:17 -0700
Subject: [PATCH 0052/1248] Cheyenne GULU test now passes with these additional
 updates

---
 src/biogeochem/CNCStateUpdate2Mod.F90 | 18 ++++++++++--------
 src/biogeochem/CNGapMortalityMod.F90  |  5 -----
 src/biogeochem/dynGrossUnrepMod.F90   |  2 +-
 src/dyn_subgrid/dynHarvestMod.F90     |  5 -----
 4 files changed, 11 insertions(+), 19 deletions(-)

diff --git a/src/biogeochem/CNCStateUpdate2Mod.F90 b/src/biogeochem/CNCStateUpdate2Mod.F90
index c59d7d47f1..5fb7a283e9 100644
--- a/src/biogeochem/CNCStateUpdate2Mod.F90
+++ b/src/biogeochem/CNCStateUpdate2Mod.F90
@@ -401,6 +401,16 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
       do fp = 1,num_soilp
          p = filter_soilp(fp)
 
+         ! xsmrpool
+         cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) &
+              - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt
+         ! gresp storage pool
+         cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) &
+              - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt
+         ! gresp transfer pool
+         cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p) &
+              - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt
+
          ! patch-level carbon fluxes from gross unrepresented landcover change mortality
          !
          ! State update without the matrix solution
@@ -422,10 +432,6 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
             cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p)                 &
                  - cf_veg%gru_deadcrootc_to_litter_patch(p) * dt
 
-            ! xsmrpool
-            cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p)                     &
-                 - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt
-
             ! storage pools
             cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p)           &
                  - cf_veg%gru_leafc_storage_to_atm_patch(p) * dt
@@ -439,8 +445,6 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
                  - cf_veg%gru_livecrootc_storage_to_atm_patch(p) * dt
             cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) &
                  - cf_veg%gru_deadcrootc_storage_to_atm_patch(p) * dt
-            cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p)           &
-                 - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt
 
             ! transfer pools
             cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p)                 &
@@ -455,8 +459,6 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, &
                  - cf_veg%gru_livecrootc_xfer_to_atm_patch(p) * dt
             cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p)       &
                  - cf_veg%gru_deadcrootc_xfer_to_atm_patch(p) * dt
-            cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p)                 &
-                 - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt
 
          else
             ! NB (slevis) The matrix equivalent of the above is in
diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90
index e9013e03b1..c99660e3c6 100644
--- a/src/biogeochem/CNGapMortalityMod.F90
+++ b/src/biogeochem/CNGapMortalityMod.F90
@@ -24,11 +24,6 @@ module CNGapMortalityMod
   use PatchType                      , only : patch
   use GridcellType                   , only : grc
   use CNSharedParamsMod              , only : use_matrixcn
-  use clm_varpar                     , only : ileaf,ileaf_st,ileaf_xf,ifroot,ifroot_st,ifroot_xf,&
-                                              ilivestem,ilivestem_st,ilivestem_xf,&
-                                              ideadstem,ideadstem_st,ideadstem_xf,&
-                                              ilivecroot,ilivecroot_st,ilivecroot_xf,&
-                                              ideadcroot,ideadcroot_st,ideadcroot_xf,iretransn,ioutc,ioutn
   use CNVegMatrixMod                 , only : matrix_update_gmc, matrix_update_gmn
   !
   implicit none
diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90
index 0c9b1e2c53..1da39a0b64 100644
--- a/src/biogeochem/dynGrossUnrepMod.F90
+++ b/src/biogeochem/dynGrossUnrepMod.F90
@@ -364,7 +364,7 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, &
                gru_livecrootc_xfer_to_atm(p)        = livecrootc_xfer(p)     * m
                gru_deadcrootc_xfer_to_atm(p)        = deadcrootc_xfer(p)     * m
                gru_gresp_xfer_to_atm(p)             = gresp_xfer(p)          * m
-	    
+
                ! patch-level gross unrepresented landcover change mortality nitrogen fluxes
                ! displayed pools
                gru_leafn_to_litter(p)               = leafn(p)               * m
diff --git a/src/dyn_subgrid/dynHarvestMod.F90 b/src/dyn_subgrid/dynHarvestMod.F90
index 609ba6679b..2936a41545 100644
--- a/src/dyn_subgrid/dynHarvestMod.F90
+++ b/src/dyn_subgrid/dynHarvestMod.F90
@@ -25,11 +25,6 @@ module dynHarvestMod
   use PatchType               , only : patch                
   use CNSharedParamsMod       , only : use_matrixcn
   use clm_varctl              , only : use_fates
-  use clm_varpar              , only : ileaf,ileaf_st,ileaf_xf,ifroot,ifroot_st,ifroot_xf,&
-                                       ilivestem,ilivestem_st,ilivestem_xf,&
-                                       ideadstem,ideadstem_st,ideadstem_xf,&
-                                       ilivecroot,ilivecroot_st,ilivecroot_xf,&
-                                       ideadcroot,ideadcroot_st,ideadcroot_xf,ioutc,ioutn 
   !
   ! !PUBLIC MEMBER FUNCTIONS:
   implicit none

From 46cbf4b3e67b1b55260b6b5b6d57778c1cc54db7 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Fri, 29 Dec 2023 16:04:20 -0700
Subject: [PATCH 0053/1248] Remove PS from SMS_Ld3_PS test for it to work with
 matrixcn

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index e1f26f0703..3551d34b1a 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -536,7 +536,7 @@
       <option name="comment"  >Transient case with isotopes with a December start</option>
     </options>
   </test>
-  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
+  <test name="SMS_Ld3" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>

From 2287bb6b7b4fdb66a97dc462d37173b72a46ec73 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Fri, 29 Dec 2023 19:04:24 -0700
Subject: [PATCH 0054/1248] Corrections for model to build and a test to pass

Used this one for testing:
SMS_D.1x1_brazil.I1850Clm51BgcCrop.cheyenne_gnu.clm-mimics_matrixcn
---
 src/biogeochem/CNCStateUpdate1Mod.F90         | 61 ++++---------------
 src/biogeochem/CNDriverMod.F90                |  8 +--
 .../SoilBiogeochemNitrogenStateType.F90       |  1 +
 3 files changed, 17 insertions(+), 53 deletions(-)

diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90
index c342e36a22..e839136e11 100644
--- a/src/biogeochem/CNCStateUpdate1Mod.F90
+++ b/src/biogeochem/CNCStateUpdate1Mod.F90
@@ -215,6 +215,18 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                   ! terms have been moved to CStateUpdateDynPatch. I think this is zeroed every
                   ! time step, but to be safe, I'm explicitly setting it to zero here.
                   cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8
+
+                  ! litter and SOM HR fluxes
+                  do k = 1, ndecomp_cascade_transitions
+                     cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
+                          cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
+                          - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) * dt
+                     if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
+                        cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
+                             cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
+                             + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k) * dt
+                     end if
+                  end do
                else
                   !
                   ! For the matrix solution the actual state update comes after the matrix
@@ -233,55 +245,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
          end if fates_if
             
       end do fc_loop
-         
-
-      ! litter and SOM HR fluxes
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               !
-               ! State update without the matrix solution
-               !
-               if (.not. use_soil_matrixcn) then
-                  cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
-                       cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
-                       - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt
-               end if !not use_soil_matrixcn 
-            end do
-         end do
-      end do
-      do k = 1, ndecomp_cascade_transitions
-         if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
-            do j = 1,nlevdecomp
-               do fc = 1,num_soilc
-                  c = filter_soilc(fc)
-                  if (.not. use_soil_matrixcn) then
-                     cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
-                          cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
-                          - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt
-                  end if !not use_soil_matrixcn 
-               end do
-            end do
-         end do
-         do k = 1, ndecomp_cascade_transitions
-            if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
-               do j = 1,nlevdecomp
-                  do fc = 1,num_soilc
-                     c = filter_soilc(fc)
-                     !
-                     ! State update without the matrix solution
-                     !
-                     if (.not. use_soil_matrixcn) then
-                        cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
-                             cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
-                             + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt
-                     end if !not use_soil_matrixcn
-                  end do
-               end do
-            end do
-         end if
-      end do
 
       soilpatch_loop: do fp = 1,num_soilp
          p = filter_soilp(fp)
diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90
index be341477a5..67eaba1013 100644
--- a/src/biogeochem/CNDriverMod.F90
+++ b/src/biogeochem/CNDriverMod.F90
@@ -1097,10 +1097,10 @@ subroutine CNDriverLeaching(bounds, &
 
     if ( use_matrixcn ) then
        call t_startf('CNVMatrix')
-       call CNVegMatrix(bounds,num_bgc_soilp,filter_bgc_soilp(1:num_bgc_soilp),num_actfirep,filter_actfirep,cnveg_carbonstate_inst,cnveg_nitrogenstate_inst,&
-                         cnveg_carbonflux_inst,  cnveg_nitrogenflux_inst,cnveg_state_inst,soilbiogeochem_nitrogenflux_inst,&
-                         c13_cnveg_carbonstate_inst,c14_cnveg_carbonstate_inst,c13_cnveg_carbonflux_inst,&
-                         c14_cnveg_carbonflux_inst)
+       call CNVegMatrix(bounds, num_bgc_vegp, filter_bgc_vegp(1:num_bgc_vegp), &
+          num_actfirep, filter_actfirep, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, &
+          cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, cnveg_state_inst,soilbiogeochem_nitrogenflux_inst, &
+          c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst)
        call t_stopf('CNVMatrix')
     end if
 
diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
index e97ed3e6eb..a0cbc81a9e 100644
--- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
+++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
@@ -15,6 +15,7 @@ module SoilBiogeochemNitrogenStateType
   use clm_varctl                         , only : iulog, override_bgc_restart_mismatch_dump, spinup_state
   use landunit_varcon                    , only : istcrop, istsoil 
   use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn
+  use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, century_decomp, decomp_method
   use LandunitType                       , only : lun                
   use ColumnType                         , only : col                
   use GridcellType                       , only : grc

From 107f854c89a237b2d1d99ad36b78ce2ef2ad2544 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Sat, 30 Dec 2023 21:42:36 -0700
Subject: [PATCH 0055/1248] Fix for FatesCold simulations to pass

---
 src/biogeochem/CNCStateUpdate1Mod.F90 | 30 +++++++++++++++++----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90
index e839136e11..4eb52d9c10 100644
--- a/src/biogeochem/CNCStateUpdate1Mod.F90
+++ b/src/biogeochem/CNCStateUpdate1Mod.F90
@@ -216,17 +216,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                   ! time step, but to be safe, I'm explicitly setting it to zero here.
                   cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8
 
-                  ! litter and SOM HR fluxes
-                  do k = 1, ndecomp_cascade_transitions
-                     cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
-                          cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
-                          - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) * dt
-                     if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
-                        cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
-                             cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
-                             + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k) * dt
-                     end if
-                  end do
                else
                   !
                   ! For the matrix solution the actual state update comes after the matrix
@@ -243,6 +232,25 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
             end do
 
          end if fates_if
+
+         do j = 1,nlevdecomp
+            !
+            ! State update without the matrix solution
+            !
+            if (.not. use_soil_matrixcn) then
+               ! litter and SOM HR fluxes
+               do k = 1, ndecomp_cascade_transitions
+                  cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
+                       cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
+                       - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) * dt
+                  if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
+                     cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
+                          cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
+                          + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k) * dt
+                  end if
+               end do
+            end if
+         end do
             
       end do fc_loop
 

From 3af4aedfbb8bc7a8b0076184197141c463e6c8fd Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 2 Jan 2024 18:39:00 -0700
Subject: [PATCH 0056/1248] Corrections from comparing model versions

---
 src/biogeochem/CNPhenologyMod.F90 | 40 +++++++++----------------------
 1 file changed, 11 insertions(+), 29 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index e1b7b2edb6..2d9ab51473 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -3506,17 +3506,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                t1 = 1.0_r8 / dt
                frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p)
 
-               ! TODO slevis: This line didn't appear in dev159. Remove?
-               ! biofuel_harvfrac is only non-zero for prognostic crops.
-               leafc_to_litter(p)  = t1 * leafc(p) * (1._r8 - biofuel_harvfrac(ivt(p))) + cpool_to_leafc(p)
-
-               ! leafc_litter and frootc_to_litter for matrix
+               ! frootc_to_litter for matrix
                if (use_matrixcn) then
-                  if(leafc(p) .gt. 0)then
-                     leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
-                  else
-                     leafc_to_litter(p) = 0
-                  end if
                   if(frootc(p) .gt. 0)then
                      frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
@@ -3618,6 +3609,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                   ! as well as leaf C:N ratio (unaffected by biofuel harvest). It thus does not
                   ! need to be updated here.
 
+                  ! Matrix for grain, livestem to litter, leaf to litter, and biofuel
                   if(use_matrixcn)then
                      if(reproductivec(p,1) .gt. 0)then
                         grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
@@ -3633,13 +3625,17 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                      end if
                      if(livestemc(p) .gt. 0)then
                         livestemc_to_litter(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_iout_phc,livestemc_to_litter(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
+                        livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
                      else
                         livestemc_to_litter(p) = 0
+                        livestemc_to_biofuelc(p) = 0
                      end if
                      if(livestemn(p) .gt. 0)then
                         livestemn_to_biofueln(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_biofueln(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
+                        livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                      else
                         livestemn_to_biofueln(p) = 0
+                        livestemn_to_litter(p) = 0
                      end if
                      if(leafn(p) > 0)then
                         leafn_to_biofueln(p) =  leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_biofueln(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
@@ -3647,14 +3643,11 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                         leafn_to_biofueln(p) = 0
                      end if
                      if (leafc(p) > 0)then
-                       leafc_to_biofuelc(p) =  leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
-                     else
-                       leafc_to_biofuelc(p) = 0
-                     end if
-                     if(livestemc(p) .gt. 0)then
-                        livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
+                        leafc_to_biofuelc(p) =  leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
+                        leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        livestemc_to_biofuelc(p) = 0
+                        leafc_to_biofuelc(p) = 0
+                        leafc_to_litter(p) = 0
                      end if
                   else
                      ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
@@ -3675,7 +3668,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                   if(frootc(p) .gt. 0)then
                      frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                   else
-                     frootc_to_litter(p) = 0
+                     frootc_to_litter(p) = 0  ! TODO slevis here and elsewhere
                   end if
                else
                   ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)
@@ -3824,17 +3817,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                endif    
             end if
 
-            ! TODO slevis: This paragraph didn't appear in dev159. Remove?
-            if (ivt(p) >= npcropmin) then
-               ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn
-               !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p))
-               ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead
-               livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p)))
-               if(use_matrixcn)then
-                  livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
-               end if
-            end if
-
             ! save the current litterfall fluxes
             prev_leafc_to_litter(p)  = leafc_to_litter(p)
             prev_frootc_to_litter(p) = frootc_to_litter(p)

From 2ea1cecedd3a00cd98d962f9de1eaac2159ace05 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 2 Jan 2024 18:46:58 -0700
Subject: [PATCH 0057/1248] Corrections to lists of tests and expected failures

---
 cime_config/testdefs/ExpectedTestFails.xml |  4 ++--
 cime_config/testdefs/testlist_clm.xml      | 18 +++++++++---------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 6be036c485..b0f7fa860b 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -50,13 +50,13 @@
       <issue>#1733</issue>
     </phase>
   </test>
-  <test name="LGRAIN2_Ly1_P72x1.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
+  <test name="LGRAIN2_Ly1_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
     </phase>
   </test>
-  <test name="LREPRSTRUCT_Ly1_P72x1.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput">
+  <test name="LREPRSTRUCT_Ly1_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 114e3781a0..5ec791b7d4 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -373,7 +373,7 @@
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
   <test name="ERS_Ld3" grid="f10_f10_mg37" compset="I2000Clm51Bgc" testmods="clm/ciso_cwd_hr">
@@ -632,7 +632,7 @@
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/vrtlay">
@@ -641,7 +641,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50SpCru" testmods="clm/drydepnomegan">
@@ -729,7 +729,7 @@
       <option name="comment"  >Transient case with isotopes with a December start, without Meier roughness</option>
     </options>
   </test>
-  <test name="SMS_Ld3" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -808,7 +808,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Test MIMICS with CN matrix on (but soil matrixcn off)</option>
+      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015' with CN matrix on but soil matrixcn off</option>
     </options>
   </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/mimics">
@@ -1005,7 +1005,7 @@
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
   <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/decStart">
@@ -1014,7 +1014,7 @@
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso">
@@ -2383,7 +2383,7 @@
       <option name="comment"  >include a production gnu test of Clm45</option>
     </options>
   </test>
-  <test name="SMS_Ld2_D" grid="f09_g17" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic_interp">
+  <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic_interp">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -2603,7 +2603,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:20:00</option>
       <option name="comment"  >Want one fates test on a large grid: Since FATES has cohorts, it has potential to be a massive memory consumer and netcdf array size maker, so the large grid test will help smoke out these types of issues (and it's a restart test to cover possible memory/netcdf size issues with the restart file).</option>
     </options>
   </test>

From 9208fde389712a1fc08a8f73760a781f2ff1cd02 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Jan 2024 00:46:45 -0700
Subject: [PATCH 0058/1248] Update CAM and CICE6 to cesm2_3_beta16 versions

---
 Externals.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index ff0e28f4cd..d75b4683a6 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -41,7 +41,7 @@ local_path = components/cice5
 required = True
 
 [cice6]
-tag = cesm_cice6_2_0_22
+tag = cesm_cice6_4_1_10
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CICE
 local_path = components/cice
@@ -49,7 +49,7 @@ externals = Externals.cfg
 required = True
 
 [cam6]
-tag = cam6_3_058
+tag = cam6_3_133
 protocol = git
 repo_url = https://github.com/ESCOMP/CAM
 local_path = components/cam

From 896713bc0971108231cafb8dc0d392fce5e8131c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Jan 2024 00:47:04 -0700
Subject: [PATCH 0059/1248] Squashed 'manage_externals/' changes from
 7b6d92ef6..0f884bfec

0f884bfec Merge pull request #205 from jedwards4b/sunset_svn_git_access
82a5edf79 merge in billsacks:svn_testing_no_github
17532c160 Use a local svn repo for testing
9c904341a different method to determine if in tests
539952ebd remove debug print statement
cc5434fa7 fix submodule testing
1d7f28840 remove broken tests
04e94a519 provide a meaningful error message
38bcc0a8c Merge pull request #201 from jedwards4b/partial_match
b4466a5aa remove debug print statement
c3cf3ec35 fix issue with partial branch match

git-subtree-dir: manage_externals
git-subtree-split: 0f884bfec8e43d0c02261de858d6ec3f6d855e51
---
 manic/repository_git.py                       |  18 +-
 manic/repository_svn.py                       |   3 +
 test/repos/README.md                          |   4 +-
 test/repos/simple-ext.svn/README.txt          |   5 +
 test/repos/simple-ext.svn/conf/authz          |  32 +++
 test/repos/simple-ext.svn/conf/hooks-env.tmpl |  19 ++
 test/repos/simple-ext.svn/conf/passwd         |   8 +
 test/repos/simple-ext.svn/conf/svnserve.conf  |  81 +++++++
 test/repos/simple-ext.svn/db/current          |   1 +
 test/repos/simple-ext.svn/db/format           |   3 +
 test/repos/simple-ext.svn/db/fs-type          |   1 +
 test/repos/simple-ext.svn/db/fsfs.conf        | 200 ++++++++++++++++++
 test/repos/simple-ext.svn/db/min-unpacked-rev |   1 +
 test/repos/simple-ext.svn/db/rep-cache.db     | Bin 0 -> 8192 bytes
 .../simple-ext.svn/db/rep-cache.db-journal    |   0
 test/repos/simple-ext.svn/db/revprops/0/0     |   5 +
 test/repos/simple-ext.svn/db/revprops/0/1     |  13 ++
 test/repos/simple-ext.svn/db/revprops/0/2     |  13 ++
 test/repos/simple-ext.svn/db/revprops/0/3     |  13 ++
 test/repos/simple-ext.svn/db/revs/0/0         | Bin 0 -> 253 bytes
 test/repos/simple-ext.svn/db/revs/0/1         | Bin 0 -> 725 bytes
 test/repos/simple-ext.svn/db/revs/0/2         | Bin 0 -> 816 bytes
 test/repos/simple-ext.svn/db/revs/0/3         | Bin 0 -> 769 bytes
 test/repos/simple-ext.svn/db/txn-current      |   1 +
 test/repos/simple-ext.svn/db/txn-current-lock |   0
 test/repos/simple-ext.svn/db/uuid             |   2 +
 test/repos/simple-ext.svn/db/write-lock       |   0
 test/repos/simple-ext.svn/format              |   1 +
 .../simple-ext.svn/hooks/post-commit.tmpl     |  62 ++++++
 .../repos/simple-ext.svn/hooks/post-lock.tmpl |  64 ++++++
 .../hooks/post-revprop-change.tmpl            |  69 ++++++
 .../simple-ext.svn/hooks/post-unlock.tmpl     |  61 ++++++
 .../simple-ext.svn/hooks/pre-commit.tmpl      |  91 ++++++++
 test/repos/simple-ext.svn/hooks/pre-lock.tmpl |  95 +++++++++
 .../hooks/pre-revprop-change.tmpl             |  79 +++++++
 .../simple-ext.svn/hooks/pre-unlock.tmpl      |  87 ++++++++
 .../simple-ext.svn/hooks/start-commit.tmpl    |  81 +++++++
 test/repos/simple-ext.svn/locks/db-logs.lock  |   3 +
 test/repos/simple-ext.svn/locks/db.lock       |   3 +
 test/test_sys_checkout.py                     |  51 ++---
 40 files changed, 1126 insertions(+), 44 deletions(-)
 create mode 100644 test/repos/simple-ext.svn/README.txt
 create mode 100644 test/repos/simple-ext.svn/conf/authz
 create mode 100644 test/repos/simple-ext.svn/conf/hooks-env.tmpl
 create mode 100644 test/repos/simple-ext.svn/conf/passwd
 create mode 100644 test/repos/simple-ext.svn/conf/svnserve.conf
 create mode 100644 test/repos/simple-ext.svn/db/current
 create mode 100644 test/repos/simple-ext.svn/db/format
 create mode 100644 test/repos/simple-ext.svn/db/fs-type
 create mode 100644 test/repos/simple-ext.svn/db/fsfs.conf
 create mode 100644 test/repos/simple-ext.svn/db/min-unpacked-rev
 create mode 100644 test/repos/simple-ext.svn/db/rep-cache.db
 create mode 100644 test/repos/simple-ext.svn/db/rep-cache.db-journal
 create mode 100644 test/repos/simple-ext.svn/db/revprops/0/0
 create mode 100644 test/repos/simple-ext.svn/db/revprops/0/1
 create mode 100644 test/repos/simple-ext.svn/db/revprops/0/2
 create mode 100644 test/repos/simple-ext.svn/db/revprops/0/3
 create mode 100644 test/repos/simple-ext.svn/db/revs/0/0
 create mode 100644 test/repos/simple-ext.svn/db/revs/0/1
 create mode 100644 test/repos/simple-ext.svn/db/revs/0/2
 create mode 100644 test/repos/simple-ext.svn/db/revs/0/3
 create mode 100644 test/repos/simple-ext.svn/db/txn-current
 create mode 100644 test/repos/simple-ext.svn/db/txn-current-lock
 create mode 100644 test/repos/simple-ext.svn/db/uuid
 create mode 100644 test/repos/simple-ext.svn/db/write-lock
 create mode 100644 test/repos/simple-ext.svn/format
 create mode 100755 test/repos/simple-ext.svn/hooks/post-commit.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/post-lock.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/post-revprop-change.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/post-unlock.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/pre-commit.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/pre-lock.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/pre-unlock.tmpl
 create mode 100755 test/repos/simple-ext.svn/hooks/start-commit.tmpl
 create mode 100644 test/repos/simple-ext.svn/locks/db-logs.lock
 create mode 100644 test/repos/simple-ext.svn/locks/db.lock
 mode change 100644 => 100755 test/test_sys_checkout.py

diff --git a/manic/repository_git.py b/manic/repository_git.py
index adc666cc57..aab1a468a8 100644
--- a/manic/repository_git.py
+++ b/manic/repository_git.py
@@ -7,6 +7,7 @@
 
 import copy
 import os
+import sys
 
 from .global_constants import EMPTY_STR, LOCAL_PATH_INDICATOR
 from .global_constants import VERBOSITY_VERBOSE
@@ -380,7 +381,6 @@ def _check_for_valid_ref(self, ref, remote_name, dirname):
         is_tag = self._ref_is_tag(ref, dirname)
         is_branch = self._ref_is_branch(ref, remote_name, dirname)
         is_hash = self._ref_is_hash(ref, dirname)
-
         is_valid = is_tag or is_branch or is_hash
         if not is_valid:
             msg = ('In repo "{0}": reference "{1}" does not appear to be a '
@@ -710,7 +710,10 @@ def _git_lsremote_branch(ref, remote_name, dirname):
         cmd = ('git -C {dirname} ls-remote --exit-code --heads '
                '{remote_name} {ref}').format(
                    dirname=dirname, remote_name=remote_name, ref=ref).split()
-        status = execute_subprocess(cmd, status_to_caller=True)
+        status, output = execute_subprocess(cmd, status_to_caller=True, output_to_caller=True)
+        if not status and not f"refs/heads/{ref}" in output:
+            # In this case the ref is contained in the branch name but is not the complete branch name
+            return -1
         return status
 
     @staticmethod
@@ -837,12 +840,19 @@ def _git_update_submodules(verbosity, dirname):
         """Run git submodule update for the side effect of updating this
         repo's submodules.
         """
+        # due to https://vielmetti.typepad.com/logbook/2022/10/git-security-fixes-lead-to-fatal-transport-file-not-allowed-error-in-ci-systems-cve-2022-39253.html
+        # submodules from file doesn't work without overriding the protocol, this is done
+        # for testing submodule support but should not be done in practice
+        file_protocol = ""
+        if 'unittest' in sys.modules.keys():
+            file_protocol = "-c protocol.file.allow=always"
+
         # First, verify that we have a .gitmodules file
         if os.path.exists(
                 os.path.join(dirname,
                              ExternalsDescription.GIT_SUBMODULES_FILENAME)):
-            cmd = ('git -C {dirname} submodule update --init --recursive'
-                   .format(dirname=dirname)).split()
+            cmd = ('git {file_protocol} -C {dirname} submodule update --init --recursive'
+                   .format(file_protocol=file_protocol, dirname=dirname)).split()
             if verbosity >= VERBOSITY_VERBOSE:
                 printlog('    {0}'.format(' '.join(cmd)))
 
diff --git a/manic/repository_svn.py b/manic/repository_svn.py
index 922855d34e..32a71184b4 100644
--- a/manic/repository_svn.py
+++ b/manic/repository_svn.py
@@ -42,6 +42,9 @@ def __init__(self, component_name, repo, ignore_ancestry=False):
         Parse repo (a <repo> XML element).
         """
         Repository.__init__(self, component_name, repo)
+        if 'github.com' in self._url:
+            msg = "SVN access to github.com is no longer supported"
+            fatal_error(msg)
         self._ignore_ancestry = ignore_ancestry
         if self._url.endswith('/'):
             # there is already a '/' separator in the URL; no need to add another
diff --git a/test/repos/README.md b/test/repos/README.md
index 8a3502c35f..026b684ea3 100644
--- a/test/repos/README.md
+++ b/test/repos/README.md
@@ -1,6 +1,6 @@
-Git repositories for testing git-related behavior.  For usage and terminology notes, see test/test_sys_checkout.py.
+Git and svn repositories for testing git and svn-related behavior.  For usage and terminology notes, see test/test_sys_checkout.py.
 
-To list files and view file contents at HEAD:
+For git repos: To list files and view file contents at HEAD:
 ```
 cd <repo_dir>
 git ls-tree --full-tree -r --name-only HEAD
diff --git a/test/repos/simple-ext.svn/README.txt b/test/repos/simple-ext.svn/README.txt
new file mode 100644
index 0000000000..9935818a1b
--- /dev/null
+++ b/test/repos/simple-ext.svn/README.txt
@@ -0,0 +1,5 @@
+This is a Subversion repository; use the 'svnadmin' and 'svnlook' 
+tools to examine it.  Do not add, delete, or modify files here 
+unless you know how to avoid corrupting the repository.
+
+Visit http://subversion.apache.org/ for more information.
diff --git a/test/repos/simple-ext.svn/conf/authz b/test/repos/simple-ext.svn/conf/authz
new file mode 100644
index 0000000000..0b9a41074e
--- /dev/null
+++ b/test/repos/simple-ext.svn/conf/authz
@@ -0,0 +1,32 @@
+### This file is an example authorization file for svnserve.
+### Its format is identical to that of mod_authz_svn authorization
+### files.
+### As shown below each section defines authorizations for the path and
+### (optional) repository specified by the section name.
+### The authorizations follow. An authorization line can refer to:
+###  - a single user,
+###  - a group of users defined in a special [groups] section,
+###  - an alias defined in a special [aliases] section,
+###  - all authenticated users, using the '$authenticated' token,
+###  - only anonymous users, using the '$anonymous' token,
+###  - anyone, using the '*' wildcard.
+###
+### A match can be inverted by prefixing the rule with '~'. Rules can
+### grant read ('r') access, read-write ('rw') access, or no access
+### ('').
+
+[aliases]
+# joe = /C=XZ/ST=Dessert/L=Snake City/O=Snake Oil, Ltd./OU=Research Institute/CN=Joe Average
+
+[groups]
+# harry_and_sally = harry,sally
+# harry_sally_and_joe = harry,sally,&joe
+
+# [/foo/bar]
+# harry = rw
+# &joe = r
+# * =
+
+# [repository:/baz/fuz]
+# @harry_and_sally = rw
+# * = r
diff --git a/test/repos/simple-ext.svn/conf/hooks-env.tmpl b/test/repos/simple-ext.svn/conf/hooks-env.tmpl
new file mode 100644
index 0000000000..ee965c316c
--- /dev/null
+++ b/test/repos/simple-ext.svn/conf/hooks-env.tmpl
@@ -0,0 +1,19 @@
+### This file is an example hook script environment configuration file.
+### Hook scripts run in an empty environment by default.
+### As shown below each section defines environment variables for a
+### particular hook script. The [default] section defines environment
+### variables for all hook scripts, unless overridden by a hook-specific
+### section.
+
+### This example configures a UTF-8 locale for all hook scripts, so that 
+### special characters, such as umlauts, may be printed to stderr.
+### If UTF-8 is used with a mod_dav_svn server, the SVNUseUTF8 option must
+### also be set to 'yes' in httpd.conf.
+### With svnserve, the LANG environment variable of the svnserve process
+### must be set to the same value as given here.
+[default]
+LANG = en_US.UTF-8
+
+### This sets the PATH environment variable for the pre-commit hook.
+[pre-commit]
+PATH = /usr/local/bin:/usr/bin:/usr/sbin
diff --git a/test/repos/simple-ext.svn/conf/passwd b/test/repos/simple-ext.svn/conf/passwd
new file mode 100644
index 0000000000..ecaa08dcec
--- /dev/null
+++ b/test/repos/simple-ext.svn/conf/passwd
@@ -0,0 +1,8 @@
+### This file is an example password file for svnserve.
+### Its format is similar to that of svnserve.conf. As shown in the
+### example below it contains one section labelled [users].
+### The name and password for each user follow, one account per line.
+
+[users]
+# harry = harryssecret
+# sally = sallyssecret
diff --git a/test/repos/simple-ext.svn/conf/svnserve.conf b/test/repos/simple-ext.svn/conf/svnserve.conf
new file mode 100644
index 0000000000..6cefc17b3e
--- /dev/null
+++ b/test/repos/simple-ext.svn/conf/svnserve.conf
@@ -0,0 +1,81 @@
+### This file controls the configuration of the svnserve daemon, if you
+### use it to allow access to this repository.  (If you only allow
+### access through http: and/or file: URLs, then this file is
+### irrelevant.)
+
+### Visit http://subversion.apache.org/ for more information.
+
+[general]
+### The anon-access and auth-access options control access to the
+### repository for unauthenticated (a.k.a. anonymous) users and
+### authenticated users, respectively.
+### Valid values are "write", "read", and "none".
+### Setting the value to "none" prohibits both reading and writing;
+### "read" allows read-only access, and "write" allows complete 
+### read/write access to the repository.
+### The sample settings below are the defaults and specify that anonymous
+### users have read-only access to the repository, while authenticated
+### users have read and write access to the repository.
+# anon-access = read
+# auth-access = write
+### The password-db option controls the location of the password
+### database file.  Unless you specify a path starting with a /,
+### the file's location is relative to the directory containing
+### this configuration file.
+### If SASL is enabled (see below), this file will NOT be used.
+### Uncomment the line below to use the default password file.
+# password-db = passwd
+### The authz-db option controls the location of the authorization
+### rules for path-based access control.  Unless you specify a path
+### starting with a /, the file's location is relative to the
+### directory containing this file.  The specified path may be a
+### repository relative URL (^/) or an absolute file:// URL to a text
+### file in a Subversion repository.  If you don't specify an authz-db,
+### no path-based access control is done.
+### Uncomment the line below to use the default authorization file.
+# authz-db = authz
+### The groups-db option controls the location of the file with the
+### group definitions and allows maintaining groups separately from the
+### authorization rules.  The groups-db file is of the same format as the
+### authz-db file and should contain a single [groups] section with the
+### group definitions.  If the option is enabled, the authz-db file cannot
+### contain a [groups] section.  Unless you specify a path starting with
+### a /, the file's location is relative to the directory containing this
+### file.  The specified path may be a repository relative URL (^/) or an
+### absolute file:// URL to a text file in a Subversion repository.
+### This option is not being used by default.
+# groups-db = groups
+### This option specifies the authentication realm of the repository.
+### If two repositories have the same authentication realm, they should
+### have the same password database, and vice versa.  The default realm
+### is repository's uuid.
+# realm = My First Repository
+### The force-username-case option causes svnserve to case-normalize
+### usernames before comparing them against the authorization rules in the
+### authz-db file configured above.  Valid values are "upper" (to upper-
+### case the usernames), "lower" (to lowercase the usernames), and
+### "none" (to compare usernames as-is without case conversion, which
+### is the default behavior).
+# force-username-case = none
+### The hooks-env options specifies a path to the hook script environment 
+### configuration file. This option overrides the per-repository default
+### and can be used to configure the hook script environment for multiple 
+### repositories in a single file, if an absolute path is specified.
+### Unless you specify an absolute path, the file's location is relative
+### to the directory containing this file.
+# hooks-env = hooks-env
+
+[sasl]
+### This option specifies whether you want to use the Cyrus SASL
+### library for authentication. Default is false.
+### Enabling this option requires svnserve to have been built with Cyrus
+### SASL support; to check, run 'svnserve --version' and look for a line
+### reading 'Cyrus SASL authentication is available.'
+# use-sasl = true
+### These options specify the desired strength of the security layer
+### that you want SASL to provide. 0 means no encryption, 1 means
+### integrity-checking only, values larger than 1 are correlated
+### to the effective key length for encryption (e.g. 128 means 128-bit
+### encryption). The values below are the defaults.
+# min-encryption = 0
+# max-encryption = 256
diff --git a/test/repos/simple-ext.svn/db/current b/test/repos/simple-ext.svn/db/current
new file mode 100644
index 0000000000..00750edc07
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/current
@@ -0,0 +1 @@
+3
diff --git a/test/repos/simple-ext.svn/db/format b/test/repos/simple-ext.svn/db/format
new file mode 100644
index 0000000000..5dd0c22198
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/format
@@ -0,0 +1,3 @@
+8
+layout sharded 1000
+addressing logical
diff --git a/test/repos/simple-ext.svn/db/fs-type b/test/repos/simple-ext.svn/db/fs-type
new file mode 100644
index 0000000000..4fdd95313f
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/fs-type
@@ -0,0 +1 @@
+fsfs
diff --git a/test/repos/simple-ext.svn/db/fsfs.conf b/test/repos/simple-ext.svn/db/fsfs.conf
new file mode 100644
index 0000000000..ac6877a727
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/fsfs.conf
@@ -0,0 +1,200 @@
+### This file controls the configuration of the FSFS filesystem.
+
+[memcached-servers]
+### These options name memcached servers used to cache internal FSFS
+### data.  See http://www.danga.com/memcached/ for more information on
+### memcached.  To use memcached with FSFS, run one or more memcached
+### servers, and specify each of them as an option like so:
+# first-server = 127.0.0.1:11211
+# remote-memcached = mymemcached.corp.example.com:11212
+### The option name is ignored; the value is of the form HOST:PORT.
+### memcached servers can be shared between multiple repositories;
+### however, if you do this, you *must* ensure that repositories have
+### distinct UUIDs and paths, or else cached data from one repository
+### might be used by another accidentally.  Note also that memcached has
+### no authentication for reads or writes, so you must ensure that your
+### memcached servers are only accessible by trusted users.
+
+[caches]
+### When a cache-related error occurs, normally Subversion ignores it
+### and continues, logging an error if the server is appropriately
+### configured (and ignoring it with file:// access).  To make
+### Subversion never ignore cache errors, uncomment this line.
+# fail-stop = true
+
+[rep-sharing]
+### To conserve space, the filesystem can optionally avoid storing
+### duplicate representations.  This comes at a slight cost in
+### performance, as maintaining a database of shared representations can
+### increase commit times.  The space savings are dependent upon the size
+### of the repository, the number of objects it contains and the amount of
+### duplication between them, usually a function of the branching and
+### merging process.
+###
+### The following parameter enables rep-sharing in the repository.  It can
+### be switched on and off at will, but for best space-saving results
+### should be enabled consistently over the life of the repository.
+### 'svnadmin verify' will check the rep-cache regardless of this setting.
+### rep-sharing is enabled by default.
+# enable-rep-sharing = true
+
+[deltification]
+### To conserve space, the filesystem stores data as differences against
+### existing representations.  This comes at a slight cost in performance,
+### as calculating differences can increase commit times.  Reading data
+### will also create higher CPU load and the data will be fragmented.
+### Since deltification tends to save significant amounts of disk space,
+### the overall I/O load can actually be lower.
+###
+### The options in this section allow for tuning the deltification
+### strategy.  Their effects on data size and server performance may vary
+### from one repository to another.  Versions prior to 1.8 will ignore
+### this section.
+###
+### The following parameter enables deltification for directories. It can
+### be switched on and off at will, but for best space-saving results
+### should be enabled consistently over the lifetime of the repository.
+### Repositories containing large directories will benefit greatly.
+### In rarely accessed repositories, the I/O overhead may be significant
+### as caches will most likely be low.
+### directory deltification is enabled by default.
+# enable-dir-deltification = true
+###
+### The following parameter enables deltification for properties on files
+### and directories.  Overall, this is a minor tuning option but can save
+### some disk space if you merge frequently or frequently change node
+### properties.  You should not activate this if rep-sharing has been
+### disabled because this may result in a net increase in repository size.
+### property deltification is enabled by default.
+# enable-props-deltification = true
+###
+### During commit, the server may need to walk the whole change history of
+### of a given node to find a suitable deltification base.  This linear
+### process can impact commit times, svnadmin load and similar operations.
+### This setting limits the depth of the deltification history.  If the
+### threshold has been reached, the node will be stored as fulltext and a
+### new deltification history begins.
+### Note, this is unrelated to svn log.
+### Very large values rarely provide significant additional savings but
+### can impact performance greatly - in particular if directory
+### deltification has been activated.  Very small values may be useful in
+### repositories that are dominated by large, changing binaries.
+### Should be a power of two minus 1.  A value of 0 will effectively
+### disable deltification.
+### For 1.8, the default value is 1023; earlier versions have no limit.
+# max-deltification-walk = 1023
+###
+### The skip-delta scheme used by FSFS tends to repeatably store redundant
+### delta information where a simple delta against the latest version is
+### often smaller.  By default, 1.8+ will therefore use skip deltas only
+### after the linear chain of deltas has grown beyond the threshold
+### specified by this setting.
+### Values up to 64 can result in some reduction in repository size for
+### the cost of quickly increasing I/O and CPU costs. Similarly, smaller
+### numbers can reduce those costs at the cost of more disk space.  For
+### rarely read repositories or those containing larger binaries, this may
+### present a better trade-off.
+### Should be a power of two.  A value of 1 or smaller will cause the
+### exclusive use of skip-deltas (as in pre-1.8).
+### For 1.8, the default value is 16; earlier versions use 1.
+# max-linear-deltification = 16
+###
+### After deltification, we compress the data to minimize on-disk size.
+### This setting controls the compression algorithm, which will be used in
+### future revisions.  It can be used to either disable compression or to
+### select between available algorithms (zlib, lz4).  zlib is a general-
+### purpose compression algorithm.  lz4 is a fast compression algorithm
+### which should be preferred for repositories with large and, possibly,
+### incompressible files.  Note that the compression ratio of lz4 is
+### usually lower than the one provided by zlib, but using it can
+### significantly speed up commits as well as reading the data.
+### lz4 compression algorithm is supported, starting from format 8
+### repositories, available in Subversion 1.10 and higher.
+### The syntax of this option is:
+###   compression = none | lz4 | zlib | zlib-1 ... zlib-9
+### Versions prior to Subversion 1.10 will ignore this option.
+### The default value is 'lz4' if supported by the repository format and
+### 'zlib' otherwise.  'zlib' is currently equivalent to 'zlib-5'.
+# compression = lz4
+###
+### DEPRECATED: The new 'compression' option deprecates previously used
+### 'compression-level' option, which was used to configure zlib compression.
+### For compatibility with previous versions of Subversion, this option can
+### still be used (and it will result in zlib compression with the
+### corresponding compression level).
+###   compression-level = 0 ... 9 (default is 5)
+
+[packed-revprops]
+### This parameter controls the size (in kBytes) of packed revprop files.
+### Revprops of consecutive revisions will be concatenated into a single
+### file up to but not exceeding the threshold given here.  However, each
+### pack file may be much smaller and revprops of a single revision may be
+### much larger than the limit set here.  The threshold will be applied
+### before optional compression takes place.
+### Large values will reduce disk space usage at the expense of increased
+### latency and CPU usage reading and changing individual revprops.
+### Values smaller than 4 kByte will not improve latency any further and 
+### quickly render revprop packing ineffective.
+### revprop-pack-size is 16 kBytes by default for non-compressed revprop
+### pack files and 64 kBytes when compression has been enabled.
+# revprop-pack-size = 16
+###
+### To save disk space, packed revprop files may be compressed.  Standard
+### revprops tend to allow for very effective compression.  Reading and
+### even more so writing, become significantly more CPU intensive.
+### Compressing packed revprops is disabled by default.
+# compress-packed-revprops = false
+
+[io]
+### Parameters in this section control the data access granularity in
+### format 7 repositories and later.  The defaults should translate into
+### decent performance over a wide range of setups.
+###
+### When a specific piece of information needs to be read from disk,  a
+### data block is being read at once and its contents are being cached.
+### If the repository is being stored on a RAID, the block size should be
+### either 50% or 100% of RAID block size / granularity.  Also, your file
+### system blocks/clusters should be properly aligned and sized.  In that
+### setup, each access will hit only one disk (minimizes I/O load) but
+### uses all the data provided by the disk in a single access.
+### For SSD-based storage systems, slightly lower values around 16 kB
+### may improve latency while still maximizing throughput.  If block-read
+### has not been enabled, this will be capped to 4 kBytes.
+### Can be changed at any time but must be a power of 2.
+### block-size is given in kBytes and with a default of 64 kBytes.
+# block-size = 64
+###
+### The log-to-phys index maps data item numbers to offsets within the
+### rev or pack file.  This index is organized in pages of a fixed maximum
+### capacity.  To access an item, the page table and the respective page
+### must be read.
+### This parameter only affects revisions with thousands of changed paths.
+### If you have several extremely large revisions (~1 mio changes), think
+### about increasing this setting.  Reducing the value will rarely result
+### in a net speedup.
+### This is an expert setting.  Must be a power of 2.
+### l2p-page-size is 8192 entries by default.
+# l2p-page-size = 8192
+###
+### The phys-to-log index maps positions within the rev or pack file to
+### to data items,  i.e. describes what piece of information is being
+### stored at any particular offset.  The index describes the rev file
+### in chunks (pages) and keeps a global list of all those pages.  Large
+### pages mean a shorter page table but a larger per-page description of
+### data items in it.  The latency sweetspot depends on the change size
+### distribution but covers a relatively wide range.
+### If the repository contains very large files,  i.e. individual changes
+### of tens of MB each,  increasing the page size will shorten the index
+### file at the expense of a slightly increased latency in sections with
+### smaller changes.
+### For source code repositories, this should be about 16x the block-size.
+### Must be a power of 2.
+### p2l-page-size is given in kBytes and with a default of 1024 kBytes.
+# p2l-page-size = 1024
+
+[debug]
+###
+### Whether to verify each new revision immediately before finalizing
+### the commit.  This is disabled by default except in maintainer-mode
+### builds.
+# verify-before-commit = false
diff --git a/test/repos/simple-ext.svn/db/min-unpacked-rev b/test/repos/simple-ext.svn/db/min-unpacked-rev
new file mode 100644
index 0000000000..573541ac97
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/min-unpacked-rev
@@ -0,0 +1 @@
+0
diff --git a/test/repos/simple-ext.svn/db/rep-cache.db b/test/repos/simple-ext.svn/db/rep-cache.db
new file mode 100644
index 0000000000000000000000000000000000000000..3193b2eaad046fba3704b0d28a50a68a94801da2
GIT binary patch
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literal 0
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diff --git a/test/repos/simple-ext.svn/db/rep-cache.db-journal b/test/repos/simple-ext.svn/db/rep-cache.db-journal
new file mode 100644
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diff --git a/test/repos/simple-ext.svn/db/revprops/0/0 b/test/repos/simple-ext.svn/db/revprops/0/0
new file mode 100644
index 0000000000..92768005d3
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/revprops/0/0
@@ -0,0 +1,5 @@
+K 8
+svn:date
+V 27
+2023-11-16T20:11:46.318861Z
+END
diff --git a/test/repos/simple-ext.svn/db/revprops/0/1 b/test/repos/simple-ext.svn/db/revprops/0/1
new file mode 100644
index 0000000000..aa95a9de9f
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/revprops/0/1
@@ -0,0 +1,13 @@
+K 10
+svn:author
+V 5
+sacks
+K 8
+svn:date
+V 27
+2023-11-16T20:15:56.917904Z
+K 7
+svn:log
+V 30
+Setting up directory structure
+END
diff --git a/test/repos/simple-ext.svn/db/revprops/0/2 b/test/repos/simple-ext.svn/db/revprops/0/2
new file mode 100644
index 0000000000..3d04d8909a
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/revprops/0/2
@@ -0,0 +1,13 @@
+K 10
+svn:author
+V 5
+sacks
+K 8
+svn:date
+V 27
+2023-11-16T20:27:31.407916Z
+K 7
+svn:log
+V 10
+Add README
+END
diff --git a/test/repos/simple-ext.svn/db/revprops/0/3 b/test/repos/simple-ext.svn/db/revprops/0/3
new file mode 100644
index 0000000000..de20268415
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/revprops/0/3
@@ -0,0 +1,13 @@
+K 10
+svn:author
+V 5
+sacks
+K 8
+svn:date
+V 27
+2023-11-16T21:14:43.366717Z
+K 7
+svn:log
+V 27
+Creating cesm2.0.beta07 tag
+END
diff --git a/test/repos/simple-ext.svn/db/revs/0/0 b/test/repos/simple-ext.svn/db/revs/0/0
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diff --git a/test/repos/simple-ext.svn/db/txn-current b/test/repos/simple-ext.svn/db/txn-current
new file mode 100644
index 0000000000..00750edc07
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/txn-current
@@ -0,0 +1 @@
+3
diff --git a/test/repos/simple-ext.svn/db/txn-current-lock b/test/repos/simple-ext.svn/db/txn-current-lock
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/repos/simple-ext.svn/db/uuid b/test/repos/simple-ext.svn/db/uuid
new file mode 100644
index 0000000000..0b16502652
--- /dev/null
+++ b/test/repos/simple-ext.svn/db/uuid
@@ -0,0 +1,2 @@
+1c80dd47-0c07-4207-8ee0-e60dd9d98853
+31d57ab1-759c-4129-a63d-898c774d96c9
diff --git a/test/repos/simple-ext.svn/db/write-lock b/test/repos/simple-ext.svn/db/write-lock
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/repos/simple-ext.svn/format b/test/repos/simple-ext.svn/format
new file mode 100644
index 0000000000..7ed6ff82de
--- /dev/null
+++ b/test/repos/simple-ext.svn/format
@@ -0,0 +1 @@
+5
diff --git a/test/repos/simple-ext.svn/hooks/post-commit.tmpl b/test/repos/simple-ext.svn/hooks/post-commit.tmpl
new file mode 100755
index 0000000000..988f041fa5
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/post-commit.tmpl
@@ -0,0 +1,62 @@
+#!/bin/sh
+
+# POST-COMMIT HOOK
+#
+# The post-commit hook is invoked after a commit.  Subversion runs
+# this hook by invoking a program (script, executable, binary, etc.)
+# named 'post-commit' (for which this file is a template) with the 
+# following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] REV          (the number of the revision just committed)
+#   [3] TXN-NAME     (the name of the transaction that has become REV)
+#
+# Because the commit has already completed and cannot be undone,
+# the exit code of the hook program is ignored.  The hook program
+# can use the 'svnlook' utility to help it examine the
+# newly-committed tree.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'post-commit'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'post-commit' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'post-commit.bat' or 'post-commit.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+REV="$2"
+TXN_NAME="$3"
+
+mailer.py commit "$REPOS" "$REV" /path/to/mailer.conf
diff --git a/test/repos/simple-ext.svn/hooks/post-lock.tmpl b/test/repos/simple-ext.svn/hooks/post-lock.tmpl
new file mode 100755
index 0000000000..96f2165209
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/post-lock.tmpl
@@ -0,0 +1,64 @@
+#!/bin/sh
+
+# POST-LOCK HOOK
+#
+# The post-lock hook is run after a path is locked.  Subversion runs
+# this hook by invoking a program (script, executable, binary, etc.)
+# named 'post-lock' (for which this file is a template) with the 
+# following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] USER         (the user who created the lock)
+#
+# The paths that were just locked are passed to the hook via STDIN.
+#
+# Because the locks have already been created and cannot be undone,
+# the exit code of the hook program is ignored.  The hook program
+# can use the 'svnlook' utility to examine the paths in the repository
+# but since the hook is invoked asynchronously the newly-created locks
+# may no longer be present.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'post-lock'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'post-lock' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'post-lock.bat' or 'post-lock.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+USER="$2"
+
+# Send email to interested parties, let them know a lock was created:
+mailer.py lock "$REPOS" "$USER" /path/to/mailer.conf
diff --git a/test/repos/simple-ext.svn/hooks/post-revprop-change.tmpl b/test/repos/simple-ext.svn/hooks/post-revprop-change.tmpl
new file mode 100755
index 0000000000..de1b914648
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/post-revprop-change.tmpl
@@ -0,0 +1,69 @@
+#!/bin/sh
+
+# POST-REVPROP-CHANGE HOOK
+#
+# The post-revprop-change hook is invoked after a revision property
+# has been added, modified or deleted.  Subversion runs this hook by
+# invoking a program (script, executable, binary, etc.) named
+# 'post-revprop-change' (for which this file is a template), with the
+# following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] REV          (the revision that was tweaked)
+#   [3] USER         (the username of the person tweaking the property)
+#   [4] PROPNAME     (the property that was changed)
+#   [5] ACTION       (the property was 'A'dded, 'M'odified, or 'D'eleted)
+#
+#   [STDIN] PROPVAL  ** the old property value is passed via STDIN.
+#
+# Because the propchange has already completed and cannot be undone,
+# the exit code of the hook program is ignored.  The hook program
+# can use the 'svnlook' utility to help it examine the
+# new property value.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'post-revprop-change'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'post-revprop-change' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'post-revprop-change.bat' or 'post-revprop-change.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+REV="$2"
+USER="$3"
+PROPNAME="$4"
+ACTION="$5"
+
+mailer.py propchange2 "$REPOS" "$REV" "$USER" "$PROPNAME" "$ACTION" /path/to/mailer.conf
diff --git a/test/repos/simple-ext.svn/hooks/post-unlock.tmpl b/test/repos/simple-ext.svn/hooks/post-unlock.tmpl
new file mode 100755
index 0000000000..e33f793c25
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/post-unlock.tmpl
@@ -0,0 +1,61 @@
+#!/bin/sh
+
+# POST-UNLOCK HOOK
+#
+# The post-unlock hook runs after a path is unlocked.  Subversion runs
+# this hook by invoking a program (script, executable, binary, etc.)
+# named 'post-unlock' (for which this file is a template) with the 
+# following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] USER         (the user who destroyed the lock)
+#
+# The paths that were just unlocked are passed to the hook via STDIN.
+#
+# Because the lock has already been destroyed and cannot be undone,
+# the exit code of the hook program is ignored.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'post-unlock'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'post-unlock' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'post-unlock.bat' or 'post-unlock.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+USER="$2"
+
+# Send email to interested parties, let them know a lock was removed:
+mailer.py unlock "$REPOS" "$USER" /path/to/mailer.conf
diff --git a/test/repos/simple-ext.svn/hooks/pre-commit.tmpl b/test/repos/simple-ext.svn/hooks/pre-commit.tmpl
new file mode 100755
index 0000000000..626e72300c
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/pre-commit.tmpl
@@ -0,0 +1,91 @@
+#!/bin/sh
+
+# PRE-COMMIT HOOK
+#
+# The pre-commit hook is invoked before a Subversion txn is
+# committed.  Subversion runs this hook by invoking a program
+# (script, executable, binary, etc.) named 'pre-commit' (for which
+# this file is a template), with the following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] TXN-NAME     (the name of the txn about to be committed)
+#
+#   [STDIN] LOCK-TOKENS ** the lock tokens are passed via STDIN.
+#
+#   If STDIN contains the line "LOCK-TOKENS:\n" (the "\n" denotes a
+#   single newline), the lines following it are the lock tokens for
+#   this commit.  The end of the list is marked by a line containing
+#   only a newline character.
+#
+#   Each lock token line consists of a URI-escaped path, followed
+#   by the separator character '|', followed by the lock token string,
+#   followed by a newline.
+#
+# If the hook program exits with success, the txn is committed; but
+# if it exits with failure (non-zero), the txn is aborted, no commit
+# takes place, and STDERR is returned to the client.   The hook
+# program can use the 'svnlook' utility to help it examine the txn.
+#
+#   ***  NOTE: THE HOOK PROGRAM MUST NOT MODIFY THE TXN, EXCEPT  ***
+#   ***  FOR REVISION PROPERTIES (like svn:log or svn:author).   ***
+#
+#   This is why we recommend using the read-only 'svnlook' utility.
+#   In the future, Subversion may enforce the rule that pre-commit
+#   hooks should not modify the versioned data in txns, or else come
+#   up with a mechanism to make it safe to do so (by informing the
+#   committing client of the changes).  However, right now neither
+#   mechanism is implemented, so hook writers just have to be careful.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'pre-commit'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'pre-commit' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'pre-commit.bat' or 'pre-commit.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+TXN="$2"
+
+# Make sure that the log message contains some text.
+SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook
+$SVNLOOK log -t "$TXN" "$REPOS" | \
+   grep "[a-zA-Z0-9]" > /dev/null || exit 1
+
+# Check that the author of this commit has the rights to perform
+# the commit on the files and directories being modified.
+commit-access-control.pl "$REPOS" "$TXN" commit-access-control.cfg || exit 1
+
+# All checks passed, so allow the commit.
+exit 0
diff --git a/test/repos/simple-ext.svn/hooks/pre-lock.tmpl b/test/repos/simple-ext.svn/hooks/pre-lock.tmpl
new file mode 100755
index 0000000000..148582a689
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/pre-lock.tmpl
@@ -0,0 +1,95 @@
+#!/bin/sh
+
+# PRE-LOCK HOOK
+#
+# The pre-lock hook is invoked before an exclusive lock is
+# created.  Subversion runs this hook by invoking a program 
+# (script, executable, binary, etc.) named 'pre-lock' (for which
+# this file is a template), with the following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] PATH         (the path in the repository about to be locked)
+#   [3] USER         (the user creating the lock)
+#   [4] COMMENT      (the comment of the lock)
+#   [5] STEAL-LOCK   (1 if the user is trying to steal the lock, else 0)
+#
+# If the hook program outputs anything on stdout, the output string will
+# be used as the lock token for this lock operation.  If you choose to use
+# this feature, you must guarantee the tokens generated are unique across
+# the repository each time.
+#
+# If the hook program exits with success, the lock is created; but
+# if it exits with failure (non-zero), the lock action is aborted
+# and STDERR is returned to the client.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'pre-lock'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'pre-lock' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'pre-lock.bat' or 'pre-lock.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+PATH="$2"
+USER="$3"
+COMMENT="$4"
+STEAL="$5"
+
+# If a lock exists and is owned by a different person, don't allow it
+# to be stolen (e.g., with 'svn lock --force ...').
+
+# (Maybe this script could send email to the lock owner?)
+SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook
+GREP=/bin/grep
+SED=/bin/sed
+
+LOCK_OWNER=`$SVNLOOK lock "$REPOS" "$PATH" | \
+            $GREP '^Owner: ' | $SED 's/Owner: //'`
+
+# If we get no result from svnlook, there's no lock, allow the lock to
+# happen:
+if [ "$LOCK_OWNER" = "" ]; then
+  exit 0
+fi
+
+# If the person locking matches the lock's owner, allow the lock to
+# happen:
+if [ "$LOCK_OWNER" = "$USER" ]; then
+  exit 0
+fi
+
+# Otherwise, we've got an owner mismatch, so return failure:
+echo "Error: $PATH already locked by ${LOCK_OWNER}." 1>&2
+exit 1
diff --git a/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl b/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl
new file mode 100755
index 0000000000..8b065d7c79
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl
@@ -0,0 +1,79 @@
+#!/bin/sh
+
+# PRE-REVPROP-CHANGE HOOK
+#
+# The pre-revprop-change hook is invoked before a revision property
+# is added, modified or deleted.  Subversion runs this hook by invoking
+# a program (script, executable, binary, etc.) named 'pre-revprop-change'
+# (for which this file is a template), with the following ordered
+# arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] REV          (the revision being tweaked)
+#   [3] USER         (the username of the person tweaking the property)
+#   [4] PROPNAME     (the property being set on the revision)
+#   [5] ACTION       (the property is being 'A'dded, 'M'odified, or 'D'eleted)
+#
+#   [STDIN] PROPVAL  ** the new property value is passed via STDIN.
+#
+# If the hook program exits with success, the propchange happens; but
+# if it exits with failure (non-zero), the propchange doesn't happen.
+# The hook program can use the 'svnlook' utility to examine the 
+# existing value of the revision property.
+#
+# WARNING: unlike other hooks, this hook MUST exist for revision
+# properties to be changed.  If the hook does not exist, Subversion 
+# will behave as if the hook were present, but failed.  The reason
+# for this is that revision properties are UNVERSIONED, meaning that
+# a successful propchange is destructive;  the old value is gone
+# forever.  We recommend the hook back up the old value somewhere.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'pre-revprop-change'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'pre-revprop-change' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'pre-revprop-change.bat' or 'pre-revprop-change.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+REV="$2"
+USER="$3"
+PROPNAME="$4"
+ACTION="$5"
+
+if [ "$ACTION" = "M" -a "$PROPNAME" = "svn:log" ]; then exit 0; fi
+
+echo "Changing revision properties other than svn:log is prohibited" >&2
+exit 1
diff --git a/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl b/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl
new file mode 100755
index 0000000000..9ba99d071b
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl
@@ -0,0 +1,87 @@
+#!/bin/sh
+
+# PRE-UNLOCK HOOK
+#
+# The pre-unlock hook is invoked before an exclusive lock is
+# destroyed.  Subversion runs this hook by invoking a program 
+# (script, executable, binary, etc.) named 'pre-unlock' (for which
+# this file is a template), with the following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] PATH         (the path in the repository about to be unlocked)
+#   [3] USER         (the user destroying the lock)
+#   [4] TOKEN        (the lock token to be destroyed)
+#   [5] BREAK-UNLOCK (1 if the user is breaking the lock, else 0)
+#
+# If the hook program exits with success, the lock is destroyed; but
+# if it exits with failure (non-zero), the unlock action is aborted
+# and STDERR is returned to the client.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'pre-unlock'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'pre-unlock' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'pre-unlock.bat' or 'pre-unlock.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+PATH="$2"
+USER="$3"
+TOKEN="$4"
+BREAK="$5"
+
+# If a lock is owned by a different person, don't allow it be broken.
+# (Maybe this script could send email to the lock owner?)
+
+SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook
+GREP=/bin/grep
+SED=/bin/sed
+
+LOCK_OWNER=`$SVNLOOK lock "$REPOS" "$PATH" | \
+            $GREP '^Owner: ' | $SED 's/Owner: //'`
+
+# If we get no result from svnlook, there's no lock, return success:
+if [ "$LOCK_OWNER" = "" ]; then
+  exit 0
+fi
+
+# If the person unlocking matches the lock's owner, return success:
+if [ "$LOCK_OWNER" = "$USER" ]; then
+  exit 0
+fi
+
+# Otherwise, we've got an owner mismatch, so return failure:
+echo "Error: $PATH locked by ${LOCK_OWNER}." 1>&2
+exit 1
diff --git a/test/repos/simple-ext.svn/hooks/start-commit.tmpl b/test/repos/simple-ext.svn/hooks/start-commit.tmpl
new file mode 100755
index 0000000000..1395e8315a
--- /dev/null
+++ b/test/repos/simple-ext.svn/hooks/start-commit.tmpl
@@ -0,0 +1,81 @@
+#!/bin/sh
+
+# START-COMMIT HOOK
+#
+# The start-commit hook is invoked immediately after a Subversion txn is
+# created and populated with initial revprops in the process of doing a
+# commit. Subversion runs this hook by invoking a program (script, 
+# executable, binary, etc.) named 'start-commit' (for which this file
+# is a template) with the following ordered arguments:
+#
+#   [1] REPOS-PATH   (the path to this repository)
+#   [2] USER         (the authenticated user attempting to commit)
+#   [3] CAPABILITIES (a colon-separated list of capabilities reported
+#                     by the client; see note below)
+#   [4] TXN-NAME     (the name of the commit txn just created)
+#
+# Note: The CAPABILITIES parameter is new in Subversion 1.5, and 1.5
+# clients will typically report at least the "mergeinfo" capability.
+# If there are other capabilities, then the list is colon-separated,
+# e.g.: "mergeinfo:some-other-capability" (the order is undefined).
+#
+# The list is self-reported by the client.  Therefore, you should not
+# make security assumptions based on the capabilities list, nor should
+# you assume that clients reliably report every capability they have.
+#
+# Note: The TXN-NAME parameter is new in Subversion 1.8.  Prior to version
+# 1.8, the start-commit hook was invoked before the commit txn was even
+# created, so the ability to inspect the commit txn and its metadata from
+# within the start-commit hook was not possible.
+# 
+# If the hook program exits with success, the commit continues; but
+# if it exits with failure (non-zero), the commit is stopped before
+# a Subversion txn is created, and STDERR is returned to the client.
+#
+# The default working directory for the invocation is undefined, so
+# the program should set one explicitly if it cares.
+#
+# On a Unix system, the normal procedure is to have 'start-commit'
+# invoke other programs to do the real work, though it may do the
+# work itself too.
+#
+# Note that 'start-commit' must be executable by the user(s) who will
+# invoke it (typically the user httpd runs as), and that user must
+# have filesystem-level permission to access the repository.
+#
+# On a Windows system, you should name the hook program
+# 'start-commit.bat' or 'start-commit.exe',
+# but the basic idea is the same.
+#
+# The hook program runs in an empty environment, unless the server is
+# explicitly configured otherwise.  For example, a common problem is for
+# the PATH environment variable to not be set to its usual value, so
+# that subprograms fail to launch unless invoked via absolute path.
+# If you're having unexpected problems with a hook program, the
+# culprit may be unusual (or missing) environment variables.
+#
+# CAUTION:
+# For security reasons, you MUST always properly quote arguments when
+# you use them, as those arguments could contain whitespace or other
+# problematic characters. Additionally, you should delimit the list
+# of options with "--" before passing the arguments, so malicious
+# clients cannot bootleg unexpected options to the commands your
+# script aims to execute.
+# For similar reasons, you should also add a trailing @ to URLs which
+# are passed to SVN commands accepting URLs with peg revisions.
+#
+# Here is an example hook script, for a Unix /bin/sh interpreter.
+# For more examples and pre-written hooks, see those in
+# the Subversion repository at
+# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
+# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
+
+
+REPOS="$1"
+USER="$2"
+
+commit-allower.pl --repository "$REPOS" --user "$USER" || exit 1
+special-auth-check.py --user "$USER" --auth-level 3 || exit 1
+
+# All checks passed, so allow the commit.
+exit 0
diff --git a/test/repos/simple-ext.svn/locks/db-logs.lock b/test/repos/simple-ext.svn/locks/db-logs.lock
new file mode 100644
index 0000000000..20dd6369be
--- /dev/null
+++ b/test/repos/simple-ext.svn/locks/db-logs.lock
@@ -0,0 +1,3 @@
+This file is not used by Subversion 1.3.x or later.
+However, its existence is required for compatibility with
+Subversion 1.2.x or earlier.
diff --git a/test/repos/simple-ext.svn/locks/db.lock b/test/repos/simple-ext.svn/locks/db.lock
new file mode 100644
index 0000000000..20dd6369be
--- /dev/null
+++ b/test/repos/simple-ext.svn/locks/db.lock
@@ -0,0 +1,3 @@
+This file is not used by Subversion 1.3.x or later.
+However, its existence is required for compatibility with
+Subversion 1.2.x or earlier.
diff --git a/test/test_sys_checkout.py b/test/test_sys_checkout.py
old mode 100644
new mode 100755
index ab4f77e88f..664160dc99
--- a/test/test_sys_checkout.py
+++ b/test/test_sys_checkout.py
@@ -97,6 +97,7 @@
 SIMPLE_REPO = 'simple-ext.git'       # Child repo
 SIMPLE_FORK_REPO = 'simple-ext-fork.git'  # Child repo
 MIXED_REPO = 'mixed-cont-ext.git'    # Both parent and child
+SVN_TEST_REPO = 'simple-ext.svn'     # Subversion repository
 
 # Standard (arbitrary) external names for test configs
 TAG_SECTION = 'simp_tag'
@@ -120,8 +121,6 @@
 # Branch that exists in both the simple and simple-fork repos.
 REMOTE_BRANCH_FEATURE2 = 'feature2'
 
-SVN_TEST_REPO = 'https://github.com/escomp/cesm'
-
 # Disable too-many-public-methods error
 # pylint: disable=R0904
 
@@ -354,7 +353,7 @@ def create_section_reference_to_subexternal(self, name):
 
         self._config.set(name, ExternalsDescription.EXTERNALS, CFG_SUB_NAME)
 
-    def create_svn_external(self, name, tag='', branch=''):
+    def create_svn_external(self, name, url, tag='', branch=''):
         """Create a config section for an svn repository.
 
         """
@@ -365,7 +364,7 @@ def create_svn_external(self, name, tag='', branch=''):
         self._config.set(name, ExternalsDescription.PROTOCOL,
                          ExternalsDescription.PROTOCOL_SVN)
 
-        self._config.set(name, ExternalsDescription.REPO_URL, SVN_TEST_REPO)
+        self._config.set(name, ExternalsDescription.REPO_URL, url)
 
         self._config.set(name, ExternalsDescription.REQUIRED, str(True))
 
@@ -1387,36 +1386,10 @@ def test_container_sparse(self):
                                                              'simple_subdir',
                                                              'subdir_file.txt'))
 
-
 class TestSysCheckoutSVN(BaseTestSysCheckout):
     """Run systems level tests of checkout_externals accessing svn repositories
 
-    SVN tests - these tests use the svn repository interface. Since
-    they require an active network connection, they are significantly
-    slower than the git tests. But svn testing is critical. So try to
-    design the tests to only test svn repository functionality
-    (checkout, switch) and leave generic testing of functionality like
-    'optional' to the fast git tests.
-
-    Example timing as of 2017-11:
-
-      * All other git and unit tests combined take between 4-5 seconds
-
-      * Just checking if svn is available for a single test takes 2 seconds.
-
-      * The single svn test typically takes between 10 and 25 seconds
-        (depending on the network)!
-
-    NOTE(bja, 2017-11) To enable CI testing we can't use a real remote
-    repository that restricts access and it seems inappropriate to hit
-    a random open source repo. For now we are just hitting one of our
-    own github repos using the github svn server interface. This
-    should be "good enough" for basic checkout and swich
-    functionality. But if additional svn functionality is required, a
-    better solution will be necessary. I think eventually we want to
-    create a small local svn repository on the fly (doesn't require an
-    svn server or network connection!) and use it for testing.
-
+    SVN tests - these tests use the svn repository interface.
     """
 
     @staticmethod
@@ -1427,6 +1400,9 @@ def _svn_branch_name():
     def _svn_tag_name():
         return './{0}/svn_tag'.format(EXTERNALS_PATH)
     
+    def _svn_test_repo_url(self):
+        return 'file://' + os.path.join(self._bare_root, SVN_TEST_REPO)
+
     def _check_tag_branch_svn_tag_clean(self, tree):
         self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
                                ExternalStatus.STATUS_OK,
@@ -1438,13 +1414,12 @@ def _check_tag_branch_svn_tag_clean(self, tree):
                                ExternalStatus.STATUS_OK,
                                ExternalStatus.STATUS_OK)
 
-    @staticmethod
-    def _have_svn_access():
+    def _have_svn_access(self):
         """Check if we have svn access so we can enable tests that use svn.
 
         """
         have_svn = False
-        cmd = ['svn', 'ls', SVN_TEST_REPO, ]
+        cmd = ['svn', 'ls', self._svn_test_repo_url(), ]
         try:
             execute_subprocess(cmd)
             have_svn = True
@@ -1472,8 +1447,8 @@ def test_container_simple_svn(self):
         self._generator.create_section(SIMPLE_REPO, TAG_SECTION, tag='tag1')
 
         # Svn repos.
-        self._generator.create_svn_external('svn_branch', branch='trunk')
-        self._generator.create_svn_external('svn_tag', tag='tags/cesm2.0.beta07')
+        self._generator.create_svn_external('svn_branch', self._svn_test_repo_url(), branch='trunk')
+        self._generator.create_svn_external('svn_tag', self._svn_test_repo_url(), tag='tags/cesm2.0.beta07')
 
         self._generator.write_config(cloned_repo_dir)
 
@@ -1557,7 +1532,7 @@ def setUp(self):
         execute_subprocess(cmd)
         cmd = ['git', 'checkout', self._bare_branch_name]
         execute_subprocess(cmd)
-        cmd = ['git', 'submodule', 'add', fork_repo_dir]
+        cmd = ['git', '-c', 'protocol.file.allow=always','submodule', 'add', fork_repo_dir]
         execute_subprocess(cmd)
         cmd = ['git', 'commit', '-am', "'Added simple-ext-fork as a submodule'"]
         execute_subprocess(cmd)
@@ -1571,7 +1546,7 @@ def setUp(self):
         execute_subprocess(cmd)
         cmd = ['git', 'checkout', self._config_branch_name]
         execute_subprocess(cmd)
-        cmd = ['git', 'submodule', 'add', '--name', SIMPLE_REPO,
+        cmd = ['git', '-c', 'protocol.file.allow=always', 'submodule', 'add', '--name', SIMPLE_REPO,
                simple_repo_dir, self._simple_ext_name]
         execute_subprocess(cmd)
         # Checkout feature2

From c4e14d165f90ac3dab2ba8bb2b778459c6c7ceaa Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Jan 2024 02:06:07 -0700
Subject: [PATCH 0060/1248] Update to cam version that no longer uses svn, but
 git

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index d75b4683a6..4e65a11aed 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -49,7 +49,7 @@ externals = Externals.cfg
 required = True
 
 [cam6]
-tag = cam6_3_133
+tag = cam6_3_135
 protocol = git
 repo_url = https://github.com/ESCOMP/CAM
 local_path = components/cam

From 6abcc1d26a1d858ae0a035ee36ffee10c6a7aa72 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <ekluzek@users.noreply.github.com>
Date: Fri, 26 Jan 2024 14:46:17 -0700
Subject: [PATCH 0061/1248] Update assign-to-project.yml

---
 .github/workflows/assign-to-project.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml
index 8c6c259c33..a5bcd10b64 100644
--- a/.github/workflows/assign-to-project.yml
+++ b/.github/workflows/assign-to-project.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Assign to High Priority project
     steps:
-    - name: Assign issues and pull requests with `priority: high` label to project 25
+    - name: Assign issues and pull requests with priority high label to project 25
       uses: srggrs/assign-one-project-github-action@1.3.1
       if: |
         contains(github.event.issue.labels.*.name, 'priority: high') ||

From 9902724bb64579cc0aa84b567f62682c1f1d24c7 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Feb 2024 00:27:30 -0700
Subject: [PATCH 0062/1248] Move datasets to under inputdata

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 57f5b3adf4..28a372de32 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2749,9 +2749,9 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <!-- =========================================  -->
 
 <stream_fldfilename_prigentroughness
->/glade/u/home/dleung/CESM2/ctsm_dustemis_dev/cdf5_Z0a_Prigent-Globe-025x025-01242023.nc</stream_fldfilename_prigentroughness>
+>lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c240127.nc</stream_fldfilename_prigentroughness>
 <stream_meshfile_prigentroughness
->/glade/u/home/dleung/CESM2/ctsm_dustemis_dev/lnd_mesh.nc</stream_meshfile_prigentroughness>
+>lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c230730.nc</stream_meshfile_prigentroughness>
 
 <!-- =========================================  -->
 <!-- Defaults for different BGC/decomp modes    -->

From 158c878451b3b0916657cf84c2f02dc262dc4b4c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Feb 2024 01:20:16 -0700
Subject: [PATCH 0063/1248] Remove whitespace at end of lines, remove commented
 out code included commented out Zender code, remove unneeded markers by Danny
 Leung

---
 src/biogeochem/DUSTMod.F90 | 84 ++++++++------------------------------
 1 file changed, 18 insertions(+), 66 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 39aa5766f4..67c22e207a 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -16,7 +16,7 @@ module DUSTMod
   use shr_log_mod          , only : errMsg => shr_log_errMsg
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
   use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr, &
-                                    natpft_lb, natpft_ub, natpft_size  
+                                    natpft_lb, natpft_ub, natpft_size
   use clm_varcon           , only : grav, spval
   use landunit_varcon      , only : istcrop, istsoil
   use clm_varctl           , only : iulog
@@ -31,7 +31,7 @@ module DUSTMod
   use LandunitType         , only : lun
   use ColumnType           , only : col
   use PatchType            , only : patch
-  use pftconMod            , only : noveg    
+  use pftconMod            , only : noveg
   use PrigentRoughnessStreamType    , only : prigentroughnessstream_type
   !  
   ! !PUBLIC TYPES
@@ -105,7 +105,7 @@ module DUSTMod
   subroutine Init(this, bounds, NLFilename)
 
     class(dust_type) :: this
-    type(bounds_type), intent(in) :: bounds 
+    type(bounds_type), intent(in) :: bounds
     character(len=*),  intent(in) :: NLFilename
 
     call this%InitAllocate (bounds)
@@ -296,8 +296,8 @@ subroutine InitCold(this, bounds)
     !
     !
     ! !ARGUMENTS:
-    class(dust_type), intent(inout) :: this  ! Danny M. Leung used class instead of type
-    type(bounds_type), intent(in) :: bounds 
+    class(dust_type), intent(inout) :: this
+    type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
     integer :: c,l
@@ -340,7 +340,7 @@ subroutine DustEmission (bounds, &
     ! !USES
     use shr_const_mod, only : SHR_CONST_RHOFW
     use subgridaveMod, only : p2g
-    use pftconMod            , only : noveg     
+    use pftconMod    , only : noveg
     !
     ! !ARGUMENTS:
     type(bounds_type)      , intent(in)    :: bounds                      
@@ -366,7 +366,6 @@ subroutine DustEmission (bounds, &
     real(r8) :: flx_mss_vrt_dst_ttl(bounds%begp:bounds%endp)
     real(r8) :: frc_thr_wet_fct
     real(r8) :: frc_thr_rgh_fct
-    !real(r8) :: wnd_frc_thr_slt    ! Danny M. Leung commented and put below
     real(r8) :: wnd_rfr_thr_slt
     real(r8) :: wnd_frc_slt
     real(r8) :: lnd_frc_mbl(bounds%begp:bounds%endp)
@@ -377,8 +376,10 @@ subroutine DustEmission (bounds, &
     real(r8) :: sumwt(bounds%begl:bounds%endl) ! sum of weights
     logical  :: found                          ! temporary for error check
     integer  :: index
-    
-    real(r8) :: tmp2   ! calculates the dry fluid threshold using Shao and Lu (2000) scheme; replace the tmp1 (Iversen and White, 1982) that was passed from Dustini to DustEmission; tmp2 will be calculated here
+
+    real(r8) :: tmp2                ! calculates the dry fluid threshold using Shao and Lu (2000) scheme;
+                                    ! replace the tmp1 (Iversen and White, 1982) that was passed from Dustini to DustEmission;
+                                    ! tmp2 will be calculated here
     real(r8) :: wnd_frc_thr_slt_std ! [m/s] The soil threshold friction speed at standard air density (1.2250 kg/m3)
     real(r8) :: frag_expt           ! fragmentation exponent
     real(r8) :: wnd_frc_thr_slt_it  ! [m/s] created for impact threshold friction velocity
@@ -430,7 +431,7 @@ subroutine DustEmission (bounds, &
          mbl_bsn_fct         => dust_inst%mbl_bsn_fct_col            , & ! Input:  [real(r8) (:)   ]  basin factor                                      
          flx_mss_vrt_dst     => dust_inst%flx_mss_vrt_dst_patch      , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
          flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch  , & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
-         
+
          dst_emiss_coeff     => dust_inst%dst_emiss_coeff_patch      , & ! Output dust emission coefficient
          wnd_frc_thr         => dust_inst%wnd_frc_thr_patch          , & ! output impact threshold
          wnd_frc_thr_dry     => dust_inst%wnd_frc_thr_dry_patch      , & ! output dry threshold
@@ -594,7 +595,7 @@ subroutine DustEmission (bounds, &
          wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold
          wnd_frc_thr_slt_it = B_it * tmp2 / sqrt(forc_rho(c)) ! define impact threshold
 
-         !wnd_frc_thr_dry(p) = tmp1 / sqrt(forc_rho(c))    ! output dry fluid threshold; tmp1 uses I&W 1982         
+         !wnd_frc_thr_dry(p) = tmp1 / sqrt(forc_rho(c))    ! output dry fluid threshold; tmp1 uses I&W 1982
          !wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold
          !wnd_frc_thr_slt_it = B_it * tmp1 / sqrt(forc_rho(c)) ! define impact threshold
          ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme
@@ -612,7 +613,7 @@ subroutine DustEmission (bounds, &
          end if
 
          !################ drag partition effect, and soil friction velocity ###########################
-         ! subsection on computing vegetation drag partition and hybrid drag partition factors 
+         ! subsection on computing vegetation drag partition and hybrid drag partition factors
          ! in Leung et al. (2022), drag partition effect is applied on the wind instead of the threshold
          !##############################################################################################
          ! the following comes from subr. frc_thr_rgh_fct_get
@@ -626,24 +627,18 @@ subroutine DustEmission (bounds, &
                lai(p)  = 1_r8   ! setting LAI ~ 0.1 to be a min value (since the value goes to infinity when LAI=0)
             end if              ! and 1 to be a max value as computing K involves 1 / LAI
 
-            ! calculate Okin's shear stress ratio (which is drag partition factor) using Pierre's equation   
+            ! calculate Okin's shear stress ratio (which is drag partition factor) using Pierre's equation
             K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup
             ssr(p) = (K_length+f_0*c_e)/(K_length+c_e)
 
-            ! dmleung added calculation of LUH2 bare vs veg fraction within a grid
-            !bare_frc = wt_lunit(g,istsoil) * wt_nat_patch(g,noveg) 
-            !veg_frc = wt_lunit(g,istsoil) * sum(wt_nat_patch(g,(noveg+1):natpft_ub)) + wt_lunit(g,istcrop)
-
-            !frc_thr_rgh_fct = (bare_frc*(roughfct(p))**3_r8 + veg_frc*(ssr(p))**3_r8 )**(0.3333_r8)   ! land cover weighted mean using LUH2 land cover
-
             ! calculation of drag partition effect using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then
                   frc_thr_rgh_fct = dpfct_rock(p)
-               else 
+               else
                   frc_thr_rgh_fct = ssr(p)
                end if
-            else 
+            else
                frc_thr_rgh_fct = 1.0_r8
             end if
 
@@ -658,30 +653,16 @@ subroutine DustEmission (bounds, &
 
          !########## end of drag partition effect #######################################################
 
-         !############ comment out Owen's offect this block; dust emission does not need to consider it  ###########
-         ! the following if-block comes from subr. wnd_frc_slt_get 
-         ! purpose: compute the saltating friction velocity
-         ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
-
-         !if (u10(p) >= wnd_rfr_thr_slt) then
-         !   wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
-         !   wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
-         !   wnd_frc_slt = wnd_frc_slt + wnd_frc_slt_dlt   ! careful that RHS is now wnd_frc_slt instead of fv(p)
-         ! ! because wnd_frc_slt takes drag partition effect into account, but fv(p) doesn't. 
-         !end if
-         !########## end of Owen effect ################################################################
-
          ! save soil friction velocity and roughness effect before the if-statement
          wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect
          ! save land mobile fraction
          lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement
-         ! only perform the following calculations if lnd_frc_mbl is non-zero 
+         ! only perform the following calculations if lnd_frc_mbl is non-zero
 
          if (lnd_frc_mbl(p) > 0.0_r8) then  ! if bare land fraction is larger than 0 then calculate the dust emission equation
 
             ! reset these variables which will be updated in the following if-block
 
-            !wnd_frc_slt = fv(p)  ! we don't need this line because its calculation is moved upward
             flx_mss_hrz_slt_ttl = 0.0_r8
             flx_mss_vrt_dst_ttl(p) = 0.0_r8
 
@@ -690,32 +671,11 @@ subroutine DustEmission (bounds, &
 
             wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)     ! keep and use if we want the default Z03 scheme
 
-            
             ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
             ! purpose: compute vertically integrated streamwise mass flux of particles
 
-            !if (wnd_frc_slt > wnd_frc_thr_slt) then! if using Zender's scheme, use fluid threshold for dust emission equation below
             if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if using Leung's scheme, use impact threshold for dust emission equation
 
-               !################### for Zender et al. (2003) scheme -dmleung ###########################
-               !################ uncomment the below block if want to use Z03 scheme ###################
-               !wnd_frc_rat = wnd_frc_thr_slt / wnd_frc_slt
-               !flx_mss_hrz_slt_ttl = cst_slt * forc_rho(c) * (wnd_frc_slt**3.0_r8) * &
-               !     (1.0_r8 - wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) / grav  ! Zender dust emission equation for emission flux
-
-               ! the following loop originates from subr. dst_mbl
-               ! purpose: apply land sfc and veg limitations and global tuning factor
-               ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect 
-               ! of frozen soil
-
-               !flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * mbl_bsn_fct(c) * &
-               !     flx_mss_fdg_fct * liqfrac
-
-               !
-               !dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )
-               !flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
-               !########################################################################################
-
                !################### for Leung et al. (2022) ################################################
                !################ uncomment the below block if want to use Leung's scheme ###################
 
@@ -733,14 +693,6 @@ subroutine DustEmission (bounds, &
             ! mean lowpass-filtered wind speed at 0.1 m saltation height (assuming aerodynamic roughness length = 1e-4 m globally for ease; also assuming neutral condition)
             u_mean_slt(p) = (wnd_frc_slt/k) * log(0.1_r8 / 1e-4_r8)  ! translating from ustar (velocity scale) to actual wind
 
-            ! sd of lowpass-filtered wind speed
-            !if (obul(p)==0) then
-            !   zetaobu = 0
-            !else 
-               !zetaobu = zii(p) / obul(p)   ! For now zii is a constant of 1000 m in CLM -dml, 24 Aug 2021
-            !   zetaobu = 1000_r8 / obul(p)   ! For now zii is a constant of 1000 m in CLM -dml, 24 Aug 2021
-            !end if
-            !stblty(p) = zetaobu    ! zetaobu get outputted as the Obukhov stability parameter
             stblty(p) = 0   ! -dmleung 2 Dec 2021: use stability = 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
             if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
                u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
@@ -775,7 +727,7 @@ subroutine DustEmission (bounds, &
 
             ! multiply dust emission flux by intermittency factor
             if (intrmtncy_fct(p) /= intrmtncy_fct(p)) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted
-               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) 
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p)
             else
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * intrmtncy_fct(p)  ! multiply dust flux by intermittency
             end if

From 1e6d8bee191777e6c1580080a1419ba07f5aa2dd Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Feb 2024 01:22:53 -0700
Subject: [PATCH 0064/1248] Add use_prigent_roughness to determine if that
 streams dataset needs to be read in, this is important when we need to flip
 between Zender and Leung

---
 bld/CLMBuildNamelist.pm                         | 14 ++++++++++++--
 bld/namelist_files/namelist_defaults_ctsm.xml   |  1 +
 bld/namelist_files/namelist_definition_ctsm.xml |  5 +++++
 bld/unit_testers/build-namelist_test.pl         |  7 ++++++-
 4 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 33299da345..7e9ae0e2d2 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4575,9 +4575,19 @@ sub setup_logic_misc {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_prigent_roughness {
+  #
+  # The Prigent roughness stream data set read in if needed
+  #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_prigentroughness' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_prigentroughness' );
+  my $var = "use_prigent_roughness";
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var );
+  my $use_prigent = $nl->get_value($var);
+  if ( &value_is_true($use_prigent) ) {
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_prigentroughness' );
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_prigentroughness' );
+  } else {
+    $log->fatal_error("variable \"$var\" MUST be true when Leung_2023 dust emission method is being used" );
+  }
 }
 
 #-------------------------------------------------------------------------------
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 28a372de32..a52477ce6c 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2748,6 +2748,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <!-- Defaults for Prigent's roughness data      -->
 <!-- =========================================  -->
 
+<use_prigent_roughness>.true.</use_prigent_roughness>
 <stream_fldfilename_prigentroughness
 >lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c240127.nc</stream_fldfilename_prigentroughness>
 <stream_meshfile_prigentroughness
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 54514f62c1..f6764b831d 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1788,6 +1788,11 @@ Mapping method from Nitrogen deposition input file to the model resolution
 <!-- Prigent roughness stream -->
 <!-- ========================================================================================  -->
 
+<entry id="use_prigent_roughness" type="logical" category="clm_physics"
+        group="prigentroughness" valid_values="" >
+If TRUE use the Prigent roughness dataset
+</entry>
+
 <entry id="stream_fldfilename_prigentroughness" type="char*256" category="datasets"
        input_pathname="abs" group="prigentroughness" valid_values="" >
 Filename of input stream data for aeolian roughness length (from Prigent's roughness dataset)
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 9b579dd9ce..e05e0857b7 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1999;
+my $ntests = 2000;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 1353;
@@ -531,6 +531,11 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
+     "LeungDust_WO_Prigent"      =>{ options=>" -envxml_dir . -bgc sp",
+                                     namelst=>"use_prigent_roughness=.false.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                   },
      "soilm_stream off w file"      =>{ options=>"-res 0.9x1.25 -envxml_dir .",
                                      namelst=>"use_soil_moisture_streams = .false.,stream_fldfilename_soilm='file_provided_when_off'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

From b9d118f4481e30fa056ac476100b4fbc9249e82a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Feb 2024 01:40:28 -0700
Subject: [PATCH 0065/1248] Remove more commented out code

---
 src/biogeochem/DUSTMod.F90 | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 67c22e207a..7a1bfcc092 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -595,9 +595,6 @@ subroutine DustEmission (bounds, &
          wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold
          wnd_frc_thr_slt_it = B_it * tmp2 / sqrt(forc_rho(c)) ! define impact threshold
 
-         !wnd_frc_thr_dry(p) = tmp1 / sqrt(forc_rho(c))    ! output dry fluid threshold; tmp1 uses I&W 1982
-         !wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold
-         !wnd_frc_thr_slt_it = B_it * tmp1 / sqrt(forc_rho(c)) ! define impact threshold
          ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme
          wnd_frc_thr(p) = wnd_frc_thr_slt          ! output fluid threshold
 

From 2d8a0cf52ff3918280e28672033415aaefc81c2a Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Mon, 12 Feb 2024 18:17:23 -0600
Subject: [PATCH 0066/1248] Resolve comments on pull request 2275 to CTSM main

Changes done:
1. Removed and modified comments as suggested
2. Changed `urban_explicit_ac` default under clm5_0 to .false.
3. Removed changes that are already/going to be on main (bugfix for view factor and number of urban layers)
---
 bld/CLMBuildNamelist.pm                       |  1 -
 bld/namelist_files/namelist_defaults_ctsm.xml |  6 +--
 .../namelist_definition_ctsm.xml              |  3 --
 src/biogeophys/UrbBuildTempOleson2015Mod.F90  | 21 ++--------
 src/biogeophys/UrbanParamsType.F90            |  6 ---
 src/cpl/share_esmf/UrbanTimeVarType.F90       | 42 +++++++------------
 src/main/clm_varpar.F90                       |  3 +-
 7 files changed, 23 insertions(+), 59 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 0895a89ebb..0b9b161c20 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2111,7 +2111,6 @@ sub setup_logic_urban {
 
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac');
-  # X. Li [dev.04]
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic');
 }
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index a3f488b8f9..0d8e45a779 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -166,11 +166,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <calc_human_stress_indices phys="clm5_0" >FAST</calc_human_stress_indices>
 <calc_human_stress_indices phys="clm4_5" >NONE</calc_human_stress_indices>
 
-<!--                                                                              -->
-<!-- X. Li [dev.04]                                                               -->
-<!-- Default urban air conditioning flux and building interior temperature scheme -->
+<!-- Explicit, time-varying urban air conditioning adoption rate scheme -->
 <urban_explicit_ac phys="clm5_1" >.true.</urban_explicit_ac>
-<urban_explicit_ac phys="clm5_0" >.true.</urban_explicit_ac>
+<urban_explicit_ac phys="clm5_0" >.false.</urban_explicit_ac>
 
 <!-- Default urban traffic flux -->
 <urban_traffic>.false.</urban_traffic>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 5f89da9d29..8334b46d2a 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -947,9 +947,6 @@ Turn urban air conditioning/heating ON or OFF and add wasteheat:
     ON_WASTEHEAT = Air conditioning/heating is ON and waste-heat sent to urban canyon
 </entry>
 
-<!--                          -->
-<!-- X. Li [dev.04]           -->
-<!--                          -->
 <entry id="urban_explicit_ac" type="logical" category="clm_physics"
        group="clmu_inparm" valid_values="" >
 If TRUE, use explicit, time-varying AC adoption rate for air-conditioning flux and interior building temperature calculations.
diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index c07b1ad0e3..2e588e2e88 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -210,9 +210,6 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     use clm_varctl      , only : iulog
     use abortutils      , only : endrun
     use clm_varpar      , only : nlevurb, nlevsno, nlevmaxurbgrnd
-    ! X. Li [orig]:
-    ! use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on
-    ! X. Li [dev.04]:
     use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on, urban_explicit_ac
 !
 ! !ARGUMENTS:
@@ -239,7 +236,6 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     real(r8) :: t_floor_bef(bounds%begl:bounds%endl)       ! floor temperature at previous time step (K)              
     real(r8) :: t_building_bef(bounds%begl:bounds%endl)    ! internal building air temperature at previous time step [K]
     real(r8) :: t_building_bef_hac(bounds%begl:bounds%endl)! internal building air temperature before applying HAC [K]
-    ! X. Li [dev.03]
     real(r8) :: eflx_urban_ac_sat(bounds%begl:bounds%endl) ! urban air conditioning flux under AC adoption saturation (W/m**2)
     real(r8) :: hcv_roofi(bounds%begl:bounds%endl)         ! roof convective heat transfer coefficient (W m-2 K-1)
     real(r8) :: hcv_sunwi(bounds%begl:bounds%endl)         ! sunwall convective heat transfer coefficient (W m-2 K-1)
@@ -329,7 +325,6 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     t_floor           => temperature_inst%t_floor_lun      , & ! InOut:  [real(r8) (:)]  floor temperature (K)
     t_building        => temperature_inst%t_building_lun   , & ! InOut:  [real(r8) (:)]  internal building air temperature (K)
 
-    ! X. Li [dev]
     p_ac              => urbantv_inst%p_ac                 , & ! Input:  [real(r8) (:)]  air-conditioning penetration rate (-)
     t_building_max    => urbantv_inst%t_building_max       , & ! Input:  [real(r8) (:)]  maximum internal building air temperature (K)
     t_building_min    => urbanparams_inst%t_building_min   , & ! Input:  [real(r8) (:)]  minimum internal building air temperature (K)
@@ -432,10 +427,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
          vf_wf(l)  = 0.5_r8*(1._r8 - vf_rf(l))
 
          ! This view factor implicitly converts from per unit floor area to per unit wall area
-         ! X. Li [orig]
-         ! vf_fw(l) = vf_wf(l) / building_hwr(l)
-         ! X. Li [bugfix]
-         vf_fw(l) = vf_wf(l)
+         vf_fw(l) = vf_wf(l) / building_hwr(l)
 
          ! This view factor implicitly converts from per unit roof area to per unit wall area
          vf_rw(l)  = vf_fw(l)
@@ -841,10 +833,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
                         + em_floori(l)*sb*t_floor_bef(l)**4._r8 &
                         + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l))
 
-         ! X. Li [orig]
-         ! qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l)
-         ! X. Li [bugfix]
-         qrd_building(l) = qrd_roof(l) + qrd_sunw(l) + qrd_shdw(l) + qrd_floor(l)
+         qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l)
 
          if (abs(qrd_building(l)) > .10_r8 ) then
            write (iulog,*) 'urban inside building net longwave radiation balance error ',qrd_building(l)
@@ -936,16 +925,14 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
 !           rho_dair(l) = pstd / (rair*t_building(l))
 
             if (t_building_bef_hac(l) > t_building_max(l)) then
-              ! X. Li [dev.04]
-              if (urban_explicit_ac) then   ! use explicit ac adoption rate:
-                ! X. Li [dev.03]            ! after the change, t_building_max is saturation setpoint
+              if (urban_explicit_ac) then   ! use explicit ac adoption rate parameterization scheme:
+                ! Here, t_building_max is the AC saturation setpoint
                 eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) &
                                      - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
                 t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) &
                               * dtime / (ht_roof(l) * rho_dair(l) * cpair * wtlunit_roof(l))
                 eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l)
               else
-                ! X. Li [orig] 
                 t_building(l) = t_building_max(l)
                 eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
                                    - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90
index 16da4b3ad0..4b7b80e4fe 100644
--- a/src/biogeophys/UrbanParamsType.F90
+++ b/src/biogeophys/UrbanParamsType.F90
@@ -101,7 +101,6 @@ module UrbanParamsType
   character(len= *), parameter, public :: urban_hac_on =  'ON'                 
   character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT'  
   character(len= 16), public           :: urban_hac = urban_hac_off
-  ! X. Li [dev.04]
   logical, public                      :: urban_explicit_ac = .true.  ! whether to use explicit, time-varying AC adoption rate
   logical, public                      :: urban_traffic = .false.     ! urban traffic fluxes
 
@@ -849,9 +848,6 @@ subroutine UrbanReadNML ( NLFilename )
     integer :: unitn                ! unit for namelist file
     character(len=32) :: subname = 'UrbanReadNML'  ! subroutine name
 
-    ! X. Li [orig]:
-    ! namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method
-    ! X. Li [dev.04]:
     namelist / clmu_inparm / urban_hac, urban_explicit_ac, urban_traffic, building_temp_method
     !EOP
     !-----------------------------------------------------------------------
@@ -880,7 +876,6 @@ subroutine UrbanReadNML ( NLFilename )
 
     ! Broadcast namelist variables read in
     call shr_mpi_bcast(urban_hac,             mpicom)
-    ! X. Li [dev.04]:
     call shr_mpi_bcast(urban_explicit_ac,     mpicom)
     call shr_mpi_bcast(urban_traffic,         mpicom)
     call shr_mpi_bcast(building_temp_method,  mpicom)
@@ -893,7 +888,6 @@ subroutine UrbanReadNML ( NLFilename )
     !
     if ( masterproc )then
        write(iulog,*) '   urban air conditioning/heating and wasteheat   = ', urban_hac
-       ! X. Li [dev.04]:
        write(iulog,*) '   urban explicit air-conditioning adoption rate   = ', urban_explicit_ac
        write(iulog,*) '   urban traffic flux   = ', urban_traffic
     end if
diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 23dbf54086..54d5c61d19 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -12,7 +12,7 @@ module UrbanTimeVarType
   use abortutils      , only : endrun
   use decompMod       , only : bounds_type, subgrid_level_landunit
   use clm_varctl      , only : iulog
-  use landunit_varcon , only : isturb_MIN, isturb_MAX ! X. Li: min and max types urban; equals 7 and 9, resp.
+  use landunit_varcon , only : isturb_MIN, isturb_MAX
   use clm_varcon      , only : spval
   use LandunitType    , only : lun
   use GridcellType    , only : grc
@@ -24,8 +24,7 @@ module UrbanTimeVarType
   type, public :: urbantv_type
      !
      real(r8), public, pointer :: t_building_max(:)    ! lun maximum internal building air temperature (K)
-     ! X. Li [dev]
-     real(r8), public, pointer :: p_ac(:)              ! lun air-conditioning ownership rate (unitless, between 0 and 1)
+     real(r8), public, pointer :: p_ac(:)              ! lun air-conditioning adoption rate (unitless, between 0 and 1)
      type(shr_strdata_type)    :: sdat_urbantv         ! urban time varying input data stream
    contains
      ! !PUBLIC MEMBER FUNCTIONS:
@@ -60,7 +59,7 @@ subroutine Init(this, bounds, NLFilename)
     character(len=*)  , intent(in) :: NLFilename   ! Namelist filename
     !
     ! !LOCAL VARIABLES:
-    integer		:: begl, endl                       ! X. Li: beginning and ending landunit index, from src/main/decompMod
+    integer		:: begl, endl
     !---------------------------------------------------------------------
 
     begl = bounds%begl; endl = bounds%endl
@@ -68,20 +67,18 @@ subroutine Init(this, bounds, NLFilename)
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
-    ! X. Li [dev]
     allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
 
     call this%urbantv_init(bounds, NLFilename)
     call this%urbantv_interp(bounds)
 
-    ! Add history fields     ! X. Li: this adds an output field. the subroutine is in scr/main/histFileMod.F90
+    ! Add history fields
     call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
           avgflag='A', long_name='prescribed maximum interior building temperature',   &
           ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
-    ! X. Li [dev] 
     call hist_addfld1d (fname='P_AC', units='unitless',      &
-          avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)',   &
+          avgflag='A', long_name='prescribed air-conditioning ownership rate (unitless, between 0 and 1)',   &
           ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
 
@@ -97,7 +94,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
     use clm_nlUtilsMod   , only : find_nlgroup_name
     use spmdMod          , only : masterproc, mpicom, iam
     use shr_mpi_mod      , only : shr_mpi_bcast
-    use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md ! X. Li: equals 7, 8 and 9
+    use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md
     use dshr_strdata_mod , only : shr_strdata_init_from_inline
     use lnd_comp_shr     , only : mesh, model_clock
     !
@@ -105,23 +102,23 @@ subroutine urbantv_init(this, bounds, NLFilename)
     implicit none
     class(urbantv_type)           :: this
     type(bounds_type), intent(in) :: bounds
-    character(len=*),  intent(in) :: NLFilename   ! Namelist filename ???is this the netCDF file name?
+    character(len=*),  intent(in) :: NLFilename   ! Namelist filename
     !
     ! !LOCAL VARIABLES:
     integer            :: n
     integer            :: stream_year_first_urbantv         ! first year in urban tv stream to use
     integer            :: stream_year_last_urbantv          ! last year in urban tv stream to use
     integer            :: model_year_align_urbantv          ! align stream_year_first_urbantv with this model year
-    integer            :: nu_nml                            ! unit for namelist file ???
+    integer            :: nu_nml                            ! unit for namelist file
     integer            :: nml_error                         ! namelist i/o error flag
-    character(len=CL)  :: stream_fldFileName_urbantv        ! urban tv streams filename ???
-    character(len=CL)  :: stream_meshfile_urbantv           ! urban tv streams filename ???
-    character(len=CL)  :: urbantvmapalgo = 'nn'             ! mapping alogrithm for urban ac ???
+    character(len=CL)  :: stream_fldFileName_urbantv        ! urban tv streams filename
+    character(len=CL)  :: stream_meshfile_urbantv           ! urban tv streams filename
+    character(len=CL)  :: urbantvmapalgo = 'nn'             ! mapping alogrithm for urban ac
     character(len=CL)  :: urbantv_tintalgo = 'linear'       ! time interpolation alogrithm
     integer            :: rc                                ! error code
     ! X. Li [orig]: this is taken out because field strings are now hard coded in
     ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string
-    character(*), parameter :: subName = "('urbantv_init')" ! ???
+    character(*), parameter :: subName = "('urbantv_init')"
     !-----------------------------------------------------------------------
 
     namelist /urbantv_streams/       &
@@ -215,7 +212,6 @@ subroutine urbantv_init(this, bounds, NLFilename)
          stream_tintalgo     = urbantv_tintalgo,                     &
          stream_name         = 'Urban time varying data',            &
          rc                  = rc)
-
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
     end if
@@ -257,11 +253,10 @@ subroutine urbantv_interp(this, bounds)
     ! Advance sdat stream
     call get_curr_date(year, mon, day, sec)
     mcdate = year*10000 + mon*100 + day
-
     call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
-    end if 
+    end if
 
     ! Create 2d array for all stream variable data
     lsize = bounds%endg - bounds%begg + 1
@@ -306,9 +301,8 @@ subroutine urbantv_interp(this, bounds)
              end if
           end do
        else
-          this%t_building_max(l) = spval ! X. Li: special value for real data, set to 1.e36 in src/main/clm_varcon
-          ! X. Li [dev]
-          this%p_ac(l) = 0._r8 ! X. Li: set to 0 for non-urban landunit
+          this%t_building_max(l) = spval
+          this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit
        end if
     end do
     deallocate(dataptr2d)
@@ -322,11 +316,8 @@ subroutine urbantv_interp(this, bounds)
              ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
-          ! X. Li [orig]
-          ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
-          ! X. Li [dev]
           if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) &
-             .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then
+             .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then   ! check if AC adoption rate is outside of range 0 to 1
              found = .true.
              gindx = g
              lindx = l
@@ -339,7 +330,6 @@ subroutine urbantv_interp(this, bounds)
        write(iulog,*)'landunit type:   ',lun%itype(lindx)
        write(iulog,*)'urban_valid:     ',urban_valid(gindx)
        write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
-       ! X. Li [dev]
        write(iulog,*)'p_ac:            ',this%p_ac(lindx)
        call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, &
             msg=errmsg(sourcefile, __LINE__))
diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90
index 3ef9cf48a2..f54b750181 100644
--- a/src/main/clm_varpar.F90
+++ b/src/main/clm_varpar.F90
@@ -203,8 +203,7 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft)
     max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb)
 
     nlevsoifl   =  10
-    ! X. Li: changed below from 5 to 10 to match new surface data
-    nlevurb     =  10 ! originally 5
+    nlevurb     =  5
 
     if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined
     if ( masterproc ) write(iulog, *) 'soil_layerstruct_userdefined varpar ', soil_layerstruct_userdefined

From 9a05842d4ad3d173b06b3d1559e62c51bfea2fb0 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 12 Feb 2024 22:43:10 -0700
Subject: [PATCH 0067/1248] Add in read of use_prigent_roughness to the FORTRAN
 source

---
 src/biogeochem/DUSTMod.F90                    |  1 +
 .../share_esmf/PrigentRoughnessStreamType.F90 | 33 ++++++++++++++++---
 2 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 7a1bfcc092..f3b3a0cd68 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -63,6 +63,7 @@ module DUSTMod
      real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
      real(r8), pointer, private :: vlc_trb_4_patch           (:)   ! turbulent deposition velocity 4(m/s)
      real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! basin factor
+
      real(r8), pointer, private :: dst_emiss_coeff_patch     (:)   ! dust emission coefficient (unitless)
      real(r8), pointer, private :: wnd_frc_thr_patch         (:)   ! wet fluid threshold (m/s)
      real(r8), pointer, private :: wnd_frc_thr_dry_patch     (:)   ! dry fluid threshold (m/s)
diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index cef34682c9..0766c0ca1a 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -39,7 +39,7 @@ module PrigentRoughnessStreamType
      character(len=CL)  :: stream_meshfile_prigentroughness      ! mesh Filename
      character(len=CL)  :: prigentroughnessmapalgo               ! map algo
   contains
-     procedure, private :: ReadNML     ! Read in namelist
+     procedure, private :: ReadNML     ! Read in namelist                 ! If will be used
   end type streamcontrol_type
 
   type(streamcontrol_type), private :: control        ! Stream control data
@@ -269,6 +269,7 @@ subroutine ReadNML(this, bounds, NLFilename)
    ! local variables
    integer            :: nu_nml    ! unit for namelist file
    integer            :: nml_error ! namelist i/o error flag
+   logical            :: use_prigent_roughness = .true.
    character(len=CL)  :: stream_fldFileName_prigentroughness = ' '
    character(len=CL)  :: stream_meshfile_prigentroughness = ' '
    character(len=CL)  :: prigentroughnessmapalgo = 'bilinear'
@@ -277,7 +278,8 @@ subroutine ReadNML(this, bounds, NLFilename)
    !-----------------------------------------------------------------------
 
    namelist /prigentroughness/ &               ! MUST agree with namelist_name above
-        prigentroughnessmapalgo,  stream_fldFileName_prigentroughness, stream_meshfile_prigentroughness
+        prigentroughnessmapalgo,  stream_fldFileName_prigentroughness, stream_meshfile_prigentroughness, &
+        use_prigent_roughness
 
    ! Default values for namelist
 
@@ -296,16 +298,37 @@ subroutine ReadNML(this, bounds, NLFilename)
       close(nu_nml)
    endif
 
+   call shr_mpi_bcast(use_prigent_roughness               , mpicom)
    call shr_mpi_bcast(prigentroughnessmapalgo             , mpicom)
    call shr_mpi_bcast(stream_fldFileName_prigentroughness , mpicom)
    call shr_mpi_bcast(stream_meshfile_prigentroughness    , mpicom)
 
+   ! Error checking
+   if ( use_prigent_roughness == .false. )then
+      if ( len_trim(stream_fldFileName_prigentroughness) /= 0 )then
+         call endrun(msg=' ERROR stream_fldFileName_prigentroughness is set, but use_prigent_roughness is FALSE'//errMsg(sourcefile, __LINE__))
+      end if
+      if ( len_trim(stream_meshfile_prigentroughness) /= 0 )then
+         call endrun(msg=' ERROR stream_meshfile_prigentroughness is set, but use_prigent_roughness is FALSE'//errMsg(sourcefile, __LINE__))
+      end if
+   else
+      if ( len_trim(stream_fldFileName_prigentroughness) == 0 )then
+         call endrun(msg=' ERROR stream_fldFileName_prigentroughness is NOT set, but use_prigent_roughness is TRUE'//errMsg(sourcefile, __LINE__))
+      end if
+      if ( len_trim(stream_meshfile_prigentroughness) == 0 )then
+         call endrun(msg=' ERROR stream_meshfile_prigentroughness is NOT set, but use_prigent_roughness is TRUE'//errMsg(sourcefile, __LINE__))
+      end if
+   end if
+
    if (masterproc) then
       write(iulog,*) ' '
       write(iulog,*) namelist_name, ' stream settings:'
-      write(iulog,*) '  stream_fldFileName_prigentroughness = ',stream_fldFileName_prigentroughness
-      write(iulog,*) '  stream_meshfile_prigentroughness    = ',stream_meshfile_prigentroughness
-      write(iulog,*) '  prigentroughnessmapalgo             = ',prigentroughnessmapalgo
+      write(iulog,*) '  use_prigent_roughness               = ',use_prigent_roughness
+      if ( use_prigent_roughness )then
+         write(iulog,*) '  stream_fldFileName_prigentroughness = ',trim(stream_fldFileName_prigentroughness)
+         write(iulog,*) '  stream_meshfile_prigentroughness    = ',trim(stream_meshfile_prigentroughness)
+         write(iulog,*) '  prigentroughnessmapalgo             = ',trim(prigentroughnessmapalgo)
+      end if
    endif
    this%stream_fldFileName_prigentroughness = stream_fldFileName_prigentroughness
    this%stream_meshfile_prigentroughness    = stream_meshfile_prigentroughness

From d8b6cb8f6c27186a252d23f8ae1d3521e9c1323e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 13 Feb 2024 11:39:16 -0700
Subject: [PATCH 0068/1248] Remove an empty call the prigentRoughness call is
 what's being used

---
 bld/CLMBuildNamelist.pm | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 7e9ae0e2d2..8081f1277e 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1706,11 +1706,6 @@ sub process_namelist_inline_logic {
   ##################################
   setup_logic_lai_streams($opts,  $nl_flags, $definition, $defaults, $nl);
 
-  ##################################
-  # namelist group: dust_emis_streams  #
-  ##################################
-  #setup_logic_dustemis_streams($opts,  $nl_flags, $definition, $defaults, $nl);
-
   ##################################
   # namelist group: cropcal_streams  #
   ##################################

From 4a72a1c9be9f1ba97a0f9ef98905a37addcc1771 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 13 Feb 2024 12:00:52 -0700
Subject: [PATCH 0069/1248] Work with some indentation, remove commented out
 code, add a deallocate that was missing, add underscore to a name for
 readability, always allocate, but allocate only 0th element if usestreams is
 false

---
 .../share_esmf/PrigentRoughnessStreamType.F90 | 24 ++++++++++++-------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 0766c0ca1a..dec9fa86fd 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -79,17 +79,18 @@ subroutine Init(this, bounds, NLFilename)
    character(len=16), allocatable :: stream_varnames(:) ! array of stream field names
    integer                        :: rc                 ! error code
    real(r8), pointer              :: dataptr1d(:)       ! temporary pointer
-   character(len=*), parameter    :: stream_name = 'prigentroughness'
+   character(len=*), parameter    :: stream_name = 'prigent_roughness'
    !-----------------------------------------------------------------------
 
-   !if ( finundation_mtd /= finundation_mtd_h2osfc )then
-      call this%InitAllocate( bounds )
       call control%ReadNML( bounds, NLFileName )
 
+      call this%InitAllocate( bounds )
+
       if ( this%useStreams() )then
 
-            allocate(stream_varnames(1))
-            stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
+
+         allocate(stream_varnames(1))
+         stream_varnames = (/"Z0a"/)  ! varname in cdf5_Z0a_Prigent-Globe-025x025-09262022.nc, in centimeter
 
          if (masterproc) then
             write(iulog,*) '  stream_varnames                  = ',stream_varnames
@@ -152,8 +153,8 @@ subroutine Init(this, bounds, NLFilename)
             end if
 
          end do
+         deallocate(stream_varnames)
       end if
-   !end if         !commented out
 
   end subroutine Init
 
@@ -161,7 +162,7 @@ end subroutine Init
   logical function UseStreams(this)
     !
     ! !DESCRIPTION:
-    ! Return true if
+    ! Return true if the Prigent Roughness stream is being used
     !
     ! !USES:
     !
@@ -171,7 +172,7 @@ logical function UseStreams(this)
     !
     ! !LOCAL VARIABLES:
     if ( trim(control%stream_fldFileName_prigentroughness) == '' )then
-       UseStreams = .false.  ! this won't happen and UseStreams will always be true
+       UseStreams = .false.  ! Prigent streams are off without a filename given
     else
        UseStreams = .true.
     end if
@@ -197,7 +198,12 @@ subroutine InitAllocate(this, bounds)
 
     begg = bounds%begg; endg = bounds%endg
 
-    allocate(this%prigent_rghn     (begg:endg))            ;  this%prigent_rghn     (:)   = nan
+    if ( this%useStreams() )then
+       allocate(this%prigent_rghn(begg:endg))
+    else
+       allocate(this%prigent_rghn(0))
+    end if
+    this%prigent_rghn(:) = nan
 
   end subroutine InitAllocate
 

From 3291040ae8d1fbe9fbf60d4e2d97f177cfba1983 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 13 Feb 2024 12:54:44 -0700
Subject: [PATCH 0070/1248] Shorten many lines (will help with nag compiler),
 add extra error checking around making sure namelist is read in and stream
 initialization has been done, this builds and runs

---
 .../share_esmf/PrigentRoughnessStreamType.F90 | 105 +++++++++++++-----
 1 file changed, 79 insertions(+), 26 deletions(-)

diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index dec9fa86fd..734c26ea8a 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -6,7 +6,7 @@ module PrigentRoughnessStreamType
   ! Contains methods for reading in the Prigent et al. (1997) roughness length streams file
   ! Created by Danny M. Leung 22 Nov 2022
   ! !USES
-  use ESMF                         
+  use ESMF
   use dshr_strdata_mod , only : shr_strdata_type
   use shr_kind_mod     , only : r8 => shr_kind_r8, CL => shr_kind_cl
   use shr_log_mod      , only : errMsg => shr_log_errMsg
@@ -20,13 +20,14 @@ module PrigentRoughnessStreamType
   private
 
   type, public :: prigentroughnessstream_type
-     real(r8), pointer, private :: prigent_rghn  (:)         ! Prigent et al. (1997) roughness length (m)
+     real(r8), pointer, public :: prigent_rghn  (:)         ! Prigent et al. (1997) roughness length (m)
   contains
 
       ! !PUBLIC MEMBER FUNCTIONS:
       procedure, public :: Init            ! Initialize and read data in
       procedure, public :: CalcDragPartition ! Calculate drag partitioning based on input streams
-      procedure, public :: UseStreams      ! If streams will be used -- dmleung set default as yes
+      procedure, public :: UseStreams      ! If Prigent rougness streams will be used
+      procedure, public :: IsStreamInit    ! If the streams have been initialized and read in, so data can be used
 
       ! !PRIVATE MEMBER FUNCTIONS:
       procedure, private :: InitAllocate   ! Allocate data
@@ -39,12 +40,14 @@ module PrigentRoughnessStreamType
      character(len=CL)  :: stream_meshfile_prigentroughness      ! mesh Filename
      character(len=CL)  :: prigentroughnessmapalgo               ! map algo
   contains
-     procedure, private :: ReadNML     ! Read in namelist                 ! If will be used
+     procedure, private :: ReadNML      ! Read in control namelist
   end type streamcontrol_type
 
-  type(streamcontrol_type), private :: control        ! Stream control data
+  type(streamcontrol_type), private :: control             ! Stream control data
+  logical                 , private :: NMLRead = .false.   ! If namelist has been read
+  logical                 , private :: InitDone = .false.  ! If initialization of streams has been done
 
-  character(len=*), parameter, private :: sourcefile = &  
+  character(len=*), parameter, private :: sourcefile = &
        __FILE__
 
 !==============================================================================
@@ -80,6 +83,7 @@ subroutine Init(this, bounds, NLFilename)
    integer                        :: rc                 ! error code
    real(r8), pointer              :: dataptr1d(:)       ! temporary pointer
    character(len=*), parameter    :: stream_name = 'prigent_roughness'
+   character(len=*), parameter    :: subname     = 'PrigentRoughnessStream::Init'
    !-----------------------------------------------------------------------
 
       call control%ReadNML( bounds, NLFileName )
@@ -138,7 +142,7 @@ subroutine Init(this, bounds, NLFilename)
          end if
 
          ! Get pointer for stream data that is time and spatially interpolate to model time and grid
-         do n = 1,size(stream_varnames) 
+         do n = 1,size(stream_varnames)
             call dshr_fldbun_getFldPtr(sdat_rghn%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc)
             if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
                call ESMF_Finalize(endflag=ESMF_END_ABORT)
@@ -154,6 +158,7 @@ subroutine Init(this, bounds, NLFilename)
 
          end do
          deallocate(stream_varnames)
+         InitDone = .true.
       end if
 
   end subroutine Init
@@ -170,7 +175,11 @@ logical function UseStreams(this)
     implicit none
     class(prigentroughnessstream_type) :: this
     !
-    ! !LOCAL VARIABLES:
+    character(len=*), parameter :: subname = 'PrigentRoughnessStream::UseStreams'
+    !
+    if ( .not. NMLRead )then
+       call endrun(msg=subname//' ERROR Namelist has NOT been read first, call Init before this')
+    end if
     if ( trim(control%stream_fldFileName_prigentroughness) == '' )then
        UseStreams = .false.  ! Prigent streams are off without a filename given
     else
@@ -178,6 +187,30 @@ logical function UseStreams(this)
     end if
   end function UseStreams
 
+  !==============================================================================
+  logical function IsStreamInit(this)
+    !
+    ! !DESCRIPTION:
+    ! Return true if the streams have been initialized
+    !
+    ! !USES:
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(prigentroughnessstream_type) :: this
+    !
+    character(len=*), parameter :: subname = 'PrigentRoughnessStream::IsStreamInit'
+    !
+    if ( .not. NMLRead )then
+       call endrun(msg=subname//' ERROR Namelist has NOT been read first, call Init before this')
+    end if
+    if ( InitDone )then
+       IsStreamInit = .true.
+    else
+       IsStreamInit = .false.
+    end if
+  end function IsStreamInit
+
   !==============================================================================
   subroutine InitAllocate(this, bounds)
     !
@@ -212,13 +245,13 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     !
     ! !DESCRIPTION:
     ! Commented below by Danny M. Leung 31 Dec 2022
-    ! Calculate the drag partition effect of friction velocity due to surface roughness following 
-    ! Leung et al. (2022).  This module is used in the dust emission module DUSTMod.F90 for 
-    ! calculating drag partitioning. The drag partition equation comes from Marticorena and 
-    ! Bergametti (1995) with constants modified by Darmenova et al. (2009). Here it is assumed 
+    ! Calculate the drag partition effect of friction velocity due to surface roughness following
+    ! Leung et al. (2022).  This module is used in the dust emission module DUSTMod.F90 for
+    ! calculating drag partitioning. The drag partition equation comes from Marticorena and
+    ! Bergametti (1995) with constants modified by Darmenova et al. (2009). Here it is assumed
     ! that this equation is used only over arid/desertic regions, such that Catherine Prigent's
     ! roughness measurements represents mostly rocks. For more vegetated areas, the vegetation
-    ! roughness and drag partitioning are calculated in the DustEmission subroutine. This 
+    ! roughness and drag partitioning are calculated in the DustEmission subroutine. This
     ! subroutine is used in the InitCold subroutine of DUSTMod.F90.
     !
     ! !USES:
@@ -228,29 +261,42 @@ subroutine CalcDragPartition(this, bounds, dpfct_rock)
     !
     ! !ARGUMENTS:
     implicit none
-    class(prigentroughnessstream_type)             :: this
-    type(bounds_type)              , intent(in)    :: bounds
-    real(r8)                       , intent(inout) :: dpfct_rock(bounds%begp:)      ! [fraction] rock drag partition factor (roughness effect)
+    class(prigentroughnessstream_type) :: this
+    type(bounds_type)  , intent(in)    :: bounds
+    real(r8)           , intent(inout) :: dpfct_rock(bounds%begp:) ! [fraction] rock drag partition factor (roughness effect)
     !
     ! !LOCAL VARIABLES:
     integer  :: g, p, fp, l    ! Indices
     real(r8) :: z0s         ! smooth roughness length (m)
-    
+
     ! constants
-    real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2022)
-    real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume estimating roughness effect at a distance of 10 m following Leung et al. (2022)
+    real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant
+                                                     ! of ~130 um following Leung et al. (2022)
+    real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume
+                                                     ! estimating roughness effect at a distance of 10 m following Leung et al. (2022)
+    character(len=*), parameter :: subname = 'PrigentRoughnessStream::CalcDragPartition'
     !---------------------------------------------------------------------
 
     SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__)
 
+    ! Make sure we've been initialized
+    if ( .not. this%IsStreamInit() )then
+       call endrun(msg=subname//' ERROR Streams have not been initialized, make sure Init is called first' &
+                              //', and streams are on')
+    end if
 
-    ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks. We save the drag partition factor as a patch level quantity.
-    z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006). Here we assume soil medium size is a global constant, and so is smooth roughness length.
+    ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks.
+    !          We save the drag partition factor as a patch level quantity.
+    ! TODO: EBK 02/13/2024: Several magic numbers here that should become parameters so the meaning is preserved
+    z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006).
+                             ! Here we assume soil medium size is a global constant, and so is smooth roughness length.
     do p = bounds%begp,bounds%endp
        g = patch%gridcell(p)
        l = patch%landunit(p)
        if (lun%itype(l) /= istdlak) then
-          dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)**0.8_r8) ) ! Calculating rock drag partition factor using Marticorena and Bergametti (1995). 0.01 is used to convert Z0a from centimeter to meter.
+          ! Calculating rock drag partition factor using Marticorena and Bergametti (1995).
+          ! 0.01 is used to convert Z0a from centimeter to meter.
+          dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)**0.8_r8) )
        end if
     end do
 
@@ -312,17 +358,21 @@ subroutine ReadNML(this, bounds, NLFilename)
    ! Error checking
    if ( use_prigent_roughness == .false. )then
       if ( len_trim(stream_fldFileName_prigentroughness) /= 0 )then
-         call endrun(msg=' ERROR stream_fldFileName_prigentroughness is set, but use_prigent_roughness is FALSE'//errMsg(sourcefile, __LINE__))
+         call endrun(msg=' ERROR stream_fldFileName_prigentroughness is set, but use_prigent_roughness is FALSE' &
+                     //errMsg(sourcefile, __LINE__))
       end if
       if ( len_trim(stream_meshfile_prigentroughness) /= 0 )then
-         call endrun(msg=' ERROR stream_meshfile_prigentroughness is set, but use_prigent_roughness is FALSE'//errMsg(sourcefile, __LINE__))
+         call endrun(msg=' ERROR stream_meshfile_prigentroughness is set, but use_prigent_roughness is FALSE' &
+                     //errMsg(sourcefile, __LINE__))
       end if
    else
       if ( len_trim(stream_fldFileName_prigentroughness) == 0 )then
-         call endrun(msg=' ERROR stream_fldFileName_prigentroughness is NOT set, but use_prigent_roughness is TRUE'//errMsg(sourcefile, __LINE__))
+         call endrun(msg=' ERROR stream_fldFileName_prigentroughness is NOT set, but use_prigent_roughness is TRUE' &
+                     //errMsg(sourcefile, __LINE__))
       end if
       if ( len_trim(stream_meshfile_prigentroughness) == 0 )then
-         call endrun(msg=' ERROR stream_meshfile_prigentroughness is NOT set, but use_prigent_roughness is TRUE'//errMsg(sourcefile, __LINE__))
+         call endrun(msg=' ERROR stream_meshfile_prigentroughness is NOT set, but use_prigent_roughness is TRUE' &
+                    //errMsg(sourcefile, __LINE__))
       end if
    end if
 
@@ -340,6 +390,9 @@ subroutine ReadNML(this, bounds, NLFilename)
    this%stream_meshfile_prigentroughness    = stream_meshfile_prigentroughness
    this%prigentroughnessmapalgo             = prigentroughnessmapalgo
 
+   ! Mark namelist read as having been done
+   NMLRead = .true.
+
  end subroutine ReadNML
 
 end module PrigentRoughnessStreamType

From 2886a18151b35cf6ee4c60433ee696a2ecce4327 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 13 Feb 2024 15:35:29 -0700
Subject: [PATCH 0071/1248] Move CalcDragPartition to DUSTMod from
 PrigentRoughnessStream object

---
 src/biogeochem/DUSTMod.F90 | 75 +++++++++++++++++++++++++++++++++++---
 1 file changed, 69 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index f3b3a0cd68..e3f9dd669c 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -84,7 +84,7 @@ module DUSTMod
      real(r8), pointer, private :: lai_patch                 (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin's drag partition, averaged to landunit level
      real(r8), pointer, private :: frc_thr_rghn_fct_patch    (:)   ! [dimless] hybrid drag partition (or called roughness) factor
      real(r8), pointer, private :: wnd_frc_thr_std_patch     (:)   ! standardized fluid threshold friction velocity (m/s)
-     type(prigentroughnessstream_type), private :: prigentroughnessstream      ! Prigent roughness stream data
+     type(prigentroughnessstream_type), private :: prigent_roughness_stream      ! Prigent roughness stream data
      real(r8), pointer, private :: dpfct_rock_patch          (:)   ! [fraction] rock drag partition factor, time-constant
    contains
 
@@ -92,7 +92,8 @@ module DUSTMod
      procedure , private :: InitAllocate 
      procedure , private :: InitHistory  
      procedure , private :: InitCold     
-     procedure , private :: InitDustVars ! Initialize variables used in subroutine Dust
+     procedure , private :: InitDustVars      ! Initialize variables used in subroutine Dust
+     procedure , private :: CalcDragPartition ! Calculate drag partitioning based on Prigent roughness stream
 
   end type dust_type
   !------------------------------------------------------------------------
@@ -111,7 +112,7 @@ subroutine Init(this, bounds, NLFilename)
 
     call this%InitAllocate (bounds)
     call this%InitHistory  (bounds)
-    call this%prigentroughnessstream%Init( bounds, NLFilename )
+    call this%prigent_roughness_stream%Init( bounds, NLFilename )
     call this%InitCold     (bounds)
     call this%InitDustVars (bounds)
 
@@ -315,9 +316,8 @@ subroutine InitCold(this, bounds)
     end do
 
       ! Caulculate Drag Partition factor
-      if ( this%prigentroughnessstream%useStreams() )then !if usestreams == true, and it should be always true
-         call this%prigentroughnessstream%CalcDragPartition( bounds, &
-                                this%dpfct_rock_patch(bounds%begp:bounds%endp) )
+      if ( this%prigent_roughness_stream%useStreams() )then !if usestreams == true, and it should be always true
+         call this%CalcDragPartition( bounds, this%prigent_roughness_stream )
       else
 
          call endrun( "ERROR:: Drag partitioning MUST now use a streams file of aeolian roughness length to calculate, it can no longer read from the fsurdat file" )
@@ -1219,4 +1219,67 @@ subroutine InitDustVars(this, bounds)
 
   end subroutine InitDustVars
 
+  !==============================================================================
+  subroutine CalcDragPartition(this, bounds, prigent_roughness_stream )
+    !
+    ! !DESCRIPTION:
+    ! Commented below by Danny M. Leung 31 Dec 2022
+    ! Calculate the drag partition effect of friction velocity due to surface roughness following
+    ! Leung et al. (2022).  This module is used in the dust emission module DUSTMod.F90 for
+    ! calculating drag partitioning. The drag partition equation comes from Marticorena and
+    ! Bergametti (1995) with constants modified by Darmenova et al. (2009). Here it is assumed
+    ! that this equation is used only over arid/desertic regions, such that Catherine Prigent's
+    ! roughness measurements represents mostly rocks. For more vegetated areas, the vegetation
+    ! roughness and drag partitioning are calculated in the DustEmission subroutine. This
+    ! subroutine is used in the InitCold subroutine of DUSTMod.F90.
+    !
+    ! !USES:
+    use PatchType               , only : patch
+    use landunit_varcon         , only : istdlak
+    use LandunitType            , only : lun
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(dust_type) , intent(inout) :: this
+    type(bounds_type), intent(in) :: bounds
+    type(prigentroughnessstream_type), intent(in) :: prigent_roughness_stream
+    !
+    ! !LOCAL VARIABLES:
+    integer  :: g, p, fp, l    ! Indices
+    real(r8) :: z0s         ! smooth roughness length (m)
+
+    ! constants
+    real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant
+                                                     ! of ~130 um following Leung et al. (2022)
+    real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume
+                                                     ! estimating roughness effect at a distance of 10 m following Leung et al. (2022)
+    character(len=*), parameter :: subname = 'PrigentRoughnessStream::CalcDragPartition'
+    !---------------------------------------------------------------------
+
+    ! Make sure we've been initialized
+    if ( .not. prigent_roughness_stream%IsStreamInit() )then
+       call endrun(msg=subname//' ERROR Streams have not been initialized, make sure Init is called first' &
+                              //', and streams are on')
+    end if
+
+    ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks.
+    !          We save the drag partition factor as a patch level quantity.
+    ! TODO: EBK 02/13/2024: Several magic numbers here that should become parameters so the meaning is preserved
+    z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006).
+                             ! Here we assume soil medium size is a global constant, and so is smooth roughness length.
+    do p = bounds%begp,bounds%endp
+       g = patch%gridcell(p)
+       l = patch%landunit(p)
+       if (lun%itype(l) /= istdlak) then
+          ! Calculating rock drag partition factor using Marticorena and Bergametti (1995).
+          ! 0.01 is used to convert Z0a from centimeter to meter.
+          this%dpfct_rock_patch(p) = 1._r8 - ( log(prigent_roughness_stream%prigent_rghn(g)*0.01_r8/z0s) &
+                             / log(0.7_r8*(X/z0s)**0.8_r8) )
+       end if
+    end do
+
+  end subroutine CalcDragPartition
+
+  !==============================================================================
+
 end module DUSTMod

From e2123b0215d8228e03f9f12d4b47ed34a3106bfe Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 13 Feb 2024 16:02:33 -0700
Subject: [PATCH 0072/1248] Move CalcDragPartition to DUSTMod from
 PrigentRoughnessStream object

---
 .../share_esmf/PrigentRoughnessStreamType.F90 | 73 ++-----------------
 1 file changed, 5 insertions(+), 68 deletions(-)

diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 734c26ea8a..751fe8458c 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -1,5 +1,5 @@
 module PrigentRoughnessStreamType
-#include "shr_assert.h"
+
 
   !-----------------------------------------------------------------------
   ! !DESCRIPTION:
@@ -25,7 +25,6 @@ module PrigentRoughnessStreamType
 
       ! !PUBLIC MEMBER FUNCTIONS:
       procedure, public :: Init            ! Initialize and read data in
-      procedure, public :: CalcDragPartition ! Calculate drag partitioning based on input streams
       procedure, public :: UseStreams      ! If Prigent rougness streams will be used
       procedure, public :: IsStreamInit    ! If the streams have been initialized and read in, so data can be used
 
@@ -101,15 +100,15 @@ subroutine Init(this, bounds, NLFilename)
          end if
 
          ! Initialize the cdeps data type sdat_rghn
-         call shr_strdata_init_from_inline(sdat_rghn,                                  &
+         call shr_strdata_init_from_inline(sdat_rghn,                                   &
               my_task             = iam,                                                &
               logunit             = iulog,                                              &
               compname            = 'LND',                                              &
               model_clock         = model_clock,                                        &
               model_mesh          = mesh,                                               &
-              stream_meshfile     = control%stream_meshfile_prigentroughness,              &
+              stream_meshfile     = control%stream_meshfile_prigentroughness,           &
               stream_lev_dimname  = 'null',                                             &
-              stream_mapalgo      = control%prigentroughnessmapalgo,                       &
+              stream_mapalgo      = control%prigentroughnessmapalgo,                    &
               stream_filenames    = (/trim(control%stream_fldFileName_prigentroughness)/), &
               stream_fldlistFile  = stream_varnames,                                    &
               stream_fldListModel = stream_varnames,                                    &
@@ -120,7 +119,7 @@ subroutine Init(this, bounds, NLFilename)
               stream_taxmode      = 'extend',                                           &
               stream_dtlimit      = 1.0e30_r8,                                          &
               stream_tintalgo     = 'linear',                                           &
-              stream_name         = 'Prigent roughness',                                 &
+              stream_name         = 'Prigent roughness',                                &
               rc                  = rc)
          if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
             call ESMF_Finalize(endflag=ESMF_END_ABORT)
@@ -240,68 +239,6 @@ subroutine InitAllocate(this, bounds)
 
   end subroutine InitAllocate
 
-  !==============================================================================
-  subroutine CalcDragPartition(this, bounds, dpfct_rock)
-    !
-    ! !DESCRIPTION:
-    ! Commented below by Danny M. Leung 31 Dec 2022
-    ! Calculate the drag partition effect of friction velocity due to surface roughness following
-    ! Leung et al. (2022).  This module is used in the dust emission module DUSTMod.F90 for
-    ! calculating drag partitioning. The drag partition equation comes from Marticorena and
-    ! Bergametti (1995) with constants modified by Darmenova et al. (2009). Here it is assumed
-    ! that this equation is used only over arid/desertic regions, such that Catherine Prigent's
-    ! roughness measurements represents mostly rocks. For more vegetated areas, the vegetation
-    ! roughness and drag partitioning are calculated in the DustEmission subroutine. This
-    ! subroutine is used in the InitCold subroutine of DUSTMod.F90.
-    !
-    ! !USES:
-    use PatchType               , only : patch
-    use landunit_varcon         , only : istdlak
-    use LandunitType            , only : lun
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(prigentroughnessstream_type) :: this
-    type(bounds_type)  , intent(in)    :: bounds
-    real(r8)           , intent(inout) :: dpfct_rock(bounds%begp:) ! [fraction] rock drag partition factor (roughness effect)
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: g, p, fp, l    ! Indices
-    real(r8) :: z0s         ! smooth roughness length (m)
-
-    ! constants
-    real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant
-                                                     ! of ~130 um following Leung et al. (2022)
-    real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume
-                                                     ! estimating roughness effect at a distance of 10 m following Leung et al. (2022)
-    character(len=*), parameter :: subname = 'PrigentRoughnessStream::CalcDragPartition'
-    !---------------------------------------------------------------------
-
-    SHR_ASSERT_ALL_FL((ubound(dpfct_rock)        == (/bounds%endp/)), sourcefile, __LINE__)
-
-    ! Make sure we've been initialized
-    if ( .not. this%IsStreamInit() )then
-       call endrun(msg=subname//' ERROR Streams have not been initialized, make sure Init is called first' &
-                              //', and streams are on')
-    end if
-
-    ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks.
-    !          We save the drag partition factor as a patch level quantity.
-    ! TODO: EBK 02/13/2024: Several magic numbers here that should become parameters so the meaning is preserved
-    z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006).
-                             ! Here we assume soil medium size is a global constant, and so is smooth roughness length.
-    do p = bounds%begp,bounds%endp
-       g = patch%gridcell(p)
-       l = patch%landunit(p)
-       if (lun%itype(l) /= istdlak) then
-          ! Calculating rock drag partition factor using Marticorena and Bergametti (1995).
-          ! 0.01 is used to convert Z0a from centimeter to meter.
-          dpfct_rock(p) = 1._r8 - ( log(this%prigent_rghn(g)*0.01_r8/z0s) / log(0.7_r8*(X/z0s)**0.8_r8) )
-       end if
-    end do
-
-  end subroutine CalcDragPartition
-
   !==============================================================================
   subroutine ReadNML(this, bounds, NLFilename)
    !

From 3e9d6b67c2af06cd2a9d699640ee3d242245cc01 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 20 Feb 2024 00:37:15 -0700
Subject: [PATCH 0073/1248] dmleung fixed many of ekluzek's comments: defining
 magic values into physical parameters, changing numbers into double
 precisions, and putting more comments into the code. 20 Feb 2024

---
 src/biogeochem/DUSTMod.F90                   | 117 +++++++++++--------
 src/biogeophys/SoilStateInitTimeConstMod.F90 |   4 +-
 2 files changed, 68 insertions(+), 53 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index e3f9dd669c..275f0a4c10 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -228,7 +228,7 @@ subroutine InitHistory(this, bounds)
          ptr_patch=this%lnd_frc_mble_patch, set_lake=0._r8, set_urb=0._r8)
     this%gwc_patch(begp:endp) = spval
     call hist_addfld1d (fname='GWC', units='kg/kg',  &
-         avgflag='A', long_name='gravimetric water content', &
+         avgflag='A', long_name='gravimetric soil moisture at the topmost soil layer', &
          ptr_patch=this%gwc_patch, set_lake=0._r8, set_urb=0._r8)
     this%liq_frac_patch(begp:endp) = spval
     call hist_addfld1d (fname='LIQ_FRAC', units='dimensionless',  &
@@ -276,7 +276,7 @@ subroutine InitHistory(this, bounds)
          ptr_patch=this%ssr_patch, set_lake=0._r8, set_urb=0._r8)
     this%lai_patch(begp:endp) = spval
     call hist_addfld1d (fname='LAI', units='m/s',  &
-         avgflag='A', long_name='landunit-mean LAI for Okin-Pierre scheme', &
+         avgflag='A', long_name='leaf area index for Okin-Pierre scheme', &
          ptr_patch=this%lai_patch, set_lake=0._r8, set_urb=0._r8)
     this%frc_thr_rghn_fct_patch(begp:endp) = spval
     call hist_addfld1d (fname='FRC_THR_RGHN_FCT', units='dimensionless',  &
@@ -395,7 +395,7 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
     !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
     character(len=*),parameter :: subname = 'DUSTEmission'
-    real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests 1, and the old 0.3 seems a bit too small
+    real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests 1, and Zender's scheme uses 0.3
     real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient
     real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent
     real(r8), parameter :: Ce = 2.0_r8                 ! [dimless] proportionality constant scaling exponential dependence of dust emission coefficient on standardized soil threshold friction speed
@@ -407,6 +407,12 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: k = 0.4_r8                  ! [dimless] von Karman constant
     real(r8), parameter :: f_0 = 0.32_r8               ! [dimless] SSR in the immediate lee of a plant
     real(r8), parameter :: c_e = 4.8_r8                ! [dimless] e-folding distance velocity recovery
+    real(r8), parameter :: D_p = 130e-6_r8             ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2023). dmleung 16 Feb 2024
+    real(r8), parameter :: gamma_Shao = 1.65e-4_r8     ! [kg s-2] interparticle cohesion: fitting parameter in Shao and Lu (2000) (S&L00). dmleung 16 Feb 2024
+    real(r8), parameter :: A_Shao = 0.0123_r8          ! [dimless] coefficient for aerodynamic force: fitting parameter in Shao and Lu (2000). dmleung 16 Feb 2024 
+    real(r8), parameter :: frag_expt_thr = 5.0_r8      ! [dimless] threshold for fragmentation exponent defined in Leung et al. (2023), somewhere within 3 to 5. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024
+    real(r8), parameter :: z0a_glob = 1e-4             ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
+    real(r8), parameter :: hgt_sal = 0.1               ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
     real(r8) :: numer                                  ! Numerator term for threshold crossing rate
     real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     !------------------------------------------------------------------------
@@ -432,28 +438,28 @@ subroutine DustEmission (bounds, &
          mbl_bsn_fct         => dust_inst%mbl_bsn_fct_col            , & ! Input:  [real(r8) (:)   ]  basin factor                                      
          flx_mss_vrt_dst     => dust_inst%flx_mss_vrt_dst_patch      , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
          flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch  , & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
-
+         ! below variables are defined in Kok et al. (2014) or (mostly) Leung et al. (2023) dust emission scheme. dmleung 16 Feb 2024
          dst_emiss_coeff     => dust_inst%dst_emiss_coeff_patch      , & ! Output dust emission coefficient
          wnd_frc_thr         => dust_inst%wnd_frc_thr_patch          , & ! output impact threshold
          wnd_frc_thr_dry     => dust_inst%wnd_frc_thr_dry_patch      , & ! output dry threshold
          lnd_frc_mble        => dust_inst%lnd_frc_mble_patch         , & ! output bare land fraction
          wnd_frc_soil        => dust_inst%wnd_frc_soil_patch         , & ! soil friction velocity u_*s = (u_*)(f_eff)
          gwc                 => dust_inst%gwc_patch                  , & ! output gravimetric water content
-         liq_frac            => dust_inst%liq_frac_patch             , &
-         intrmtncy_fct       => dust_inst%intrmtncy_fct_patch        , &
-         stblty              => dust_inst%stblty_patch               , &
-         u_mean_slt          => dust_inst%u_mean_slt_patch           , &
-         u_sd_slt            => dust_inst%u_sd_slt_patch             , &
-         u_fld_thr           => dust_inst%u_fld_thr_patch            , &
-         u_impct_thr         => dust_inst%u_impct_thr_patch          , &
-         thr_crs_rate        => dust_inst%thr_crs_rate_patch         , &
-         prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , &
-         prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , &
-         ssr                 => dust_inst%ssr_patch                  , &
-         lai                 => dust_inst%lai_patch                  , &
-         frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , &
-         wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch      , &
-         dpfct_rock          => dust_inst%dpfct_rock_patch            &
+         liq_frac            => dust_inst%liq_frac_patch             , & ! output fraction of liquid moisture
+         intrmtncy_fct       => dust_inst%intrmtncy_fct_patch        , & ! output intermittency factor eta (fraction of time that dust emission is active within a timestep)
+         stblty              => dust_inst%stblty_patch               , & ! stability in similarity theory (no need to output)
+         u_mean_slt          => dust_inst%u_mean_slt_patch           , & ! output mean wind speed at 0.1 m height translated from friction velocity using the log law of the wall, assuming neutral condition
+         u_sd_slt            => dust_inst%u_sd_slt_patch             , & ! output standard deviation of wind speed from similarity theory
+         u_fld_thr           => dust_inst%u_fld_thr_patch            , & ! output fluid threshold wind speed at 0.1 m height translated from the log law of the wall
+         u_impct_thr         => dust_inst%u_impct_thr_patch          , & ! output impact threshold wind speed at 0.1 m height translated from the log law of the wall
+         thr_crs_rate        => dust_inst%thr_crs_rate_patch         , & ! output threshold crossing rate in Comola 2019 intermittency parameterization
+         prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , & ! output probability of instantaneous wind crossing fluid threshold in Comola 2019 intermittency parameterization
+         prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , & ! output probability of instantaneous wind crossing impact threshold in Comola 2019 intermittency parameterization
+         ssr                 => dust_inst%ssr_patch                  , & ! output vegetation drag partition factor in Okin 2008 vegetation roughness effect (called shear stress ratio, SSR in Okin 2008)
+         lai                 => dust_inst%lai_patch                  , & ! leaf area index for calculating vegetation drag partitioning. lai=0 in the ssr equation will lead to infinity, so for now a small value is added into this lai dmleung defined. (no need to output) 16 Feb 2024
+         frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , & ! output hybrid/total drag partition factor considering both rock and vegetation drag partition factors.
+         wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch      , & ! standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
+         dpfct_rock          => dust_inst%dpfct_rock_patch            & ! output rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -570,10 +576,17 @@ subroutine DustEmission (bounds, &
          !--------------------------------------------------------------------------------------------------
          ! put dust emission calculation here to output threshold friction velocity for the whole globe,
          ! not just when lnd_frc_mbl = 0. Danny M. Leung 27 Nov 2021
-         bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
+
+         !####################################################################################################
+         ! calculate soil moisture effect for dust emission threshold
+         ! following Fecan, Marticorena et al. (1999)
+         ! also see Zender et al. (2003) for DEAD emission scheme and Kok et al. (2014b) for K14 emission scheme in CESM
+         bd = (1._r8-watsat(c,1))*dns_slt      ![kg m-3] Bulk density of dry surface soil (dmleung changed from 2700 to dns_slt, soil particle density, on 16 Feb 2024. Note that dns_slt=2650 kg m-3 so the value is changed by a tiny bit from 2700 to 2650. dns_slt has been here for many years so dns_slt should be used here instead of explicitly tpying the value out. dmleung 16 Feb 2024)
+
+         ! Here convert h2osoi_vol (H2OSOI) at the topmost CTSM soil layer from volumetric (m3 water / m3 soil) to gravimetric soil moisture (kg water / kg soil)
          gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
          if (gwc_sfc > gwc_thr(c)) then
-            frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)
+            frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)   ! dmleung's comment: this is an empirical equation by Fecan, Marticorena et al. (1999) on relating the soil moisture factor on enhancing dust emission threshold to gravimetric soil moisture. 1.21 and 0.68 are fitting parameters in the regression done by Fecan; 100 is to convert gracimetric soil moisture from fraction (kg water / kg soil) to percentage. Note that gwc_thr was defined in SoilStateInitConst.F90 as a fraction. 1.0_r8 means there is no soil moisture effect on enhancing dust emission threhsold. dmleung 16 Feb 2024.
          else
             frc_thr_wet_fct = 1.0_r8
          end if
@@ -583,17 +596,17 @@ subroutine DustEmission (bounds, &
 
          ! slevis: adding liqfrac here, because related to effects from soil water
          liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
-         ! output liquid fraction
+         ! dmleung: output liquid fraction
          liq_frac(p) = liqfrac
 
          !#######################################################################################################
          ! calculate Shao & Lu (2000) dust emission threshold scheme here
          ! use tmp1 from DUSTini for Iversen and White I&W (1982) (~75 um is optimal); use tmp2 for S&L (2000) (~80 um is optimal)
+         ! see Danny M. Leung et al. (2023)
          !#######################################################################################################
-
-         tmp2 = 1.0_r8*sqrt(0.0123_r8 * (dns_slt*grav*130.0e-6_r8 + 1.65e-4_r8/130.0e-6_r8)) ! calculate S&L (2000) scheme here for threshold; gamma = 1.65e-4 following S&L00, D_p = 127 um ~ 130 um following Leung et al. (2022). As this is a global constant, this line can be put outside the loop to save computational power.
-         wnd_frc_thr_dry(p) = tmp2 / sqrt(forc_rho(c))    ! output dry fluid threshold
-         wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold
+         tmp2 = sqrt(A_Shao * (dns_slt*grav*D_p + gamma_Shao/D_p))  ! calculate S&L (2000) scheme here for threshold; gamma = 1.65e-4 following S&L00, D_p = 127 um ~ 130 um following Leung et al. (2023). dmleung use defined parameters instead of typing numerical values 16 Feb 2024
+         wnd_frc_thr_dry(p) = tmp2 / sqrt(forc_rho(c))    ! dry fluid threshold
+         wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold. dmleung commented out frc_thr_rgh_fct since it is used to modify the wind, not the wind threshold.
          wnd_frc_thr_slt_it = B_it * tmp2 / sqrt(forc_rho(c)) ! define impact threshold
 
          ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme
@@ -606,13 +619,13 @@ subroutine DustEmission (bounds, &
 
          ! framentation exponent
          frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a)
-         if (frag_expt > 5.0_r8) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
-            frag_expt = 5.0_r8
+         if (frag_expt > frag_expt_thr) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
+            frag_expt = frag_expt_thr
          end if
 
          !################ drag partition effect, and soil friction velocity ###########################
          ! subsection on computing vegetation drag partition and hybrid drag partition factors
-         ! in Leung et al. (2022), drag partition effect is applied on the wind instead of the threshold
+         ! in Leung et al. (2023), drag partition effect is applied on the wind instead of the threshold
          !##############################################################################################
          ! the following comes from subr. frc_thr_rgh_fct_get
          ! purpose: compute factor by which surface roughness increases threshold
@@ -620,7 +633,7 @@ subroutine DustEmission (bounds, &
 
          if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
             ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
-            lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0 so we add in a small number. Then lai is saved for output
+            lai(p) = tlai_lu(l)+0.01_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0 so we add in a small number.
             if (lai(p) > 1_r8) then
                lai(p)  = 1_r8   ! setting LAI ~ 0.1 to be a min value (since the value goes to infinity when LAI=0)
             end if              ! and 1 to be a max value as computing K involves 1 / LAI
@@ -629,7 +642,7 @@ subroutine DustEmission (bounds, &
             K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup
             ssr(p) = (K_length+f_0*c_e)/(K_length+c_e)
 
-            ! calculation of drag partition effect using LUH2 bare and veg fractions within a grid
+            ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then
                   frc_thr_rgh_fct = dpfct_rock(p)
@@ -646,7 +659,7 @@ subroutine DustEmission (bounds, &
 
          else
             wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
-            frc_thr_rghn_fct(p) = 0.0_r8            ! save and output hybrid drag partition factor
+            frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > 1, the drag partition effect is zero. dmleung 16 Feb 2024.
          end if
 
          !########## end of drag partition effect #######################################################
@@ -674,7 +687,7 @@ subroutine DustEmission (bounds, &
 
             if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if using Leung's scheme, use impact threshold for dust emission equation
 
-               !################### for Leung et al. (2022) ################################################
+               !################### for Leung et al. (2023) ################################################
                !################ uncomment the below block if want to use Leung's scheme ###################
 
                flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
@@ -688,8 +701,8 @@ subroutine DustEmission (bounds, &
             ! subsection for intermittency factor calculation (only used by Leung's scheme, not Zender's scheme)
             ! 2 Dec 2021: assume no buoyancy contribution to the wind fluctuation (u_sd_slt), so no obul(p) is needed. It is shown to be important for the wind fluctuations contribute little to the intermittency factor. We might add this back in the future revisions.
 
-            ! mean lowpass-filtered wind speed at 0.1 m saltation height (assuming aerodynamic roughness length = 1e-4 m globally for ease; also assuming neutral condition)
-            u_mean_slt(p) = (wnd_frc_slt/k) * log(0.1_r8 / 1e-4_r8)  ! translating from ustar (velocity scale) to actual wind
+            ! mean lowpass-filtered wind speed at hgt_sal = 0.1 m saltation height (assuming aerodynamic roughness length z0a_glob = 1e-4 m globally for ease; also assuming neutral condition)
+            u_mean_slt(p) = (wnd_frc_slt/k) * log(hgt_sal / z0a_glob)  ! translating from ustar (velocity scale) to actual wind
 
             stblty(p) = 0   ! -dmleung 2 Dec 2021: use stability = 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
             if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
@@ -701,27 +714,27 @@ subroutine DustEmission (bounds, &
             ! threshold velocities
             ! Here wnd_frc_thr_slt is the fluid threshold; wnd_frc_thr_dry(p) is the dry fluid threshold; B_it*wnd_frc_thr_dry(p) is the impact threshold
             ! fluid threshold wind at 0.1 m saltation height
-            u_fld_thr(p) = (wnd_frc_thr_slt/k) * log(0.1_r8 / 1e-4_r8)
+            u_fld_thr(p) = (wnd_frc_thr_slt/k) * log(hgt_sal / z0a_glob)  ! assume a globally constant z0a value for the log law of the wall, but it can be z0m from CLM or, better, z0a from Prigent's roughness dataset. Danny M. Leung et al. (2023) chose to assume a global constant z0a = 1e-4 m. dmleung 20 Feb 2024
             ! impact threshold wind at 0.1 m saltation height
-            u_impct_thr(p) = (wnd_frc_thr_slt_it/k) * log(0.1_r8 / 1e-4_r8)  ! to avoid model error
+            u_impct_thr(p) = (wnd_frc_thr_slt_it/k) * log(hgt_sal / z0a_glob)
 
             ! threshold crossing rate
-            numer = (u_fld_thr(p)**2_r8 - u_impct_thr(p)**2_r8 - 2_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p)))
-            denom = (2_r8 * u_sd_slt(p)**2_r8)
+            numer = (u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p)))
+            denom = (2.0_r8 * u_sd_slt(p)**2.0_r8)
             ! Truncate to zero if the expression inside exp is becoming too large
             if ( numer/denom < 30._r8 )then
-               thr_crs_rate(p) = (exp((u_fld_thr(p)**2_r8 - u_impct_thr(p)**2_r8 - 2_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2_r8 * u_sd_slt(p)**2_r8)) + 1_r8)**(-1_r8)
+               thr_crs_rate(p) = (exp((u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2.0_r8 * u_sd_slt(p)**2.0_r8)) + 1.0_r8)**(-1.0_r8)
             else
                thr_crs_rate(p) = 0.0_r8
             end if
 
             ! probability that lowpass-filtered wind speed does not exceed u_ft
-            prb_crs_fld_thr(p) = 0.5_r8 * (1_r8 + erf((u_fld_thr(p) - u_mean_slt(p)) / (1.414_r8 * u_sd_slt(p))))
+            prb_crs_fld_thr(p) = 0.5_r8 * (1.0_r8 + erf((u_fld_thr(p) - u_mean_slt(p)) / ( sqrt(2.0_r8) * u_sd_slt(p))))
             ! probability that lowpass-filtered wind speed does not exceed u_it
-            prb_crs_impct_thr(p) = 0.5_r8 * (1_r8 + erf((u_impct_thr(p) - u_mean_slt(p)) / (1.414_r8 * u_sd_slt(p))))
+            prb_crs_impct_thr(p) = 0.5_r8 * (1.0_r8 + erf((u_impct_thr(p) - u_mean_slt(p)) / ( sqrt(2.0_r8 * u_sd_slt(p))))
 
-            ! intermittency factor (from 0 to 1)
-            intrmtncy_fct(p) = 1_r8 - prb_crs_fld_thr(p) + thr_crs_rate(p) * (prb_crs_fld_thr(p) - prb_crs_impct_thr(p))
+            ! intermittency factor (eta; ranging from 0 to 1)
+            intrmtncy_fct(p) = 1.0_r8 - prb_crs_fld_thr(p) + thr_crs_rate(p) * (prb_crs_fld_thr(p) - prb_crs_impct_thr(p))
 
             ! multiply dust emission flux by intermittency factor
             if (intrmtncy_fct(p) /= intrmtncy_fct(p)) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted
@@ -1250,31 +1263,33 @@ subroutine CalcDragPartition(this, bounds, prigent_roughness_stream )
 
     ! constants
     real(r8), parameter :: D_p = 130e-6_r8           ! [m] Medium soil particle diameter, assuming a global constant
-                                                     ! of ~130 um following Leung et al. (2022)
+                                                     ! of ~130 um following Leung et al. (2023)
     real(r8), parameter :: X = 10_r8                 ! [m] distance downwind of the roughness element (rock). Assume
-                                                     ! estimating roughness effect at a distance of 10 m following Leung et al. (2022)
+                                                     ! estimating roughness effect at a distance of 10 m following Leung et al. (2023)
+    real(r8), parameter :: b1 = 0.7_r8               ! [dimless] first fitting coefficient for the drag partition equation by Marticorena and Bergametti (1995), later modified by Darmenova et al. (2009).
+    real(r8), parameter :: b2 = 0.8_r8               ! [dimless] second fitting coefficient for the drag partition equation by Marticorena and Bergametti (1995), later modified by Darmenova et al. (2009).
     character(len=*), parameter :: subname = 'PrigentRoughnessStream::CalcDragPartition'
     !---------------------------------------------------------------------
 
-    ! Make sure we've been initialized
+    ! Make sure we've initialized the Prigent roughness streams
     if ( .not. prigent_roughness_stream%IsStreamInit() )then
-       call endrun(msg=subname//' ERROR Streams have not been initialized, make sure Init is called first' &
+       call endrun(msg=subname//' ERROR: Streams have not been initialized, make sure Init is called first' &
                               //', and streams are on')
     end if
 
     ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks.
     !          We save the drag partition factor as a patch level quantity.
     ! TODO: EBK 02/13/2024: Several magic numbers here that should become parameters so the meaning is preserved
-    z0s = 2_r8 * D_p / 30_r8 ! equation from Frank M. White (2006).
+    z0s = 2_r8/30_r8 * D_p   ! equation for smooth roughness length for soil grain. See Danny M. Leung et al. (2023) and Martin Klose et al. (2021) for instance. 1/15 is a coefficient that relates roughness to soil particle diameter D_p.
                              ! Here we assume soil medium size is a global constant, and so is smooth roughness length.
     do p = bounds%begp,bounds%endp
        g = patch%gridcell(p)
        l = patch%landunit(p)
        if (lun%itype(l) /= istdlak) then
           ! Calculating rock drag partition factor using Marticorena and Bergametti (1995).
-          ! 0.01 is used to convert Z0a from centimeter to meter.
+          ! 0.01 is used to convert Prigent's roughness length dataset from centimeter to meter.
           this%dpfct_rock_patch(p) = 1._r8 - ( log(prigent_roughness_stream%prigent_rghn(g)*0.01_r8/z0s) &
-                             / log(0.7_r8*(X/z0s)**0.8_r8) )
+                             / log(b1 * (X/z0s)**b2 ) )
        end if
     end do
 
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 0e31cc2c53..bf2de65a29 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -703,8 +703,8 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     do c = begc,endc
        g = col%gridcell(c)
 
-       soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Danny M. Leung modified the equation of soil moisture effect for dust emissions using a scale factor of 1. 0.01 is to convert from % to fraction.
-       !soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with 1 / (clay fraction) being the scaling factor.
+       !soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Jasper Kok et al. (2014) modified the equation of soil moisture effect for dust emissions using a tuning factor of a = 1. 0.01 is to convert the threshold gravimetric soil moisture from % to fraction. Danny M. Leung et al. (2023) followed K14 and used this equation for the paper's results. However, Danny Leung later (Dec 2023) decided to revert to Zender's choice and use a = 1 / (clay fraction), which overall encourages more dust emissions from seriamid and more marginal dust sources. dmleung added this detailed comment on 19 Feb 2024.
+       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with a = 1 / (clay fraction) being the tuning factor for soil moisture effect in Zender's dust emission scheme. Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) dust emission scheme in the CESM will use Zender's tuning of a = 1 / (clay fraction), which overall encourages more dust emissions from seriamid and more marginal dust sources. Another advantage of using this tuning factor instead of a = 1 is that the dust emission threshold is linearly dependent on the clay fraction instead of parabolically dependent on clay fraction as in the above line. This means that dust emission becomes a little less sensitive to clay content (soil texture). 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to convert surface clay fraction from percentage to fraction. dmleung added this detailed comment on 19 Feb 2024.
        soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
     end do
 

From fcf1fb93aef1d813d4eeeeb2bc5b4b2920a9775c Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 20 Feb 2024 00:44:54 -0700
Subject: [PATCH 0074/1248] small bug fix to the previous commit. dmleung 20
 Feb 2024

---
 src/biogeochem/DUSTMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 275f0a4c10..d096cc9e2a 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -731,7 +731,7 @@ subroutine DustEmission (bounds, &
             ! probability that lowpass-filtered wind speed does not exceed u_ft
             prb_crs_fld_thr(p) = 0.5_r8 * (1.0_r8 + erf((u_fld_thr(p) - u_mean_slt(p)) / ( sqrt(2.0_r8) * u_sd_slt(p))))
             ! probability that lowpass-filtered wind speed does not exceed u_it
-            prb_crs_impct_thr(p) = 0.5_r8 * (1.0_r8 + erf((u_impct_thr(p) - u_mean_slt(p)) / ( sqrt(2.0_r8 * u_sd_slt(p))))
+            prb_crs_impct_thr(p) = 0.5_r8 * (1.0_r8 + erf((u_impct_thr(p) - u_mean_slt(p)) / ( sqrt(2.0_r8) * u_sd_slt(p))))
 
             ! intermittency factor (eta; ranging from 0 to 1)
             intrmtncy_fct(p) = 1.0_r8 - prb_crs_fld_thr(p) + thr_crs_rate(p) * (prb_crs_fld_thr(p) - prb_crs_impct_thr(p))

From b1fad336249cc7e9c0870d85375ec4f30c366716 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 20 Feb 2024 16:43:46 -0700
Subject: [PATCH 0075/1248] dmleung added more comments in the code blocks for
 the dust emission process in the DustEmission subroutine. 20 Feb 2024

---
 src/biogeochem/DUSTMod.F90 | 36 +++++++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 13 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index d096cc9e2a..9b72549e3c 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -530,7 +530,7 @@ subroutine DustEmission (bounds, &
             write(iulog,*)'Error dstmbl: pft= ',p,' lnd_frc_mbl(p)= ',lnd_frc_mbl(p)
             call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__))
          end if
-      end do
+      end doflx_mss_hrz_slt_ttl = 0.0_r8
 
       ! dmleung add output for bare_frc and veg_frc here if wanted !!!!----------------------
 
@@ -581,7 +581,9 @@ subroutine DustEmission (bounds, &
          ! calculate soil moisture effect for dust emission threshold
          ! following Fecan, Marticorena et al. (1999)
          ! also see Zender et al. (2003) for DEAD emission scheme and Kok et al. (2014b) for K14 emission scheme in CESM
-         bd = (1._r8-watsat(c,1))*dns_slt      ![kg m-3] Bulk density of dry surface soil (dmleung changed from 2700 to dns_slt, soil particle density, on 16 Feb 2024. Note that dns_slt=2650 kg m-3 so the value is changed by a tiny bit from 2700 to 2650. dns_slt has been here for many years so dns_slt should be used here instead of explicitly tpying the value out. dmleung 16 Feb 2024)
+         bd = (1._r8-watsat(c,1))*dns_slt      ![kg m-3] Bulk density of dry surface soil (dmleung changed from 2700 to dns_slt, soil particle density, on 16 Feb 2024. Note that dns_slt=2650 kg m-3 so the value is changed by a tiny bit from 2700 to 2650. dns_slt has been here for many years so dns_slt should be used here instead of explicitly typing the value out. dmleung 16 Feb 2024)
+
+         ! use emission threshold to calculate standardized threshold and dust emission coefficient
 
          ! Here convert h2osoi_vol (H2OSOI) at the topmost CTSM soil layer from volumetric (m3 water / m3 soil) to gravimetric soil moisture (kg water / kg soil)
          gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
@@ -612,18 +614,22 @@ subroutine DustEmission (bounds, &
          ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme
          wnd_frc_thr(p) = wnd_frc_thr_slt          ! output fluid threshold
 
-         ! use emission threshold to calculate standardized threshold and dust emission coefficient
+         !##############################################################################################
+         ! dmleung: here, calculate quantities relevant to the fluid threshold
+         ! standardized fluid threshold
          wnd_frc_thr_slt_std = wnd_frc_thr_slt * sqrt(forc_rho(c) / forc_rho_std) ! standardized soil threshold friction speed (defined using fluid threshold)
          wnd_frc_thr_std(p) = wnd_frc_thr_slt_std          ! output standardized fluid threshold
+         ! dust emission coefficient or soil erodibility coefficient (this is analogous to the soil erodibility map or prefenertial source filter in Zender; see zendersoilerodstream)
          dst_emiss_coeff(p) = Cd0 * exp(-Ce * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min) ! save dust emission coefficient here for all grids
 
-         ! framentation exponent
+         ! framentation exponent (dependent on fluid threshold)
          frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a)
          if (frag_expt > frag_expt_thr) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
             frag_expt = frag_expt_thr
          end if
 
-         !################ drag partition effect, and soil friction velocity ###########################
+         !##############################################################################################
+         !################ drag partition effect, and soil-surface friction velocity ###################
          ! subsection on computing vegetation drag partition and hybrid drag partition factors
          ! in Leung et al. (2023), drag partition effect is applied on the wind instead of the threshold
          !##############################################################################################
@@ -644,12 +650,12 @@ subroutine DustEmission (bounds, &
 
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-               if (patch%itype(p) == noveg) then
+               if (patch%itype(p) == noveg) then ! if bare, uses rock drag partition factor
                   frc_thr_rgh_fct = dpfct_rock(p)
-               else
-                  frc_thr_rgh_fct = ssr(p)
+               else   ! if vegetation, uses vegetation drag partition factor
+                  frc_thr_rgh_fct = ssr(p)  
                end if
-            else
+            else   
                frc_thr_rgh_fct = 1.0_r8
             end if
 
@@ -657,7 +663,7 @@ subroutine DustEmission (bounds, &
 
             frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor
 
-         else
+         else    ! for lnd_frc_mbl=0, do not change friction velocity and assume drag partition factor = 0
             wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
             frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > 1, the drag partition effect is zero. dmleung 16 Feb 2024.
          end if
@@ -666,6 +672,8 @@ subroutine DustEmission (bounds, &
 
          ! save soil friction velocity and roughness effect before the if-statement
          wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect
+         ! 20 Feb 2024: dmleung notes that Leung does not consider the Owen's effect. This is Jasper Kok's decision. The Owen's effect should be in Zender's DEAD emission scheme.
+
          ! save land mobile fraction
          lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement
          ! only perform the following calculations if lnd_frc_mbl is non-zero
@@ -673,19 +681,18 @@ subroutine DustEmission (bounds, &
          if (lnd_frc_mbl(p) > 0.0_r8) then  ! if bare land fraction is larger than 0 then calculate the dust emission equation
 
             ! reset these variables which will be updated in the following if-block
-
             flx_mss_hrz_slt_ttl = 0.0_r8
             flx_mss_vrt_dst_ttl(p) = 0.0_r8
 
             ! the following line comes from subr. dst_mbl
             ! purpose: threshold saltation wind speed
 
-            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)     ! keep and use if we want the default Z03 scheme
+            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)     ! use if we want the default Z03 scheme; for Leung 2023 this is not needed
 
             ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
             ! purpose: compute vertically integrated streamwise mass flux of particles
 
-            if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if using Leung's scheme, use impact threshold for dust emission equation
+            if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if using Leung's scheme, use impact threshold for dust emission equation; if Zender, uses fluid threshold (wnd_frc_thr_slt) for dust emission equation
 
                !################### for Leung et al. (2023) ################################################
                !################ uncomment the below block if want to use Leung's scheme ###################
@@ -699,7 +706,10 @@ subroutine DustEmission (bounds, &
 
             !############## Danny M. Leung added the intermittency calculation #################################
             ! subsection for intermittency factor calculation (only used by Leung's scheme, not Zender's scheme)
+            ! Leung et al. (2023) uses the Comola et al. (2019) intermittency scheme for the calculation of intermittent dust emissions.
+            ! This part takes care of the sub-timestep, high-frequency (< 1 minute period) turblent wind fluctuations occuring at the planetary boundary layer (PBL) near surface. Subtimestep wind gusts and episodes are important for generating emissions in marginal dust source regions, such as semiarid areas and high-latitude polar deserts.
             ! 2 Dec 2021: assume no buoyancy contribution to the wind fluctuation (u_sd_slt), so no obul(p) is needed. It is shown to be important for the wind fluctuations contribute little to the intermittency factor. We might add this back in the future revisions.
+            ! 20 Feb 2024: dmleung notes that dmleung may revise Comola's scheme in the future to improve Comola's formulation of the statistical parameterization.
 
             ! mean lowpass-filtered wind speed at hgt_sal = 0.1 m saltation height (assuming aerodynamic roughness length z0a_glob = 1e-4 m globally for ease; also assuming neutral condition)
             u_mean_slt(p) = (wnd_frc_slt/k) * log(hgt_sal / z0a_glob)  ! translating from ustar (velocity scale) to actual wind

From 4d732449d6dcd6094ca028aacbadca9908ab5212 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 20 Feb 2024 17:23:18 -0700
Subject: [PATCH 0076/1248] dmleung: small bug fix to the previous commit. 20
 Feb 2024

---
 src/biogeochem/DUSTMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 9b72549e3c..f0b8931459 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -530,7 +530,7 @@ subroutine DustEmission (bounds, &
             write(iulog,*)'Error dstmbl: pft= ',p,' lnd_frc_mbl(p)= ',lnd_frc_mbl(p)
             call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__))
          end if
-      end doflx_mss_hrz_slt_ttl = 0.0_r8
+      end do
 
       ! dmleung add output for bare_frc and veg_frc here if wanted !!!!----------------------
 

From 5aa94945e03fff81ef9c76ad30e74820dd2402b8 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Thu, 22 Feb 2024 21:46:37 -0700
Subject: [PATCH 0077/1248] A bug fix for z0s inside CalcDragPartition in
 DUSTMod.F90. dmleung 22 Feb 2024

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 src/biogeochem/DUSTMod.F90                    | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index a52477ce6c..e57a768e67 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2752,7 +2752,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <stream_fldfilename_prigentroughness
 >lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c240127.nc</stream_fldfilename_prigentroughness>
 <stream_meshfile_prigentroughness
->lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c230730.nc</stream_meshfile_prigentroughness>
+>lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c240221.nc</stream_meshfile_prigentroughness>
 
 <!-- =========================================  -->
 <!-- Defaults for different BGC/decomp modes    -->
diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index f0b8931459..8b77d355e1 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -1290,7 +1290,8 @@ subroutine CalcDragPartition(this, bounds, prigent_roughness_stream )
     ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks.
     !          We save the drag partition factor as a patch level quantity.
     ! TODO: EBK 02/13/2024: Several magic numbers here that should become parameters so the meaning is preserved
-    z0s = 2_r8/30_r8 * D_p   ! equation for smooth roughness length for soil grain. See Danny M. Leung et al. (2023) and Martin Klose et al. (2021) for instance. 1/15 is a coefficient that relates roughness to soil particle diameter D_p.
+    !z0s = 2_r8/30_r8 * D_p   ! equation for smooth roughness length for soil grain. See Danny M. Leung et al. (2023) and Martina Klose et al. (2021) for instance. 1/15 is a coefficient that relates roughness to soil particle diameter D_p.
+    z0s = 2_r8 * D_p / 30_r8 ! equation for smooth roughness length for soil grain. See Danny M. Leung et al. (2023) and Martina Klose et al. (2021) for instance. 1/15 is a coefficient that relates roughness to soil particle diameter D_p.
                              ! Here we assume soil medium size is a global constant, and so is smooth roughness length.
     do p = bounds%begp,bounds%endp
        g = patch%gridcell(p)

From 0c62e5bde7016a60bf07d4d9eb9ef990d37d3b9a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 24 Feb 2024 21:39:22 -0700
Subject: [PATCH 0078/1248] Fix meshfile names so the resolution name is
 correct, as pointed out by @dmleung

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e57a768e67..7bb58dcd61 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2752,7 +2752,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <stream_fldfilename_prigentroughness
 >lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c240127.nc</stream_fldfilename_prigentroughness>
 <stream_meshfile_prigentroughness
->lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c240221.nc</stream_meshfile_prigentroughness>
+>lnd/clm2/dustemisdata/dust_0.25x0.25_ESMFmesh_cdf5_c240222.nc</stream_meshfile_prigentroughness>
 
 <!-- =========================================  -->
 <!-- Defaults for different BGC/decomp modes    -->

From 942a3aecdc985c056b4231acf4422cb978da04f2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 25 Feb 2024 20:50:25 -0700
Subject: [PATCH 0079/1248] Fix a logical comparison so will compile with gnu
 on Derecho

---
 src/cpl/share_esmf/PrigentRoughnessStreamType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 751fe8458c..6287b5f552 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -293,7 +293,7 @@ subroutine ReadNML(this, bounds, NLFilename)
    call shr_mpi_bcast(stream_meshfile_prigentroughness    , mpicom)
 
    ! Error checking
-   if ( use_prigent_roughness == .false. )then
+   if ( .not. use_prigent_roughness )then
       if ( len_trim(stream_fldFileName_prigentroughness) /= 0 )then
          call endrun(msg=' ERROR stream_fldFileName_prigentroughness is set, but use_prigent_roughness is FALSE' &
                      //errMsg(sourcefile, __LINE__))

From c27f2093b1a803af46d666de8f464d25b41f9b85 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 26 Feb 2024 18:13:33 -0700
Subject: [PATCH 0080/1248] dmleung: improved LAI treatment in Okin's
 vegetation drag partitioning. Also added precision in other defined
 parameters. 26 Feb 2024

---
 src/biogeochem/DUSTMod.F90 | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 8b77d355e1..4eb33c625d 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -275,10 +275,10 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='Okin-Pierre vegetation shear stress ratio (drag partition factor)', &
          ptr_patch=this%ssr_patch, set_lake=0._r8, set_urb=0._r8)
     this%lai_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LAI', units='m/s',  &
-         avgflag='A', long_name='leaf area index for Okin-Pierre scheme', &
-         ptr_patch=this%lai_patch, set_lake=0._r8, set_urb=0._r8)
-    this%frc_thr_rghn_fct_patch(begp:endp) = spval
+    !call hist_addfld1d (fname='LAI', units='m/s',  &
+    !     avgflag='A', long_name='leaf area index for Okin-Pierre scheme', &
+    !     ptr_patch=this%lai_patch, set_lake=0._r8, set_urb=0._r8)
+    !this%frc_thr_rghn_fct_patch(begp:endp) = spval
     call hist_addfld1d (fname='FRC_THR_RGHN_FCT', units='dimensionless',  &
          avgflag='A', long_name='hybrid drag partition (or roughness) factor', &
          ptr_patch=this%frc_thr_rghn_fct_patch, set_lake=0._r8, set_urb=0._r8)
@@ -411,8 +411,9 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: gamma_Shao = 1.65e-4_r8     ! [kg s-2] interparticle cohesion: fitting parameter in Shao and Lu (2000) (S&L00). dmleung 16 Feb 2024
     real(r8), parameter :: A_Shao = 0.0123_r8          ! [dimless] coefficient for aerodynamic force: fitting parameter in Shao and Lu (2000). dmleung 16 Feb 2024 
     real(r8), parameter :: frag_expt_thr = 5.0_r8      ! [dimless] threshold for fragmentation exponent defined in Leung et al. (2023), somewhere within 3 to 5. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024
-    real(r8), parameter :: z0a_glob = 1e-4             ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
-    real(r8), parameter :: hgt_sal = 0.1               ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
+    real(r8), parameter :: z0a_glob = 1e-4_r8          ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
+    real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
+    real(r8), parameter :: lai0_Okin = 0.1_r8          ! [m2/m2] minimum LAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
     real(r8) :: numer                                  ! Numerator term for threshold crossing rate
     real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     !------------------------------------------------------------------------
@@ -456,7 +457,7 @@ subroutine DustEmission (bounds, &
          prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , & ! output probability of instantaneous wind crossing fluid threshold in Comola 2019 intermittency parameterization
          prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , & ! output probability of instantaneous wind crossing impact threshold in Comola 2019 intermittency parameterization
          ssr                 => dust_inst%ssr_patch                  , & ! output vegetation drag partition factor in Okin 2008 vegetation roughness effect (called shear stress ratio, SSR in Okin 2008)
-         lai                 => dust_inst%lai_patch                  , & ! leaf area index for calculating vegetation drag partitioning. lai=0 in the ssr equation will lead to infinity, so for now a small value is added into this lai dmleung defined. (no need to output) 16 Feb 2024
+         lai                 => dust_inst%lai_patch                  , & ! leaf area index for calculating Okin-Pierre vegetation drag partitioning. lai=0 in the ssr equation will lead to infinity, so a small value is added into this lai dmleung defined. (no need to output) 16 Feb 2024
          frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , & ! output hybrid/total drag partition factor considering both rock and vegetation drag partition factors.
          wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch      , & ! standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
          dpfct_rock          => dust_inst%dpfct_rock_patch            & ! output rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
@@ -639,14 +640,15 @@ subroutine DustEmission (bounds, &
 
          if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
             ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
-            lai(p) = tlai_lu(l)+0.01_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0 so we add in a small number.
+            !lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
+            lai(p) = ttlai(p) + lai0_Okin     ! ttlai = tlai+tsai. Okin-Pierre's equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
             if (lai(p) > 1_r8) then
-               lai(p)  = 1_r8   ! setting LAI ~ 0.1 to be a min value (since the value goes to infinity when LAI=0)
-            end if              ! and 1 to be a max value as computing K involves 1 / LAI
+               lai(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
+            end if              ! 
 
             ! calculate Okin's shear stress ratio (which is drag partition factor) using Pierre's equation
-            K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup
-            ssr(p) = (K_length+f_0*c_e)/(K_length+c_e)
+            K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023)
+            ssr(p) = (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023).
 
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then

From ac5873b968f0a9dabaa460b9d052a1d76c276683 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 27 Feb 2024 15:47:48 -0700
Subject: [PATCH 0081/1248] dmleung: Now we call the vegetation in Okin scheme
 VAI instead of LAI. Also set output for impact threshold. 27 Feb 2024

---
 src/biogeochem/DUSTMod.F90 | 63 +++++++++++++++++++++++---------------
 1 file changed, 38 insertions(+), 25 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 4eb33c625d..17deda7375 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -67,6 +67,7 @@ module DUSTMod
      real(r8), pointer, private :: dst_emiss_coeff_patch     (:)   ! dust emission coefficient (unitless)
      real(r8), pointer, private :: wnd_frc_thr_patch         (:)   ! wet fluid threshold (m/s)
      real(r8), pointer, private :: wnd_frc_thr_dry_patch     (:)   ! dry fluid threshold (m/s)
+     real(r8), pointer, private :: wnd_frc_thr_it_patch     (:)   ! impact threshold (m/s)
      real(r8), pointer, private :: lnd_frc_mble_patch        (:)   ! land mobile fraction
      real(r8), pointer, private :: liq_frac_patch            (:)   ! liquid fraction of total water
      real(r8), pointer, private :: wnd_frc_soil_patch        (:)   ! soil wind friction velocity (m/s)
@@ -81,7 +82,7 @@ module DUSTMod
      real(r8), pointer, private :: prb_crs_fld_thr_patch     (:)   ! probability of wind speed crossing fluid threshold
      real(r8), pointer, private :: prb_crs_impct_thr_patch   (:)   ! probability of wind speed crossing impact threshold
      real(r8), pointer, private :: ssr_patch                 (:)   ! [dimless] integrated shear stress ratiio, defined by Okin (2008) and then integrated by Caroline Pierre et al. (2014)
-     real(r8), pointer, private :: lai_patch                 (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin's drag partition, averaged to landunit level
+     real(r8), pointer, private :: vai_Okin_patch             (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin drag partition
      real(r8), pointer, private :: frc_thr_rghn_fct_patch    (:)   ! [dimless] hybrid drag partition (or called roughness) factor
      real(r8), pointer, private :: wnd_frc_thr_std_patch     (:)   ! standardized fluid threshold friction velocity (m/s)
      type(prigentroughnessstream_type), private :: prigent_roughness_stream      ! Prigent roughness stream data
@@ -144,6 +145,7 @@ subroutine InitAllocate(this, bounds)
     allocate(this%dst_emiss_coeff_patch     (begp:endp))        ; this%dst_emiss_coeff_patch     (:)   = nan
     allocate(this%wnd_frc_thr_patch         (begp:endp))        ; this%wnd_frc_thr_patch         (:)   = nan
     allocate(this%wnd_frc_thr_dry_patch     (begp:endp))        ; this%wnd_frc_thr_dry_patch     (:)   = nan
+    allocate(this%wnd_frc_thr_it_patch      (begp:endp))        ; this%wnd_frc_thr_it_patch      (:)   = nan
     allocate(this%lnd_frc_mble_patch        (begp:endp))        ; this%lnd_frc_mble_patch        (:)   = nan
     allocate(this%wnd_frc_soil_patch        (begp:endp))        ; this%wnd_frc_soil_patch        (:)   = nan
     allocate(this%gwc_patch                 (begp:endp))        ; this%gwc_patch                 (:)   = nan
@@ -158,7 +160,7 @@ subroutine InitAllocate(this, bounds)
     allocate(this%prb_crs_fld_thr_patch     (begp:endp))        ; this%prb_crs_fld_thr_patch     (:)   = nan
     allocate(this%prb_crs_impct_thr_patch   (begp:endp))        ; this%prb_crs_impct_thr_patch   (:)   = nan
     allocate(this%ssr_patch                 (begp:endp))        ; this%ssr_patch                 (:)   = nan
-    allocate(this%lai_patch                 (begp:endp))        ; this%lai_patch                 (:)   = nan
+    allocate(this%vai_Okin_patch            (begp:endp))        ; this%vai_Okin_patch            (:)   = nan
     allocate(this%frc_thr_rghn_fct_patch    (begp:endp))        ; this%frc_thr_rghn_fct_patch    (:)   = nan
     allocate(this%wnd_frc_thr_std_patch     (begp:endp))        ; this%wnd_frc_thr_std_patch     (:)   = nan
     allocate(this%dpfct_rock_patch          (begp:endp))        ; this%dpfct_rock_patch          (:)   = nan
@@ -207,8 +209,8 @@ subroutine InitHistory(this, bounds)
          ptr_patch=this%vlc_trb_4_patch, default='inactive')
 
     this%dst_emiss_coeff_patch(begp:endp) = spval
-    call hist_addfld1d (fname='C_d', units='dimensionless',  &
-         avgflag='A', long_name='dust emission coefficient', &
+    call hist_addfld1d (fname='DUST_EMIS_COEFF', units='dimensionless',  &
+         avgflag='A', long_name='soil erodibility or dust emission coefficient for Kok emission scheme', &
          ptr_patch=this%dst_emiss_coeff_patch, set_lake=0._r8, set_urb=0._r8)
     this%wnd_frc_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_FT', units='m/s',  &
@@ -218,6 +220,10 @@ subroutine InitHistory(this, bounds)
     call hist_addfld1d (fname='WND_FRC_FT_DRY', units='m/s',  &
          avgflag='A', long_name='dry fluid threshold friction velocity', &
          ptr_patch=this%wnd_frc_thr_dry_patch, set_lake=0._r8, set_urb=0._r8)
+    this%wnd_frc_thr_it_patch(begp:endp) = spval
+    call hist_addfld1d (fname='WND_FRC_IT', units='m/s',  &
+         avgflag='A', long_name='impact threshold friction velocity', &
+         ptr_patch=this%wnd_frc_thr_it_patch, set_lake=0._r8, set_urb=0._r8)
     this%wnd_frc_soil_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_SOIL', units='m/s',  &
          avgflag='A', long_name='soil surface wind friction velocity', &
@@ -274,11 +280,11 @@ subroutine InitHistory(this, bounds)
     call hist_addfld1d (fname='SSR', units='m/s',  &
          avgflag='A', long_name='Okin-Pierre vegetation shear stress ratio (drag partition factor)', &
          ptr_patch=this%ssr_patch, set_lake=0._r8, set_urb=0._r8)
-    this%lai_patch(begp:endp) = spval
-    !call hist_addfld1d (fname='LAI', units='m/s',  &
-    !     avgflag='A', long_name='leaf area index for Okin-Pierre scheme', &
-    !     ptr_patch=this%lai_patch, set_lake=0._r8, set_urb=0._r8)
-    !this%frc_thr_rghn_fct_patch(begp:endp) = spval
+    this%vai_Okin_patch(begp:endp) = spval
+    call hist_addfld1d (fname='VAI_OKIN', units='m/s',  &
+         avgflag='A', long_name='vegetation area index used in the Okin-Pierre plant drag partition scheme', &
+         ptr_patch=this%vai_Okin_patch, set_lake=0._r8, set_urb=0._r8)
+    this%frc_thr_rghn_fct_patch(begp:endp) = spval
     call hist_addfld1d (fname='FRC_THR_RGHN_FCT', units='dimensionless',  &
          avgflag='A', long_name='hybrid drag partition (or roughness) factor', &
          ptr_patch=this%frc_thr_rghn_fct_patch, set_lake=0._r8, set_urb=0._r8)
@@ -315,7 +321,7 @@ subroutine InitCold(this, bounds)
        end if
     end do
 
-      ! Caulculate Drag Partition factor
+      ! Caulculate Drag Partition factor (Marticorena and Bergametti 1995 formulation)
       if ( this%prigent_roughness_stream%useStreams() )then !if usestreams == true, and it should be always true
          call this%CalcDragPartition( bounds, this%prigent_roughness_stream )
       else
@@ -413,7 +419,7 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: frag_expt_thr = 5.0_r8      ! [dimless] threshold for fragmentation exponent defined in Leung et al. (2023), somewhere within 3 to 5. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024
     real(r8), parameter :: z0a_glob = 1e-4_r8          ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
     real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
-    real(r8), parameter :: lai0_Okin = 0.1_r8          ! [m2/m2] minimum LAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
+    real(r8), parameter :: vai0_Okin = 0.1_r8          ! [m2/m2] minimum VAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
     real(r8) :: numer                                  ! Numerator term for threshold crossing rate
     real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     !------------------------------------------------------------------------
@@ -441,8 +447,9 @@ subroutine DustEmission (bounds, &
          flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch  , & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
          ! below variables are defined in Kok et al. (2014) or (mostly) Leung et al. (2023) dust emission scheme. dmleung 16 Feb 2024
          dst_emiss_coeff     => dust_inst%dst_emiss_coeff_patch      , & ! Output dust emission coefficient
-         wnd_frc_thr         => dust_inst%wnd_frc_thr_patch          , & ! output impact threshold
-         wnd_frc_thr_dry     => dust_inst%wnd_frc_thr_dry_patch      , & ! output dry threshold
+         wnd_frc_thr         => dust_inst%wnd_frc_thr_patch          , & ! output fluid threshold
+         wnd_frc_thr_dry     => dust_inst%wnd_frc_thr_dry_patch      , & ! output dry fluid threshold
+         wnd_frc_thr_it      => dust_inst%wnd_frc_thr_it_patch       , & ! output impact threshold
          lnd_frc_mble        => dust_inst%lnd_frc_mble_patch         , & ! output bare land fraction
          wnd_frc_soil        => dust_inst%wnd_frc_soil_patch         , & ! soil friction velocity u_*s = (u_*)(f_eff)
          gwc                 => dust_inst%gwc_patch                  , & ! output gravimetric water content
@@ -457,7 +464,7 @@ subroutine DustEmission (bounds, &
          prb_crs_fld_thr     => dust_inst%prb_crs_fld_thr_patch      , & ! output probability of instantaneous wind crossing fluid threshold in Comola 2019 intermittency parameterization
          prb_crs_impct_thr   => dust_inst%prb_crs_impct_thr_patch    , & ! output probability of instantaneous wind crossing impact threshold in Comola 2019 intermittency parameterization
          ssr                 => dust_inst%ssr_patch                  , & ! output vegetation drag partition factor in Okin 2008 vegetation roughness effect (called shear stress ratio, SSR in Okin 2008)
-         lai                 => dust_inst%lai_patch                  , & ! leaf area index for calculating Okin-Pierre vegetation drag partitioning. lai=0 in the ssr equation will lead to infinity, so a small value is added into this lai dmleung defined. (no need to output) 16 Feb 2024
+         vai_Okin            => dust_inst%vai_Okin_patch             , & ! vegetation area index for calculating Okin-Pierre vegetation drag partitioning. vai=0 in the ssr equation will lead to infinity, so a small value is added into this vai dmleung defined. (no need to output) 16 Feb 2024
          frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , & ! output hybrid/total drag partition factor considering both rock and vegetation drag partition factors.
          wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch      , & ! standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
          dpfct_rock          => dust_inst%dpfct_rock_patch            & ! output rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
@@ -557,7 +564,7 @@ subroutine DustEmission (bounds, &
          prb_crs_impct_thr(p) = 0.0_r8
          intrmtncy_fct(p) = 0.0_r8
          ssr(p) = 0.0_r8
-         lai(p) = 0.0_r8
+         vai_Okin(p) = 0.0_r8
          frc_thr_rghn_fct(p) = 0.0_r8
          wnd_frc_thr_std(p) = 0.0_r8
       end do
@@ -614,6 +621,7 @@ subroutine DustEmission (bounds, &
 
          ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme
          wnd_frc_thr(p) = wnd_frc_thr_slt          ! output fluid threshold
+         wnd_frc_thr_it(p) = wnd_frc_thr_slt_it    ! output impact threshold
 
          !##############################################################################################
          ! dmleung: here, calculate quantities relevant to the fluid threshold
@@ -638,17 +646,22 @@ subroutine DustEmission (bounds, &
          ! purpose: compute factor by which surface roughness increases threshold
          !          friction velocity (currently a constant)
 
-         if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
+         !if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
+         if (lnd_frc_mbl(p) > 0.0_r8  .AND. ttlai(p)<=1_r8) then
             ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
             !lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
-            lai(p) = ttlai(p) + lai0_Okin     ! ttlai = tlai+tsai. Okin-Pierre's equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
-            if (lai(p) > 1_r8) then
-               lai(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
-            end if              ! 
+            !lai(p) = ttlai(p) + lai0_Okin     ! ttlai = tlai+tsai. Okin-Pierre's equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
+            !if (lai(p) > 1_r8) then
+            !   lai(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
+            !end if              ! 
 
-            ! calculate Okin's shear stress ratio (which is drag partition factor) using Pierre's equation
-            K_length = 2_r8 * (1_r8/lai(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023)
-            ssr(p) = (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023).
+            if (ttlai(p) + vai0_Okin <= 1_r8) then
+               vai_Okin(p) = ttlai(p) + vai0_Okin     ! ttlai = vai = tlai+tsai. Okin-Pierre's equation is undefined at vai=0, and VAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
+            end if                                    ! In the Okin-Pierre formulation, VAI has to be 0 < VAI <= 1.
+
+            ! calculate Okin's shear stress ratio (SSR, which is vegetation drag partition factor) using Pierre's equation
+            K_length = 2_r8 * (1_r8/vai_Okin(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
+            ssr(p) = (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023). This line is Pierre's formulation.
 
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
@@ -1250,7 +1263,7 @@ subroutine CalcDragPartition(this, bounds, prigent_roughness_stream )
     ! !DESCRIPTION:
     ! Commented below by Danny M. Leung 31 Dec 2022
     ! Calculate the drag partition effect of friction velocity due to surface roughness following
-    ! Leung et al. (2022).  This module is used in the dust emission module DUSTMod.F90 for
+    ! Leung et al. (2023).  This module is used in the dust emission module DUSTMod.F90 for
     ! calculating drag partitioning. The drag partition equation comes from Marticorena and
     ! Bergametti (1995) with constants modified by Darmenova et al. (2009). Here it is assumed
     ! that this equation is used only over arid/desertic regions, such that Catherine Prigent's
@@ -1299,7 +1312,7 @@ subroutine CalcDragPartition(this, bounds, prigent_roughness_stream )
        g = patch%gridcell(p)
        l = patch%landunit(p)
        if (lun%itype(l) /= istdlak) then
-          ! Calculating rock drag partition factor using Marticorena and Bergametti (1995).
+          ! Calculating rock drag partition factor using the Marticorena and Bergametti (1995) formulation.
           ! 0.01 is used to convert Prigent's roughness length dataset from centimeter to meter.
           this%dpfct_rock_patch(p) = 1._r8 - ( log(prigent_roughness_stream%prigent_rghn(g)*0.01_r8/z0s) &
                              / log(b1 * (X/z0s)**b2 ) )

From 3b4d882878204b3dcda3a651375d12a9a074940f Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 12 Mar 2024 15:51:13 -0600
Subject: [PATCH 0082/1248] Add matrixcn code for residue removal variables

---
 src/biogeochem/CNPhenologyMod.F90 | 42 ++++++++++++++++++-------------
 1 file changed, 25 insertions(+), 17 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 619b28801b..b53c195418 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -3605,43 +3605,51 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
 
                   ! Matrix for grain, livestem to litter, leaf to litter, and biofuel
                   if(use_matrixcn)then
-                     if(reproductivec(p,1) .gt. 0)then
+                     if(reproductivec(p,1) > 0._r8)then
                         grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        repr_grainc_to_seed(p,1) = 0
-                        repr_grainc_to_food(p,1) = 0
+                        repr_grainc_to_seed(p,1) = 0._r8
+                        repr_grainc_to_food(p,1) = 0._r8
                      end if
-                     if(reproductiven(p,1) .gt. 0)then
+                     if(reproductiven(p,1) > 0._r8)then
                         grainn_to_out = reproductiven(p,1) * matrix_update_phn(p,igrain_to_iout_phn,(repr_grainn_to_seed(p,1) + repr_grainn_to_food(p,1)) / reproductiven(p,1),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        repr_grainn_to_seed(p,1) = 0
-                        repr_grainn_to_food(p,1) = 0
+                        repr_grainn_to_seed(p,1) = 0._r8
+                        repr_grainn_to_food(p,1) = 0._r8
                      end if
-                     if(livestemc(p) .gt. 0)then
+                     if(livestemc(p) > 0._r8)then
                         livestemc_to_litter(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_iout_phc,livestemc_to_litter(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
+                        livestemc_to_removedresiduec(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_removedresiduec(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
                         livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
                      else
-                        livestemc_to_litter(p) = 0
-                        livestemc_to_biofuelc(p) = 0
+                        livestemc_to_litter(p) = 0._r8
+                        livestemc_to_removedresiduec(p) = 0._r8
+                        livestemc_to_biofuelc(p) = 0._r8
                      end if
-                     if(livestemn(p) .gt. 0)then
+                     if(livestemn(p) > 0._r8)then
                         livestemn_to_biofueln(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_biofueln(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
+                        livestemn_to_removedresiduen(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_removedresiduen(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
                         livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        livestemn_to_biofueln(p) = 0
-                        livestemn_to_litter(p) = 0
+                        livestemn_to_biofueln(p) = 0._r8
+                        livestemn_to_removedresiduen(p) = 0._r8
+                        livestemn_to_litter(p) = 0._r8
                      end if
-                     if(leafn(p) > 0)then
+                     if(leafn(p) > 0._r8)then
                         leafn_to_biofueln(p) =  leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_biofueln(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
+                        leafn_to_removedresiduen(p) = leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_removedresiduen(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
                      else
-                        leafn_to_biofueln(p) = 0
+                        leafn_to_biofueln(p) = 0._r8
+                        leafn_to_removedresiduen(p) = 0._r8
                      end if
-                     if (leafc(p) > 0)then
+                     if (leafc(p) > 0._r8)then
                         leafc_to_biofuelc(p) =  leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
+                        leafc_to_removedresiduec(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_removedresiduec(p) / leafc(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
                         leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
-                        leafc_to_biofuelc(p) = 0
-                        leafc_to_litter(p) = 0
+                        leafc_to_biofuelc(p) = 0._r8
+                        leafc_to_removedresiduec(p) = 0._r8
+                        leafc_to_litter(p) = 0._r8
                      end if
                   else
                      ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019)

From fe50ce16c03446c86b7018d1c655ca9a71b61982 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 12 Mar 2024 16:08:18 -0600
Subject: [PATCH 0083/1248] Update comment based on most recent code changes

---
 src/biogeochem/CNPhenologyMod.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index b53c195418..c6e6cf3635 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -3603,7 +3603,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                   ! as well as leaf C:N ratio (unaffected by biofuel harvest). It thus does not
                   ! need to be updated here.
 
-                  ! Matrix for grain, livestem to litter, leaf to litter, and biofuel
+                  ! Matrix for grain
+                  ! Matrix for livestem/leaf to litter, biofuel, and removed residue
                   if(use_matrixcn)then
                      if(reproductivec(p,1) > 0._r8)then
                         grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)

From acd1413ef75868c873e72c17810704049495c00f Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 12 Mar 2024 16:25:36 -0600
Subject: [PATCH 0084/1248] Correction to latest code mods

---
 src/biogeochem/CNPhenologyMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index c6e6cf3635..c81dd4215d 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -3645,7 +3645,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                      end if
                      if (leafc(p) > 0._r8)then
                         leafc_to_biofuelc(p) =  leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
-                        leafc_to_removedresiduec(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_removedresiduec(p) / leafc(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.)
+                        leafc_to_removedresiduec(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_removedresiduec(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.)
                         leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph)
                      else
                         leafc_to_biofuelc(p) = 0._r8

From 82c1903287d254dc5b8ed5084c38118029eab90c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 19 Mar 2024 11:23:05 -0600
Subject: [PATCH 0085/1248] Corrections for PEM...till test to PASS

---
 .../SoilBiogeochemDecompCascadeBGCMod.F90     | 21 +++++----------
 .../SoilBiogeochemDecompCascadeMIMICSMod.F90  | 26 +++++++++++++++++--
 2 files changed, 31 insertions(+), 16 deletions(-)

diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
index 139cdbba32..49fc95d6f5 100644
--- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
+++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
@@ -911,23 +911,16 @@ subroutine decomp_rate_constants_bgc(bounds, num_bgc_soilc, filter_bgc_soilc, &
 
             ! Above into soil matrix
             if(use_soil_matrixcn)then
-               Ksoil%DM(c,j+nlevdecomp*(i_met_lit-1)) = k_l1    * t_scalar(c,j) * w_scalar(c,j) * &
-                  depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_l1(c) * dt
-               Ksoil%DM(c,j+nlevdecomp*(i_cel_lit-1)) = k_l2_l3 * t_scalar(c,j) * w_scalar(c,j) * &
-                  depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_l23(c) * dt
-               Ksoil%DM(c,j+nlevdecomp*(i_lig_lit-1)) = k_l2_l3 * t_scalar(c,j) * w_scalar(c,j) * &
-                  depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_l23(c) * dt
-               Ksoil%DM(c,j+nlevdecomp*(i_act_som-1)) = k_s1    * t_scalar(c,j) * w_scalar(c,j) * &
-                  depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_s1(c) * dt
-               Ksoil%DM(c,j+nlevdecomp*(i_slo_som-1)) = k_s2    * t_scalar(c,j) * w_scalar(c,j) * &
-                  depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_s2(c) * dt
-               Ksoil%DM(c,j+nlevdecomp*(i_pas_som-1)) = k_s3    * t_scalar(c,j) * w_scalar(c,j) * &
-                  depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_s3(c) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_met_lit-1)) = decomp_k(c,j,i_met_lit) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_cel_lit-1)) = decomp_k(c,j,i_cel_lit) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_lig_lit-1)) = decomp_k(c,j,i_lig_lit) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_act_som-1)) = decomp_k(c,j,i_act_som) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_slo_som-1)) = decomp_k(c,j,i_slo_som) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_pas_som-1)) = decomp_k(c,j,i_pas_som) * dt
                ! same for cwd but only if fates is not enabled; fates handles CWD
                ! on its own structure
                if (.not. use_fates) then
-                  Ksoil%DM(c,j+nlevdecomp*(i_cwd-1))   = k_frag  * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * &
-                     o_scalar(c,j) * spinup_geogterm_cwd(c) * dt
+                  Ksoil%DM(c,j+nlevdecomp*(i_cwd-1))   = decomp_k(c,j,i_cwd) * dt
                end if
             end if !use_soil_matrixcn
          end do
diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90
index 65091755f5..e9bb60bcec 100644
--- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90
+++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90
@@ -18,7 +18,7 @@ module SoilBiogeochemDecompCascadeMIMICSMod
   use spmdMod                            , only : masterproc
   use abortutils                         , only : endrun
   use CNSharedParamsMod                  , only : CNParamsShareInst, nlev_soildecomp_standard 
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
+  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, InitSoilTransfer, use_soil_matrixcn
   use SoilBiogeochemStateType            , only : soilbiogeochem_state_type
   use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
   use SoilBiogeochemCarbonStateType      , only : soilbiogeochem_carbonstate_type
@@ -734,6 +734,8 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat
          nue_decomp_cascade(i_cwdl2) = 1.0_r8
       end if
 
+      if (use_soil_matrixcn) call InitSoilTransfer()
+
       deallocate(params_inst%mimics_mge)
       deallocate(params_inst%mimics_vmod)
       deallocate(params_inst%mimics_vint)
@@ -763,7 +765,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
     ! decomposition cascade model
     !
     ! !USES:
-    use clm_time_manager , only : get_average_days_per_year
+    use clm_time_manager , only : get_average_days_per_year, get_step_size
     use clm_varcon       , only : secspday, secsphr, tfrz
     use clm_varcon       , only : g_to_mg, cm3_to_m3
     use subgridAveMod    , only : p2c
@@ -822,6 +824,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
     integer :: p, fp, c, fc, j, k, l, s  ! indices
     integer :: pf  ! fates patch index
     integer :: nc  ! clump index
+    real(r8):: dt                           ! decomposition time step
     real(r8):: days_per_year                ! days per year
     real(r8):: depth_scalar(bounds%begc:bounds%endc,1:nlevdecomp) 
     real(r8):: w_d_o_scalars  ! product of w_scalar * depth_scalar * o_scalar
@@ -882,6 +885,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
          cn_col         => soilbiogeochem_carbonflux_inst%cn_col       , & ! Output: [real(r8) (:,:)   ]  C:N ratio
          ligninNratioAvg => soilbiogeochem_carbonflux_inst%litr_lig_c_to_n_col, &  ! Input: [real(r8) (:) ] C:N ratio of litter lignin
          decomp_k       => soilbiogeochem_carbonflux_inst%decomp_k_col , & ! Output: [real(r8) (:,:,:) ]  rate for decomposition (1./sec)
+         Ksoil          => soilbiogeochem_carbonflux_inst%Ksoil        , & ! Output: [real(r8) (:,:,:) ]  rate constant for decomposition (1./sec)
          spinup_factor  => decomp_cascade_con%spinup_factor              & ! Input:  [real(r8)          (:)     ]  factor for AD spinup associated with each pool           
          )
 
@@ -892,6 +896,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
       mino2lim = CNParamsShareInst%mino2lim
 
       days_per_year = get_average_days_per_year()
+      dt = real( get_step_size(), r8 )
 
 !     ! Set "decomp_depth_efolding" parameter
 !     decomp_depth_efolding = CNParamsShareInst%decomp_depth_efolding
@@ -1311,6 +1316,23 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
             if (get_do_tillage()) then
                call get_apply_tillage_multipliers(idop, c, j, decomp_k(c,j,:))
             end if
+
+! Above into soil matrix
+            if(use_soil_matrixcn)then
+               Ksoil%DM(c,j+nlevdecomp*(i_met_lit-1)) = decomp_k(c,j,i_met_lit) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_str_lit-1)) = decomp_k(c,j,i_str_lit) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_avl_som-1)) = decomp_k(c,j,i_avl_som) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_phys_som-1)) = decomp_k(c,j,i_phys_som) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_chem_som-1)) = decomp_k(c,j,i_chem_som) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_cop_mic-1)) = decomp_k(c,j,i_cop_mic) * dt
+               Ksoil%DM(c,j+nlevdecomp*(i_oli_mic-1)) = decomp_k(c,j,i_oli_mic) * dt
+               ! same for cwd but only if fates is not enabled; fates handles
+               ! CWD
+               ! on its own structure
+               if (.not. use_fates) then
+                  Ksoil%DM(c,j+nlevdecomp*(i_cwd-1))   = decomp_k(c,j,i_cwd) * dt
+               end if
+            end if !use_soil_matrixcn
          end do
       end do
 

From d1d21137041ea091b8743ce3801eb7ff99960a34 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Wed, 20 Mar 2024 15:17:23 -0500
Subject: [PATCH 0086/1248] Fix backward compatibility & p_ac dynamic read-in

1. set different paths for default stream_fldfilename_urbantv based on urban_explicit_ac (currently points to the file in my work directory when urban_explicit_ac=.true.)
2. only read in p_ac when urban_explicit_ac is true
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 15 +++++
 src/biogeophys/UrbBuildTempOleson2015Mod.F90  |  2 +-
 src/cpl/share_esmf/UrbanTimeVarType.F90       | 57 ++++++++++++++-----
 3 files changed, 60 insertions(+), 14 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 0d8e45a779..0f7d9b948a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1744,6 +1744,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <stream_year_first_urbantv sim_year="constant" sim_year_range="1850-2000" >1850</stream_year_first_urbantv>
 <stream_year_last_urbantv  sim_year="constant" sim_year_range="1850-2000" >2106</stream_year_last_urbantv>
 
+<!-- X Li. [03.19] 
 <stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25"
 >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 <stream_meshfile_urbantv    phys="clm5_1"  hgrid="0.9x1.25"
@@ -1753,6 +1754,20 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 <stream_meshfile_urbantv    phys="clm5_0"  hgrid="0.9x1.25"
 >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1_ESMFmesh_cdf5_100621.nc</stream_meshfile_urbantv>
+-->
+<stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25" urban_explicit_ac=".false."
+>lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
+<stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25" urban_explicit_ac=".true."
+>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+<stream_meshfile_urbantv    phys="clm5_1"  hgrid="0.9x1.25"
+>lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1_ESMFmesh_cdf5_100621.nc</stream_meshfile_urbantv>
+
+<stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".false."
+>lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
+<stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".true."
+>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+<stream_meshfile_urbantv    phys="clm5_0"  hgrid="0.9x1.25"
+>lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1_ESMFmesh_cdf5_100621.nc</stream_meshfile_urbantv>
 
 <stream_fldfilename_urbantv phys="clm4_5" hgrid="0.9x1.25"
 >lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
index 2e588e2e88..ee824931cd 100644
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
@@ -325,7 +325,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec,
     t_floor           => temperature_inst%t_floor_lun      , & ! InOut:  [real(r8) (:)]  floor temperature (K)
     t_building        => temperature_inst%t_building_lun   , & ! InOut:  [real(r8) (:)]  internal building air temperature (K)
 
-    p_ac              => urbantv_inst%p_ac                 , & ! Input:  [real(r8) (:)]  air-conditioning penetration rate (-)
+    p_ac              => urbantv_inst%p_ac                 , & ! Input:  [real(r8) (:)]  air-conditioning penetration rate (a fraction between 0 and 1)
     t_building_max    => urbantv_inst%t_building_max       , & ! Input:  [real(r8) (:)]  maximum internal building air temperature (K)
     t_building_min    => urbanparams_inst%t_building_min   , & ! Input:  [real(r8) (:)]  minimum internal building air temperature (K)
 
diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 54d5c61d19..5f507a1e9c 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -36,7 +36,11 @@ module UrbanTimeVarType
   ! X. Li [orig]
   ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX)
   ! X. Li [dev]: 
-  character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
+  ! character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
+  ! X. Li [03.19]
+  integer      , private :: stream_varname_MIN       ! minimum index for stream_varnames
+  integer      , private :: stream_varname_MAX       ! maximum index for stream_varnames
+  character(15), private :: stream_varnames(:)       ! urban time varying variable names
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -67,7 +71,9 @@ subroutine Init(this, bounds, NLFilename)
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
-    allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
+    ! X. Li [03.19]
+    ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
+    allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8
 
     call this%urbantv_init(bounds, NLFilename)
     call this%urbantv_interp(bounds)
@@ -77,8 +83,8 @@ subroutine Init(this, bounds, NLFilename)
           avgflag='A', long_name='prescribed maximum interior building temperature',   &
           ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
-    call hist_addfld1d (fname='P_AC', units='unitless',      &
-          avgflag='A', long_name='prescribed air-conditioning ownership rate (unitless, between 0 and 1)',   &
+    call hist_addfld1d (fname='P_AC', units='a fraction between 0 and 1',      &
+          avgflag='A', long_name='prescribed air-conditioning ownership rate',   &
           ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
 
@@ -97,6 +103,8 @@ subroutine urbantv_init(this, bounds, NLFilename)
     use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md
     use dshr_strdata_mod , only : shr_strdata_init_from_inline
     use lnd_comp_shr     , only : mesh, model_clock
+    ! X. Li [03.19]
+    use UrbanParamsType  , only : urban_explicit_ac
     !
     ! !ARGUMENTS:
     implicit none
@@ -136,6 +144,15 @@ subroutine urbantv_init(this, bounds, NLFilename)
     model_year_align_urbantv   = 1       ! align stream_year_first_urbantv with this model year
     stream_fldFileName_urbantv = ' '
     stream_meshfile_urbantv    = ' '
+    ! X. Li [03.19]
+    stream_varname_MIN = 1
+    ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, 
+    ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes;
+    ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. 
+    if (urban_explicit_ac) then
+       stream_varname_MAX = 6
+    else
+       stream_varname_MAX = 3
     ! X. Li [orig]
     ! stream_varnames(isturb_tbd) = urbantvString//"TBD"
     ! stream_varnames(isturb_hd)  = urbantvString//"HD"
@@ -144,9 +161,11 @@ subroutine urbantv_init(this, bounds, NLFilename)
     stream_varnames(1) = "tbuildmax_TBD"
     stream_varnames(2) = "tbuildmax_HD"
     stream_varnames(3) = "tbuildmax_MD"
-    stream_varnames(4) = "p_ac_TBD"
-    stream_varnames(5) = "p_ac_HD"
-    stream_varnames(6) = "p_ac_MD"
+    ! X. Li [03.19]
+    if (urban_explicit_ac) then
+       stream_varnames(4) = "p_ac_TBD"
+       stream_varnames(5) = "p_ac_HD"
+       stream_varnames(6) = "p_ac_MD"
 
     ! Read urbantv_streams namelist
     if (masterproc) then
@@ -180,7 +199,9 @@ subroutine urbantv_init(this, bounds, NLFilename)
        ! X. Li [orig]
        ! do n = isturb_tbd,isturb_md
        ! X. Li [dev]
-       do n = 1,6
+       ! do n = 1,6
+       ! X. Li [03.19]
+       do n = stream_varname_MIN,stream_varname_MAX
           write(iulog,'(a,a)' ) '  stream_varname         = ',trim(stream_varnames(n))
        end do
        write(iulog,*) ' '
@@ -201,8 +222,11 @@ subroutine urbantv_init(this, bounds, NLFilename)
          ! stream_fldlistFile  = stream_varnames(isturb_tbd:isturb_md),&
          ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),&
          ! X. Li [dev]
-         stream_fldlistFile  = stream_varnames(1:6),                 &
-         stream_fldListModel = stream_varnames(1:6),                 &
+         ! stream_fldlistFile  = stream_varnames(1:6),                 &
+         ! stream_fldListModel = stream_varnames(1:6),                 &
+         ! X. Li [03.19]
+         stream_fldlistFile  = stream_varnames(stream_varname_MIN:stream_varname_MAX), &
+         stream_fldListModel = stream_varnames(stream_varname_MIN:stream_varname_MAX), &
          stream_yearFirst    = stream_year_first_urbantv,            &
          stream_yearLast     = stream_year_last_urbantv,             &
          stream_yearAlign    = model_year_align_urbantv,             &
@@ -266,6 +290,9 @@ subroutine urbantv_interp(this, bounds)
     ! X. Li [dev]
     allocate(dataptr2d(lsize, 1:6))
     do n = 1,6
+    ! X. Li [03.19]
+    allocate(dataptr2d(lsize, stream_varname_MIN:stream_varname_MAX))
+    do n = stream_varname_MIN,stream_varname_MAX
        call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), &
             fldptr1=dataptr1d, rc=rc)
        if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
@@ -278,7 +305,7 @@ subroutine urbantv_interp(this, bounds)
        end do
     end do
 
-    ! Determine this%tbuilding_max for all landunits
+    ! Determine this%tbuilding_max (and this%p_ac, if applicable) for all landunits
     do l = bounds%begl,bounds%endl
        if (lun%urbpoi(l)) then
           ig = 0
@@ -289,7 +316,9 @@ subroutine urbantv_interp(this, bounds)
           ! X. Li [orig]
           ! do n = isturb_MIN,isturb_MAX
           ! X. Li [dev]
-          do n = 1,6
+          ! do n = 1,6
+          ! X. Li [03.19]
+          do n = stream_varname_MIN,stream_varname_MAX
              ! X. Li [orig]
              ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
              ! X. Li [dev.02]
@@ -302,7 +331,9 @@ subroutine urbantv_interp(this, bounds)
           end do
        else
           this%t_building_max(l) = spval
-          this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit
+          ! this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit
+          ! X. Li [03.19]
+          this%p_ac(l) = nan ! set to nan for non-urban landunit
        end if
     end do
     deallocate(dataptr2d)

From 79790a0d392178ca95b4a0bcf2b7e3a02618896c Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 21 Mar 2024 16:08:23 -0500
Subject: [PATCH 0087/1248] Bug fix

Closed if blocks, commented out extra lines, defined nan
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 5f507a1e9c..fc670ca830 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -38,9 +38,9 @@ module UrbanTimeVarType
   ! X. Li [dev]: 
   ! character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
   ! X. Li [03.19]
-  integer      , private :: stream_varname_MIN       ! minimum index for stream_varnames
-  integer      , private :: stream_varname_MAX       ! maximum index for stream_varnames
-  character(15), private :: stream_varnames(:)       ! urban time varying variable names
+  integer      , private              :: stream_varname_MIN       ! minimum index for stream_varnames
+  integer      , private              :: stream_varname_MAX       ! maximum index for stream_varnames
+  character(15), private, allocatable :: stream_varnames(:)       ! urban time varying variable names
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -153,6 +153,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
        stream_varname_MAX = 6
     else
        stream_varname_MAX = 3
+    end if
     ! X. Li [orig]
     ! stream_varnames(isturb_tbd) = urbantvString//"TBD"
     ! stream_varnames(isturb_hd)  = urbantvString//"HD"
@@ -166,6 +167,7 @@ subroutine urbantv_init(this, bounds, NLFilename)
        stream_varnames(4) = "p_ac_TBD"
        stream_varnames(5) = "p_ac_HD"
        stream_varnames(6) = "p_ac_MD"
+    end if
 
     ! Read urbantv_streams namelist
     if (masterproc) then
@@ -253,6 +255,7 @@ subroutine urbantv_interp(this, bounds)
     use clm_instur       , only : urban_valid
     use dshr_methods_mod , only : dshr_fldbun_getfldptr
     use dshr_strdata_mod , only : shr_strdata_advance
+    use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
     !
     ! !ARGUMENTS:
     class(urbantv_type)           :: this
@@ -288,8 +291,8 @@ subroutine urbantv_interp(this, bounds)
     ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX))
     ! do n = isturb_MIN,isturb_MAX
     ! X. Li [dev]
-    allocate(dataptr2d(lsize, 1:6))
-    do n = 1,6
+    ! allocate(dataptr2d(lsize, 1:6))
+    ! do n = 1,6
     ! X. Li [03.19]
     allocate(dataptr2d(lsize, stream_varname_MIN:stream_varname_MAX))
     do n = stream_varname_MIN,stream_varname_MAX

From c383dee0be598f52766c330ff59965fd6b4eaa0c Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Fri, 22 Mar 2024 16:55:12 -0500
Subject: [PATCH 0088/1248] Fixing error SIGSEGV, segmentation fault occurred

Trying to fix this error by changing "allocatable" to "pointer" for the variable `stream_varnames`, since the error message points to the line where this variable was first assigned values.
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index fc670ca830..5cd3f607ca 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -40,7 +40,7 @@ module UrbanTimeVarType
   ! X. Li [03.19]
   integer      , private              :: stream_varname_MIN       ! minimum index for stream_varnames
   integer      , private              :: stream_varname_MAX       ! maximum index for stream_varnames
-  character(15), private, allocatable :: stream_varnames(:)       ! urban time varying variable names
+  character(15), private, pointer     :: stream_varnames(:)       ! urban time varying variable names
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__

From 0081443d8662dacce74da1790b922c98a7edfd64 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Fri, 22 Mar 2024 18:12:21 -0500
Subject: [PATCH 0089/1248] Fixing the error SIGSEGV cont'd

Adding parameter" attribute to `stream_varname_MIN/MAX` to see if it helps
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 5cd3f607ca..ffecf07c2d 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -38,9 +38,9 @@ module UrbanTimeVarType
   ! X. Li [dev]: 
   ! character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
   ! X. Li [03.19]
-  integer      , private              :: stream_varname_MIN       ! minimum index for stream_varnames
-  integer      , private              :: stream_varname_MAX       ! maximum index for stream_varnames
-  character(15), private, pointer     :: stream_varnames(:)       ! urban time varying variable names
+  integer      , private, parameter   :: stream_varname_MIN       ! minimum index for stream_varnames
+  integer      , private, parameter   :: stream_varname_MAX       ! maximum index for stream_varnames
+  character(15), private, pointer     :: stream_varnames(stream_varname_MIN:stream_varname_MAX)       ! urban time varying variable names
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__

From e4a42c8fec448dacd53bcb37c18fd05bc05161cb Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Fri, 22 Mar 2024 18:55:02 -0500
Subject: [PATCH 0090/1248] Fixing the error SIGSEGV cont'd

Trying out determining `stream_varname_MIN/MAX` and allocating `stream_varnames` in a different subroutine, before stream_varnames are assigned values
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 39 +++++++++++++++++--------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index ffecf07c2d..f9aab74b09 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -38,9 +38,9 @@ module UrbanTimeVarType
   ! X. Li [dev]: 
   ! character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
   ! X. Li [03.19]
-  integer      , private, parameter   :: stream_varname_MIN       ! minimum index for stream_varnames
-  integer      , private, parameter   :: stream_varname_MAX       ! maximum index for stream_varnames
-  character(15), private, pointer     :: stream_varnames(stream_varname_MIN:stream_varname_MAX)       ! urban time varying variable names
+  integer      , private              :: stream_varname_MIN       ! minimum index for stream_varnames
+  integer      , private              :: stream_varname_MAX       ! maximum index for stream_varnames
+  character(15), private, pointer     :: stream_varnames(:)       ! urban time varying variable names
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -56,6 +56,8 @@ subroutine Init(this, bounds, NLFilename)
     ! !USES:
     use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
     use histFileMod     , only : hist_addfld1d
+    ! X. Li [03.22]
+    use UrbanParamsType , only : urban_explicit_ac
     !
     ! !ARGUMENTS:
     class(urbantv_type) :: this
@@ -68,12 +70,25 @@ subroutine Init(this, bounds, NLFilename)
 
     begl = bounds%begl; endl = bounds%endl
 
+    ! X. Li [03.22]
+    ! Determine the minimum and maximum indices for stream_varnames
+    stream_varname_MIN = 1
+    ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, 
+    ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes;
+    ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. 
+    if (urban_explicit_ac) then
+       stream_varname_MAX = 6
+    else
+       stream_varname_MAX = 3
+    end if
+
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
     ! X. Li [03.19]
     ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
     allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8
+    allocate(this%stream_varnames(stream_varname_MIN:stream_varname_MAX))
 
     call this%urbantv_init(bounds, NLFilename)
     call this%urbantv_interp(bounds)
@@ -145,15 +160,15 @@ subroutine urbantv_init(this, bounds, NLFilename)
     stream_fldFileName_urbantv = ' '
     stream_meshfile_urbantv    = ' '
     ! X. Li [03.19]
-    stream_varname_MIN = 1
-    ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, 
-    ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes;
-    ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. 
-    if (urban_explicit_ac) then
-       stream_varname_MAX = 6
-    else
-       stream_varname_MAX = 3
-    end if
+    ! stream_varname_MIN = 1
+    ! ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, 
+    ! ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes;
+    ! ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. 
+    ! if (urban_explicit_ac) then
+    !    stream_varname_MAX = 6
+    ! else
+    !    stream_varname_MAX = 3
+    ! end if
     ! X. Li [orig]
     ! stream_varnames(isturb_tbd) = urbantvString//"TBD"
     ! stream_varnames(isturb_hd)  = urbantvString//"HD"

From f69173523060c05c06a665fd9c500fae43f5dab2 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Fri, 22 Mar 2024 19:05:49 -0500
Subject: [PATCH 0091/1248] Fixing the error SIGSEGV cont'd

Previous build had error "This is not a component name that is defined in the encompassing structure" for `stream_varnames` allocation, so removed "this%"
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index f9aab74b09..1a29abb9af 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -88,7 +88,7 @@ subroutine Init(this, bounds, NLFilename)
     ! X. Li [03.19]
     ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
     allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8
-    allocate(this%stream_varnames(stream_varname_MIN:stream_varname_MAX))
+    allocate(stream_varnames(stream_varname_MIN:stream_varname_MAX))
 
     call this%urbantv_init(bounds, NLFilename)
     call this%urbantv_interp(bounds)

From 64870fa5b51fef1f93a4d05488c0a18e2d65d7d4 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Mon, 25 Mar 2024 09:53:37 -0600
Subject: [PATCH 0092/1248] Getting around "file not found" error for /run
 directory

---
 cime_config/SystemTests/sspmatrixcn.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py
index bd41d84651..5f2d3e065e 100644
--- a/cime_config/SystemTests/sspmatrixcn.py
+++ b/cime_config/SystemTests/sspmatrixcn.py
@@ -207,7 +207,9 @@ def run_phase(self):
                      linkfile = os.path.join(rundir, os.path.basename(item))
                      if os.path.exists(linkfile):
                          os.remove( linkfile )
-                     os.symlink(item, linkfile )
+                     self._case.flush()
+                     if os.path.exists(rundir):
+                         os.symlink(item, linkfile )
    
                  for item in glob.glob("{}/*rpointer*".format(rest_path)):
                      shutil.copy(item, rundir)
@@ -215,7 +217,8 @@ def run_phase(self):
            #
            # Run the case (Archiving on)
            #
-           self._case.flush()
+           if not os.path.exists(rundir):
+               self._case.flush()
            self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True)
 
            #

From ccb91e21abd4f8bb6437f551b025444126787c94 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Mon, 25 Mar 2024 20:03:01 -0500
Subject: [PATCH 0093/1248] Prepare for PR review

Remove comments no longer needed to prepare for PR review
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 11 ----
 src/cpl/share_esmf/UrbanTimeVarType.F90       | 57 -------------------
 2 files changed, 68 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 0f7d9b948a..be3d776c2f 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1744,17 +1744,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <stream_year_first_urbantv sim_year="constant" sim_year_range="1850-2000" >1850</stream_year_first_urbantv>
 <stream_year_last_urbantv  sim_year="constant" sim_year_range="1850-2000" >2106</stream_year_last_urbantv>
 
-<!-- X Li. [03.19] 
-<stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25"
->lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
-<stream_meshfile_urbantv    phys="clm5_1"  hgrid="0.9x1.25"
->lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1_ESMFmesh_cdf5_100621.nc</stream_meshfile_urbantv>
-
-<stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25"
->lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
-<stream_meshfile_urbantv    phys="clm5_0"  hgrid="0.9x1.25"
->lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1_ESMFmesh_cdf5_100621.nc</stream_meshfile_urbantv>
--->
 <stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25" urban_explicit_ac=".true."
diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 1a29abb9af..e6ceed7173 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -33,11 +33,6 @@ module UrbanTimeVarType
      procedure, public :: urbantv_interp    ! Interpolate urban time varying stream
   end type urbantv_type
   
-  ! X. Li [orig]
-  ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX)
-  ! X. Li [dev]: 
-  ! character(15), private :: stream_varnames(1:6)       ! 1-3 for t_building_max, 4-6 for p_ac
-  ! X. Li [03.19]
   integer      , private              :: stream_varname_MIN       ! minimum index for stream_varnames
   integer      , private              :: stream_varname_MAX       ! maximum index for stream_varnames
   character(15), private, pointer     :: stream_varnames(:)       ! urban time varying variable names
@@ -56,7 +51,6 @@ subroutine Init(this, bounds, NLFilename)
     ! !USES:
     use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
     use histFileMod     , only : hist_addfld1d
-    ! X. Li [03.22]
     use UrbanParamsType , only : urban_explicit_ac
     !
     ! !ARGUMENTS:
@@ -70,7 +64,6 @@ subroutine Init(this, bounds, NLFilename)
 
     begl = bounds%begl; endl = bounds%endl
 
-    ! X. Li [03.22]
     ! Determine the minimum and maximum indices for stream_varnames
     stream_varname_MIN = 1
     ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, 
@@ -85,8 +78,6 @@ subroutine Init(this, bounds, NLFilename)
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
-    ! X. Li [03.19]
-    ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
     allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8
     allocate(stream_varnames(stream_varname_MIN:stream_varname_MAX))
 
@@ -118,7 +109,6 @@ subroutine urbantv_init(this, bounds, NLFilename)
     use landunit_varcon  , only : isturb_tbd, isturb_hd, isturb_md
     use dshr_strdata_mod , only : shr_strdata_init_from_inline
     use lnd_comp_shr     , only : mesh, model_clock
-    ! X. Li [03.19]
     use UrbanParamsType  , only : urban_explicit_ac
     !
     ! !ARGUMENTS:
@@ -139,8 +129,6 @@ subroutine urbantv_init(this, bounds, NLFilename)
     character(len=CL)  :: urbantvmapalgo = 'nn'             ! mapping alogrithm for urban ac
     character(len=CL)  :: urbantv_tintalgo = 'linear'       ! time interpolation alogrithm
     integer            :: rc                                ! error code
-    ! X. Li [orig]: this is taken out because field strings are now hard coded in
-    ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string
     character(*), parameter :: subName = "('urbantv_init')"
     !-----------------------------------------------------------------------
 
@@ -159,25 +147,9 @@ subroutine urbantv_init(this, bounds, NLFilename)
     model_year_align_urbantv   = 1       ! align stream_year_first_urbantv with this model year
     stream_fldFileName_urbantv = ' '
     stream_meshfile_urbantv    = ' '
-    ! X. Li [03.19]
-    ! stream_varname_MIN = 1
-    ! ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, 
-    ! ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes;
-    ! ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. 
-    ! if (urban_explicit_ac) then
-    !    stream_varname_MAX = 6
-    ! else
-    !    stream_varname_MAX = 3
-    ! end if
-    ! X. Li [orig]
-    ! stream_varnames(isturb_tbd) = urbantvString//"TBD"
-    ! stream_varnames(isturb_hd)  = urbantvString//"HD"
-    ! stream_varnames(isturb_md)  = urbantvString//"MD"
-    ! X. Li [dev]
     stream_varnames(1) = "tbuildmax_TBD"
     stream_varnames(2) = "tbuildmax_HD"
     stream_varnames(3) = "tbuildmax_MD"
-    ! X. Li [03.19]
     if (urban_explicit_ac) then
        stream_varnames(4) = "p_ac_TBD"
        stream_varnames(5) = "p_ac_HD"
@@ -213,11 +185,6 @@ subroutine urbantv_init(this, bounds, NLFilename)
        write(iulog,'(a,a)' ) '  stream_fldFileName_urbantv = ',stream_fldFileName_urbantv
        write(iulog,'(a,a)' ) '  stream_meshfile_urbantv    = ',stream_meshfile_urbantv
        write(iulog,'(a,a)' ) '  urbantv_tintalgo           = ',urbantv_tintalgo
-       ! X. Li [orig]
-       ! do n = isturb_tbd,isturb_md
-       ! X. Li [dev]
-       ! do n = 1,6
-       ! X. Li [03.19]
        do n = stream_varname_MIN,stream_varname_MAX
           write(iulog,'(a,a)' ) '  stream_varname         = ',trim(stream_varnames(n))
        end do
@@ -235,13 +202,6 @@ subroutine urbantv_init(this, bounds, NLFilename)
          stream_lev_dimname  = 'null',                               &
          stream_mapalgo      = trim(urbantvmapalgo),                 &
          stream_filenames    = (/trim(stream_fldfilename_urbantv)/), &
-         ! X. Li [orig]
-         ! stream_fldlistFile  = stream_varnames(isturb_tbd:isturb_md),&
-         ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),&
-         ! X. Li [dev]
-         ! stream_fldlistFile  = stream_varnames(1:6),                 &
-         ! stream_fldListModel = stream_varnames(1:6),                 &
-         ! X. Li [03.19]
          stream_fldlistFile  = stream_varnames(stream_varname_MIN:stream_varname_MAX), &
          stream_fldListModel = stream_varnames(stream_varname_MIN:stream_varname_MAX), &
          stream_yearFirst    = stream_year_first_urbantv,            &
@@ -302,13 +262,6 @@ subroutine urbantv_interp(this, bounds)
 
     ! Create 2d array for all stream variable data
     lsize = bounds%endg - bounds%begg + 1
-    ! X. Li [orig]
-    ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX))
-    ! do n = isturb_MIN,isturb_MAX
-    ! X. Li [dev]
-    ! allocate(dataptr2d(lsize, 1:6))
-    ! do n = 1,6
-    ! X. Li [03.19]
     allocate(dataptr2d(lsize, stream_varname_MIN:stream_varname_MAX))
     do n = stream_varname_MIN,stream_varname_MAX
        call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), &
@@ -331,15 +284,7 @@ subroutine urbantv_interp(this, bounds)
              ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
-          ! X. Li [orig]
-          ! do n = isturb_MIN,isturb_MAX
-          ! X. Li [dev]
-          ! do n = 1,6
-          ! X. Li [03.19]
           do n = stream_varname_MIN,stream_varname_MAX
-             ! X. Li [orig]
-             ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
-             ! X. Li [dev.02]
              if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then
                 this%t_building_max(l) = dataptr2d(ig,n)
              end if
@@ -349,8 +294,6 @@ subroutine urbantv_interp(this, bounds)
           end do
        else
           this%t_building_max(l) = spval
-          ! this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit
-          ! X. Li [03.19]
           this%p_ac(l) = nan ! set to nan for non-urban landunit
        end if
     end do

From 25f0236576b01044df8509e865dbce35587983ca Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 26 Mar 2024 09:49:24 -0600
Subject: [PATCH 0094/1248] Getting around "file not found" error for rundir
 (this time test passes)

---
 cime_config/SystemTests/sspmatrixcn.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py
index 5f2d3e065e..eec462e72c 100644
--- a/cime_config/SystemTests/sspmatrixcn.py
+++ b/cime_config/SystemTests/sspmatrixcn.py
@@ -207,9 +207,9 @@ def run_phase(self):
                      linkfile = os.path.join(rundir, os.path.basename(item))
                      if os.path.exists(linkfile):
                          os.remove( linkfile )
-                     self._case.flush()
-                     if os.path.exists(rundir):
-                         os.symlink(item, linkfile )
+                     if not os.path.isdir(rundir):
+                         os.makedirs(rundir)
+                     os.symlink(item, linkfile )
    
                  for item in glob.glob("{}/*rpointer*".format(rest_path)):
                      shutil.copy(item, rundir)
@@ -217,8 +217,7 @@ def run_phase(self):
            #
            # Run the case (Archiving on)
            #
-           if not os.path.exists(rundir):
-               self._case.flush()
+           self._case.flush()
            self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True)
 
            #

From d4cbc8c58570b027adbc155b7f39d0c2faaf3f38 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 26 Mar 2024 13:03:46 -0600
Subject: [PATCH 0095/1248] Bug-fix discovered by izumi_nag test

---
 src/main/surfrdUtilsMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/surfrdUtilsMod.F90 b/src/main/surfrdUtilsMod.F90
index 97f5b7d80f..ac7c1304b8 100644
--- a/src/main/surfrdUtilsMod.F90
+++ b/src/main/surfrdUtilsMod.F90
@@ -282,8 +282,8 @@ subroutine collapse_to_dominant(weight, lower_bound, upper_bound, begg, endg, n_
           ! original sum of all the weights
           wt_sum(g) = sum(weight(g,:))
 
-          if (present(do_not_collapse) .and. do_not_collapse(g)) then
-             cycle
+          if (present(do_not_collapse)) then
+             if (do_not_collapse(g)) cycle
           end if
 
           max_indices = 0  ! initialize

From f06ceb8c8e3b47d96f363a7d2c681c7a68c1432e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 26 Mar 2024 13:15:26 -0600
Subject: [PATCH 0096/1248] Update derecho test from failing P64x2 to passing
 P24x2

---
 cime_config/testdefs/testlist_clm.xml | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 3d713e98ec..04200b7271 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2835,19 +2835,7 @@
 
     </machines>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpBgcCropGswp" testmods="clm/default">
-    <machines>
-
-      <machine name="cheyenne" compiler="intel" category="aux_clm">
-        <options>
-          <option name="wallclock">00:30:00</option>
-          <option name="comment">A debug ERP test of the NWP configuration with active BGC and CROP.</option>
-        </options>
-      </machine>
-
-    </machines>
-  </test>
-  <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpBgcCropGswp" testmods="clm/default">
+  <test name="ERP_P24x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpBgcCropGswp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>

From 0ebb7e0415809c49250ecbc1bbd355227068ae35 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Wed, 27 Mar 2024 13:22:13 -0600
Subject: [PATCH 0097/1248] Rename isspinup -> spinup_matrixcn, is_outmatrix ->
 hist_wrt_matrixcn_diag

Ran aux_clm on derecho and got expected results
---
 bld/CLMBuildNamelist.pm                       | 28 +++++++++----------
 bld/namelist_files/namelist_defaults_ctsm.xml | 16 +++++------
 .../namelist_definition_ctsm.xml              |  6 ++--
 bld/unit_testers/build-namelist_test.pl       | 18 ++++++------
 cime_config/SystemTests/sspmatrixcn.py        |  2 +-
 .../clm/ciso_monthly_matrixcn/user_nl_clm     |  2 +-
 src/biogeochem/CNVegMatrixMod.F90             | 14 +++++-----
 src/main/clm_varctl.F90                       |  4 +--
 src/main/controlMod.F90                       | 10 +++----
 src/soilbiogeochem/CNSoilMatrixMod.F90        | 16 +++++------
 10 files changed, 58 insertions(+), 58 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 67b8bd3b5c..ca0221277f 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -114,7 +114,7 @@ OPTIONS
                                   off : run in normal mode                 (spinup_state = 0)
 
                               To spinup using the CN soil matrix method use "sasu" SemiAnalytic Spin-Up (SASU)
-                                  sasu: Turn on matrix spinup               (isspinup=T)
+                                  sasu: Turn on matrix spinup               (spinup_matrixcn=T)
                               Normal spinup sequence is: on, sasu, off
 
                               Default is set by clm_accelerated_spinup mode.
@@ -1234,21 +1234,21 @@ sub setup_cmdl_spinup {
   }
   $nl_flags->{$var} = $val;
   if ( &value_is_true($nl_flags->{'use_soil_matrixcn'}) ) {
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "isspinup",
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "spinup_matrixcn",
                  , 'use_fates'=>$nl_flags->{'use_fates'}, 'bgc_mode'=>$nl_flags->{'bgc_mode'}
                  , 'phys'=>$nl_flags->{'phys'}, 'use_soil_matrixcn'=>$nl_flags->{'use_soil_matrixcn'},
                  , clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} );
      my $spinup;
-     if ( &value_is_true($nl->get_value("isspinup") ) ) {
+     if ( &value_is_true($nl->get_value("spinup_matrixcn") ) ) {
         $spinup = ".true.";
      } else {
         $spinup = ".false.";
      }
-     $nl_flags->{'isspinup'} = $spinup;
-     if ( &value_is_true($nl_flags->{'isspinup'}) ) {
+     $nl_flags->{'spinup_matrixcn'} = $spinup;
+     if ( &value_is_true($nl_flags->{'spinup_matrixcn'}) ) {
         $nl_flags->{'bgc_spinup'} = "on";
         if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) {
-           $log->fatal_error("matrix spinup (isspinup) is True, but clm_accelerated_spinup is off, change one or the other");
+           $log->fatal_error("matrix spinup (spinup_matrixcn) is True, but clm_accelerated_spinup is off, change one or the other");
         }
      } else {
         $nl_flags->{'bgc_spinup'} = "off";
@@ -4569,14 +4569,14 @@ sub setup_logic_cnmatrix {
     #
     my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-    my @matrixlist = ( "use_matrixcn", "is_outmatrix" );
+    my @matrixlist = ( "use_matrixcn", "hist_wrt_matrixcn_diag" );
     foreach my $var ( @matrixlist ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var
                 , 'use_fates'=>$nl_flags->{'use_fates'}, 'bgc_mode'=>$nl_flags->{'bgc_mode'}
                 , 'phys'=>$nl_flags->{'phys'}, 'use_soil_matrixcn'=>$nl_flags->{'use_soil_matrixcn'},
-                , 'isspinup'=>$nl_flags->{'isspinup'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
+                , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
     }
-    @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "is_outmatrix", "isspinup" );
+    @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" );
     # Matrix items can't be on for SP mode
     if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
        foreach my $var ( @matrixlist ) {
@@ -4607,14 +4607,14 @@ sub setup_logic_cnmatrix {
       }
       # If both matrixcn and soil_matrix are off outmatrix can't be on
       if ( ! &value_is_true($nl->get_value("use_matrixcn")) && ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) {
-         my $var = "is_outmatrix";
+         my $var = "hist_wrt_matrixcn_diag";
          if ( &value_is_true($nl->get_value($var)) ) {
             $log->fatal_error("$var can NOT be on when both use_matrixcn and use_soil_matrixcn are off" );
          }
       }
       # If soil_matrix is off ispspinup can't be on
       if ( ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) {
-         my $var = "isspinup";
+         my $var = "spinup_matrixcn";
          if ( &value_is_true($nl->get_value($var)) ) {
             $log->fatal_error("$var can NOT be on when use_soil_matrixcn is off" );
          }
@@ -4623,10 +4623,10 @@ sub setup_logic_cnmatrix {
     # if soil matrix is on and spinup is on, set spinup specific variables
     my @spinup_vars = ( "nyr_forcing", "nyr_sasu", "iloop_avg" );
     foreach my $var ( @spinup_vars ) {
-       if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'isspinup'}) ) {
+       if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'spinup_matrixcn'}) ) {
           if ( $var ne "nyr_sasu" ) {
              add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                       , 'phys'=>$nl_flags->{'phys'}, 'isspinup'=>$nl_flags->{'isspinup'} );
+                       , 'phys'=>$nl_flags->{'phys'}, 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'} );
           } else {
              # Set SASU spinup period to nyr_forcing (slow mode) by default
              add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
@@ -4644,7 +4644,7 @@ sub setup_logic_cnmatrix {
           }
        }
     }
-    if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'isspinup'}) ) {
+    if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'spinup_matrixcn'}) ) {
        my $nyr_forcing = $nl->get_value('nyr_forcing');
        my $nyr_sasu    = $nl->get_value('nyr_sasu');
        if ( $nyr_sasu > $nyr_forcing ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index f2e42dd6e0..1455bbf873 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -661,18 +661,18 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_soil_matrixcn               bgc_mode="fates" >.false.</use_soil_matrixcn>
 <use_soil_matrixcn                                >.false.</use_soil_matrixcn>
 
-<is_outmatrix clm_accelerated_spinup="on"                             >.false.</is_outmatrix>
-<is_outmatrix clm_accelerated_spinup="sasu"                           >.false.</is_outmatrix>
-<is_outmatrix clm_accelerated_spinup="off"                            >.false.</is_outmatrix>
-<isspinup     clm_accelerated_spinup="on"   use_soil_matrixcn=".true.">.true.</isspinup>
-<isspinup     clm_accelerated_spinup="sasu" use_soil_matrixcn=".true.">.true.</isspinup>
-<isspinup     clm_accelerated_spinup="off"                            >.false.</isspinup>
+<hist_wrt_matrixcn_diag clm_accelerated_spinup="on"                             >.false.</hist_wrt_matrixcn_diag>
+<hist_wrt_matrixcn_diag clm_accelerated_spinup="sasu"                           >.false.</hist_wrt_matrixcn_diag>
+<hist_wrt_matrixcn_diag clm_accelerated_spinup="off"                            >.false.</hist_wrt_matrixcn_diag>
+<spinup_matrixcn     clm_accelerated_spinup="on"   use_soil_matrixcn=".true.">.true.</spinup_matrixcn>
+<spinup_matrixcn     clm_accelerated_spinup="sasu" use_soil_matrixcn=".true.">.true.</spinup_matrixcn>
+<spinup_matrixcn     clm_accelerated_spinup="off"                            >.false.</spinup_matrixcn>
 <nyr_forcing                                                          >1</nyr_forcing>
-<nyr_forcing  isspinup=".true."             use_soil_matrixcn=".true.">20</nyr_forcing>
+<nyr_forcing  spinup_matrixcn=".true."             use_soil_matrixcn=".true.">20</nyr_forcing>
 <!-- for SASU spinup nyr_sasu will normally be set to nyr_forcing (slow mode spinup) -->
 <nyr_sasu                                                             >1</nyr_sasu>
 <iloop_avg                                                            >-999</iloop_avg>
-<iloop_avg    isspinup=".true."             use_soil_matrixcn=".true.">-999</iloop_avg>
+<iloop_avg    spinup_matrixcn=".true."             use_soil_matrixcn=".true.">-999</iloop_avg>
 
 
 <!-- General CN options -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 5214c20942..4cf8b8ad7d 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1149,12 +1149,12 @@ Turn on the Matrix solution for above ground biogeochemistry, requires CN to be
 Turn on the Matrix solution for soil biogeochemistry
 </entry>
 
-<entry id="is_outmatrix" type="logical" category="bgc"
+<entry id="hist_wrt_matrixcn_diag" type="logical" category="bgc"
        group="clm_inparm" valid_values="" value=".false.">
 Turn on extra output for the matrix solution
 </entry>
 
-<entry id="isspinup" type="logical" category="bgc"
+<entry id="spinup_matrixcn" type="logical" category="bgc"
        group="clm_inparm" valid_values="" value=".false.">
 Turn on semi-analytic spinup solution for the CN/Soil matrix, requires soil matrix to be on
 This will drive the solution to equilibrium
@@ -1162,7 +1162,7 @@ This will drive the solution to equilibrium
 
 <entry id="nyr_forcing" type="integer" category="bgc"
        group="clm_inparm" valid_values="" value="1">
-Number of years to average the storage capacitance over for the soil Matrix solution during semi-analytic spinup (isspinup=T)
+Number of years to average the storage capacitance over for the soil Matrix solution during semi-analytic spinup (spinup_matrixcn=T)
 Normally should be the same as the number of years the atmospheric forcing is run over
 </entry>
 
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 3c3a42abc9..83429d2f18 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -326,8 +326,8 @@ sub cat_and_create_namelistinfile {
                          "-res 0.9x1.25 -use_case 1850_control",
                          "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'",
                          "-res 1x1_brazil",
-                         "-namelist '&a use_matrixcn=F,use_soil_matrixcn=F,is_outmatrix=F,isspinup=F/' -bgc sp",
-                         "-namelist '&a use_matrixcn=T,use_soil_matrixcn=T,is_outmatrix=T,isspinup=T/' -bgc bgc -crop -clm_accelerated_spinup on",
+                         "-namelist '&a use_matrixcn=F,use_soil_matrixcn=F,hist_wrt_matrixcn_diag=F,spinup_matrixcn=F/' -bgc sp",
+                         "-namelist '&a use_matrixcn=T,use_soil_matrixcn=T,hist_wrt_matrixcn_diag=T,spinup_matrixcn=T/' -bgc bgc -crop -clm_accelerated_spinup on",
                          "-namelist \"&a soil_decomp_method='MIMICSWieder2015',use_matrixcn=F/\" -bgc bgc -crop",
                          "-namelist \"&a soil_decomp_method='MIMICSWieder2015',use_matrixcn=T/\" -bgc bgc -crop",
                          "-bgc bgc -crop -clm_accelerated_spinup sasu",
@@ -970,12 +970,12 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "outmatrixWOmatrix"         =>{ options=>"-envxml_dir . -bgc bgc",
-                                     namelst=>"use_soil_matrixcn=.false.,use_matrixcn=F,is_outmatrix=T",
+                                     namelst=>"use_soil_matrixcn=.false.,use_matrixcn=F,hist_wrt_matrixcn_diag=T",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
      "spinupWOsoilmatrix"         =>{ options=>"-envxml_dir . -bgc bgc",
-                                     namelst=>"use_soil_matrixcn=F,use_matrixcn=T,isspinup=T",
+                                     namelst=>"use_soil_matrixcn=F,use_matrixcn=T,spinup_matrixcn=T",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
@@ -990,27 +990,27 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_1",
                                    },
      "nyrforceWOspinup"          =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu",
-                                     namelst=>"use_matrixcn=.false.,isspinup=F,nyr_forcing=20",
+                                     namelst=>"use_matrixcn=.false.,spinup_matrixcn=F,nyr_forcing=20",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
      "nyrsasuGTnyrforce"         =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu",
-                                     namelst=>"use_matrixcn=.false.,isspinup=T,nyr_forcing=20,nyr_sasu=21",
+                                     namelst=>"use_matrixcn=.false.,spinup_matrixcn=T,nyr_forcing=20,nyr_sasu=21",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
      "iloopZero"                 =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu",
-                                     namelst=>"use_matrixcn=.false.,isspinup=T,iloop_avg=0",
+                                     namelst=>"use_matrixcn=.false.,spinup_matrixcn=T,iloop_avg=0",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
      "matrixspinupWADmode"        =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu",
-                                     namelst=>"isspinup=T,spinup_state=2",
+                                     namelst=>"spinup_matrixcn=T,spinup_state=2",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
      "matrixspinupWclmaccell"     =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup off",
-                                     namelst=>"use_soil_matrixcn=T,isspinup=T",
+                                     namelst=>"use_soil_matrixcn=T,spinup_matrixcn=T",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py
index eec462e72c..0e0d57e6c2 100644
--- a/cime_config/SystemTests/sspmatrixcn.py
+++ b/cime_config/SystemTests/sspmatrixcn.py
@@ -130,7 +130,7 @@ def append_user_nl(self, caseroot, n=0):
         # For all but last step turn extra matrix output to off
         b4last = self.n_steps() - 1
         if ( n < b4last ):
-           contents_to_append = contents_to_append + ", is_outmatrix = .False."
+           contents_to_append = contents_to_append + ", hist_wrt_matrixcn_diag = .False."
         # For matrix spinup steps, set the matrix spinup and other variables associated with it
         if ( self.spin[n] == "sasu" ):
             contents_to_append = contents_to_append + ", nyr_forcing = "+str(self.nyr_forcing)
diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm
index 56d4261a45..6b7eb4347d 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm
@@ -1,3 +1,3 @@
  use_matrixcn = .true.
  use_soil_matrixcn = .true.
- is_outmatrix = .true.
+ hist_wrt_matrixcn_diag = .true.
diff --git a/src/biogeochem/CNVegMatrixMod.F90 b/src/biogeochem/CNVegMatrixMod.F90
index c171490bf0..bf7527bc71 100644
--- a/src/biogeochem/CNVegMatrixMod.F90
+++ b/src/biogeochem/CNVegMatrixMod.F90
@@ -41,7 +41,7 @@ module CNVegMatrixMod
   use CNVegNitrogenFluxType          , only : cnveg_nitrogenflux_type
   use CNVegStateType                 , only : cnveg_state_type
   use SoilBiogeochemNitrogenFluxType , only : soilbiogeochem_nitrogenflux_type
-  use clm_varctl                     , only : isspinup, is_outmatrix, nyr_forcing, nyr_SASU, iloop_avg 
+  use clm_varctl                     , only : spinup_matrixcn, hist_wrt_matrixcn_diag, nyr_forcing, nyr_SASU, iloop_avg 
   use clm_varctl                     , only : use_c13, use_c14 
   use SparseMatrixMultiplyMod        , only : sparse_matrix_type,diag_matrix_type,vector_type
   use MatrixMod                      , only : inverse
@@ -1253,7 +1253,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire
          if(mod(iyr-1,nyr_forcing) .eq. 0)then
             iloop = iloop + 1
          end if
-         if(.not. isspinup .or. isspinup .and. mod(iyr-1,nyr_SASU) .eq. 0)then
+         if(.not. spinup_matrixcn .or. spinup_matrixcn .and. mod(iyr-1,nyr_SASU) .eq. 0)then
             do fp = 1,num_soilp
                p = filter_soilp(fp)
                leafc0(p)                = max(leafc(p),  epsi)
@@ -1683,7 +1683,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire
   ! Accumulate transfers during the whole calendar year
 
          call t_startf('CN veg matrix-accum. trans.')
-         if(isspinup .or. is_outmatrix)then
+         if(spinup_matrixcn .or. hist_wrt_matrixcn_diag)then
             do fp = 1,num_soilp
                p = filter_soilp(fp)
                matrix_calloc_leaf_acc(p)        = matrix_calloc_leaf_acc(p)        + vegmatrixc_input%V(p,ileaf)
@@ -2439,8 +2439,8 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire
          call t_stopf('CN veg matrix-assign new value')
 
   ! Calculate C storage capacity. 2D matrix instead of sparse matrix is still used when calculating the inverse
-         if(isspinup .or. is_outmatrix)then
-            if((.not. isspinup .and. is_end_curr_year()) .or. (isspinup .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then
+         if(spinup_matrixcn .or. hist_wrt_matrixcn_diag)then
+            if((.not. spinup_matrixcn .and. is_end_curr_year()) .or. (spinup_matrixcn .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then
                do fp = 1,num_soilp
                   call t_startf('CN veg matrix-prepare AK^-1')
                   p = filter_soilp(fp)
@@ -2881,7 +2881,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire
  
                   call t_startf('CN veg matrix-finalize spinup')
                   
-                  if(isspinup .and. .not. is_first_step_of_this_run_segment())then
+                  if(spinup_matrixcn .and. .not. is_first_step_of_this_run_segment())then
                      deadstemc(p)              = vegmatrixc_rt(ideadstem)
                      deadstemc_storage(p)      = vegmatrixc_rt(ideadstem_st)
                      deadcrootc(p)             = vegmatrixc_rt(ideadcroot)
@@ -3184,7 +3184,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire
                   end if
 
   ! Save C storage capacity from temporary variables to module variables
-                  if(is_outmatrix)then
+                  if(hist_wrt_matrixcn_diag)then
                      matrix_cap_leafc(p)                  = vegmatrixc_rt(ileaf)
                      matrix_cap_leafc_storage(p)          = vegmatrixc_rt(ileaf_st)
                      matrix_cap_leafc_xfer(p)             = vegmatrixc_rt(ileaf_xf)
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index ffc43b4200..faead44399 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -280,8 +280,8 @@ module clm_varctl
   !----------------------------------------------------------
   ! CN matrix
   !----------------------------------------------------------  
-  logical, public :: isspinup = .false.  !.false.              ! true => use acc spinup
-  logical, public :: is_outmatrix = .false.!.false.              ! true => use acc spinup
+  logical, public :: spinup_matrixcn = .false.  !.false.              ! true => use acc spinup
+  logical, public :: hist_wrt_matrixcn_diag = .false.!.false.              ! true => use acc spinup
   ! SASU 
   integer, public :: nyr_forcing  = 10   ! length of forcing years for the spin up. eg. if DATM_CLMNCEP_YR_START=1901;DATM_CLMNCEP_YR_END=1920, then nyr_forcing = 20
   integer, public :: nyr_SASU     = 1    ! length of each semi-analytic solution. eg. nyr_SASU=5, analytic solutions will be calculated every five years.
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index ef006bcc42..acb4d6491b 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -189,7 +189,7 @@ subroutine control_init(dtime)
 
     ! CN Matrix solution
     namelist /clm_inparm / &
-         use_matrixcn, use_soil_matrixcn, is_outmatrix, isspinup, nyr_forcing, nyr_sasu, iloop_avg
+         use_matrixcn, use_soil_matrixcn, hist_wrt_matrixcn_diag, spinup_matrixcn, nyr_forcing, nyr_sasu, iloop_avg
 
     ! lake_melt_icealb is of dimension numrad
 
@@ -325,8 +325,8 @@ subroutine control_init(dtime)
     if(use_fates)then
        use_matrixcn = .false.
        use_soil_matrixcn = .false.
-       is_outmatrix = .false.
-       isspinup = .false.
+       hist_wrt_matrixcn_diag = .false.
+       spinup_matrixcn = .false.
     end if
     nyr_forcing = 10
 
@@ -850,8 +850,8 @@ subroutine control_spmd()
     call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_matrixcn, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_soil_matrixcn, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (is_outmatrix, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (isspinup, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (hist_wrt_matrixcn_diag, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (spinup_matrixcn, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (nyr_forcing, 1, MPI_INTEGER, 0, mpicom, ier)
     call mpi_bcast (nyr_sasu, 1, MPI_INTEGER, 0, mpicom, ier)
     call mpi_bcast (iloop_avg, 1, MPI_INTEGER, 0, mpicom, ier)
diff --git a/src/soilbiogeochem/CNSoilMatrixMod.F90 b/src/soilbiogeochem/CNSoilMatrixMod.F90
index 1248c5e1d6..56c1f11b5c 100644
--- a/src/soilbiogeochem/CNSoilMatrixMod.F90
+++ b/src/soilbiogeochem/CNSoilMatrixMod.F90
@@ -34,7 +34,7 @@ module CNSoilMatrixMod
   use SoilBiogeochemNitrogenFluxType     , only : soilbiogeochem_nitrogenflux_type  
   use CNSharedParamsMod                  , only : CNParamsShareInst
   use SoilStateType                      , only : soilstate_type  
-  use clm_varctl                         , only : isspinup, is_outmatrix, nyr_forcing, nyr_SASU, iloop_avg
+  use clm_varctl                         , only : spinup_matrixcn, hist_wrt_matrixcn_diag, nyr_forcing, nyr_SASU, iloop_avg
   use ColumnType                         , only : col                
   use GridcellType                       , only : grc
   use clm_varctl                         , only : use_c13, use_c14, iulog
@@ -67,14 +67,14 @@ subroutine CNSoilMatrixInit( )
     if ( use_soil_matrixcn ) then
        write(iulog,*) 'CN Soil matrix solution is on'
        write(iulog,*) '*****************************'
-       if ( isspinup ) then
+       if ( spinup_matrixcn ) then
           write(iulog,*) '   Matrix spinup is on'
           write(iulog,*) '   *******************'
           write(iulog,*) '   nyr_forcing = ', nyr_forcing
           write(iulog,*) '   nyr_SASU    = ', nyr_SASU
           write(iulog,*) '   iloop_avg   = ', iloop_avg
        end if
-       if ( is_outmatrix )then
+       if ( hist_wrt_matrixcn_diag )then
           write(iulog,*) '   Extra matrix solution tracability output is turned on'
        else
           write(iulog,*) '   no extra matrix solution tracability output'
@@ -343,7 +343,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act
          if(mod(iyr-1,nyr_forcing) .eq. 0)then
             iloop = iloop + 1
          end if
-         if(.not. isspinup .or. isspinup .and. mod(iyr-1,nyr_SASU) .eq. 0)then
+         if(.not. spinup_matrixcn .or. spinup_matrixcn .and. mod(iyr-1,nyr_SASU) .eq. 0)then
             do i = 1,ndecomp_pools
                do j = 1, nlevdecomp
                   do fc = 1,num_soilc
@@ -550,7 +550,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act
 
       call t_stopf('CN Soil matrix-assign back')
 
-      if(use_soil_matrixcn .and. (is_outmatrix .or. isspinup))then
+      if(use_soil_matrixcn .and. (hist_wrt_matrixcn_diag .or. spinup_matrixcn))then
             
          ! Accumulate C transfers during a whole calendar year to calculate the C and N capacity
          do j=1,ndecomp_pools*nlevdecomp
@@ -665,7 +665,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act
          end if
 
          call t_startf('CN Soil matrix-calc. C capacity')
-         if((.not. isspinup .and. is_end_curr_year()) .or. (isspinup .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then
+         if((.not. spinup_matrixcn .and. is_end_curr_year()) .or. (spinup_matrixcn .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then
             ! Copy C transfers from sparse matrix to 2D temporary variables tran_acc and tran_nacc
             ! Calculate the C and N transfer rate by dividing CN transfer by base value saved at begin of each year.
             do fc = 1,num_soilc
@@ -816,7 +816,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act
                do j = 1,nlevdecomp
                   do fc = 1,num_soilc
                      c = filter_soilc(fc)
-                     if(isspinup .and. .not. is_first_step_of_this_run_segment())then
+                     if(spinup_matrixcn .and. .not. is_first_step_of_this_run_segment())then
                         cs_soil%decomp_cpools_vr_col(c,j,i) =  soilmatrixc_cap(c,j+(i-1)*nlevdecomp,1)
                         if(use_c13)then
                            cs13_soil%decomp_cpools_vr_col(c,j,i) =  soilmatrixc13_cap(c,j+(i-1)*nlevdecomp,1)
@@ -871,7 +871,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act
                end do
             end do
          
-            if(isspinup)call update_DA_nstep()
+            if(spinup_matrixcn)call update_DA_nstep()
             if(iloop .eq. iloop_avg .and. iyr .eq. nyr_forcing)iloop = 0
             if(iyr .eq. nyr_forcing)iyr = 0
 

From 1a2ddffdffbae8b3140b0e751b530f21db9c5afb Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Wed, 27 Mar 2024 13:24:58 -0600
Subject: [PATCH 0098/1248] Replace 1.e+36 with spval in cnmatrix code

---
 src/biogeochem/CNVegMatrixMod.F90 | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/CNVegMatrixMod.F90 b/src/biogeochem/CNVegMatrixMod.F90
index bf7527bc71..5582afeffe 100644
--- a/src/biogeochem/CNVegMatrixMod.F90
+++ b/src/biogeochem/CNVegMatrixMod.F90
@@ -23,6 +23,7 @@ module CNVegMatrixMod
   use clm_time_manager               , only : get_step_size,is_end_curr_year,is_first_step_of_this_run_segment,&
                                               is_beg_curr_year,update_DA_nstep
   use decompMod                      , only : bounds_type 
+  use clm_varcon                     , only : spval
   use clm_varpar                     , only : nlevdecomp, nvegcpool, nvegnpool
   use clm_varpar                     , only : ileaf,ileaf_st,ileaf_xf,ifroot,ifroot_st,ifroot_xf,&
                                               ilivestem,ilivestem_st,ilivestem_xf,&
@@ -2711,27 +2712,27 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire
                   matrix_ntransfer_acc(iretransn,iretransn)         = -matrix_nturnover_retransn_acc(p)               
 
                   do i=1,nvegcpool
-                    if(matrix_ctransfer_acc(i,i) .eq. 0)then
-                       matrix_ctransfer_acc(i,i) = 1.e+36
+                    if(matrix_ctransfer_acc(i,i) == 0)then
+                       matrix_ctransfer_acc(i,i) = spval
                     end if
                   end do
                   if(use_c13)then
                      do i=1,nvegcpool
-                       if(matrix_c13transfer_acc(i,i) .eq. 0)then
-                          matrix_c13transfer_acc(i,i) = 1.e+36
+                       if(matrix_c13transfer_acc(i,i) == 0)then
+                          matrix_c13transfer_acc(i,i) = spval
                        end if
                      end do
                   end if
                   if(use_c14)then
                      do i=1,nvegcpool
-                       if(matrix_c14transfer_acc(i,i) .eq. 0)then
-                          matrix_c14transfer_acc(i,i) = 1.e+36
+                       if(matrix_c14transfer_acc(i,i) == 0)then
+                          matrix_c14transfer_acc(i,i) = spval
                        end if
                      end do
                   end if
                   do i=1,nvegnpool
-                    if(matrix_ntransfer_acc(i,i) .eq. 0)then
-                       matrix_ntransfer_acc(i,i) = 1.e+36
+                    if(matrix_ntransfer_acc(i,i) == 0)then
+                       matrix_ntransfer_acc(i,i) = spval
                     end if
                   end do
 

From 47839a77229c61555e3b8932927bb54cdc511b27 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Wed, 27 Mar 2024 14:39:43 -0600
Subject: [PATCH 0099/1248] Black reformatting of two files

---
 cime_config/SystemTests/sspmatrixcn.py | 455 ++++++++++++++-----------
 cime_config/buildnml                   |  72 ++--
 2 files changed, 295 insertions(+), 232 deletions(-)

diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py
index 0e0d57e6c2..37d4154121 100644
--- a/cime_config/SystemTests/sspmatrixcn.py
+++ b/cime_config/SystemTests/sspmatrixcn.py
@@ -14,15 +14,15 @@
 """
 import shutil, glob, os, sys
 
-if __name__ == '__main__':
-   CIMEROOT = os.environ.get("CIMEROOT")
-   if CIMEROOT is None:
-      CIMEROOT = "../../cime";
+if __name__ == "__main__":
+    CIMEROOT = os.environ.get("CIMEROOT")
+    if CIMEROOT is None:
+        CIMEROOT = "../../cime"
 
-   sys.path.append(os.path.join( CIMEROOT, "scripts", "lib"))
-   sys.path.append(os.path.join( CIMEROOT, "scripts" ) )
+    sys.path.append(os.path.join(CIMEROOT, "scripts", "lib"))
+    sys.path.append(os.path.join(CIMEROOT, "scripts"))
 else:
-   from CIME.utils import append_testlog
+    from CIME.utils import append_testlog
 
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
@@ -31,123 +31,170 @@
 
 logger = logging.getLogger(__name__)
 
+
 class SSPMATRIXCN(SystemTestsCommon):
 
     # Class data
     nyr_forcing = 2
     # Get different integer multiples of the number of forcing years
-    full   = nyr_forcing
-    twice  = 2 * nyr_forcing
+    full = nyr_forcing
+    twice = 2 * nyr_forcing
     thrice = 3 * nyr_forcing
     # Define the settings that will be used for each step
-    steps  = ["0-AD",                        "1-SASU",                               "2-norm" ]
-    desc   = ["Accell-Decomp(AD)-coldstart", "slow-mode Semi-Analytic SpinUp(SASU)", "normal" ]
-    runtyp = ["startup",                     "hybrid",                               "branch" ]
-    spin   = ["on",                          "sasu",                                 "off"    ]
-    stop_n = [5,                             thrice,                                 thrice   ]
-    cold   = [True,                          False,                                  False    ]
-    iloop  = [-999,                          -999,                                   -999     ]
-    sasu   = [-999,                          -999,                                   -999     ]
+    steps = ["0-AD", "1-SASU", "2-norm"]
+    desc = [
+        "Accell-Decomp(AD)-coldstart",
+        "slow-mode Semi-Analytic SpinUp(SASU)",
+        "normal",
+    ]
+    runtyp = ["startup", "hybrid", "branch"]
+    spin = ["on", "sasu", "off"]
+    stop_n = [5, thrice, thrice]
+    cold = [True, False, False]
+    iloop = [-999, -999, -999]
+    sasu = [-999, -999, -999]
 
     def __init__(self, case=None):
         """
         initialize an object interface to the SSPMATRIXCN system test
         """
-        expect ( len(self.steps) == len(self.sasu),   "length of steps must be the same as sasu" )
-        expect ( len(self.steps) == len(self.spin),   "length of steps must be the same as spin" )
-        expect ( len(self.steps) == len(self.desc),   "length of steps must be the same as desc" )
-        expect ( len(self.steps) == len(self.cold),   "length of steps must be the same as cold" )
-        expect ( len(self.steps) == len(self.runtyp), "length of steps must be the same as runtyp" )
-        expect ( len(self.steps) == len(self.iloop),  "length of steps must be the same as iloop" )
-        expect ( len(self.steps) == len(self.stop_n), "length of steps must be the same as stop_n" )
-
-        if __name__ != '__main__':
-           SystemTestsCommon.__init__(self, case)
-           ystart = int(self._case.get_value("DATM_YR_START"))
-           yend   = int(self._case.get_value("DATM_YR_END"))
-           self.comp = self._case.get_value("COMP_LND") 
+        expect(
+            len(self.steps) == len(self.sasu),
+            "length of steps must be the same as sasu",
+        )
+        expect(
+            len(self.steps) == len(self.spin),
+            "length of steps must be the same as spin",
+        )
+        expect(
+            len(self.steps) == len(self.desc),
+            "length of steps must be the same as desc",
+        )
+        expect(
+            len(self.steps) == len(self.cold),
+            "length of steps must be the same as cold",
+        )
+        expect(
+            len(self.steps) == len(self.runtyp),
+            "length of steps must be the same as runtyp",
+        )
+        expect(
+            len(self.steps) == len(self.iloop),
+            "length of steps must be the same as iloop",
+        )
+        expect(
+            len(self.steps) == len(self.stop_n),
+            "length of steps must be the same as stop_n",
+        )
+
+        if __name__ != "__main__":
+            SystemTestsCommon.__init__(self, case)
+            ystart = int(self._case.get_value("DATM_YR_START"))
+            yend = int(self._case.get_value("DATM_YR_END"))
+            self.comp = self._case.get_value("COMP_LND")
         else:
-           self._case = None
-           self.comp = "clm"
-           ystart = 2000
-           yend   = 2001
+            self._case = None
+            self.comp = "clm"
+            ystart = 2000
+            yend = 2001
 
         for n in range(len(self.steps)):
-           if ( n == 0 ):
-              expect( self.cold[n]   == True,      "First step MUST be a cold-start" )
-              expect( self.runtyp[n] == "startup", "First step MUST be a startup" )
-           else:
-              expect( self.cold[n] == False, "Other steps must NOT be a cold-start" )
-              expect( self.runtyp[n] != "startup", "Other steps MUST NOT be a startup" )
-
-           if ( self.spin[n] == "sasu" ):
-              expect( self.cold[n] == False,            "SASU step should NOT be a cold-start" )
-              if ( self.sasu[n] != -999 ):
-                 expect( self.sasu[n] > 0,                 "SASU steps must set SASU cycle" )
-                 expect( self.sasu[n] <= self.nyr_forcing, "SASU cycles can't be greater than a full forcing cycle" )
-
-        expect( yend-ystart+1 == self.nyr_forcing, "Number of years run over MUST correspond to nyr_forcing" )
+            if n == 0:
+                expect(self.cold[n] == True, "First step MUST be a cold-start")
+                expect(self.runtyp[n] == "startup", "First step MUST be a startup")
+            else:
+                expect(self.cold[n] == False, "Other steps must NOT be a cold-start")
+                expect(self.runtyp[n] != "startup", "Other steps MUST NOT be a startup")
+
+            if self.spin[n] == "sasu":
+                expect(self.cold[n] == False, "SASU step should NOT be a cold-start")
+                if self.sasu[n] != -999:
+                    expect(self.sasu[n] > 0, "SASU steps must set SASU cycle")
+                    expect(
+                        self.sasu[n] <= self.nyr_forcing,
+                        "SASU cycles can't be greater than a full forcing cycle",
+                    )
+
+        expect(
+            yend - ystart + 1 == self.nyr_forcing,
+            "Number of years run over MUST correspond to nyr_forcing",
+        )
         self._testname = "SSPMATRIX"
 
-    def check_n( self, n):
+    def check_n(self, n):
         "Check if n is within range"
-        expect( ( (n >= 0) and (n < self.n_steps()) ), "Step number is out of range = " + str(n) )
+        expect(
+            ((n >= 0) and (n < self.n_steps())),
+            "Step number is out of range = " + str(n),
+        )
 
     def __logger__(self, n=0):
         "Log info on this step"
 
-        self.check_n( n )
-        msg = "Step {}: {}: doing a {} run for {} years".format( self.steps[n], self.runtyp[n], self.desc[n], self.stop_n[n] )
+        self.check_n(n)
+        msg = "Step {}: {}: doing a {} run for {} years".format(
+            self.steps[n], self.runtyp[n], self.desc[n], self.stop_n[n]
+        )
         logger.info(msg)
-        logger.info("  spinup type: {}".format( self.spin[n] ) )
-        if __name__ != '__main__':
-           append_testlog(msg)
-        if ( n+1 < self.n_steps() ):
-           logger.info("  writing restarts at end of run")
-           logger.info("  short term archiving is on ")
+        logger.info("  spinup type: {}".format(self.spin[n]))
+        if __name__ != "__main__":
+            append_testlog(msg)
+        if n + 1 < self.n_steps():
+            logger.info("  writing restarts at end of run")
+            logger.info("  short term archiving is on ")
 
     def n_steps(self):
         "Total number of steps"
 
-        return( len(self.steps) )
+        return len(self.steps)
 
     def total_years(self):
         "Total number of years needed to do the full spinup"
 
         ysum = 0
         for nyr in self.stop_n:
-           ysum = ysum + nyr
+            ysum = ysum + nyr
 
-        return( ysum )
+        return ysum
 
     def append_user_nl(self, caseroot, n=0):
         "Append needed settings to the user_nl files"
 
-        self.check_n( n )
+        self.check_n(n)
         # For all set output to yearly
         contents_to_append = "hist_nhtfrq = -8760"
-        contents_to_append = contents_to_append + ", hist_mfilt = "+str(self.nyr_forcing)
+        contents_to_append = (
+            contents_to_append + ", hist_mfilt = " + str(self.nyr_forcing)
+        )
         # For all but last step turn extra matrix output to off
         b4last = self.n_steps() - 1
-        if ( n < b4last ):
-           contents_to_append = contents_to_append + ", hist_wrt_matrixcn_diag = .False."
+        if n < b4last:
+            contents_to_append = (
+                contents_to_append + ", hist_wrt_matrixcn_diag = .False."
+            )
         # For matrix spinup steps, set the matrix spinup and other variables associated with it
-        if ( self.spin[n] == "sasu" ):
-            contents_to_append = contents_to_append + ", nyr_forcing = "+str(self.nyr_forcing)
-            if ( self.sasu[n] != -999 ):
-               contents_to_append = contents_to_append + ", nyr_sasu = " + str(self.sasu[n])
-            if ( self.iloop[n] != -999 ):
-               contents_to_append = contents_to_append + ", iloop_avg = " + str(self.iloop[n])
+        if self.spin[n] == "sasu":
+            contents_to_append = (
+                contents_to_append + ", nyr_forcing = " + str(self.nyr_forcing)
+            )
+            if self.sasu[n] != -999:
+                contents_to_append = (
+                    contents_to_append + ", nyr_sasu = " + str(self.sasu[n])
+                )
+            if self.iloop[n] != -999:
+                contents_to_append = (
+                    contents_to_append + ", iloop_avg = " + str(self.iloop[n])
+                )
 
         # For cold start, run with matrix off
-        if ( self.cold[n] ):
+        if self.cold[n]:
             contents_to_append = contents_to_append + ", use_matrixcn = .False."
             contents_to_append = contents_to_append + ", use_soil_matrixcn = .False."
 
         # Always append to the end
-        user_nl_utils.append_to_user_nl_files(caseroot = caseroot,
-                                              component = self.comp,
-                                              contents = contents_to_append)
+        user_nl_utils.append_to_user_nl_files(
+            caseroot=caseroot, component=self.comp, contents=contents_to_append
+        )
 
     def run_phase(self):
         "Run phase"
@@ -156,77 +203,80 @@ def run_phase(self):
         orig_case = self._case
         orig_casevar = self._case.get_value("CASE")
 
-
         # Get a clone of each step except the last one
         b4last = self.n_steps() - 1
         for n in range(b4last):
-           #
-           # Clone the main case, and get it setup for the next step
-           #
-           clone_path =  "{}.step{}".format(caseroot,self.steps[n])
-           if os.path.exists(clone_path):
-               shutil.rmtree(clone_path)
-           if ( n > 0 ): 
-             del clone
-           self._set_active_case(orig_case)
-           clone = self._case.create_clone(clone_path, keepexe=True)
-           os.chdir(clone_path)
-           self._set_active_case(clone)
-
-           self.__logger__(n)
-
-           with clone:
-              clone.set_value("RUN_TYPE", self.runtyp[n] )
-              clone.set_value("STOP_N", self.stop_n[n] )
-
-              clone.set_value("CLM_ACCELERATED_SPINUP", self.spin[n] )
-
-              if ( self.cold[n] ):
-                 clone.set_value("CLM_FORCE_COLDSTART", "on" )
-              else:
-                 clone.set_value("CLM_FORCE_COLDSTART", "off" )
-
-              self.append_user_nl( clone_path, n )
-
-           dout_sr = clone.get_value("DOUT_S_ROOT")
-
-           self._skip_pnl = False
-           #
-           # Start up from the previous case
-           #
-           rundir = clone.get_value("RUNDIR")
-           with clone:
-              if ( n > 0 ):
-                 clone.set_value("GET_REFCASE", False)
-                 expect( "refcase" in locals(), "refcase was NOT previously set" )
-                 clone.set_value("RUN_REFCASE", refcase )
-                 expect( "refdate" in locals(), "refdate was NOT previously set" )
-                 clone.set_value("RUN_STARTDATE", refdate )
-                 clone.set_value("RUN_REFDATE", refdate )
-                 for item in glob.glob("{}/*{}*".format(rest_path, refdate)):
-                     linkfile = os.path.join(rundir, os.path.basename(item))
-                     if os.path.exists(linkfile):
-                         os.remove( linkfile )
-                     if not os.path.isdir(rundir):
-                         os.makedirs(rundir)
-                     os.symlink(item, linkfile )
-   
-                 for item in glob.glob("{}/*rpointer*".format(rest_path)):
-                     shutil.copy(item, rundir)
-   
-           #
-           # Run the case (Archiving on)
-           #
-           self._case.flush()
-           self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True)
-
-           #
-           # Get the reference case from this step for the next step
-           #
-           refcase = clone.get_value("CASE")
-           refdate = run_cmd_no_fail(r'ls -1dt {}/rest/*-00000* | head -1 | sed "s/-00000.*//" | sed "s/^.*rest\///"'.format(dout_sr))
-           refsec = "00000"
-           rest_path = os.path.join(dout_sr, "rest", "{}-{}".format(refdate, refsec))
+            #
+            # Clone the main case, and get it setup for the next step
+            #
+            clone_path = "{}.step{}".format(caseroot, self.steps[n])
+            if os.path.exists(clone_path):
+                shutil.rmtree(clone_path)
+            if n > 0:
+                del clone
+            self._set_active_case(orig_case)
+            clone = self._case.create_clone(clone_path, keepexe=True)
+            os.chdir(clone_path)
+            self._set_active_case(clone)
+
+            self.__logger__(n)
+
+            with clone:
+                clone.set_value("RUN_TYPE", self.runtyp[n])
+                clone.set_value("STOP_N", self.stop_n[n])
+
+                clone.set_value("CLM_ACCELERATED_SPINUP", self.spin[n])
+
+                if self.cold[n]:
+                    clone.set_value("CLM_FORCE_COLDSTART", "on")
+                else:
+                    clone.set_value("CLM_FORCE_COLDSTART", "off")
+
+                self.append_user_nl(clone_path, n)
+
+            dout_sr = clone.get_value("DOUT_S_ROOT")
+
+            self._skip_pnl = False
+            #
+            # Start up from the previous case
+            #
+            rundir = clone.get_value("RUNDIR")
+            with clone:
+                if n > 0:
+                    clone.set_value("GET_REFCASE", False)
+                    expect("refcase" in locals(), "refcase was NOT previously set")
+                    clone.set_value("RUN_REFCASE", refcase)
+                    expect("refdate" in locals(), "refdate was NOT previously set")
+                    clone.set_value("RUN_STARTDATE", refdate)
+                    clone.set_value("RUN_REFDATE", refdate)
+                    for item in glob.glob("{}/*{}*".format(rest_path, refdate)):
+                        linkfile = os.path.join(rundir, os.path.basename(item))
+                        if os.path.exists(linkfile):
+                            os.remove(linkfile)
+                        if not os.path.isdir(rundir):
+                            os.makedirs(rundir)
+                        os.symlink(item, linkfile)
+
+                    for item in glob.glob("{}/*rpointer*".format(rest_path)):
+                        shutil.copy(item, rundir)
+
+            #
+            # Run the case (Archiving on)
+            #
+            self._case.flush()
+            self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True)
+
+            #
+            # Get the reference case from this step for the next step
+            #
+            refcase = clone.get_value("CASE")
+            refdate = run_cmd_no_fail(
+                r'ls -1dt {}/rest/*-00000* | head -1 | sed "s/-00000.*//" | sed "s/^.*rest\///"'.format(
+                    dout_sr
+                )
+            )
+            refsec = "00000"
+            rest_path = os.path.join(dout_sr, "rest", "{}-{}".format(refdate, refsec))
 
         #
         # Last step in original case
@@ -239,25 +289,25 @@ def run_phase(self):
         self._set_active_case(orig_case)
         self.__logger__(n)
         self._case.set_value("DOUT_S", False)
-        self._case.set_value("RUN_TYPE", self.runtyp[n] )
-        self._case.set_value("STOP_N", self.stop_n[n] )
+        self._case.set_value("RUN_TYPE", self.runtyp[n])
+        self._case.set_value("STOP_N", self.stop_n[n])
         rundir = self._case.get_value("RUNDIR")
         self._case.set_value("GET_REFCASE", False)
-        expect( "refcase" in locals(), "refcase was NOT previously set" )
+        expect("refcase" in locals(), "refcase was NOT previously set")
         self._case.set_value("RUN_REFCASE", refcase)
-        expect( "refdate" in locals(), "refdate was NOT previously set" )
+        expect("refdate" in locals(), "refdate was NOT previously set")
         self._case.set_value("RUN_REFDATE", refdate)
-        self._case.set_value("RUN_STARTDATE", refdate )
+        self._case.set_value("RUN_STARTDATE", refdate)
         for item in glob.glob("{}/*{}*".format(rest_path, refdate)):
             linkfile = os.path.join(rundir, os.path.basename(item))
             if os.path.exists(linkfile):
-               os.remove( linkfile )
-            os.symlink(item, linkfile )
+                os.remove(linkfile)
+            os.symlink(item, linkfile)
 
         for item in glob.glob("{}/*rpointer*".format(rest_path)):
             shutil.copy(item, rundir)
 
-        self.append_user_nl( clone_path, n )
+        self.append_user_nl(clone_path, n)
         #
         # Don't need to set COLDSTART or ACCEL_SPINUP
         #
@@ -266,7 +316,8 @@ def run_phase(self):
         # Run the case (short term archiving is off)
         #
         self._case.flush()
-        self.run_indv( suffix="step{}".format(self.steps[n]), st_archive=False )
+        self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=False)
+
 
 #
 # Unit testing for above
@@ -274,59 +325,57 @@ def run_phase(self):
 import unittest
 from CIME.case import Case
 from CIME.utils import _LessThanFilter
-from argparse  import RawTextHelpFormatter
+from argparse import RawTextHelpFormatter
+
 
 class test_ssp_matrixcn(unittest.TestCase):
+    def setUp(self):
+        self.ssp = SSPMATRIXCN()
+
+    def test_logger(self):
+        # Test the logger
+        stream_handler = logging.StreamHandler(sys.stdout)
+        logger.addHandler(stream_handler)
+        logger.level = logging.DEBUG
+        logger.info("nyr_forcing = {}".format(self.ssp.nyr_forcing))
+        for n in range(self.ssp.n_steps()):
+            self.ssp.__logger__(n)
+            if self.ssp.spin[n] == "sasu":
+                logger.info("  SASU spinup is .true.")
+                if self.ssp.sasu[n] != -999:
+                    logger.info("  nyr_sasu = {}".format(self.ssp.sasu[n]))
+                if self.ssp.iloop[n] != -999:
+                    logger.info("  iloop_avg = {}".format(self.ssp.iloop[n]))
+
+        logger.info("Total number of years {}".format(self.ssp.total_years()))
+        logger.removeHandler(stream_handler)
+
+    def test_n_steps(self):
+        self.assertTrue(self.ssp.n_steps() == 3)
+
+    def test_valid_n(self):
+        for n in range(self.ssp.n_steps()):
+            self.ssp.check_n(n)
+
+    def test_negative_n(self):
+        self.assertRaises(SystemExit, self.ssp.check_n, -1)
+
+    def test_n_too_big(self):
+        self.assertRaises(SystemExit, self.ssp.check_n, self.ssp.n_steps())
+
+    def test_append_user_nl_step2(self):
+        ufile = "user_nl_clm"
+        if not os.path.exists(ufile):
+            os.mknod(ufile)
+        else:
+            expect(0, ufile + " file already exists, not overwritting it")
 
-   def setUp( self ):
-     self.ssp = SSPMATRIXCN()
-
-   def test_logger( self ):
-     # Test the logger
-     stream_handler = logging.StreamHandler(sys.stdout)
-     logger.addHandler(stream_handler)
-     logger.level = logging.DEBUG
-     logger.info( "nyr_forcing = {}".format(self.ssp.nyr_forcing) )
-     for n in range(self.ssp.n_steps()):
-       self.ssp.__logger__(n)
-       if ( self.ssp.spin[n] == "sasu" ):
-          logger.info( "  SASU spinup is .true." )
-          if ( self.ssp.sasu[n] != -999 ):
-             logger.info( "  nyr_sasu = {}".format(self.ssp.sasu[n]) )
-          if ( self.ssp.iloop[n] != -999 ):
-             logger.info( "  iloop_avg = {}".format(self.ssp.iloop[n]) )
-
-     logger.info( "Total number of years {}".format( self.ssp.total_years() ) )
-     logger.removeHandler(stream_handler)
-
-   def test_n_steps( self ):
-       self.assertTrue( self.ssp.n_steps() == 3)
-
-   def test_valid_n( self ):
-       for n in range(self.ssp.n_steps()):
-          self.ssp.check_n(n)
-    
-   def test_negative_n( self ):
-       self.assertRaises(SystemExit, self.ssp.check_n, -1 )
-
-   def test_n_too_big( self ):
-       self.assertRaises(SystemExit, self.ssp.check_n, self.ssp.n_steps()  )
-
-   def test_append_user_nl_step2( self ):
-       ufile = "user_nl_clm"
-       if not os.path.exists(ufile):
-         os.mknod(ufile)
-       else:
-         expect( 0, ufile+" file already exists, not overwritting it" )
-
-       self.ssp.append_user_nl( caseroot=".", n=2)
-       print( ufile+" for step 2" )
-       log = open(ufile, "r").read()
-       print( log )
-       os.remove(ufile)
-
-
-if __name__ == '__main__':
-     unittest.main()
+        self.ssp.append_user_nl(caseroot=".", n=2)
+        print(ufile + " for step 2")
+        log = open(ufile, "r").read()
+        print(log)
+        os.remove(ufile)
 
 
+if __name__ == "__main__":
+    unittest.main()
diff --git a/cime_config/buildnml b/cime_config/buildnml
index 11112b81f0..2f27473732 100755
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -51,24 +51,24 @@ def buildnml(case, caseroot, compname):
     clm_accelerated_spinup = case.get_value("CLM_ACCELERATED_SPINUP")
     comp_interface = case.get_value("COMP_INTERFACE")
     lilac_mode = case.get_value("LILAC_MODE")
-    if ( comp_interface == "nuopc" ):
-       yr_start = case.get_value("DATM_YR_START")
-       yr_end   = case.get_value("DATM_YR_END")
+    if comp_interface == "nuopc":
+        yr_start = case.get_value("DATM_YR_START")
+        yr_end = case.get_value("DATM_YR_END")
     else:
-       yr_start = case.get_value("DATM_CLMNCEP_YR_START")
-       yr_end   = case.get_value("DATM_CLMNCEP_YR_END")
+        yr_start = case.get_value("DATM_CLMNCEP_YR_START")
+        yr_end = case.get_value("DATM_CLMNCEP_YR_END")
 
-    if ( yr_start != None and yr_start < 0 ):
-       yr_start = case.get_value("DATM_CPLHIST_YR_START")
-       yr_end   = case.get_value("DATM_CPLHIST_YR_END")
+    if yr_start != None and yr_start < 0:
+        yr_start = case.get_value("DATM_CPLHIST_YR_START")
+        yr_end = case.get_value("DATM_CPLHIST_YR_END")
 
     # For LILAC
-    if ( yr_start == None or lilac_mode == "on" ):
-       yr_start = "0"
-       yr_end   = "0"
+    if yr_start == None or lilac_mode == "on":
+        yr_start = "0"
+        yr_end = "0"
 
     yr_start = int(yr_start)
-    yr_end   = int(yr_end)
+    yr_end = int(yr_end)
 
     comp_atm = case.get_value("COMP_ATM")
     lnd_grid = case.get_value("LND_GRID")
@@ -117,7 +117,9 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_path = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -206,22 +208,28 @@ def buildnml(case, caseroot, compname):
     else:
         ignore = "-ignore_ic_date"
 
-    tuning = "-lnd_tuning_mode %s "%lnd_tuning_mode
-    
+    tuning = "-lnd_tuning_mode %s " % lnd_tuning_mode
+
     #
     # Spinup settings and specifics for SASU spinup
     #
-    spinup = "-clm_accelerated_spinup %s "%clm_accelerated_spinup
-    if ( clm_accelerated_spinup == "sasu" ):
-       if ( (yr_start != None) and (yr_end != None) ):
-         nyr = yr_end - yr_start + 1
-         if ( (yr_end <= 0) or (yr_start <= 0) ): 
-            logger.error( "ERROR: Year start and end are both negative and should not be" )
-         clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts)
-       else:
-         logger.warning( "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model" )
-         logger.warning( "         as it expects regular atmosphere forcing that is cycled over" )
-    
+    spinup = "-clm_accelerated_spinup %s " % clm_accelerated_spinup
+    if clm_accelerated_spinup == "sasu":
+        if (yr_start != None) and (yr_end != None):
+            nyr = yr_end - yr_start + 1
+            if (yr_end <= 0) or (yr_start <= 0):
+                logger.error(
+                    "ERROR: Year start and end are both negative and should not be"
+                )
+            clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts)
+        else:
+            logger.warning(
+                "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model"
+            )
+            logger.warning(
+                "         as it expects regular atmosphere forcing that is cycled over"
+            )
+
     infile = os.path.join(ctsmconf, "namelist")
 
     inputdata_file = os.path.join(caseroot, "Buildconf", "ctsm.input_data_list")
@@ -234,7 +242,9 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_file = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
 
     # -----------------------------------------------------
     # Clear out old data
@@ -297,7 +307,9 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
+                logger.warning(
+                    "WARNING: Could NOT find a start file to use using" + clm_startfile
+                )
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -308,7 +320,9 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
+        create_namelist_infile(
+            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
+        )
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From 4cef2cc63b6282c1792ef45803cfad33f2dc3737 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Wed, 27 Mar 2024 14:45:05 -0600
Subject: [PATCH 0100/1248] Update .git-blame-ignore-revs

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 4798c37853..2c92251e93 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -32,3 +32,4 @@ d866510188d26d51bcd6d37239283db690af7e82
 6fccf682eaf718615407d9bacdd3903b8786a03d
 2500534eb0a83cc3aff94b30fb62e915054030bf
 78d05967c2b027dc9776a884716597db6ef7f57c
+47839a77229c61555e3b8932927bb54cdc511b27

From eede6f8fa03d00f997fa8b4a5b39535be6d89a00 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 1 Apr 2024 17:08:52 -0600
Subject: [PATCH 0101/1248] dmleung reverted to the landunit level VAI for
 Okin's vegetation drag partitioning, which worked much better than the patch
 level VAI. 1 Apr 2024

---
 src/biogeochem/DUSTMod.F90 | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 17deda7375..9161076e4f 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -646,8 +646,8 @@ subroutine DustEmission (bounds, &
          ! purpose: compute factor by which surface roughness increases threshold
          !          friction velocity (currently a constant)
 
-         !if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
-         if (lnd_frc_mbl(p) > 0.0_r8  .AND. ttlai(p)<=1_r8) then
+         if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
+         !if (lnd_frc_mbl(p) > 0.0_r8  .AND. ttlai(p)<=1_r8) then
             ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
             !lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
             !lai(p) = ttlai(p) + lai0_Okin     ! ttlai = tlai+tsai. Okin-Pierre's equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
@@ -655,9 +655,17 @@ subroutine DustEmission (bounds, &
             !   lai(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
             !end if              ! 
 
-            if (ttlai(p) + vai0_Okin <= 1_r8) then
-               vai_Okin(p) = ttlai(p) + vai0_Okin     ! ttlai = vai = tlai+tsai. Okin-Pierre's equation is undefined at vai=0, and VAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
-            end if                                    ! In the Okin-Pierre formulation, VAI has to be 0 < VAI <= 1.
+            !if (ttlai(p) + vai0_Okin <= 1_r8) then
+            !   vai_Okin(p) = ttlai(p) + vai0_Okin     ! ttlai = vai = tlai+tsai. Okin-Pierre's equation is undefined at vai=0, and VAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
+            !if (tlai_lu(l) + vai0_Okin <= 1_r8) then
+            !   vai_Okin(p) = tlai_lu(l) + vai0_Okin   ! testing on 27 Feb 2024
+            !end if                                    ! In the Okin-Pierre formulation, VAI has to be 0 < VAI <= 1.
+
+            vai_Okin(p) = tlai_lu(l)+vai0_Okin       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
+            if (vai_Okin(p) > 1_r8) then
+               vai_Okin(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
+            end if 
+
 
             ! calculate Okin's shear stress ratio (SSR, which is vegetation drag partition factor) using Pierre's equation
             K_length = 2_r8 * (1_r8/vai_Okin(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation

From 53871f47af026a51210e5feacb6fd43f9b3c5bd2 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 1 Apr 2024 17:15:21 -0600
Subject: [PATCH 0102/1248] Typo fix: Some users told me that the denominator
 of the dust emission equation in Leung 2023 should be impact threshold
 instead of standardized fluid threshold. So, that was corrected in the code.
 dmleung 1 Apr 2024

---
 src/biogeochem/DUSTMod.F90 | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 9161076e4f..438468a532 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -657,15 +657,12 @@ subroutine DustEmission (bounds, &
 
             !if (ttlai(p) + vai0_Okin <= 1_r8) then
             !   vai_Okin(p) = ttlai(p) + vai0_Okin     ! ttlai = vai = tlai+tsai. Okin-Pierre's equation is undefined at vai=0, and VAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
-            !if (tlai_lu(l) + vai0_Okin <= 1_r8) then
-            !   vai_Okin(p) = tlai_lu(l) + vai0_Okin   ! testing on 27 Feb 2024
             !end if                                    ! In the Okin-Pierre formulation, VAI has to be 0 < VAI <= 1.
 
             vai_Okin(p) = tlai_lu(l)+vai0_Okin       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
             if (vai_Okin(p) > 1_r8) then
                vai_Okin(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
-            end if 
-
+            end if
 
             ! calculate Okin's shear stress ratio (SSR, which is vegetation drag partition factor) using Pierre's equation
             K_length = 2_r8 * (1_r8/vai_Okin(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
@@ -720,7 +717,8 @@ subroutine DustEmission (bounds, &
                !################### for Leung et al. (2023) ################################################
                !################ uncomment the below block if want to use Leung's scheme ###################
 
-               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
+               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
+               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
 
                ! account for bare soil fraction, frozen soil fraction, and apply global tuning parameter (Kok et al. 2014)
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * lnd_frc_mbl(p) * C_tune * liqfrac

From f488309777bd6cd3ba8ac61bc1d60c4448e905f2 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 1 Apr 2024 17:25:47 -0600
Subject: [PATCH 0103/1248] Important change: Used Monin-Obukhov length to
 calculate the buoyancy contribution to the subtimestep wind fluctuations,
 instead of assuming zero buoyancy contributions. dmleung 1 Apr 2024

---
 src/biogeochem/DUSTMod.F90 | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 438468a532..2986ed579b 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -420,6 +420,7 @@ subroutine DustEmission (bounds, &
     real(r8), parameter :: z0a_glob = 1e-4_r8          ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
     real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
     real(r8), parameter :: vai0_Okin = 0.1_r8          ! [m2/m2] minimum VAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
+    real(r8), parameter :: zii = 1000.0_r8             ! [m] convective boundary layer height added by dmleung 20 Feb 2024, following other CTSM modules (e.g., CanopyFluxesMod). Should we transfer PBL height (PBLH) from CAM?
     real(r8) :: numer                                  ! Numerator term for threshold crossing rate
     real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     !------------------------------------------------------------------------
@@ -467,7 +468,8 @@ subroutine DustEmission (bounds, &
          vai_Okin            => dust_inst%vai_Okin_patch             , & ! vegetation area index for calculating Okin-Pierre vegetation drag partitioning. vai=0 in the ssr equation will lead to infinity, so a small value is added into this vai dmleung defined. (no need to output) 16 Feb 2024
          frc_thr_rghn_fct    => dust_inst%frc_thr_rghn_fct_patch     , & ! output hybrid/total drag partition factor considering both rock and vegetation drag partition factors.
          wnd_frc_thr_std     => dust_inst%wnd_frc_thr_std_patch      , & ! standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
-         dpfct_rock          => dust_inst%dpfct_rock_patch            & ! output rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
+         dpfct_rock          => dust_inst%dpfct_rock_patch           , & ! output rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
+         obu                 => frictionvel_inst%obu_patch             & ! Input:  [real(r8) (:)   ] Monin-Obukhov length from the friction Velocity module 
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -735,7 +737,8 @@ subroutine DustEmission (bounds, &
             ! mean lowpass-filtered wind speed at hgt_sal = 0.1 m saltation height (assuming aerodynamic roughness length z0a_glob = 1e-4 m globally for ease; also assuming neutral condition)
             u_mean_slt(p) = (wnd_frc_slt/k) * log(hgt_sal / z0a_glob)  ! translating from ustar (velocity scale) to actual wind
 
-            stblty(p) = 0   ! -dmleung 2 Dec 2021: use stability = 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
+            !stblty(p) = 0_r8   ! -dmleung 2 Dec 2021: use stability = 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
+            stblty(p) = zii / obu(p)   ! -dmleung 20 Feb 2024: use obu from CTSM and PBL height = zii (= 1000_r8) which is default in CTSM. Should we transfer PBL height from CAM?
             if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
                u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
             else

From e79364382b7f6a555a60070c6f84f52366c9c663 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 2 Apr 2024 18:08:20 -0600
Subject: [PATCH 0104/1248] testlist updates for LGRAIN2 and LREPRSTRUCT tests

---
 cime_config/testdefs/testlist_clm.xml | 67 ++-------------------------
 1 file changed, 4 insertions(+), 63 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 04200b7271..f44a8e84ab 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3377,9 +3377,9 @@
     </options>
   </test>
 
-  <test name="LGRAIN2_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
+  <test name="LGRAIN2_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
+      <machine name="derecho" compiler="gnu" category="aux_clm">
         <options>
           <option name="wallclock">02:00:00</option>
           <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). This and other tests with the ciso_soil_matrixcn_only testmods become redundant when default use_matrixcn = .false.. There are 2 more LGRAIN and two more LREPR tests with the same names but ciso testmods for when default use_matrixcn = .true..</option>
@@ -3387,19 +3387,9 @@
       </machine>
     </machines>
   </test>
-  <test name="LGRAIN2_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
-  <test name="LREPRSTRUCT_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
+  <test name="LREPRSTRUCT_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
+      <machine name="derecho" compiler="gnu" category="aux_clm">
         <options>
           <option name="wallclock">02:00:00</option>
           <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
@@ -3407,26 +3397,6 @@
       </machine>
     </machines>
   </test>
-  <test name="LREPRSTRUCT_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
-  <test name="LGRAIN2_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="LGRAIN2_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -3436,16 +3406,6 @@
       <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
     </options>
   </test>
-  <test name="LGRAIN2_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="LGRAIN2_Ly2_P128x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -3455,16 +3415,6 @@
       <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
     </options>
   </test>
-  <test name="LREPRSTRUCT_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="LREPRSTRUCT_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -3474,15 +3424,6 @@
       <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
     </options>
   </test>
-  <test name="LREPRSTRUCT_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">02:00:00</option>
-      <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
-    </options>
-  </test>
   <test name="LREPRSTRUCT_Ly2_P128x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>

From 306d11a6dcb9c16f29fbc3937b1110110a5d436c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Wed, 3 Apr 2024 14:15:58 -0600
Subject: [PATCH 0105/1248] testlist updates for already existing matrixcn
 tests

---
 cime_config/testdefs/testlist_clm.xml | 30 ++++++---------------------
 1 file changed, 6 insertions(+), 24 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index f44a8e84ab..a47d74de5d 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -530,7 +530,7 @@
   </test>
   <test name="SMS_D" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/ciso_soil_matrixcn_only">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
     </machines>
     <options>
@@ -540,7 +540,7 @@
   </test>
   <test name="ERS_Lm13" grid="f10_f10_mg37" compset="I1850Clm51Bgc" testmods="clm/monthly_matrixcn_fast_spinup">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi"    compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -548,27 +548,9 @@
       <option name="comment"  >Run matrix solution fast spinup for restart beyond a year (to trigger next year logic) turning off extra options to make faster (so without crop or isotopes). This test would've caught a previous bug.</option>
     </options>
   </test>
-  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm45Bgc" testmods="clm/clm45_monthly_matrixcn_soilCN30">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:20:00</option>
-      <option name="comment"  >Smoke test of soil CN-matrix on with soil CN ratio set to 30, since this crashes</option>
-    </options>
-  </test>
-  <test name="ERS_D_Lm3" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:20:00</option>
-      <option name="comment"  >Run in DEBUG with the matrix solution on with all options it interacts with (requires Bgc, but also turn on Crop and Carbon isotopes)</option>
-    </options>
-  </test>
   <test name="ERS_D" grid="f19_g17" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi"    compiler="nag" category="aux_clm"/>
     </machines>
     <options>
@@ -578,7 +560,7 @@
   </test>
   <test name="ERS_Lm54_Mmpi-serial" grid="1x1_numaIA" compset="I1850Clm50BgcCropQian" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -587,7 +569,7 @@
   </test>
   <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -804,7 +786,7 @@
   </test>
   <test name="SMS_D" grid="1x1_brazil" compset="I1850Clm51BgcCrop" testmods="clm/mimics_matrixcn">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>

From 99ba6ced5d9fbfcfb42d3b4c4cd253ccc7d72c9c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 4 Apr 2024 18:05:23 -0600
Subject: [PATCH 0106/1248] Removed testmod directory not in use

---
 .../clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods

diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods
deleted file mode 100644
index 442d7afb24..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods
+++ /dev/null
@@ -1,2 +0,0 @@
-../decStart
-../ciso_monthly_matrixcn_spinup

From 45dbe6247da94965e4c37593ca38592f3e25da9e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 4 Apr 2024 18:16:10 -0600
Subject: [PATCH 0107/1248] Adding matrixcnOn testmods

---
 .../testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods    | 1 +
 cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm  | 3 +++
 2 files changed, 4 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm
new file mode 100644
index 0000000000..185d6a2410
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm
@@ -0,0 +1,3 @@
+hist_wrt_matrixcn_diag = .true.
+use_matrixcn = .true.
+use_soil_matrixcn = .true.

From fef58b6d383fd750233ab4fe64086a738a41f2e2 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Thu, 4 Apr 2024 20:23:43 -0600
Subject: [PATCH 0108/1248] Relax tolerance for truncating small snocan values
 in CanopyFluxes

The default of 1e-13 was letting through some state updates that look
like they should have been truncated to 0: each time step, snocan was
decreasing by about 12 orders of magnitude.

Addresses ESCOMP/CTSM#2444
---
 src/biogeophys/CanopyFluxesMod.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90
index 58334a70c0..a969dc0583 100644
--- a/src/biogeophys/CanopyFluxesMod.F90
+++ b/src/biogeophys/CanopyFluxesMod.F90
@@ -1624,7 +1624,8 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
       ! snocan < rel_epsilon * snocan_baseline will be set to zero
       ! See NumericsMod for rel_epsilon value
       call truncate_small_values(fn, filterp, begp, endp, &
-         snocan_baseline(begp:endp), snocan(begp:endp))
+         snocan_baseline(begp:endp), snocan(begp:endp), &
+         custom_rel_epsilon=1.e-10_r8)
       
       if ( use_fates ) then
          

From 0d07eb28518db409863bab811dbc3b7919f967c7 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Mon, 8 Apr 2024 16:46:20 -0600
Subject: [PATCH 0109/1248] 45 new tests with matrixcnOn testmods

---
 cime_config/testdefs/testlist_clm.xml | 456 +++++++++++++++++++-------
 1 file changed, 343 insertions(+), 113 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index a47d74de5d..6056439278 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2,17 +2,23 @@
 <testlist version="2.0">
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm51Bgc" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm51Bgc" testmods="clm/default--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERI_D_Ld9...default test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm50BgcNoAnthro" testmods="clm/decStart1851_noinitial">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
     </machines>
@@ -21,6 +27,16 @@
       <option name="comment"  >No anthropogenic compset</option>
     </options>
   </test>
+  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm50BgcNoAnthro" testmods="clm/decStart1851_noinitial--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="prebeta"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >No anthropogenic compset, repeated with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_Ld5" grid="f09_g17" compset="I1850Clm45BgcCru" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
@@ -139,13 +155,21 @@
   </test>
   <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/vrtlay">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
+  <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/vrtlay--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:60:00</option>
+      <option name="comment"  >Repeat last ERI_D_Ld9...vrtlay test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERI_D_Ld9" grid="T31_g37" compset="I2000Clm50Sp" testmods="clm/SNICARFRC">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -350,13 +374,21 @@
   </test>
   <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm50BgcCru" testmods="clm/nofire">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm50BgcCru" testmods="clm/nofire--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERI_Ld9...nofire test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERI_Ld9" grid="f09_g17" compset="I2000Clm51BgcCrop" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
@@ -378,13 +410,21 @@
   </test>
   <test name="ERS_Ld3" grid="f10_f10_mg37" compset="I2000Clm51Bgc" testmods="clm/ciso_cwd_hr">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERS_Ld3" grid="f10_f10_mg37" compset="I2000Clm51Bgc" testmods="clm/ciso_cwd_hr--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERS_Ld3...ciso_cwd_hr test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_Ld9" grid="f45_g37" compset="I2000Clm51Bgc" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -396,8 +436,6 @@
   </test>
   <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm51Bgc" testmods="clm/decStart">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -405,6 +443,15 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm51Bgc" testmods="clm/decStart--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERP_D...decStart test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld3_P36x2" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -501,7 +548,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -509,9 +555,17 @@
       <option name="comment">Use a transient compset so we allocate and run all PFTs (non-transient cases only allocate memory for non-zero-weight PFTs)</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Repeat ERP_D_Ld5_allActive test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/anoxia">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -519,15 +573,32 @@
       <option name="comment">Run a test with anoxia turned on</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/anoxia--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Repeat anoxia test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/ciso_flexCN_FUN">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/ciso_flexCN_FUN--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Repeat ERP_D_Ld5...ciso_flexCN_FUN test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_D" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/ciso_soil_matrixcn_only">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -675,13 +746,13 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/ciso_decStart">
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I1850Clm51Bgc" testmods="clm/ciso--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment"  >Transient case with isotopes with a December start</option>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERP_D_Ld5_P48x1...ciso test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/ciso_decStart">
@@ -693,13 +764,13 @@
       <option name="comment"  >Transient case with isotopes with a December start</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/default">
+  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/ciso_decStart--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
-      <option name="comment"  >Transient case with isotopes with a December start, without Meier roughness</option>
+      <option name="comment"  >Repeat ERP_D_Ld10_P64x2...ciso_decStart test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/default">
@@ -711,9 +782,17 @@
       <option name="comment"  >Transient case with isotopes with a December start, without Meier roughness</option>
     </options>
   </test>
+  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/default--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment"  >Repeat ERP_D_Ld10_P64x2...default test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -721,6 +800,15 @@
       <option name="comment"  >Transient case with a December 1990 start, and Gross Unrepresented Land Use and Land Cover change on, with f09 datasets with non-zero GU_LULCC values</option>
     </options>
   </test>
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment"  >Repeat SMS_Ld3_PS...GU_LULCC test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/reduceOutput">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
@@ -759,12 +847,14 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm51BgcCrop" testmods="clm/coldStart">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="clm_short"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERP_D_P64x2_Ld3...default test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm51BgcCrop" testmods="clm/coldStart">
@@ -775,13 +865,13 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/mimics">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm51BgcCrop" testmods="clm/coldStart--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
+      <option name="comment"  >Repeat last ERP_D_P64x2_Ld3...coldStart test with matrixcnOn</option>
     </options>
   </test>
   <test name="SMS_D" grid="1x1_brazil" compset="I1850Clm51BgcCrop" testmods="clm/mimics_matrixcn">
@@ -820,36 +910,38 @@
       <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015' with Newton-Krylov spinup variables on</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERP_D_P64x2_Ld3...flexCN_FUN test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last ERP_D_P64x2_Ld3...noFUN_flexCN test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/luna">
@@ -961,6 +1053,16 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D_P48x1" grid="f10_f10_mg37" compset="IHistClm51Bgc" testmods="clm/decStart--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="prealpha"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat ERP_D_P48x1...decStart test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/drydepnomegan">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
@@ -972,8 +1074,6 @@
   </test>
   <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -981,6 +1081,15 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/default--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat ERP_Ld5...default test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_Ld5" grid="f09_g17" compset="I2000Clm50Vic" testmods="clm/vrtlay">
     <machines>
       <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
@@ -1007,6 +1116,15 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat ERP_D_Ld5_P48x1...ciso test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_Ld3" grid="f09_g17" compset="I1850Clm50BgcCropCru" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
@@ -1035,6 +1153,15 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat ERP_D_Ld5_P48x1...flexCN_FUN test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
@@ -1043,6 +1170,15 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat ERP_D_Ld5_P48x1...noFUN_flexCN test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/luna">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
@@ -1051,27 +1187,26 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_Ly3_P72x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput">
+  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
     </options>
   </test>
-  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput">
+  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
+      <option name="comment"  >Repeat ERP_Ly3_P64x2...cropMonthOutput test with matrixcnOn</option>
     </options>
   </test>
   <test name="SMS_Ld5" grid="f09_g17" compset="I1850Clm45Bgc" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
@@ -1117,14 +1252,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1133,13 +1260,13 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm45Sp" testmods="clm/default">
+  <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a debug test of I2000Clm45Sp</option>
+      <option name="comment"  >Repeat ERP_P64x2_D_Ld5...ciso test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm45Sp" testmods="clm/default">
@@ -1238,16 +1365,6 @@
       <option name="comment"  >Science support for IHistClm45Sp at f19</option>
     </options>
   </test>
-  <test name="ERP_P36x2_Lm13" grid="f10_f10_mg37" compset="IHistClm51Bgc" testmods="clm/monthly">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">02:00:00</option>
-      <option name="tput_tolerance">0.5</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm51Bgc" testmods="clm/monthly">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1258,14 +1375,14 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D" grid="f10_f10_mg37" compset="I2000Clm50SpRtmFl" testmods="clm/default">
+  <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm51Bgc" testmods="clm/monthly--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a debug test with flooding on</option>
+      <option name="wallclock">02:00:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >Repeat ERP_P64x2_Lm13...monthly test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERP_P64x2_D" grid="f10_f10_mg37" compset="I2000Clm50SpRtmFl" testmods="clm/default">
@@ -1278,16 +1395,6 @@
       <option name="comment"  >include a debug test with flooding on</option>
     </options>
   </test>
-  <test name="ERP_P72x2_D_Ld5" grid="f19_g17_gris4" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_increase">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >cism is not answer preserving across processor changes, but short test length should be ok.</option>
-    </options>
-  </test>
   <test name="ERP_P256x2_D_Ld5" grid="f19_g17_gris4" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_increase">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1446,13 +1553,21 @@
   </test>
   <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/reseedresetsnow">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/reseedresetsnow--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat ERS_D...reseedresetsnow test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERP_P36x2_D_Ld10" grid="f10_f10_mg37" compset="IHistClm50SpG" testmods="clm/glcMEC_decrease">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -1531,10 +1646,6 @@
   </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="clm_short"/>
-      <machine name="cheyenne" compiler="gnu" category="clm_short"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_short"/>
@@ -1544,6 +1655,16 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="clm_short"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat ERS_D_Ld3...default test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/clm50dynroots">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -1619,6 +1740,15 @@
       <option name="comment"  >multi-year test with crops and isotopes that includes all crop types; added (2020-05-21) in order to test the new switchgrass and miscanthus crops (which otherwise aren't currently tested)</option>
     </options>
   </test>
+  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/ciso_monthly--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">02:00:00</option>
+      <option name="comment"  >Repeat ERS_Ly5_Mmpi-serial...ciso_monthly test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERS_Lm40_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
@@ -1647,6 +1777,16 @@
       <option name="comment"       >20 year single point tests with BGC-Crop starting from cold start (crop keeps a 20 year running mean, so this tests the sequence of that running mean being established)</option>
     </options>
   </test>
+  <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock"     >04:00:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment"       >Repeat ERS_Ly20_Mmpi-serial...cropMonthlyNoinitial test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -1666,15 +1806,6 @@
       <option name="comment"  >restart is right before the transition from 100% nat veg to 100% crop</option>
     </options>
   </test>
-  <test name="ERS_Ly3_P72x2" grid="f10_f10_mg37" compset="IHistClm50BgcCropG" testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use glacier evolution with ERS test</option>
-    </options>
-  </test>
   <test name="ERS_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCropG" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1684,13 +1815,13 @@
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use glacier evolution with ERS test</option>
     </options>
   </test>
-  <test name="ERS_Ly5_P144x1" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/cropMonthOutput">
+  <test name="ERS_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCropG" testmods="clm/cropMonthOutput--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Want a multi-year global test of transient crops; also want a multi-year transient restart test.  Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test</option>
+      <option name="comment"  >Repeat ERS_Ly3_P64x2...cropMonthOutput test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/cropMonthOutput">
@@ -1702,13 +1833,13 @@
       <option name="comment"  >Want a multi-year global test of transient crops; also want a multi-year transient restart test.  Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test</option>
     </options>
   </test>
-  <test name="ERS_Ly5_P72x1" grid="f10_f10_mg37" compset="IHistClm45BgcCrop" testmods="clm/cropMonthOutput">
+  <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">03:00:00</option>
-      <option name="comment"  >include a long Clm45 test, and include a production intel test of Clm45</option>
+      <option name="wallclock">01:40:00</option>
+      <option name="comment"  >Repeat ERS_Ly5_P128x1...cropMonthOutput test with matrixcnOn</option>
     </options>
   </test>
   <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm45BgcCrop" testmods="clm/cropMonthOutput">
@@ -1762,6 +1893,16 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
+  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">02:00:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >Repeat ERS_Ly6_Mmpi-serial...cropMonthOutput</option>
+    </options>
+  </test>
   <test name="SMS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/gregorian_cropMonthOutput">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
@@ -1774,7 +1915,6 @@
   </test>
   <test name="LII_D_Ld3_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1782,13 +1922,13 @@
       <option name="comment"  >Basic LII test, covering the standard range of subgrid heterogeneity - particularly, including crop. Uses a year-2000 restart file so that the restart file has non-zero product pools, so that we exercise the gridcell-level code in init_interp.</option>
     </options>
   </test>
-  <test name="LII2FINIDATAREAS_D_P72x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default">
+  <test name="LII_D_Ld3_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Exercise the init_interp_method='use_finidat_areas' option. See documentation at the top of the python script implementing this test for more details and rationale. This test requires a compatible finidat file (i.e., a file that can be used without interpolation). If no such file is available out-of-the-box, then the test will need to use a testmod that points to a compatible file.</option>
+      <option name="comment"  >Repeat LII_D... test with matrixcnOn</option>
     </options>
   </test>
   <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default">
@@ -1800,6 +1940,15 @@
       <option name="comment"  >Exercise the init_interp_method='use_finidat_areas' option. See documentation at the top of the python script implementing this test for more details and rationale. This test requires a compatible finidat file (i.e., a file that can be used without interpolation). If no such file is available out-of-the-box, then the test will need to use a testmod that points to a compatible file.</option>
     </options>
   </test>
+  <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat LII2... test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="LVG_Ld5_D" grid="f10_f10_mg37" compset="I1850Clm51Bgc" testmods="clm/no_vector_output">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -1812,8 +1961,6 @@
   </test>
   <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/ciso_monthly">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
     </machines>
@@ -1822,6 +1969,16 @@
       <option name="comment"  >Make sure Carbon isotopes on and off with land-use change, does NOT change answers. To verify for landuse change must go beyond a year boundary, because of #404 we can't use a December start, so need to run for beyond the year boundary.</option>
     </options>
   </test>
+  <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="prebeta"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:30:00</option>
+      <option name="comment"  >Repeat LCISO_Lm13...ciso_monthly test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="NCK_Ld1" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -1853,14 +2010,14 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="PET_P36x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
+  <test name="PEM_Ld1" grid="f10_f10_mg37" compset="I2000Clm51BgcCrop" testmods="clm/till--clm/matrixcnOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="prebeta"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >The main purpose of this test is to test threading of init_interp, exercising the OpenMP directives in initInterp. (Note that ERP tests don't compare threaded vs. non-threaded runs of init_interp, since init_interp won't run in the restart case.) Note that this test will use init_interp as long as we don't have out-of-the-box initial conditions at f10 resolution. We could probably get a similar level of confidence in the threading directives by deleting this test and instead changing the LII test to use threading; the main loss would be that that wouldn't test threading combined with interpolating from one resolution to another, as this one does.</option>
-      <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >Repeat PEM_Ld1...till test with matrixcnOn</option>
     </options>
   </test>
   <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
@@ -1873,6 +2030,16 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
+  <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat PET_P64x2_D...default test with matrixcnOn</option>
+      <option name="tput_tolerance">0.5</option>
+    </options>
+  </test>
   <test name="SMS" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/crop">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
@@ -1896,8 +2063,6 @@
   </test>
   <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
@@ -1905,6 +2070,16 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="prealpha"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last SMS_D_Ld1...cplhist test with matrixcnOn"</option>
+    </options>
+  </test>
   <test name="SMS_D_Ld1_PS" grid="f19_f19_mg17" compset="I2010Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -2091,10 +2266,6 @@
   </test>
   <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="clm_short"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
-      <machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_short"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -2104,6 +2275,18 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="clm_short"/>
+      <machine name="derecho" compiler="intel" category="prealpha"/>
+      <machine name="derecho" compiler="intel" category="aux_cime_baselines"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Repeat last SMS_D_Ld3...default test with matrixcnOn"</option>
+    </options>
+  </test>
   <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -2170,6 +2353,17 @@
       <option name="comment"  >Add at least one test of a NEON site</option>
     </options>
   </test>
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/default--clm/NEON/NIWO--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho"  compiler="gnu" category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >Repeat SMS_Ld10_D_Mmpi-serial...NIWO test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51SpRs" testmods="clm/default--clm/NEON/TOOL">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
@@ -2255,7 +2449,6 @@
   </test>
   <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2263,6 +2456,15 @@
       <option name="comment"  >Want a test of the c13 and c14 timeseries that crosses the year boundary. Ideally this test would include crops (in order to cover as much code as possible combined with the c13/c14 timeseries, even though there are no direct interactions between these timeseries and crops), but crop DecStart tests currently fail because of https://github.com/ESCOMP/ctsm/issues/404 and I didn't want to add another long test just to test these options, so for now using a compset without crops. Using a compset with SGLC to avoid problems with CISM in DecStart tests; the only IHistClm50Bgc compset we have with SGLC is this Qian compset, so I'm using this one.</option>
     </options>
   </test>
+  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment"  >Repeat ciso_bombspike1963DecStart test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_D_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm45BgcCropQianRs" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
@@ -2427,6 +2629,15 @@
       </machine>
     </machines>
   </test>
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/nlevgrnd_small--clm/matrixcnOn">
+    <machines>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">0:20:00</option>
+      <option name="comment">Repeat nlevgrnd_small test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="SMS_Lm13_PS" grid="f19_g17" compset="I2000Clm51BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -2756,7 +2967,6 @@
   </test>
   <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2765,6 +2975,16 @@
       <option name="comment">60 day exact restart test providing coverage for the FATES logging mode on an f45 grid.</option>
     </options>
   </test>
+  <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment">Repeat this SMS_Ld5...FatesCold test with matrixcnOn</option>
+    </options>
+  </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSizeAgeMort">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -3312,7 +3532,6 @@
   </test>
   <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm50BgcCrop">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -3322,6 +3541,17 @@
       <option name="tput_tolerance">0.1</option>
     </options>
   </test>
+  <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+      <option name="comment">Repeat PFS_Ld10_PS test with matrixcnOn</option>
+      <!-- standard throughput tolerance is 25%, but for this PFS test we want a stricter tolerance -->
+      <option name="tput_tolerance">0.1</option>
+    </options>
+  </test>
 
   <test name="FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1" grid="5x5_amazon" compset="I2000Clm50SpRs">
     <machines>

From 3e0ee1a0a4150e3cc3daf80549c0cf665001afe3 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 11 Apr 2024 05:14:22 -0600
Subject: [PATCH 0110/1248] Add tsoi coldstart, get streams out of waterstate
 and plumb them back

---
 src/biogeophys/TemperatureType.F90 | 25 ++++++---
 src/biogeophys/WaterStateType.F90  | 90 +++++++++++++-----------------
 src/main/clm_instMod.F90           | 22 +++++++-
 3 files changed, 77 insertions(+), 60 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index ab310650c8..7906773b26 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -8,7 +8,7 @@ module TemperatureType
   use decompMod       , only : bounds_type
   use abortutils      , only : endrun
   use clm_varctl      , only : use_cndv, iulog, use_luna, use_crop, use_biomass_heat_storage
-  use clm_varpar      , only : nlevsno, nlevgrnd, nlevlak, nlevurb, nlevmaxurbgrnd
+  use clm_varpar      , only : nlevsno, nlevgrnd, nlevlak, nlevurb, nlevmaxurbgrnd, nlevsoi
   use clm_varcon      , only : spval, ispval
   use GridcellType    , only : grc
   use LandunitType    , only : lun
@@ -141,7 +141,7 @@ module TemperatureType
   !------------------------------------------------------------------------
   subroutine Init(this, bounds, &
        em_roof_lun,  em_wall_lun, em_improad_lun, em_perroad_lun, &
-       is_simple_buildtemp, is_prog_buildtemp)
+       is_simple_buildtemp, is_prog_buildtemp, exice_init_stream_col)
     !
     ! !DESCRIPTION:
     !
@@ -156,6 +156,7 @@ subroutine Init(this, bounds, &
     real(r8)          , intent(in) :: em_perroad_lun(bounds%begl:)
     logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
     logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
+    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:)  ! initial excess ice concentration from the stream file
 
     call this%InitAllocate ( bounds )
     call this%InitHistory ( bounds, is_simple_buildtemp, is_prog_buildtemp )
@@ -164,7 +165,8 @@ subroutine Init(this, bounds, &
          em_wall_lun(bounds%begl:bounds%endl),    &
          em_improad_lun(bounds%begl:bounds%endl), &
          em_perroad_lun(bounds%begl:bounds%endl), &
-         is_simple_buildtemp, is_prog_buildtemp)
+         is_simple_buildtemp, is_prog_buildtemp,  &
+         exice_init_stream_col(bounds%begc:bounds%endc) )
 
   end subroutine Init
 
@@ -639,7 +641,7 @@ end subroutine InitHistory
   !-----------------------------------------------------------------------
   subroutine InitCold(this, bounds, &
        em_roof_lun,  em_wall_lun, em_improad_lun, em_perroad_lun, &
-       is_simple_buildtemp, is_prog_buildtemp)
+       is_simple_buildtemp, is_prog_buildtemp, exice_init_stream_col)
     !
     ! !DESCRIPTION:
     ! Initialize cold start conditions for module variables
@@ -647,11 +649,12 @@ subroutine InitCold(this, bounds, &
     ! !USES:
     use shr_kind_mod   , only : r8 => shr_kind_r8
     use shr_const_mod  , only : SHR_CONST_TKFRZ
-    use clm_varcon     , only : denice, denh2o
+    use clm_varcon     , only : denice, denh2o, zisoi
     use landunit_varcon, only : istwet, istsoil, istdlak, istice, istcrop
     use column_varcon  , only : icol_road_imperv, icol_roof, icol_sunwall
     use column_varcon  , only : icol_shadewall, icol_road_perv
     use clm_varctl     , only : iulog, use_vancouver, use_mexicocity, use_excess_ice
+    use initVerticalMod , only : find_soil_layer_containing_depth
     !
     ! !ARGUMENTS:
     class(temperature_type)        :: this
@@ -662,6 +665,7 @@ subroutine InitCold(this, bounds, &
     real(r8)          , intent(in) :: em_perroad_lun(bounds%begl:)
     logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
     logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
+    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from the stream file
     !
     ! !LOCAL VARIABLES:
     integer  :: j,l,c,p ! indices
@@ -669,6 +673,7 @@ subroutine InitCold(this, bounds, &
     real(r8) :: snowbd  ! temporary calculation of snow bulk density (kg/m3)
     real(r8) :: fmelt   ! snowbd/100
     integer  :: lev
+    integer  :: n05m    ! layer number containing 0.5 meter depth
     !-----------------------------------------------------------------------
 
     SHR_ASSERT_ALL_FL((ubound(em_roof_lun)    == (/bounds%endl/)), sourcefile, __LINE__)
@@ -742,8 +747,14 @@ subroutine InitCold(this, bounds, &
                end if
             else
                this%t_soisno_col(c,1:nlevgrnd) = 272._r8
-               if (use_excess_ice .and. (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop)) then
-                  this%t_soisno_col(c,1:nlevgrnd) = SHR_CONST_TKFRZ - 5.0_r8 !needs to be below freezing to properly initiate excess ice
+               if (use_excess_ice .and. exice_init_stream_col(c) > 0.0_r8) then
+                  n05m = nlevsoi - 1
+                  if (zisoi(nlevsoi) >= 0.5_r8) then
+                     call find_soil_layer_containing_depth(0.5_r8,n05m)
+                  else
+                       n05m=nlevsoi-1
+                  endif
+                  this%t_soisno_col(c,n05m:nlevgrnd) = SHR_CONST_TKFRZ - 12.15_r8 !needs to be below freezing to properly initiate excess ice
                end if
             endif
          endif
diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90
index 390e9e8691..4c82e4efa6 100644
--- a/src/biogeophys/WaterStateType.F90
+++ b/src/biogeophys/WaterStateType.F90
@@ -56,8 +56,6 @@ module WaterStateType
      real(r8), pointer :: excess_ice_col         (:,:)  ! col excess ice (kg/m2) (new) (-nlevsno+1:nlevgrnd)
      real(r8), pointer :: exice_bulk_init        (:)    ! inital value for excess ice (new) (unitless)
 
-     type(excessicestream_type), private :: exicestream ! stream type for excess ice initialization NUOPC only
-
      ! Hillslope stream variables
      real(r8), pointer :: stream_water_volume_lun(:)   ! landunit volume of water in the streams (m3)
 
@@ -82,7 +80,7 @@ module WaterStateType
 
   !------------------------------------------------------------------------
   subroutine Init(this, bounds, info, tracer_vars, &
-       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename)
+       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
 
     class(waterstate_type), intent(inout) :: this
     type(bounds_type) , intent(in) :: bounds  
@@ -91,8 +89,9 @@ subroutine Init(this, bounds, info, tracer_vars, &
     real(r8)          , intent(in) :: h2osno_input_col(bounds%begc:)
     real(r8)          , intent(in) :: watsat_col(bounds%begc:, 1:)          ! volumetric soil water at saturation (porosity)
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
-    logical           , intent(in)    :: use_aquifer_layer ! whether an aquifer layer is used in this run
-    character(len=*) , intent(in)     :: NLFilename ! Namelist filename
+    logical           , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run
+    character(len=*)  , intent(in) :: NLFilename ! Namelist filename
+    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:bounds%endc) ! initial ammount of excess ice from stream
 
     this%info => info
 
@@ -104,7 +103,7 @@ subroutine Init(this, bounds, info, tracer_vars, &
       watsat_col = watsat_col, &
       t_soisno_col = t_soisno_col, &
       use_aquifer_layer = use_aquifer_layer, &
-      NLFilename = NLFilename)
+      NLFilename = NLFilename, exice_init_stream_col = exice_init_stream_col)
 
   end subroutine Init
 
@@ -323,7 +322,7 @@ end subroutine InitHistory
 
   !-----------------------------------------------------------------------
   subroutine InitCold(this, bounds, &
-       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename)
+       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
     !
     ! !DESCRIPTION:
     ! Initialize time constant variables and cold start conditions 
@@ -344,6 +343,7 @@ subroutine InitCold(this, bounds, &
     real(r8)              , intent(in)    :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical               , intent(in)    :: use_aquifer_layer                       ! whether an aquifer layer is used in this run
     character(len=*)      , intent(in)    :: NLFilename                              ! Namelist filename
+    real(r8)              , intent(in)    :: exice_init_stream_col(bounds%begc:bounds%endc) ! initial ammount of excess ice from stream
     !
     ! !LOCAL VARIABLES:
     integer            :: c,j,l,nlevs,g 
@@ -550,52 +550,40 @@ subroutine InitCold(this, bounds, &
       this%dynbal_baseline_ice_col(bounds%begc:bounds%endc) = 0._r8
 
       !Initialize excess ice
-      if (use_excess_ice .and. NLFilename /= '') then
-         ! enforce initialization with 0 for everything
-         this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8
-         this%exice_bulk_init(bounds%begc:bounds%endc)=0.0_r8
-         call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column
-         !
-         ! If excess ice is being read from streams, use the streams to
-         ! initialize
-         !
-         if ( UseExcessIceStreams() )then
-            call this%exicestream%CalcExcessIce(bounds, this%exice_bulk_init)
-            do c = bounds%begc,bounds%endc
-               g = col%gridcell(c)
-               l = col%landunit(c)
-               if (.not. lun%lakpoi(l)) then  !not lake
-                  if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-                     if (zisoi(nlevsoi) >= 0.5_r8) then
-                       call find_soil_layer_containing_depth(0.5_r8,n05m)
-                     else
-                       n05m=nlevsoi-1
-                     endif
-                     if (use_bedrock .and. col%nbedrock(c) <=nlevsoi) then
-                        nbedrock = col%nbedrock(c)
-                     else
-                        nbedrock = nlevsoi
-                     endif
-                     do j = 2, nlevmaxurbgrnd ! ignore first layer
-                        if (n05m<nbedrock) then ! bedrock below 1 m
-                           if (j >= n05m .and. j<nbedrock .and. t_soisno_col(c,j) <= tfrz ) then
-                              this%excess_ice_col(c,j) = col%dz(c,j)*denice*(this%exice_bulk_init(c))
-                           else
-                              this%excess_ice_col(c,j) = 0.0_r8
-                           endif
-                        else 
-                           this%excess_ice_col(c,j) = 0.0_r8
-                        end if
-                     end do
+      this%exice_bulk_init(bounds%begc:bounds%endc) = exice_init_stream_col(bounds%begc:bounds%endc)
+      this%excess_ice_col(bounds%begc:bounds%endc,:) = 0.0_r8
+      if (use_excess_ice) then
+         do c = bounds%begc,bounds%endc
+            g = col%gridcell(c)
+            l = col%landunit(c)
+            if (.not. lun%lakpoi(l)) then  !not lake
+               if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
+                  if (zisoi(nlevsoi) >= 0.5_r8) then
+                     call find_soil_layer_containing_depth(0.5_r8,n05m)
+                  else
+                     n05m=nlevsoi-1
+                  endif
+                  if (use_bedrock .and. col%nbedrock(c) <=nlevsoi) then
+                     nbedrock = col%nbedrock(c)
+                  else
+                     nbedrock = nlevsoi
                   endif
-               else ! just in case zeros for lakes and other columns
-                  this%excess_ice_col(c,-nlevsno+1:nlevmaxurbgrnd) = 0.0_r8
+                  do j = 2, nlevmaxurbgrnd ! ignore first layer
+                     if (n05m<nbedrock) then ! bedrock below 1 m
+                        if (j >= n05m .and. j<nbedrock .and. t_soisno_col(c,j) <= tfrz ) then
+                           this%excess_ice_col(c,j) = col%dz(c,j)*denice*(this%exice_bulk_init(c))
+                        else
+                           this%excess_ice_col(c,j) = 0.0_r8
+                        endif
+                     else 
+                        this%excess_ice_col(c,j) = 0.0_r8
+                     end if
+                  end do
                endif
-            enddo
-         end if
-      else ! use_excess_ice is false
-         this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8
-         this%exice_bulk_init(bounds%begc:bounds%endc)=0.0_r8
+            else ! just in case zeros for lakes and other columns
+               this%excess_ice_col(c,-nlevsno+1:nlevmaxurbgrnd) = 0.0_r8
+            endif
+         enddo
       end if
     end associate
 
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index b9d74c418a..145a2b856c 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -11,6 +11,7 @@ module clm_instMod
   use clm_varctl      , only : use_cn, use_c13, use_c14, use_lch4, use_cndv, use_fates, use_fates_bgc
   use clm_varctl      , only : iulog
   use clm_varctl      , only : use_crop, snow_cover_fraction_method, paramfile
+  use clm_varctl      , only : use_excess_ice
   use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, no_soil_decomp, century_decomp, decomp_method
   use clm_varcon      , only : bdsno, c13ratio, c14ratio
   use landunit_varcon , only : istice, istsoil
@@ -193,6 +194,8 @@ subroutine clm_instInit(bounds)
     use SoilBiogeochemDecompCascadeBGCMod  , only : init_decompcascade_bgc
     use SoilBiogeochemDecompCascadeContype , only : init_decomp_cascade_constants
     use SoilBiogeochemCompetitionMod       , only : SoilBiogeochemCompetitionInit
+    use clm_varctl                         , only : use_excess_ice
+    use ExcessIceStreamType                , only : excessicestream_type, UseExcessIceStreams
     
     use initVerticalMod                    , only : initVertical
     use SnowHydrologyMod                   , only : InitSnowLayers
@@ -218,6 +221,8 @@ subroutine clm_instInit(bounds)
     type(file_desc_t)     :: params_ncid  ! pio netCDF file id for parameter file
     real(r8), allocatable :: h2osno_col(:)
     real(r8), allocatable :: snow_depth_col(:)
+    real(r8), allocatable :: exice_init_stream_col(:)
+    type(excessicestream_type)  :: exice_stream
 
     integer :: dummy_to_make_pgi_happy
     !----------------------------------------------------------------------
@@ -295,12 +300,23 @@ subroutine clm_instInit(bounds)
 
     ! Initialization of public data types
 
+    ! If excess ice is read from the stream, it has to be read before we coldstart the temperature
+    allocate(exice_init_stream_col(bounds%begc:bounds%endc))
+    exice_init_stream_col(bounds%begc:bounds%endc) = 0.0_r8
+    if (use_excess_ice) then
+       call exice_stream%Init(bounds, NLFilename)
+       if (UseExcessIceStreams()) then
+          call exice_stream%CalcExcessIce(bounds, exice_init_stream_col(bounds%begc:bounds%endc))
+       endif
+    endif
+
     call temperature_inst%Init(bounds,           &
          urbanparams_inst%em_roof(begl:endl),    &
          urbanparams_inst%em_wall(begl:endl),    &
          urbanparams_inst%em_improad(begl:endl), &
          urbanparams_inst%em_perroad(begl:endl), &
-         IsSimpleBuildTemp(), IsProgBuildTemp() )
+         IsSimpleBuildTemp(), IsProgBuildTemp(), &
+         exice_init_stream_col(begc:endc) )
 
     call active_layer_inst%Init(bounds)
 
@@ -314,7 +330,8 @@ subroutine clm_instInit(bounds)
          snow_depth_col = snow_depth_col(begc:endc), &
          watsat_col = soilstate_inst%watsat_col(begc:endc, 1:), &
          t_soisno_col = temperature_inst%t_soisno_col(begc:endc, -nlevsno+1:), &
-         use_aquifer_layer = use_aquifer_layer())
+         use_aquifer_layer = use_aquifer_layer(), &
+         exice_init_stream_col = exice_init_stream_col(begc:endc))
 
     call glacier_smb_inst%Init(bounds)
 
@@ -452,6 +469,7 @@ subroutine clm_instInit(bounds)
 
     deallocate (h2osno_col)
     deallocate (snow_depth_col)
+    deallocate (exice_init_stream_col)
 
     ! ------------------------------------------------------------------------
     ! Initialize accumulated fields

From 89ceeeb1129e311d5a884552d2c0b6f1e937b0b4 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 11 Apr 2024 05:14:52 -0600
Subject: [PATCH 0111/1248] Add use_streams default for coldstart

---
 bld/CLMBuildNamelist.pm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fd8def8845..4a338201d5 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4564,6 +4564,10 @@ sub setup_logic_exice {
   my $use_exice = $nl->get_value( 'use_excess_ice' );
   my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' );
   # IF excess ice streams is on
+  if ( (not defined($use_exice_streams) && value_is_true($use_exice)) && ($nl_flags->{'clm_start_type'} == /cold/  || $nl_flags->{'clm_start_type'} == /arb_ic/ ) ) {
+   $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.true.');
+   $use_exice_streams = '.true.'
+   }
   if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
      # Can only be true if excess ice is also on, otherwise fail
      if (defined($use_exice) && not value_is_true($use_exice)) {

From a3179995bcd7149edf1de4cc5aa32e23ae71ac9c Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 11 Apr 2024 05:15:04 -0600
Subject: [PATCH 0112/1248] plumbing

---
 src/biogeophys/WaterStateBulkType.F90 |  5 +++--
 src/biogeophys/WaterType.F90          | 23 +++++++++++++++--------
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90
index ba3f0513c5..4f03ba177e 100644
--- a/src/biogeophys/WaterStateBulkType.F90
+++ b/src/biogeophys/WaterStateBulkType.F90
@@ -47,7 +47,7 @@ module WaterStateBulkType
 
   !------------------------------------------------------------------------
   subroutine InitBulk(this, bounds, info, vars, &
-       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename)
+       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
 
     class(waterstatebulk_type), intent(inout) :: this
     type(bounds_type) , intent(in) :: bounds
@@ -58,6 +58,7 @@ subroutine InitBulk(this, bounds, info, vars, &
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical           , intent(in) :: use_aquifer_layer                       ! whether an aquifer layer is used in this run
     character(len=*)  , intent(in) :: NLFilename                              ! Namelist filename
+    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
 
     call this%Init(bounds = bounds, &
          info = info, &
@@ -66,7 +67,7 @@ subroutine InitBulk(this, bounds, info, vars, &
          watsat_col = watsat_col, &
          t_soisno_col = t_soisno_col, &
          use_aquifer_layer = use_aquifer_layer, & 
-         NLFilename = NLFilename)
+         NLFilename = NLFilename, exice_init_stream_col = exice_init_stream_col(bounds%begc:bounds%endc))
 
     call this%InitBulkAllocate(bounds) 
 
diff --git a/src/biogeophys/WaterType.F90 b/src/biogeophys/WaterType.F90
index bc257f27ad..e92dc0c759 100644
--- a/src/biogeophys/WaterType.F90
+++ b/src/biogeophys/WaterType.F90
@@ -213,7 +213,7 @@ end function water_params_constructor
 
   !-----------------------------------------------------------------------
   subroutine Init(this, bounds, NLFilename, &
-       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer)
+       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, exice_init_stream_col)
     !
     ! !DESCRIPTION:
     ! Initialize all water variables
@@ -227,6 +227,7 @@ subroutine Init(this, bounds, NLFilename, &
     real(r8)          , intent(in) :: watsat_col(bounds%begc:, 1:)          ! volumetric soil water at saturation (porosity)
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical           , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run
+    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
     !
     ! !LOCAL VARIABLES:
 
@@ -240,14 +241,14 @@ subroutine Init(this, bounds, NLFilename, &
          watsat_col = watsat_col, &
          t_soisno_col = t_soisno_col, &
          use_aquifer_layer = use_aquifer_layer, &
-         NLFilename = NLFilename)
+         NLFilename = NLFilename, exice_init_stream_col = exice_init_stream_col)
 
   end subroutine Init
 
   !-----------------------------------------------------------------------
   subroutine InitForTesting(this, bounds, params, &
        h2osno_col, snow_depth_col, watsat_col, &
-       t_soisno_col, use_aquifer_layer, NLFilename)
+       t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
     !
     ! !DESCRIPTION:
     ! Version of Init routine just for unit tests
@@ -262,8 +263,9 @@ subroutine InitForTesting(this, bounds, params, &
     real(r8)          , intent(in) :: snow_depth_col(bounds%begc:)
     real(r8)          , intent(in) :: watsat_col(bounds%begc:, 1:)            ! volumetric soil water at saturation (porosity)
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
-    character(len=*) , intent(in) :: NLFilename                               ! Namelist filename
+    character(len=*)  , intent(in) :: NLFilename                               ! Namelist filename
     logical , intent(in), optional :: use_aquifer_layer                       ! whether an aquifer layer is used in this run (false by default)
+    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
     !
     ! !LOCAL VARIABLES:
     logical :: l_use_aquifer_layer
@@ -283,13 +285,14 @@ subroutine InitForTesting(this, bounds, params, &
          watsat_col = watsat_col, &
          t_soisno_col = t_soisno_col, &
          use_aquifer_layer = l_use_aquifer_layer, &
-         NLFilename = NLFilename)
+         NLFilename = NLFilename, &
+          exice_init_stream_col = exice_init_stream_col )
 
   end subroutine InitForTesting
 
   !-----------------------------------------------------------------------
   subroutine DoInit(this, bounds, &
-       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename)
+       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
     !
     ! !DESCRIPTION:
     ! Actually do the initialization (shared between main Init routine and InitForTesting)
@@ -305,6 +308,7 @@ subroutine DoInit(this, bounds, &
     real(r8)         , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical          , intent(in) :: use_aquifer_layer                       ! whether an aquifer layer is used in this run
     character(len=*) , intent(in) :: NLFilename                              ! Namelist filename
+    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
     !
     ! !LOCAL VARIABLES:
     integer :: begc, endc
@@ -321,6 +325,7 @@ subroutine DoInit(this, bounds, &
     SHR_ASSERT_ALL_FL((ubound(snow_depth_col) == [endc]), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(watsat_col, 1) == endc), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(t_soisno_col, 1) == endc), sourcefile, __LINE__)
+    SHR_ASSERT_ALL_FL((ubound(exice_init_stream_col, 1) == endc), sourcefile, __LINE__)
 
     call this%SetupTracerInfo()
 
@@ -340,7 +345,8 @@ subroutine DoInit(this, bounds, &
          watsat_col = watsat_col(begc:endc, 1:),   &
          t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), &
          use_aquifer_layer = use_aquifer_layer, & 
-         NLFilename = NLFilename)
+         NLFilename = NLFilename, &
+         exice_init_stream_col = exice_init_stream_col)
 
     call this%waterdiagnosticbulk_inst%InitBulk(bounds, &
          bulk_info, &
@@ -381,7 +387,8 @@ subroutine DoInit(this, bounds, &
             watsat_col = watsat_col(begc:endc, 1:),   &
             t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), &
             use_aquifer_layer = use_aquifer_layer, &
-            NLFilename = NLFilename)
+            NLFilename = NLFilename, &
+            exice_init_stream_col = exice_init_stream_col)
 
        call this%bulk_and_tracers(i)%waterdiagnostic_inst%Init(bounds, &
             this%bulk_and_tracers(i)%info, &

From a8fad1df11260ce6f106a067399b2d008e926a1a Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 11 Apr 2024 06:50:53 -0600
Subject: [PATCH 0113/1248] add parameters for coldstart initialization. rename
 vars.

---
 bld/CLMBuildNamelist.pm                         |  4 +++-
 bld/namelist_files/namelist_defaults_ctsm.xml   |  2 ++
 bld/namelist_files/namelist_definition_ctsm.xml | 11 +++++++++++
 src/biogeophys/TemperatureType.F90              | 15 ++++++++-------
 src/main/clm_varctl.F90                         |  6 +++++-
 src/main/controlMod.F90                         | 11 ++++++++++-
 6 files changed, 39 insertions(+), 10 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 4a338201d5..1a69d59d0c 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4575,7 +4575,7 @@ sub setup_logic_exice {
      }
   # Otherwise if ice streams are off
   } else {
-     my @list = ( "stream_meshfile_exice", "stream_fldfilename_exice" );
+     my @list = ( "stream_meshfile_exice", "stream_fldfilename_exice" , "excess_ice_coldstart_temp" , "excess_ice_coldstart_depth");
      # fail is excess ice streams files are set
      foreach my $var ( @list ) {
         if ( defined($nl->get_value($var)) ) {
@@ -4594,6 +4594,8 @@ sub setup_logic_exice {
      if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice');
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice');
+       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_temp');
+       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_depth');
        # If excess ice streams on, but NOT the NUOPC driver fail
        if ( not $opts->{'driver'} eq "nuopc" ) {
           $log->fatal_error("nuopc driver is required when use_excess_ice_streams is set to true" );
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index a01839836d..380e3f875a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2891,6 +2891,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 
 <use_excess_ice>.false.</use_excess_ice>
 
+<excess_ice_coldstart_temp use_excess_ice=".true.">-12.15</excess_ice_coldstart_temp>
+<excess_ice_coldstart_depth use_excess_ice=".true.">1.5</excess_ice_coldstart_depth>
 <stream_fldfilename_exice use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc</stream_fldfilename_exice>
 <stream_meshfile_exice    use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc</stream_meshfile_exice>
 <stream_mapalgo_exice     use_excess_ice=".true.">bilinear</stream_mapalgo_exice>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index a2e9fb86da..61c16cd4cb 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -3050,6 +3050,17 @@ use case.)
 If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020)
 </entry>
 
+<entry id="excess_ice_coldstart_temp" type="real" category="clm_physics"
+       group="clm_inparm" >
+Initial soil temperature to use for gridcells with excess ice present during a run starting with coldstart (deg C)
+</entry>
+
+<entry id="excess_ice_coldstart_depth" type="real" category="clm_physics"
+       group="clm_inparm" >
+Soil depth below which initial excess ice concentration will be applied during a run starting with coldstart (m)
+</entry>
+
+
 <entry id="use_excess_ice_streams" type="logical" category="clm_physics"
         group="exice_streams" valid_values="" >
 If TRUE and use_excess_ice is TRUE, use the excess ice stream to determine the initial values of the excess ice field
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 7906773b26..0a31bba6e6 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -653,7 +653,8 @@ subroutine InitCold(this, bounds, &
     use landunit_varcon, only : istwet, istsoil, istdlak, istice, istcrop
     use column_varcon  , only : icol_road_imperv, icol_roof, icol_sunwall
     use column_varcon  , only : icol_shadewall, icol_road_perv
-    use clm_varctl     , only : iulog, use_vancouver, use_mexicocity, use_excess_ice
+    use clm_varctl     , only : iulog, use_vancouver, use_mexicocity
+    use clm_varctl     , only : use_excess_ice, excess_ice_coldstart_depth, excess_ice_coldstart_temp
     use initVerticalMod , only : find_soil_layer_containing_depth
     !
     ! !ARGUMENTS:
@@ -673,7 +674,7 @@ subroutine InitCold(this, bounds, &
     real(r8) :: snowbd  ! temporary calculation of snow bulk density (kg/m3)
     real(r8) :: fmelt   ! snowbd/100
     integer  :: lev
-    integer  :: n05m    ! layer number containing 0.5 meter depth
+    integer  :: nexice_start    ! layer number containing 0.5 meter depth
     !-----------------------------------------------------------------------
 
     SHR_ASSERT_ALL_FL((ubound(em_roof_lun)    == (/bounds%endl/)), sourcefile, __LINE__)
@@ -748,13 +749,13 @@ subroutine InitCold(this, bounds, &
             else
                this%t_soisno_col(c,1:nlevgrnd) = 272._r8
                if (use_excess_ice .and. exice_init_stream_col(c) > 0.0_r8) then
-                  n05m = nlevsoi - 1
-                  if (zisoi(nlevsoi) >= 0.5_r8) then
-                     call find_soil_layer_containing_depth(0.5_r8,n05m)
+                  nexice_start = nlevsoi - 1
+                  if (zisoi(nlevsoi) >= excess_ice_coldstart_depth) then
+                     call find_soil_layer_containing_depth(0.5_r8,nexice_start)
                   else
-                       n05m=nlevsoi-1
+                       nexice_start=nlevsoi-1
                   endif
-                  this%t_soisno_col(c,n05m:nlevgrnd) = SHR_CONST_TKFRZ - 12.15_r8 !needs to be below freezing to properly initiate excess ice
+                  this%t_soisno_col(c,nexice_start:nlevgrnd) = SHR_CONST_TKFRZ + excess_ice_coldstart_temp !needs to be below freezing to properly initiate excess ice
                end if
             endif
          endif
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 389ed50f88..09f3dd176a 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -411,10 +411,14 @@ module clm_varctl
   logical, public :: use_hillslope_routing = .false. ! true => use surface water routing in hillslope hydrology
 
   !----------------------------------------------------------
-  ! excess ice physics switch
+  ! excess ice physics switch and params
   !----------------------------------------------------------
   logical, public :: use_excess_ice = .false. ! true. => use excess ice physics
 
+  real(r8), public :: excess_ice_coldstart_temp = rundef ! initial coldstart soil temperature for gridcells where excess ice is present
+
+  real(r8), public :: excess_ice_coldstart_depth = rundef ! initial coldstart depth at which excess ice might be present and excess_ice_coldstart_temp will be applied
+
   !----------------------------------------------------------
   ! plant hydraulic stress switch
   !----------------------------------------------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index dc9622ddac..8ec95c9e81 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -256,7 +256,8 @@ subroutine control_init(dtime)
 
     namelist /clm_inparm/ use_soil_moisture_streams
 
-    namelist /clm_inparm/ use_excess_ice
+    ! excess ice flag and parameters
+    namelist /clm_inparm/ use_excess_ice , excess_ice_coldstart_depth, excess_ice_coldstart_temp
 
     namelist /clm_inparm/ use_lai_streams
 
@@ -823,6 +824,10 @@ subroutine control_spmd()
 
     call mpi_bcast (use_excess_ice, 1, MPI_LOGICAL, 0, mpicom,ier)
 
+    call mpi_bcast (excess_ice_coldstart_depth, 1, MPI_REAL8, 0, mpicom, ier)
+
+    call mpi_bcast (excess_ice_coldstart_temp, 1, MPI_REAL8, 0, mpicom, ier)
+
     call mpi_bcast (use_lai_streams, 1, MPI_LOGICAL, 0, mpicom, ier)
 
     call mpi_bcast (use_cropcal_streams, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -977,6 +982,10 @@ subroutine control_print ()
     write(iulog,*) '    use_extralakelayers = ', use_extralakelayers
     write(iulog,*) '    use_vichydro = ', use_vichydro
     write(iulog,*) '    use_excess_ice = ', use_excess_ice
+    if (use_excess_ice) then
+       write(iulog,*) '    excess_ice_coldstart_depth = ', excess_ice_coldstart_depth
+       write(iulog,*) '    excess_ice_coldstart_temp = ', excess_ice_coldstart_temp
+    endif
     write(iulog,*) '    use_cn = ', use_cn
     write(iulog,*) '    use_cndv = ', use_cndv
     write(iulog,*) '    use_crop = ', use_crop

From 9b3527e333ae50e300a363af1a20b9e2e2a3c04c Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 11 Apr 2024 07:04:41 -0600
Subject: [PATCH 0114/1248] change default values for new namelist vars

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 380e3f875a..2e346038f4 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2891,8 +2891,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 
 <use_excess_ice>.false.</use_excess_ice>
 
-<excess_ice_coldstart_temp use_excess_ice=".true.">-12.15</excess_ice_coldstart_temp>
-<excess_ice_coldstart_depth use_excess_ice=".true.">1.5</excess_ice_coldstart_depth>
+<excess_ice_coldstart_temp use_excess_ice=".true.">-2.15</excess_ice_coldstart_temp>
+<excess_ice_coldstart_depth use_excess_ice=".true.">0.5</excess_ice_coldstart_depth>
 <stream_fldfilename_exice use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc</stream_fldfilename_exice>
 <stream_meshfile_exice    use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc</stream_meshfile_exice>
 <stream_mapalgo_exice     use_excess_ice=".true.">bilinear</stream_mapalgo_exice>

From a2fc12b8be573434ef95e23e00efecffc87a6c18 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 11 Apr 2024 12:44:38 -0600
Subject: [PATCH 0115/1248] Change matrixcnOn tests to Clm51 and remove
 redundant tests

---
 cime_config/testdefs/testlist_clm.xml | 95 ++++++++-------------------
 1 file changed, 29 insertions(+), 66 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 6056439278..c3bda24655 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -27,7 +27,7 @@
       <option name="comment"  >No anthropogenic compset</option>
     </options>
   </test>
-  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm50BgcNoAnthro" testmods="clm/decStart1851_noinitial--clm/matrixcnOn">
+  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm51BgcNoAnthro" testmods="clm/decStart1851_noinitial--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
@@ -161,7 +161,7 @@
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/vrtlay--clm/matrixcnOn">
+  <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm51BgcCru" testmods="clm/vrtlay--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -380,7 +380,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm50BgcCru" testmods="clm/nofire--clm/matrixcnOn">
+  <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm51BgcCru" testmods="clm/nofire--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -555,7 +555,7 @@
       <option name="comment">Use a transient compset so we allocate and run all PFTs (non-transient cases only allocate memory for non-zero-weight PFTs)</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive--clm/matrixcnOn">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/allActive--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -573,7 +573,7 @@
       <option name="comment">Run a test with anoxia turned on</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/anoxia--clm/matrixcnOn">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/anoxia--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -590,7 +590,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/ciso_flexCN_FUN--clm/matrixcnOn">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/ciso_flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -800,7 +800,7 @@
       <option name="comment"  >Transient case with a December 1990 start, and Gross Unrepresented Land Use and Land Cover change on, with f09 datasets with non-zero GU_LULCC values</option>
     </options>
   </test>
-  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn">
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm51BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -847,10 +847,10 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm"/>
-      <machine name="derecho" compiler="gnu" category="clm_short"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="clm_short"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -918,7 +918,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -935,7 +935,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1081,15 +1081,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/default--clm/matrixcnOn">
-    <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Repeat ERP_Ld5...default test with matrixcnOn</option>
-    </options>
-  </test>
   <test name="ERP_Ld5" grid="f09_g17" compset="I2000Clm50Vic" testmods="clm/vrtlay">
     <machines>
       <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
@@ -1116,15 +1107,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso--clm/matrixcnOn">
-    <machines>
-      <machine name="izumi" compiler="nag" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Repeat ERP_D_Ld5_P48x1...ciso test with matrixcnOn</option>
-    </options>
-  </test>
   <test name="SMS_Ld3" grid="f09_g17" compset="I1850Clm50BgcCropCru" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
@@ -1153,7 +1135,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -1170,7 +1152,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -1196,7 +1178,7 @@
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
     </options>
   </test>
-  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn">
+  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1260,7 +1242,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso--clm/matrixcnOn">
+  <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm51Bgc" testmods="clm/ciso--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1559,7 +1541,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/reseedresetsnow--clm/matrixcnOn">
+  <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/reseedresetsnow--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1655,16 +1637,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-      <machine name="derecho" compiler="intel" category="clm_short"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Repeat ERS_D_Ld3...default test with matrixcnOn</option>
-    </options>
-  </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/clm50dynroots">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -1740,7 +1712,7 @@
       <option name="comment"  >multi-year test with crops and isotopes that includes all crop types; added (2020-05-21) in order to test the new switchgrass and miscanthus crops (which otherwise aren't currently tested)</option>
     </options>
   </test>
-  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/ciso_monthly--clm/matrixcnOn">
+  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm51BgcCropQianRs" testmods="clm/ciso_monthly--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -1777,7 +1749,7 @@
       <option name="comment"       >20 year single point tests with BGC-Crop starting from cold start (crop keeps a 20 year running mean, so this tests the sequence of that running mean being established)</option>
     </options>
   </test>
-  <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial--clm/matrixcnOn">
+  <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm51BgcCropQianRs" testmods="clm/cropMonthlyNoinitial--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1815,15 +1787,6 @@
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use glacier evolution with ERS test</option>
     </options>
   </test>
-  <test name="ERS_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCropG" testmods="clm/cropMonthOutput--clm/matrixcnOn">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Repeat ERS_Ly3_P64x2...cropMonthOutput test with matrixcnOn</option>
-    </options>
-  </test>
   <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1893,7 +1856,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn">
+  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm51BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1922,7 +1885,7 @@
       <option name="comment"  >Basic LII test, covering the standard range of subgrid heterogeneity - particularly, including crop. Uses a year-2000 restart file so that the restart file has non-zero product pools, so that we exercise the gridcell-level code in init_interp.</option>
     </options>
   </test>
-  <test name="LII_D_Ld3_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="LII_D_Ld3_PS" grid="f19_g17" compset="I2000Clm51BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1940,7 +1903,7 @@
       <option name="comment"  >Exercise the init_interp_method='use_finidat_areas' option. See documentation at the top of the python script implementing this test for more details and rationale. This test requires a compatible finidat file (i.e., a file that can be used without interpolation). If no such file is available out-of-the-box, then the test will need to use a testmod that points to a compatible file.</option>
     </options>
   </test>
-  <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm51BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2030,7 +1993,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2070,7 +2033,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm51BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -2275,7 +2238,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_short"/>
@@ -2456,7 +2419,7 @@
       <option name="comment"  >Want a test of the c13 and c14 timeseries that crosses the year boundary. Ideally this test would include crops (in order to cover as much code as possible combined with the c13/c14 timeseries, even though there are no direct interactions between these timeseries and crops), but crop DecStart tests currently fail because of https://github.com/ESCOMP/ctsm/issues/404 and I didn't want to add another long test just to test these options, so for now using a compset without crops. Using a compset with SGLC to avoid problems with CISM in DecStart tests; the only IHistClm50Bgc compset we have with SGLC is this Qian compset, so I'm using this one.</option>
     </options>
   </test>
-  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn">
+  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm51BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2629,7 +2592,7 @@
       </machine>
     </machines>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/nlevgrnd_small--clm/matrixcnOn">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm51Bgc" testmods="clm/nlevgrnd_small--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2975,7 +2938,7 @@
       <option name="comment">60 day exact restart test providing coverage for the FATES logging mode on an f45 grid.</option>
     </options>
   </test>
-  <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
+  <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I2000Clm51FatesRs" testmods="clm/FatesCold--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
@@ -3541,7 +3504,7 @@
       <option name="tput_tolerance">0.1</option>
     </options>
   </test>
-  <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/matrixcnOn">
+  <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm51BgcCrop" testmods="clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>

From bd7d031760665a5cdc920ef61c2a519bb5116b6e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 11 Apr 2024 14:51:17 -0600
Subject: [PATCH 0116/1248] Rename failing Clm51 tests back to Clm50 due to
 missing compsets

---
 cime_config/testdefs/testlist_clm.xml | 28 +++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index b730b62720..54c9d0fb62 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -27,7 +27,7 @@
       <option name="comment"  >No anthropogenic compset</option>
     </options>
   </test>
-  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm51BgcNoAnthro" testmods="clm/decStart1851_noinitial--clm/matrixcnOn">
+  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm50BgcNoAnthro" testmods="clm/decStart1851_noinitial--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
@@ -199,7 +199,7 @@
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm51BgcCru" testmods="clm/vrtlay--clm/matrixcnOn">
+  <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/vrtlay--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -418,7 +418,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm51BgcCru" testmods="clm/nofire--clm/matrixcnOn">
+  <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm50BgcCru" testmods="clm/nofire--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -611,7 +611,7 @@
       <option name="comment">Run a test with anoxia turned on</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/anoxia--clm/matrixcnOn">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/anoxia--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -628,7 +628,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/ciso_flexCN_FUN--clm/matrixcnOn">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/ciso_flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -956,7 +956,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -973,7 +973,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1173,7 +1173,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -1190,7 +1190,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm51BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -1750,7 +1750,7 @@
       <option name="comment"  >multi-year test with crops and isotopes that includes all crop types; added (2020-05-21) in order to test the new switchgrass and miscanthus crops (which otherwise aren't currently tested)</option>
     </options>
   </test>
-  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm51BgcCropQianRs" testmods="clm/ciso_monthly--clm/matrixcnOn">
+  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/ciso_monthly--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -1787,7 +1787,7 @@
       <option name="comment"       >20 year single point tests with BGC-Crop starting from cold start (crop keeps a 20 year running mean, so this tests the sequence of that running mean being established)</option>
     </options>
   </test>
-  <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm51BgcCropQianRs" testmods="clm/cropMonthlyNoinitial--clm/matrixcnOn">
+  <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1894,7 +1894,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm51BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn">
+  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2071,7 +2071,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm51BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -2457,7 +2457,7 @@
       <option name="comment"  >Want a test of the c13 and c14 timeseries that crosses the year boundary. Ideally this test would include crops (in order to cover as much code as possible combined with the c13/c14 timeseries, even though there are no direct interactions between these timeseries and crops), but crop DecStart tests currently fail because of https://github.com/ESCOMP/ctsm/issues/404 and I didn't want to add another long test just to test these options, so for now using a compset without crops. Using a compset with SGLC to avoid problems with CISM in DecStart tests; the only IHistClm50Bgc compset we have with SGLC is this Qian compset, so I'm using this one.</option>
     </options>
   </test>
-  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm51BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn">
+  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>

From 5d0a037a71c8e97e6f7e4c12535715bfbc16722d Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Thu, 11 Apr 2024 19:45:40 -0600
Subject: [PATCH 0117/1248] Remove a clm/FatesCold--clm/matrixcnOn test as
 invalid

---
 cime_config/testdefs/testlist_clm.xml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 54c9d0fb62..aea06d7f1e 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2976,16 +2976,6 @@
       <option name="comment">60 day exact restart test providing coverage for the FATES logging mode on an f45 grid.</option>
     </options>
   </test>
-  <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I2000Clm51FatesRs" testmods="clm/FatesCold--clm/matrixcnOn">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-      <machine name="izumi" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment">Repeat this SMS_Ld5...FatesCold test with matrixcnOn</option>
-    </options>
-  </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSizeAgeMort">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>

From 7cc2965bef7a75966fdc69c52513bb88f027027a Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Wed, 17 Apr 2024 14:51:22 -0600
Subject: [PATCH 0118/1248] Fix to get correct urbantv streams file

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 0b9b161c20..0b4893dbb6 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -3610,7 +3610,7 @@ sub setup_logic_urbantv_streams {
                  'sim_year_range'=>$nl_flags->{'sim_year_range'});
   }
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_urbantv', 'phys'=>$nl_flags->{'phys'},
-              'hgrid'=>"0.9x1.25" );
+              'hgrid'=>"0.9x1.25", 'urban_explicit_ac'=>$nl->get_value('urban_explicit_ac') );
   if ($opts->{'driver'} eq "nuopc" ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_urbantv', 'phys'=>$nl_flags->{'phys'},
                   'hgrid'=>"0.9x1.25" );

From 48b52dc5179a4ba3388a911a8aea7f1c682ce62c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 17 Apr 2024 17:08:50 -0600
Subject: [PATCH 0119/1248] Point FATES external at Charlie's LUH2 branch.

---
 Externals_CLM.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
index dc1bc3f0e7..1494217277 100644
--- a/Externals_CLM.cfg
+++ b/Externals_CLM.cfg
@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.70.0_api.32.0.0
+repo_url = https://github.com/ckoven/fates
+hash = d37d9733b5970dfe67a
 required = True
 
 [externals_description]

From 52962a5e9e5f9ada9119a0beb7bccc313c71d955 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 18 Apr 2024 16:46:42 -0500
Subject: [PATCH 0120/1248] Fix stream_varnames out of bounds error

---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index e6ceed7173..b4bb592e91 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -288,8 +288,10 @@ subroutine urbantv_interp(this, bounds)
              if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then
                 this%t_building_max(l) = dataptr2d(ig,n)
              end if
-             if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then
-                this%p_ac(l) = dataptr2d(ig,n)
+             if (urban_explicit_ac) then
+                if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then
+                   this%p_ac(l) = dataptr2d(ig,n)
+                end if
              end if
           end do
        else

From d9402b92d78b016603342dcff668ecef1435ce78 Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 18 Apr 2024 17:00:39 -0500
Subject: [PATCH 0121/1248] Add missing "use" statement

---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index b4bb592e91..98d1d51989 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -231,6 +231,7 @@ subroutine urbantv_interp(this, bounds)
     use dshr_methods_mod , only : dshr_fldbun_getfldptr
     use dshr_strdata_mod , only : shr_strdata_advance
     use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
+    use UrbanParamsType  , only : urban_explicit_ac
     !
     ! !ARGUMENTS:
     class(urbantv_type)           :: this

From a1cb4db82f7709677fa7d1311358600cfe75a05a Mon Sep 17 00:00:00 2001
From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com>
Date: Thu, 18 Apr 2024 23:22:02 -0500
Subject: [PATCH 0122/1248] Trying to fix "floating invalid" error

Previous commit has "floating invalid" error if I try to output P_AC as an h0 history field.

After P_AC is taken out from history field, it allows I2000Clm51Sp to run without an error under DEBUG mode, but leads to "floating invalid" error for I2000Clm50Sp run after 18-20mins.
---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 98d1d51989..c8566dcc82 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -297,7 +297,8 @@ subroutine urbantv_interp(this, bounds)
           end do
        else
           this%t_building_max(l) = spval
-          this%p_ac(l) = nan ! set to nan for non-urban landunit
+          ! this%p_ac(l) = nan ! set to nan for non-urban landunit
+          this%p_ac(l) = 0._r8
        end if
     end do
     deallocate(dataptr2d)

From 496d0903ad5bea1c1935e93f9666450579abcfa2 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Tue, 23 Apr 2024 08:32:34 -0600
Subject: [PATCH 0123/1248] Only output P_AC if urban_explicit_ac is .true.

---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index c8566dcc82..23e30f3909 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -89,10 +89,12 @@ subroutine Init(this, bounds, NLFilename)
           avgflag='A', long_name='prescribed maximum interior building temperature',   &
           ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
           l2g_scale_type='unity')
-    call hist_addfld1d (fname='P_AC', units='a fraction between 0 and 1',      &
-          avgflag='A', long_name='prescribed air-conditioning ownership rate',   &
-          ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
-          l2g_scale_type='unity')
+    if (urban_explicit_ac) then
+       call hist_addfld1d (fname='P_AC', units='a fraction between 0 and 1',      &
+             avgflag='A', long_name='prescribed air-conditioning ownership rate',   &
+             ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, &
+             l2g_scale_type='unity')
+    end if
 
   end subroutine Init
 

From 1ae7a195ffcf5cbfe312d9e83497c36cd97876f2 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Tue, 23 Apr 2024 12:11:42 -0600
Subject: [PATCH 0124/1248] Make P_AC history output consistent with
 TBUILD_MAX, TSA_U, etc. and only check for valid p_ac data if
 urban_explicit_ac is .true.

---
 src/cpl/share_esmf/UrbanTimeVarType.F90 | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90
index 23e30f3909..01f37da564 100644
--- a/src/cpl/share_esmf/UrbanTimeVarType.F90
+++ b/src/cpl/share_esmf/UrbanTimeVarType.F90
@@ -78,7 +78,7 @@ subroutine Init(this, bounds, NLFilename)
     ! Allocate urbantv data structure
 
     allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan
-    allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8
+    allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan
     allocate(stream_varnames(stream_varname_MIN:stream_varname_MAX))
 
     call this%urbantv_init(bounds, NLFilename)
@@ -299,8 +299,7 @@ subroutine urbantv_interp(this, bounds)
           end do
        else
           this%t_building_max(l) = spval
-          ! this%p_ac(l) = nan ! set to nan for non-urban landunit
-          this%p_ac(l) = 0._r8
+          this%p_ac(l) = spval
        end if
     end do
     deallocate(dataptr2d)
@@ -314,8 +313,13 @@ subroutine urbantv_interp(this, bounds)
              ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
-          if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) &
-             .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then   ! check if AC adoption rate is outside of range 0 to 1
+          ! Check for valid urban data
+          if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
+             found = .true.
+             gindx = g
+             lindx = l
+             exit
+          else if (urban_explicit_ac .and. (this%p_ac(l) < 0._r8 .or. this%p_ac(l) > 1._r8)) then
              found = .true.
              gindx = g
              lindx = l

From d863c13be015ec1624bf74b8eb1b4a993f6cfb49 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 25 Apr 2024 17:51:28 -0600
Subject: [PATCH 0125/1248] Add 1979 and 1979-2026 ne0np4 files to namelist
 defaults

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index ecced7a6e2..e4f4c331d9 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1428,6 +1428,14 @@ lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c24
 <fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" >
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240221.nc</fsurdat>
 
+<!-- for 1979 simulations (SSP2 label is irrelevant in these files) -->
+<fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="1979">
+lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979_78pfts_c240425.nc</fsurdat>
+<fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="1979">
+lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979_78pfts_c240425.nc</fsurdat>
+<fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="1979">
+lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4CONUS.ne30x8_SSP2-4.5_1979_78pfts_c240425.nc</fsurdat>
+
 <!-- for pre-industrial simulations - year 1850 -->
 
 <fsurdat hgrid="360x720cru"  sim_year="1850">
@@ -1498,6 +1506,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/surfdata_esmf/NEON/landuse.timeseries_NEON_${NEONSITE}_hist_78pfts_simyr2018-2023_c230931.nc</flanduse_timeseries>
 -->
 
+<!-- Historical 1850-2000 (SSP2 label is irrelevant in these files) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000"
  >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000"
@@ -1571,6 +1580,13 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
+<flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year_range="1979-2026" ssp_rcp="SSP2-4.5"
+>lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" sim_year_range="1979-2026" ssp_rcp="SSP2-4.5"
+>lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" sim_year_range="1979-2026" ssp_rcp="SSP2-4.5"
+>lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+
 <!-- SSP3-RCP7.0 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP3-7.0"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP3-7.0_1850-2100_78pfts_c240216.nc</flanduse_timeseries>

From 66c100482afdb26bb431d5c1e71deda28e3cdb69 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Apr 2024 13:56:24 -0600
Subject: [PATCH 0126/1248] Update cmeps to the branch

---
 Externals.cfg | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 185f412cab..1aa8991883 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -48,9 +48,12 @@ tag = cime6.0.217_httpsbranch03
 required = True
 
 [cmeps]
-tag = cmeps0.14.50
+#tag = cmeps0.14.50
+#branch = dust_emis_mod
+hash = d79e34f67df825f9265bdaaf3091f8995d5df1a2
 protocol = git
-repo_url = https://github.com/ESCOMP/CMEPS.git
+#repo_url = https://github.com/ESCOMP/CMEPS.git
+repo_url = https://github.com/ekluzek/CMEPS.git
 local_path = components/cmeps
 required = True
 

From c4debee33f97dc0ac503683e7cbc956c2380c377 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 26 Apr 2024 14:34:10 -0600
Subject: [PATCH 0127/1248] Replace 3 vr-grid test compsets with
 ISSP245Clm50BgcCrop compset

---
 cime_config/testdefs/testlist_clm.xml | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 05526b3529..918d86c213 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2034,17 +2034,16 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode_1979Start">
+  <test name="ERS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="ISSP245Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode_1979Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Run ARCTIC for transient case starting in 1979 as for AMIP CAM cases, with latest CLM version
-                (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
+      <option name="comment"  >Run ARCTIC for transient case starting in 1979 as for AMIP CAM cases (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode_1979Start">
+  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="ISSP245Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode_1979Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2059,10 +2058,10 @@
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
-      <option name="comment"  >Run ARCTICGRIS for future transient case (do not run this expensive test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
+      <option name="comment"  >Run ARCTICGRIS for 1850 case (do not run this expensive test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode_2013Start">
+  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="ISSP245Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode_2013Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2141,12 +2140,11 @@
   </test>
   <test name="SMS_Ln9" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Run course resolution ne3pg3_ne3pg3_mg37 to make sure will work for CAM"</option>
+      <option name="comment"  >Run coarse resolution ne3pg3_ne3pg3_mg37 to make sure will work for CAM"</option>
     </options>
   </test>
   <test name="SMS_D" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/crop">

From 73ac9d72a9a478ed839238d2e73c5fae45f0a24f Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 26 Apr 2024 14:37:07 -0600
Subject: [PATCH 0128/1248] Remove sim_year_range from new flanduse_timeseries
 for xml file to work

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e4f4c331d9..ac4f7252d2 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1580,11 +1580,11 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
-<flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year_range="1979-2026" ssp_rcp="SSP2-4.5"
+<flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" sim_year_range="1979-2026" ssp_rcp="SSP2-4.5"
+<flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" sim_year_range="1979-2026" ssp_rcp="SSP2-4.5"
+<flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
 
 <!-- SSP3-RCP7.0 - relative to {csmdata}) -->

From f8aa6eac32a00c821824478860c06a26fbdb9010 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Apr 2024 15:02:04 -0600
Subject: [PATCH 0129/1248] Add shr_dust_emis_mod.F90 to the files needed for
 unit testing, fails, because ESMF is currently needed and not available

---
 src/CMakeLists.txt | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 568b53cd15..9d2e6041b5 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -20,9 +20,11 @@ add_subdirectory(${CLM_ROOT}/share/src csm_share)
 add_subdirectory(${CLM_ROOT}/share/unit_test_stubs/util csm_share_stubs)
 add_subdirectory(${CLM_ROOT}/share/src/esmf_wrf_timemgr esmf_wrf_timemgr)
 
-# Add the single file we need from CMEPS
-set (drv_sources_needed
-  ${CLM_ROOT}/components/cmeps/cesm/nuopc_cap_share/glc_elevclass_mod.F90)
+# Add files needed from CMEPS
+list ( APPEND drv_sources_needed
+  ${CLM_ROOT}/components/cmeps/cesm/nuopc_cap_share/glc_elevclass_mod.F90
+  ${CLM_ROOT}/components/cmeps/cesm/nuopc_cap_share/shr_dust_emis_mod.F90
+  )
 
 # Add CLM source directories
 add_subdirectory(${CLM_ROOT}/src/utils clm_utils)

From e95f9eaa9bcb4c85d57335fd9e4ae57d5e1ad827 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 26 Apr 2024 17:08:35 -0600
Subject: [PATCH 0130/1248] Add to Makefile for automatic generation 1979-2026
 fsurdat/landuse files

---
 .../ctsm/toolchain/gen_mksurfdata_jobscript_multi.py   | 10 ++++++++++
 tools/mksurfdata_esmf/Makefile                         |  5 +++++
 2 files changed, 15 insertions(+)

diff --git a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
index 6deb50ebfb..6c38efdd0d 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
@@ -48,6 +48,7 @@
     "crop-global-SSP2-4.5-f19",
     "crop-global-SSP2-4.5-f10",
     "crop-global-SSP2-4.5-f45",
+    "crop-global-SSP2-4.5-ne0np4",
     "crop-global-SSP2-4.5-ne3",
     "crop-global-SSP2-4.5-ne16",
     "crop-global-SSP2-4.5-ne30",
@@ -204,6 +205,11 @@ def main():
         "ne3": ["ne3np4.pg3"],
         "ne16": ["ne16np4.pg3"],
         "ne30": ["ne30np4.pg3", "ne30np4.pg2", "ne30np4"],
+        "ne0np4": [
+            "ne0np4.ARCTICGRIS.ne30x8",
+            "ne0np4.ARCTIC.ne30x4",
+            "ne0np4CONUS.ne30x8",
+        ],
         "ne120": [
             "ne0np4.ARCTICGRIS.ne30x8",
             "ne0np4.ARCTIC.ne30x4",
@@ -333,6 +339,10 @@ def main():
             "--start-year 1850 --end-year 2100 --nosurfdata --ssp-rcp SSP2-4.5 --res",
             "f45",
         ),
+        "crop-global-SSP2-4.5-ne0np4": (
+            "--start-year 1979 --end-year 2026 --ssp-rcp SSP2-4.5 --res",
+            "ne0np4",
+        ),
         "crop-global-SSP2-4.5-ne3": (
             "--start-year 1850 --end-year 2100 --nosurfdata --ssp-rcp SSP2-4.5 --res",
             "ne3",
diff --git a/tools/mksurfdata_esmf/Makefile b/tools/mksurfdata_esmf/Makefile
index fc81d48079..00e90efa45 100644
--- a/tools/mksurfdata_esmf/Makefile
+++ b/tools/mksurfdata_esmf/Makefile
@@ -275,6 +275,7 @@ crop-global-SSP2-4.5         : crop-global-SSP2-4.5-f09 \
                                crop-global-SSP2-4.5-hcru \
                                crop-global-SSP2-4.5-ne16 \
                                crop-global-SSP2-4.5-ne30 \
+                               crop-global-SSP2-4.5-ne0np4 \
                                crop-global-SSP2-4.5-C96 \
                                crop-global-SSP2-4.5-mpasa120
 
@@ -318,6 +319,10 @@ crop-global-SSP2-4.5-ne30 : FORCE
 	$(MKSURFDATA)  --number-of-nodes 9 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
 	$(BATCHJOBS) $@.sh
 
+crop-global-SSP2-4.5-ne0np4 : FORCE
+	$(MKSURFDATA)  --number-of-nodes 9 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
+	$(BATCHJOBS) $@.sh
+
 crop-global-SSP2-4.5-C96 : FORCE
 	$(MKSURFDATA)  --number-of-nodes 9 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
 	$(BATCHJOBS) $@.sh

From 526bc19b068546e4d92828cf44c86596010e9482 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 17 Apr 2024 15:39:56 -0600
Subject: [PATCH 0131/1248] Update CTSM to work with FATES LUH2. Some issues
 remain.

---
 bld/CLMBuildNamelist.pm                       |  26 +-
 bld/namelist_files/namelist_defaults_ctsm.xml |  10 +-
 .../namelist_definition_ctsm.xml              |  26 +-
 bld/unit_testers/build-namelist_test.pl       |   1 +
 .../testmods_dirs/clm/Fates/user_nl_clm       |   2 +-
 .../clm/FatesColdLogging/user_nl_clm          |   1 +
 .../usermods_dirs/fates_sp/user_nl_clm        |   2 +-
 src/dyn_subgrid/dynFATESLandUseChangeMod.F90  |  80 +++++-
 src/main/clm_instMod.F90                      |   3 +-
 src/main/clm_varctl.F90                       |   4 +-
 src/main/controlMod.F90                       |  14 +-
 src/utils/clmfates_interfaceMod.F90           | 227 ++++++++++++++++--
 12 files changed, 351 insertions(+), 45 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 4df42d5e74..bcf68a8d61 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -783,7 +783,7 @@ sub setup_cmdl_fates_mode {
        # dis-allow fates specific namelist items with non-fates runs
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
-                      "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
+                      "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
                       "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
@@ -4370,7 +4370,7 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
-                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" );
+                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" );
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
@@ -4426,6 +4426,28 @@ sub setup_logic_fates {
               }
            }
         }
+
+        # Check fates_harvest_mode compatibility
+        my $var = "fates_harvest_mode";
+        if ( defined($nl->get_value($var))  ) {
+           # using fates_harvest_mode with CLM landuse driver data - for user convienence
+           # if ( $nl->get_value($var) == 2) {
+           #    # Make sure that do_harvest is set to true
+           #    if ( ! &value_is_true($nl->get_value('do_harvest')) ) {
+           #      fatal_error("do_harvest must be true when $var is equal to 2" );
+           # }
+           # using fates_harvest mode with raw luh2 harvest data
+           if ( $nl->get_value($var) > 2) {
+              # Make sure that use_fates_luh is true when using raw fates luh2 harvest data
+              if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
+                fatal_error("use_fates_luh is required to be true when $var is greater than 2" );
+              }
+              # do_harvest can not be on if we are using the raw fates luh2 harvest data
+              if ( &value_is_true($nl->get_value('do_harvest')) ) {
+                fatal_error("do_harvest can not be true when $var is greater than 2" );
+              }
+           }
+        }
     }
 }
 
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 7891361238..bc962d1b0f 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1572,11 +1572,14 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2100" ssp_rcp="SSP5-3.4"
  use_crop=".false."   >lnd/clm2/surfdata_map/release-clm5.0.18/landuse.timeseries_10x15_SSP5-3.4_16pfts_Irrig_CMIP6_simyr1850-2100_c190228.nc</flanduse_timeseries>
 
-<!-- Land Use Harmonization unified data sets for dynamic FATES land use change -->
+<!-- Land Use Harmonization unified timeseries data sets for dynamic FATES land use change -->
 
 <fluh_timeseries hgrid="4x5" sim_year_range="1850-2000" use_fates=".true."
  >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
 
+<!-- Land Use Harmonization static landuse x pft mapping data sets for FATES land use change -->
+<flandusepftdat hgrid="4x5" use_fates=".true." >lnd/clm2/surfdata_map/fates-sci.1.73.0_api.33.0.0/fates_landuse_pft_map_4x5_240206.nc</flandusepftdat>
+
 <!-- This one is just for testing until Issue #2304 is resolved -->
 <fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."
  >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
@@ -2756,14 +2759,17 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 
 <!-- ===== FATES DEFAULTS =========== -->
 <fates_spitfire_mode           use_fates=".true.">0</fates_spitfire_mode>
+<fates_harvest_mode            use_fates=".true.">0</fates_harvest_mode>
 <use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
 <use_fates_tree_damage         use_fates=".true.">.false.</use_fates_tree_damage>
 <use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
 <use_fates_ed_st3              use_fates=".true.">.false.</use_fates_ed_st3>
 <use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
-<use_fates_logging             use_fates=".true.">.false.</use_fates_logging>
 <use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
+<use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="3">.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="4">.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true.">.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index b672b43125..fa2d83a3c9 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -734,10 +734,15 @@ Toggle to turn on no competition mode (only relevant if FATES is being used).
 Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used).                        
 </entry>
 
-<entry id="use_fates_logging" type="logical" category="physics"
-        group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the logging module
-(Only relevant if FATES is on)
+<entry id="fates_harvest_mode" type="integer" category="physics"
+        group="clm_inparm" valid_values="0,1,2,3,4", value="0" >
+Set FATES harvesting mode by setting fates_harvest_mode > 0.
+Allowed values are:
+ 0 : no fates harvesting of any kind
+ 1 : fates logging via fates logging event codes (see fates parameter file) only
+ 2 : fates harvest driven by CLM landuse timeseries data (dynHarvestMod)
+ 3 : fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
+ 4 : fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
 </entry>
 
 <entry id="use_fates_planthydro" type="logical" category="physics"
@@ -781,9 +786,17 @@ Full pathname to the inventory initialization control file.
 <entry id="use_fates_luh" type="logical" category="physics"
        group="clm_inparm" valid_values="" >
 If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file.
+This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harvest
+data (fates_harvest_mode >= 3)
 (Also, only valid for use_fates = true and is incompatible with transient runs currently.)
 </entry>
 
+<entry id="use_fates_potentialveg" type="logical" category="physics"
+       group="clm_inparm" valid_values="" >
+If TRUE, ignore the land-use state vector and transitions, and assert that all lands
+are primary, and that there is no harvest.
+</entry>
+
 <!-- This could eventually be included in the "dynamic_subgrid" -->
 <entry id="fluh_timeseries" type="char*256" category="datasets"
        input_pathname="abs" group="clm_inparm" valid_values="" >
@@ -793,6 +806,11 @@ types to vary over time.
 (Only relevant if FATES is on).
 </entry>
 
+<entry id="flandusepftdat" type="char*256" category="datasets"
+       input_pathname="abs" group="clm_inparm" valid_values="" >
+Full pathname of fates landuse x pft data map.
+</entry>
+
 <entry id="use_luna" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the LUNA model, to effect Photosynthesis by leaf Nitrogen
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 9b579dd9ce..899bd10b9c 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1046,6 +1046,7 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
+     # TODO SSR: Replace this with fates_harvest_mode
      "useloggingButNOTFATES"     =>{ options=>"-envxml_dir . -no-megan",
                                      namelst=>"use_fates_logging=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
index 406fb598f6..91df3e2e61 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -16,7 +16,7 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
-'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE',
+'FATES_HARVEST_WOODPROD_C_FLUX', 'FATES_DISTURBANCE_RATE_FIRE',
 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
 'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP',
 'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY',
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm
index 3b74a4fd37..5f457f3f1c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm
@@ -1 +1,2 @@
+! TODO SSR: Replace this with fates_harvest_mode
 use_fates_logging= .true.
diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/fates_sp/user_nl_clm
index 093ecd7eda..37da8d1c67 100644
--- a/cime_config/usermods_dirs/fates_sp/user_nl_clm
+++ b/cime_config/usermods_dirs/fates_sp/user_nl_clm
@@ -22,7 +22,7 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLD
               'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 
               'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
               'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
-              'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY',
+              'FATES_HARVEST_WOODPROD_C_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY',
               'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX',
               'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY', 
               'FATES_DDBH_CANOPY_SZ', 'FATES_DDBH_USTORY_SZ', 'FATES_BASALAREA_SZ',
diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
index 45f4340d6a..4f326d82a5 100644
--- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
+++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
@@ -26,13 +26,39 @@ module dynFATESLandUseChangeMod
   ! Landuse state at beginning of year (fraction of gridcell), landuse state name x gridcell
   real(r8), allocatable, public :: landuse_states(:,:)
 
+  ! TODO SSR: Ask Charlie for description to go here
+  real(r8), allocatable, public :: landuse_harvest(:,:)
+
   ! Number of landuse transition and state names
   integer, public, parameter    :: num_landuse_transition_vars = 108
   integer, public, parameter    :: num_landuse_state_vars = 12
+  integer, public, parameter    :: num_landuse_harvest_vars = 5
+
+  ! Define the fates landuse namelist mode switch values
+  integer, public, parameter    :: fates_harvest_no_logging   = 0
+  integer, public, parameter    :: fates_harvest_logging_only = 1
+  integer, public, parameter    :: fates_harvest_clmlanduse   = 2
+  integer, public, parameter    :: fates_harvest_luh_area     = 3
+  integer, public, parameter    :: fates_harvest_luh_mass     = 4
+
+  ! Define landuse harvest unit integer representation
+  integer, public, parameter    :: landuse_harvest_area_units = 1
+  integer, public, parameter    :: landuse_harvest_mass_units = 2
+  integer, public               :: landuse_harvest_units
 
   ! landuse filename
   type(dyn_file_type), target   :: dynFatesLandUse_file
 
+  ! LUH2 raw wood harvest area fraction
+  character(len=10), target :: landuse_harvest_area_varnames(num_landuse_harvest_vars) = &
+       [character(len=10) :: 'primf_harv', 'primn_harv', 'secmf_harv', 'secyf_harv', 'secnf_harv']
+
+  ! LUH2 raw wood harvest biomass carbon
+  character(len=10), target :: landuse_harvest_mass_varnames(num_landuse_harvest_vars) = &
+       [character(len=10) :: 'primf_bioh', 'primn_bioh', 'secmf_bioh', 'secyf_bioh', 'secnf_bioh']
+
+  character(len=10), public, pointer :: landuse_harvest_varnames(:) => null()
+
   ! Land use name arrays
   character(len=5), public, parameter  :: landuse_state_varnames(num_landuse_state_vars) = &
                     [character(len=5)  :: 'primf','primn','secdf','secdn','pastr','range', &
@@ -64,8 +90,9 @@ module dynFATESLandUseChangeMod
                                           'c3nfx_to_c3ann','c3nfx_to_c4ann','c3nfx_to_c3per','c3nfx_to_c4per', &
                                           'c3nfx_to_secdf','c3nfx_to_secdn','c3nfx_to_pastr','c3nfx_to_range','c3nfx_to_urban']
 
-  type(dyn_var_time_uninterp_type) :: landuse_transition_vars(num_landuse_transition_vars) ! value of each landuse variable
-  type(dyn_var_time_uninterp_type) :: landuse_state_vars(num_landuse_state_vars)           ! value of each landuse variable
+  type(dyn_var_time_uninterp_type) :: landuse_transition_vars(num_landuse_transition_vars) ! value of each transitions variable
+  type(dyn_var_time_uninterp_type) :: landuse_state_vars(num_landuse_state_vars)           ! value of each state variable
+  type(dyn_var_time_uninterp_type) :: landuse_harvest_vars(num_landuse_harvest_vars)       ! value of each harvest variable
 
   public :: dynFatesLandUseInit
   public :: dynFatesLandUseInterp
@@ -79,14 +106,14 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename)
     ! Initialize data structures for land use information.
 
     ! !USES:
-    use clm_varctl            , only : use_cn, use_fates_luh
+    use clm_varctl            , only : use_cn, use_fates_luh, fates_harvest_mode
     use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type
     use dynTimeInfoMod        , only : YEAR_POSITION_START_OF_TIMESTEP
     use dynTimeInfoMod        , only : YEAR_POSITION_END_OF_TIMESTEP
 
     ! !ARGUMENTS:
     type(bounds_type), intent(in) :: bounds        ! proc-level bounds
-    character(len=*) , intent(in) :: landuse_filename  ! name of file containing land use information
+    character(len=*) , intent(in) :: landuse_filename  ! name of file containing landuse timeseries information (fates luh2)
 
     ! !LOCAL VARIABLES
     integer :: varnum, i      ! counter for harvest variables
@@ -111,17 +138,23 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename)
     if (ier /= 0) then
        call endrun(msg=' allocation error for landuse_transitions'//errMsg(__FILE__, __LINE__))
     end if
+    allocate(landuse_harvest(num_landuse_harvest_vars,bounds%begg:bounds%endg),stat=ier)
+    if (ier /= 0) then
+       call endrun(msg=' allocation error for landuse_harvest'//errMsg(__FILE__, __LINE__))
+    end if
 
+    ! Initialize the states, transitions and harvest mapping percentages as zero by default
     landuse_states = 0._r8
     landuse_transitions = 0._r8
+    landuse_harvest = 0._r8
 
     if (use_fates_luh) then
 
-       ! Generate the dyn_file_type object.  Note that the land use data being read in is for the
-       ! transitions occuring within the current year
+       ! Generate the dyn_file_type object.
+       ! Start calls get_prev_date, whereas end calls get_curr_date
        dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP)
 
-       ! Get initial land use data
+       ! Get initial land use data from the fates luh2 timeseries dataset
        num_points = (bounds%endg - bounds%begg + 1)
        landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor?
        do varnum = 1, num_landuse_transition_vars
@@ -136,6 +169,28 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename)
                dim1name=grlnd, conversion_factor=1.0_r8, &
                do_check_sums_equal_1=.false., data_shape=landuse_shape)
        end do
+
+       ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled
+       if (fates_harvest_mode .ge. fates_harvest_luh_area ) then
+
+          ! change the harvest varnames being used depending on the mode selected
+          if (fates_harvest_mode .eq. fates_harvest_luh_area ) then
+             landuse_harvest_varnames => landuse_harvest_area_varnames
+             landuse_harvest_units = landuse_harvest_area_units
+          elseif (fates_harvest_mode .eq. fates_harvest_luh_mass ) then
+             landuse_harvest_varnames => landuse_harvest_mass_varnames
+             landuse_harvest_units = landuse_harvest_mass_units
+          else
+             call endrun(msg=' undefined fates harvest mode selected'//errMsg(__FILE__, __LINE__))
+          end if
+
+          do varnum = 1, num_landuse_harvest_vars
+             landuse_harvest_vars(varnum) = dyn_var_time_uninterp_type( &
+                  dyn_file=dynFatesLandUse_file, varname=landuse_harvest_varnames(varnum), &
+                  dim1name=grlnd, conversion_factor=1.0_r8, &
+                  do_check_sums_equal_1=.false., data_shape=landuse_shape)
+          end do
+       end if
     end if
 
     ! Since fates needs state data during initialization, make sure to call
@@ -159,7 +214,7 @@ subroutine dynFatesLandUseInterp(bounds, init_state)
 
     ! !USES:
     use dynTimeInfoMod , only : time_info_type
-    use clm_varctl     , only : use_cn
+    use clm_varctl     , only : use_cn, fates_harvest_mode
 
     ! !ARGUMENTS:
     type(bounds_type), intent(in) :: bounds       ! proc-level bounds
@@ -181,13 +236,14 @@ subroutine dynFatesLandUseInterp(bounds, init_state)
        init_flag = init_state
     end if
 
-    ! Get the current year
+    ! Get the data for the current year
     call dynFatesLandUse_file%time_info%set_current_year()
 
     if (dynFatesLandUse_file%time_info%is_before_time_series() .and. .not.(init_flag)) then
        ! Reset the land use transitions to zero for safety
        landuse_transitions(1:num_landuse_transition_vars,bounds%begg:bounds%endg) = 0._r8
        landuse_states(1:num_landuse_state_vars,bounds%begg:bounds%endg) = 0._r8
+       landuse_harvest(1:num_landuse_harvest_vars,bounds%begg:bounds%endg) = 0._r8
     else
        ! Loop through all variables on the data file and put data into the temporary array
        ! then update the global state and transitions array.
@@ -200,6 +256,12 @@ subroutine dynFatesLandUseInterp(bounds, init_state)
           call landuse_state_vars(varnum)%get_current_data(this_data)
           landuse_states(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg)
        end do
+       if (fates_harvest_mode .ge. fates_harvest_luh_area ) then
+          do varnum = 1, num_landuse_harvest_vars
+             call landuse_harvest_vars(varnum)%get_current_data(this_data)
+             landuse_harvest(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg)
+          end do
+       end if
        deallocate(this_data)
     end if
 
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index 1ca450b48d..830dcfcca7 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -200,6 +200,7 @@ subroutine clm_instInit(bounds)
     use SoilWaterRetentionCurveFactoryMod  , only : create_soil_water_retention_curve
     use decompMod                          , only : get_proc_bounds
     use BalanceCheckMod                    , only : GetBalanceCheckSkipSteps
+    use clm_varctl                         , only : flandusepftdat
     !
     ! !ARGUMENTS    
     type(bounds_type), intent(in) :: bounds  ! processor bounds
@@ -436,7 +437,7 @@ subroutine clm_instInit(bounds)
     ! Initialize the Functionaly Assembled Terrestrial Ecosystem Simulator (FATES)
     ! 
     if (use_fates) then
-       call clm_fates%Init(bounds)
+       call clm_fates%Init(bounds, flandusepftdat)
     end if
 
     deallocate (h2osno_col)
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index e0d142bffd..9ab6c631c7 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -302,7 +302,7 @@ module clm_varctl
                                                                         ! > 1 for external data (lightning and/or anthropogenic ignitions)
                                                                         ! see bld/namelist_files/namelist_definition_clm4_5.xml for details
   logical, public            :: use_fates_tree_damage = .false.         ! true => turn on tree damage module
-  logical, public            :: use_fates_logging = .false.             ! true => turn on logging module
+  integer, public            :: fates_harvest_mode = 0                  ! 0 for no harvest/logging; 1-4 for harvest mode options
   logical, public            :: use_fates_planthydro = .false.          ! true => turn on fates hydro
   logical, public            :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking
   logical, public            :: use_fates_ed_st3   = .false.            ! true => static stand structure
@@ -311,7 +311,9 @@ module clm_varctl
   logical, public            :: use_fates_fixed_biogeog = .false.       ! true => use fixed biogeography mode
   logical, public            :: use_fates_nocomp = .false.              ! true => use no comopetition mode
   logical, public            :: use_fates_luh = .false.                 ! true => use FATES landuse data mode
+  logical, public            :: use_fates_potentialveg = .false.        ! true => FATES potential veg only
   character(len=256), public :: fluh_timeseries = ''                    ! filename for fates landuse timeseries data
+  character(len=256), public :: flandusepftdat = ''                     ! filename for fates landuse x pft data
   character(len=256), public :: fates_inventory_ctrl_filename = ''      ! filename for inventory control
 
   ! FATES SP AND FATES BGC are MUTUTALLY EXCLUSIVE, THEY CAN'T BOTH BE ON
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 44efec4eeb..196bc141ff 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -222,7 +222,7 @@ subroutine control_init(dtime)
 
     ! FATES Flags
     namelist /clm_inparm/ fates_paramfile, use_fates,   &
-          fates_spitfire_mode, use_fates_logging,       &
+          fates_spitfire_mode, fates_harvest_mode,      &
           use_fates_planthydro, use_fates_ed_st3,       &
           use_fates_cohort_age_tracking,                &
           use_fates_ed_prescribed_phys,                 &
@@ -231,7 +231,9 @@ subroutine control_init(dtime)
           use_fates_nocomp,                             &
           use_fates_sp,                                 &
           use_fates_luh,                                &
+          use_fates_potentialveg,                       &
           fluh_timeseries,                              &
+          flandusepftdat,                               &
           fates_inventory_ctrl_filename,                &
           fates_parteh_mode,                            &
           fates_seeddisp_cadence,                       &
@@ -772,7 +774,7 @@ subroutine control_spmd()
     call mpi_bcast (for_testing_allow_interp_non_ciso_to_ciso, 1, MPI_LOGICAL, 0, mpicom, ier)
 
     call mpi_bcast (fates_spitfire_mode, 1, MPI_INTEGER, 0, mpicom, ier)
-    call mpi_bcast (use_fates_logging, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (fates_harvest_mode, 1, MPI_INTEGER, 0, mpicom, ier)
     call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_tree_damage, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_cohort_age_tracking, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -783,10 +785,12 @@ subroutine control_spmd()
     call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_luh, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (use_fates_potentialveg, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier)
-    call mpi_bcast (fluh_timeseries, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (fluh_timeseries, len(fluh_timeseries) , MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (flandusepftdat, len(flandusepftdat) , MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fates_parteh_mode, 1, MPI_INTEGER, 0, mpicom, ier)
     call mpi_bcast (fates_seeddisp_cadence, 1, MPI_INTEGER, 0, mpicom, ier)
 
@@ -1144,7 +1148,7 @@ subroutine control_print ()
     write(iulog, *) '    use_fates = ', use_fates
     if (use_fates) then
        write(iulog, *) '    fates_spitfire_mode = ', fates_spitfire_mode
-       write(iulog, *) '    use_fates_logging = ', use_fates_logging
+       write(iulog, *) '    fates_harvest_mode = ', fates_harvest_mode
        write(iulog, *) '    fates_paramfile = ', fates_paramfile
        write(iulog, *) '    fates_parteh_mode = ', fates_parteh_mode
        write(iulog, *) '    use_fates_planthydro = ', use_fates_planthydro
@@ -1157,7 +1161,9 @@ subroutine control_print ()
        write(iulog, *) '    use_fates_nocomp = ', use_fates_nocomp
        write(iulog, *) '    use_fates_sp = ', use_fates_sp
        write(iulog, *) '    use_fates_luh= ', use_fates_luh
+       write(iulog, *) '    use_fates_potentialveg = ', use_fates_potentialveg
        write(iulog, *) '    fluh_timeseries = ', trim(fluh_timeseries)
+       write(iulog, *) '    flandusepftdat = ', trim(flandusepftdat)
        write(iulog, *) '    fates_seeddisp_cadence = ', fates_seeddisp_cadence
        write(iulog, *) '    fates_seeddisp_cadence: 0, 1, 2, 3 => off, daily, monthly, or yearly dispersal'
        write(iulog, *) '    fates_inventory_ctrl_filename = ', trim(fates_inventory_ctrl_filename)
diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 83d7186021..3f84a28508 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -54,12 +54,14 @@ module CLMFatesInterfaceMod
    use clm_varctl        , only : use_fates_cohort_age_tracking
    use clm_varctl        , only : use_fates_ed_st3
    use clm_varctl        , only : use_fates_ed_prescribed_phys
-   use clm_varctl        , only : use_fates_logging
+   use clm_varctl        , only : fates_harvest_mode
    use clm_varctl        , only : use_fates_inventory_init
    use clm_varctl        , only : use_fates_fixed_biogeog
    use clm_varctl        , only : use_fates_nocomp
    use clm_varctl        , only : use_fates_sp
    use clm_varctl        , only : use_fates_luh
+   use clm_varctl        , only : use_fates_potentialveg
+   use clm_varctl        , only : flandusepftdat
    use clm_varctl        , only : fates_seeddisp_cadence
    use clm_varctl        , only : fates_inventory_ctrl_filename
    use clm_varctl        , only : use_nitrif_denitrif
@@ -180,6 +182,12 @@ module CLMFatesInterfaceMod
    use dynFATESLandUseChangeMod, only : landuse_transitions, landuse_states
    use dynFATESLandUseChangeMod, only : landuse_transition_varnames, landuse_state_varnames
    use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp
+   use dynFATESLandUseChangeMod, only : num_landuse_harvest_vars
+   use dynFATESLandUseChangeMod, only : fates_harvest_no_logging
+   use dynFATESLandUseChangeMod, only : fates_harvest_luh_area
+   use dynFATESLandUseChangeMod, only : landuse_harvest
+   use dynFATESLandUseChangeMod, only : landuse_harvest_units
+   use dynFATESLandUseChangeMod, only : landuse_harvest_varnames
 
    implicit none
 
@@ -272,6 +280,8 @@ module CLMFatesInterfaceMod
    character(len=*), parameter, private :: sourcefile = &
         __FILE__
 
+   integer, parameter :: num_landuse_pft_vars = 4
+
    public  :: CLMFatesGlobals1
    public  :: CLMFatesGlobals2
 
@@ -384,8 +394,10 @@ subroutine CLMFatesGlobals2()
      integer                                        :: pass_cohort_age_tracking
      integer                                        :: pass_tree_damage
      integer                                        :: pass_use_luh
+     integer                                        :: pass_use_potentialveg
      integer                                        :: pass_num_luh_states
      integer                                        :: pass_num_luh_transitions
+     integer                                        :: pass_lupftdat
 
      call t_startf('fates_globals2')
 
@@ -477,7 +489,7 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_ed_st3',ival=pass_ed_st3)
 
-        if(use_fates_logging) then
+        if (fates_harvest_mode > fates_harvest_no_logging) then
            pass_logging = 1
         else
            pass_logging = 0
@@ -505,8 +517,8 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking)
 
-        ! check fates logging namelist value first because hlm harvest overrides it
-        if(use_fates_logging) then
+        ! check fates logging namelist value first because hlm harvest can override it
+        if (fates_harvest_mode > fates_harvest_no_logging) then
            pass_logging = 1
         else
            pass_logging = 0
@@ -521,23 +533,53 @@ subroutine CLMFatesGlobals2()
            pass_num_lu_harvest_cats = 0
         end if
 
-        call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest)
-        call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats)
-        call set_fates_ctrlparms('use_logging',ival=pass_logging)
-
         if(use_fates_luh) then
            pass_use_luh = 1
            pass_num_luh_states = num_landuse_state_vars
            pass_num_luh_transitions = num_landuse_transition_vars
+
+           ! Do not set harvest passing variables to zero not in luh harvest modes
+           ! as the user may want to use the CLM landuse harvest with luh2 transitions
+           if(fates_harvest_mode >= fates_harvest_luh_area) then
+              ! End the run if do_harvest is true with this run mode.
+              ! This should be caught be the build namelist.
+              if(get_do_harvest()) then
+                 call endrun(msg="do_harvest and fates_harvest_mode using luh2 harvest data are incompatible"//&
+                      errmsg(sourcefile, __LINE__))
+              else
+                 pass_lu_harvest = 1
+              end if
+           end if
         else
            pass_use_luh = 0
            pass_num_luh_states = 0
            pass_num_luh_transitions = 0
         end if
+
         call set_fates_ctrlparms('use_luh2',ival=pass_use_luh)
         call set_fates_ctrlparms('num_luh2_states',ival=pass_num_luh_states)
         call set_fates_ctrlparms('num_luh2_transitions',ival=pass_num_luh_transitions)
 
+        if ( use_fates_potentialveg ) then
+           pass_use_potentialveg = 1
+        else
+           pass_use_potentialveg = 0
+        end if
+        call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg)
+
+        if(flandusepftdat /= '') then
+           pass_lupftdat = 1
+        else
+           pass_lupftdat = 0
+        end if
+        call set_fates_ctrlparms('use_landusepft_data',ival=pass_lupftdat)
+
+        ! Wait to set the harvest and logging variables after checking get_do_harvest
+        ! and fates_harvest_modes
+        call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest)
+        call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats)
+        call set_fates_ctrlparms('use_logging',ival=pass_logging)
+
         if(use_fates_inventory_init) then
            pass_inventory_init = 1
         else
@@ -585,7 +627,7 @@ end subroutine CLMFatesTimesteps
    
    ! ====================================================================================
 
-   subroutine init(this, bounds_proc )
+   subroutine init(this, bounds_proc, flandusepftdat)
 
       ! ---------------------------------------------------------------------------------
       ! This initializes the hlm_fates_interface_type
@@ -614,6 +656,7 @@ subroutine init(this, bounds_proc )
       ! Input Arguments
       class(hlm_fates_interface_type), intent(inout) :: this
       type(bounds_type),intent(in)                   :: bounds_proc
+      character(len=*), intent(in)                   :: flandusepftdat
 
       ! local variables
       integer                                        :: nclumps   ! Number of threads
@@ -631,6 +674,9 @@ subroutine init(this, bounds_proc )
       integer                                        :: ndecomp
       integer                                        :: numg
 
+      real(r8), allocatable :: landuse_pft_map(:,:,:)
+      real(r8), allocatable :: landuse_bareground(:)
+
       ! Initialize the FATES communicators with the HLM
       ! This involves to stages
       ! 1) allocate the vectors
@@ -663,6 +709,13 @@ subroutine init(this, bounds_proc )
          write(iulog,*) 'clm_fates%init():  allocating for ',nclumps,' threads'
       end if
 
+      ! Retrieve the landuse x pft static data if the file is present
+      if (flandusepftdat /= '') then
+         call GetLandusePFTData(bounds_proc, flandusepftdat, landuse_pft_map, landuse_bareground)
+      end if
+
+      nclumps = get_proc_clumps()
+
       allocate(copy_fates_var(bounds_proc%begc:bounds_proc%endc))
       copy_fates_var(:) = .false.
 
@@ -767,18 +820,26 @@ subroutine init(this, bounds_proc )
             this%fates(nc)%sites(s)%lat = grc%latdeg(g)
             this%fates(nc)%sites(s)%lon = grc%londeg(g)
 
-            this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8
-            ! initialize static layers for reduced complexity FATES versions from HLM
-            ! maybe make this into a subroutine of it's own later.
-            do m = surfpft_lb,surfpft_ub
-               ft = m - surfpft_lb
-               this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m)
-            end do
+            ! Transfer the landuse x pft data to fates via bc_in if file is given
+            if (flandusepftdat /= '') then
+               this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars)
+               this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g)
+            end if
 
-            if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > sum_to_1_tol) then
-               write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)%pft_areafrac(:)) - 1.0_r8
-               call endrun(msg=errMsg(sourcefile, __LINE__))
-              end if
+            if (flandusepftdat == '') then
+               ! initialize static layers for reduced complexity FATES versions from HLM
+               ! maybe make this into a subroutine of it's own later.
+               this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8
+               do m = surfpft_lb,surfpft_ub
+                  ft = m - surfpft_lb
+                  this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m)
+               end do
+
+               if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) >    sum_to_1_tol) then
+                  write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)   %pft_areafrac(:)) - 1.0_r8
+                  call endrun(msg=errMsg(sourcefile, __LINE__))
+               end if
+            end if
           end do !site
 
         ! Initialize site-level static quantities dictated by the HLM
@@ -820,6 +881,12 @@ subroutine init(this, bounds_proc )
       ! Fire data to send to FATES
       call create_fates_fire_data_method( this%fates_fire_data_method )
 
+      ! deallocate the local landuse x pft array
+      if (flandusepftdat /= '') then
+         deallocate(landuse_pft_map)
+         deallocate(landuse_bareground)
+      end if
+
       call t_stopf('fates_init')
 
     end subroutine init
@@ -1087,6 +1154,12 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
                this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames
                this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g)
                this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames
+
+               if (fates_harvest_mode >= fates_harvest_luh_area) then
+                  this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g)
+                  this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames
+                  this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units
+               end if
          end if
 
       end do
@@ -2033,6 +2106,12 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, &
                     this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames
                     this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g)
                     this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames
+
+                    if (fates_harvest_mode >= fates_harvest_luh_area ) then
+                       this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g)
+                       this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames
+                       this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units
+                    end if
               end if
            end do
 
@@ -3646,6 +3725,114 @@ subroutine GetAndSetTime()
 
  end subroutine GetAndSetTime
 
+ ! ======================================================================================
+
+ subroutine GetLandusePFTData(bounds, landuse_pft_file, landuse_pft_map, landuse_bareground)
+
+   ! !DESCRIPTION:
+   ! Read in static landuse x pft file
+
+   ! !USES:
+   use fileutils , only : getfil
+   use ncdio_pio , only : file_desc_t, ncd_io, ncd_inqdlen
+   use ncdio_pio , only : ncd_pio_openfile, ncd_pio_closefile
+   use decompMod , only : BOUNDS_LEVEL_PROC
+   use clm_varcon, only : grlnd
+   use FatesConstantsMod, only : fates_unset_r8
+
+
+   ! !ARGUMENTS:
+   type(bounds_type), intent(in)        :: bounds            ! proc-level bounds
+   character(len=*) , intent(in)        :: landuse_pft_file  ! name of file containing static landuse x pft information
+   real(r8), allocatable, intent(inout) :: landuse_pft_map(:,:,:)
+   real(r8), allocatable, intent(inout) :: landuse_bareground(:)
+
+   ! !LOCAL VARIABLES
+   integer            :: varnum                    ! variable number
+   integer            :: dimid, dimlen             ! dimension id number and length
+   integer            :: ier                       ! error id
+   character(len=256) :: locfn                     ! local file name
+   type(file_desc_t)  :: ncid                      ! netcdf id
+   real(r8), pointer  :: arraylocal(:,:)           ! local array for reading fraction data
+   real(r8), pointer  :: arraylocal_bareground(:)  ! local array for reading bareground data
+   logical            :: readvar                   ! true => variable is on dataset
+   !character(len=16), parameter :: grlnd  = 'lndgrid'      ! name of lndgrid
+
+   integer, parameter :: dim_landuse_pft = 14
+
+   ! Land use name arrays
+   character(len=10), parameter  :: landuse_pft_map_varnames(num_landuse_pft_vars) = &
+                    [character(len=10)  :: 'frac_primr','frac_secnd','frac_pastr','frac_range'] !need to move 'frac_surf' to a different variable
+
+   character(len=*), parameter :: subname = 'GetLandusePFTData'
+
+   !-----------------------------------------------------------------------
+
+   ! Check to see if the landuse file name has been provided
+   ! Note: getfile checks this as well
+   if (masterproc) then
+      write(iulog,*) 'Attempting to read landuse x pft data .....'
+      if (landuse_pft_file == ' ') then
+         write(iulog,*)'landuse_pft_file must be specified'
+         call endrun(msg=errMsg(__FILE__, __LINE__))
+      endif
+   endif
+
+   ! Initialize the landuse x pft arrays and initialize to unset
+    allocate(landuse_pft_map(bounds%begg:bounds%endg,dim_landuse_pft,num_landuse_pft_vars),stat=ier)
+    if (ier /= 0) then
+       call endrun(msg=' allocation error for landuse_pft_map'//errMsg(__FILE__, __LINE__))
+    end if
+    landuse_pft_map = fates_unset_r8
+
+    allocate(landuse_bareground(bounds%begg:bounds%endg),stat=ier)
+    if (ier /= 0) then
+       call endrun(msg=' allocation error for landuse_bareground'//errMsg(__FILE__, __LINE__))
+    end if
+    landuse_bareground = fates_unset_r8
+
+
+   ! Get the local filename and open the file
+   call getfil(landuse_pft_file, locfn, 0)
+   call ncd_pio_openfile (ncid, trim(locfn), 0)
+
+   ! Check that natpft dimension on the file matches the target array dimensions
+   call ncd_inqdlen(ncid, dimid, dimlen, 'natpft')
+   if (dimlen /= dim_landuse_pft) then
+      write(iulog,*) 'natpft dimensions on the landuse x pft file do not match target array size'
+      call endrun(msg=errMsg(__FILE__, __LINE__))
+   end if
+
+   ! Allocate a temporary array since ncdio expects a pointer
+   allocate(arraylocal(bounds%begg:bounds%endg,dim_landuse_pft))
+   allocate(arraylocal_bareground(bounds%begg:bounds%endg))
+
+   ! Read the landuse x pft data from file
+   do varnum = 1, num_landuse_pft_vars
+      call ncd_io(ncid=ncid, varname=landuse_pft_map_varnames(varnum), flag='read', &
+                  data=arraylocal, dim1name=grlnd, readvar=readvar)
+      if (.not. readvar) &
+         call endrun(msg='ERROR: '//trim(landuse_pft_map_varnames(varnum))// &
+                         ' NOT on landuse x pft file'//errMsg(__FILE__, __LINE__))
+      landuse_pft_map(bounds%begg:bounds%endg,:,varnum) = arraylocal(bounds%begg:bounds%endg,:)
+   end do
+
+   ! Read the bareground data from file.  This is per gridcell only.
+   call ncd_io(ncid=ncid, varname='frac_brgnd', flag='read', &
+               data=arraylocal_bareground, dim1name=grlnd, readvar=readvar)
+   if (.not. readvar) call endrun(msg='ERROR: frac_brgnd NOT on landuse x pft file'//errMsg(__FILE__, __LINE__))
+   landuse_bareground(bounds%begg:bounds%endg) = arraylocal_bareground(bounds%begg:bounds%endg)
+
+   ! Deallocate the temporary local array point and close the file
+   deallocate(arraylocal)
+   deallocate(arraylocal_bareground)
+   call ncd_pio_closefile(ncid)
+
+   ! Check that sums equal to unity
+
+ end subroutine GetLandusePFTData
+
+
  !-----------------------------------------------------------------------
 
 end module CLMFatesInterfaceMod

From 46420cfb64f4ebb2b092daef9071a3f070b403bf Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Apr 2024 09:40:21 -0600
Subject: [PATCH 0132/1248] Add fates_landuse_v2 test suite.

---
 cime_config/testdefs/testlist_clm.xml         | 36 +++++++++++++++++++
 .../clm/FatesColdLUH2Mode1/include_user_mods  |  1 +
 .../clm/FatesColdLUH2Mode1/user_nl_clm        |  1 +
 .../clm/FatesColdLUH2Mode2/include_user_mods  |  1 +
 .../clm/FatesColdLUH2Mode2/user_nl_clm        |  1 +
 .../clm/FatesColdLUH2Mode3/include_user_mods  |  1 +
 .../clm/FatesColdLUH2Mode3/user_nl_clm        |  1 +
 .../clm/FatesColdLUH2Mode4/include_user_mods  |  1 +
 .../clm/FatesColdLUH2Mode4/user_nl_clm        |  1 +
 9 files changed, 44 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index dec8cf49d8..4184cc7e1f 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2910,6 +2910,42 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode1">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
+      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode2">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
+      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode3">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
+      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode4">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
+      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld3" grid="f19_g17" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods
new file mode 100644
index 0000000000..7eb8bb1579
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods
@@ -0,0 +1 @@
+../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm
new file mode 100644
index 0000000000..dea75b71e7
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm
@@ -0,0 +1 @@
+fates_harvest_mode = 1
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods
new file mode 100644
index 0000000000..7eb8bb1579
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods
@@ -0,0 +1 @@
+../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm
new file mode 100644
index 0000000000..fd4c74fe57
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm
@@ -0,0 +1 @@
+fates_harvest_mode = 2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods
new file mode 100644
index 0000000000..7eb8bb1579
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods
@@ -0,0 +1 @@
+../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm
new file mode 100644
index 0000000000..3332e9e526
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm
@@ -0,0 +1 @@
+fates_harvest_mode = 3
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods
new file mode 100644
index 0000000000..7eb8bb1579
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods
@@ -0,0 +1 @@
+../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm
new file mode 100644
index 0000000000..13dae9efee
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm
@@ -0,0 +1 @@
+fates_harvest_mode = 4

From e4c8b6a0f1dfd0392fc956cf5d3f41e197508ba5 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Apr 2024 11:32:05 -0600
Subject: [PATCH 0133/1248] Point FATES external to my repo: Nag array index
 fix.

---
 Externals_CLM.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
index 1494217277..ef4406545e 100644
--- a/Externals_CLM.cfg
+++ b/Externals_CLM.cfg
@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/ckoven/fates
-hash = d37d9733b5970dfe67a
+repo_url = https://github.com/samsrabin/fates
+hash = c03a4ba64a7e59817658f1c3357ffff681d8b958
 required = True
 
 [externals_description]

From 7216006b1c2400d1ca2932899671f9bcec85b6af Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Apr 2024 16:48:41 -0600
Subject: [PATCH 0134/1248] Apply relevant changes from
 rgknox/fates-auto-params.

---
 .../testdefs/testmods_dirs/clm/Fates/shell_commands   |  5 +++++
 .../testdefs/testmods_dirs/clm/Fates/user_nl_clm      |  1 +
 .../testdefs/testmods_dirs/clm/_scripts/README        |  2 ++
 .../clm/_scripts/get_fates_shell_commands_vars.sh     | 11 +++++++++++
 4 files changed, 19 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/_scripts/README
 create mode 100755 cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh

diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands
index 41a2342a51..3443bacef0 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands
@@ -1,2 +1,7 @@
 ./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
 ./xmlchange BFBFLAG="TRUE"
+
+SRCROOT=`./xmlquery SRCROOT --value`
+. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
+
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
index 91df3e2e61..57adea1ff6 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -4,6 +4,7 @@ hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 hist_ndens = 1
 fates_spitfire_mode = 1
+fates_paramfile='${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc'
 hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD',
 'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON',
diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/README b/cime_config/testdefs/testmods_dirs/clm/_scripts/README
new file mode 100644
index 0000000000..66eb22a375
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/_scripts/README
@@ -0,0 +1,2 @@
+This directory contains scripts that can be called in
+shell_commands of multiple testmods.
diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh b/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
new file mode 100755
index 0000000000..382fb4e53e
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
@@ -0,0 +1,11 @@
+# This script should be called in shell_commands with
+#    . "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
+# where the leading period ensures it's run in the same shell.
+
+CASE=`./xmlquery CASE --value`
+FATESDIR="${SRCROOT}/src/fates"
+FATESPARAMDIR="${SRCROOT}/src/fates/parameter_files/binaries"
+mkdir -p "${FATESPARAMDIR}"
+FATESPARAMFILE="${FATESPARAMDIR}/${CASE}-params.nc"
+
+# No exit status because it should be called in the same shell.

From a7c21a752224c09361b4280a730e5c61273244fa Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 23 Apr 2024 12:26:35 -0600
Subject: [PATCH 0135/1248] Don't allow flandusepftdat to be set in non-FATES
 runs.

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index bcf68a8d61..e3ceedeccc 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -784,7 +784,7 @@ sub setup_cmdl_fates_mode {
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
-                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" );
+                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat");
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {

From 90a40281134953f3d371a6454642773035efe137 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 23 Apr 2024 12:27:16 -0600
Subject: [PATCH 0136/1248] Actually set flandusepftdat in CLMBuildNamelist.pm.

---
 bld/CLMBuildNamelist.pm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index e3ceedeccc..0f7f6891c5 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4424,6 +4424,9 @@ sub setup_logic_fates {
               } elsif ( ! -f "$fname" ) {
                  $log->fatal_error("$fname does NOT point to a valid filename" );
               }
+
+              $var = "flandusepftdat";
+              add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
            }
         }
 

From d88fda01ba5904e80cf432f609cc10d4392f2767 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 23 Apr 2024 12:27:43 -0600
Subject: [PATCH 0137/1248] Update path for default flandusepftdat.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index bc962d1b0f..66c0f837e0 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1578,7 +1578,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
  >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
 
 <!-- Land Use Harmonization static landuse x pft mapping data sets for FATES land use change -->
-<flandusepftdat hgrid="4x5" use_fates=".true." >lnd/clm2/surfdata_map/fates-sci.1.73.0_api.33.0.0/fates_landuse_pft_map_4x5_240206.nc</flandusepftdat>
+<flandusepftdat hgrid="4x5" use_fates=".true." >lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc</flandusepftdat>
 
 <!-- This one is just for testing until Issue #2304 is resolved -->
 <fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."

From a731954707bc67e40282ed26a72192c53cb46208 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 28 Apr 2024 13:45:50 -0600
Subject: [PATCH 0138/1248] Point FATES external back at Charlie's branch.

---
 Externals_CLM.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
index ef4406545e..b689141aaf 100644
--- a/Externals_CLM.cfg
+++ b/Externals_CLM.cfg
@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/samsrabin/fates
-hash = c03a4ba64a7e59817658f1c3357ffff681d8b958
+repo_url = https://github.com/ckoven/fates
+hash = c1a7453c8331277a156a0ee158a870c1b8598a9f
 required = True
 
 [externals_description]

From 0191278f95a35f90c76b7922fb51d8e42d68b24e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 28 Apr 2024 13:48:21 -0600
Subject: [PATCH 0139/1248] Add missing potential veg to build list.

Manually cherry-picked from Greg Lemieux's b33a722.
---
 bld/CLMBuildNamelist.pm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 0f7f6891c5..7e2e4294af 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -784,7 +784,8 @@ sub setup_cmdl_fates_mode {
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
-                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat");
+                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat",
+                      "use_fates_potentialveg");
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {

From ee5efecb0630adae98b5839bb206edf14fe01144 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Apr 2024 17:12:41 -0600
Subject: [PATCH 0140/1248] Fix the clm6_0 issues identified in #2492

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 147a23f49a..03b5afd1ef 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -116,9 +116,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <atm_c14_filename use_c14=".true." use_c14_bombspike =".true." ssp_rcp="SSP5-8.5" >lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP5B_3x1_global_1850-2100_yearly_c181209.nc</atm_c14_filename>
 
 <!-- Irrigation default -->
-<irrigate >.false.</irrigate>
 <irrigate               use_cndv=".false."  sim_year_range="1850-2100">.true.</irrigate>
 <irrigate phys="clm4_5" use_cndv=".false."  sim_year_range="1850-2100">.false.</irrigate>
+<irrigate >.false.</irrigate>
 
 <!-- Saturation excess runoff for crops  -->
 <crop_fsat_equals_zero>.false.</crop_fsat_equals_zero>
@@ -430,6 +430,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <snow_thermal_cond_method>Jordan1991</snow_thermal_cond_method>
 <snow_thermal_cond_method phys="clm5_1">Sturm1997</snow_thermal_cond_method>
+<snow_thermal_cond_method phys="clm6_0">Sturm1997</snow_thermal_cond_method>
 
 <!-- Default glacier behavior is:
      Mountain glaciers: single_at_atm_topo
@@ -1638,6 +1639,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <snicar_snodst_intmix>.false.</snicar_snodst_intmix>
 <snicar_snobc_intmix>.false.</snicar_snobc_intmix>
 <snicar_snobc_intmix phys="clm5_1">.true.</snicar_snobc_intmix>
+<snicar_snobc_intmix phys="clm6_0">.true.</snicar_snobc_intmix>
 <snicar_use_aerosol  >.true.</snicar_use_aerosol>
 <do_sno_oc           >.false.</do_sno_oc>
 

From 9769e2f47bddfb9c39c1c776e0b6b834bb038c47 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Apr 2024 17:13:05 -0600
Subject: [PATCH 0141/1248] Start adding a namelist comparision tool

---
 bld/unit_testers/compare_namelists | 108 +++++++++++++++++++++++++++++
 1 file changed, 108 insertions(+)
 create mode 100755 bld/unit_testers/compare_namelists

diff --git a/bld/unit_testers/compare_namelists b/bld/unit_testers/compare_namelists
new file mode 100755
index 0000000000..1a5d76fa65
--- /dev/null
+++ b/bld/unit_testers/compare_namelists
@@ -0,0 +1,108 @@
+#! /bin/bash
+# Compare namelists made by the unit-tester to either themselves (for different physics versions)
+# or to a baseline also made by the unit-tester
+#
+
+#----------------------------------------------------------------------
+# Usage subroutine
+usage() {
+  echo ""
+  echo "***********************************************************************"
+  echo "usage:"
+  echo "./compare_namelists <options>"
+  echo ""
+  echo "valid options: "
+  echo "[-h|--help]  "
+  echo "     Displays this help message"
+  echo "[-v|--verbose]  "
+  echo "     Run in verbose mode"
+  echo "[-pa|--physicsA <physics-version>]  "
+  echo "     Namelists of first physics version for comparison"
+  echo "     (in current directory)"
+  echo "[-pb|--physicsB <physics-version>]  "
+  echo "     Namelists of second physics version to compare to the first one"
+  echo "     (in baseline directory)"
+  echo "[-b|--baseline <baseline>]  "
+  echo "     Baseline directory to compare to (default current directory)"
+  echo "  "
+  echo "NOTE: When --physicsA or --physicsB is chosen you must also set the other"
+  echo "***********************************************************************"
+}
+
+
+# Current working directory: the location of this script
+cwd=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+# Default settings
+verbose="No"
+PHYSA="all"
+PHYSB="all"
+baseline="."
+
+# Parse command-line options
+while [ $# -gt 0 ]; do
+   case $1 in
+       -h|--help )
+           usage
+           exit 0
+           ;;
+       -v|--verbose )
+           verbose="YES"
+           ;;
+       -pa|--physicsA )
+           PHYSA=$2
+           shift
+           ;;
+       -pb|--physicsB )
+           PHYSB=$2
+           shift
+           ;;
+       -b|--baseline )
+           baseline=$2
+           shift
+           ;;
+       * )
+           echo "ERROR:: invalid argument sent in: $2"
+           usage
+           exit 1
+           ;;
+   esac
+   shift
+done
+if [ "$PHYSA" = "all" ] && [ "$PHYSB" != "all" ]; then
+   echo "When setting --physicsB you MUST also set --physicsA"
+   echo "$PHYSA $PHYSB"
+   exit 1
+fi
+if [ "$PHYSB" = "all" ] && [ "$PHYSA" != "all" ]; then
+   echo "When setting --physicsA you MUST also set --physicsB"
+   exit 1
+fi
+
+if [ "$verbose" = "YES" ]; then echo "Get list of lnd_in.* files"; fi
+filepat="lnd_in.*"
+filenames=($filepat)
+if [ "$verbose" = "YES" ]; then echo "filename list = $filenames"; fi
+if [ "${filenames[*]}" = "$filepat" ]; then
+   echo "No lnd_in files exist in the current directory -- run ./build-namelist_test.pl first"
+   exit 1
+fi
+for file in ${filenames[*]}
+do
+   fileA="./$file"
+   fileB="$baseline/$file"
+   #if [[ $file =~ $pattern ]]; then
+   if ! test -f $fileB; then
+      if [ "$verbose" = "YES" ]; then echo "$fileB does NOT exist -- skipping"; fi
+   fi
+   if [ "$verbose" = "YES" ]; then echo "Compare namelists for $file"; fi
+   if [ "$fileA" = "$fileB" ]; then
+      echo "Comparing files to themself:"
+      echo "fileA = $fileA"
+      echo "fileB = $fileB"
+      exit 1
+   fi
+   # send standard error to /dev/null to ignore it
+   $cwd/../../cime/CIME/Tools/compare_namelists $fileA $fileB 2>/dev/null
+done
+if [ "$verbose" = "YES" ]; then echo "Successfully ran through lnd_in files to compare"; fi
\ No newline at end of file

From cb32dd1dab6f73ae852d7f4b8249aa7b03e21613 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Apr 2024 17:37:31 -0600
Subject: [PATCH 0142/1248] Get the physicsA and physicsB options working

---
 bld/unit_testers/compare_namelists | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/bld/unit_testers/compare_namelists b/bld/unit_testers/compare_namelists
index 1a5d76fa65..e0c6263555 100755
--- a/bld/unit_testers/compare_namelists
+++ b/bld/unit_testers/compare_namelists
@@ -91,18 +91,22 @@ for file in ${filenames[*]}
 do
    fileA="./$file"
    fileB="$baseline/$file"
-   #if [[ $file =~ $pattern ]]; then
-   if ! test -f $fileB; then
-      if [ "$verbose" = "YES" ]; then echo "$fileB does NOT exist -- skipping"; fi
-   fi
-   if [ "$verbose" = "YES" ]; then echo "Compare namelists for $file"; fi
-   if [ "$fileA" = "$fileB" ]; then
-      echo "Comparing files to themself:"
-      echo "fileA = $fileA"
-      echo "fileB = $fileB"
-      exit 1
-   fi
-   # send standard error to /dev/null to ignore it
-   $cwd/../../cime/CIME/Tools/compare_namelists $fileA $fileB 2>/dev/null
+   # If physicsA option used and the file matches the physics input
+   if [[ $fileA =~ "-phys+$PHYSA" ]]; then
+      # Replace physicsB for fileB
+      fileB=${fileB/-phys+$PHYSA/-phys+$PHYSB}
+      if ! test -f $fileB; then
+         if [ "$verbose" = "YES" ]; then echo "$fileB does NOT exist -- skipping"; fi
+      else
+         if [ "$verbose" = "YES" ]; then echo "Compare namelists for $file"; fi
+         if [ "$fileA" = "$fileB" ]; then
+            echo "Comparing files to themself:"
+            echo "fileA = $fileA"
+            echo "fileB = $fileB"
+            exit 1
+         fi
+         $cwd/../../cime/CIME/Tools/compare_namelists $fileA $fileB
+      fi
+    fi
 done
 if [ "$verbose" = "YES" ]; then echo "Successfully ran through lnd_in files to compare"; fi
\ No newline at end of file

From 24e9e191f17abf3dae0c2cffa91a620ad9baedcc Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 29 Apr 2024 18:26:14 -0600
Subject: [PATCH 0143/1248] Temporary updates of raw pft data in
 gen_mksurfdata_namelist.xml

---
 .../gen_mksurfdata_namelist.xml               | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index 32fb7d51bf..f4318880ea 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -10,7 +10,7 @@
 
   <mksrf_flai>
     <entry>
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c20230226/mksrf_pftlaihgt_ctsm52_histLUH2_2005.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histMKSRFDeg025_231228/mksrf_landuse_ctsm52_pftlai_CLIM.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
     <entry pft_years="2005" hires_pft='on'>
@@ -25,7 +25,7 @@
 
   <mksrf_fsoicol>
     <entry>
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c20230226/mksrf_soilcolor_ctsm52_histLUH2_2005.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histMKSRFDeg025_231228/mksrf_landuse_ctsm52_soilcolor_CLIM.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
     <entry pft_years="2005" hires_pft='on'>
@@ -221,14 +221,14 @@ version of the raw dataset will probably go away.
     </entry>
 
     <entry pft_years="1850">
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c20230226/mksrf_landuse_ctsm52_histLUH2_1850.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histLUH2Deg025_231228/mksrf_landuse_ctsm52_histLUH2_1850.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_1850.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
     </entry>
 
     <entry pft_years="2000">
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c20230226/mksrf_landuse_ctsm52_histLUH2_2000.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histLUH2Deg025_231228/mksrf_landuse_ctsm52_histLUH2_2000.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_2000.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_2000_cdf5_c20220910.nc</urban_filename>
@@ -258,7 +258,7 @@ version of the raw dataset will probably go away.
 
     <!-- Historical period from 1850 to 2015 -->
     <entry pft_years="1850-2015" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c20230226/mksrf_landuse_ctsm52_histLUH2_%y.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histLUH2Deg025_231228/mksrf_landuse_ctsm52_histLUH2_%y.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_%y_cdf5_c20220910.nc</urban_filename>
@@ -272,7 +272,7 @@ version of the raw dataset will probably go away.
 
     <!-- SSP1-RCP 2.6 -->
     <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2016-2100" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP1-2.6.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP1-2.6_%y.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP126Deg025_231228/mksrf_landuse_ctsm52_SSP126_%y.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
@@ -285,21 +285,21 @@ version of the raw dataset will probably go away.
     </entry>
     <!-- SSP1-RCP 1.9 -->
     <entry  ssp_rcp="SSP1-1.9" pft_years_ssp="2016-2100" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP1-1.9.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP1-1.9_%y.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP119Deg025_231228/mksrf_landuse_ctsm52_SSP119_%y.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP2-RCP 4.5 -->
     <entry  ssp_rcp="SSP2-4.5" pft_years_ssp="2016-2100" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP2-4.5.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP2-4.5_%y.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP245Deg025_231228/mksrf_landuse_ctsm52_SSP245_%y.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp2/urban_properties_GaoOneil_05deg_ThreeClass_ssp2_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP3-RCP 7.0 -->
     <entry  ssp_rcp="SSP3-7.0" pft_years_ssp="2016-2100" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP3-7.0.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP3-7.0_%y.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP370Deg025_231228/mksrf_landuse_ctsm52_SSP370_2100.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp3/urban_properties_GaoOneil_05deg_ThreeClass_ssp3_%y_cdf5_c20220910.nc</urban_filename>
@@ -313,14 +313,14 @@ version of the raw dataset will probably go away.
     </entry>
     <!-- SSP4-RCP 6.0 -->
     <entry  ssp_rcp="SSP4-6.0" pft_years_ssp="2016-2100" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP4-6.0_%y.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP460Deg025_231228/mksrf_landuse_ctsm52_SSP460_%y.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp4/urban_properties_GaoOneil_05deg_ThreeClass_ssp4_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP5-RCP 8.5 -->
     <entry  ssp_rcp="SSP5-8.5" pft_years_ssp="2016-2100" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP5-8.5.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP5-8.5_%y.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP585Deg025_231228/mksrf_landuse_ctsm52_SSP585_%y.c231228.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp5/urban_properties_GaoOneil_05deg_ThreeClass_ssp5_%y_cdf5_c20220910.nc</urban_filename>

From b767a82b5eb448817e2e36609bde1633e105e358 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Apr 2024 18:59:30 -0600
Subject: [PATCH 0144/1248] Start adding the unit testing for dust emission in
 cmeps

---
 Externals.cfg                                 |  2 +-
 src/CMakeLists.txt                            |  4 ++
 src/drv_test/CMakeLists.txt                   |  1 +
 .../shr_dust_emis_test/CMakeLists.txt         |  3 ++
 .../shr_dust_emis_test/test_shr_dust_emis.pf  | 50 +++++++++++++++++++
 5 files changed, 59 insertions(+), 1 deletion(-)
 create mode 100644 src/drv_test/CMakeLists.txt
 create mode 100644 src/drv_test/shr_dust_emis_test/CMakeLists.txt
 create mode 100644 src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf

diff --git a/Externals.cfg b/Externals.cfg
index 1aa8991883..70c0bd6124 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -50,7 +50,7 @@ required = True
 [cmeps]
 #tag = cmeps0.14.50
 #branch = dust_emis_mod
-hash = d79e34f67df825f9265bdaaf3091f8995d5df1a2
+hash = 492faf0014ad9d91c22bb92e2570e558a76093fe
 protocol = git
 #repo_url = https://github.com/ESCOMP/CMEPS.git
 repo_url = https://github.com/ekluzek/CMEPS.git
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9d2e6041b5..9388e65bc2 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -105,3 +105,7 @@ add_subdirectory(${CLM_ROOT}/src/dyn_subgrid/test clm_dyn_subgrid_test)
 add_subdirectory(${CLM_ROOT}/src/main/test clm_main_test)
 add_subdirectory(${CLM_ROOT}/src/init_interp/test clm_init_interp_test)
 add_subdirectory(${CLM_ROOT}/src/self_tests/test clm_self_tests_test)
+
+# Add driver unit test directories
+add_subdirectory(${CLM_ROOT}/src/drv_test drv_test)
+
diff --git a/src/drv_test/CMakeLists.txt b/src/drv_test/CMakeLists.txt
new file mode 100644
index 0000000000..adf66b8b92
--- /dev/null
+++ b/src/drv_test/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(shr_dust_emis_test)
diff --git a/src/drv_test/shr_dust_emis_test/CMakeLists.txt b/src/drv_test/shr_dust_emis_test/CMakeLists.txt
new file mode 100644
index 0000000000..21fb9c8d47
--- /dev/null
+++ b/src/drv_test/shr_dust_emis_test/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_pfunit_ctest(dust_emis
+  TEST_SOURCES "test_shr_dust_emis.pf"
+  LINK_LIBRARIES clm csm_share)
diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
new file mode 100644
index 0000000000..aa60427eac
--- /dev/null
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -0,0 +1,50 @@
+module test_shr_dust_emis
+
+  ! Tests of shr_dust_emis_mod.F90 from CMEPS nuopc_cap_share
+
+  use funit
+  use shr_dust_emis_mod, only : check_if_initialized
+  use unittestUtils, only : endrun_msg
+
+  implicit none
+
+  @TestCase
+  type, extends(TestCase) :: TestDustEmis
+   contains
+     procedure :: setUp
+     procedure :: tearDown
+  end type TestDustEmis
+
+contains
+
+  ! ========================================================================
+  ! Helper routines
+  ! ========================================================================
+
+  subroutine setUp(this)
+    class(TestDustEmis), intent(inout) :: this
+  end subroutine setUp
+
+  subroutine tearDown(this)
+    class(TestDustEmis), intent(inout) :: this
+
+  end subroutine tearDown
+
+
+
+  ! ========================================================================
+  ! Begin tests
+  ! ========================================================================
+
+   @Test
+  subroutine check_if_initialized_aborts(this)
+    ! Test that the check_if_initialized check aborts when called initially
+    class(TestDustEmis), intent(inout) :: this
+
+    call check_if_initialized()
+    @assertExceptionRaised(endrun_msg('ERROR: dust emission namelist has NOT been read in yet, shr_dust_emis_mod is NOT initialized') )
+
+  end subroutine check_if_initialized_aborts
+
+ 
+end module test_shr_dust_emis

From 82704fe7e86aa68f2bd7254d83bb62c53f4aabeb Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 09:21:16 -0600
Subject: [PATCH 0145/1248] Change call to is_NOT_initialized function, unit
 test works

---
 src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index aa60427eac..a619618e1d 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -3,7 +3,7 @@ module test_shr_dust_emis
   ! Tests of shr_dust_emis_mod.F90 from CMEPS nuopc_cap_share
 
   use funit
-  use shr_dust_emis_mod, only : check_if_initialized
+  use shr_dust_emis_mod, only : is_NOT_initialized
   use unittestUtils, only : endrun_msg
 
   implicit none
@@ -40,9 +40,11 @@ contains
   subroutine check_if_initialized_aborts(this)
     ! Test that the check_if_initialized check aborts when called initially
     class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
 
-    call check_if_initialized()
+    not_init = is_NOT_initialized()
     @assertExceptionRaised(endrun_msg('ERROR: dust emission namelist has NOT been read in yet, shr_dust_emis_mod is NOT initialized') )
+    @assertTrue(not_init)
 
   end subroutine check_if_initialized_aborts
 

From 118010da9524fa08401ba6af3c2b6be560b0d2c7 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 10:51:45 -0600
Subject: [PATCH 0146/1248] add a test that is expected to fail

---
 .../shr_dust_emis_test/test_shr_dust_emis.pf      | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index a619618e1d..646b3cfce1 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -3,8 +3,8 @@ module test_shr_dust_emis
   ! Tests of shr_dust_emis_mod.F90 from CMEPS nuopc_cap_share
 
   use funit
-  use shr_dust_emis_mod, only : is_NOT_initialized
-  use unittestUtils, only : endrun_msg
+  use shr_dust_emis_mod
+  use unittestUtils    , only : endrun_msg
 
   implicit none
 
@@ -48,5 +48,16 @@ contains
 
   end subroutine check_if_initialized_aborts
 
+   @Test
+  subroutine check_when_initialized_runs(this)
+    ! Test that the initializiation check runs when it is initialized
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'Zender_2003', 'lnd')
+    not_init = is_NOT_initialized()
+    @assertFalse(not_init)
+
+  end subroutine check_when_initialized_runs
  
 end module test_shr_dust_emis

From 516d14721ae3f29c40316c6fb7fbd4fd7d9970d2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 11:10:03 -0600
Subject: [PATCH 0147/1248] Update cmeps version so will work

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index 70c0bd6124..3753aac874 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -50,7 +50,7 @@ required = True
 [cmeps]
 #tag = cmeps0.14.50
 #branch = dust_emis_mod
-hash = 492faf0014ad9d91c22bb92e2570e558a76093fe
+hash = ecb6d45aa00a4960564ea963b00754fb4c3b7d2c
 protocol = git
 #repo_url = https://github.com/ESCOMP/CMEPS.git
 repo_url = https://github.com/ekluzek/CMEPS.git

From 5cf5dc04734ff81fc77b43e8a003af826e9553a4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 14:31:23 -0600
Subject: [PATCH 0148/1248] Add more tests that pass

---
 .../shr_dust_emis_test/test_shr_dust_emis.pf  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index 646b3cfce1..efe6a5c2a8 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -60,4 +60,35 @@ contains
 
   end subroutine check_when_initialized_runs
  
+   @Test
+  subroutine check_dust_emis(this)
+    ! Test that the dust_emis logical functions work as expected
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'Zender_2003', 'lnd')
+    @assertTrue( is_dust_emis_zender() )
+    @assertFalse( is_dust_emis_leung() )
+    call dust_emis_set_options( 'Leung_2023', 'lnd')
+    @assertFalse( is_dust_emis_zender() )
+    @assertTrue( is_dust_emis_leung() )
+
+  end subroutine check_dust_emis
+
+   
+  @Test
+  subroutine check_zender_soil(this)
+    ! Test that the dust_emis_Zender logical functions work as expected
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'Zender_2003', 'lnd')
+    @assertTrue( is_zender_soil_erod_from_land() )
+    @assertFalse( is_zender_soil_erod_from_atm() )
+    call dust_emis_set_options( 'Zender_2003', 'atm')
+    @assertFalse( is_zender_soil_erod_from_land() )
+    @assertTrue( is_zender_soil_erod_from_atm() )
+
+  end subroutine check_zender_soil
+ 
 end module test_shr_dust_emis

From de8406be596eb73e593645190d5e8eb1f839c357 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 30 Apr 2024 17:11:38 -0600
Subject: [PATCH 0149/1248] Update namelist_defaults_ctsm.xml for 1979 fsurdat
 files

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index ac4f7252d2..6b98dc1482 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1428,14 +1428,6 @@ lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c24
 <fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" >
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240221.nc</fsurdat>
 
-<!-- for 1979 simulations (SSP2 label is irrelevant in these files) -->
-<fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="1979">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979_78pfts_c240425.nc</fsurdat>
-<fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="1979">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979_78pfts_c240425.nc</fsurdat>
-<fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="1979">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4CONUS.ne30x8_SSP2-4.5_1979_78pfts_c240425.nc</fsurdat>
-
 <!-- for pre-industrial simulations - year 1850 -->
 
 <fsurdat hgrid="360x720cru"  sim_year="1850">
@@ -1477,11 +1469,11 @@ lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240216.n
 <fsurdat hgrid="ne120np4.pg3"             sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne120np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1979_78pfts_c240425.nc</fsurdat>
 <fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4CONUS.ne30x8_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
 
 <!-- Potential vegetation land use dataset, crop is off, and zeroed, all areas are natural vegetation without human disturbance -->
 <fsurdat hgrid="0.9x1.25" sim_year="PtVg" use_crop=".false."

From 99d710015b83ebed8082a5ca0a980f317403bd77 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 30 Apr 2024 17:22:15 -0600
Subject: [PATCH 0150/1248] Draft modifications to address new compset and new
 test for 1979-2026

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++---
 cime_config/config_component.xml              | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 6b98dc1482..2f3a7efd72 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1572,11 +1572,11 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
-<flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" ssp_rcp="SSP2-4.5"
+<flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" ssp_rcp="SSP2-4.5"
+<flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" ssp_rcp="SSP2-4.5"
+<flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
 
 <!-- SSP3-RCP7.0 - relative to {csmdata}) -->
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index f7adab268f..984ba5ecdf 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -210,6 +210,7 @@
       <value compset="^SSP370_"	                    >1850-2100_SSP3-7.0_transient</value>
       <value compset="^SSP534_"	                    >1850-2100_SSP5-3.4_transient</value>
       <value compset="^SSP245_"	                    >1850-2100_SSP2-4.5_transient</value>
+      <value compset="^HIST_ne0np4"                 >1850-2100_SSP2-4.5_transient</value>
       <value compset="^SSP119_"	                    >1850-2100_SSP1-1.9_transient</value>
       <value compset="^SSP434_"	                    >1850-2100_SSP4-3.4_transient</value>
       <value compset="^SSP460_"	                    >1850-2100_SSP4-6.0_transient</value>

From 75cdcd24a4c19ec66aa53fc895b17090c35f6a7a Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 30 Apr 2024 17:38:27 -0600
Subject: [PATCH 0151/1248] Improve a comment in namelist_defaults_ctsm.xml

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 2f3a7efd72..0f533a56ff 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1498,7 +1498,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/surfdata_esmf/NEON/landuse.timeseries_NEON_${NEONSITE}_hist_78pfts_simyr2018-2023_c230931.nc</flanduse_timeseries>
 -->
 
-<!-- Historical 1850-2000 (SSP2 label is irrelevant in these files) -->
+<!-- Historical 1850-2000 -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000"
  >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000"

From c06306031518a79eba39dbbc94cf0c70162f44ae Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 30 Apr 2024 17:44:17 -0600
Subject: [PATCH 0152/1248] Request same #tasks in Makefile as when I generated
 the ne0np4 files

...which I generated manually one at a time
---
 tools/mksurfdata_esmf/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mksurfdata_esmf/Makefile b/tools/mksurfdata_esmf/Makefile
index 00e90efa45..d8bacdc5dd 100644
--- a/tools/mksurfdata_esmf/Makefile
+++ b/tools/mksurfdata_esmf/Makefile
@@ -320,7 +320,7 @@ crop-global-SSP2-4.5-ne30 : FORCE
 	$(BATCHJOBS) $@.sh
 
 crop-global-SSP2-4.5-ne0np4 : FORCE
-	$(MKSURFDATA)  --number-of-nodes 9 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
+	$(MKSURFDATA)  --number-of-nodes 2 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
 	$(BATCHJOBS) $@.sh
 
 crop-global-SSP2-4.5-C96 : FORCE

From c2d226c20c1ae3cbbf5f3e2b91a7bee67fd0e5aa Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 1 May 2024 13:50:29 -0600
Subject: [PATCH 0153/1248] Add new tests and get working again

---
 .../shr_dust_emis_test/test_shr_dust_emis.pf  | 22 ++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index efe6a5c2a8..467d00de59 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -69,7 +69,7 @@ contains
     call dust_emis_set_options( 'Zender_2003', 'lnd')
     @assertTrue( is_dust_emis_zender() )
     @assertFalse( is_dust_emis_leung() )
-    call dust_emis_set_options( 'Leung_2023', 'lnd')
+    call dust_emis_set_options( 'Leung_2023', 'none')
     @assertFalse( is_dust_emis_zender() )
     @assertTrue( is_dust_emis_leung() )
 
@@ -90,5 +90,25 @@ contains
     @assertTrue( is_zender_soil_erod_from_atm() )
 
   end subroutine check_zender_soil
+
+     
+  @Test
+  subroutine check_options(this)
+    ! Test that the check_options subroutine catches errors that should die
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'zztop', 'zztop')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: dust_emis_method namelist item is not valid'))
+    call dust_emis_set_options( 'Leung_2023', 'lnd')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source should NOT be set, when dust_emis_method=Leung_2023'))
+    call dust_emis_set_options( 'Leung_2023', 'atm')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source should NOT be set, when dust_emis_method=Leung_2023'))
+    call dust_emis_set_options( 'Zender_2003', 'none')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source can only be lnd or atm'))
+    call dust_emis_set_options( 'Zender_2003', 'zztop')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source can only be lnd or atm'))
+
+  end subroutine check_options
  
 end module test_shr_dust_emis

From 0ff68d77dc824f6dbb0c8f6cac0a9ec3773e0b8c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 1 May 2024 14:05:25 -0600
Subject: [PATCH 0154/1248] Update cmeps with unit-testing completed

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index 3753aac874..39818b0fdc 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -50,7 +50,7 @@ required = True
 [cmeps]
 #tag = cmeps0.14.50
 #branch = dust_emis_mod
-hash = ecb6d45aa00a4960564ea963b00754fb4c3b7d2c
+hash = 0285eeb59605df44bc3abf38a61e8436361e7e8c
 protocol = git
 #repo_url = https://github.com/ESCOMP/CMEPS.git
 repo_url = https://github.com/ekluzek/CMEPS.git

From fffb79409b29ed741c119d9fb37496898a689cd9 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 1 May 2024 15:46:26 -0700
Subject: [PATCH 0155/1248] add use_fates_lupft switch

---
 bld/CLMBuildNamelist.pm                       | 25 +++++++++++++++++++
 bld/namelist_files/namelist_defaults_ctsm.xml | 18 +++++++------
 .../namelist_definition_ctsm.xml              |  6 +++++
 src/main/clm_varctl.F90                       |  1 +
 src/main/controlMod.F90                       |  3 +++
 src/utils/clmfates_interfaceMod.F90           | 16 ++++--------
 6 files changed, 51 insertions(+), 18 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 7e2e4294af..021381a18e 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4414,6 +4414,31 @@ sub setup_logic_fates {
               }
            }
         }
+        # make sure that fates landuse x pft mode has the necessary run mode configurations
+        # and add the necessary landuse x pft static mapping data default if not defined
+        my $var = "use_fates_lupft";
+        if ( defined($nl->get_value($var))  ) {
+          if ( &value_is_true($nl->get_value($var)) ) {
+            $var = "flandusepftdat";
+            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
+                        'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
+            my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+            if ( ! defined($nl->get_value($var))  ) {
+              fatal_error("$var is required when use_fates_lupft is set" );
+            } elsif ( ! -f "$fname" ) {
+              fatal_error("$fname does NOT point to a valid filename" );
+            }
+          }
+          # make sure that nocomp and fbg mode are enabled as well as use_fates_luh
+          my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" );
+          foreach my $var ( @list ) {
+            if ( ! &value_is_true($nl->get_value($var)) ) {
+              fatal_error("$var is required when use_fates_lupft is true" );
+            }
+          }
+        }
+        # check that fates landuse change mode has the necessary luh2 landuse timeseries data
+        # and add the default if not defined
         my $var = "use_fates_luh";
         if ( defined($nl->get_value($var))  ) {
            if ( &value_is_true($nl->get_value($var)) ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 66c0f837e0..49109c6591 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2767,17 +2767,21 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
 <use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
+<use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="3">.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="4">.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true.">.false.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="3"  >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="4"  >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true."                         >.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 
-<use_fates_nocomp              use_fates=".true." use_fates_sp=".true.">.true.</use_fates_nocomp>
-<use_fates_nocomp              use_fates=".true."                      >.false.</use_fates_nocomp>
-<use_fates_fixed_biogeog       use_fates=".true." use_fates_sp=".true.">.true.</use_fates_fixed_biogeog>
-<use_fates_fixed_biogeog       use_fates=".true."                      >.false.</use_fates_fixed_biogeog>
+<use_fates_nocomp              use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>
+<use_fates_nocomp              use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
+<use_fates_nocomp              use_fates=".true."                         >.false.</use_fates_nocomp>
+<use_fates_fixed_biogeog       use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_fixed_biogeog>
+<use_fates_fixed_biogeog       use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_fixed_biogeog>
+<use_fates_fixed_biogeog       use_fates=".true."                         >.false.</use_fates_fixed_biogeog>
 
 <!-- =========================================  -->
 <!-- Defaults for dynamic subgrid               -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index fa2d83a3c9..a2df9b1d1e 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -791,6 +791,12 @@ data (fates_harvest_mode >= 3)
 (Also, only valid for use_fates = true and is incompatible with transient runs currently.)
 </entry>
 
+<entry id="use_fates_lupft" type="logical" category="physics"
+       group="elm_inparm" valid_values="" value=".false.">
+If TRUE, enable use of fates land use x pft mapping data file.
+(Only valid for use_fates = true and is incompatible with transient runs currently.)
+</entry>
+
 <entry id="use_fates_potentialveg" type="logical" category="physics"
        group="clm_inparm" valid_values="" >
 If TRUE, ignore the land-use state vector and transitions, and assert that all lands
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 9ab6c631c7..64d6e15747 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -311,6 +311,7 @@ module clm_varctl
   logical, public            :: use_fates_fixed_biogeog = .false.       ! true => use fixed biogeography mode
   logical, public            :: use_fates_nocomp = .false.              ! true => use no comopetition mode
   logical, public            :: use_fates_luh = .false.                 ! true => use FATES landuse data mode
+  logical, public            :: use_fates_lupft = .false.               ! true => use FATES landuse x pft static mapping mode
   logical, public            :: use_fates_potentialveg = .false.        ! true => FATES potential veg only
   character(len=256), public :: fluh_timeseries = ''                    ! filename for fates landuse timeseries data
   character(len=256), public :: flandusepftdat = ''                     ! filename for fates landuse x pft data
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 196bc141ff..55dd92305d 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -231,6 +231,7 @@ subroutine control_init(dtime)
           use_fates_nocomp,                             &
           use_fates_sp,                                 &
           use_fates_luh,                                &
+          use_fates_lupft,                              &
           use_fates_potentialveg,                       &
           fluh_timeseries,                              &
           flandusepftdat,                               &
@@ -785,6 +786,7 @@ subroutine control_spmd()
     call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_luh, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (use_fates_lupft, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_potentialveg, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier)
@@ -1161,6 +1163,7 @@ subroutine control_print ()
        write(iulog, *) '    use_fates_nocomp = ', use_fates_nocomp
        write(iulog, *) '    use_fates_sp = ', use_fates_sp
        write(iulog, *) '    use_fates_luh= ', use_fates_luh
+       write(iulog, *) '    use_fates_lupft= ', use_fates_lupft
        write(iulog, *) '    use_fates_potentialveg = ', use_fates_potentialveg
        write(iulog, *) '    fluh_timeseries = ', trim(fluh_timeseries)
        write(iulog, *) '    flandusepftdat = ', trim(flandusepftdat)
diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 3f84a28508..b0ae0044f3 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -60,6 +60,7 @@ module CLMFatesInterfaceMod
    use clm_varctl        , only : use_fates_nocomp
    use clm_varctl        , only : use_fates_sp
    use clm_varctl        , only : use_fates_luh
+   use clm_varctl        , only : use_fates_lupft
    use clm_varctl        , only : use_fates_potentialveg
    use clm_varctl        , only : flandusepftdat
    use clm_varctl        , only : fates_seeddisp_cadence
@@ -567,13 +568,6 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg)
 
-        if(flandusepftdat /= '') then
-           pass_lupftdat = 1
-        else
-           pass_lupftdat = 0
-        end if
-        call set_fates_ctrlparms('use_landusepft_data',ival=pass_lupftdat)
-
         ! Wait to set the harvest and logging variables after checking get_do_harvest
         ! and fates_harvest_modes
         call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest)
@@ -710,7 +704,7 @@ subroutine init(this, bounds_proc, flandusepftdat)
       end if
 
       ! Retrieve the landuse x pft static data if the file is present
-      if (flandusepftdat /= '') then
+      if (use_fates_lupft) then
          call GetLandusePFTData(bounds_proc, flandusepftdat, landuse_pft_map, landuse_bareground)
       end if
 
@@ -821,12 +815,12 @@ subroutine init(this, bounds_proc, flandusepftdat)
             this%fates(nc)%sites(s)%lon = grc%londeg(g)
 
             ! Transfer the landuse x pft data to fates via bc_in if file is given
-            if (flandusepftdat /= '') then
+            if (use_fates_lupft) then
                this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars)
                this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g)
             end if
 
-            if (flandusepftdat == '') then
+            if (.not. use_fates_lupft) then
                ! initialize static layers for reduced complexity FATES versions from HLM
                ! maybe make this into a subroutine of it's own later.
                this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8
@@ -882,7 +876,7 @@ subroutine init(this, bounds_proc, flandusepftdat)
       call create_fates_fire_data_method( this%fates_fire_data_method )
 
       ! deallocate the local landuse x pft array
-      if (flandusepftdat /= '') then
+      if (use_fates_lupft) then
          deallocate(landuse_pft_map)
          deallocate(landuse_bareground)
       end if

From 5d11bcf5c1ad64bb8898e54f15852315439c5d57 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 1 May 2024 15:52:27 -0700
Subject: [PATCH 0156/1248] add fates use_potentialveg namelist defaults
 settings and checks

---
 bld/CLMBuildNamelist.pm                       | 13 ++++++++++++-
 bld/namelist_files/namelist_defaults_ctsm.xml |  9 +++++----
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 021381a18e..7999e9a31d 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4455,7 +4455,18 @@ sub setup_logic_fates {
               add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
            }
         }
-
+        # check that fates landuse is on and harvest mode is off when potential veg switch is true
+        my $var = "use_potentialveg";
+        if ( defined($nl->get_value($var))  ) {
+          if ( &value_is_true($nl->get_value($var)) ) {
+            if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
+              fatal_error("use_fates_luh must be true when $var is true" );
+            }
+            if ( $nl->get_value('fates_harvest_mode') > 0) {
+              fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" );
+            }
+          }
+        }
         # Check fates_harvest_mode compatibility
         my $var = "fates_harvest_mode";
         if ( defined($nl->get_value($var))  ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 49109c6591..68a122e9bc 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2769,10 +2769,11 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="3"  >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="4"  >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true."                         >.false.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="3"         >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="4"         >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." use_fates_lupft=".true."       >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true."                                >.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 

From f0f2b9e17c17cc095832e4439313192fdea28a75 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 1 May 2024 16:58:18 -0600
Subject: [PATCH 0157/1248] Additional conflict resolution in testlist_clm.xml

---
 cime_config/testdefs/testlist_clm.xml | 35 +--------------------------
 1 file changed, 1 insertion(+), 34 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index d3ee1eae35..ff3d113c53 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -955,14 +955,6 @@
       <option name="comment"  >Repeat last ERP_D_Ld5_P48x1...ciso test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart">
-    <machines>
-      <machine name="izumi" compiler="nag" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -981,14 +973,6 @@
       <option name="comment"  >Repeat ERP_D_Ld10_P64x2...ciso_decStart test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1062,15 +1046,6 @@
       <option name="comment"  >Repeat last ERP_D_P64x2_Ld3...default test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/coldStart">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-      <machine name="derecho" compiler="intel" category="clm_short"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/coldStart">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1088,14 +1063,6 @@
       <option name="comment"  >Repeat last ERP_D_P64x2_Ld3...coldStart test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/mimics">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="SMS_D" grid="1x1_brazil" compset="I1850Clm60BgcCrop" testmods="clm/mimics_matrixcn">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -2875,7 +2842,7 @@
 
     </machines>
   </test>
-  <test name="ERP_P24x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpBgcCropGswp" testmods="clm/default">
+  <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpBgcCropGswp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>

From 4c07dcc2a5079a0d30cca0c520632f24925ea789 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 1 May 2024 18:50:43 -0600
Subject: [PATCH 0158/1248] Add basic script to compare testlist baseline
 lnd_in files

---
 bld/unit_testers/cmp_baseline_lnd_in_files.sh | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100755 bld/unit_testers/cmp_baseline_lnd_in_files.sh

diff --git a/bld/unit_testers/cmp_baseline_lnd_in_files.sh b/bld/unit_testers/cmp_baseline_lnd_in_files.sh
new file mode 100755
index 0000000000..de32cddf76
--- /dev/null
+++ b/bld/unit_testers/cmp_baseline_lnd_in_files.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+baseline=$1
+compare=$2
+
+cwd=`pwd`
+if [ -z "$1" ]; then
+   echo "Need to enter a baseline directory tag name"
+   exit 1
+fi
+if [ -z "$2" ]; then
+   echo "Need to enter a comparison directory tag name"
+   exit 1
+fi
+
+BASELINE_ROOT=/glade/campaign/cgd/tss/ctsm_baselines
+root=$BASELINE_ROOT/$baseline
+if ! test -d "$root"; then
+   echo "Root directory of $root does NOT exist"
+   exit 1
+fi
+comp_root=$BASELINE_ROOT/$compare
+if ! test -d "$comp_root"; then
+   echo "Root comparison directory of $comp_root does NOT exist"
+   exit 1
+fi
+cd $root
+filepat="*"
+dirnames=($filepat)
+if [ "${filenames[*]}" = "$filepat" ]; then
+   echo "No directoctories exist in this directory"
+   exit 1
+fi
+for dir in ${dirnames[*]}
+do
+   echo $dir
+   base=$dir/CaseDocs/lnd_in
+   comp=$BASELINE_ROOT/$compare/$dir/CaseDocs/lnd_in
+   if ! test -f "$base"; then
+      echo "$base, does NOT exist, skipping"
+   elif ! test -f "$comp"; then
+      echo "$comp, does NOT exist, skipping"
+   else
+      $cwd/../../cime/CIME/Tools/compare_namelists $base $comp
+   fi
+done

From 5192bd1520f93a00f085d31b266e3913f722652e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 1 May 2024 22:16:32 -0600
Subject: [PATCH 0159/1248] Fix for #2504 so tests of use-cases is done, and
 also done over all physics options

---
 bld/unit_testers/build-namelist_test.pl | 44 +++++++++++++++----------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 7b654337af..74dbcef3f4 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 2513;
+my $ntests = 3665;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1545;
+   $ntests += 2313;
 }
 plan( tests=>$ntests );
 
@@ -1421,32 +1421,40 @@ sub cat_and_create_namelistinfile {
 }
 
 print "\n==================================================\n";
-print " Rest all use-cases \n";
+print " Test all use-cases over all physics options\n";
 print "==================================================\n";
 
 # Run over all use-cases...
 my $list = `$bldnml -use_case list 2>&1 | grep "use case"`;
 my @usecases;
 if ( $list =~ /build-namelist : use cases : (.+)$/ ) {
-  my @usecases  = split( / /, $list );
+  @usecases  = split( / /, $1 );
 } else {
   die "ERROR:: Trouble getting list of use-cases\n";
 }
-foreach my $usecase ( @usecases ) {
-   $options = "-use_case $usecase  -envxml_dir .";
-   &make_env_run();
-   eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
-   is( $@, '', "options: $options" );
-   $cfiles->checkfilesexist( "$options", $mode );
-   $cfiles->shownmldiff( "default", "standard" );
-   if ( defined($opts{'compare'}) ) {
-      $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
-   }
-   if ( defined($opts{'generate'}) ) {
-      $cfiles->copyfiles( "$options", $mode );
+if ( $#usecases != 15 ) {
+  print "use-cases = @usecases\n";
+  die "ERROR:: Number of use-cases isn't what's expected\n";
+}
+foreach my $phys ( "clm4_5", "clm5_0", "clm5_1", "clm6_0" ) {
+   print "physics = $phys\n";
+   foreach my $usecase ( @usecases ) {
+      print "usecase = $usecase\n";
+      $options = "-use_case $usecase  -envxml_dir .";
+      &make_env_run();
+      eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
+      is( $@, '', "options: $options" );
+      $cfiles->checkfilesexist( "$options", $mode );
+      $cfiles->shownmldiff( "default", "standard" );
+      if ( defined($opts{'compare'}) ) {
+         $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+         $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+      }
+      if ( defined($opts{'generate'}) ) {
+         $cfiles->copyfiles( "$options", $mode );
+      }
+      &cleanup();
    }
-   &cleanup();
 }
 
 print "\n==================================================\n";

From 480ae1b5ce1557f1848447bd8981690a25bbeaa1 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 2 May 2024 00:53:17 -0600
Subject: [PATCH 0160/1248] Simplify and correct the use-cases, with this the
 difference between clm5_1 and clm6_0 physics options is only the params_file
 which is what's expected this finishes out issues in #2492

---
 bld/namelist_files/use_cases/1850_control.xml | 45 +++------------
 .../use_cases/1850_noanthro_control.xml       | 33 ++---------
 bld/namelist_files/use_cases/2000_control.xml | 38 +++----------
 bld/namelist_files/use_cases/2010_control.xml | 45 +++------------
 .../use_cases/20thC_transient.xml             | 56 +++++--------------
 bld/namelist_files/use_cases/stdurbpt_pd.xml  |  8 +--
 6 files changed, 50 insertions(+), 175 deletions(-)

diff --git a/bld/namelist_files/use_cases/1850_control.xml b/bld/namelist_files/use_cases/1850_control.xml
index 94ee8c5d0d..6ea033629f 100644
--- a/bld/namelist_files/use_cases/1850_control.xml
+++ b/bld/namelist_files/use_cases/1850_control.xml
@@ -8,47 +8,18 @@
 
 <sim_year_range>constant</sim_year_range>
 
-<irrigate use_crop=".true." phys="clm5_1">.false.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0" >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm4_5" >.false.</irrigate>
+<irrigate use_crop=".true." >.false.</irrigate>
 
-<stream_year_first_ndep phys="clm4_5" use_cn=".true." >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm4_5" use_cn=".true." >1850</stream_year_last_ndep>
+<stream_year_first_ndep use_cn=".true." >1850</stream_year_first_ndep>
+<stream_year_last_ndep  use_cn=".true." >1850</stream_year_last_ndep>
 
-<stream_year_first_ndep phys="clm5_0" use_cn=".true." >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_0" use_cn=".true." >1850</stream_year_last_ndep>
+<stream_year_first_popdens cnfireson=".true." >1850</stream_year_first_popdens>
+<stream_year_last_popdens  cnfireson=".true." >1850</stream_year_last_popdens>
 
-<stream_year_first_ndep phys="clm5_1" use_cn=".true." >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_1" use_cn=".true." >1850</stream_year_last_ndep>
+<stream_year_first_urbantv >1850</stream_year_first_urbantv>
+<stream_year_last_urbantv  >1850</stream_year_last_urbantv>
 
-<stream_year_first_popdens phys="clm4_5" cnfireson=".true." >1850</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm4_5" cnfireson=".true." >1850</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_0" cnfireson=".true." >1850</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_0" cnfireson=".true." >1850</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_1" cnfireson=".true." >1850</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_1" cnfireson=".true." >1850</stream_year_last_popdens>
-
-<stream_year_first_urbantv phys="clm4_5"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm4_5"  >1850</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm5_0"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0"  >1850</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm5_1"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_1"  >1850</stream_year_last_urbantv>
-
-<stream_fldfilename_ndep phys="clm5_1" use_cn=".true."
->lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc</stream_fldfilename_ndep>
-
-<stream_fldfilename_ndep phys="clm5_0" use_cn=".true."
->lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc</stream_fldfilename_ndep>
- 
-<stream_fldfilename_ndep phys="clm4_5" use_cn=".true."
+<stream_fldfilename_ndep use_cn=".true."
 >lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc</stream_fldfilename_ndep>
- 
-<ndep_taxmode            phys="clm5_0"  use_cn=".true." >cycle</ndep_taxmode>
-<ndep_taxmode            phys="clm5_1"  use_cn=".true." >cycle</ndep_taxmode>
 
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/1850_noanthro_control.xml b/bld/namelist_files/use_cases/1850_noanthro_control.xml
index 636164a729..d84903f43c 100644
--- a/bld/namelist_files/use_cases/1850_noanthro_control.xml
+++ b/bld/namelist_files/use_cases/1850_noanthro_control.xml
@@ -10,26 +10,11 @@
 
 <irrigate>.false.</irrigate>
 
-<stream_year_first_ndep phys="clm4_5" use_cn=".true." >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm4_5" use_cn=".true." >1850</stream_year_last_ndep>
+<stream_year_first_ndep use_cn=".true." >1850</stream_year_first_ndep>
+<stream_year_last_ndep  use_cn=".true." >1850</stream_year_last_ndep>
 
-<stream_year_first_ndep phys="clm5_0" use_cn=".true." >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_0" use_cn=".true." >1850</stream_year_last_ndep>
-
-<stream_year_first_ndep phys="clm5_1"  use_cn=".true.">1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_1"  use_cn=".true.">1850</stream_year_last_ndep>
-
-<ndep_taxmode            phys="clm5_0"  use_cn=".true." >cycle</ndep_taxmode>
-<ndep_taxmode            phys="clm5_1"  use_cn=".true." >cycle</ndep_taxmode>
-
-<stream_year_first_popdens phys="clm4_5" cnfireson=".true." >1925</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm4_5" cnfireson=".true." >1925</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_0" cnfireson=".true." >1925</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_0" cnfireson=".true." >1925</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_1"  cnfireson=".true.">1925</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_1"  cnfireson=".true.">1925</stream_year_last_popdens>
+<stream_year_first_popdens cnfireson=".true." >1925</stream_year_first_popdens>
+<stream_year_last_popdens  cnfireson=".true." >1925</stream_year_last_popdens>
 
 <!-- zero population density file -->
 <stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true."
@@ -37,14 +22,8 @@
 <stream_meshfile_popdens hgrid="0.5x0.5"   use_cn=".true.">none</stream_meshfile_popdens>
 <popdensmapalgo use_cn=".true.">nn</popdensmapalgo>
 
-<stream_year_first_urbantv phys="clm5_1"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_1"  >1850</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm5_0"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0"  >1850</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm4_5"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm4_5"  >1850</stream_year_last_urbantv>
+<stream_year_first_urbantv >1850</stream_year_first_urbantv>
+<stream_year_last_urbantv  >1850</stream_year_last_urbantv>
 
 <!-- Turn calculation of human stress indices all the way off to save some CPU -->
 <calc_human_stress_indices     >NONE</calc_human_stress_indices>
diff --git a/bld/namelist_files/use_cases/2000_control.xml b/bld/namelist_files/use_cases/2000_control.xml
index f3c4980fc8..2fce7c5cce 100644
--- a/bld/namelist_files/use_cases/2000_control.xml
+++ b/bld/namelist_files/use_cases/2000_control.xml
@@ -8,37 +8,17 @@
 
 <sim_year_range>constant</sim_year_range>
 
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".false.">.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".true." >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0" use_cndv=".false." >.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0" use_cndv=".true."  >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm4_5"                    >.false.</irrigate>
+<irrigate use_crop=".true." use_cndv=".false.">.true.</irrigate>
+<irrigate use_crop=".true." use_cndv=".true." >.false.</irrigate>
+<irrigate use_crop=".true." phys="clm4_5"     >.false.</irrigate>
 
-<stream_year_first_ndep phys="clm4_5" use_cn=".true." >2000</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm4_5" use_cn=".true." >2000</stream_year_last_ndep>
+<stream_year_first_ndep use_cn=".true." >2000</stream_year_first_ndep>
+<stream_year_last_ndep  use_cn=".true." >2000</stream_year_last_ndep>
 
-<stream_year_first_ndep phys="clm5_0" use_cn=".true." >2000</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_0" use_cn=".true." >2000</stream_year_last_ndep>
+<stream_year_first_popdens cnfireson=".true." >2000</stream_year_first_popdens>
+<stream_year_last_popdens  cnfireson=".true." >2000</stream_year_last_popdens>
 
-<stream_year_first_ndep phys="clm5_1"  use_cn=".true.">2000</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_1"  use_cn=".true.">2000</stream_year_last_ndep>
-
-<stream_year_first_popdens phys="clm4_5" cnfireson=".true." >2000</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm4_5" cnfireson=".true." >2000</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_0" cnfireson=".true." >2000</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_0" cnfireson=".true." >2000</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_1"  cnfireson=".true.">2000</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_1"  cnfireson=".true.">2000</stream_year_last_popdens>
-
-<stream_year_first_urbantv phys="clm4_5" >2000</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm4_5" >2000</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm5_0" >2000</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0" >2000</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm5_1" >2000</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_1" >2000</stream_year_last_urbantv>
+<stream_year_first_urbantv >2000</stream_year_first_urbantv>
+<stream_year_last_urbantv  >2000</stream_year_last_urbantv>
 
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/2010_control.xml b/bld/namelist_files/use_cases/2010_control.xml
index 9316ecfb7f..d4c2a9c9c0 100644
--- a/bld/namelist_files/use_cases/2010_control.xml
+++ b/bld/namelist_files/use_cases/2010_control.xml
@@ -8,44 +8,17 @@
 
 <sim_year_range>constant</sim_year_range>
 
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".false.">.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".false.">.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".true." >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0"  use_cndv=".false.">.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0"  use_cndv=".true." >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm4_5"                    >.false.</irrigate>
+<irrigate use_crop=".true." =".false."    >.true.</irrigate>
+<irrigate use_crop=".true." =".false."    >.true.</irrigate>
+<irrigate use_crop=".true." phys="clm4_5" >.false.</irrigate>
 
-<stream_year_first_ndep phys="clm4_0"  bgc="cn"   >2010</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm4_0"  bgc="cn"   >2010</stream_year_last_ndep>
+<stream_year_first_ndep bgc="cn"   >2010</stream_year_first_ndep>
+<stream_year_last_ndep  bgc="cn"   >2010</stream_year_last_ndep>
 
-<stream_year_first_ndep phys="clm4_0"  bgc="cndv" >2010</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm4_0"  bgc="cndv" >2010</stream_year_last_ndep>
+<stream_year_first_popdens cnfireson=".true." >2010</stream_year_first_popdens>
+<stream_year_last_popdens  cnfireson=".true." >2010</stream_year_last_popdens>
 
-<stream_year_first_ndep phys="clm4_5"  use_cn=".true." >2010</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm4_5"  use_cn=".true." >2010</stream_year_last_ndep>
-
-<stream_year_first_ndep phys="clm5_0"  use_cn=".true." >2010</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_0"  use_cn=".true." >2010</stream_year_last_ndep>
-
-<stream_year_first_ndep phys="clm5_1"  use_cn=".true." >2010</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_1"  use_cn=".true." >2010</stream_year_last_ndep>
-
-<stream_year_first_popdens phys="clm4_5"  cnfireson=".true." >2010</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm4_5"  cnfireson=".true." >2010</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_0"  cnfireson=".true." >2010</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_0"  cnfireson=".true." >2010</stream_year_last_popdens>
-
-<stream_year_first_popdens phys="clm5_1"  cnfireson=".true." >2010</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_1"  cnfireson=".true." >2010</stream_year_last_popdens>
-
-<stream_year_first_urbantv phys="clm5_1"  >2010</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_1"  >2010</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm5_0"  >2010</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0"  >2010</stream_year_last_urbantv>
-
-<stream_year_first_urbantv phys="clm4_5"  >2010</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm4_5"  >2010</stream_year_last_urbantv>
+<stream_year_first_urbantv >2010</stream_year_first_urbantv>
+<stream_year_last_urbantv  >2010</stream_year_last_urbantv>
 
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/20thC_transient.xml b/bld/namelist_files/use_cases/20thC_transient.xml
index d6dd729b35..b88ca3d3b1 100644
--- a/bld/namelist_files/use_cases/20thC_transient.xml
+++ b/bld/namelist_files/use_cases/20thC_transient.xml
@@ -18,46 +18,20 @@
 
 <clm_demand >flanduse_timeseries</clm_demand>
 
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".false.">.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".true." >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0" use_cndv=".false." >.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0" use_cndv=".true."  >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm4_5"                    >.false.</irrigate>
-
-<stream_year_first_ndep phys="clm4_5" use_cn=".true."   >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm4_5" use_cn=".true."   >2015</stream_year_last_ndep>
-<model_year_align_ndep  phys="clm4_5" use_cn=".true."   >1850</model_year_align_ndep>
-
-<stream_year_first_ndep phys="clm5_0" use_cn=".true."   >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_0" use_cn=".true."   >2015</stream_year_last_ndep>
-<model_year_align_ndep  phys="clm5_0" use_cn=".true."   >1850</model_year_align_ndep>
-
-<stream_year_first_ndep phys="clm5_1"  use_cn=".true."  >1850</stream_year_first_ndep>
-<stream_year_last_ndep  phys="clm5_1"  use_cn=".true."  >2015</stream_year_last_ndep>
-<model_year_align_ndep  phys="clm5_1"  use_cn=".true."  >1850</model_year_align_ndep>
-
-<stream_year_first_popdens phys="clm4_5" cnfireson=".true."   >1850</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm4_5" cnfireson=".true."   >2016</stream_year_last_popdens>
-<model_year_align_popdens  phys="clm4_5" cnfireson=".true."   >1850</model_year_align_popdens>
-
-<stream_year_first_popdens phys="clm5_0" cnfireson=".true."   >1850</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_0" cnfireson=".true."   >2016</stream_year_last_popdens>
-<model_year_align_popdens  phys="clm5_0" cnfireson=".true."   >1850</model_year_align_popdens>
-
-<stream_year_first_popdens phys="clm5_1"  cnfireson=".true."  >1850</stream_year_first_popdens>
-<stream_year_last_popdens  phys="clm5_1"  cnfireson=".true."  >2016</stream_year_last_popdens>
-<model_year_align_popdens  phys="clm5_1"  cnfireson=".true."  >1850</model_year_align_popdens>
-
-<stream_year_first_urbantv phys="clm4_5"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm4_5"  >2106</stream_year_last_urbantv>
-<model_year_align_urbantv  phys="clm4_5"  >1850</model_year_align_urbantv>
-
-<stream_year_first_urbantv phys="clm5_0"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0"  >2106</stream_year_last_urbantv>
-<model_year_align_urbantv  phys="clm5_0"  >1850</model_year_align_urbantv>
-
-<stream_year_first_urbantv phys="clm5_1"  >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_1"  >2106</stream_year_last_urbantv>
-<model_year_align_urbantv  phys="clm5_1"  >1850</model_year_align_urbantv>
+<irrigate use_crop=".true."               use_cndv=".false.">.true.</irrigate>
+<irrigate use_crop=".true."               use_cndv=".true." >.false.</irrigate>
+<irrigate use_crop=".true." phys="clm4_5"                   >.false.</irrigate>
+
+<stream_year_first_ndep use_cn=".true."   >1850</stream_year_first_ndep>
+<stream_year_last_ndep  use_cn=".true."   >2015</stream_year_last_ndep>
+<model_year_align_ndep  use_cn=".true."   >1850</model_year_align_ndep>
+
+<stream_year_first_popdens cnfireson=".true."   >1850</stream_year_first_popdens>
+<stream_year_last_popdens  cnfireson=".true."   >2016</stream_year_last_popdens>
+<model_year_align_popdens  cnfireson=".true."   >1850</model_year_align_popdens>
+
+<stream_year_first_urbantv >1850</stream_year_first_urbantv>
+<stream_year_last_urbantv  >2106</stream_year_last_urbantv>
+<model_year_align_urbantv  >1850</model_year_align_urbantv>
 
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/stdurbpt_pd.xml b/bld/namelist_files/use_cases/stdurbpt_pd.xml
index 65786f32ae..6f5e754ba0 100644
--- a/bld/namelist_files/use_cases/stdurbpt_pd.xml
+++ b/bld/namelist_files/use_cases/stdurbpt_pd.xml
@@ -18,10 +18,8 @@
 
 <urban_hac>'OFF'</urban_hac>
 
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".false.">.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_1"  use_cndv=".true." >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0"  use_cndv=".false.">.true.</irrigate>
-<irrigate use_crop=".true." phys="clm5_0"  use_cndv=".true." >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm4_5"                    >.false.</irrigate>
+<irrigate use_crop=".true." use_cndv=".false.">.true.</irrigate>
+<irrigate use_crop=".true." use_cndv=".true." >.false.</irrigate>
+<irrigate use_crop=".true." phys="clm4_5"     >.false.</irrigate>
 
 </namelist_defaults>

From 3900cc438ca9888efa1ae5c31adf7eeab3b0ff49 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Thu, 2 May 2024 10:09:05 -0600
Subject: [PATCH 0161/1248] Fix RH2M_R long_name

---
 src/biogeophys/WaterDiagnosticBulkType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90
index dd556a2df6..f91aaca761 100644
--- a/src/biogeophys/WaterDiagnosticBulkType.F90
+++ b/src/biogeophys/WaterDiagnosticBulkType.F90
@@ -346,7 +346,7 @@ subroutine InitBulkHistory(this, bounds)
          fname=this%info%fname('RH2M_R'), &
          units='%',  &
          avgflag='A', &
-         long_name=this%info%lname('Rural 2m specific humidity'), &
+         long_name=this%info%lname('Rural 2m relative humidity'), &
          ptr_patch=this%rh_ref2m_r_patch, set_spec=spval, default='inactive')
 
     this%rh_ref2m_u_patch(begp:endp) = spval

From feda43c5c4199a1b2981980502a23f7ee489fefa Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Thu, 2 May 2024 11:57:16 -0600
Subject: [PATCH 0162/1248] Fix long name for AZSUN

---
 src/biogeophys/SurfaceAlbedoType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90
index ddb57d88f7..e90caeecbb 100644
--- a/src/biogeophys/SurfaceAlbedoType.F90
+++ b/src/biogeophys/SurfaceAlbedoType.F90
@@ -226,7 +226,7 @@ subroutine InitHistory(this, bounds)
 
     this%azsun_grc(begg:endg) = spval
     call hist_addfld1d (fname='AZSUN', units='radians', &
-         avgflag='A', long_name='cosine of solar zenith angle', &
+         avgflag='A', long_name='azimuth angle of the sun', &
          ptr_lnd=this%azsun_grc, default='inactive')
 
     this%coszen_grc(begg:endg) = spval

From 3cc33e59813be988d983cfca47f2e9ef99819f1d Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 2 May 2024 12:24:55 -0600
Subject: [PATCH 0163/1248] Update test to use a valid compset

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index ff3d113c53..cfd81a5a2b 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -830,7 +830,7 @@
       <option name="comment"  >Run in DEBUG with the matrix solution on for spinup with all options it interacts with (requires Bgc, but also turn on Crop and Carbon isotopes)</option>
     </options>
   </test>
-  <test name="ERS_Lm54_Mmpi-serial" grid="1x1_numaIA" compset="I1850Clm50BgcCropQian" testmods="clm/ciso_monthly_matrixcn_spinup">
+  <test name="ERS_Lm54_Mmpi-serial" grid="1x1_numaIA" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>

From 6bd7d37a956edb0fc2bb20f7d593c64e4fa6eb0c Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 2 May 2024 11:49:28 -0700
Subject: [PATCH 0164/1248] add use_fates_lupft to default namelist

---
 bld/CLMBuildNamelist.pm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 7999e9a31d..23505492bd 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -785,7 +785,7 @@ sub setup_cmdl_fates_mode {
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
                       "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat",
-                      "use_fates_potentialveg");
+                      "use_fates_potentialveg","use_fates_lupft");
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -4371,7 +4371,8 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
-                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" );
+                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
+                       "use_fates_luh","use_fates_lupft" );
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );

From 115281fde88bb91999609d77511a8b41df33d403 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Thu, 2 May 2024 13:00:00 -0600
Subject: [PATCH 0165/1248] Updates to history field list documentation in
 User's Guide

---
 .../history_fields_fates.rst                  | 158 +++++++++++-------
 .../history_fields_nofates.rst                |  56 +++++--
 2 files changed, 144 insertions(+), 70 deletions(-)

diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst
index ec10de5080..84caf92465 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst
@@ -1,18 +1,18 @@
 =============================
 CTSM History Fields (fates)
 =============================
-
+ 
 CAUTION: Not all variables are relevant / present for all CTSM cases.
 Key flags used in this CTSM case:
 use_cn =  F
 use_crop =  F
 use_fates =  T
-
-=================================== ================ ============================================================================================== ================================================================= =======
+ 
+=================================== ================ ============================================================================================== ================================================================= ======= 
 CTSM History Fields
 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
                       Variable Name       Level Dim.                                                                               Long Description                                                             Units Active?
-=================================== ================ ============================================================================================== ================================================================= =======
+=================================== ================ ============================================================================================== ================================================================= ======= 
 A5TMIN                              -                5-day running mean of min 2-m temperature                                                      K                                                                      F
 ACTUAL_IMMOB                        -                actual N immobilization                                                                        gN/m^2/s                                                               T
 AGLB                                -                Aboveground leaf biomass                                                                       kg/m^2                                                                 F
@@ -22,13 +22,27 @@ ALTMAX                              -                maximum annual active layer
 ALTMAX_LASTYEAR                     -                maximum prior year active layer thickness                                                      m                                                                      F
 ATM_O3                              -                atmospheric ozone partial pressure                                                             mol/mol                                                                F
 ATM_TOPO                            -                atmospheric surface height                                                                     m                                                                      T
+AZSUN                               -                azimuth angle of the sun                                                                       radians                                                                F
 AnnET                               -                Annual ET                                                                                      mm/s                                                                   F
 BCDEP                               -                total BC deposition (dry+wet) from atmosphere                                                  kg/m^2/s                                                               T
+BCPHIDRY                            -                black carbon deposition (phidry) from atmosphere                                               kg/m^2/s                                                               F
+BCPHIWET                            -                black carbon deposition (phiwet) from atmosphere                                               kg/m^2/s                                                               F
+BCPHODRY                            -                black carbon deposition (phodry) from atmosphere                                               kg/m^2/s                                                               F
 BTRAN                               -                transpiration beta factor                                                                      unitless                                                               T
 BTRANMN                             -                daily minimum of transpiration beta factor                                                     unitless                                                               T
+CH4PROD                             -                Gridcell total production of CH4                                                               gC/m2/s                                                                T
+CH4_EBUL_TOTAL_SAT                  -                ebullition surface CH4 flux; (+ to atm)                                                        mol/m2/s                                                               F
+CH4_EBUL_TOTAL_UNSAT                -                ebullition surface CH4 flux; (+ to atm)                                                        mol/m2/s                                                               F
+CH4_SURF_AERE_SAT                   -                aerenchyma surface CH4 flux for inundated area; (+ to atm)                                     mol/m2/s                                                               T
+CH4_SURF_AERE_UNSAT                 -                aerenchyma surface CH4 flux for non-inundated area; (+ to atm)                                 mol/m2/s                                                               T
+CH4_SURF_DIFF_SAT                   -                diffusive surface CH4 flux for inundated / lake area; (+ to atm)                               mol/m2/s                                                               T
+CH4_SURF_DIFF_UNSAT                 -                diffusive surface CH4 flux for non-inundated area; (+ to atm)                                  mol/m2/s                                                               T
+CH4_SURF_EBUL_SAT                   -                ebullition surface CH4 flux for inundated / lake area; (+ to atm)                              mol/m2/s                                                               T
+CH4_SURF_EBUL_UNSAT                 -                ebullition surface CH4 flux for non-inundated area; (+ to atm)                                 mol/m2/s                                                               T
 COL_CTRUNC                          -                column-level sink for C truncation                                                             gC/m^2                                                                 F
 COL_NTRUNC                          -                column-level sink for N truncation                                                             gN/m^2                                                                 F
-COSZEN                              -                cosine of solar zenith angle                                                                   none                                                                   F
+COSZEN                              -                cosine of solar zenith angle (downscaled if downscaling is activated)                          none                                                                   F
+COSZEN_GRC                          -                cosine of solar zenith angle                                                                   none                                                                   F
 CROPPROD1C                          -                1-yr crop product (grain+biofuel) C                                                            gC/m^2                                                                 T
 CROPPROD1C_LOSS                     -                loss from 1-yr crop product pool                                                               gC/m^2/s                                                               T
 CROPPROD1N                          -                1-yr crop product (grain+biofuel) N                                                            gN/m^2                                                                 T
@@ -43,7 +57,15 @@ DPVLTRB3                            -                turbulent deposition veloci
 DPVLTRB4                            -                turbulent deposition velocity 4                                                                m/s                                                                    F
 DSL                                 -                dry surface layer thickness                                                                    mm                                                                     T
 DSTDEP                              -                total dust deposition (dry+wet) from atmosphere                                                kg/m^2/s                                                               T
+DSTDRY1                             -                dust deposition (dry1) from atmosphere                                                         kg/m^2/s                                                               F
+DSTDRY2                             -                dust deposition (dry2) from atmosphere                                                         kg/m^2/s                                                               F
+DSTDRY3                             -                dust deposition (dry3) from atmosphere                                                         kg/m^2/s                                                               F
+DSTDRY4                             -                dust deposition (dry4) from atmosphere                                                         kg/m^2/s                                                               F
 DSTFLXT                             -                total surface dust emission                                                                    kg/m2/s                                                                T
+DSTWET1                             -                dust deposition (wet1) from atmosphere                                                         kg/m^2/s                                                               F
+DSTWET2                             -                dust deposition (wet2) from atmosphere                                                         kg/m^2/s                                                               F
+DSTWET3                             -                dust deposition (wet3) from atmosphere                                                         kg/m^2/s                                                               F
+DSTWET4                             -                dust deposition (wet4) from atmosphere                                                         kg/m^2/s                                                               F
 DWT_CROPPROD1C_GAIN                 -                landcover change-driven addition to 1-year crop product pool                                   gC/m^2/s                                                               T
 DWT_CROPPROD1N_GAIN                 -                landcover change-driven addition to 1-year crop product pool                                   gN/m^2/s                                                               T
 DWT_PROD100C_GAIN                   -                landcover change-driven addition to 100-yr wood product pool                                   gC/m^2/s                                                               F
@@ -52,6 +74,7 @@ DWT_PROD10C_GAIN                    -                landcover change-driven add
 DWT_PROD10N_GAIN                    -                landcover change-driven addition to 10-yr wood product pool                                    gN/m^2/s                                                               F
 DWT_WOODPRODC_GAIN                  -                landcover change-driven addition to wood product pools                                         gC/m^2/s                                                               T
 DWT_WOODPRODN_GAIN                  -                landcover change-driven addition to wood product pools                                         gN/m^2/s                                                               T
+DYN_COL_ADJUSTMENTS_CH4             -                Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2                                                                 F
 DYN_COL_SOIL_ADJUSTMENTS_C          -                Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level:  gC/m^2                                                                 F
 DYN_COL_SOIL_ADJUSTMENTS_N          -                Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2                                                                 F
 DYN_COL_SOIL_ADJUSTMENTS_NH4        -                Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2                                                                 F
@@ -95,10 +118,6 @@ FATES_DAYSINCE_COLDLEAFON           -                site-level days elapsed sin
 FATES_DEMOTION_CARBONFLUX           -                demotion-associated biomass carbon flux from canopy to understory in kg carbon per m2 per seco kg m-2 s-1                                                             T
 FATES_DISTURBANCE_RATE_FIRE         -                disturbance rate from fire                                                                     m2 m-2 yr-1                                                            T
 FATES_DISTURBANCE_RATE_LOGGING      -                disturbance rate from logging                                                                  m2 m-2 yr-1                                                            T
-FATES_DISTURBANCE_RATE_P2P          -                disturbance rate from primary to primary lands                                                 m2 m-2 yr-1                                                            T
-FATES_DISTURBANCE_RATE_P2S          -                disturbance rate from primary to secondary lands                                               m2 m-2 yr-1                                                            T
-FATES_DISTURBANCE_RATE_POTENTIAL    -                potential (i.e., including unresolved) disturbance rate                                        m2 m-2 yr-1                                                            T
-FATES_DISTURBANCE_RATE_S2S          -                disturbance rate from secondary to secondary lands                                             m2 m-2 yr-1                                                            T
 FATES_DISTURBANCE_RATE_TREEFALL     -                disturbance rate from treefall                                                                 m2 m-2 yr-1                                                            T
 FATES_EFFECT_WSPEED                 -                effective wind speed for fire spread in meters per second                                      m s-1                                                                  T
 FATES_EXCESS_RESP                   -                respiration of un-allocatable carbon gain                                                      kg m-2 s-1                                                             T
@@ -128,6 +147,7 @@ FATES_HARVEST_DEBT                  -                Accumulated carbon failed t
 FATES_HARVEST_DEBT_SEC              -                Accumulated carbon failed to be harvested from secondary patches                               kg C                                                                   T
 FATES_HET_RESP                      -                heterotrophic respiration in kg carbon per m2 per second                                       kg m-2 s-1                                                             T
 FATES_IGNITIONS                     -                number of successful fire ignitions per m2 land area per second                                m-2 s-1                                                                T
+FATES_L2FR                          -                The leaf to fineroot biomass multiplier for target allometry                                   kg kg-1                                                                T
 FATES_LAI                           -                leaf area index per m2 land area                                                               m2 m-2                                                                 T
 FATES_LAI_SECONDARY                 -                leaf area index per m2 land area, secondary patches                                            m2 m-2                                                                 T
 FATES_LBLAYER_COND                  -                mean leaf boundary layer conductance                                                           mol m-2 s-1                                                            T
@@ -139,7 +159,7 @@ FATES_LITTER_OUT                    -                litter flux out in kg carbo
 FATES_LSTEMMAINTAR                  -                live stem maintenance autotrophic respiration in kg carbon per m2 per second                   kg m-2 s-1                                                             T
 FATES_MAINT_RESP                    -                maintenance respiration in kg carbon per m2 land area per second                               kg m-2 s-1                                                             T
 FATES_MAINT_RESP_SECONDARY          -                maintenance respiration in kg carbon per m2 land area per second, secondary patches            kg m-2 s-1                                                             T
-FATES_MAINT_RESP_UNREDUCED          -                diagnostic maintenance respiration if the low-carbon-storage reduction is ignored              kg m-2 s-1                                                             F
+FATES_MAINT_RESP_UNREDUCED          -                diagnostic maintenance respiration if the low-carbon-storage reduction is ignored              kg m-2 s-1                                                             T
 FATES_MORTALITY_CFLUX_CANOPY        -                flux of biomass carbon from live to dead pools from mortality of canopy plants in kg carbon pe kg m-2 s-1                                                             T
 FATES_MORTALITY_CFLUX_USTORY        -                flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbo kg m-2 s-1                                                             T
 FATES_NCHILLDAYS                    -                site-level number of chill days                                                                days                                                                   T
@@ -148,6 +168,7 @@ FATES_NCOHORTS_SECONDARY            -                total number of cohorts per
 FATES_NCOLDDAYS                     -                site-level number of cold days                                                                 days                                                                   T
 FATES_NEP                           -                net ecosystem production in kg carbon per m2 per second                                        kg m-2 s-1                                                             T
 FATES_NESTEROV_INDEX                -                nesterov fire danger index                                                                                                                                            T
+FATES_NIR_RAD_ERROR                 -                mean two-stream solver error for NIR                                                           -                                                                      T
 FATES_NONSTRUCTC                    -                non-structural biomass (sapwood + leaf + fineroot) in kg carbon per m2                         kg m-2                                                                 T
 FATES_NPATCHES                      -                total number of patches per site                                                                                                                                      T
 FATES_NPATCHES_SECONDARY            -                total number of patches per site                                                                                                                                      T
@@ -155,7 +176,6 @@ FATES_NPP                           -                net primary production in k
 FATES_NPP_SECONDARY                 -                net primary production in kg carbon per m2 per second, secondary patches                       kg m-2 s-1                                                             T
 FATES_PRIMARY_PATCHFUSION_ERR       -                error in total primary lands associated with patch fusion                                      m2 m-2 yr-1                                                            T
 FATES_PROMOTION_CARBONFLUX          -                promotion-associated biomass carbon flux from understory to canopy in kg carbon per m2 per sec kg m-2 s-1                                                             T
-FATES_RAD_ERROR                     -                radiation error in FATES RTM                                                                   W m-2                                                                  T
 FATES_REPROC                        -                total biomass in live plant reproductive tissues in kg carbon per m2                           kg m-2                                                                 T
 FATES_ROS                           -                fire rate of spread in meters per second                                                       m s-1                                                                  T
 FATES_SAPWOODC                      -                total biomass in live plant sapwood in kg carbon per m2                                        kg m-2                                                                 T
@@ -181,8 +201,12 @@ FATES_UNGERM_SEED_BANK              -                ungerminated seed mass of a
 FATES_USTORY_VEGC                   -                biomass of understory plants in kg carbon per m2 land area                                     kg m-2                                                                 T
 FATES_VEGC                          -                total biomass in live plants in kg carbon per m2 land area                                     kg m-2                                                                 T
 FATES_VEGC_ABOVEGROUND              -                aboveground biomass in kg carbon per m2 land area                                              kg m-2                                                                 T
+FATES_VIS_RAD_ERROR                 -                mean two-stream solver error for VIS                                                           -                                                                      T
 FATES_WOOD_PRODUCT                  -                total wood product from logging in kg carbon per m2 land area                                  kg m-2                                                                 T
 FCEV                                -                canopy evaporation                                                                             W/m^2                                                                  T
+FCH4                                -                Gridcell surface CH4 flux to atmosphere (+ to atm)                                             kgC/m2/s                                                               T
+FCH4TOCO2                           -                Gridcell oxidation of CH4 to CO2                                                               gC/m2/s                                                                T
+FCH4_DFSAT                          -                CH4 additional flux due to changing fsat, natural vegetated and crop landunits only            kgC/m2/s                                                               T
 FCO2                                -                CO2 flux to atmosphere (+ to atm)                                                              kgCO2/m2/s                                                             F
 FCOV                                -                fractional impermeable area                                                                    unitless                                                               T
 FCTR                                -                canopy transpiration                                                                           W/m^2                                                                  T
@@ -194,6 +218,8 @@ FGR_R                               -                Rural heat flux into soil/s
 FGR_U                               -                Urban heat flux into soil/snow including snow melt                                             W/m^2                                                                  F
 FH2OSFC                             -                fraction of ground covered by surface water                                                    unitless                                                               T
 FH2OSFC_NOSNOW                      -                fraction of ground covered by surface water (if no snow present)                               unitless                                                               F
+FINUNDATED                          -                fractional inundated area of vegetated columns                                                 unitless                                                               T
+FINUNDATED_LAG                      -                time-lagged inundated fraction of vegetated columns                                            unitless                                                               F
 FIRA                                -                net infrared (longwave) radiation                                                              W/m^2                                                                  T
 FIRA_ICE                            -                net infrared (longwave) radiation (ice landunits only)                                         W/m^2                                                                  F
 FIRA_R                              -                Rural net infrared (longwave) radiation                                                        W/m^2                                                                  T
@@ -202,8 +228,9 @@ FIRE                                -                emitted infrared (longwave)
 FIRE_ICE                            -                emitted infrared (longwave) radiation (ice landunits only)                                     W/m^2                                                                  F
 FIRE_R                              -                Rural emitted infrared (longwave) radiation                                                    W/m^2                                                                  T
 FIRE_U                              -                Urban emitted infrared (longwave) radiation                                                    W/m^2                                                                  F
-FLDS                                -                atmospheric longwave radiation (downscaled to columns in glacier regions)                      W/m^2                                                                  T
-FLDS_ICE                            -                atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2                                                                  F
+FLDS                                -                atmospheric longwave radiation (downscaled for glacier and hillslope columns)                  W/m^2                                                                  T
+FLDS_ICE                            -                atmospheric longwave radiation (downscaled for glacier and hillslope columns) (ice landunits o W/m^2                                                                  F
+FLDS_NOT_DOWNSCALED                 -                atmospheric longwave radiation (pre-downscaling)                                               W/m^2                                                                  F
 FPG                                 -                fraction of potential gpp                                                                      proportion                                                             T
 FPI                                 -                fraction of potential immobilization                                                           proportion                                                             T
 FROST_TABLE                         -                frost table depth (natural vegetated and crop landunits only)                                  m                                                                      F
@@ -214,7 +241,7 @@ FSA_R                               -                Rural absorbed solar radiat
 FSA_U                               -                Urban absorbed solar radiation                                                                 W/m^2                                                                  F
 FSD24                               -                direct radiation (last 24hrs)                                                                  K                                                                      F
 FSD240                              -                direct radiation (last 240hrs)                                                                 K                                                                      F
-FSDS                                -                atmospheric incident solar radiation                                                           W/m^2                                                                  T
+FSDS                                -                atmospheric incident solar radiation (downscaled for glacier and hillslope columns)            W/m^2                                                                  T
 FSDSND                              -                direct nir incident solar radiation                                                            W/m^2                                                                  T
 FSDSNDLN                            -                direct nir incident solar radiation at local noon                                              W/m^2                                                                  T
 FSDSNI                              -                diffuse nir incident solar radiation                                                           W/m^2                                                                  T
@@ -222,6 +249,7 @@ FSDSVD                              -                direct vis incident solar r
 FSDSVDLN                            -                direct vis incident solar radiation at local noon                                              W/m^2                                                                  T
 FSDSVI                              -                diffuse vis incident solar radiation                                                           W/m^2                                                                  T
 FSDSVILN                            -                diffuse vis incident solar radiation at local noon                                             W/m^2                                                                  T
+FSDS_from_atm                       -                atmospheric incident solar radiation received from atmosphere (pre-downscaling)                W/m^2                                                                  T
 FSH                                 -                sensible heat not including correction for land use change and rain/snow conversion            W/m^2                                                                  T
 FSH_G                               -                sensible heat from ground                                                                      W/m^2                                                                  T
 FSH_ICE                             -                sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2                                                                  F
@@ -320,7 +348,7 @@ LIT_MET_N                           -                LIT_MET N
 LIT_MET_N_1m                        -                LIT_MET N to 1 meter                                                                           gN/m^2                                                                 F
 LIT_MET_N_TO_SOM_ACT_N              -                decomp. of metabolic litter N to active soil organic N                                         gN/m^2                                                                 F
 LNC                                 -                leaf N concentration                                                                           gN leaf/m^2                                                            T
-LWdown                              -                atmospheric longwave radiation (downscaled to columns in glacier regions)                      W/m^2                                                                  F
+LWdown                              -                atmospheric longwave radiation (downscaled for glacier and hillslope columns)                  W/m^2                                                                  F
 LWup                                -                upwelling longwave radiation                                                                   W/m^2                                                                  F
 MORTALITY_CROWNAREA_CANOPY          -                Crown area of canopy trees that died                                                           m2/ha/year                                                             T
 MORTALITY_CROWNAREA_UNDERSTORY      -                Crown aera of understory trees that died                                                       m2/ha/year                                                             T
@@ -337,13 +365,19 @@ M_SOM_PAS_N_TO_LEACHING             -                passive soil organic N leac
 M_SOM_SLO_C_TO_LEACHING             -                slow soil organic ma C leaching loss                                                           gC/m^2/s                                                               F
 M_SOM_SLO_N_TO_LEACHING             -                slow soil organic ma N leaching loss                                                           gN/m^2/s                                                               F
 NDEP_TO_SMINN                       -                atmospheric N deposition to soil mineral N                                                     gN/m^2/s                                                               T
+NEM                                 -                Gridcell net adjustment to net carbon exchange passed to atm. for methane production           gC/m2/s                                                                T
 NET_NMIN                            -                net rate of N mineralization                                                                   gN/m^2/s                                                               T
 NFIX_TO_SMINN                       -                symbiotic/asymbiotic N fixation to soil mineral N                                              gN/m^2/s                                                               T
 NSUBSTEPS                           -                number of adaptive timesteps in CLM timestep                                                   unitless                                                               F
 OBU                                 -                Monin-Obukhov length                                                                           m                                                                      F
 OCDEP                               -                total OC deposition (dry+wet) from atmosphere                                                  kg/m^2/s                                                               T
+OCPHIDRY                            -                organic carbon deposition (phidry) from atmosphere                                             kg/m^2/s                                                               F
+OCPHIWET                            -                organic carbon deposition (phiwet) from atmosphere                                             kg/m^2/s                                                               F
+OCPHODRY                            -                black carbon deposition (phodry) from atmosphere                                               kg/m^2/s                                                               F
 PARVEGLN                            -                absorbed par by vegetation at local noon                                                       W/m^2                                                                  T
-PBOT                                -                atmospheric pressure at surface (downscaled to columns in glacier regions)                     Pa                                                                     T
+PBOT                                -                atmospheric pressure at surface (downscaled for glacier and hillslope columns)                 Pa                                                                     T
+PBOT_NOT_DOWNSCALED                 -                atmospheric pressure at surface (pre-downscaling)                                              Pa                                                                     F
+PCH4                                -                atmospheric partial pressure of CH4                                                            Pa                                                                     T
 PCO2                                -                atmospheric partial pressure of CO2                                                            Pa                                                                     T
 POTENTIAL_IMMOB                     -                potential N immobilization                                                                     gN/m^2/s                                                               T
 POT_F_DENIT                         -                potential denitrification flux                                                                 gN/m^2/s                                                               T
@@ -356,10 +390,11 @@ PROD10C                             -                10-yr wood product C
 PROD10C_LOSS                        -                loss from 10-yr wood product pool                                                              gC/m^2/s                                                               F
 PROD10N                             -                10-yr wood product N                                                                           gN/m^2                                                                 F
 PROD10N_LOSS                        -                loss from 10-yr wood product pool                                                              gN/m^2/s                                                               F
-PSurf                               -                atmospheric pressure at surface (downscaled to columns in glacier regions)                     Pa                                                                     F
+PSurf                               -                atmospheric pressure at surface (downscaled for glacier and hillslope columns)                 Pa                                                                     F
 Q2M                                 -                2m specific humidity                                                                           kg/kg                                                                  T
 QAF                                 -                canopy air humidity                                                                            kg/kg                                                                  F
 QBOT                                -                atmospheric specific humidity (downscaled to columns in glacier regions)                       kg/kg                                                                  T
+QBOT_NOT_DOWNSCALED                 -                atmospheric specific humidity (pre-downscaling)                                                kg/kg                                                                  F
 QDIRECT_THROUGHFALL                 -                direct throughfall of liquid (rain + above-canopy irrigation)                                  mm/s                                                                   F
 QDIRECT_THROUGHFALL_SNOW            -                direct throughfall of snow                                                                     mm/s                                                                   F
 QDRAI                               -                sub-surface drainage                                                                           mm/s                                                                   T
@@ -396,6 +431,7 @@ QIRRIG_FROM_GW_UNCONFINED           -                water added through unconfi
 QIRRIG_FROM_SURFACE                 -                water added through surface water irrigation                                                   mm/s                                                                   T
 QIRRIG_SPRINKLER                    -                water added via sprinkler irrigation                                                           mm/s                                                                   F
 QOVER                               -                total surface runoff (includes QH2OSFC)                                                        mm/s                                                                   T
+QOVER_LAG                           -                time-lagged surface runoff for soil columns                                                    mm/s                                                                   F
 QPHSNEG                             -                net negative hydraulic redistribution flux                                                     mm/s                                                                   F
 QRGWL                               -                surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s                                                                   T
 QRUNOFF                             -                total liquid runoff not including correction for land use change                               mm/s                                                                   T
@@ -436,7 +472,7 @@ RAW2                                -                aerodynamical resistance
 RB                                  -                leaf boundary resistance                                                                       s/m                                                                    F
 RH                                  -                atmospheric relative humidity                                                                  %                                                                      F
 RH2M                                -                2m relative humidity                                                                           %                                                                      T
-RH2M_R                              -                Rural 2m specific humidity                                                                     %                                                                      F
+RH2M_R                              -                Rural 2m relative humidity                                                                     %                                                                      F
 RH2M_U                              -                Urban 2m relative humidity                                                                     %                                                                      F
 RHAF                                -                fractional humidity of canopy air                                                              fraction                                                               F
 RH_LEAF                             -                fractional humidity at leaf surface                                                            fraction                                                               F
@@ -444,6 +480,7 @@ RSCANOPY                            -                canopy resistance
 RSSHA                               -                shaded leaf stomatal resistance                                                                s/m                                                                    T
 RSSUN                               -                sunlit leaf stomatal resistance                                                                s/m                                                                    T
 Rainf                               -                atmospheric rain, after rain/snow repartitioning based on temperature                          mm/s                                                                   F
+Rho_from_atm                        -                atmospheric density (pre-downscaling)                                                          kg/m^3                                                                 F
 Rnet                                -                net radiation                                                                                  W/m^2                                                                  F
 SABG                                -                solar rad absorbed by ground                                                                   W/m^2                                                                  T
 SABG_PEN                            -                Rural solar rad penetrating top soil or snow layer                                             watt/m^2                                                               T
@@ -546,21 +583,24 @@ T10                                 -                10-day running mean of 2-m
 TAF                                 -                canopy air temperature                                                                         K                                                                      F
 TAUX                                -                zonal surface stress                                                                           kg/m/s^2                                                               T
 TAUY                                -                meridional surface stress                                                                      kg/m/s^2                                                               T
-TBOT                                -                atmospheric air temperature (downscaled to columns in glacier regions)                         K                                                                      T
+TBOT                                -                atmospheric air temperature (downscaled for glacier and hillslope columns)                     K                                                                      T
 TBUILD                              -                internal urban building air temperature                                                        K                                                                      T
 TBUILD_MAX                          -                prescribed maximum interior building temperature                                               K                                                                      F
+TDEPTH                              -                tributary water depth                                                                          m                                                                      F
+TDEPTHMAX                           -                tributary bankfull water depth                                                                 m                                                                      F
 TFLOOR                              -                floor temperature                                                                              K                                                                      F
 TG                                  -                ground temperature                                                                             K                                                                      T
 TG_ICE                              -                ground temperature (ice landunits only)                                                        K                                                                      F
 TG_R                                -                Rural ground temperature                                                                       K                                                                      F
 TG_U                                -                Urban ground temperature                                                                       K                                                                      F
 TH2OSFC                             -                surface water temperature                                                                      K                                                                      T
-THBOT                               -                atmospheric air potential temperature (downscaled to columns in glacier regions)               K                                                                      T
+THBOT                               -                atmospheric air potential temperature (downscaled for glacier and hillslope columns)           K                                                                      T
 TKE1                                -                top lake level eddy thermal conductivity                                                       W/(mK)                                                                 T
 TLAI                                -                total projected leaf area index                                                                m^2/m^2                                                                T
 TOPO_COL                            -                column-level topographic height                                                                m                                                                      F
 TOPO_COL_ICE                        -                column-level topographic height (ice landunits only)                                           m                                                                      F
 TOTCOLC                             -                total column carbon, incl veg and cpool but excl product pools                                 gC/m^2                                                                 T
+TOTCOLCH4                           -                total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits)   gC/m2                                                                  T
 TOTCOLN                             -                total column-level N, excluding product pools                                                  gN/m^2                                                                 T
 TOTECOSYSC                          -                total ecosystem carbon, incl veg but excl cpool and product pools                              gC/m^2                                                                 T
 TOTECOSYSN                          -                total ecosystem N, excluding product pools                                                     gN/m^2                                                                 T
@@ -600,8 +640,9 @@ TV                                  -                vegetation temperature
 TV24                                -                vegetation temperature (last 24hrs)                                                            K                                                                      F
 TV240                               -                vegetation temperature (last 240hrs)                                                           K                                                                      F
 TWS                                 -                total water storage                                                                            mm                                                                     T
-Tair                                -                atmospheric air temperature (downscaled to columns in glacier regions)                         K                                                                      F
+Tair                                -                atmospheric air temperature (downscaled for glacier and hillslope columns)                     K                                                                      F
 Tair_from_atm                       -                atmospheric air temperature received from atmosphere (pre-downscaling)                         K                                                                      F
+Thair_from_atm                      -                atmospheric air potential temperature (pre-downscaling)                                        K                                                                      F
 U10                                 -                10-m wind                                                                                      m/s                                                                    T
 U10_DUST                            -                10-m wind for dust model                                                                       m/s                                                                    T
 U10_ICE                             -                10-m wind (ice landunits only)                                                                 m/s                                                                    F
@@ -611,6 +652,7 @@ URBAN_AC                            -                urban air conditioning flux
 URBAN_HEAT                          -                urban heating flux                                                                             W/m^2                                                                  T
 USTAR                               -                aerodynamical resistance                                                                       s/m                                                                    F
 UST_LAKE                            -                friction velocity (lakes only)                                                                 m/s                                                                    F
+UWIND                               -                atmospheric U wind velocity magnitude                                                          m/s                                                                    F
 VA                                  -                atmospheric wind speed plus convective velocity                                                m/s                                                                    F
 VENTILATION                         -                sensible heat flux from building ventilation                                                   W/m^2                                                                  T
 VOLR                                -                river channel total water storage                                                              m3                                                                     T
@@ -618,11 +660,13 @@ VOLRMCH                             -                river channel main channel
 VPD                                 -                vpd                                                                                            Pa                                                                     F
 VPD2M                               -                2m vapor pressure deficit                                                                      Pa                                                                     T
 VPD_CAN                             -                canopy vapor pressure deficit                                                                  kPa                                                                    T
+VWIND                               -                atmospheric V wind velocity magnitude                                                          m/s                                                                    F
 WASTEHEAT                           -                sensible heat flux from heating/cooling sources of urban waste heat                            W/m^2                                                                  T
 WBT                                 -                2 m Stull Wet Bulb                                                                             C                                                                      T
 WBT_R                               -                Rural 2 m Stull Wet Bulb                                                                       C                                                                      T
 WBT_U                               -                Urban 2 m Stull Wet Bulb                                                                       C                                                                      T
 WIND                                -                atmospheric wind velocity magnitude                                                            m/s                                                                    T
+WTGQ                                -                surface tracer conductance                                                                     m/s                                                                    T
 Wind                                -                atmospheric wind velocity magnitude                                                            m/s                                                                    F
 Z0HG                                -                roughness length over ground, sensible heat (vegetated landunits only)                         m                                                                      F
 Z0MG                                -                roughness length over ground, momentum (vegetated landunits only)                              m                                                                      F
@@ -633,6 +677,7 @@ ZBOT                                -                atmospheric reference heigh
 ZETA                                -                dimensionless stability parameter                                                              unitless                                                               F
 ZII                                 -                convective boundary height                                                                     m                                                                      F
 ZWT                                 -                water table depth (natural vegetated and crop landunits only)                                  m                                                                      T
+ZWT_CH4_UNSAT                       -                depth of water table for methane production used in non-inundated area                         m                                                                      T
 ZWT_PERCH                           -                perched water table depth (natural vegetated and crop landunits only)                          m                                                                      T
 num_iter                            -                number of iterations                                                                           unitless                                                               F
 QICE_FORC                           elevclas         qice forcing sent to GLC                                                                       mm/s                                                                   F
@@ -660,39 +705,28 @@ FATES_SCORCH_HEIGHT_APPF            fates_levagepft  SPITFIRE flame Scorch Heigh
 FATES_VEGC_APPF                     fates_levagepft  biomass per PFT in each age bin in kg carbon per m2                                            kg m-2                                                                 F
 FATES_MORTALITY_AGESCEN_AC          fates_levcacls   age senescence mortality by cohort age in number of plants per m2 per year                     m-2 yr-1                                                               T
 FATES_NPLANT_AC                     fates_levcacls   number of plants per m2 by cohort age class                                                    m-2                                                                    T
-FATES_CROWNAREA_CL                  fates_levcan     total crown area in each canopy layer                                                          m2 m-2                                                                 T
-FATES_FABD_SHA_TOPLF_CL             fates_levcan     shade fraction of direct light absorbed by the top leaf layer of each canopy layer             1                                                                      F
-FATES_FABD_SUN_TOPLF_CL             fates_levcan     sun fraction of direct light absorbed by the top leaf layer of each canopy layer               1                                                                      F
-FATES_FABI_SHA_TOPLF_CL             fates_levcan     shade fraction of indirect light absorbed by the top leaf layer of each canopy layer           1                                                                      F
-FATES_FABI_SUN_TOPLF_CL             fates_levcan     sun fraction of indirect light absorbed by the top leaf layer of each canopy layer             1                                                                      F
-FATES_LAISHA_TOP_CL                 fates_levcan     LAI in the shade by the top leaf layer of each canopy layer                                    m2 m-2                                                                 F
-FATES_LAISUN_TOP_CL                 fates_levcan     LAI in the sun by the top leaf layer of each canopy layer                                      m2 m-2                                                                 F
-FATES_PARSHA_Z_CL                   fates_levcan     PAR absorbed in the shade by top leaf layer in each canopy layer                               W m-2                                                                  F
-FATES_PARSUN_Z_CL                   fates_levcan     PAR absorbed in the sun by top leaf layer in each canopy layer                                 W m-2                                                                  F
+FATES_CROWNAREA_CL                  fates_levcan     area fraction of the canopy footprint occupied by each canopy-leaf layer                       m2 m-2                                                                 T
+FATES_LAISHA_CL                     fates_levcan     LAI of shaded leaves by canopy layer                                                           m2 m-2                                                                 F
+FATES_LAISUN_CL                     fates_levcan     LAI of sunlit leaves by canopy layer                                                           m2 m-2                                                                 F
+FATES_PARSHA_CL                     fates_levcan     PAR absorbed by shaded leaves in each canopy layer                                             W m-2                                                                  F
+FATES_PARSUN_CL                     fates_levcan     PAR absorbed by sunlit leaves in each canopy layer                                             W m-2                                                                  F
 FATES_MORTALITY_AGESCEN_ACPF        fates_levcapf    age senescence mortality by pft/cohort age in number of plants per m2 per year                 m-2 yr-1                                                               F
 FATES_NPLANT_ACPF                   fates_levcapf    stem number density by pft and age class                                                       m-2                                                                    F
-FATES_CROWNAREA_CLLL                fates_levcnlf    total crown area that is occupied by leaves in each canopy and leaf layer                      m2 m-2                                                                 F
-FATES_FABD_SHA_CLLL                 fates_levcnlf    shade fraction of direct light absorbed by each canopy and leaf layer                          1                                                                      F
-FATES_FABD_SUN_CLLL                 fates_levcnlf    sun fraction of direct light absorbed by each canopy and leaf layer                            1                                                                      F
-FATES_FABI_SHA_CLLL                 fates_levcnlf    shade fraction of indirect light absorbed by each canopy and leaf layer                        1                                                                      F
-FATES_FABI_SUN_CLLL                 fates_levcnlf    sun fraction of indirect light absorbed by each canopy and leaf layer                          1                                                                      F
-FATES_LAISHA_Z_CLLL                 fates_levcnlf    LAI in the shade by each canopy and leaf layer                                                 m2 m-2                                                                 F
-FATES_LAISUN_Z_CLLL                 fates_levcnlf    LAI in the sun by each canopy and leaf layer                                                   m2 m-2                                                                 F
+FATES_CROWNAREA_CLLL                fates_levcnlf    area fraction of the total ground occupied by each canopy-leaf layer                           m2 m-2                                                                 F
+FATES_LAISHA_CLLL                   fates_levcnlf    LAI in the shade by each canopy and leaf layer                                                 m2 m-2                                                                 F
+FATES_LAISUN_CLLL                   fates_levcnlf    LAI in the sun by each canopy and leaf layer                                                   m2 m-2                                                                 F
 FATES_NET_C_UPTAKE_CLLL             fates_levcnlf    net carbon uptake in kg carbon per m2 per second by each canopy and leaf layer per unit ground kg m-2 s-1                                                             F
 FATES_PARPROF_DIF_CLLL              fates_levcnlf    radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs)     W m-2                                                                  F
 FATES_PARPROF_DIR_CLLL              fates_levcnlf    radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs)      W m-2                                                                  F
-FATES_PARSHA_Z_CLLL                 fates_levcnlf    PAR absorbed in the shade by each canopy and leaf layer                                        W m-2                                                                  F
-FATES_PARSUN_Z_CLLL                 fates_levcnlf    PAR absorbed in the sun by each canopy and leaf layer                                          W m-2                                                                  F
-FATES_FABD_SHA_CLLLPF               fates_levcnlfpf  shade fraction of direct light absorbed by each canopy, leaf, and PFT                          1                                                                      F
-FATES_FABD_SUN_CLLLPF               fates_levcnlfpf  sun fraction of direct light absorbed by each canopy, leaf, and PFT                            1                                                                      F
-FATES_FABI_SHA_CLLLPF               fates_levcnlfpf  shade fraction of indirect light absorbed by each canopy, leaf, and PFT                        1                                                                      F
-FATES_FABI_SUN_CLLLPF               fates_levcnlfpf  sun fraction of indirect light absorbed by each canopy, leaf, and PFT                          1                                                                      F
-FATES_LAISHA_Z_CLLLPF               fates_levcnlfpf  LAI in the shade by each canopy, leaf, and PFT                                                 m2 m-2                                                                 F
-FATES_LAISUN_Z_CLLLPF               fates_levcnlfpf  LAI in the sun by each canopy, leaf, and PFT                                                   m2 m-2                                                                 F
+FATES_PARSHA_CLLL                   fates_levcnlf    PAR absorbed in the shade by each canopy and leaf layer                                        W m-2                                                                  F
+FATES_PARSUN_CLLL                   fates_levcnlf    PAR absorbed in the sun by each canopy and leaf layer                                          W m-2                                                                  F
+FATES_CROWNFRAC_CLLLPF              fates_levcnlfpf  area fraction of the canopy footprint occupied by each canopy-leaf-pft layer                   m2 m-2                                                                 F
+FATES_LAISHA_CLLLPF                 fates_levcnlfpf  Shaded leaf area by each canopy, leaf, and PFT                                                 m2 m-2                                                                 F
+FATES_LAISUN_CLLLPF                 fates_levcnlfpf  Sunlit leaf area by each canopy, leaf, and PFT                                                 m2 m-2                                                                 F
 FATES_PARPROF_DIF_CLLLPF            fates_levcnlfpf  radiative profile of diffuse PAR through each canopy, leaf, and PFT                            W m-2                                                                  F
 FATES_PARPROF_DIR_CLLLPF            fates_levcnlfpf  radiative profile of direct PAR through each canopy, leaf, and PFT                             W m-2                                                                  F
-FATES_PARSHA_Z_CLLLPF               fates_levcnlfpf  PAR absorbed in the shade by each canopy, leaf, and PFT                                        W m-2                                                                  F
-FATES_PARSUN_Z_CLLLPF               fates_levcnlfpf  PAR absorbed in the sun by each canopy, leaf, and PFT                                          W m-2                                                                  F
+FATES_PARSHA_CLLLPF                 fates_levcnlfpf  PAR absorbed in the shade by each canopy, leaf, and PFT                                        W m-2                                                                  F
+FATES_PARSUN_CLLLPF                 fates_levcnlfpf  PAR absorbed in the sun by each canopy, leaf, and PFT                                          W m-2                                                                  F
 FATES_CWD_ABOVEGROUND_DC            fates_levcwdsc   debris class-level aboveground coarse woody debris stocks in kg carbon per m2                  kg m-2                                                                 F
 FATES_CWD_ABOVEGROUND_IN_DC         fates_levcwdsc   debris class-level aboveground coarse woody debris input in kg carbon per m2 per second        kg m-2 s-1                                                             F
 FATES_CWD_ABOVEGROUND_OUT_DC        fates_levcwdsc   debris class-level aboveground coarse woody debris output in kg carbon per m2 per second       kg m-2 s-1                                                             F
@@ -718,6 +752,8 @@ FATES_FUEL_BURNT_BURNFRAC_FC        fates_levfuel    product of fraction (0-1) o
 FATES_FUEL_MOISTURE_FC              fates_levfuel    spitfire fuel class-level fuel moisture (volumetric)                                           m3 m-3                                                                 T
 FATES_CANOPYAREA_HT                 fates_levheight  canopy area height distribution                                                                m2 m-2                                                                 T
 FATES_LEAFAREA_HT                   fates_levheight  leaf area height distribution                                                                  m2 m-2                                                                 T
+FATES_PATCHAREA_LU                  fates_levlanduse patch area by land use type                                                                    m2 m-2                                                                 T
+FATES_DISTURBANCE_RATE_MATRIX_LULU  fates_levlulu    disturbance rates by land use type x land use type matrix                                      m2 m-2 yr-1                                                            T
 FATES_CANOPYCROWNAREA_PF            fates_levpft     total PFT-level canopy-layer crown area per m2 land area                                       m2 m-2                                                                 T
 FATES_CROWNAREA_PF                  fates_levpft     total PFT-level crown area per m2 land area                                                    m2 m-2                                                                 T
 FATES_DAYSINCE_DROUGHTLEAFOFF_PF    fates_levpft     PFT-level days elapsed since drought leaf drop                                                 days                                                                   T
@@ -726,14 +762,17 @@ FATES_DROUGHT_STATUS_PF             fates_levpft     PFT-level drought status, <
 FATES_ELONG_FACTOR_PF               fates_levpft     PFT-level mean elongation factor (partial flushing/abscission)                                 1                                                                      T
 FATES_GPP_PF                        fates_levpft     total PFT-level GPP in kg carbon per m2 land area per second                                   kg m-2 s-1                                                             T
 FATES_GPP_SE_PF                     fates_levpft     total PFT-level GPP in kg carbon per m2 land area per second, secondary patches                kg m-2 s-1                                                             T
+FATES_L2FR_CANOPY_REC_PF            fates_levpft     The leaf to fineroot biomass multiplier for recruits (canopy)                                  kg kg-1                                                                T
+FATES_L2FR_USTORY_REC_PF            fates_levpft     The leaf to fineroot biomass multiplier for recruits (understory)                              kg kg-1                                                                T
 FATES_LEAFC_PF                      fates_levpft     total PFT-level leaf biomass in kg carbon per m2 land area                                     kg m-2                                                                 T
 FATES_MEANLIQVOL_DROUGHTPHEN_PF     fates_levpft     PFT-level mean liquid water volume for drought phenolgy                                        m3 m-3                                                                 T
 FATES_MEANSMP_DROUGHTPHEN_PF        fates_levpft     PFT-level mean soil matric potential for drought phenology                                     Pa                                                                     T
 FATES_MORTALITY_CFLUX_PF            fates_levpft     PFT-level flux of biomass carbon from live to dead pool from mortality                         kg m-2 s-1                                                             T
-FATES_MORTALITY_CSTARV_CFLUX_PF     fates_levpft     PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality       kg m-2 s-1                                                             T
+FATES_MORTALITY_CSTARV_CFLUX_PF     fates_levpft     PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality (both kg m-2 s-1                                                             T
 FATES_MORTALITY_FIRE_CFLUX_PF       fates_levpft     PFT-level flux of biomass carbon from live to dead pool from fire mortality                    kg m-2 s-1                                                             T
 FATES_MORTALITY_HYDRO_CFLUX_PF      fates_levpft     PFT-level flux of biomass carbon from live to dead pool from hydraulic failure mortality       kg m-2 s-1                                                             T
 FATES_MORTALITY_PF                  fates_levpft     PFT-level mortality rate in number of individuals per m2 land area per year                    m-2 yr-1                                                               T
+FATES_MORT_CSTARV_CONT_CFLUX_PF     fates_levpft     PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality (Cont kg m-2 s-1                                                             T
 FATES_NPLANT_PF                     fates_levpft     total PFT-level number of individuals per m2 land area                                         m-2                                                                    T
 FATES_NPLANT_SEC_PF                 fates_levpft     total PFT-level number of individuals per m2 land area, secondary patches                      m-2                                                                    T
 FATES_NPP_PF                        fates_levpft     total PFT-level NPP in kg carbon per m2 land area per second                                   kg m-2 s-1                                                             T
@@ -776,8 +815,8 @@ FATES_LEAF_ALLOC_CANOPY_SZ          fates_levscls    allocation to leaves for ca
 FATES_LEAF_ALLOC_USTORY_SZ          fates_levscls    allocation to leaves for understory plants by size class in kg carbon per m2 per second        kg m-2 s-1                                                             F
 FATES_LSTEMMAINTAR_CANOPY_SZ        fates_levscls    live stem maintenance autotrophic respiration for canopy plants in kg carbon per m2 per second kg m-2 s-1                                                             F
 FATES_LSTEMMAINTAR_USTORY_SZ        fates_levscls    live stem maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1                                                             F
-FATES_M3_MORTALITY_CANOPY_SZ        fates_levscls    C starvation mortality of canopy plants by size                                                N/ha/yr                                                                F
-FATES_M3_MORTALITY_USTORY_SZ        fates_levscls    C starvation mortality of understory plants by size                                            N/ha/yr                                                                F
+FATES_M3_MORTALITY_CANOPY_SZ        fates_levscls    C starvation mortality of canopy plants by size                                                m-2 yr-1                                                               F
+FATES_M3_MORTALITY_USTORY_SZ        fates_levscls    C starvation mortality of understory plants by size                                            m-2 yr-1                                                               F
 FATES_MAINTAR_CANOPY_SZ             fates_levscls    maintenance autotrophic respiration of canopy plants in kg carbon per m2 per second by size    kg m-2 s-1                                                             F
 FATES_MAINTAR_USTORY_SZ             fates_levscls    maintenance autotrophic respiration of understory plants in kg carbon per m2 per second by siz kg m-2 s-1                                                             F
 FATES_MORTALITY_AGESCEN_SE_SZ       fates_levscls    age senescence mortality by size in number of plants per m2 per year, secondary patches        m-2 yr-1                                                               T
@@ -787,7 +826,7 @@ FATES_MORTALITY_BACKGROUND_SZ       fates_levscls    background mortality by siz
 FATES_MORTALITY_CANOPY_SE_SZ        fates_levscls    total mortality of canopy trees by size class in number of plants per m2, secondary patches    m-2 yr-1                                                               T
 FATES_MORTALITY_CANOPY_SZ           fates_levscls    total mortality of canopy trees by size class in number of plants per m2                       m-2 yr-1                                                               T
 FATES_MORTALITY_CSTARV_SE_SZ        fates_levscls    carbon starvation mortality by size in number of plants per m2 per year, secondary patches     m-2 yr-1                                                               T
-FATES_MORTALITY_CSTARV_SZ           fates_levscls    carbon starvation mortality by size in number of plants per m2 per year                        m-2 yr-1                                                               T
+FATES_MORTALITY_CSTARV_SZ           fates_levscls    carbon starvation mortality by size in number of plants per m2 per year (both continous and te m-2 yr-1                                                               T
 FATES_MORTALITY_FIRE_SZ             fates_levscls    fire mortality by size in number of plants per m2 per year                                     m-2 yr-1                                                               T
 FATES_MORTALITY_FREEZING_SE_SZ      fates_levscls    freezing mortality by size in number of plants per m2 per event, secondary patches             m-2 event-1                                                            T
 FATES_MORTALITY_FREEZING_SZ         fates_levscls    freezing mortality by size in number of plants per m2 per year                                 m-2 yr-1                                                               T
@@ -798,7 +837,7 @@ FATES_MORTALITY_LOGGING_SE_SZ       fates_levscls    logging mortality by size i
 FATES_MORTALITY_LOGGING_SZ          fates_levscls    logging mortality by size in number of plants per m2 per year                                  m-2 yr-1                                                               T
 FATES_MORTALITY_SENESCENCE_SE_SZ    fates_levscls    senescence mortality by size in number of plants per m2 per event, secondary patches           m-2 yr-1                                                               T
 FATES_MORTALITY_SENESCENCE_SZ       fates_levscls    senescence mortality by size in number of plants per m2 per year                               m-2 yr-1                                                               T
-FATES_MORTALITY_TERMINATION_SZ      fates_levscls    termination mortality by size in number of plants per m2 per year                              m-2 yr-1                                                               T
+FATES_MORTALITY_TERMINATION_SZ      fates_levscls    termination mortality (excluding C-starvation) by size in number of plants per m2 per year     m-2 yr-1                                                               T
 FATES_MORTALITY_USTORY_SZ           fates_levscls    total mortality of understory trees by size class in individuals per m2 per year               m-2 yr-1                                                               T
 FATES_NPLANT_CANOPY_SZ              fates_levscls    number of canopy plants per m2 by size class                                                   m-2                                                                    T
 FATES_NPLANT_SZ                     fates_levscls    number of plants per m2 by size class                                                          m-2                                                                    T
@@ -845,6 +884,8 @@ FATES_BGSAPMAINTAR_SZPF             fates_levscpf    below-ground sapwood mainte
 FATES_BGSAPWOOD_ALLOC_SZPF          fates_levscpf    allocation to below-ground sapwood by pft/size in kg carbon per m2 per second                  kg m-2 s-1                                                             F
 FATES_BGSTRUCT_ALLOC_SZPF           fates_levscpf    allocation to below-ground structural (deadwood) by pft/size in kg carbon per m2 per second    kg m-2 s-1                                                             F
 FATES_C13DISC_SZPF                  fates_levscpf    C13 discrimination by pft/size                                                                 per mil                                                                F
+FATES_CROWNAREA_CANOPY_SZPF         fates_levscpf    Total crown area of canopy plants by pft/size                                                  m2 m-2                                                                 F
+FATES_CROWNAREA_USTORY_SZPF         fates_levscpf    Total crown area of understory plants by pft/size                                              m2 m-2                                                                 F
 FATES_DDBH_CANOPY_SZPF              fates_levscpf    diameter growth increment by pft/size                                                          m m-2 yr-1                                                             F
 FATES_DDBH_SZPF                     fates_levscpf    diameter growth increment by pft/size                                                          m m-2 yr-1                                                             F
 FATES_DDBH_USTORY_SZPF              fates_levscpf    diameter growth increment by pft/size                                                          m m-2 yr-1                                                             F
@@ -863,22 +904,22 @@ FATES_LEAFC_CANOPY_SZPF             fates_levscpf    biomass in leaves of canopy
 FATES_LEAFC_SZPF                    fates_levscpf    leaf carbon mass by size-class x pft in kg carbon per m2                                       kg m-2                                                                 F
 FATES_LEAFC_USTORY_SZPF             fates_levscpf    biomass in leaves of understory plants by pft/size in kg carbon per m2                         kg m-2                                                                 F
 FATES_LEAF_ALLOC_SZPF               fates_levscpf    allocation to leaves by pft/size in kg carbon per m2 per second                                kg m-2 s-1                                                             F
-FATES_M3_MORTALITY_CANOPY_SZPF      fates_levscpf    C starvation mortality of canopy plants by pft/size                                            N/ha/yr                                                                F
-FATES_M3_MORTALITY_USTORY_SZPF      fates_levscpf    C starvation mortality of understory plants by pft/size                                        N/ha/yr                                                                F
+FATES_M3_MORTALITY_CANOPY_SZPF      fates_levscpf    C starvation mortality of canopy plants by pft/size                                            m-2 yr-1                                                               F
+FATES_M3_MORTALITY_USTORY_SZPF      fates_levscpf    C starvation mortality of understory plants by pft/size                                        m-2 yr-1                                                               F
 FATES_MAINTAR_SZPF                  fates_levscpf    maintenance autotrophic respiration in kg carbon per m2 per second by pft/size                 kg m-2 s-1                                                             F
 FATES_MORTALITY_AGESCEN_SZPF        fates_levscpf    age senescence mortality by pft/size in number of plants per m2 per year                       m-2 yr-1                                                               F
 FATES_MORTALITY_BACKGROUND_SZPF     fates_levscpf    background mortality by pft/size in number of plants per m2 per year                           m-2 yr-1                                                               F
 FATES_MORTALITY_CAMBIALBURN_SZPF    fates_levscpf    fire mortality from cambial burn by pft/size in number of plants per m2 per year               m-2 yr-1                                                               F
 FATES_MORTALITY_CANOPY_SZPF         fates_levscpf    total mortality of canopy plants by pft/size in number of plants per m2 per year               m-2 yr-1                                                               F
 FATES_MORTALITY_CROWNSCORCH_SZPF    fates_levscpf    fire mortality from crown scorch by pft/size in number of plants per m2 per year               m-2 yr-1                                                               F
-FATES_MORTALITY_CSTARV_SZPF         fates_levscpf    carbon starvation mortality by pft/size in number of plants per m2 per year                    m-2 yr-1                                                               F
+FATES_MORTALITY_CSTARV_SZPF         fates_levscpf    carbon starvation mortality by pft/size in number of plants per m2 per year (both continous an m-2 yr-1                                                               F
 FATES_MORTALITY_FIRE_SZPF           fates_levscpf    fire mortality by pft/size in number of plants per m2 per year                                 m-2 yr-1                                                               F
 FATES_MORTALITY_FREEZING_SZPF       fates_levscpf    freezing mortality by pft/size in number of plants per m2 per year                             m-2 yr-1                                                               F
 FATES_MORTALITY_HYDRAULIC_SZPF      fates_levscpf    hydraulic mortality by pft/size in number of plants per m2 per year                            m-2 yr-1                                                               F
 FATES_MORTALITY_IMPACT_SZPF         fates_levscpf    impact mortality by pft/size in number of plants per m2 per year                               m-2 yr-1                                                               F
 FATES_MORTALITY_LOGGING_SZPF        fates_levscpf    logging mortality by pft/size in number of plants per m2 per year                              m-2 yr-1                                                               F
 FATES_MORTALITY_SENESCENCE_SZPF     fates_levscpf    senescence mortality by pft/size in number of plants per m2 per year                           m-2 yr-1                                                               F
-FATES_MORTALITY_TERMINATION_SZPF    fates_levscpf    termination mortality by pft/size in number pf plants per m2 per year                          m-2 yr-1                                                               F
+FATES_MORTALITY_TERMINATION_SZPF    fates_levscpf    termination mortality (excluding C-starvation) by pft/size in number pf plants per m2 per year m-2 yr-1                                                               F
 FATES_MORTALITY_USTORY_SZPF         fates_levscpf    total mortality of understory plants by pft/size in number of plants per m2 per year           m-2 yr-1                                                               F
 FATES_NPLANT_CANOPY_SZPF            fates_levscpf    number of canopy plants by size/pft per m2                                                     m-2                                                                    F
 FATES_NPLANT_SZPF                   fates_levscpf    stem number density by pft/size                                                                m-2                                                                    F
@@ -1008,8 +1049,11 @@ ratio_k1                            levdcmp          ratio_k1
 ratio_no3_co2                       levdcmp          ratio_no3_co2                                                                                  ratio                                                                  F
 soil_bulkdensity                    levdcmp          soil_bulkdensity                                                                               kg/m3                                                                  F
 soil_co2_prod                       levdcmp          soil_co2_prod                                                                                  ug C / g soil / day                                                    F
+CONC_CH4_SAT                        levgrnd          CH4 soil Concentration for inundated / lake area                                               mol/m3                                                                 F
+CONC_CH4_UNSAT                      levgrnd          CH4 soil Concentration for non-inundated area                                                  mol/m3                                                                 F
 FGR_SOIL_R                          levgrnd          Rural downward heat flux at interface below each soil layer                                    watt/m^2                                                               F
 HK                                  levgrnd          hydraulic conductivity (natural vegetated and crop landunits only)                             mm/s                                                                   F
+O2_DECOMP_DEPTH_UNSAT               levgrnd          O2 consumption from HR and AR for non-inundated area                                           mol/m3/s                                                               F
 SMP                                 levgrnd          soil matric potential (natural vegetated and crop landunits only)                              mm                                                                     T
 SOILPSI                             levgrnd          soil water potential in each soil layer                                                        MPa                                                                    F
 TSOI                                levgrnd          soil temperature (natural vegetated and crop landunits only)                                   K                                                                      T
@@ -1035,6 +1079,8 @@ SNO_TK_ICE                          levsno           Thermal conductivity (ice l
 SNO_T_ICE                           levsno           Snow temperatures (ice landunits only)                                                         K                                                                      F
 SNO_Z                               levsno           Snow layer thicknesses                                                                         m                                                                      F
 SNO_Z_ICE                           levsno           Snow layer thicknesses (ice landunits only)                                                    m                                                                      F
+CONC_O2_SAT                         levsoi           O2 soil Concentration for inundated / lake area                                                mol/m3                                                                 T
+CONC_O2_UNSAT                       levsoi           O2 soil Concentration for non-inundated area                                                   mol/m3                                                                 T
 FATES_FRAGMENTATION_SCALER_SL       levsoi           factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer                                                                            T
 FATES_FROOTC_SL                     levsoi           Total carbon in live plant fine-roots over depth                                               kg m-3                                                                 T
 H2OSOI                              levsoi           volumetric soil water (natural vegetated and crop landunits only)                              mm3/mm3                                                                T
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst
index 89e7dd23fc..67868f75b1 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst
@@ -8,11 +8,11 @@ use_cn = T
 use_crop = T
 use_fates = F
 
-=================================== ================ ============================================================================================== ================================================================= =======
+=================================== ================ ============================================================================================== ================================================================= ======= 
 CTSM History Fields
 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
                       Variable Name       Level Dim.                                                                               Long Description                                                             Units Active?
-=================================== ================ ============================================================================================== ================================================================= =======
+=================================== ================ ============================================================================================== ================================================================= ======= 
 A10TMIN                             -                10-day running mean of min 2-m temperature                                                     K                                                                      F
 A5TMIN                              -                5-day running mean of min 2-m temperature                                                      K                                                                      F
 ACTUAL_IMMOB                        -                actual N immobilization                                                                        gN/m^2/s                                                               T
@@ -36,10 +36,14 @@ ATM_O3                              -                atmospheric ozone partial p
 ATM_TOPO                            -                atmospheric surface height                                                                     m                                                                      T
 AVAILC                              -                C flux available for allocation                                                                gC/m^2/s                                                               F
 AVAIL_RETRANSN                      -                N flux available from retranslocation pool                                                     gN/m^2/s                                                               F
+AZSUN                               -                azimuth angle of the sun                                                                       radians                                                                F
 AnnET                               -                Annual ET                                                                                      mm/s                                                                   F
 BAF_CROP                            -                fractional area burned for crop                                                                s-1                                                                    T
 BAF_PEATF                           -                fractional area burned in peatland                                                             s-1                                                                    T
 BCDEP                               -                total BC deposition (dry+wet) from atmosphere                                                  kg/m^2/s                                                               T
+BCPHIDRY                            -                black carbon deposition (phidry) from atmosphere                                               kg/m^2/s                                                               F
+BCPHIWET                            -                black carbon deposition (phiwet) from atmosphere                                               kg/m^2/s                                                               F
+BCPHODRY                            -                black carbon deposition (phodry) from atmosphere                                               kg/m^2/s                                                               F
 BETA                                -                coefficient of convective velocity                                                             none                                                                   F
 BGLFR                               -                background litterfall rate                                                                     1/s                                                                    F
 BGNPP                               -                belowground NPP                                                                                gC/m^2/s                                                               T
@@ -66,7 +70,8 @@ COL_NTRUNC                          -                column-level sink for N tru
 COST_NACTIVE                        -                Cost of active uptake                                                                          gN/gC                                                                  T
 COST_NFIX                           -                Cost of fixation                                                                               gN/gC                                                                  T
 COST_NRETRANS                       -                Cost of retranslocation                                                                        gN/gC                                                                  T
-COSZEN                              -                cosine of solar zenith angle                                                                   none                                                                   F
+COSZEN                              -                cosine of solar zenith angle (downscaled if downscaling is activated)                          none                                                                   F
+COSZEN_GRC                          -                cosine of solar zenith angle                                                                   none                                                                   F
 CPHASE                              -                crop phenology phase                                                                           0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest       T
 CPOOL                               -                temporary photosynthate C pool                                                                 gC/m^2                                                                 T
 CPOOL_DEADCROOT_GR                  -                dead coarse root growth respiration                                                            gC/m^2/s                                                               F
@@ -158,7 +163,15 @@ DPVLTRB3                            -                turbulent deposition veloci
 DPVLTRB4                            -                turbulent deposition velocity 4                                                                m/s                                                                    F
 DSL                                 -                dry surface layer thickness                                                                    mm                                                                     T
 DSTDEP                              -                total dust deposition (dry+wet) from atmosphere                                                kg/m^2/s                                                               T
+DSTDRY1                             -                dust deposition (dry1) from atmosphere                                                         kg/m^2/s                                                               F
+DSTDRY2                             -                dust deposition (dry2) from atmosphere                                                         kg/m^2/s                                                               F
+DSTDRY3                             -                dust deposition (dry3) from atmosphere                                                         kg/m^2/s                                                               F
+DSTDRY4                             -                dust deposition (dry4) from atmosphere                                                         kg/m^2/s                                                               F
 DSTFLXT                             -                total surface dust emission                                                                    kg/m2/s                                                                T
+DSTWET1                             -                dust deposition (wet1) from atmosphere                                                         kg/m^2/s                                                               F
+DSTWET2                             -                dust deposition (wet2) from atmosphere                                                         kg/m^2/s                                                               F
+DSTWET3                             -                dust deposition (wet3) from atmosphere                                                         kg/m^2/s                                                               F
+DSTWET4                             -                dust deposition (wet4) from atmosphere                                                         kg/m^2/s                                                               F
 DT_VEG                              -                change in t_veg, last iteration                                                                K                                                                      F
 DWT_CONV_CFLUX                      -                conversion C flux (immediate loss to atm) (0 at all times except first timestep of year)       gC/m^2/s                                                               T
 DWT_CONV_CFLUX_DRIBBLED             -                conversion C flux (immediate loss to atm), dribbled throughout the year                        gC/m^2/s                                                               T
@@ -246,8 +259,9 @@ FIRE                                -                emitted infrared (longwave)
 FIRE_ICE                            -                emitted infrared (longwave) radiation (ice landunits only)                                     W/m^2                                                                  F
 FIRE_R                              -                Rural emitted infrared (longwave) radiation                                                    W/m^2                                                                  T
 FIRE_U                              -                Urban emitted infrared (longwave) radiation                                                    W/m^2                                                                  F
-FLDS                                -                atmospheric longwave radiation (downscaled to columns in glacier regions)                      W/m^2                                                                  T
-FLDS_ICE                            -                atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2                                                                  F
+FLDS                                -                atmospheric longwave radiation (downscaled for glacier and hillslope columns)                  W/m^2                                                                  T
+FLDS_ICE                            -                atmospheric longwave radiation (downscaled for glacier and hillslope columns) (ice landunits o W/m^2                                                                  F
+FLDS_NOT_DOWNSCALED                 -                atmospheric longwave radiation (pre-downscaling)                                               W/m^2                                                                  F
 FPI                                 -                fraction of potential immobilization                                                           proportion                                                             T
 FPSN                                -                photosynthesis                                                                                 umol m-2 s-1                                                           T
 FPSN24                              -                24 hour accumulative patch photosynthesis starting from mid-night                              umol CO2/m^2 ground/day                                                F
@@ -278,7 +292,7 @@ FSA_R                               -                Rural absorbed solar radiat
 FSA_U                               -                Urban absorbed solar radiation                                                                 W/m^2                                                                  F
 FSD24                               -                direct radiation (last 24hrs)                                                                  K                                                                      F
 FSD240                              -                direct radiation (last 240hrs)                                                                 K                                                                      F
-FSDS                                -                atmospheric incident solar radiation                                                           W/m^2                                                                  T
+FSDS                                -                atmospheric incident solar radiation (downscaled for glacier and hillslope columns)            W/m^2                                                                  T
 FSDSND                              -                direct nir incident solar radiation                                                            W/m^2                                                                  T
 FSDSNDLN                            -                direct nir incident solar radiation at local noon                                              W/m^2                                                                  T
 FSDSNI                              -                diffuse nir incident solar radiation                                                           W/m^2                                                                  T
@@ -286,6 +300,7 @@ FSDSVD                              -                direct vis incident solar r
 FSDSVDLN                            -                direct vis incident solar radiation at local noon                                              W/m^2                                                                  T
 FSDSVI                              -                diffuse vis incident solar radiation                                                           W/m^2                                                                  T
 FSDSVILN                            -                diffuse vis incident solar radiation at local noon                                             W/m^2                                                                  T
+FSDS_from_atm                       -                atmospheric incident solar radiation received from atmosphere (pre-downscaling)                W/m^2                                                                  T
 FSH                                 -                sensible heat not including correction for land use change and rain/snow conversion            W/m^2                                                                  T
 FSH_G                               -                sensible heat from ground                                                                      W/m^2                                                                  T
 FSH_ICE                             -                sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2                                                                  F
@@ -426,6 +441,7 @@ LEAFC_STORAGE_XFER_ACC              -                Accumulated leaf C transfer
 LEAFC_TO_BIOFUELC                   -                leaf C to biofuel C                                                                            gC/m^2/s                                                               T
 LEAFC_TO_LITTER                     -                leaf C litterfall                                                                              gC/m^2/s                                                               F
 LEAFC_TO_LITTER_FUN                 -                leaf C litterfall used by FUN                                                                  gC/m^2/s                                                               T
+LEAFC_TO_REMOVEDRESIDUEC            -                leaf C to removed residue C                                                                    gC/m^2/s                                                               F
 LEAFC_XFER                          -                leaf C transfer                                                                                gC/m^2                                                                 F
 LEAFC_XFER_TO_LEAFC                 -                leaf C growth from storage                                                                     gC/m^2/s                                                               F
 LEAFN                               -                leaf N                                                                                         gN/m^2                                                                 T
@@ -487,6 +503,7 @@ LIVESTEMC_STORAGE                   -                live stem C storage
 LIVESTEMC_STORAGE_TO_XFER           -                live stem C shift storage to transfer                                                          gC/m^2/s                                                               F
 LIVESTEMC_TO_BIOFUELC               -                livestem C to biofuel C                                                                        gC/m^2/s                                                               T
 LIVESTEMC_TO_DEADSTEMC              -                live stem C turnover                                                                           gC/m^2/s                                                               F
+LIVESTEMC_TO_REMOVEDRESIDUEC        -                livestem C to removed residue C                                                                gC/m^2/s                                                               F
 LIVESTEMC_XFER                      -                live stem C transfer                                                                           gC/m^2                                                                 F
 LIVESTEMC_XFER_TO_LIVESTEMC         -                live stem C growth from storage                                                                gC/m^2/s                                                               F
 LIVESTEMN                           -                live stem N                                                                                    gN/m^2                                                                 T
@@ -498,7 +515,7 @@ LIVESTEMN_XFER                      -                live stem N transfer
 LIVESTEMN_XFER_TO_LIVESTEMN         -                live stem N growth from storage                                                                gN/m^2/s                                                               F
 LIVESTEM_MR                         -                live stem maintenance respiration                                                              gC/m^2/s                                                               F
 LNC                                 -                leaf N concentration                                                                           gN leaf/m^2                                                            T
-LWdown                              -                atmospheric longwave radiation (downscaled to columns in glacier regions)                      W/m^2                                                                  F
+LWdown                              -                atmospheric longwave radiation (downscaled for glacier and hillslope columns)                  W/m^2                                                                  F
 LWup                                -                upwelling longwave radiation                                                                   W/m^2                                                                  F
 MEG_acetaldehyde                    -                MEGAN flux                                                                                     kg/m2/sec                                                              T
 MEG_acetic_acid                     -                MEGAN flux                                                                                     kg/m2/sec                                                              T
@@ -700,6 +717,9 @@ NUPTAKE_NPP_FRACTION                -                frac of NPP used in N uptak
 N_ALLOMETRY                         -                N allocation index                                                                             none                                                                   F
 OBU                                 -                Monin-Obukhov length                                                                           m                                                                      F
 OCDEP                               -                total OC deposition (dry+wet) from atmosphere                                                  kg/m^2/s                                                               T
+OCPHIDRY                            -                organic carbon deposition (phidry) from atmosphere                                             kg/m^2/s                                                               F
+OCPHIWET                            -                organic carbon deposition (phiwet) from atmosphere                                             kg/m^2/s                                                               F
+OCPHODRY                            -                black carbon deposition (phodry) from atmosphere                                               kg/m^2/s                                                               F
 OFFSET_COUNTER                      -                offset days counter                                                                            days                                                                   F
 OFFSET_FDD                          -                offset freezing degree days counter                                                            C degree-days                                                          F
 OFFSET_FLAG                         -                offset flag                                                                                    none                                                                   F
@@ -719,8 +739,9 @@ PAR24_sun                           -                sunlit PAR (24 hrs)
 PARVEGLN                            -                absorbed par by vegetation at local noon                                                       W/m^2                                                                  T
 PAR_shade                           -                shade PAR                                                                                      umol/m2/s                                                              F
 PAR_sun                             -                sunlit PAR                                                                                     umol/m2/s                                                              F
-PBOT                                -                atmospheric pressure at surface (downscaled to columns in glacier regions)                     Pa                                                                     T
+PBOT                                -                atmospheric pressure at surface (downscaled for glacier and hillslope columns)                 Pa                                                                     T
 PBOT_240                            -                10 day running mean of air pressure                                                            Pa                                                                     F
+PBOT_NOT_DOWNSCALED                 -                atmospheric pressure at surface (pre-downscaling)                                              Pa                                                                     F
 PCH4                                -                atmospheric partial pressure of CH4                                                            Pa                                                                     T
 PCO2                                -                atmospheric partial pressure of CO2                                                            Pa                                                                     T
 PCO2_240                            -                10 day running mean of CO2 pressure                                                            Pa                                                                     F
@@ -754,10 +775,11 @@ PSNSHA                              -                shaded leaf photosynthesis
 PSNSHADE_TO_CPOOL                   -                C fixation from shaded canopy                                                                  gC/m^2/s                                                               T
 PSNSUN                              -                sunlit leaf photosynthesis                                                                     umolCO2/m^2/s                                                          T
 PSNSUN_TO_CPOOL                     -                C fixation from sunlit canopy                                                                  gC/m^2/s                                                               T
-PSurf                               -                atmospheric pressure at surface (downscaled to columns in glacier regions)                     Pa                                                                     F
+PSurf                               -                atmospheric pressure at surface (downscaled for glacier and hillslope columns)                 Pa                                                                     F
 Q2M                                 -                2m specific humidity                                                                           kg/kg                                                                  T
 QAF                                 -                canopy air humidity                                                                            kg/kg                                                                  F
 QBOT                                -                atmospheric specific humidity (downscaled to columns in glacier regions)                       kg/kg                                                                  T
+QBOT_NOT_DOWNSCALED                 -                atmospheric specific humidity (pre-downscaling)                                                kg/kg                                                                  F
 QDIRECT_THROUGHFALL                 -                direct throughfall of liquid (rain + above-canopy irrigation)                                  mm/s                                                                   F
 QDIRECT_THROUGHFALL_SNOW            -                direct throughfall of snow                                                                     mm/s                                                                   F
 QDRAI                               -                sub-surface drainage                                                                           mm/s                                                                   T
@@ -839,7 +861,7 @@ RETRANSN                            -                plant pool of retranslocate
 RETRANSN_TO_NPOOL                   -                deployment of retranslocated N                                                                 gN/m^2/s                                                               T
 RH                                  -                atmospheric relative humidity                                                                  %                                                                      F
 RH2M                                -                2m relative humidity                                                                           %                                                                      T
-RH2M_R                              -                Rural 2m specific humidity                                                                     %                                                                      F
+RH2M_R                              -                Rural 2m relative humidity                                                                     %                                                                      F
 RH2M_U                              -                Urban 2m relative humidity                                                                     %                                                                      F
 RH30                                -                30-day running mean of relative humidity                                                       %                                                                      F
 RHAF                                -                fractional humidity of canopy air                                                              fraction                                                               F
@@ -849,6 +871,7 @@ RR                                  -                root respiration (fine root
 RSSHA                               -                shaded leaf stomatal resistance                                                                s/m                                                                    T
 RSSUN                               -                sunlit leaf stomatal resistance                                                                s/m                                                                    T
 Rainf                               -                atmospheric rain, after rain/snow repartitioning based on temperature                          mm/s                                                                   F
+Rho_from_atm                        -                atmospheric density (pre-downscaling)                                                          kg/m^3                                                                 F
 Rnet                                -                net radiation                                                                                  W/m^2                                                                  F
 SABG                                -                solar rad absorbed by ground                                                                   W/m^2                                                                  T
 SABG_PEN                            -                Rural solar rad penetrating top soil or snow layer                                             watt/m^2                                                               T
@@ -977,9 +1000,11 @@ T10                                 -                10-day running mean of 2-m
 TAF                                 -                canopy air temperature                                                                         K                                                                      F
 TAUX                                -                zonal surface stress                                                                           kg/m/s^2                                                               T
 TAUY                                -                meridional surface stress                                                                      kg/m/s^2                                                               T
-TBOT                                -                atmospheric air temperature (downscaled to columns in glacier regions)                         K                                                                      T
+TBOT                                -                atmospheric air temperature (downscaled for glacier and hillslope columns)                     K                                                                      T
 TBUILD                              -                internal urban building air temperature                                                        K                                                                      T
 TBUILD_MAX                          -                prescribed maximum interior building temperature                                               K                                                                      F
+TDEPTH                              -                tributary water depth                                                                          m                                                                      F
+TDEPTHMAX                           -                tributary bankfull water depth                                                                 m                                                                      F
 TEMPAVG_T2M                         -                temporary average 2m air temperature                                                           K                                                                      F
 TEMPMAX_RETRANSN                    -                temporary annual max of retranslocated N pool                                                  gN/m^2                                                                 F
 TEMPSUM_POTENTIAL_GPP               -                temporary annual sum of potential GPP                                                          gC/m^2/yr                                                              F
@@ -992,7 +1017,7 @@ TG_ICE                              -                ground temperature (ice lan
 TG_R                                -                Rural ground temperature                                                                       K                                                                      F
 TG_U                                -                Urban ground temperature                                                                       K                                                                      F
 TH2OSFC                             -                surface water temperature                                                                      K                                                                      T
-THBOT                               -                atmospheric air potential temperature (downscaled to columns in glacier regions)               K                                                                      T
+THBOT                               -                atmospheric air potential temperature (downscaled for glacier and hillslope columns)           K                                                                      T
 THIC                                -                2 m Temp Hum Index Comfort                                                                     C                                                                      T
 THIC_R                              -                Rural 2 m Temp Hum Index Comfort                                                               C                                                                      T
 THIC_U                              -                Urban 2 m Temp Hum Index Comfort                                                               C                                                                      T
@@ -1060,8 +1085,9 @@ TV240                               -                vegetation temperature (las
 TVEGD10                             -                10 day running mean of patch daytime vegetation temperature                                    Kelvin                                                                 F
 TVEGN10                             -                10 day running mean of patch night-time vegetation temperature                                 Kelvin                                                                 F
 TWS                                 -                total water storage                                                                            mm                                                                     T
-Tair                                -                atmospheric air temperature (downscaled to columns in glacier regions)                         K                                                                      F
+Tair                                -                atmospheric air temperature (downscaled for glacier and hillslope columns)                     K                                                                      F
 Tair_from_atm                       -                atmospheric air temperature received from atmosphere (pre-downscaling)                         K                                                                      F
+Thair_from_atm                      -                atmospheric air potential temperature (pre-downscaling)                                        K                                                                      F
 U10                                 -                10-m wind                                                                                      m/s                                                                    T
 U10_DUST                            -                10-m wind for dust model                                                                       m/s                                                                    T
 U10_ICE                             -                10-m wind (ice landunits only)                                                                 m/s                                                                    F
@@ -1072,6 +1098,7 @@ URBAN_AC                            -                urban air conditioning flux
 URBAN_HEAT                          -                urban heating flux                                                                             W/m^2                                                                  T
 USTAR                               -                aerodynamical resistance                                                                       s/m                                                                    F
 UST_LAKE                            -                friction velocity (lakes only)                                                                 m/s                                                                    F
+UWIND                               -                atmospheric U wind velocity magnitude                                                          m/s                                                                    F
 VA                                  -                atmospheric wind speed plus convective velocity                                                m/s                                                                    F
 VCMX25T                             -                canopy profile of vcmax25                                                                      umol/m2/s                                                              T
 VENTILATION                         -                sensible heat flux from building ventilation                                                   W/m^2                                                                  T
@@ -1081,6 +1108,7 @@ VOLRMCH                             -                river channel main channel
 VPD                                 -                vpd                                                                                            Pa                                                                     F
 VPD2M                               -                2m vapor pressure deficit                                                                      Pa                                                                     T
 VPD_CAN                             -                canopy vapor pressure deficit                                                                  kPa                                                                    T
+VWIND                               -                atmospheric V wind velocity magnitude                                                          m/s                                                                    F
 Vcmx25Z                             -                canopy profile of vcmax25 predicted by LUNA model                                              umol/m2/s                                                              T
 WASTEHEAT                           -                sensible heat flux from heating/cooling sources of urban waste heat                            W/m^2                                                                  T
 WBA                                 -                2 m Wet Bulb                                                                                   C                                                                      T
@@ -1261,7 +1289,7 @@ STEM_PROF                           levdcmp          profile for litter C and N
 SUPPLEMENT_TO_SMINN_vr              levdcmp          supplemental N supply                                                                          gN/m^3/s                                                               F
 WFPS                                levdcmp          WFPS                                                                                           percent                                                                F
 anaerobic_frac                      levdcmp          anaerobic_frac                                                                                 m3/m3                                                                  F
-diffus                              levdcmp          diffusivity (from nitrification-denitrification)                                               m^2/s                                                                  F
+diffus                              levdcmp          diffusivity                                                                                    m^2/s                                                                  F
 fr_WFPS                             levdcmp          fr_WFPS                                                                                        fraction                                                               F
 n2_n2o_ratio_denit                  levdcmp          n2_n2o_ratio_denit                                                                             gN/gN                                                                  F
 r_psi                               levdcmp          r_psi                                                                                          m                                                                      F

From bbfe2b4542fc56b08cfeeffefc1b4e54f9572181 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 2 May 2024 15:07:50 -0600
Subject: [PATCH 0166/1248] Correction to last commit (1850 should have been
 2000)

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index cfd81a5a2b..bf20c1241a 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -830,7 +830,7 @@
       <option name="comment"  >Run in DEBUG with the matrix solution on for spinup with all options it interacts with (requires Bgc, but also turn on Crop and Carbon isotopes)</option>
     </options>
   </test>
-  <test name="ERS_Lm54_Mmpi-serial" grid="1x1_numaIA" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
+  <test name="ERS_Lm54_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>

From 57004d92e39e6f83393f6f7c74cf3e21062e18c3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 3 May 2024 17:34:08 -0600
Subject: [PATCH 0167/1248] New conflict resolution in testlist_clm.xml, this
 time for an izumi test

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index bf20c1241a..c2bb819572 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1652,7 +1652,7 @@
       <option name="comment"  >multi-year test with crops and isotopes that includes all crop types; added (2020-05-21) in order to test the new switchgrass and miscanthus crops (which otherwise aren't currently tested)</option>
     </options>
   </test>
-  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/ciso_monthly--clm/matrixcnOn">
+  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
     </machines>

From f65de8fc0968316fe7e9a4c99bbc6e897dee5a92 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 4 May 2024 11:08:24 -0600
Subject: [PATCH 0168/1248] Add LND_SETS_DUST_EMIS_DRV_FLDS which will be used
 to NOT set dust_emis drv_flds_in settings when CAM is going to set them

---
 cime_config/config_component.xml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index f7adab268f..c474b7e0c1 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -162,6 +162,20 @@
     This is typically set by the compset.</desc>
   </entry>
 
+  <entry id="LND_SETS_DUST_EMIS_DRV_FLDS">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>TRUE</default_value>
+    <values>
+      <!-- Until CAM sets dust settings in drv_flds_in this should only be TRUE
+      <value compset="CAM"  >FALSE</value>
+      -->
+    </values>
+    <group>run_component_cpl</group>
+    <file>env_run.xml</file>
+    <desc>If CTSM will set the dust settings in drv_flds_in (TRUE), or if ATM (i.e. CAM) will - DO NOT EDIT (set by compset name)</desc>
+  </entry>
+
   <entry id="CLM_CONFIGURATION">
     <type>char</type>
     <valid_values>clm,nwp</valid_values>

From 89f08710f61275cb0ac1dea22b5de849787682b2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 4 May 2024 11:17:34 -0600
Subject: [PATCH 0169/1248] Move dust_emis and soil_erod namelist items to the
 drv_fld_in namelist file in CMEPS

---
 bld/CLMBuildNamelist.pm                            | 13 ++++++++-----
 bld/namelist_files/namelist_defaults_ctsm.xml      |  2 --
 bld/namelist_files/namelist_definition_ctsm.xml    | 14 --------------
 .../namelist_definition_drv_flds.xml               | 13 +++++++++++++
 bld/unit_testers/build-namelist_test.pl            | 14 +++++++++++++-
 5 files changed, 34 insertions(+), 22 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fb44023cd5..ce2c2a81d2 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -517,6 +517,7 @@ sub read_namelist_defaults {
                             "$cfgdir/namelist_files/namelist_defaults_ctsm.xml",
                             "$cfgdir/namelist_files/namelist_defaults_drv.xml",
                             "$cfgdir/namelist_files/namelist_defaults_fire_emis.xml",
+                            "$cfgdir/namelist_files/namelist_defaults_dust_emis.xml",
                             "$cfgdir/namelist_files/namelist_defaults_drydep.xml" );
 
   # Add the location of the use case defaults files to the options hash
@@ -3988,7 +3989,7 @@ sub setup_logic_fire_emis {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_dust_emis {
-  # Logic to handle the dust emissions
+  # Logic to handle the dust emissions namelists, both drv_flds_in and lnd_in files
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   # First get the dust emission method
@@ -4011,14 +4012,16 @@ sub setup_logic_dust_emis {
                        'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source,
                        'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} );
         }
-     } else {
+     } elsif ( $zender_source eq "atm" ) {
         foreach my $option ( @zender_files_in_lnd_opts ) {
            if ( defined($nl->get_value($option)) ) {
-             $log->fatal_error("zender_soil_erod_source is NOT lnd, but the file option $option is being set" .
-                               " and should NOT be unless you want it handled here in the LAND model, " .
+             $log->fatal_error("zender_soil_erod_source is atm, and the file option $option is being set" .
+                               " which should NOT be unless you want it handled here in the LAND model, " .
                                "otherwise the equivalent option is set in CAM" );
            }
         }
+     } elsif ( $zender_source eq "none" ) {
+        $log->fatal_error("zender_soil_erod_source is set to none and only atm or lnd should be used when $var is Zender_2002" );
      }
   } else {
      # Verify that NONE of the Zender options are being set if Zender is NOT being used
@@ -4736,7 +4739,7 @@ sub write_output_files {
   $log->verbose_message("Writing clm namelist to $outfile");
 
   # Drydep, fire-emission or MEGAN namelist for driver
-  @groups = qw(drydep_inparm megan_emis_nl fire_emis_nl carma_inparm);
+  @groups = qw(drydep_inparm megan_emis_nl fire_emis_nl carma_inparm dust_emis_inparm);
   $outfile = "$opts->{'dir'}/drv_flds_in";
   $nl->write($outfile, 'groups'=>\@groups, 'note'=>"$note" );
   $log->verbose_message("Writing @groups namelists to $outfile");
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 147a23f49a..6fde63ee02 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1991,8 +1991,6 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- Defaults for Zender's soil erodibility data  -->
 <!-- ===========================================  -->
 
-<dust_emis_method>Zender_2003</dust_emis_method>
-<zender_soil_erod_source dust_emis_method="Zender_2003">atm</zender_soil_erod_source>
 <zendersoilerod_mapalgo>bilinear</zendersoilerod_mapalgo>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 37c457141c..e730082e90 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1612,20 +1612,6 @@ Mapping method from Nitrogen deposition input file to the model resolution
 <!-- Dust namelist and Zender soil erodibility stream                                          -->
 <!-- ========================================================================================  -->
 
-<entry id="dust_emis_method" type="char*12" category="physics"
-       group="clm_inparm" valid_values="Zender_2003,Leung_2023" >
-Which dust emission method is going to be used. Either the Zender 2003 scheme or the Leung 2023
-scheme.
-(NOTE: The Leung 2023 method is NOT currently available)
-</entry>
-
-<entry id="zender_soil_erod_source" type="char*3" category="physics"
-       group="zendersoilerod" valid_values="lnd,atm" >
-Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
-here in CTSM, or in the ATM model.
-(only used when dust_emis_method is Zender_2003)
-</entry>
-
 <entry id="zendersoilerod_mapalgo" type="char*256" category="physics"
        group="zendersoilerod" valid_values="bilinear,nn,nnoni,nnonj,spval,copy" >
 Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
diff --git a/bld/namelist_files/namelist_definition_drv_flds.xml b/bld/namelist_files/namelist_definition_drv_flds.xml
index 088f5c5fa9..89bab07f4f 100644
--- a/bld/namelist_files/namelist_definition_drv_flds.xml
+++ b/bld/namelist_files/namelist_definition_drv_flds.xml
@@ -123,4 +123,17 @@
     List of fluxes needed by the CARMA model, from CLM to CAM.
   </entry>
 
+  <entry id="dust_emis_method" type="char*80" category="dust_emissions"
+    group="dust_emis_inparm" valid_values="Zender_2003,Leung_2023" >
+     Which dust emission method is going to be used. Either the Zender 2003 scheme or the Leung 2023 scheme.
+     (NOTE: The Leung 2023 method is NOT currently available)
+  </entry>
+
+  <entry id="zender_soil_erod_source" type="char*80" category="dust_emissions"
+    group="dust_emis_inparm" valid_values="none,lnd,atm" >
+     Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
+     in the active LAND model or in the ATM model.
+     (only used when dust_emis_method is Zender_2003)
+  </entry>
+
 </namelist_definition>
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 7b654337af..114fb0c36c 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 2513;
+my $ntests = 2515;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 1545;
@@ -1255,6 +1255,18 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                      },
+     "soil_erod_none_w_Zender"  =>{ options=>"--envxml_dir .",
+                                     namelst=>"dust_emis_method='Zender_2003', " .
+                                     "zender_soil_erod_source='none'",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                     },
+     "soil_erod_bad_w_Zender"   =>{ options=>"--envxml_dir .",
+                                     namelst=>"dust_emis_method='Zender_2003', " .
+                                     "zender_soil_erod_source='zztop'",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                     },
                );
 foreach my $key ( keys(%failtest) ) {
    print( "$key\n" );

From edae95a1013439e234e7d56d57c01efc74ce063f Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sat, 4 May 2024 13:08:16 -0600
Subject: [PATCH 0170/1248] manually revert defaults for use_fates_lupft and
 fix calls to fatal_error

---
 bld/CLMBuildNamelist.pm                       | 25 +++++++++++--------
 bld/namelist_files/namelist_defaults_ctsm.xml |  7 ++----
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 23505492bd..01d583eb16 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4371,12 +4371,16 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
-                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
-                       "use_fates_luh","use_fates_lupft" );
+                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage");
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
         }
+
+ 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
+ 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
+                      'use_fates_lupft'=>$nl_flags->{'use_fates_lupft'} );
+
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');
         if ( ($parteh_mode == 1) &&  ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
@@ -4384,6 +4388,7 @@ sub setup_logic_fates {
                             "but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" . 
                             "Change suplnitro back to ALL");
         }
+
         #
         # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
         # And also check for other settings that can't be trigged on as well
@@ -4425,16 +4430,16 @@ sub setup_logic_fates {
                         'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
             my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
             if ( ! defined($nl->get_value($var))  ) {
-              fatal_error("$var is required when use_fates_lupft is set" );
+              $log->fatal_error("$var is required when use_fates_lupft is set" );
             } elsif ( ! -f "$fname" ) {
-              fatal_error("$fname does NOT point to a valid filename" );
+              $log->fatal_error("$fname does NOT point to a valid filename" );
             }
           }
           # make sure that nocomp and fbg mode are enabled as well as use_fates_luh
           my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" );
           foreach my $var ( @list ) {
             if ( ! &value_is_true($nl->get_value($var)) ) {
-              fatal_error("$var is required when use_fates_lupft is true" );
+              $log->fatal_error("$var is required when use_fates_lupft is true" );
             }
           }
         }
@@ -4461,10 +4466,10 @@ sub setup_logic_fates {
         if ( defined($nl->get_value($var))  ) {
           if ( &value_is_true($nl->get_value($var)) ) {
             if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
-              fatal_error("use_fates_luh must be true when $var is true" );
+              $log->fatal_error("use_fates_luh must be true when $var is true" );
             }
             if ( $nl->get_value('fates_harvest_mode') > 0) {
-              fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" );
+              $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" );
             }
           }
         }
@@ -4475,17 +4480,17 @@ sub setup_logic_fates {
            # if ( $nl->get_value($var) == 2) {
            #    # Make sure that do_harvest is set to true
            #    if ( ! &value_is_true($nl->get_value('do_harvest')) ) {
-           #      fatal_error("do_harvest must be true when $var is equal to 2" );
+           #      $log->fatal_error("do_harvest must be true when $var is equal to 2" );
            # }
            # using fates_harvest mode with raw luh2 harvest data
            if ( $nl->get_value($var) > 2) {
               # Make sure that use_fates_luh is true when using raw fates luh2 harvest data
               if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
-                fatal_error("use_fates_luh is required to be true when $var is greater than 2" );
+                $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" );
               }
               # do_harvest can not be on if we are using the raw fates luh2 harvest data
               if ( &value_is_true($nl->get_value('do_harvest')) ) {
-                fatal_error("do_harvest can not be true when $var is greater than 2" );
+                $log->fatal_error("do_harvest can not be true when $var is greater than 2" );
               }
            }
         }
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 68a122e9bc..1195ba5329 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2769,19 +2769,16 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="3"         >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="4"         >.true.</use_fates_luh>
+
 <use_fates_luh                 use_fates=".true." use_fates_lupft=".true."       >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true."                                >.false.</use_fates_luh>
+
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 
 <use_fates_nocomp              use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>
-<use_fates_nocomp              use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
 <use_fates_nocomp              use_fates=".true."                         >.false.</use_fates_nocomp>
 <use_fates_fixed_biogeog       use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_fixed_biogeog>
-<use_fates_fixed_biogeog       use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_fixed_biogeog>
 <use_fates_fixed_biogeog       use_fates=".true."                         >.false.</use_fates_fixed_biogeog>
 
 <!-- =========================================  -->

From af6a1c0e87a4f3d03e3fe6976b00af3ac94398f1 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sat, 4 May 2024 13:37:22 -0600
Subject: [PATCH 0171/1248] remove old flandusepftdat add_default and fix
 use_fates_lupft check

this also temporarily removes the use_fates_lupft check for the use_fates_luh
namelist defaults
---
 bld/CLMBuildNamelist.pm                       | 17 +++++++----------
 bld/namelist_files/namelist_defaults_ctsm.xml |  6 +-----
 2 files changed, 8 insertions(+), 15 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 01d583eb16..1cb14878e7 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4389,7 +4389,6 @@ sub setup_logic_fates {
                             "Change suplnitro back to ALL");
         }
 
-        #
         # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
         # And also check for other settings that can't be trigged on as well
         #
@@ -4434,12 +4433,13 @@ sub setup_logic_fates {
             } elsif ( ! -f "$fname" ) {
               $log->fatal_error("$fname does NOT point to a valid filename" );
             }
-          }
-          # make sure that nocomp and fbg mode are enabled as well as use_fates_luh
-          my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" );
-          foreach my $var ( @list ) {
-            if ( ! &value_is_true($nl->get_value($var)) ) {
-              $log->fatal_error("$var is required when use_fates_lupft is true" );
+
+            # make sure that nocomp and fbg mode are enabled as well as use_fates_luh
+            my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" );
+            foreach my $var ( @list ) {
+              if ( ! &value_is_true($nl->get_value($var)) ) {
+                $log->fatal_error("$var is required when use_fates_lupft is true" );
+              }
             }
           }
         }
@@ -4456,9 +4456,6 @@ sub setup_logic_fates {
               } elsif ( ! -f "$fname" ) {
                  $log->fatal_error("$fname does NOT point to a valid filename" );
               }
-
-              $var = "flandusepftdat";
-              add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
            }
         }
         # check that fates landuse is on and harvest mode is off when potential veg switch is true
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 1195ba5329..e6f6b736a6 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2769,13 +2769,9 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-
-<use_fates_luh                 use_fates=".true." use_fates_lupft=".true."       >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true."                                >.false.</use_fates_luh>
-
+<use_fates_luh                 use_fates=".true.">.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
-
 <use_fates_nocomp              use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>
 <use_fates_nocomp              use_fates=".true."                         >.false.</use_fates_nocomp>
 <use_fates_fixed_biogeog       use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_fixed_biogeog>

From d5575d5c31e0013b8e303b3bc6966f6c8e405f55 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sat, 4 May 2024 14:42:15 -0600
Subject: [PATCH 0172/1248] correct call to add_default for use_fates_lupft
 dependency with use_fates_luh

---
 bld/CLMBuildNamelist.pm                       | 2 +-
 bld/namelist_files/namelist_defaults_ctsm.xml | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 1cb14878e7..7ad35584aa 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4379,7 +4379,7 @@ sub setup_logic_fates {
 
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
-                      'use_fates_lupft'=>$nl_flags->{'use_fates_lupft'} );
+                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft') );
 
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e6f6b736a6..38a0fe6493 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2769,7 +2769,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-<use_fates_luh                 use_fates=".true.">.false.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true."                         >.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 <use_fates_nocomp              use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>

From ea773e451b78b3b7011a534a73352693600be95e Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sat, 4 May 2024 14:53:16 -0600
Subject: [PATCH 0173/1248] add use_fates_lupft dependencies for nocomp and fbg

---
 bld/CLMBuildNamelist.pm                       | 10 ++++++++--
 bld/namelist_files/namelist_defaults_ctsm.xml |  2 ++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 7ad35584aa..261c775fbd 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4370,7 +4370,7 @@ sub setup_logic_fates {
     if (&value_is_true( $nl_flags->{'use_fates'})  ) {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
-                       "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
+                       "use_fates_inventory_init","fates_seeddisp_cadence",
                        "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage");
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
@@ -4380,6 +4380,12 @@ sub setup_logic_fates {
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_lupft'=>$nl->get_value('use_fates_lupft') );
+ 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'},
+                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
+                      'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
+ 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'},
+                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
+                      'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
 
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');
@@ -4435,7 +4441,7 @@ sub setup_logic_fates {
             }
 
             # make sure that nocomp and fbg mode are enabled as well as use_fates_luh
-            my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" );
+            my @list = ( "use_fates_luh", "use_fates_nocomp", "use_fates_fixed_biogeog" );
             foreach my $var ( @list ) {
               if ( ! &value_is_true($nl->get_value($var)) ) {
                 $log->fatal_error("$var is required when use_fates_lupft is true" );
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 38a0fe6493..216ad74ca1 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2774,8 +2774,10 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 <use_fates_nocomp              use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>
+<use_fates_nocomp              use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
 <use_fates_nocomp              use_fates=".true."                         >.false.</use_fates_nocomp>
 <use_fates_fixed_biogeog       use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_fixed_biogeog>
+<use_fates_fixed_biogeog       use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_fixed_biogeog>
 <use_fates_fixed_biogeog       use_fates=".true."                         >.false.</use_fates_fixed_biogeog>
 
 <!-- =========================================  -->

From a21181f1b3e4a89f426e4b9bdce52e76b06ffc39 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sun, 5 May 2024 12:24:05 -0600
Subject: [PATCH 0174/1248] add fates_harvest_mode to use_fates_luh check

---
 bld/CLMBuildNamelist.pm                       | 3 ++-
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 ++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 261c775fbd..8af5f035e9 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4379,7 +4379,8 @@ sub setup_logic_fates {
 
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
-                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft') );
+                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), 
+                      'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') );
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 216ad74ca1..206ab7cd1b 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2769,6 +2769,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="3">.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="4">.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true."                         >.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>

From d8178e415a399f2f0fd61b15f92b4c43f9dd4484 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sun, 5 May 2024 12:54:52 -0600
Subject: [PATCH 0175/1248] add use_fates_potentialveg to use_fates_luh check

---
 bld/CLMBuildNamelist.pm                       | 4 +++-
 bld/namelist_files/namelist_defaults_ctsm.xml | 7 ++++---
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 8af5f035e9..b450060736 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4377,9 +4377,11 @@ sub setup_logic_fates {
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
         }
 
+ 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_potentialveg', 'use_fates'=>$nl_flags->{'use_fates'});
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), 
+                      'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'), 
                       'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') );
  	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
@@ -4466,7 +4468,7 @@ sub setup_logic_fates {
            }
         }
         # check that fates landuse is on and harvest mode is off when potential veg switch is true
-        my $var = "use_potentialveg";
+        my $var = "use_fates_potentialveg";
         if ( defined($nl->get_value($var))  ) {
           if ( &value_is_true($nl->get_value($var)) ) {
             if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 206ab7cd1b..9d2a34b7bf 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2769,10 +2769,11 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="3">.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="4">.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="3"  >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="4"  >.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true."                         >.false.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true."                                >.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 <use_fates_nocomp              use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>

From 9751fb68174903134e301472087edc263bc4822e Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sun, 5 May 2024 13:01:20 -0600
Subject: [PATCH 0176/1248] add check to fates sp mode to make sure landuse
 isn't enabled

---
 bld/CLMBuildNamelist.pm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b450060736..54f0c0c997 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4414,6 +4414,10 @@ sub setup_logic_fates {
               if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
                     $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
               }
+              # fates landuse can't be on with FATES SP mode is active
+              if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
+                    $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
+              }
            }
         }
         my $var = "use_fates_inventory_init";

From 39cd37dd5d1da5ea96b2327ecc10ac7f72d37383 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 6 May 2024 13:05:29 -0600
Subject: [PATCH 0177/1248] Provide scalar cth and cbh in unit tests. Failing.

---
 python/ctsm/test/test_unit_singlept_data_surfdata.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/python/ctsm/test/test_unit_singlept_data_surfdata.py b/python/ctsm/test/test_unit_singlept_data_surfdata.py
index a29fa05b33..2106799a4b 100755
--- a/python/ctsm/test/test_unit_singlept_data_surfdata.py
+++ b/python/ctsm/test/test_unit_singlept_data_surfdata.py
@@ -47,8 +47,8 @@ class TestSinglePointCaseSurfaceNoCrop(unittest.TestCase):
     evenly_split_cropland = False
     pct_pft = None
     num_pft = 16
-    cth = [0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9]
-    cbh = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]
+    cth = 0.9
+    cbh = 0.1
     include_nonveg = False
     uni_snow = True
     cap_saturation = True
@@ -668,8 +668,8 @@ class TestSinglePointCaseSurfaceCrop(unittest.TestCase):
     evenly_split_cropland = False
     pct_pft = None
     num_pft = 78
-    cth = [0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9]
-    cbh = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]
+    cth = 0.9
+    cbh = 0.1
     include_nonveg = False
     uni_snow = False
     cap_saturation = False

From 486d634d9e930987a61a3609eafaf6c35ffeb133 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 6 May 2024 13:17:17 -0600
Subject: [PATCH 0178/1248] Ensure cth and cbh are iterable before zipping.
 Unit tests now pass.

---
 python/ctsm/site_and_regional/single_point_case.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py
index 86dabe609d..b197b29578 100644
--- a/python/ctsm/site_and_regional/single_point_case.py
+++ b/python/ctsm/site_and_regional/single_point_case.py
@@ -27,6 +27,14 @@
 LAST_MONTH = 12
 
 
+def _ensure_iterable(thing_we_want_iterable, iterable_length):
+    try:
+        iter(thing_we_want_iterable)
+        return thing_we_want_iterable
+    except TypeError:
+        return [thing_we_want_iterable] * iterable_length
+
+
 class SinglePointCase(BaseCase):
     """
     A class to encapsulate everything for single point cases.
@@ -415,7 +423,10 @@ def modify_surfdata_atpoint(self, f_orig):
             # f_mod["PCT_CROP"][:, :] = 0
 
             # -- loop over all dom_pft and pct_pft
-            zip_pfts = zip(self.dom_pft, self.pct_pft, self.cth, self.cbh)
+            iterable_length = len(self.dom_pft)
+            cth_to_zip = _ensure_iterable(self.cth, iterable_length)
+            cbh_to_zip = _ensure_iterable(self.cbh, iterable_length)
+            zip_pfts = zip(self.dom_pft, self.pct_pft, cth_to_zip, cbh_to_zip)
             for dom_pft, pct_pft, cth, cbh in zip_pfts:
                 if cth is not None:
                     f_mod["MONTHLY_HEIGHT_TOP"][:, :, :, dom_pft] = cth

From af672fb3f0727bad7490c131499e9c151779c574 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 6 May 2024 13:53:07 -0600
Subject: [PATCH 0179/1248] Fix comparison to a baseline directory

---
 bld/unit_testers/compare_namelists | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/bld/unit_testers/compare_namelists b/bld/unit_testers/compare_namelists
index e0c6263555..7a8badc288 100755
--- a/bld/unit_testers/compare_namelists
+++ b/bld/unit_testers/compare_namelists
@@ -80,9 +80,10 @@ if [ "$PHYSB" = "all" ] && [ "$PHYSA" != "all" ]; then
 fi
 
 if [ "$verbose" = "YES" ]; then echo "Get list of lnd_in.* files"; fi
+if [ "$verbose" = "YES" ]; then pwd; fi
 filepat="lnd_in.*"
 filenames=($filepat)
-if [ "$verbose" = "YES" ]; then echo "filename list = $filenames"; fi
+if [ "$verbose" = "YES" ]; then echo "filename list = ${filenames[*]}"; fi
 if [ "${filenames[*]}" = "$filepat" ]; then
    echo "No lnd_in files exist in the current directory -- run ./build-namelist_test.pl first"
    exit 1
@@ -92,9 +93,11 @@ do
    fileA="./$file"
    fileB="$baseline/$file"
    # If physicsA option used and the file matches the physics input
-   if [[ $fileA =~ "-phys+$PHYSA" ]]; then
+   if [[ "$fileA" =~ "-phys+$PHYSA" ]] || [ "$PHYSA" = "all" ]; then
       # Replace physicsB for fileB
-      fileB=${fileB/-phys+$PHYSA/-phys+$PHYSB}
+      if [ ! "$PHYSA" = "all" ]; then
+         fileB=${fileB/-phys+$PHYSA/-phys+$PHYSB}
+      fi
       if ! test -f $fileB; then
          if [ "$verbose" = "YES" ]; then echo "$fileB does NOT exist -- skipping"; fi
       else
@@ -109,4 +112,4 @@ do
       fi
     fi
 done
-if [ "$verbose" = "YES" ]; then echo "Successfully ran through lnd_in files to compare"; fi
\ No newline at end of file
+if [ "$verbose" = "YES" ]; then echo "Successfully ran through lnd_in files to compare"; fi

From cfeb9d6301b4ef455762f83262da831fe5e2b129 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 6 May 2024 14:00:33 -0600
Subject: [PATCH 0180/1248] Move ensure_iterable() to utils.py and add testing.
 One failure.

---
 .../site_and_regional/single_point_case.py    | 14 ++------
 python/ctsm/test/test_unit_utils.py           | 34 ++++++++++++++++++-
 python/ctsm/utils.py                          | 11 ++++++
 3 files changed, 47 insertions(+), 12 deletions(-)

diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py
index b197b29578..2c2aebad52 100644
--- a/python/ctsm/site_and_regional/single_point_case.py
+++ b/python/ctsm/site_and_regional/single_point_case.py
@@ -14,7 +14,7 @@
 
 # -- import local classes for this script
 from ctsm.site_and_regional.base_case import BaseCase, USRDAT_DIR, DatmFiles
-from ctsm.utils import add_tag_to_filename
+from ctsm.utils import add_tag_to_filename, ensure_iterable
 
 logger = logging.getLogger(__name__)
 
@@ -27,14 +27,6 @@
 LAST_MONTH = 12
 
 
-def _ensure_iterable(thing_we_want_iterable, iterable_length):
-    try:
-        iter(thing_we_want_iterable)
-        return thing_we_want_iterable
-    except TypeError:
-        return [thing_we_want_iterable] * iterable_length
-
-
 class SinglePointCase(BaseCase):
     """
     A class to encapsulate everything for single point cases.
@@ -424,8 +416,8 @@ def modify_surfdata_atpoint(self, f_orig):
 
             # -- loop over all dom_pft and pct_pft
             iterable_length = len(self.dom_pft)
-            cth_to_zip = _ensure_iterable(self.cth, iterable_length)
-            cbh_to_zip = _ensure_iterable(self.cbh, iterable_length)
+            cth_to_zip = ensure_iterable(self.cth, iterable_length)
+            cbh_to_zip = ensure_iterable(self.cbh, iterable_length)
             zip_pfts = zip(self.dom_pft, self.pct_pft, cth_to_zip, cbh_to_zip)
             for dom_pft, pct_pft, cth, cbh in zip_pfts:
                 if cth is not None:
diff --git a/python/ctsm/test/test_unit_utils.py b/python/ctsm/test/test_unit_utils.py
index 85ba2515dd..cc22401d1e 100755
--- a/python/ctsm/test/test_unit_utils.py
+++ b/python/ctsm/test/test_unit_utils.py
@@ -9,7 +9,7 @@
 import os
 
 from ctsm import unit_testing
-from ctsm.utils import fill_template_file
+from ctsm.utils import fill_template_file, ensure_iterable
 from ctsm.config_utils import lon_range_0_to_360, _handle_config_value
 
 # Allow names that pylint doesn't like, because otherwise I find it hard
@@ -328,6 +328,38 @@ def test_handleConfigValue_isListFalse(self):
         self.assertEqual(val_out, float(val_in))
 
 
+class TestUtilsEnsureIterable(unittest.TestCase):
+    """Tests of utils: ensure_iterable"""
+
+    def test_ensure_iterable_number(self):
+        """
+        Tests that ensure_iterable(NUMBER, 3) produces a list of 3 NUMBERs
+        """
+        val = 724.1987
+        self.assertEqual(ensure_iterable(val, 3), [val, val, val])
+
+    def test_ensure_iterable_none(self):
+        """
+        Tests that ensure_iterable(None, 2) produces a list of 2 Nones
+        """
+        val = None
+        self.assertEqual(ensure_iterable(val, 2), [val, val])
+
+    def test_ensure_iterable_already(self):
+        """
+        Tests that ensure_iterable() returns the input if it's already iterable
+        """
+        val = [11, 12]
+        self.assertEqual(ensure_iterable(val, 2), val)
+
+    def test_ensure_iterable_error_wrong_length(self):
+        """
+        Tests that ensure_iterable() errors if input is iterable but of the wrong length
+        """
+        with self.assertRaisesRegex(SystemExit, "Input is iterable but wrong length"):
+            ensure_iterable([11, 12], 3)
+
+
 if __name__ == "__main__":
     unit_testing.setup_for_tests()
     unittest.main()
diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py
index 8578ea860c..f7d4e163c6 100644
--- a/python/ctsm/utils.py
+++ b/python/ctsm/utils.py
@@ -26,6 +26,17 @@ def abort(errmsg):
     sys.exit("ERROR: {}".format(errmsg))
 
 
+def ensure_iterable(thing_we_want_iterable, iterable_length):
+    """
+    Ensure that a variable is iterable
+    """
+    try:
+        iter(thing_we_want_iterable)
+        return thing_we_want_iterable
+    except TypeError:
+        return [thing_we_want_iterable] * iterable_length
+
+
 def fill_template_file(path_to_template, path_to_final, substitutions):
     """Given a template file (based on python's template strings), write a copy of the
     file with template values filled in.

From a696d9551f619d58e307aa09b95239e6e2a6874b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 6 May 2024 14:05:52 -0600
Subject: [PATCH 0181/1248] ensure_iterable() now errors if already iterable
 but wrong length. Tests pass.

---
 python/ctsm/test/test_unit_utils.py |  2 +-
 python/ctsm/utils.py                | 11 +++++++++--
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/test/test_unit_utils.py b/python/ctsm/test/test_unit_utils.py
index cc22401d1e..aed43cfede 100755
--- a/python/ctsm/test/test_unit_utils.py
+++ b/python/ctsm/test/test_unit_utils.py
@@ -356,7 +356,7 @@ def test_ensure_iterable_error_wrong_length(self):
         """
         Tests that ensure_iterable() errors if input is iterable but of the wrong length
         """
-        with self.assertRaisesRegex(SystemExit, "Input is iterable but wrong length"):
+        with self.assertRaisesRegex(ValueError, "Input is iterable but wrong length"):
             ensure_iterable([11, 12], 3)
 
 
diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py
index f7d4e163c6..3f4149c163 100644
--- a/python/ctsm/utils.py
+++ b/python/ctsm/utils.py
@@ -30,11 +30,18 @@ def ensure_iterable(thing_we_want_iterable, iterable_length):
     """
     Ensure that a variable is iterable
     """
+    already_iterable = True
     try:
         iter(thing_we_want_iterable)
-        return thing_we_want_iterable
     except TypeError:
-        return [thing_we_want_iterable] * iterable_length
+        already_iterable = False
+    
+    if not already_iterable:
+        thing_we_want_iterable = [thing_we_want_iterable] * iterable_length
+    elif len(thing_we_want_iterable) != iterable_length:
+        raise ValueError(f"Input is iterable but wrong length")
+    
+    return thing_we_want_iterable
 
 
 def fill_template_file(path_to_template, path_to_final, substitutions):

From 475831f0fb0e31e97f630eac4e078c886558b61c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 6 May 2024 14:08:50 -0600
Subject: [PATCH 0182/1248] Clean up ctsm/utils.py with black and pylint.

---
 python/ctsm/utils.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py
index 3f4149c163..a5a02a5c9d 100644
--- a/python/ctsm/utils.py
+++ b/python/ctsm/utils.py
@@ -35,12 +35,12 @@ def ensure_iterable(thing_we_want_iterable, iterable_length):
         iter(thing_we_want_iterable)
     except TypeError:
         already_iterable = False
-    
+
     if not already_iterable:
         thing_we_want_iterable = [thing_we_want_iterable] * iterable_length
     elif len(thing_we_want_iterable) != iterable_length:
-        raise ValueError(f"Input is iterable but wrong length")
-    
+        raise ValueError("Input is iterable but wrong length")
+
     return thing_we_want_iterable
 
 

From 0819983f37aadf9f7c9dde290dd7f65b4870b3f6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 6 May 2024 14:09:27 -0600
Subject: [PATCH 0183/1248] Add previous commit to .git-blame-ignore-revs.

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index f86a330408..e769d3187c 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -25,6 +25,7 @@ a9d96219902cf609636886c7073a84407f450d9a
 d866510188d26d51bcd6d37239283db690af7e82
 0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 e096358c832ab292ddfd22dd5878826c7c788968
+475831f0fb0e31e97f630eac4e078c886558b61c
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

From 75f9cc54227f39f7baabc430de7a12506b892192 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 6 May 2024 15:35:56 -0700
Subject: [PATCH 0184/1248] rename luh unit test that matched old test

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 899bd10b9c..0bf0ea5390 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1062,7 +1062,7 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
-     "useinventorybutnotfile"    =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan",
+     "useLUH2butnotfile"         =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan",
                                      namelst=>"use_fates_luh=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",

From ff3af55931b98e9cb7b9553717d10f2388954197 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 6 May 2024 16:24:30 -0700
Subject: [PATCH 0185/1248] add build namelist unit tests for fates landuse v2

---
 bld/unit_testers/build-namelist_test.pl | 41 +++++++++++++++++++++++--
 1 file changed, 38 insertions(+), 3 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 0bf0ea5390..70243c5843 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1999;
+my $ntests = 2006;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1353;
+   $ntests += 1360;
 }
 plan( tests=>$ntests );
 
@@ -1062,11 +1062,16 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
-     "useLUH2butnotfile"         =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan",
+     "useFATESLUH2butnotfile"    =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan",
                                      namelst=>"use_fates_luh=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
+     "useFATESLUPFTbutnotfile"   =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan",
+                                     namelst=>"use_fates_lupft=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm4_5",
+                                   },
      "inventoryfileDNE"          =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_fates_luh=.true., fluh_timeseries='zztop'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1092,6 +1097,36 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "useFATESSPwithLUH"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_sp=T,use_fates_luh=T",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_potentialveg=T,fates_harvest_mode=1",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "useFATESHARVEST3WOLUH"     =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_luh=F,fates_harvest_mode=3",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "useFATESLUPFTWOLUH"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_lupft=T,use_fates_luh=F",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "useFATESLUPFTWONOCOMP"     =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_lupft=T,use_fates_nocomp=F",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "useFATESLUPFTWOFBG"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_lupft=T,use_fates_fixedbiogeog=F",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
      "useFATESTRANSWdynPFT"      =>{ options=>"-bgc fates -envxml_dir . -use_case 20thC_transient -no-megan",
                                      namelst=>"do_transient_pfts=T",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

From 69154dab7b33706491bdabc634d9a80142bf0b35 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 6 May 2024 16:37:07 -0700
Subject: [PATCH 0186/1248] update fates logging unit test to use new fates
 harvest mode

---
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 bld/unit_testers/build-namelist_test.pl         | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index a2df9b1d1e..edcfa36d27 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -814,7 +814,7 @@ types to vary over time.
 
 <entry id="flandusepftdat" type="char*256" category="datasets"
        input_pathname="abs" group="clm_inparm" valid_values="" >
-Full pathname of fates landuse x pft data map.
+Full pathname of fates landuse x pft static data map.
 </entry>
 
 <entry id="use_luna" type="logical" category="physics"
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 70243c5843..3b2dabd057 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1046,9 +1046,8 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
-     # TODO SSR: Replace this with fates_harvest_mode
      "useloggingButNOTFATES"     =>{ options=>"-envxml_dir . -no-megan",
-                                     namelst=>"use_fates_logging=.true.",
+                                     namelst=>"fates_harvest_mode=1",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },

From 5c5ca6f8e40cc6fe69d9b9a7edf32ce5242a7629 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 6 May 2024 17:49:34 -0600
Subject: [PATCH 0187/1248] minor update

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 3b2dabd057..f674849b6f 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 2006;
+my $ntests = 2007;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 1360;

From eec4e79bb867aa671ad52a9c52028f1df00358e1 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 7 May 2024 03:23:41 -0600
Subject: [PATCH 0188/1248] Update testlist based on what's needed for CAM and
 CESM test lists

---
 cime_config/testdefs/testlist_clm.xml | 32 +++++++++++++++++++++------
 1 file changed, 25 insertions(+), 7 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index c2a90507ba..56ba176cfe 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -73,7 +73,7 @@
       <option name="comment">Simple test use soil eroditability in CTSM for CAM5 tuning</option>
     </options>
   </test>
-  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningModeZDustSoilErod">
+  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningModeZDustSoilErod">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -102,7 +102,7 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="IHistClm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="IHistClm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -111,7 +111,7 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution for transient</option>
     </options>
   </test>
-  <test name="PEM_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="PEM_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -120,7 +120,7 @@
       <option name="comment">CESM3 development test with change in the processor count at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERS_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="ERS_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -129,7 +129,7 @@
       <option name="comment">CESM3 development simple exact restart test at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERI_D" grid="ne30pg3_t232" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="ERI_D" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -138,7 +138,7 @@
       <option name="comment">CESM3 development Exact restart test for all startup types at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="SMS_Lm1" grid="ne30pg3_t232" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Lm1" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -331,6 +331,24 @@
       <option name="comment"  >Science support for 1850 with clm5_1 for SP mode at f19</option>
     </options>
   </test>
+  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam60LndTuningMode">
+    <machines>
+      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Science support for 1850 with clm5_1 for SP mode at f09 with cam60</option>
+    </options>
+  </test>
+  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam60LndTuningMode">
+    <machines>
+      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Science support for 1850 with clm5_1 for SP mode at f19 with cam60</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50Sp" testmods="clm/prescribed">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -685,7 +703,7 @@
       <option name="comment">Workhorse SE grid for running with CAM and with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>

From e529c2f119f8561a7203f0f3588ded549094e6e6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 7 May 2024 03:27:31 -0600
Subject: [PATCH 0189/1248] Add IHistClm60BgcCropG which is needed for CESM
 testing, change NoAnthro compsets to run with RTM as required for Paleo work,
 best guess as to what needs science support

---
 cime_config/config_compsets.xml | 30 +++++++++++++++++++++++++-----
 1 file changed, 25 insertions(+), 5 deletions(-)

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
index 2de911da86..538329e523 100644
--- a/cime_config/config_compsets.xml
+++ b/cime_config/config_compsets.xml
@@ -91,6 +91,8 @@
   <compset>
     <alias>I2000Clm60Sp</alias>
     <lname>2000_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+    <science_support grid="f09_g17"/>
+    <science_support grid="f19_g17"/>
   </compset>
 
   <!-- Primarily for testing -->
@@ -182,6 +184,8 @@
   <compset>
     <alias>I1850Clm60Sp</alias>
     <lname>1850_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+    <science_support grid="f09_g17"/>
+    <science_support grid="f19_g17"/>
   </compset>
 
   <compset>
@@ -291,22 +295,24 @@
 
   <compset>
      <alias>I1850Clm60BgcNoAnthro</alias>
-     <lname>1850_DATM%GSWP3v1_CLM60%BGC-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+     <lname>1850_DATM%GSWP3v1_CLM60%BGC-NOANTHRO_SICE_SOCN_RTM_SGLC_SWAV</lname>
+     <science_support grid="f09_g17"/>
    </compset>
 
   <compset>
      <alias>I1850Clm60SpNoAnthro</alias>
-     <lname>1850_DATM%GSWP3v1_CLM60%SP-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+     <lname>1850_DATM%GSWP3v1_CLM60%SP-NOANTHRO_SICE_SOCN_RTM_SGLC_SWAV</lname>
+     <science_support grid="f09_g17"/>
    </compset>
 
   <compset>
      <alias>I1850Clm50BgcNoAnthro</alias>
-     <lname>1850_DATM%GSWP3v1_CLM50%BGC-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+     <lname>1850_DATM%GSWP3v1_CLM50%BGC-NOANTHRO_SICE_SOCN_RTM_SGLC_SWAV</lname>
    </compset>
 
   <compset>
      <alias>I1850Clm50SpNoAnthro</alias>
-     <lname>1850_DATM%GSWP3v1_CLM50%SP-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+     <lname>1850_DATM%GSWP3v1_CLM50%SP-NOANTHRO_SICE_SOCN_RTM_SGLC_SWAV</lname>
    </compset>
 
 
@@ -319,12 +325,15 @@
 
   <compset>
      <alias>I1850Clm60SpNoAnthro</alias>
-     <lname>1850_DATM%GSWP3v1_CLM60%SP-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+     <lname>1850_DATM%GSWP3v1_CLM60%SP-NOANTHRO_SICE_SOCN_RTM_SGLC_SWAV</lname>
+    <science_support grid="f09_g17"/>
    </compset>
 
   <compset>
     <alias>IHistClm60Sp</alias>
     <lname>HIST_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+    <science_support grid="f09_g17"/>
+    <science_support grid="f19_g17"/>
   </compset>
 
   <!-- Needed for testing until CAM removes used of CLM51 in compsets-->
@@ -631,6 +640,17 @@
   <compset>
     <alias>I1850Clm60BgcCropG</alias>
     <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV</lname>
+    <science_support grid="f09_g17"/>
+    <science_support grid="f19_g17"/>
+    <science_support grid="ne30pg3_t232"/>
+  </compset>
+
+  <compset>
+    <alias>IHistClm60BgcCropG</alias>
+    <lname>HIST_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV</lname>
+    <science_support grid="f09_g17"/>
+    <science_support grid="f19_g17"/>
+    <science_support grid="ne30pg3_t232"/>
   </compset>
   <!-- Needed for testing until removed by CESM -->
   <compset>

From 6f8021cb9be81521f4f905b27b353ce9de1980be Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 7 May 2024 03:30:20 -0600
Subject: [PATCH 0190/1248] Start adding reference for
 LND_SETS_DUST_EMIS_DRV_FLDS in unit tester

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 114fb0c36c..30110d92f7 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -42,7 +42,7 @@ sub make_env_run {
     my %settings = @_;
 
     # Set default settings
-    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" );
+    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE",  LND_SETS_DUST_EMIS_DRV_FLDS=>"TRUE", NEONSITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
        $env_vars{$item} = $settings{$item};

From f52f76fc0c71f3521a0680207141b1545dd6098a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 7 May 2024 03:31:04 -0600
Subject: [PATCH 0191/1248] Add dust emis namelist default for drv_flds_in

---
 .../namelist_defaults_dust_emis.xml           | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 bld/namelist_files/namelist_defaults_dust_emis.xml

diff --git a/bld/namelist_files/namelist_defaults_dust_emis.xml b/bld/namelist_files/namelist_defaults_dust_emis.xml
new file mode 100644
index 0000000000..40bf3d9078
--- /dev/null
+++ b/bld/namelist_files/namelist_defaults_dust_emis.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+
+<?xml-stylesheet type="text/xsl" href="namelist_defaults.xsl"?>
+
+<namelist_defaults>
+
+<!--
+Values to use by default for creation of CLM model driver namelists.
+The element names are the same as the corresponding namelist
+variables.  Values that depend on the model configuration use
+attributes to express the dependency.  The recognized attributes
+are: RESOLUTION, defaults, mask, ic_ymd, ic_tod, sim_year and all configuration
+attributes from the config_cache.xml file (with keys converted to upper-case).
+-->
+
+<!-- Defaults for dust_emis_inparm namelist  -->
+<dust_emis_method>Zender_2003</dust_emis_method>
+
+<zender_soil_erod_source>atm</zender_soil_erod_source>
+
+</namelist_defaults>

From 2a88002ea1a916d21da69b05c6621774cca74b39 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 7 May 2024 10:26:16 -0700
Subject: [PATCH 0192/1248] change lupft check to fbg + luh check to mirror
 fates-side logic

---
 src/utils/clmfates_interfaceMod.F90 | 37 ++++++++++++++---------------
 1 file changed, 18 insertions(+), 19 deletions(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index b0ae0044f3..048824a83a 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -398,7 +398,6 @@ subroutine CLMFatesGlobals2()
      integer                                        :: pass_use_potentialveg
      integer                                        :: pass_num_luh_states
      integer                                        :: pass_num_luh_transitions
-     integer                                        :: pass_lupftdat
 
      call t_startf('fates_globals2')
 
@@ -704,7 +703,7 @@ subroutine init(this, bounds_proc, flandusepftdat)
       end if
 
       ! Retrieve the landuse x pft static data if the file is present
-      if (use_fates_lupft) then
+      if (use_fates_fixed_biogeog .and. use_fates_luh) then
          call GetLandusePFTData(bounds_proc, flandusepftdat, landuse_pft_map, landuse_bareground)
       end if
 
@@ -815,23 +814,23 @@ subroutine init(this, bounds_proc, flandusepftdat)
             this%fates(nc)%sites(s)%lon = grc%londeg(g)
 
             ! Transfer the landuse x pft data to fates via bc_in if file is given
-            if (use_fates_lupft) then
-               this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars)
-               this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g)
-            end if
-
-            if (.not. use_fates_lupft) then
-               ! initialize static layers for reduced complexity FATES versions from HLM
-               ! maybe make this into a subroutine of it's own later.
-               this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8
-               do m = surfpft_lb,surfpft_ub
-                  ft = m - surfpft_lb
-                  this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m)
-               end do
+            if (use_fates_fixed_biogeog) then
+               if (use_fates_luh) then
+                  this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars)
+                  this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g)
+               else
+                  ! initialize static layers for reduced complexity FATES versions from HLM
+                  ! maybe make this into a subroutine of it's own later.
+                  this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8
+                  do m = surfpft_lb,surfpft_ub
+                     ft = m - surfpft_lb
+                     this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m)
+                  end do
 
-               if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) >    sum_to_1_tol) then
-                  write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)   %pft_areafrac(:)) - 1.0_r8
-                  call endrun(msg=errMsg(sourcefile, __LINE__))
+                  if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) >    sum_to_1_tol) then
+                     write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)   %pft_areafrac(:)) - 1.0_r8
+                     call endrun(msg=errMsg(sourcefile, __LINE__))
+                  end if
                end if
             end if
           end do !site
@@ -876,7 +875,7 @@ subroutine init(this, bounds_proc, flandusepftdat)
       call create_fates_fire_data_method( this%fates_fire_data_method )
 
       ! deallocate the local landuse x pft array
-      if (use_fates_lupft) then
+      if (use_fates_fixed_biogeog .and. use_fates_luh) then
          deallocate(landuse_pft_map)
          deallocate(landuse_bareground)
       end if

From 9b5001d0026e0de26bc0b20608f3924ea0cca214 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 7 May 2024 17:02:30 -0600
Subject: [PATCH 0193/1248] Fix #2519 so that the mksurfdata_esmf build can
 work in a CESM checkout

---
 tools/mksurfdata_esmf/gen_mksurfdata_build | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_build b/tools/mksurfdata_esmf/gen_mksurfdata_build
index 974c1929a5..864b5915b9 100755
--- a/tools/mksurfdata_esmf/gen_mksurfdata_build
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_build
@@ -127,7 +127,16 @@ if [ "$existing_bld" = "No" ]; then
    if [ "$verbose" != "YES" ]; then
      options="$options --silent"
    fi
-   $cwd/../../cime/CIME/scripts/configure --macros-format CMake --machine $MACH $options
+   # Try finding configure file assuming a CTSM standalone checkout and then try for a CESM checkout
+   configure="$cwd/../../cime/CIME/scripts/configure"
+   if [ ! -f "$configure" ]; then
+      configure="$cwd/../../../../cime/CIME/scripts/configure"
+      if [ ! -f "$configure" ]; then
+         echo "Error $configure file does NOT exist in expected location, either for a standalone checkout or CESM/CAM checkout"
+         exit 1
+      fi
+   fi
+   $configure --macros-format CMake --machine $MACH $options
 
    if [ $? != 0 ]; then
      echo "Error doing configure for machine name: $MACH"

From 89a4d1d0d02b655a10790fdee043dd65f8c65ab5 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 7 May 2024 17:42:19 -0600
Subject: [PATCH 0194/1248] Update ctsm_sci tests for 3 VR grids

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++---
 cime_config/config_component.xml              | 2 +-
 cime_config/testdefs/testlist_clm.xml         | 6 +++---
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 0f533a56ff..67b21c1259 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -939,12 +939,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
 >hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
@@ -956,7 +956,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </init_interp_attributes>
 
 <!-- 2013 IC's - exact match for CONUS grid ... -->
-<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
 			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
 >hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 984ba5ecdf..be6916ae0c 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -210,7 +210,7 @@
       <value compset="^SSP370_"	                    >1850-2100_SSP3-7.0_transient</value>
       <value compset="^SSP534_"	                    >1850-2100_SSP5-3.4_transient</value>
       <value compset="^SSP245_"	                    >1850-2100_SSP2-4.5_transient</value>
-      <value compset="^HIST_ne0np4"                 >1850-2100_SSP2-4.5_transient</value>
+      <value compset="^HIST" grid="ne0np4"          >1850-2100_SSP2-4.5_transient</value>
       <value compset="^SSP119_"	                    >1850-2100_SSP1-1.9_transient</value>
       <value compset="^SSP434_"	                    >1850-2100_SSP4-3.4_transient</value>
       <value compset="^SSP460_"	                    >1850-2100_SSP4-6.0_transient</value>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 918d86c213..f8c0a1bd79 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2034,7 +2034,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="ISSP245Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode_1979Start">
+  <test name="SMS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode_1979Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2043,7 +2043,7 @@
       <option name="comment"  >Run ARCTIC for transient case starting in 1979 as for AMIP CAM cases (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="ISSP245Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode_1979Start">
+  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode_1979Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2061,7 +2061,7 @@
       <option name="comment"  >Run ARCTICGRIS for 1850 case (do not run this expensive test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="ISSP245Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode_2013Start">
+  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode_2013Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>

From 0bcf80acea865f2df37d13911aa6b9d167622a66 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 1 May 2024 16:37:32 -0600
Subject: [PATCH 0195/1248] FatesColdLUH2 tests now use use_fates_nocomp false.

---
 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
index 854c21407f..917ba314b3 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
@@ -1 +1,2 @@
 use_fates_luh = .true.
+use_fates_nocomp = .false.

From 0edcb1b5b118c7029807a05e1ce3773396c6ec7f Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Wed, 8 May 2024 10:22:47 -0600
Subject: [PATCH 0196/1248] Update FATES external to latest
 ckoven/luh2_nocomp_merge.

---
 Externals_CLM.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
index b689141aaf..e1bc1696af 100644
--- a/Externals_CLM.cfg
+++ b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/ckoven/fates
-hash = c1a7453c8331277a156a0ee158a870c1b8598a9f
+hash = 153b0bda9c96f18e8d2a93887a082bc7a31b574b
 required = True
 
 [externals_description]

From b64ceb6b1f7a5a462842c88861f2c5becc7e8c1e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 8 May 2024 11:05:37 -0600
Subject: [PATCH 0197/1248] Change an expected failure "status" from PEND to
 FAIL

---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index fe6a54c221..e346e6e7af 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -31,7 +31,7 @@
   <!-- ctsm_sci test suite failures -->
   <test name="RXCROPMATURITY_Lm61.f09_g17.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput">
     <phase name="RUN">
-      <status>PEND</status>
+      <status>FAIL</status>
       <issue>#2460</issue>
     </phase>
   </test>

From 92fb80687f707c1799cacea85bc64bc9c1cd9f89 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 8 May 2024 13:25:19 -0600
Subject: [PATCH 0198/1248] Update FatesColdLUH2 testdef.

---
 .../testmods_dirs/clm/FatesColdLUH2/user_nl_clm       | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
index 917ba314b3..970e7df7cd 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
@@ -1,2 +1,11 @@
+
+! Run a transient case, with vegetation starting from bare ground, but land use starting from LUH state vector on starting date, in a nocomp configuration.
+! From Charlie's list of valid FATES configurations:
+! https://docs.google.com/spreadsheets/d/1eE3sRMYxfocZKbT8uIQhXpjjtfM2feXPRSWXJNoo4jM/edit#gid=0
+flandusepftdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc'
 use_fates_luh = .true.
-use_fates_nocomp = .false.
+use_fates_nocomp = .true.
+use_fates_fixed_biogeog = .true.
+use_fates_sp = .false.
+use_fates_potentialveg = .false.
+fluh_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc'

From f6728017c7726f947492179f88031cccfa81181f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 8 May 2024 13:26:56 -0600
Subject: [PATCH 0199/1248] Add FatesColdLUH2Mode0 testdef.

---
 cime_config/testdefs/testlist_clm.xml                    | 9 +++++++++
 .../clm/FatesColdLUH2Mode0/include_user_mods             | 1 +
 .../testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm     | 1 +
 3 files changed, 11 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 4184cc7e1f..022bb9ad73 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2910,6 +2910,15 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode0">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
+      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode1">
     <machines>
       <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods
new file mode 100644
index 0000000000..7eb8bb1579
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods
@@ -0,0 +1 @@
+../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm
new file mode 100644
index 0000000000..929a8e6e14
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm
@@ -0,0 +1 @@
+fates_harvest_mode = 0

From f33040751bcf1fdb566119f6f91d5c9695e97386 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 8 May 2024 13:55:17 -0600
Subject: [PATCH 0200/1248] Change comments about clm5_1 to clm6_0

---
 cime_config/testdefs/testlist_clm.xml | 32 +++++++++++++--------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 56ba176cfe..5350b4716b 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -312,14 +312,14 @@
       <option name="comment"  >Science support for I1850Clm50SpCru at f19</option>
     </options>
   </test>
-  <!-- science support for workhorse resolutions with CLM5_1 physics -->
+  <!-- science support for workhorse resolutions with CLM6_0 physics -->
   <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm5_1 for SP mode at f09</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f09</option>
     </options>
   </test>
   <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/default">
@@ -328,7 +328,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm5_1 for SP mode at f19</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19</option>
     </options>
   </test>
   <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam60LndTuningMode">
@@ -337,7 +337,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm5_1 for SP mode at f09 with cam60</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f09 with cam60</option>
     </options>
   </test>
   <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam60LndTuningMode">
@@ -346,7 +346,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm5_1 for SP mode at f19 with cam60</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19 with cam60</option>
     </options>
   </test>
   <test name="ERP_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50Sp" testmods="clm/prescribed">
@@ -586,14 +586,14 @@
       <option name="comment"  >Science support for 1850 clm5_0 physics for Bgc at f09</option>
     </options>
   </test>
-  <!-- clm5_1 physics workhorse resolution BGC science test list -->
+  <!-- clm6_0 physics workhorse resolution BGC science test list -->
   <test name="SMS_Ld5" grid="f19_g17" compset="I1850Clm60Bgc" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 Clm5_1 physics for Bgc at f19</option>
+      <option name="comment"  >Science support for 1850 Clm6_0 physics for Bgc at f19</option>
     </options>
   </test>
   <test name="SMS_Ld5" grid="f09_g17" compset="I1850Clm60Bgc" testmods="clm/default">
@@ -602,7 +602,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 Clm5_1 physics for Bgc at f09</option>
+      <option name="comment"  >Science support for 1850 Clm6_0 physics for Bgc at f09</option>
     </options>
   </test>
   <test name="ERP_D_Ld5" grid="ne30_g17" compset="I1850Clm50BgcCrop" testmods="clm/default">
@@ -749,14 +749,14 @@
       <option name="comment"  >Science support for Historical clm5_0 physics with BGC-Crop at f19</option>
     </options>
   </test>
-  <!-- Historical clm5_1 physics BgcCrop science support -->
+  <!-- Historical clm6_0 physics BgcCrop science support -->
   <test name="SMS_Ld5" grid="f09_g17" compset="IHistClm60BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for Historical clm5_1 physics with BGC-Crop at f09</option>
+      <option name="comment"  >Science support for Historical clm6_0 physics with BGC-Crop at f09</option>
     </options>
   </test>
   <test name="SMS_Ld5" grid="f19_g17" compset="IHistClm60BgcCrop" testmods="clm/default">
@@ -765,7 +765,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for Historical clm5_1 physics with BGC-Crop at f19</option>
+      <option name="comment"  >Science support for Historical clm6_0 physics with BGC-Crop at f19</option>
     </options>
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive">
@@ -2108,14 +2108,14 @@
       <option name="comment"  >Science support for historical clm5_0 physics with SP mode at f19</option>
     </options>
   </test>
-  <!-- Historical science support for clm5_1 workhorse resolutions -->
+  <!-- Historical science support for clm6_0 workhorse resolutions -->
   <test name="SMS_Ld5" grid="f09_g17" compset="IHistClm60Sp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for historical clm5_1 physics with SP mode at f09</option>
+      <option name="comment"  >Science support for historical clm6_0 physics with SP mode at f09</option>
     </options>
   </test>
   <test name="SMS_Ld5" grid="f19_g17" compset="IHistClm60Sp" testmods="clm/default">
@@ -2124,7 +2124,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for historical clm5_1 physics with SP mode at f19</option>
+      <option name="comment"  >Science support for historical clm6_0 physics with SP mode at f19</option>
     </options>
   </test>
   <test name="SMS_Ln9" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
@@ -2798,7 +2798,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Fates with clm5_1</option>
+      <option name="comment"  >Fates with clm6_0</option>
     </options>
   </test>
   <test name="ERS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60FatesRs" testmods="clm/FatesCold">
@@ -2808,7 +2808,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Run a Fates test with latest Clm5_1</option>
+      <option name="comment"  >Run a Fates test with latest Clm6_0</option>
     </options>
   </test>
   <test name="SMS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm45Fates" testmods="clm/FatesCold">

From 524cbc06a30a6820f72c60e9c44d9748977afe48 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 8 May 2024 13:58:33 -0600
Subject: [PATCH 0201/1248] Revert order of irrigate and add note that it's
 also set in the use-cases

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 25b0c80cf9..6f2f265da4 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -115,10 +115,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <atm_c14_filename use_c14=".true." use_c14_bombspike =".true." ssp_rcp="SSP5-3.4" >lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP534os_3x1_global_1850-2100_yearly_c181209.nc</atm_c14_filename>
 <atm_c14_filename use_c14=".true." use_c14_bombspike =".true." ssp_rcp="SSP5-8.5" >lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP5B_3x1_global_1850-2100_yearly_c181209.nc</atm_c14_filename>
 
-<!-- Irrigation default -->
+<!-- Irrigation default (Note, the use-cases also set this) -->
+<irrigate                                                             >.false.</irrigate>
 <irrigate               use_cndv=".false."  sim_year_range="1850-2100">.true.</irrigate>
 <irrigate phys="clm4_5" use_cndv=".false."  sim_year_range="1850-2100">.false.</irrigate>
-<irrigate >.false.</irrigate>
 
 <!-- Saturation excess runoff for crops  -->
 <crop_fsat_equals_zero>.false.</crop_fsat_equals_zero>

From b9e947d76e40fbf39c0bdcfbae3de9e14b751b1c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 8 May 2024 16:58:20 -0600
Subject: [PATCH 0202/1248] Get mksurfdata_esmf build and namelist build
 working under a CESM checkout

---
 python/ctsm/.pylintrc                            | 2 ++
 python/ctsm/toolchain/gen_mksurfdata_namelist.py | 8 ++++----
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/python/ctsm/.pylintrc b/python/ctsm/.pylintrc
index db78949288..230f8acba8 100644
--- a/python/ctsm/.pylintrc
+++ b/python/ctsm/.pylintrc
@@ -436,6 +436,8 @@ good-names=i,
            ds,
            m,
            n,
+           ni,
+           nj,
            l1,
            l2,
            ax,
diff --git a/python/ctsm/toolchain/gen_mksurfdata_namelist.py b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
index 8a953c39df..361616419f 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_namelist.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
@@ -12,7 +12,7 @@
 from datetime import datetime
 import netCDF4
 
-from ctsm.path_utils import path_to_ctsm_root
+from ctsm.path_utils import path_to_ctsm_root, path_to_cime
 from ctsm.ctsm_logging import setup_logging_pre_config, add_logging_args, process_logging_args
 
 logger = logging.getLogger(__name__)
@@ -326,7 +326,7 @@ def main():
     )
 
     # determine output mesh
-    determine_output_mesh(res, force_model_mesh_file, input_path, rawdata_files, tool_path)
+    determine_output_mesh(res, force_model_mesh_file, input_path, rawdata_files)
 
     # Determine num_pft
     if nocrop_flag:
@@ -752,11 +752,11 @@ def handle_transient_run(
     return landuse_fname, must_run_download_input_data
 
 
-def determine_output_mesh(res, force_model_mesh_file, input_path, rawdata_files, tool_path):
+def determine_output_mesh(res, force_model_mesh_file, input_path, rawdata_files):
     """
     determine output mesh
     """
-    xml_path = os.path.join(tool_path, "../../ccs_config/component_grids_nuopc.xml")
+    xml_path = os.path.join(path_to_cime(), "../ccs_config/component_grids_nuopc.xml")
     tree2 = ET.parse(xml_path)
     root = tree2.getroot()
     model_mesh = ""

From 7d91ac1d991003e9c953f5e1bb903064d789e1bd Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 8 May 2024 17:16:23 -0600
Subject: [PATCH 0203/1248] Correct clm60 typo in testlist

---
 cime_config/testdefs/testlist_clm.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 5350b4716b..75bdf63e19 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -331,22 +331,22 @@
       <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam60LndTuningMode">
+  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f09 with cam60</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f09 with CAM6</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam60LndTuningMode">
+  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19 with cam60</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19 with CAM6</option>
     </options>
   </test>
   <test name="ERP_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50Sp" testmods="clm/prescribed">

From 010a008396e8edab3870270da919a706a543ee71 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 8 May 2024 17:32:03 -0600
Subject: [PATCH 0204/1248] Add a description and usage and error check command
 line args

---
 bld/unit_testers/cmp_baseline_lnd_in_files.sh | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/bld/unit_testers/cmp_baseline_lnd_in_files.sh b/bld/unit_testers/cmp_baseline_lnd_in_files.sh
index de32cddf76..ebeeffc72a 100755
--- a/bld/unit_testers/cmp_baseline_lnd_in_files.sh
+++ b/bld/unit_testers/cmp_baseline_lnd_in_files.sh
@@ -1,15 +1,39 @@
 #!/bin/bash
+#
+# A simple script to compare lnd_in namelists between two baselines on Derecho
+#
 
+#----------------------------------------------------------------------
+# Usage subroutine
+usage() {
+  echo ""
+  echo "***********************************************************************"
+  echo "usage:"
+  echo "./cmp_baseline_lnd_in_files.sh <baseline> <comparison-baseline>"
+  echo "  "
+  echo "Compares lnd_in files between two baselines on Derecho"
+  echo "***********************************************************************"
+}
+
+#----------------------------------------------------------------------
+
+if [ "$#" -ne 2 ]; then
+   echo "Need to give two baseline directories to compare"
+   usage
+   exit 1
+fi
 baseline=$1
 compare=$2
 
 cwd=`pwd`
 if [ -z "$1" ]; then
    echo "Need to enter a baseline directory tag name"
+   usage
    exit 1
 fi
 if [ -z "$2" ]; then
    echo "Need to enter a comparison directory tag name"
+   usage
    exit 1
 fi
 
@@ -22,6 +46,7 @@ fi
 comp_root=$BASELINE_ROOT/$compare
 if ! test -d "$comp_root"; then
    echo "Root comparison directory of $comp_root does NOT exist"
+   usage
    exit 1
 fi
 cd $root

From fc0261376e1499fe06d6b41adfc3c2270bd373a6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 8 May 2024 17:47:52 -0600
Subject: [PATCH 0205/1248] Adjustments to the testlist

Make sure CESM testing compsets with cam6
forcing are being exercised. Update NoAnthro
to Clm60.
---
 cime_config/testdefs/testlist_clm.xml | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 75bdf63e19..1b825f0d40 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -21,11 +21,10 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm50BgcNoAnthro" testmods="clm/decStart1851_noinitial">
+  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm60SpNoAnthro" testmods="clm/decStart1851_noinitial">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
     </machines>
     <options>
@@ -33,6 +32,15 @@
       <option name="comment"  >No anthropogenic compset</option>
     </options>
   </test>
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="I1850Clm60BgcNoAnthro" testmods="clm/decStart1851_noinitial">
+    <machines>
+      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >No anthropogenic compset for Bgc and ctsm_sci test list</option>
+    </options>
+  </test>
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
@@ -141,6 +149,7 @@
   <test name="SMS_Lm1" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>

From f8c6a49539c3b1ce86dd2ca491c953b0c8856766 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 9 May 2024 02:05:20 -0600
Subject: [PATCH 0206/1248] Add a ctsm_sci test for I1850Clm50BgcCropG to
 verify that current B1850 will work

---
 cime_config/testdefs/testlist_clm.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 1b825f0d40..f0dc3ee270 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -576,6 +576,15 @@
       <option name="comment"  >cism is not answer preserving across processor changes, but short test length should be ok.</option>
     </options>
   </test>
+  <test name="SMS" grid="f09_mg17" compset="I1850Clm50BgcCropG" testmods="clm/default">
+    <machines>
+      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Science support for 1850 clm5_0 physics for BgcCrop wtih CISM at f09</option>
+    </options>
+  </test>
   <!-- clm5_0 physics workhorse resolution BGC science test list -->
   <test name="SMS_Ld5" grid="f19_g17" compset="I1850Clm50Bgc" testmods="clm/default">
     <machines>

From 05332fb117e7ed94abcc09c5c66f5db8d8885638 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 9 May 2024 10:53:59 -0700
Subject: [PATCH 0207/1248] Remove get_do_harvest dependency for fates harvest
 modes

---
 src/dyn_subgrid/dynSubgridDriverMod.F90 |  7 ++-
 src/utils/clmfates_interfaceMod.F90     | 71 +++++++++----------------
 2 files changed, 32 insertions(+), 46 deletions(-)

diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90
index e5ca3f002e..b12b135b59 100644
--- a/src/dyn_subgrid/dynSubgridDriverMod.F90
+++ b/src/dyn_subgrid/dynSubgridDriverMod.F90
@@ -89,6 +89,11 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst)
     ! Note that dynpft_init needs to be called from outside any loops over clumps - so
     ! this routine needs to be called from outside any loops over clumps.
     !
+    !
+    ! !USES:
+    use clm_varctl               , only : fates_harvest_mode
+    use dynFATESLandUseChangeMod , only : fates_harvest_clmlanduse
+    !
     ! !ARGUMENTS:
     type(bounds_type)       , intent(in)    :: bounds_proc ! processor-level bounds
     type(glc_behavior_type) , intent(in)    :: glc_behavior
@@ -123,7 +128,7 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst)
     ! flanduse_timeseries file. However, this could theoretically be changed so that the
     ! harvest data were separated from the pftdyn data, allowing them to differ in the
     ! years over which they apply.
-    if (get_do_harvest()) then
+    if (get_do_harvest() .or. fates_harvest_mode >= fates_harvest_clmlanduse) then
        call dynHarvest_init(bounds_proc, harvest_filename=get_flanduse_timeseries())
     end if
 
diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 048824a83a..308d5cee8e 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -169,7 +169,6 @@ module CLMFatesInterfaceMod
    use FATESFireBase          , only : fates_fire_base_type
    use FATESFireFactoryMod    , only : no_fire, scalar_lightning, successful_ignitions,&
                                        anthro_ignitions, anthro_suppression
-   use dynSubgridControlMod   , only : get_do_harvest
    use dynHarvestMod          , only : num_harvest_inst, harvest_varnames
    use dynHarvestMod          , only : harvest_units, mass_units, unitless_units
    use dynHarvestMod          , only : dynHarvest_interp_resolve_harvesttypes
@@ -185,6 +184,7 @@ module CLMFatesInterfaceMod
    use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp
    use dynFATESLandUseChangeMod, only : num_landuse_harvest_vars
    use dynFATESLandUseChangeMod, only : fates_harvest_no_logging
+   use dynFATESLandUseChangeMod, only : fates_harvest_clmlanduse
    use dynFATESLandUseChangeMod, only : fates_harvest_luh_area
    use dynFATESLandUseChangeMod, only : landuse_harvest
    use dynFATESLandUseChangeMod, only : landuse_harvest_units
@@ -489,13 +489,6 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_ed_st3',ival=pass_ed_st3)
 
-        if (fates_harvest_mode > fates_harvest_no_logging) then
-           pass_logging = 1
-        else
-           pass_logging = 0
-        end if
-        call set_fates_ctrlparms('use_logging',ival=pass_logging)
-
         if(use_fates_ed_prescribed_phys) then
            pass_ed_prescribed_phys = 1
         else
@@ -517,39 +510,28 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking)
 
-        ! check fates logging namelist value first because hlm harvest can override it
+        ! FATES logging and harvest modes
         if (fates_harvest_mode > fates_harvest_no_logging) then
-           pass_logging = 1
-        else
-           pass_logging = 0
-        end if
-
-        if(get_do_harvest()) then
-           pass_logging = 1
-           pass_num_lu_harvest_cats = num_harvest_inst
-           pass_lu_harvest = 1
-        else
-           pass_lu_harvest = 0
-           pass_num_lu_harvest_cats = 0
-        end if
+           pass_logging = 1 ! Time driven logging, without landuse harvest
+           ! CLM landuse timeseries driven harvest rates
+           if (fates_harvest_mode == fates_harvest_clmlanduse)
+              pass_num_lu_harvest_cats = num_harvest_inst
+              pass_lu_harvest = 1
+
+           ! LUH2 landuse timeseries driven  harvest rates
+           else if (fates_harvest_mode >= fates_harvest_luh_area) then
+              pass_lu_harvest = 1
+              pass_num_lu_harvest_types = num_landuse_harvest_vars
+           else
+              pass_lu_harvest = 0
+              pass_num_lu_harvest_cats = 0
+           end if
 
+        ! FATES landuse modes
         if(use_fates_luh) then
            pass_use_luh = 1
            pass_num_luh_states = num_landuse_state_vars
            pass_num_luh_transitions = num_landuse_transition_vars
-
-           ! Do not set harvest passing variables to zero not in luh harvest modes
-           ! as the user may want to use the CLM landuse harvest with luh2 transitions
-           if(fates_harvest_mode >= fates_harvest_luh_area) then
-              ! End the run if do_harvest is true with this run mode.
-              ! This should be caught be the build namelist.
-              if(get_do_harvest()) then
-                 call endrun(msg="do_harvest and fates_harvest_mode using luh2 harvest data are incompatible"//&
-                      errmsg(sourcefile, __LINE__))
-              else
-                 pass_lu_harvest = 1
-              end if
-           end if
         else
            pass_use_luh = 0
            pass_num_luh_states = 0
@@ -567,8 +549,7 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg)
 
-        ! Wait to set the harvest and logging variables after checking get_do_harvest
-        ! and fates_harvest_modes
+        ! Wait to set the harvest and logging variables after checking fates_harvest_modes
         call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest)
         call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats)
         call set_fates_ctrlparms('use_logging',ival=pass_logging)
@@ -996,7 +977,8 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
       ! Set the FATES global time and date variables
       call GetAndSetTime
 
-      if (get_do_harvest()) then
+      ! Get harvest rates for CLM landuse timeseries driven rates
+      if (fates_harvest_mode == fates_harvest_clmlanduse)
          call dynHarvest_interp_resolve_harvesttypes(bounds_clump, &
               harvest_rates=harvest_rates(begg:endg,1:num_harvest_inst), &
               after_start_of_harvest_ts=after_start_of_harvest_ts)
@@ -1122,7 +1104,7 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
          ! for now there is one veg column per gridcell, so store all harvest data in each site
          ! this will eventually change
          ! today's hlm harvest flag needs to be set no matter what
-         if (get_do_harvest()) then
+         if (fates_harvest_mode == fates_harvest_clmlanduse)
             if (after_start_of_harvest_ts) then
                this%fates(nc)%bc_in(s)%hlm_harvest_rates(1:num_harvest_inst) = harvest_rates(g,1:num_harvest_inst)
             else
@@ -1140,6 +1122,11 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
                write(iulog,*) harvest_units
                call endrun(msg=errMsg(sourcefile, __LINE__))
            end if
+
+         else if (fates_harvest_mode >= fates_harvest_luh_area) then
+              this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g)
+              this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames
+              this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units
          endif
 
          if (use_fates_luh) then
@@ -1147,12 +1134,6 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
                this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames
                this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g)
                this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames
-
-               if (fates_harvest_mode >= fates_harvest_luh_area) then
-                  this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g)
-                  this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames
-                  this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units
-               end if
          end if
 
       end do

From a35f91d53444c2ac7af2ee1434ae0f85431208b4 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 9 May 2024 11:15:18 -0700
Subject: [PATCH 0208/1248] fix check to be only during use of clm landuse
 timeseries for fates

---
 src/dyn_subgrid/dynSubgridDriverMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90
index b12b135b59..162247a0ff 100644
--- a/src/dyn_subgrid/dynSubgridDriverMod.F90
+++ b/src/dyn_subgrid/dynSubgridDriverMod.F90
@@ -128,7 +128,7 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst)
     ! flanduse_timeseries file. However, this could theoretically be changed so that the
     ! harvest data were separated from the pftdyn data, allowing them to differ in the
     ! years over which they apply.
-    if (get_do_harvest() .or. fates_harvest_mode >= fates_harvest_clmlanduse) then
+    if (get_do_harvest() .or. fates_harvest_mode == fates_harvest_clmlanduse) then
        call dynHarvest_init(bounds_proc, harvest_filename=get_flanduse_timeseries())
     end if
 

From 74e86669d21c18043a057d955f55e17bd5e7913e Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 9 May 2024 11:48:57 -0700
Subject: [PATCH 0209/1248] fix passing num landuse harvest vars to the fates
 landuse harvest categories

---
 src/utils/clmfates_interfaceMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 308d5cee8e..cd94b6a15c 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -521,7 +521,7 @@ subroutine CLMFatesGlobals2()
            ! LUH2 landuse timeseries driven  harvest rates
            else if (fates_harvest_mode >= fates_harvest_luh_area) then
               pass_lu_harvest = 1
-              pass_num_lu_harvest_types = num_landuse_harvest_vars
+              pass_num_lu_harvest_cats = num_landuse_harvest_vars
            else
               pass_lu_harvest = 0
               pass_num_lu_harvest_cats = 0

From fd07890223b3e92d91caa1a034055d1184bcff2e Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 9 May 2024 11:51:20 -0700
Subject: [PATCH 0210/1248] fix missing end if

---
 src/utils/clmfates_interfaceMod.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index cd94b6a15c..b9e9bf3031 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -526,6 +526,7 @@ subroutine CLMFatesGlobals2()
               pass_lu_harvest = 0
               pass_num_lu_harvest_cats = 0
            end if
+        end if
 
         ! FATES landuse modes
         if(use_fates_luh) then

From c37f743023dc4bf8fd26b7bd88336cbb7bc61d68 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 9 May 2024 14:57:59 -0600
Subject: [PATCH 0211/1248] Add more tests of finidat file settings, a bunch of
 things fail because of a problem in the use-case changes I made

---
 bld/unit_testers/build-namelist_test.pl | 164 ++++++++++++++++--------
 1 file changed, 114 insertions(+), 50 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 74dbcef3f4..2b65b18f38 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3665;
+my $ntests = 3385;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2313;
+   $ntests += 2097;
 }
 plan( tests=>$ntests );
 
@@ -1424,7 +1424,7 @@ sub cat_and_create_namelistinfile {
 print " Test all use-cases over all physics options\n";
 print "==================================================\n";
 
-# Run over all use-cases...
+# Run over all use-cases for f09 and all physics...
 my $list = `$bldnml -use_case list 2>&1 | grep "use case"`;
 my @usecases;
 if ( $list =~ /build-namelist : use cases : (.+)$/ ) {
@@ -1436,27 +1436,128 @@ sub cat_and_create_namelistinfile {
   print "use-cases = @usecases\n";
   die "ERROR:: Number of use-cases isn't what's expected\n";
 }
+my @expect_fails = ( "1850-2100_SSP5-3.4_transient", "1850-2100_SSP4-3.4", "1850-2100_SSP1-1.9_transient",
+                      "1850-2100_SSP4-6.0_transient" );
 foreach my $phys ( "clm4_5", "clm5_0", "clm5_1", "clm6_0" ) {
    print "physics = $phys\n";
    foreach my $usecase ( @usecases ) {
       print "usecase = $usecase\n";
-      $options = "-use_case $usecase  -envxml_dir .";
+      $options = "-res 0.9x1.25 -use_case $usecase  -envxml_dir .";
       &make_env_run();
       eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
-      is( $@, '', "options: $options" );
-      $cfiles->checkfilesexist( "$options", $mode );
-      $cfiles->shownmldiff( "default", "standard" );
-      if ( defined($opts{'compare'}) ) {
-         $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-         $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+      my $expect_fail = 0;
+      foreach my $failusecase ( @expect_fails ) {
+         if ( $failusecase eq $usecase ) {
+            $expect_fail = 1;
+         }
       }
-      if ( defined($opts{'generate'}) ) {
-         $cfiles->copyfiles( "$options", $mode );
+      if ( not $expect_fail ) {
+         is( $@, '', "options: $options" );
+         $cfiles->checkfilesexist( "$options", $mode );
+         $cfiles->shownmldiff( "default", "standard" );
+         if ( defined($opts{'compare'}) ) {
+            $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+            $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+         }
+         if ( defined($opts{'generate'}) ) {
+            $cfiles->copyfiles( "$options", $mode );
+         }
+      } else {
+         isnt( $@, '', "options: $options" );
       }
       &cleanup();
    }
 }
 
+print "\n=======================================================================================\n";
+print " Test the seperate initial condition files, for ones not tested elsewhere\n";
+print "=========================================================================================\n";
+
+my %finidat_files = (
+     "f091850Clm45BgcGSW"        =>{ phys =>"clm4_5",
+                                     atm_forc=>"GSWP3v1",
+                                     res => "0.9x1.25",
+                                     bgc => "bgc",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+     "f091850Clm45BgcCRU"        =>{ phys =>"clm4_5",
+                                     atm_forc=>"CRUv7",
+                                     res => "0.9x1.25",
+                                     bgc => "bgc",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+     "f091850Clm45BgcCAM6"       =>{ phys =>"clm4_5",
+                                     atm_forc=>"cam6.0",
+                                     res => "0.9x1.25",
+                                     bgc => "bgc",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+     "f091850Clm50BgcGSW"        =>{ phys =>"clm5_0",
+                                     atm_forc=>"GSWP3v1",
+                                     res => "0.9x1.25",
+                                     bgc => "bgc",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+     "f091850Clm50SpGSW"         =>{ phys =>"clm5_0",
+                                     atm_forc=>"GSWP3v1",
+                                     res => "0.9x1.25",
+                                     bgc => "sp",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+     "f091850Clm50BgcCRU"        =>{ phys =>"clm5_0",
+                                     atm_forc=>"CRUv7",
+                                     res => "0.9x1.25",
+                                     bgc => "bgc",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+     "f091850Clm50SpCRU"         =>{ phys =>"clm5_0",
+                                     atm_forc=>"CRUv7",
+                                     res => "0.9x1.25",
+                                     bgc => "sp",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+     "f091850Clm50BgcCAM6"       =>{ phys =>"clm5_0",
+                                     atm_forc=>"cam6.0",
+                                     res => "0.9x1.25",
+                                     bgc => "bgc",
+                                     use_case => "1850_control",
+                                     start_ymd => "18500101",
+                                   },
+   );
+
+foreach my $key ( keys(%finidat_files) ) {
+   print( "$key\n" );
+   my $phys = $finidat_files{$key}{'phys'};
+   print "physics = $phys\n";
+   &make_config_cache($phys);
+   my $usecase = $finidat_files{$key}{'use_case'};
+   my $bgc = $finidat_files{$key}{'bgc'};
+   my $res = $finidat_files{$key}{'res'};
+   my $start_ymd = $finidat_files{$key}{'start_ymd'};
+   my $lnd_tuning_mode = "${phys}_" . $finidat_files{$key}{'atm_forc'};
+   $options = "-bgc $bgc -res $res -use_case $usecase -envxml_dir . --lnd_tuning_mode $lnd_tuning_mode -namelist '&a start_ymd=$start_ymd/'";
+   &make_env_run();
+   eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
+   is( $@, '', "options: $options" );
+   $cfiles->checkfilesexist( "$options", $mode );
+   $cfiles->shownmldiff( "default", "standard" );
+   if ( defined($opts{'compare'}) ) {
+         $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+         $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+   }
+   if ( defined($opts{'generate'}) ) {
+         $cfiles->copyfiles( "$options", $mode );
+   }
+   &cleanup();
+}
+
 print "\n==================================================\n";
 print "Test crop resolutions \n";
 print "==================================================\n";
@@ -1519,7 +1620,7 @@ sub cat_and_create_namelistinfile {
                   "20thC_transient",
                  );
 foreach my $res ( @glc_res ) {
-   foreach my $usecase ( @usecases ) {
+   foreach my $usecase ( @use_cases ) {
       my $startymd = undef;
       if ( ($usecase eq "1850_control") || ($usecase eq "20thC_transient") ) {
          $startymd = 18500101;
@@ -1591,43 +1692,6 @@ sub cat_and_create_namelistinfile {
 #
 # End loop over versions
 #
-#
-# Test ALL SSP's for f09...
-#
-$phys = "clm6_0";
-$mode = "-phys $phys";
-&make_config_cache($phys);
-my $res = "0.9x1.25";
-foreach my $usecase ( "1850-2100_SSP5-8.5_transient", "1850-2100_SSP2-4.5_transient", "1850-2100_SSP1-2.6_transient", "1850-2100_SSP3-7.0_transient" ) {
-      $options = "-res $res -bgc bgc -crop -use_case $usecase -envxml_dir . -namelist '&a start_ymd=20150101/'";
-      &make_env_run();
-      eval{ system( "$bldnml $options > $tempfile 2>&1 " ); };
-      is( $@, '', "$options" );
-      $cfiles->checkfilesexist( "$options", $mode );
-      $cfiles->shownmldiff( "default", "standard" );
-      if ( defined($opts{'compare'}) ) {
-         $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-         $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
-      }
-      if ( defined($opts{'generate'}) ) {
-         $cfiles->copyfiles( "$options", $mode );
-      }
-      &cleanup();
-}
-
-# The SSP's that fail because of missing ndep files...
-$phys = "clm5_0";
-$mode = "-phys $phys";
-&make_config_cache($phys);
-my $res = "0.9x1.25";
-foreach my $usecase ( "1850-2100_SSP5-3.4_transient", "1850-2100_SSP4-3.4", "1850-2100_SSP1-1.9_transient",
-                      "1850-2100_SSP4-6.0_transient" ) {
-      $options = "-res $res -bgc bgc -crop -use_case $usecase -envxml_dir . -namelist '&a start_ymd=20150101/'";
-      &make_env_run();
-      eval{ system( "$bldnml $options > $tempfile 2>&1 " ); };
-      isnt( $?, 0, $usecase );
-      system( "cat $tempfile" );
-}
 
 print "\n==================================================\n";
 print "Test clm4.5/clm5.0/clm5_1/clm6_0 resolutions \n";

From f9974947dfebaba2c02bca5c3c87f0a2424b2849 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 9 May 2024 15:14:30 -0600
Subject: [PATCH 0212/1248] Updated ChangeLog/ChangeSum

---
 doc/ChangeLog | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 106 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e0a5e45cb6..3307c8df88 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,109 @@
 ===============================================================
+Tag name: ctsm5.2.004
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 09 May 2024 03:10:52 PM MDT
+One-line Summary: CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes
+
+Purpose and description of changes
+----------------------------------
+
+ Includes work by multiple people:
+ @slevis-lmwg: new fsurdat/landuse files and corresponding infrastructure for
+ the three so-called VR grids (ne0np4)
+ @samsrabin: a subset_data fix
+ @olyson: corrections to a couple of history long-names and updates to
+ history_fields_fates.rst and history_fields_nofates.rst
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2487 VR grids
+ Fixes #2527 subset_data is broken
+ Fixes #2511 a hist long name is incorrect
+ Fixes #2506 a hist long name is incorrect
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+ The so-called VR grids now use 1979 fsurdat files for 1850 compsets
+ and 1979-2026 landuse for historical compsets. The latter cross over into
+ SSP years and use SSP2-4.5 for that.
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ Same comment.
+
+Changes to documentation:
+ See Purpose and Description above.
+
+Substantial timing or memory changes:
+ Not considered.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ Updated the ctsm_sci tests for the three VR grids.
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ---- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+ However, note that the ctsm_sci test-suite showed diffs in
+ - Fates cases as expected since the last available baseline was ctsm_sci-ctsm5.2.0.
+ - the preexisting VR grid test for 1850 as expected since the fsurdat changed to 1979.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2590
+ https://github.com/ESCOMP/ctsm/pull/2512
+ https://github.com/ESCOMP/ctsm/pull/2528
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.003
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Thu May  2 14:06:54 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index b48e04889d..17ad670f17 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes
        ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev
        ctsm5.2.002 glemieux 04/26/2024 FATES default allometry parameter file update
        ctsm5.2.001     erik 04/22/2024 Merge b4b-dev

From 72ed62381b8312b0f0355b938d30c8b1a852cb31 Mon Sep 17 00:00:00 2001
From: loaner <loaner@eesaloaner-m53.local>
Date: Thu, 9 May 2024 16:25:53 -0700
Subject: [PATCH 0213/1248] update do_harvest to not be compatible with fates

---
 bld/CLMBuildNamelist.pm | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 54f0c0c997..e422109078 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2932,7 +2932,7 @@ sub setup_logic_do_harvest {
          $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
       }
 
-      elsif (!&value_is_true($nl->get_value('use_cn')) && !&value_is_true($nl->get_value('use_fates'))) {
+      elsif (!&value_is_true($nl->get_value('use_cn')) && &value_is_true($nl->get_value('use_fates'))) {
          $cannot_be_true = "$var can only be set to true when running with either CN or FATES";
       }
 
@@ -4486,22 +4486,12 @@ sub setup_logic_fates {
         # Check fates_harvest_mode compatibility
         my $var = "fates_harvest_mode";
         if ( defined($nl->get_value($var))  ) {
-           # using fates_harvest_mode with CLM landuse driver data - for user convienence
-           # if ( $nl->get_value($var) == 2) {
-           #    # Make sure that do_harvest is set to true
-           #    if ( ! &value_is_true($nl->get_value('do_harvest')) ) {
-           #      $log->fatal_error("do_harvest must be true when $var is equal to 2" );
-           # }
            # using fates_harvest mode with raw luh2 harvest data
            if ( $nl->get_value($var) > 2) {
               # Make sure that use_fates_luh is true when using raw fates luh2 harvest data
               if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
                 $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" );
               }
-              # do_harvest can not be on if we are using the raw fates luh2 harvest data
-              if ( &value_is_true($nl->get_value('do_harvest')) ) {
-                $log->fatal_error("do_harvest can not be true when $var is greater than 2" );
-              }
            }
         }
     }

From cf1a297864938fae60288ce742adfb2150e5caf8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 9 May 2024 17:28:23 -0600
Subject: [PATCH 0214/1248] Update Externals.cfg to cesm2_3_beta17

---
 Externals.cfg | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 185f412cab..80bfb45db8 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_99
+tag = cismwrap_2_1_100
 externals = Externals_CISM.cfg
 required = True
 
@@ -29,12 +29,12 @@ required = True
 [mizuRoute]
 local_path = components/mizuRoute
 protocol = git
-repo_url = https://github.com/nmizukami/mizuRoute
-hash = 34723c2
+repo_url = https://github.com/ESCOMP/mizuRoute
+hash = 81c720c
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.92
+tag = ccs_config_cesm0.0.106
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,18 +44,18 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.217_httpsbranch03
+tag = cime6.0.238_httpsbranch01
 required = True
 
 [cmeps]
-tag = cmeps0.14.50
+tag = cmeps0.14.60
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.28
+tag = cdeps1.0.33
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps

From 2aa76c4b3f841d35d465a254285daeb075f9d7cc Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 9 May 2024 17:46:05 -0600
Subject: [PATCH 0215/1248] Remove mct from Externals.cfg

---
 Externals.cfg | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 80bfb45db8..e8a2121df5 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -76,13 +76,6 @@ repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
 required = True
 
-[mct]
-tag = MCT_2.11.0
-protocol = git
-repo_url = https://github.com/MCSclimate/MCT
-local_path = libraries/mct
-required = True
-
 [parallelio]
 tag = pio2_6_2
 protocol = git

From ccce061987e7dc193aec37e53d7f46fa441d2147 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 9 May 2024 17:49:34 -0600
Subject: [PATCH 0216/1248] Remove cpl7 from Externals.cfg

---
 Externals.cfg | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index e8a2121df5..a8a77a40f1 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -62,13 +62,6 @@ local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
-[cpl7]
-tag = cpl77.0.7
-protocol = git
-repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
-local_path = components/cpl7
-required = True
-
 [share]
 tag = share1.0.18
 protocol = git

From f00ba49d552a3dc3578012f1cf32e6925ac224f9 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 9 May 2024 17:58:07 -0600
Subject: [PATCH 0217/1248] remove fates from the do_harvest section altogether

---
 bld/CLMBuildNamelist.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index e422109078..aafc7739a3 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2932,8 +2932,8 @@ sub setup_logic_do_harvest {
          $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
       }
 
-      elsif (!&value_is_true($nl->get_value('use_cn')) && &value_is_true($nl->get_value('use_fates'))) {
-         $cannot_be_true = "$var can only be set to true when running with either CN or FATES";
+      elsif (!&value_is_true($nl->get_value('use_cn'))) {
+         $cannot_be_true = "$var can only be set to true when running with CN.  Please set use_cn to true.";
       }
 
       if ($cannot_be_true) {

From 278a901fc4821e0c6abef4e0c5ed9bbf41f64516 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 10 May 2024 10:43:41 -0700
Subject: [PATCH 0218/1248] fix if statements

---
 src/utils/clmfates_interfaceMod.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index b9e9bf3031..5c23f1c1dc 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -514,7 +514,7 @@ subroutine CLMFatesGlobals2()
         if (fates_harvest_mode > fates_harvest_no_logging) then
            pass_logging = 1 ! Time driven logging, without landuse harvest
            ! CLM landuse timeseries driven harvest rates
-           if (fates_harvest_mode == fates_harvest_clmlanduse)
+           if (fates_harvest_mode == fates_harvest_clmlanduse) then
               pass_num_lu_harvest_cats = num_harvest_inst
               pass_lu_harvest = 1
 
@@ -979,7 +979,7 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
       call GetAndSetTime
 
       ! Get harvest rates for CLM landuse timeseries driven rates
-      if (fates_harvest_mode == fates_harvest_clmlanduse)
+      if (fates_harvest_mode == fates_harvest_clmlanduse) then
          call dynHarvest_interp_resolve_harvesttypes(bounds_clump, &
               harvest_rates=harvest_rates(begg:endg,1:num_harvest_inst), &
               after_start_of_harvest_ts=after_start_of_harvest_ts)
@@ -1105,7 +1105,7 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
          ! for now there is one veg column per gridcell, so store all harvest data in each site
          ! this will eventually change
          ! today's hlm harvest flag needs to be set no matter what
-         if (fates_harvest_mode == fates_harvest_clmlanduse)
+         if (fates_harvest_mode == fates_harvest_clmlanduse) then
             if (after_start_of_harvest_ts) then
                this%fates(nc)%bc_in(s)%hlm_harvest_rates(1:num_harvest_inst) = harvest_rates(g,1:num_harvest_inst)
             else

From 4861125a7a9c81008de5cb218755cd9792db0bb9 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 13:11:58 -0600
Subject: [PATCH 0219/1248] Remove MCT from README and .config_files.xml

---
 .config_files.xml | 3 ---
 README            | 5 ++---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/.config_files.xml b/.config_files.xml
index d1a592e5db..7f0d6bb11a 100644
--- a/.config_files.xml
+++ b/.config_files.xml
@@ -19,11 +19,8 @@
     <values>
       <value component="clm"                         >$SRCROOT</value>
       <value component="slim"                        >$SRCROOT/components/slim/</value>
-      <value component="dlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/data_comps_$COMP_INTERFACE/dlnd</value>
       <value component="dlnd" comp_interface="nuopc" >$SRCROOT/components/cdeps/dlnd</value>
-      <value component="slnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/stub_comps_$COMP_INTERFACE/slnd</value>
       <value component="slnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
-      <value component="xlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
       <value component="xlnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
     </values>
     <group>case_comps</group>
diff --git a/README b/README
index 18cc2b1458..4699fec858 100644
--- a/README
+++ b/README
@@ -57,7 +57,7 @@ python ------------ Python modules used in tools and testing and automated check
 Directory structure only for a CTSM checkout:
 
 components -------- Other active sub-components needed for CTSM to run (river routing and land-ice models)
-libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO (deprecated)
+libraries --------- CESM libraries: PIO (deprecated)
 share ------------- CESM shared code
 ccs_config -------- CIME configure files (for grids, compsets, and machines) for CESM
 
@@ -68,7 +68,6 @@ components/cdeps -------------------- CESM top level data model shared code (for
 components/cism --------------------- CESM Community land Ice Sheet Model.
 components/mosart ------------------- Model for Scale Adaptive River Transport
 components/rtm ---------------------- CESM River Transport Model.
-components/cpl7 --------------------- CESM top level driver for MCT driver (deprecated will be removed)
 
 Top level documentation ($CTSMROOT):
 
@@ -154,7 +153,7 @@ Source code directory structure:
 
 src/biogeochem ---- Biogeochemisty
 src/main ---------- Main control and high level code
-src/cpl ----------- Land model high level caps for NUOPC driver (and MCT and LILAC)
+src/cpl ----------- Land model high level caps for NUOPC driver (and LILAC)
 src/biogeophys ---- Biogeophysics (Hydrology)
 src/dyn_subgrid --- Dynamic land unit change
 src/init_interp --- Online interpolation

From db147cd616ea8a52e4bc64e88299c8fe76036396 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 13:57:37 -0600
Subject: [PATCH 0220/1248] Remove MCT from CLMBuildNamelist.pm

---
 bld/CLMBuildNamelist.pm | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fb44023cd5..731589289c 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -71,7 +71,7 @@ REQUIRED OPTIONS
                               (if read they allow user_nl_clm and CLM_BLDNML_OPTS to expand
                                variables [for example to use \$DIN_LOC_ROOT])
                               (default current directory)
-     -lnd_frac "domainfile"   Land fraction file (the input domain file) (needed for MCT driver and LILAC)
+     -lnd_frac "domainfile"   Land fraction file (the input domain file) (needed for LILAC)
      -res "resolution"        Specify horizontal grid.  Use nlatxnlon for spectral grids;
                               dlatxdlon for fv grids (dlat and dlon are the grid cell size
                               in degrees for latitude and longitude respectively)
@@ -83,7 +83,7 @@ REQUIRED OPTIONS
                               (default 2000)
      -structure "structure"   The overall structure being used [ standard | fast ]
 OPTIONS
-     -driver "value"          CESM driver type you will run with [ mct | nuopc ]
+     -driver "value"          CESM driver type you will run with [ nuopc ]
      -bgc "value"             Build CLM with BGC package [ sp | bgc | fates ]
                               (default is sp).
                                 CLM Biogeochemistry mode
@@ -1893,10 +1893,10 @@ sub setup_logic_lnd_frac {
   my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;
 
   #
-  # fatmlndfrc is required for the MCT driver (or LILAC), but uneeded for NUOPC
+  # fatmlndfrc is required for LILAC but uneeded for NUOPC
   #
   my $var = "lnd_frac";
-  if ( ($opts->{'driver'} eq "mct") || $opts->{'lilac'} ) {
+  if ( $opts->{'lilac'} ) {
      if ( defined($opts->{$var}) ) {
        if ( defined($nl->get_value('fatmlndfrc')) ) {
          $log->fatal_error("Can NOT set both -lnd_frac option (set via LND_DOMAIN_PATH/LND_DOMAIN_FILE " .
@@ -3838,9 +3838,7 @@ sub setup_logic_popd_streams {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'},
                  'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
-     #
-     # TODO (mvertens, 2021-06-22) the following is needed for MCT since a use case enforces this  - so for now stream_meshfile_popdens will be added to the mct
-     # stream namelist but simply not used
+
     if ($opts->{'driver'} eq "nuopc" ) {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_popdens', 'hgrid'=>"0.5x0.5");
         my $inputdata_rootdir = $nl_flags->{'inputdata_rootdir'};
@@ -3854,12 +3852,6 @@ sub setup_logic_popd_streams {
             $val = &quote_string( $val );
             $nl->set_variable_value($group, $var, $val);
         }
-    } else {
-        my $var = 'stream_meshfile_popdens';
-        my $group = $definition->get_group_name($var);
-        my $val = "none";
-        $val = &quote_string( $val );
-        $nl->set_variable_value($group, $var, $val);
     }
   } else {
      # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set

From 68d46b68f92ebe08ce04d61527638d6997275b38 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 14:03:49 -0600
Subject: [PATCH 0221/1248] Remove MCT from build-namelist_test.pl

---
 bld/unit_testers/build-namelist_test.pl | 30 ++-----------------------
 1 file changed, 2 insertions(+), 28 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 7b654337af..12a5f4bd38 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -314,7 +314,7 @@ sub cat_and_create_namelistinfile {
 print "=================================================================================\n";
 
 my $startfile = "clmrun.clm2.r.1964-05-27-00000.nc";
-foreach my $driver ( "mct", "nuopc" ) {
+foreach my $driver ( "nuopc" ) {
    print "   For $driver driver\n\n";
    # configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case
    foreach my $options ( "-res 0.9x1.25 -configuration nwp",
@@ -335,13 +335,7 @@ sub cat_and_create_namelistinfile {
       my $file = $startfile;
       &make_env_run();
       my $base_options = "-envxml_dir . -driver $driver";
-      if ( $driver eq "mct" ) {
-         $base_options = "$base_options -lnd_frac $DOMFILE";
-         # Skip the MCT test for excess ice streams
-         if ( $options =~ /use_excess_ice_streams=.true./ ) {
-           next;
-         }
-      } else {
+      if ( $driver eq "nuopc" ) {
          $base_options = "$base_options -namelist '&a force_send_to_atm = .false./'";
       }
       eval{ system( "$bldnml $base_options $options > $tempfile 2>&1 " ); };
@@ -548,11 +542,6 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
-     "exice stream on, but mct"    =>{ options=>"--res 0.9x1.25 --envxml_dir . --driver mct --lnd_frac $DOMFILE ",
-                                     namelst=>"use_excess_ice=.true., use_excess_ice_streams=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_0",
-                                   },
      "clm50CNDVwtransient"       =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -898,16 +887,6 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
-     "both lnd_frac and on nml"  =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .",
-                                     namelst=>"fatmlndfrc='frac.nc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_0",
-                                   },
-     "lnd_frac set to UNSET"     =>{ options=>"-driver mct -lnd_frac UNSET -envxml_dir .",
-                                     namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm6_0",
-                                   },
      "lnd_frac set but nuopc"    =>{ options=>"-driver nuopc -lnd_frac $DOMFILE -envxml_dir .",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -923,11 +902,6 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
-     "force_send but not nuopc"  =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .",
-                                     namelst=>"force_send_to_atm = .false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm6_0",
-                                   },
      "branch but NO nrevsn"      =>{ options=>"-clm_start_type branch -envxml_dir .",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

From 190be8bd937ce545ad636c7c339f8b5497968ab6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 10 May 2024 14:21:11 -0600
Subject: [PATCH 0222/1248] Fix the 2010 use case, and get the namelist testing
 working better

---
 bld/namelist_files/use_cases/2010_control.xml |  4 ++--
 bld/unit_testers/build-namelist_test.pl       | 24 ++++++++++++-------
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/bld/namelist_files/use_cases/2010_control.xml b/bld/namelist_files/use_cases/2010_control.xml
index d4c2a9c9c0..d16177301c 100644
--- a/bld/namelist_files/use_cases/2010_control.xml
+++ b/bld/namelist_files/use_cases/2010_control.xml
@@ -12,8 +12,8 @@
 <irrigate use_crop=".true." =".false."    >.true.</irrigate>
 <irrigate use_crop=".true." phys="clm4_5" >.false.</irrigate>
 
-<stream_year_first_ndep bgc="cn"   >2010</stream_year_first_ndep>
-<stream_year_last_ndep  bgc="cn"   >2010</stream_year_last_ndep>
+<stream_year_first_ndep bgc="cn" use_cn=".true." >2010</stream_year_first_ndep>
+<stream_year_last_ndep  bgc="cn" use_cn=".true." >2010</stream_year_last_ndep>
 
 <stream_year_first_popdens cnfireson=".true." >2010</stream_year_first_popdens>
 <stream_year_last_popdens  cnfireson=".true." >2010</stream_year_last_popdens>
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 2b65b18f38..25545dcf8a 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3385;
+my $ntests = 3313;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2097;
+   $ntests += 2001;
 }
 plan( tests=>$ntests );
 
@@ -1436,22 +1436,24 @@ sub cat_and_create_namelistinfile {
   print "use-cases = @usecases\n";
   die "ERROR:: Number of use-cases isn't what's expected\n";
 }
-my @expect_fails = ( "1850-2100_SSP5-3.4_transient", "1850-2100_SSP4-3.4", "1850-2100_SSP1-1.9_transient",
-                      "1850-2100_SSP4-6.0_transient" );
+my @expect_fails = ( "1850-2100_SSP5-3.4_transient", "1850-2100_SSP4-3.4_transient", "2018-PD_transient", "1850-2100_SSP1-1.9_transient",
+                      "1850-2100_SSP4-6.0_transient", "2018_control" );
 foreach my $phys ( "clm4_5", "clm5_0", "clm5_1", "clm6_0" ) {
    print "physics = $phys\n";
+   &make_config_cache($phys);
    foreach my $usecase ( @usecases ) {
       print "usecase = $usecase\n";
       $options = "-res 0.9x1.25 -use_case $usecase  -envxml_dir .";
       &make_env_run();
-      eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
-      my $expect_fail = 0;
+      my $expect_fail = undef;
       foreach my $failusecase ( @expect_fails ) {
          if ( $failusecase eq $usecase ) {
             $expect_fail = 1;
+            last;
          }
       }
-      if ( not $expect_fail ) {
+      eval{ system( "$bldnml $options > $tempfile 2>&1 " ); };
+      if ( ! defined($expect_fail) ) {
          is( $@, '', "options: $options" );
          $cfiles->checkfilesexist( "$options", $mode );
          $cfiles->shownmldiff( "default", "standard" );
@@ -1463,7 +1465,7 @@ sub cat_and_create_namelistinfile {
             $cfiles->copyfiles( "$options", $mode );
          }
       } else {
-         isnt( $@, '', "options: $options" );
+         isnt( $@, 0, "options: $options" );
       }
       &cleanup();
    }
@@ -1546,6 +1548,12 @@ sub cat_and_create_namelistinfile {
    &make_env_run();
    eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
    is( $@, '', "options: $options" );
+   my $finidat = `grep finidat lnd_in`;
+   if ( $finidat =~ /initdata_map/ ) {
+      my $result;
+      eval( $result = `grep use_init_interp lnd_in` );
+      isnt( $#, 0, "use_init_interp needs to be set here and was not: $result")
+   }
    $cfiles->checkfilesexist( "$options", $mode );
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {

From f3386bcd5c0ec78d6d2be660aaa7b4c257910030 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 15:58:49 -0600
Subject: [PATCH 0223/1248] Remove MCT from config_definition_ctsm.xml

---
 bld/config_files/config_definition_ctsm.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/config_files/config_definition_ctsm.xml b/bld/config_files/config_definition_ctsm.xml
index dfe6378f17..e6628b1d94 100644
--- a/bld/config_files/config_definition_ctsm.xml
+++ b/bld/config_files/config_definition_ctsm.xml
@@ -18,11 +18,11 @@ Root directory of CLM source distribution (directory above CLM configure).
 </entry>
 
 <entry id="comp_intf" 
-       valid_values="ESMF,MCT,cpl_\$COMP" 
-       value="MCT"
+       valid_values="ESMF,cpl_\$COMP"
+       value="ESMF"
        category="directories">
 Component framework interface to use 
-(Model Coupling Toolkit, or Earth System Modeling Framework)
+(Earth System Modeling Framework)
 </entry>
 
 <entry id="usr_src" 

From dc70323e5fe7e5d5c7c580de9b3877554debba4a Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 16:08:42 -0600
Subject: [PATCH 0224/1248] Remove MCT from ExpectedTestFails.xml and update
 README.NUOPC_driver.md

---
 README.NUOPC_driver.md                     | 5 +----
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 2 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/README.NUOPC_driver.md b/README.NUOPC_driver.md
index ba0b70c2c0..9eb5d5b2cb 100644
--- a/README.NUOPC_driver.md
+++ b/README.NUOPC_driver.md
@@ -43,9 +43,6 @@ by having an updated copy in your case directory.
 
 ## What if I want to use the MCT driver?
 
-The MCT driver is now deprecated, and will be removed. So at this point we don't
-suggest using it anymore.
-
-For more notes see:
+The MCT driver is now removed. For more notes see:
 
 https://docs.google.com/presentation/d/1yjiKSEV53JDAJbYxhpY2T9GTxlWFzQAn
diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 8ee60cf4b8..f600444547 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -51,13 +51,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld1_Mmpi-serial_Vmct.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsRLA">
-    <phase name="SHAREDLIB_BUILD">
-      <status>FAIL</status>
-      <issue>#1887</issue>
-    </phase>
-  </test>
-
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>

From 629961c2afa8d86be3101b90dfe040a8d9603ac2 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 16:11:33 -0600
Subject: [PATCH 0225/1248] Remove reference to MCT in fsurdat_modifier.py

---
 python/ctsm/modify_input_files/fsurdat_modifier.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py
index bd060cb9dc..1a45590872 100644
--- a/python/ctsm/modify_input_files/fsurdat_modifier.py
+++ b/python/ctsm/modify_input_files/fsurdat_modifier.py
@@ -254,8 +254,8 @@ def modify_optional(
     """Modify the dataset according to the optional settings"""
 
     # Set fsurdat variables in a rectangle that could be global (default).
-    # Note that the land/ocean mask gets specified in the domain file for
-    # MCT or the ocean mesh files for NUOPC. Here the user may specify
+    # Note that the land/ocean mask gets specified in
+    # the ocean mesh files. Here the user may specify
     # fsurdat variables inside a box but cannot change which points will
     # run as land and which as ocean.
     if idealized:

From fb5b6310be60477a7c4cb67656a68a9c71cb8b6e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 16:15:09 -0600
Subject: [PATCH 0226/1248] Remove src/unit_test_stubs/csm_share/CMakeLists.txt

---
 src/unit_test_stubs/csm_share/CMakeLists.txt | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100644 src/unit_test_stubs/csm_share/CMakeLists.txt

diff --git a/src/unit_test_stubs/csm_share/CMakeLists.txt b/src/unit_test_stubs/csm_share/CMakeLists.txt
deleted file mode 100644
index 33ddbfb342..0000000000
--- a/src/unit_test_stubs/csm_share/CMakeLists.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-list(APPEND share_sources
-  shr_mpi_mod_stub.F90
-  )
-
-sourcelist_to_parent(share_sources)

From 3d1ab9be7da02a53107786a952582462049611db Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 16:18:43 -0600
Subject: [PATCH 0227/1248] Remove MCT from test_driver.sh

---
 test/tools/test_driver.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh
index f93301a530..307d1accf8 100755
--- a/test/tools/test_driver.sh
+++ b/test/tools/test_driver.sh
@@ -463,8 +463,7 @@ if [ ! -d \$CLM_TESTDIR ]; then
     fi
 fi
 
-## MCT and PIO build directorys
-export MCT_LIBDIR=\$CLM_TESTDIR/mct
+## PIO build directory
 export PIO_LIBDIR=\$CLM_TESTDIR/pio
 
 ##set our own environment vars

From 371f093e02a7820e8beec823c97dd23b94277c05 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 16:20:13 -0600
Subject: [PATCH 0228/1248] Remove the src/cpl/mct directory

---
 src/cpl/mct/ExcessIceStreamType.F90       | 144 -----
 src/cpl/mct/FireDataBaseType.F90          | 561 -------------------
 src/cpl/mct/SoilMoistureStreamMod.F90     | 418 --------------
 src/cpl/mct/UrbanTimeVarType.F90          | 314 -----------
 src/cpl/mct/ch4FInundatedStreamType.F90   | 389 -------------
 src/cpl/mct/clm_cpl_indices.F90           | 330 -----------
 src/cpl/mct/laiStreamMod.F90              | 241 ---------
 src/cpl/mct/lnd_comp_mct.F90              | 632 ----------------------
 src/cpl/mct/lnd_import_export.F90         | 354 ------------
 src/cpl/mct/lnd_set_decomp_and_domain.F90 | 352 ------------
 src/cpl/mct/ndepStreamMod.F90             | 376 -------------
 11 files changed, 4111 deletions(-)
 delete mode 100644 src/cpl/mct/ExcessIceStreamType.F90
 delete mode 100644 src/cpl/mct/FireDataBaseType.F90
 delete mode 100644 src/cpl/mct/SoilMoistureStreamMod.F90
 delete mode 100644 src/cpl/mct/UrbanTimeVarType.F90
 delete mode 100644 src/cpl/mct/ch4FInundatedStreamType.F90
 delete mode 100644 src/cpl/mct/clm_cpl_indices.F90
 delete mode 100644 src/cpl/mct/laiStreamMod.F90
 delete mode 100644 src/cpl/mct/lnd_comp_mct.F90
 delete mode 100644 src/cpl/mct/lnd_import_export.F90
 delete mode 100644 src/cpl/mct/lnd_set_decomp_and_domain.F90
 delete mode 100644 src/cpl/mct/ndepStreamMod.F90

diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90
deleted file mode 100644
index 5c5394233c..0000000000
--- a/src/cpl/mct/ExcessIceStreamType.F90
+++ /dev/null
@@ -1,144 +0,0 @@
-module ExcessIceStreamType
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Stub for ExcessIceStreams for the MCT driver. So that MCT can be used
-  ! without excess ice streams.
-  !
-  ! !USES
-  use shr_kind_mod     , only : r8 => shr_kind_r8, CL => shr_kind_CL
-  use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use spmdMod          , only : mpicom, masterproc
-  use clm_varctl       , only : iulog
-  use abortutils       , only : endrun
-  use decompMod        , only : bounds_type
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-
-  public  :: UseExcessIceStreams      ! If streams will be used
-
-  type, public :: excessicestream_type
-  contains
-
-      ! !PUBLIC MEMBER FUNCTIONS:
-      procedure, public  :: Init            ! Initialize and read data in
-      procedure, public  :: CalcExcessIce   ! Calculate excess ice ammount
-
-      ! !PRIVATE MEMBER FUNCTIONS:
-      procedure, private :: ReadNML     ! Read in namelist
-
-  end type excessicestream_type
-  ! ! PRIVATE DATA:
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-!==============================================================================
-contains
-!==============================================================================
-
-  subroutine Init(this, bounds, NLFilename)
-    !
-    !
-    ! arguments
-    implicit none
-    class(excessicestream_type) :: this
-    type(bounds_type), intent(in)   :: bounds
-    character(len=*),  intent(in)   :: NLFilename   ! Namelist filename
-
-    !
-    ! local variables
-
-    call this%ReadNML( bounds, NLFileName )
-  end subroutine Init
-
-  subroutine CalcExcessIce(this,bounds,exice_bulk_init)
-  
-  ! only transfers grid values to columns
-   implicit none
-   class(excessicestream_type)        :: this
-   type(bounds_type),  intent(in)     :: bounds
-   real(r8)         ,  intent(inout)  :: exice_bulk_init(bounds%begc:bounds%endc) 
-   !
-   ! !LOCAL VARIABLES:
-   
-  end subroutine CalcExcessIce
-
-  logical function UseExcessIceStreams()
-  !
-  ! !DESCRIPTION:
-  ! Return true if
-  !
-  ! !USES:
-  !
-  ! !ARGUMENTS:
-  implicit none
-  !
-  ! !LOCAL VARIABLES:
-  UseExcessIceStreams = .false.
-end function UseExcessIceStreams
-
-subroutine ReadNML(this, bounds, NLFilename)
-  !
-  ! Read the namelist data stream information.
-  !
-  ! Uses:
-  use shr_nl_mod       , only : shr_nl_find_group_name
-  use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use shr_mpi_mod      , only : shr_mpi_bcast
-  !
-  ! arguments
-  implicit none
-  class(excessicestream_type)   :: this
-  type(bounds_type), intent(in) :: bounds
-  character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-  !
-  ! local variables
-  integer            :: nu_nml    ! unit for namelist file
-  integer            :: nml_error ! namelist i/o error flag
-  logical            :: use_excess_ice_streams = .false.         ! logical to turn on use of excess ice streams
-  character(len=CL)  :: stream_fldFileName_exice = ' '
-  character(len=CL)  :: stream_mapalgo_exice = 'none'
-  character(len=*), parameter :: namelist_name = 'exice_streams'    ! MUST agree with name in namelist and read
-  character(len=*), parameter :: subName = "('exice_streams::ReadNML')"
-  !-----------------------------------------------------------------------
-
-  namelist /exice_streams/ &               ! MUST agree with namelist_name above
-       stream_mapalgo_exice,  stream_fldFileName_exice, use_excess_ice_streams
-  !-----------------------------------------------------------------------
-  ! Default values for namelist
-
-  ! Read excess ice namelist
-  if (masterproc) then
-     open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-     call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error)
-     if (nml_error == 0) then
-        read(nu_nml, nml=exice_streams,iostat=nml_error)   ! MUST agree with namelist_name above
-        if (nml_error /= 0) then
-           call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-        end if
-     else
-        call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-     end if
-     close(nu_nml)
-  endif
-
-  call shr_mpi_bcast(use_excess_ice_streams   , mpicom)
-
-  if (masterproc) then
-     if ( use_excess_ice_streams ) then
-        call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__))
-     end if
-     if ( trim(stream_fldFileName_exice) /= ''  ) then
-        call endrun(msg=' ERROR stream_fldFileName_exice can NOT be set for the MCT driver'//errMsg(sourcefile, __LINE__))
-     end if
-     if ( trim(stream_mapalgo_exice) /= 'none'  ) then
-        call endrun(msg=' ERROR stream_mapalgo_exice can only be none for the MCT driver'//errMsg(sourcefile, __LINE__))
-     end if
-  endif
-
-end subroutine ReadNML
-
-end module ExcessIceStreamType
diff --git a/src/cpl/mct/FireDataBaseType.F90 b/src/cpl/mct/FireDataBaseType.F90
deleted file mode 100644
index 0ee635b2fa..0000000000
--- a/src/cpl/mct/FireDataBaseType.F90
+++ /dev/null
@@ -1,561 +0,0 @@
-module FireDataBaseType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! module for handling of fire data
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8, CL => shr_kind_CL
-  use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create, shr_strdata_print
-  use shr_strdata_mod , only : shr_strdata_advance
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use clm_varctl      , only : iulog, inst_name
-  use spmdMod         , only : masterproc, mpicom, comp_id
-  use fileutils       , only : getavu, relavu
-  use domainMod       , only : ldomain
-  use abortutils      , only : endrun
-  use decompMod       , only : bounds_type
-  use FireMethodType  , only : fire_method_type
-  use lnd_set_decomp_and_domain, only : gsmap_global
-  use mct_mod
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC TYPES:
-  public :: fire_base_type
-
-  !
-  type, abstract, extends(fire_method_type) :: fire_base_type
-    private
-      ! !PRIVATE MEMBER DATA:
-
-      real(r8), public, pointer :: forc_lnfm(:)    ! Lightning frequency
-      real(r8), public, pointer :: forc_hdm(:)     ! Human population density
-      
-      real(r8), public, pointer :: gdp_lf_col(:)   ! col global real gdp data (k US$/capita)
-      real(r8), public, pointer :: peatf_lf_col(:) ! col global peatland fraction data (0-1)
-      integer , public, pointer :: abm_lf_col(:)   ! col global peak month of crop fire emissions
-
-      type(shr_strdata_type) :: sdat_hdm    ! Human population density input data stream
-      type(shr_strdata_type) :: sdat_lnfm   ! Lightning input data stream
-
-    contains
-      !
-      ! !PUBLIC MEMBER FUNCTIONS:
-      procedure, public :: FireInit => BaseFireInit     ! Initialization of Fire
-      procedure, public :: BaseFireInit                 ! Initialization of Fire
-      procedure(FireReadNML_interface), public, deferred :: FireReadNML       ! Read in namelist for Fire
-      procedure, public :: FireInterp        ! Interpolate fire data
-      procedure(need_lightning_and_popdens_interface), public, deferred :: &
-           need_lightning_and_popdens ! Returns true if need lightning & popdens
-      !
-      ! !PRIVATE MEMBER FUNCTIONS:
-      procedure, private :: hdm_init     ! position datasets for dynamic human population density
-      procedure, private :: hdm_interp   ! interpolates between two years of human pop. density file data
-      procedure, private :: lnfm_init    ! position datasets for Lightning
-      procedure, private :: lnfm_interp  ! interpolates between two years of Lightning file data
-      procedure, private :: surfdataread ! read fire related data from surface data set
-  end type fire_base_type
-  !-----------------------------------------------------------------------
-
-  abstract interface
-     !-----------------------------------------------------------------------
-     function need_lightning_and_popdens_interface(this) result(need_lightning_and_popdens)
-       !
-       ! !DESCRIPTION:
-       ! Returns true if need lightning and popdens, false otherwise
-       !
-       ! USES
-       import :: fire_base_type
-       !
-       ! !ARGUMENTS:
-       class(fire_base_type), intent(in) :: this
-       logical :: need_lightning_and_popdens  ! function result
-       !-----------------------------------------------------------------------
-     end function need_lightning_and_popdens_interface
-  end interface
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine FireReadNML_interface( this, NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Read the namelist for Fire
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(fire_base_type) :: this
-    character(len=*), intent(in) :: NLFilename ! Namelist filename
-  end subroutine FireReadNML_interface
-
-  !-----------------------------------------------------------------------
-  subroutine BaseFireInit( this, bounds, NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Initialize CN Fire module
-    ! !USES:
-    use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(fire_base_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    character(len=*),  intent(in) :: NLFilename
-    !-----------------------------------------------------------------------
-
-    if ( this%need_lightning_and_popdens() ) then
-       ! Allocate lightning forcing data
-       allocate( this%forc_lnfm(bounds%begg:bounds%endg) )
-       this%forc_lnfm(bounds%begg:) = nan
-       ! Allocate pop dens forcing data
-       allocate( this%forc_hdm(bounds%begg:bounds%endg) )
-       this%forc_hdm(bounds%begg:) = nan
-       
-       ! Allocate real gdp data
-       allocate(this%gdp_lf_col(bounds%begc:bounds%endc))
-       ! Allocate peatland fraction data
-       allocate(this%peatf_lf_col(bounds%begc:bounds%endc))
-       ! Allocates peak month of crop fire emissions
-       allocate(this%abm_lf_col(bounds%begc:bounds%endc))
-   
-
-       call this%hdm_init(bounds, NLFilename)
-       call this%hdm_interp(bounds)
-       call this%lnfm_init(bounds, NLFilename)
-       call this%lnfm_interp(bounds)
-       call this%surfdataread(bounds)
-    end if
-
-  end subroutine BaseFireInit
-
-  !-----------------------------------------------------------------------
-  subroutine FireInterp(this,bounds)
-    !
-    ! !DESCRIPTION:
-    ! Interpolate CN Fire datasets
-    !
-    ! !ARGUMENTS:
-    class(fire_base_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !-----------------------------------------------------------------------
-
-    if ( this%need_lightning_and_popdens() ) then
-       call this%hdm_interp(bounds)
-       call this%lnfm_interp(bounds)
-    end if
-
-  end subroutine FireInterp
-
-  !-----------------------------------------------------------------------
-  subroutine hdm_init( this, bounds, NLFilename )
-   !
-   ! !DESCRIPTION:
-   ! Initialize data stream information for population density.
-   !
-   ! !USES:
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use clm_nlUtilsMod   , only : find_nlgroup_name
-   use ndepStreamMod    , only : clm_domain_mct
-   use histFileMod      , only : hist_addfld1d
-   !
-   ! !ARGUMENTS:
-   implicit none
-   class(fire_base_type)         :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! !LOCAL VARIABLES:
-   integer            :: stream_year_first_popdens   ! first year in pop. dens. stream to use
-   integer            :: stream_year_last_popdens    ! last year in pop. dens. stream to use
-   integer            :: model_year_align_popdens    ! align stream_year_first_hdm with
-   integer            :: nu_nml                      ! unit for namelist file
-   integer            :: nml_error                   ! namelist i/o error flag
-   type(mct_ggrid)    :: dom_clm                     ! domain information
-   character(len=CL)  :: stream_fldFileName_popdens  ! population density streams filename
-   character(len=CL)  :: popdensmapalgo = 'bilinear' ! mapping alogrithm for population density
-   character(len=CL)  :: popdens_tintalgo = 'nearest'! time interpolation alogrithm for population density
-   character(len=CL)  :: stream_meshfile_popdens     ! not used
-   character(*), parameter :: subName = "('hdmdyn_init')"
-   character(*), parameter :: F00 = "('(hdmdyn_init) ',4a)"
-   !-----------------------------------------------------------------------
-
-   namelist /popd_streams/          &
-        stream_year_first_popdens,  &
-        stream_year_last_popdens,   &
-        model_year_align_popdens,   &
-        popdensmapalgo,             &
-        stream_fldFileName_popdens, &
-        stream_meshfile_popdens   , &
-        popdens_tintalgo
-
-   ! Default values for namelist
-   stream_year_first_popdens  = 1       ! first year in stream to use
-   stream_year_last_popdens   = 1       ! last  year in stream to use
-   model_year_align_popdens   = 1       ! align stream_year_first_popdens with this model year
-   stream_fldFileName_popdens = ' '
-
-   ! Read popd_streams namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call find_nlgroup_name(nu_nml, 'popd_streams', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=popd_streams,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg='ERROR reading popd_streams namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_year_first_popdens, mpicom)
-   call shr_mpi_bcast(stream_year_last_popdens, mpicom)
-   call shr_mpi_bcast(model_year_align_popdens, mpicom)
-   call shr_mpi_bcast(stream_fldFileName_popdens, mpicom)
-   call shr_mpi_bcast(popdens_tintalgo, mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'popdens_streams settings:'
-      write(iulog,*) '  stream_year_first_popdens  = ',stream_year_first_popdens
-      write(iulog,*) '  stream_year_last_popdens   = ',stream_year_last_popdens
-      write(iulog,*) '  model_year_align_popdens   = ',model_year_align_popdens
-      write(iulog,*) '  stream_fldFileName_popdens = ',stream_fldFileName_popdens
-      write(iulog,*) '  popdens_tintalgo           = ',popdens_tintalgo
-      write(iulog,*) ' '
-   endif
-
-   call clm_domain_mct (bounds, dom_clm)
-
-   call shr_strdata_create(this%sdat_hdm,name="clmhdm", &
-        pio_subsystem=pio_subsystem,                    &
-        pio_iotype=shr_pio_getiotype(inst_name),        &
-        mpicom=mpicom, compid=comp_id,                  &
-        gsmap=gsmap_global, ggrid=dom_clm,              &
-        nxg=ldomain%ni, nyg=ldomain%nj,                 &
-        yearFirst=stream_year_first_popdens,            &
-        yearLast=stream_year_last_popdens,              &
-        yearAlign=model_year_align_popdens,             &
-        offset=0,                                       &
-        domFilePath='',                                 &
-        domFileName=trim(stream_fldFileName_popdens),   &
-        domTvarName='time',                             &
-        domXvarName='lon' ,                             &
-        domYvarName='lat' ,                             &
-        domAreaName='area',                             &
-        domMaskName='mask',                             &
-        filePath='',                                    &
-        filename=(/trim(stream_fldFileName_popdens)/) , &
-        fldListFile='hdm',                              &
-        fldListModel='hdm',                             &
-        fillalgo='none',                                &
-        mapalgo=popdensmapalgo,                         &
-        calendar=get_calendar(),                        &
-        tintalgo=popdens_tintalgo,                      &
-        taxmode='extend'                           )
-
-   if (masterproc) then
-      call shr_strdata_print(this%sdat_hdm,'population density data')
-   endif
-
-   ! Add history fields
-   call hist_addfld1d (fname='HDM', units='counts/km^2',      &
-         avgflag='A', long_name='human population density',   &
-         ptr_lnd=this%forc_hdm, default='inactive')
-
-  end subroutine hdm_init
-
-  !-----------------------------------------------------------------------
-  subroutine hdm_interp( this, bounds)
-  !
-  ! !DESCRIPTION:
-  ! Interpolate data stream information for population density.
-  !
-  ! !USES:
-  use clm_time_manager, only : get_curr_date
-  !
-  ! !ARGUMENTS:
-  class(fire_base_type)       :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  integer :: g, ig
-  integer :: year    ! year (0, ...) for nstep+1
-  integer :: mon     ! month (1, ..., 12) for nstep+1
-  integer :: day     ! day of month (1, ..., 31) for nstep+1
-  integer :: sec     ! seconds into current date for nstep+1
-  integer :: mcdate  ! Current model date (yyyymmdd)
-  !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(this%sdat_hdm, mcdate, sec, mpicom, 'hdmdyn')
-
-   ig = 0
-   do g = bounds%begg,bounds%endg
-      ig = ig+1
-      this%forc_hdm(g) = this%sdat_hdm%avs(1)%rAttr(1,ig)
-   end do
-
-  end subroutine hdm_interp
-
-  !-----------------------------------------------------------------------
-  subroutine lnfm_init( this, bounds, NLFilename )
-  !
-  ! !DESCRIPTION:
-  !
-  ! Initialize data stream information for Lightning.
-  !
-  ! !USES:
-  use clm_time_manager , only : get_calendar
-  use ncdio_pio        , only : pio_subsystem
-  use shr_pio_mod      , only : shr_pio_getiotype
-  use clm_nlUtilsMod   , only : find_nlgroup_name
-  use ndepStreamMod    , only : clm_domain_mct
-  use histFileMod      , only : hist_addfld1d
-  !
-  ! !ARGUMENTS:
-  implicit none
-  class(fire_base_type)       :: this
-  type(bounds_type), intent(in) :: bounds
-  character(len=*),  intent(in) :: NLFilename
-  !
-  ! !LOCAL VARIABLES:
-  integer            :: stream_year_first_lightng  ! first year in Lightning stream to use
-  integer            :: stream_year_last_lightng   ! last year in Lightning stream to use
-  integer            :: model_year_align_lightng   ! align stream_year_first_lnfm with
-  integer            :: nu_nml                     ! unit for namelist file
-  integer            :: nml_error                  ! namelist i/o error flag
-  type(mct_ggrid)    :: dom_clm                    ! domain information
-  character(len=CL)  :: stream_fldFileName_lightng ! lightning stream filename to read
-  character(len=CL)  :: lightng_tintalgo = 'linear'! time interpolation alogrithm
-  character(len=CL)  :: lightngmapalgo = 'bilinear'! Mapping alogrithm
-  character(*), parameter :: subName = "('lnfmdyn_init')"
-  character(*), parameter :: F00 = "('(lnfmdyn_init) ',4a)"
-  !-----------------------------------------------------------------------
-
-   namelist /light_streams/         &
-        stream_year_first_lightng,  &
-        stream_year_last_lightng,   &
-        model_year_align_lightng,   &
-        lightngmapalgo,             &
-        stream_fldFileName_lightng, &
-        lightng_tintalgo
-
-   ! Default values for namelist
-    stream_year_first_lightng  = 1      ! first year in stream to use
-    stream_year_last_lightng   = 1      ! last  year in stream to use
-    model_year_align_lightng   = 1      ! align stream_year_first_lnfm with this model year
-    stream_fldFileName_lightng = ' '
-
-   ! Read light_streams namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call find_nlgroup_name(nu_nml, 'light_streams', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=light_streams,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg='ERROR reading light_streams namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_year_first_lightng, mpicom)
-   call shr_mpi_bcast(stream_year_last_lightng, mpicom)
-   call shr_mpi_bcast(model_year_align_lightng, mpicom)
-   call shr_mpi_bcast(stream_fldFileName_lightng, mpicom)
-   call shr_mpi_bcast(lightng_tintalgo, mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'light_stream settings:'
-      write(iulog,*) '  stream_year_first_lightng  = ',stream_year_first_lightng
-      write(iulog,*) '  stream_year_last_lightng   = ',stream_year_last_lightng
-      write(iulog,*) '  model_year_align_lightng   = ',model_year_align_lightng
-      write(iulog,*) '  stream_fldFileName_lightng = ',stream_fldFileName_lightng
-      write(iulog,*) '  lightng_tintalgo           = ',lightng_tintalgo
-      write(iulog,*) ' '
-   endif
-
-   call clm_domain_mct (bounds, dom_clm)
-
-   call shr_strdata_create(this%sdat_lnfm,name="clmlnfm", &
-        pio_subsystem=pio_subsystem,                      &
-        pio_iotype=shr_pio_getiotype(inst_name),          &
-        mpicom=mpicom, compid=comp_id,                    &
-        gsmap=gsmap_global, ggrid=dom_clm,                &
-        nxg=ldomain%ni, nyg=ldomain%nj,                   &
-        yearFirst=stream_year_first_lightng,              &
-        yearLast=stream_year_last_lightng,                &
-        yearAlign=model_year_align_lightng,               &
-        offset=0,                                         &
-        domFilePath='',                                   &
-        domFileName=trim(stream_fldFileName_lightng),     &
-        domTvarName='time',                               &
-        domXvarName='lon' ,                               &
-        domYvarName='lat' ,                               &
-        domAreaName='area',                               &
-        domMaskName='mask',                               &
-        filePath='',                                      &
-        filename=(/trim(stream_fldFileName_lightng)/),    &
-        fldListFile='lnfm',                               &
-        fldListModel='lnfm',                              &
-        fillalgo='none',                                  &
-        tintalgo=lightng_tintalgo,                        &
-        mapalgo=lightngmapalgo,                           &
-        calendar=get_calendar(),                          &
-        taxmode='cycle'                            )
-
-   if (masterproc) then
-      call shr_strdata_print(this%sdat_lnfm,'Lightning data')
-   endif
-
-   ! Add history fields
-   call hist_addfld1d (fname='LNFM', units='counts/km^2/hr',  &
-         avgflag='A', long_name='Lightning frequency',        &
-         ptr_lnd=this%forc_lnfm, default='inactive')
-
-  end subroutine lnfm_init
-
-  !-----------------------------------------------------------------------
-  subroutine lnfm_interp(this, bounds )
-  !
-  ! !DESCRIPTION:
-  ! Interpolate data stream information for Lightning.
-  !
-  ! !USES:
-  use clm_time_manager, only : get_curr_date
-  !
-  ! !ARGUMENTS:
-  class(fire_base_type)       :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  integer :: g, ig
-  integer :: year    ! year (0, ...) for nstep+1
-  integer :: mon     ! month (1, ..., 12) for nstep+1
-  integer :: day     ! day of month (1, ..., 31) for nstep+1
-  integer :: sec     ! seconds into current date for nstep+1
-  integer :: mcdate  ! Current model date (yyyymmdd)
-  !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(this%sdat_lnfm, mcdate, sec, mpicom, 'lnfmdyn')
-
-   ig = 0
-   do g = bounds%begg,bounds%endg
-      ig = ig+1
-      this%forc_lnfm(g) = this%sdat_lnfm%avs(1)%rAttr(1,ig)
-   end do
-
-  end subroutine lnfm_interp
-
-  !-----------------------------------------------------------------------
-  subroutine surfdataread(this, bounds)
-  !
-  ! !DESCRIPTION:
-  ! Read surface data set to populate relevant fire-related variables
-  !
-  ! !USES:
-  use spmdMod    , only : masterproc
-  use clm_varctl , only : nsrest, nsrStartup, fsurdat
-  use clm_varcon , only : grlnd
-  use ColumnType , only : col
-  use fileutils  , only : getfil
-  use ncdio_pio
-  !
-  ! !ARGUMENTS:
-  class(fire_base_type) :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  integer               :: g,c       ! indices
-  type(file_desc_t)     :: ncid      ! netcdf id
-  logical               :: readvar   ! true => variable is on initial dataset
-  character(len=256)    :: locfn     ! local filename
-  real(r8), pointer     :: gdp(:)    ! global gdp data (needs to be a pointer for use in ncdio)
-  real(r8), pointer     :: peatf(:)  ! global peatf data (needs to be a pointer for use in ncdio)
-  integer,  pointer     :: abm(:)    ! global abm data (needs to be a pointer for use in ncdio)
-  !-----------------------------------------------------------------------
-
-   ! --------------------------------------------------------------------
-   ! Open surface dataset
-   ! --------------------------------------------------------------------
-
-   call getfil (fsurdat, locfn, 0)
-   call ncd_pio_openfile (ncid, locfn, 0)
-
-   ! --------------------------------------------------------------------
-   ! Read in GDP data
-   ! --------------------------------------------------------------------
-
-   allocate(gdp(bounds%begg:bounds%endg))
-   call ncd_io(ncid=ncid, varname='gdp', flag='read', data=gdp, dim1name=grlnd, readvar=readvar)
-   if (.not. readvar) then
-      call endrun(msg=' ERROR: gdp NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-   end if
-   do c = bounds%begc, bounds%endc
-      g = col%gridcell(c)
-      this%gdp_lf_col(c) = gdp(g)
-   end do
-   deallocate(gdp)
-
-   ! --------------------------------------------------------------------
-   ! Read in peatf data
-   ! --------------------------------------------------------------------
-
-   allocate(peatf(bounds%begg:bounds%endg))
-   call ncd_io(ncid=ncid, varname='peatf', flag='read', data=peatf, dim1name=grlnd, readvar=readvar)
-   if (.not. readvar) then
-      call endrun(msg=' ERROR: peatf NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-   end if
-   do c = bounds%begc, bounds%endc
-      g = col%gridcell(c)
-      this%peatf_lf_col(c) = peatf(g)
-   end do
-   deallocate(peatf)
-
-   ! --------------------------------------------------------------------
-   ! Read in ABM data
-   ! --------------------------------------------------------------------
-
-   allocate(abm(bounds%begg:bounds%endg))
-   call ncd_io(ncid=ncid, varname='abm', flag='read', data=abm, dim1name=grlnd, readvar=readvar)
-   if (.not. readvar) then
-      call endrun(msg=' ERROR: abm NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-   end if
-   do c = bounds%begc, bounds%endc
-      g = col%gridcell(c)
-      this%abm_lf_col(c) = abm(g)
-   end do
-   deallocate(abm)
-
-   ! Close file
-
-   call ncd_pio_closefile(ncid)
-
-   if (masterproc) then
-      write(iulog,*) 'Successfully read fmax, soil color, sand and clay boundary data'
-      write(iulog,*)
-   endif
-   
-  end subroutine surfdataread
-  
-  
-end module FireDataBaseType
diff --git a/src/cpl/mct/SoilMoistureStreamMod.F90 b/src/cpl/mct/SoilMoistureStreamMod.F90
deleted file mode 100644
index 8b366d6c8e..0000000000
--- a/src/cpl/mct/SoilMoistureStreamMod.F90
+++ /dev/null
@@ -1,418 +0,0 @@
-module SoilMoistureStreamMod
-
-  ! **********************************************************************
-  ! --------------------------- IMPORTANT NOTE ---------------------------
-  !
-  ! In cases using the NUOPC driver/mediator, we use a different version of this module,
-  ! based on CDEPS, which resides in src/cpl/nuopc/. Changes to the science here should
-  ! also be made in the similar file in src/cpl/nuopc. Once we start using CDEPS by
-  ! default, we can remove this version and move the CDEPS-based version into its place.
-  ! **********************************************************************
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Read in soil moisture from data stream
-  !
-  ! !USES:
-  use shr_strdata_mod           , only : shr_strdata_type, shr_strdata_create
-  use shr_strdata_mod           , only : shr_strdata_print, shr_strdata_advance
-  use shr_kind_mod              , only : r8 => shr_kind_r8
-  use shr_kind_mod              , only : CL => shr_kind_CL, CXX => shr_kind_CXX
-  use shr_log_mod               , only : errMsg => shr_log_errMsg
-  use decompMod                 , only : bounds_type, subgrid_level_column
-  use abortutils                , only : endrun
-  use clm_varctl                , only : iulog, use_soil_moisture_streams, inst_name
-  use clm_varcon                , only : grlnd
-  use controlMod                , only : NLFilename
-  use domainMod                 , only : ldomain
-  use LandunitType              , only : lun
-  use ColumnType                , only : col
-  use SoilStateType             , only : soilstate_type
-  use WaterStateBulkType        , only : waterstatebulk_type
-  use perf_mod                  , only : t_startf, t_stopf
-  use spmdMod                   , only : masterproc, mpicom, comp_id
-  use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo
-  use mct_mod
-  use ncdio_pio
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: PrescribedSoilMoistureInit    ! position datasets for soil moisture
-  public :: PrescribedSoilMoistureAdvance ! Advance the soil moisture stream (outside of Open-MP loops)
-  public :: PrescribedSoilMoistureInterp  ! interpolates between two periods of soil moisture data
-
-  ! !PRIVATE MEMBER DATA:
-  type(shr_strdata_type) :: sdat_soilm    ! soil moisture input data stream
-  integer :: ism                          ! Soil moisture steram index
-  integer, allocatable :: g_to_ig(:)      ! Array matching gridcell index to data index
-  logical :: soilm_ignore_data_if_missing ! If should ignore overridding a point with soil moisture data
-                                          ! from the streams file, if the streams file shows that point
-                                          ! as missing (namelist item)
-  !
-  ! !PRIVATE TYPES:
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  !
-  ! soil_moisture_init
-  !
-  !-----------------------------------------------------------------------
-  subroutine PrescribedSoilMoistureInit(bounds)
-    !
-    ! Initialize data stream information for soil moisture.
-    !
-    !
-    ! !USES:
-    use clm_time_manager , only : get_calendar
-    use ncdio_pio        , only : pio_subsystem
-    use shr_pio_mod      , only : shr_pio_getiotype
-    use clm_nlUtilsMod   , only : find_nlgroup_name
-    use ndepStreamMod    , only : clm_domain_mct
-    use shr_stream_mod   , only : shr_stream_file_null
-    use shr_string_mod   , only : shr_string_listCreateField
-    use clm_varpar       , only : nlevsoi
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds          ! bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: i                          ! index
-    integer            :: stream_year_first_soilm    ! first year in Ustar stream to use
-    integer            :: stream_year_last_soilm     ! last year in Ustar stream to use
-    integer            :: model_year_align_soilm     ! align stream_year_first_soilm with
-    integer            :: nu_nml                     ! unit for namelist file
-    integer            :: nml_error                  ! namelist i/o error flag
-    integer            :: soilm_offset               ! Offset in time for dataset (sec)
-    type(mct_ggrid)    :: dom_clm                    ! domain information
-    character(len=CL)  :: stream_fldfilename_soilm   ! ustar stream filename to read
-    character(len=CL)  :: soilm_tintalgo = 'linear'  ! Time interpolation alogrithm
-
-    character(*), parameter    :: subName = "('PrescribedSoilMoistureInit')"
-    character(*), parameter    :: F00 = "('(PrescribedSoilMoistureInit) ',4a)"
-    character(*), parameter    :: soilmString = "H2OSOI"  ! base string for field string
-    character(CXX)             :: fldList            ! field string
-    !-----------------------------------------------------------------------
-    !
-    ! deal with namelist variables here in init
-    !
-    namelist /soil_moisture_streams/   &
-         stream_year_first_soilm,      &
-         stream_year_last_soilm,       &
-         model_year_align_soilm,       &
-         soilm_tintalgo,               &
-         soilm_offset,                 &
-         soilm_ignore_data_if_missing, &
-         stream_fldfilename_soilm
-
-    ! Default values for namelist
-    stream_year_first_soilm      = 1      ! first year in stream to use
-    stream_year_last_soilm       = 1      ! last  year in stream to use
-    model_year_align_soilm       = 1      ! align stream_year_first_soilm with this model year
-    stream_fldfilename_soilm     = shr_stream_file_null
-    soilm_offset                 = 0
-    soilm_ignore_data_if_missing = .false.
-
-    ! Read soilm_streams namelist
-    if (masterproc) then
-       open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-       call find_nlgroup_name(nu_nml, 'soil_moisture_streams', status=nml_error)
-       if (nml_error == 0) then
-          read(nu_nml, nml=soil_moisture_streams,iostat=nml_error)
-          if (nml_error /= 0) then
-             call endrun(subname // ':: ERROR reading soil_moisture_streams namelist')
-          end if
-       else
-          call endrun(subname // ':: ERROR finding soilm_streams namelist')
-       end if
-       close(nu_nml)
-    endif
-
-    call shr_mpi_bcast(stream_year_first_soilm, mpicom)
-    call shr_mpi_bcast(stream_year_last_soilm, mpicom)
-    call shr_mpi_bcast(model_year_align_soilm, mpicom)
-    call shr_mpi_bcast(stream_fldfilename_soilm, mpicom)
-    call shr_mpi_bcast(soilm_tintalgo, mpicom)
-    call shr_mpi_bcast(soilm_offset, mpicom)
-    call shr_mpi_bcast(soilm_ignore_data_if_missing, mpicom)
-
-    if (masterproc) then
-
-       write(iulog,*) ' '
-       write(iulog,*) 'soil_moisture_stream settings:'
-       write(iulog,*) '  stream_year_first_soilm  = ',stream_year_first_soilm
-       write(iulog,*) '  stream_year_last_soilm   = ',stream_year_last_soilm
-       write(iulog,*) '  model_year_align_soilm   = ',model_year_align_soilm
-       write(iulog,*) '  stream_fldfilename_soilm = ',trim(stream_fldfilename_soilm)
-       write(iulog,*) '  soilm_tintalgo = ',trim(soilm_tintalgo)
-       write(iulog,*) '  soilm_offset = ',soilm_offset
-       if ( soilm_ignore_data_if_missing )then
-          write(iulog,*) '  Do NOT override a point with streams data if the streams data is missing'
-       else
-          write(iulog,*) '  Abort, if you find a model point where the input streams data is set to missing value'
-       end if
-
-    endif
-
-    call clm_domain_mct (bounds, dom_clm, nlevels=nlevsoi)
-
-    ! create the field list for these fields...use in shr_strdata_create
-    fldList = trim(soilmString)
-    if (masterproc) write(iulog,*) 'fieldlist: ', trim(fldList)
-
-    call shr_strdata_create(sdat_soilm,name="soil_moisture",    &
-         pio_subsystem=pio_subsystem,                  &
-         pio_iotype=shr_pio_getiotype(inst_name),          &
-         mpicom=mpicom, compid=comp_id,                &
-         gsmap=gsMap_lnd2Dsoi_gdc2glo, ggrid=dom_clm,  &
-         nxg=ldomain%ni, nyg=ldomain%nj,               &
-         nzg=nlevsoi,                                  &
-         yearFirst=stream_year_first_soilm,            &
-         yearLast=stream_year_last_soilm,              &
-         yearAlign=model_year_align_soilm,             &
-         offset=soilm_offset,                          &
-         domFilePath='',                               &
-         domFileName=trim(stream_fldFileName_soilm),   &
-         domTvarName='time',                           &
-         domXvarName='lon' ,                           &
-         domYvarName='lat' ,                           &
-         domZvarName='levsoi' ,                        &
-         domAreaName='area',                           &
-         domMaskName='mask',                           &
-         filePath='',                                  &
-         filename=(/stream_fldFileName_soilm/),        &
-         fldListFile=fldList,                          &
-         fldListModel=fldList,                         &
-         fillalgo='none',                              &
-         mapalgo='none',                               &
-         tintalgo=soilm_tintalgo,                      &
-         calendar=get_calendar(),                      &
-         dtlimit = 15._r8,                             &
-         taxmode='cycle'                               )
-
-    if (masterproc) then
-       call shr_strdata_print(sdat_soilm,'soil moisture data')
-    endif
-
-  end subroutine PrescribedSoilMoistureInit
-
-
-  !-----------------------------------------------------------------------
-  !
-  ! PrescribedSoilMoistureAdvance
-  !
-  !-----------------------------------------------------------------------
-  subroutine PrescribedSoilMoistureAdvance( bounds )
-    !
-    ! Advanace the prescribed soil moisture stream
-    !
-    ! !USES:
-    use clm_time_manager, only : get_curr_date
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)         , intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    character(len=CL)  :: stream_var_name
-    integer :: g, ig
-    integer :: ier    ! error code
-    integer :: year    ! year (0, ...) for nstep+1
-    integer :: mon     ! month (1, ..., 12) for nstep+1
-    integer :: day     ! day of month (1, ..., 31) for nstep+1
-    integer :: sec     ! seconds into current date for nstep+1
-    integer :: mcdate  ! Current model date (yyyymmdd)
-
-    call get_curr_date(year, mon, day, sec)
-    mcdate = year*10000 + mon*100 + day
-
-    stream_var_name = 'H2OSOI'
-
-    ! Determine variable index
-    ism = mct_aVect_indexRA(sdat_soilm%avs(1),trim(stream_var_name))
-
-    call shr_strdata_advance(sdat_soilm, mcdate, sec, mpicom, trim(stream_var_name))
-
-    ! Map gridcell to AV index
-    ier = 0
-    if ( .not. allocated(g_to_ig) )then
-       allocate (g_to_ig(bounds%begg:bounds%endg), stat=ier)
-       if (ier /= 0) then
-          write(iulog,*) 'Prescribed soil moisture allocation error'
-          call endrun(msg=errMsg(sourcefile, __LINE__))
-       end if
-
-       ig = 0
-       do g = bounds%begg,bounds%endg
-          ig = ig+1
-          g_to_ig(g) = ig
-       end do
-    end if
-
-  end subroutine PrescribedSoilMoistureAdvance
-
-  !-----------------------------------------------------------------------
-  !
-  ! PrescribedSoilMoistureInterp
-  !
-  !-----------------------------------------------------------------------
-  subroutine PrescribedSoilMoistureInterp(bounds, soilstate_inst, &
-       waterstatebulk_inst)
-    !
-    ! Assign data stream information for prescribed soil moisture.
-    !
-    ! !USES:
-    use clm_time_manager, only : get_curr_date
-    use clm_varpar      , only : nlevsoi
-    use clm_varcon      , only : denh2o, denice, watmin, spval
-    use landunit_varcon , only : istsoil, istcrop
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)         , intent(in)    :: bounds
-    type(soilstate_type)      , intent(in)    :: soilstate_inst
-    type(waterstatebulk_type) , intent(inout) :: waterstatebulk_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c, g, j, ig, n
-    real(r8) :: soilm_liq_frac            ! liquid fraction of soil moisture
-    real(r8) :: soilm_ice_frac            ! ice fraction of soil moisture
-    real(r8) :: moisture_increment        ! soil moisture adjustment increment
-    real(r8) :: h2osoi_vol_initial        ! initial vwc value
-    character(*), parameter    :: subName = "('PrescribedSoilMoistureInterp')"
-
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,2) >= g_to_ig(bounds%endg)+(nlevsoi-1)*size(g_to_ig) ), sourcefile, __LINE__)
-    associate( &
-         dz               =>    col%dz                                , & ! Input:  [real(r8) (:,:) ]  layer depth (m)
-         watsat           =>    soilstate_inst%watsat_col             , & ! Input:  [real(r8) (:,:) ]  volumetric soil water at saturation (porosity)
-         h2osoi_liq       =>    waterstatebulk_inst%h2osoi_liq_col        , & ! Input/Output:  [real(r8) (:,:) ]  liquid water (kg/m2)
-         h2osoi_ice       =>    waterstatebulk_inst%h2osoi_ice_col        , & ! Input/Output:  [real(r8) (:,:) ]  ice water (kg/m2)
-         h2osoi_vol       =>    waterstatebulk_inst%h2osoi_vol_col        , & ! Output: volumetric soil water (m3/m3)
-         h2osoi_vol_prs   =>    waterstatebulk_inst%h2osoi_vol_prs_grc      & ! Output: prescribed volumetric soil water (m3/m3)
-         )
-      SHR_ASSERT_FL( (lbound(h2osoi_vol,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_vol,2) == 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(dz,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(dz,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(dz,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(dz,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(watsat,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(watsat,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(watsat,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(watsat,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_liq,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_liq,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_liq,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_liq,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_ice,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_ice,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_ice,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_ice,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,1) <= bounds%begg ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,1) >= bounds%endg ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,2) == 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,2) >= nlevsoi ),     sourcefile, __LINE__)
-      !
-      ! Set the prescribed soil moisture read from the file everywhere
-      !
-      do g = bounds%begg, bounds%endg
-         ig = g_to_ig(g)
-         do j = 1, nlevsoi
-
-             !n = ig + (j-1)*size(g_to_ig)
-             n = ig + (j-1)*size(g_to_ig)
-
-             h2osoi_vol_prs(g,j) = sdat_soilm%avs(1)%rAttr(ism,n)
-
-             ! If soil moiture is being interpolated in time and the result is
-             ! large that probably means one of the two data points is missing (set to spval)
-             if ( h2osoi_vol_prs(g,j) > 10.0_r8 .and. (h2osoi_vol_prs(g,j) /= spval) )then
-                h2osoi_vol_prs(g,j) = spval
-             end if
-
-         end do
-      end do
-
-      do c = bounds%begc, bounds%endc
-         !
-         ! Set variable for each gridcell/column combination
-         !
-         g = col%gridcell(c)
-         ig = g_to_ig(g)
-
-         ! EBK Jan/2020, also check weights on gridcell (See https://github.com/ESCOMP/CTSM/issues/847)
-         if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) .and. &
-              (col%wtgcell(c) /= 0._r8) ) then
-            !       this is a 2d field (gridcell/nlevsoi) !
-            do j = 1, nlevsoi
-
-               n = ig + (j-1)*size(g_to_ig)
-
-               ! if soil water is zero, liq/ice fractions cannot be calculated
-               if((h2osoi_liq(c, j) + h2osoi_ice(c, j)) > 0._r8) then
-
-                  ! save original soil moisture value
-                  h2osoi_vol_initial = h2osoi_vol(c,j)
-
-                  ! Check if the vegetated land mask from the dataset on the
-                  ! file is different
-                  if ( (h2osoi_vol_prs(g,j) == spval) .and. (h2osoi_vol_initial /= spval) )then
-                     if ( soilm_ignore_data_if_missing )then
-                        cycle
-                     else
-                        write(iulog,*) 'Input soil moisture dataset is not vegetated as expected: gridcell=', &
-                                        g, ' active = ', col%active(c)
-                        call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, &
-                             msg = subname // &
-                             ' ERROR:: The input soil moisture stream is NOT vegetated for one of the land points' )
-                     end if
-                  end if
-
-                  ! update volumetric soil moisture from data prescribed from the file
-                  h2osoi_vol(c,j) = h2osoi_vol_prs(g,j)
-
-
-                  ! calculate liq/ice mass fractions
-                  soilm_liq_frac  = h2osoi_liq(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j))
-                  soilm_ice_frac  = h2osoi_ice(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j))
-
-                  ! calculate moisture increment
-                  moisture_increment = h2osoi_vol(c,j) - h2osoi_vol_initial
-                  ! add limitation check
-                  moisture_increment = min((watsat(c,j) - h2osoi_vol_initial),max(-(h2osoi_vol_initial-watmin),moisture_increment))
-
-                  ! update liq/ice water mass due to (volumetric) moisture increment
-                  h2osoi_liq(c,j) = h2osoi_liq(c,j) + (soilm_liq_frac * moisture_increment * dz(c, j) * denh2o)
-                  h2osoi_ice(c,j) = h2osoi_ice(c,j) + (soilm_ice_frac * moisture_increment * dz(c, j) * denice)
-
-               else
-                  call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, &
-                       msg = subname // ':: ERROR h2osoil liquid plus ice is zero')
-               endif
-            enddo
-         endif
-      end do
-
-    end associate
-
-  end subroutine PrescribedSoilMoistureInterp
-
-end module SoilMoistureStreamMod
diff --git a/src/cpl/mct/UrbanTimeVarType.F90 b/src/cpl/mct/UrbanTimeVarType.F90
deleted file mode 100644
index 805ac47fbf..0000000000
--- a/src/cpl/mct/UrbanTimeVarType.F90
+++ /dev/null
@@ -1,314 +0,0 @@
-module UrbanTimeVarType
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Urban Time Varying Data
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8, CL => shr_kind_CL
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use abortutils      , only : endrun
-  use decompMod       , only : bounds_type, subgrid_level_landunit
-  use clm_varctl      , only : iulog, inst_name
-  use landunit_varcon , only : isturb_MIN, isturb_MAX
-  use clm_varcon      , only : spval
-  use LandunitType    , only : lun
-  use GridcellType    , only : grc
-  use mct_mod
-  use shr_strdata_mod , only : shr_strdata_type
-  !
-  implicit none
-  save
-  private
-  !
-  !
-
-  ! !PUBLIC TYPE
-  type, public :: urbantv_type
-
-     real(r8), public, pointer     :: t_building_max(:)    ! lun maximum internal building air temperature (K)
-     type(shr_strdata_type)        :: sdat_urbantv         ! urban time varying input data stream
-   contains
-
-     ! !PUBLIC MEMBER FUNCTIONS:
-     procedure, public :: Init              ! Allocate and initialize urbantv
-     procedure, public :: urbantv_init      ! Initialize urban time varying stream
-     procedure, public :: urbantv_interp    ! Interpolate urban time varying stream
-
-  end type urbantv_type
-
-  !-----------------------------------------------------------------------
-  character(15), private :: stream_var_name(isturb_MIN:isturb_MAX)
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
-    !
-    ! Allocate module variables and data structures
-    !
-    ! !USES:
-    use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-    use histFileMod     , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(urbantv_type) :: this
-    type(bounds_type) , intent(in) :: bounds
-    character(len=*)  , intent(in) :: NLFilename   ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer		:: begl, endl
-    !---------------------------------------------------------------------
-
-    begl = bounds%begl; endl = bounds%endl
-
-    ! Allocate urbantv data structure
-
-    allocate(this%t_building_max      (begl:endl))          ; this%t_building_max      (:)   = nan
-
-    call this%urbantv_init(bounds, NLFilename)
-    call this%urbantv_interp(bounds)
-
-    ! Add history fields
-    call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
-          avgflag='A', long_name='prescribed maximum interior building temperature',   &
-          ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
-          l2g_scale_type='unity')
-
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  subroutine urbantv_init(this, bounds, NLFilename)
-   !
-   ! !DESCRIPTION:
-   ! Initialize data stream information for urban time varying data
-   !
-   ! !USES:
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use clm_nlUtilsMod   , only : find_nlgroup_name
-   use ndepStreamMod    , only : clm_domain_mct
-   use spmdMod          , only : masterproc, mpicom, comp_id
-   use fileutils        , only : getavu, relavu
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use shr_string_mod   , only : shr_string_listAppend
-   use shr_strdata_mod  , only : shr_strdata_create, shr_strdata_print
-   use domainMod        , only : ldomain
-   use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
-   use landunit_varcon  , only : isturb_TBD, isturb_HD, isturb_MD
-   use lnd_set_decomp_and_domain , only : gsmap_global
-   !
-   ! !ARGUMENTS:
-   implicit none
-   class(urbantv_type)           :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! !LOCAL VARIABLES:
-   integer            :: begl, endl                           ! landunits
-   integer            :: ifield                               ! field index
-   integer            :: stream_year_first_urbantv            ! first year in urban tv stream to use
-   integer            :: stream_year_last_urbantv             ! last year in urban tv stream to use
-   integer            :: model_year_align_urbantv             ! align stream_year_first_urbantv
-                                                              !  with this model year
-   integer            :: nu_nml                               ! unit for namelist file
-   integer            :: nml_error                            ! namelist i/o error flag
-   type(mct_ggrid)    :: dom_clm                              ! domain information
-   character(len=CL)  :: stream_fldFileName_urbantv           ! urban tv streams filename
-   character(len=CL)  :: urbantvmapalgo = 'nn'                ! mapping alogrithm for urban ac
-   character(len=CL)  :: urbantv_tintalgo = 'linear'          ! time interpolation alogrithm
-   character(len=CL)  :: fldList                              ! field string
-   character(*), parameter :: urbantvString = "tbuildmax_"    ! base string for field string
-   character(*), parameter :: subName = "('urbantv_init')"
-   character(*), parameter :: F00 = "('(urbantv_init) ',4a)"
-   !-----------------------------------------------------------------------
-   namelist /urbantv_streams/       &
-        stream_year_first_urbantv,  &
-        stream_year_last_urbantv,   &
-        model_year_align_urbantv,   &
-        urbantvmapalgo,             &
-        stream_fldFileName_urbantv, &
-        urbantv_tintalgo
-   !-----------------------------------------------------------------------
-
-   begl = bounds%begl; endl = bounds%endl
-
-   ! Default values for namelist
-   stream_year_first_urbantv  = 1       ! first year in stream to use
-   stream_year_last_urbantv   = 1       ! last  year in stream to use
-   model_year_align_urbantv   = 1       ! align stream_year_first_urbantv with this model year
-   stream_fldFileName_urbantv = ' '
-
-   ! Read urbantv_streams namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call find_nlgroup_name(nu_nml, 'urbantv_streams', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=urbantv_streams,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg='ERROR reading urbantv_streams namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_year_first_urbantv, mpicom)
-   call shr_mpi_bcast(stream_year_last_urbantv, mpicom)
-   call shr_mpi_bcast(model_year_align_urbantv, mpicom)
-   call shr_mpi_bcast(stream_fldFileName_urbantv, mpicom)
-   call shr_mpi_bcast(urbantv_tintalgo, mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'urbantv_streams settings:'
-      write(iulog,*) '  stream_year_first_urbantv  = ',stream_year_first_urbantv
-      write(iulog,*) '  stream_year_last_urbantv   = ',stream_year_last_urbantv
-      write(iulog,*) '  model_year_align_urbantv   = ',model_year_align_urbantv
-      write(iulog,*) '  stream_fldFileName_urbantv = ',stream_fldFileName_urbantv
-      write(iulog,*) '  urbantv_tintalgo           = ',urbantv_tintalgo
-      write(iulog,*) ' '
-   endif
-
-   call clm_domain_mct (bounds, dom_clm)
-
-   ! create the field list for these urbantv fields...use in shr_strdata_create
-   stream_var_name(:)          = "NOT_SET"
-   stream_var_name(isturb_TBD) = urbantvString//"TBD"
-   stream_var_name(isturb_HD)  = urbantvString//"HD"
-   stream_var_name(isturb_MD)  = urbantvString//"MD"
-   fldList = ""
-   do ifield = isturb_MIN, isturb_MAX
-      call shr_string_listAppend( fldList, stream_var_name(ifield) )
-   end do
-
-   call shr_strdata_create(this%sdat_urbantv,name="clmurbantv", &
-        pio_subsystem=pio_subsystem,                            &
-        pio_iotype=shr_pio_getiotype(inst_name),                &
-        mpicom=mpicom, compid=comp_id,                          &
-        gsmap=gsmap_global, ggrid=dom_clm,                      &
-        nxg=ldomain%ni, nyg=ldomain%nj,                         &
-        yearFirst=stream_year_first_urbantv,                    &
-        yearLast=stream_year_last_urbantv,                      &
-        yearAlign=model_year_align_urbantv,                     &
-        offset=0,                                               &
-        domFilePath='',                                         &
-        domFileName=trim(stream_fldFileName_urbantv),           &
-        domTvarName='time',                                     &
-        domXvarName='lon' ,                                     &
-        domYvarName='lat' ,                                     &
-        domAreaName='area',                                     &
-        domMaskName='LANDMASK',                                 &
-        filePath='',                                            &
-        filename=(/trim(stream_fldFileName_urbantv)/) ,         &
-        fldListFile=fldList,                                    &
-        fldListModel=fldList,                                   &
-        fillalgo='none',                                        &
-        mapalgo=urbantvmapalgo,                                 &
-        calendar=get_calendar(),                                &
-        tintalgo=urbantv_tintalgo,                              &
-        taxmode='extend'                                 )
-
-   if (masterproc) then
-      call shr_strdata_print(this%sdat_urbantv,'urban time varying data')
-   endif
-
-
-  end subroutine urbantv_init
-
-  !-----------------------------------------------------------------------
-  subroutine urbantv_interp(this, bounds)
-  !
-  ! !DESCRIPTION:
-  ! Interpolate data stream information for urban time varying data.
-  !
-  ! !USES:
-  use clm_time_manager, only : get_curr_date
-  use spmdMod         , only : mpicom
-  use shr_strdata_mod , only : shr_strdata_advance
-  use clm_instur      , only : urban_valid
-  !
-  ! !ARGUMENTS:
-  class(urbantv_type)           :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  logical :: found
-  integer :: l, glun, ig, g, ip
-  integer :: year    ! year (0, ...) for nstep+1
-  integer :: mon     ! month (1, ..., 12) for nstep+1
-  integer :: day     ! day of month (1, ..., 31) for nstep+1
-  integer :: sec     ! seconds into current date for nstep+1
-  integer :: mcdate  ! Current model date (yyyymmdd)
-  integer :: lindx   ! landunit index
-  integer :: gindx   ! gridcell index
-  !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(this%sdat_urbantv, mcdate, sec, mpicom, 'urbantvdyn')
-
-   do l = bounds%begl,bounds%endl
-      if (lun%urbpoi(l)) then
-         glun  = lun%gridcell(l)
-         ip = mct_aVect_indexRA(this%sdat_urbantv%avs(1),trim(stream_var_name(lun%itype(l))))
-         !
-         ! Determine vector index corresponding to glun
-         !
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if (g == glun) exit
-         end do
-
-         this%t_building_max(l) = this%sdat_urbantv%avs(1)%rAttr(ip,ig)
-      else
-         this%t_building_max(l) = spval
-      end if
-   end do
-
-   found = .false.
-   do l = bounds%begl,bounds%endl
-      if (lun%urbpoi(l)) then
-         glun  = lun%gridcell(l)
-         !
-         ! Determine vector index corresponding to glun
-         !
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if (g == glun) exit
-         end do
-
-         if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
-            found = .true.
-            gindx = g
-            lindx = l
-            exit
-         end if
-      end if
-   end do
-   if ( found ) then
-      write(iulog,*)'ERROR: no valid urban data for g= ',gindx
-      write(iulog,*)'landunit type:   ',lun%itype(lindx)
-      write(iulog,*)'urban_valid:     ',urban_valid(gindx)
-      write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
-      call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, &
-           msg=errmsg(sourcefile, __LINE__))
-   end if
-
-
-  end subroutine urbantv_interp
-
-  !-----------------------------------------------------------------------
-
-end module UrbanTimeVarType
diff --git a/src/cpl/mct/ch4FInundatedStreamType.F90 b/src/cpl/mct/ch4FInundatedStreamType.F90
deleted file mode 100644
index 3c26f4d109..0000000000
--- a/src/cpl/mct/ch4FInundatedStreamType.F90
+++ /dev/null
@@ -1,389 +0,0 @@
-module ch4FInundatedStreamType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Contains methods for reading in finundated streams file for methane code.
-  !
-  ! !USES
-  use shr_kind_mod   , only: r8 => shr_kind_r8, CL => shr_kind_cl
-  use spmdMod        , only: mpicom, masterproc
-  use clm_varctl     , only: iulog, inst_name
-  use abortutils     , only: endrun
-  use decompMod      , only: bounds_type
-  use ch4varcon      , only: finundation_mtd
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-
-  type, public :: ch4finundatedstream_type
-     real(r8), pointer, private :: zwt0_gdc  (:)         ! col coefficient for determining finundated (m)
-     real(r8), pointer, private :: f0_gdc    (:)         ! col maximum inundated fraction for a gridcell (for methane code)
-     real(r8), pointer, private :: p3_gdc    (:)         ! col coefficient for determining finundated (m)
-     real(r8), pointer, private :: fws_slope_gdc     (:) ! col slope in fws = slope * tws + intercept (A coefficient)
-     real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient)
-  contains
-
-      ! !PUBLIC MEMBER FUNCTIONS:
-      procedure, public :: Init            ! Initialize and read data in
-      procedure, public :: CalcFinundated  ! Calculate finundated based on input streams
-      procedure, public :: UseStreams      ! If streams will be used
-
-      ! !PRIVATE MEMBER FUNCTIONS:
-      procedure, private :: InitAllocate   ! Allocate data
-
-  end type ch4finundatedstream_type
-
-
-  ! ! PRIVATE DATA:
-
-  type, private :: streamcontrol_type
-     character(len=CL)  :: stream_fldFileName_ch4finundated   ! Filename
-     character(len=CL)  :: ch4finundatedmapalgo               ! map algo
-     character(len=CL)  :: fldList                            ! List of fields to read
-  contains
-     procedure, private :: ReadNML     ! Read in namelist
-  end type streamcontrol_type
-
-  type(streamcontrol_type), private :: control        ! Stream control data
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !==============================================================================
-
-contains
-
-  !==============================================================================
-
-  subroutine Init(this, bounds, NLFilename)
-   !
-   ! Initialize the ch4 finundated stream object
-   !
-   ! Uses:
-   use clm_time_manager , only : get_calendar, get_curr_date
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use shr_nl_mod       , only : shr_nl_find_group_name
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use ndepStreamMod    , only : clm_domain_mct
-   use domainMod        , only : ldomain
-   use decompMod        , only : bounds_type
-   use mct_mod          , only : mct_ggrid, mct_avect_indexra
-   use shr_strdata_mod  , only : shr_strdata_type, shr_strdata_create
-   use shr_strdata_mod  , only : shr_strdata_print, shr_strdata_advance
-   use spmdMod          , only : comp_id, iam
-   use ch4varcon        , only : finundation_mtd_h2osfc
-   use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
-   use lnd_set_decomp_and_domain , only : gsmap_global
-   !
-   ! arguments
-   implicit none
-   class(ch4finundatedstream_type) :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! local variables
-   integer            :: ig, g            ! Indices
-   type(mct_ggrid)    :: dom_clm          ! domain information
-   type(shr_strdata_type) :: sdat         ! input data stream
-   integer            :: index_ZWT0       = 0 ! Index of ZWT0 field
-   integer            :: index_F0         = 0 ! Index of F0 field
-   integer            :: index_P3         = 0 ! Index of P3 field
-   integer            :: index_FWS_TWS_A  = 0 ! Index of FWS_TWS_A field
-   integer            :: index_FWS_TWS_B  = 0 ! Index of FWS_TWS_B field
-   integer            :: year                 ! year (0, ...) for nstep+1
-   integer            :: mon                  ! month (1, ..., 12) for nstep+1
-   integer            :: day                  ! day of month (1, ..., 31) for nstep+1
-   integer            :: sec                  ! seconds into current date for nstep+1
-   integer            :: mcdate               ! Current model date (yyyymmdd)
-   character(len=*), parameter :: stream_name = 'ch4finundated'
-   character(*), parameter :: subName = "('ch4finundatedstream::Init')"
-   !-----------------------------------------------------------------------
-   if ( finundation_mtd /= finundation_mtd_h2osfc )then
-      call this%InitAllocate( bounds )
-      call control%ReadNML( bounds, NLFileName )
-
-      if ( this%useStreams() )then
-         call clm_domain_mct (bounds, dom_clm)
-
-         call shr_strdata_create(sdat,name=stream_name,                 &
-           pio_subsystem=pio_subsystem,                                 &
-           pio_iotype=shr_pio_getiotype(inst_name),                     &
-           mpicom=mpicom, compid=comp_id,                               &
-           gsmap=gsmap_global, ggrid=dom_clm,                           &
-           nxg=ldomain%ni, nyg=ldomain%nj,                              &
-           yearFirst=1996,                                              &
-           yearLast=1996,                                               &
-           yearAlign=1,                                                 &
-           offset=0,                                                    &
-           domFilePath='',                                              &
-           domFileName=trim(control%stream_fldFileName_ch4finundated),  &
-           domTvarName='time',                                          &
-           domXvarName='LONGXY' ,                                       &
-           domYvarName='LATIXY' ,                                       &
-           domAreaName='AREA',                                          &
-           domMaskName='LANDMASK',                                      &
-           filePath='',                                                 &
-           filename=(/trim(control%stream_fldFileName_ch4finundated)/), &
-           fldListFile=control%fldList,                                 &
-           fldListModel=control%fldList,                                &
-           fillalgo='none',                                             &
-           mapalgo=control%ch4finundatedmapalgo,                        &
-           calendar=get_calendar(),                                     &
-           taxmode='extend'                           )
-
-         if (masterproc) then
-            call shr_strdata_print(sdat,'CLM '//stream_name//' data')
-         endif
-
-         if( finundation_mtd == finundation_mtd_ZWT_inversion )then
-            index_ZWT0      = mct_avect_indexra(sdat%avs(1),'ZWT0')
-            index_F0        = mct_avect_indexra(sdat%avs(1),'F0' )
-            index_P3        = mct_avect_indexra(sdat%avs(1),'P3' )
-         else if( finundation_mtd == finundation_mtd_TWS_inversion )then
-            index_FWS_TWS_A = mct_avect_indexra(sdat%avs(1),'FWS_TWS_A')
-            index_FWS_TWS_B = mct_avect_indexra(sdat%avs(1),'FWS_TWS_B')
-         end if
-
-
-         ! Explicitly set current date to a hardcoded constant value. Otherwise
-         ! using the real date can cause roundoff differences that are
-         ! detrected as issues with exact restart.  EBK M05/20/2017
-         !call get_curr_date(year, mon, day, sec)
-         year = 1996
-         mon  = 12
-         day  = 31
-         sec  = 0
-         mcdate = year*10000 + mon*100 + day
-
-         call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ch4finundated')
-
-         ! Get the data
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if ( index_ZWT0 > 0 )then
-               this%zwt0_gdc(g) = sdat%avs(1)%rAttr(index_ZWT0,ig)
-            end if
-            if ( index_F0 > 0 )then
-               this%f0_gdc(g) = sdat%avs(1)%rAttr(index_F0,ig)
-            end if
-            if ( index_P3 > 0 )then
-               this%p3_gdc(g) = sdat%avs(1)%rAttr(index_P3,ig)
-            end if
-            if ( index_FWS_TWS_A > 0 )then
-               this%fws_slope_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_A,ig)
-            end if
-            if ( index_FWS_TWS_B > 0 )then
-               this%fws_intercept_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_B,ig)
-            end if
-         end do
-      end if
-   end if
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  logical function UseStreams(this)
-    !
-    ! !DESCRIPTION:
-    ! Return true if
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(ch4finundatedstream_type) :: this
-    !
-    ! !LOCAL VARIABLES:
-    if ( trim(control%stream_fldFileName_ch4finundated) == '' )then
-       UseStreams = .false.
-    else
-       UseStreams = .true.
-    end if
-  end function UseStreams
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Allocate module variables and data structures
-    !
-    ! !USES:
-    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    use ch4varcon     , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(ch4finundatedstream_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begc, endc
-    integer  :: begg, endg
-    !---------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    if( finundation_mtd == finundation_mtd_ZWT_inversion )then
-       allocate(this%zwt0_gdc         (begg:endg))            ;  this%zwt0_gdc         (:)   = nan
-       allocate(this%f0_gdc           (begg:endg))            ;  this%f0_gdc           (:)   = nan
-       allocate(this%p3_gdc           (begg:endg))            ;  this%p3_gdc           (:)   = nan
-    else if( finundation_mtd == finundation_mtd_TWS_inversion )then
-       allocate(this%fws_slope_gdc    (begg:endg))            ;  this%fws_slope_gdc    (:)   = nan
-       allocate(this%fws_intercept_gdc(begg:endg))            ;  this%fws_intercept_gdc(:)   = nan
-    end if
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, &
-                            waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated )
-    !
-    ! !DESCRIPTION:
-    !
-    ! Calculate finundated according to the appropriate methodology
-    !
-    ! !USES:
-    use ColumnType       , only : col
-    use ch4varcon        , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion
-    use ch4varcon        , only : finundation_mtd_TWS_inversion
-    use clm_varpar       , only : nlevsoi
-    use SoilHydrologyType, only : soilhydrology_type
-    use WaterDiagnosticBulkType   , only : waterdiagnosticbulk_type
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(ch4finundatedstream_type)                        :: this
-    type(bounds_type)                      , intent(in)    :: bounds
-    integer                                , intent(in)    :: num_soilc          ! number of column soil points in column filter
-    integer                                , intent(in)    :: filter_soilc(:)    ! column filter for soil points
-    type(soilhydrology_type)               , intent(in)    :: soilhydrology_inst
-    type(waterdiagnosticbulk_type)                  , intent(in)    :: waterdiagnosticbulk_inst
-    real(r8)                               , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
-    real(r8)                               , intent(inout) :: finundated(bounds%begc:)        ! fractional inundated area in soil column (excluding dedicated wetland columns)
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: g, c, fc    ! Indices
-    real(r8) :: zwt_actual  ! Total water storage (ZWT) to use either perched or total depending on conditions
-
-    SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__)
-    SHR_ASSERT_ALL_FL((ubound(finundated)        == (/bounds%endc/)), sourcefile, __LINE__)
-
-    associate(                                                                 &
-         z                    =>   col%z                                     , & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
-         zwt                  =>   soilhydrology_inst%zwt_col                , & ! Input:  [real(r8) (:)   ]  water table depth (m)
-         zwt_perched          =>   soilhydrology_inst%zwt_perched_col        , & ! Input:  [real(r8) (:)   ]  perched water table depth (m)
-         tws                  =>   waterdiagnosticbulk_inst%tws_grc                   , & ! Input:  [real(r8) (:)   ]  total water storage (kg m-2)
-         frac_h2osfc          =>   waterdiagnosticbulk_inst%frac_h2osfc_col             & ! Input:  [real(r8) (:)   ]  fraction of ground covered by surface water (0 to 1)
-    )
-
-    ! Calculate finundated
-    do fc = 1, num_soilc
-       c = filter_soilc(fc)
-       g = col%gridcell(c)
-       select case( finundation_mtd )
-          case ( finundation_mtd_h2osfc )
-             finundated(c) = frac_h2osfc(c)
-          case ( finundation_mtd_ZWT_inversion )
-             if (this%zwt0_gdc(g) > 0._r8) then
-                if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then
-                   zwt_actual = zwt_perched(c)
-                else
-                   zwt_actual = zwt(c)
-                end if
-                finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c)
-             else
-                finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c)
-             end if
-          case ( finundation_mtd_TWS_inversion )
-             finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g)
-       end select
-       finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) )
-    end do
-    end associate
-
-  end subroutine CalcFinundated
-  !==============================================================================
-
-  subroutine ReadNML(this, bounds, NLFilename)
-   !
-   ! Read the namelist data stream information.
-   !
-   ! Uses:
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use shr_nl_mod       , only : shr_nl_find_group_name
-   use shr_log_mod      , only : errMsg => shr_log_errMsg
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use fileutils        , only : getavu, relavu
-   use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
-   !
-   ! arguments
-   implicit none
-   class(streamcontrol_type)    :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! local variables
-   integer            :: nu_nml    ! unit for namelist file
-   integer            :: nml_error ! namelist i/o error flag
-   character(len=CL)  :: stream_fldFileName_ch4finundated = ' '
-   character(len=CL)  :: ch4finundatedmapalgo = 'bilinear'
-   character(len=*), parameter :: namelist_name = 'ch4finundated'    ! MUST agree with name in namelist and read
-   character(len=*), parameter :: shr_strdata_unset = 'NOT_SET'
-   character(len=*), parameter :: subName = "('ch4finundated::ReadNML')"
-   character(len=*), parameter :: F00 = "('(ch4finundated_readnml) ',4a)"
-   !-----------------------------------------------------------------------
-
-   namelist /ch4finundated/        &               ! MUST agree with namelist_name above
-        ch4finundatedmapalgo,  stream_fldFileName_ch4finundated
-
-   ! Default values for namelist
-
-   ! Read ch4finundated namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=ch4finundated,iostat=nml_error)   ! MUST agree with namelist_name above
-         if (nml_error /= 0) then
-            call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      else
-         call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_fldFileName_ch4finundated, mpicom)
-   call shr_mpi_bcast(ch4finundatedmapalgo            , mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) namelist_name, ' stream settings:'
-      write(iulog,*) '  stream_fldFileName_ch4finundated = ',stream_fldFileName_ch4finundated
-      write(iulog,*) '  ch4finundatedmapalgo             = ',ch4finundatedmapalgo
-      write(iulog,*) ' '
-   endif
-   this%stream_fldFileName_ch4finundated = stream_fldFileName_ch4finundated
-   this%ch4finundatedmapalgo             = ch4finundatedmapalgo
-   if (      finundation_mtd == finundation_mtd_ZWT_inversion  )then
-       this%fldList = "ZWT0:F0:P3"
-   else if ( finundation_mtd == finundation_mtd_TWS_inversion  )then
-       this%fldList = "FWS_TWS_A:FWS_TWS_B"
-   else
-       call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// &
-                   errMsg(sourcefile, __LINE__))
-   end if
-
- end subroutine ReadNML
-
-end module ch4FInundatedStreamType
diff --git a/src/cpl/mct/clm_cpl_indices.F90 b/src/cpl/mct/clm_cpl_indices.F90
deleted file mode 100644
index 09ed89e92d..0000000000
--- a/src/cpl/mct/clm_cpl_indices.F90
+++ /dev/null
@@ -1,330 +0,0 @@
-module clm_cpl_indices
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  !    Module containing the indices for the fields passed between CLM and
-  !    the driver. Includes the River Transport Model fields (RTM) and the
-  !    fields needed by the land-ice component (sno).
-  !
-  ! !USES:
-
-  use shr_sys_mod,    only : shr_sys_abort
-  implicit none
-
-  SAVE
-  private                              ! By default make data private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: clm_cpl_indices_set        ! Set the coupler indices
-  !
-  ! !PUBLIC DATA MEMBERS:
-  !
-  integer , public :: glc_nec     ! number of elevation classes for glacier_mec landunits
-                                  ! (from coupler) - must equal maxpatch_glc from namelist
-
-  ! lnd -> drv (required)
-
-  integer, public ::index_l2x_Flrl_rofsur     ! lnd->rtm input liquid surface fluxes
-  integer, public ::index_l2x_Flrl_rofgwl     ! lnd->rtm input liquid gwl fluxes
-  integer, public ::index_l2x_Flrl_rofsub     ! lnd->rtm input liquid subsurface fluxes
-  integer, public ::index_l2x_Flrl_rofi       ! lnd->rtm input frozen fluxes
-  integer, public ::index_l2x_Flrl_irrig      ! irrigation withdrawal
-
-  integer, public ::index_l2x_Sl_t            ! temperature
-  integer, public ::index_l2x_Sl_tref         ! 2m reference temperature
-  integer, public ::index_l2x_Sl_qref         ! 2m reference specific humidity
-  integer, public ::index_l2x_Sl_avsdr        ! albedo: direct , visible
-  integer, public ::index_l2x_Sl_anidr        ! albedo: direct , near-ir
-  integer, public ::index_l2x_Sl_avsdf        ! albedo: diffuse, visible
-  integer, public ::index_l2x_Sl_anidf        ! albedo: diffuse, near-ir
-  integer, public ::index_l2x_Sl_snowh        ! snow height
-  integer, public ::index_l2x_Sl_u10          ! 10m wind
-  integer, public ::index_l2x_Sl_ddvel        ! dry deposition velocities (optional)
-  integer, public ::index_l2x_Sl_fv           ! friction velocity
-  integer, public ::index_l2x_Sl_ram1         ! aerodynamical resistance
-  integer, public ::index_l2x_Sl_soilw        ! volumetric soil water
-  integer, public ::index_l2x_Fall_taux       ! wind stress, zonal
-  integer, public ::index_l2x_Fall_tauy       ! wind stress, meridional
-  integer, public ::index_l2x_Fall_lat        ! latent          heat flux
-  integer, public ::index_l2x_Fall_sen        ! sensible        heat flux
-  integer, public ::index_l2x_Fall_lwup       ! upward longwave heat flux
-  integer, public ::index_l2x_Fall_evap       ! evaporation     water flux
-  integer, public ::index_l2x_Fall_swnet      ! heat flux       shortwave net
-  integer, public ::index_l2x_Fall_fco2_lnd   ! co2 flux **For testing set to 0
-  integer, public ::index_l2x_Fall_flxdst1    ! dust flux size bin 1
-  integer, public ::index_l2x_Fall_flxdst2    ! dust flux size bin 2
-  integer, public ::index_l2x_Fall_flxdst3    ! dust flux size bin 3
-  integer, public ::index_l2x_Fall_flxdst4    ! dust flux size bin 4
-  integer, public ::index_l2x_Fall_flxvoc     ! MEGAN fluxes
-  integer, public ::index_l2x_Fall_flxfire    ! Fire fluxes
-  integer, public ::index_l2x_Sl_ztopfire     ! Top of fire emissions (m)
-
-  ! In the following, index 0 is bare land, other indices are glc elevation classes
-  integer, allocatable, public ::index_l2x_Sl_tsrf(:)   ! glc MEC temperature
-  integer, allocatable, public ::index_l2x_Sl_topo(:)   ! glc MEC topo height
-  integer, allocatable, public ::index_l2x_Flgl_qice(:) ! glc MEC ice flux
-
-  integer, public ::index_x2l_Sa_methane
-  integer, public ::index_l2x_Fall_methane
-
-  integer, public :: nflds_l2x = 0
-
-  ! drv -> lnd (required)
-
-  integer, public ::index_x2l_Sa_z            ! bottom atm level height
-  integer, public ::index_x2l_Sa_topo         ! atm surface height (m)
-  integer, public ::index_x2l_Sa_u            ! bottom atm level zon wind
-  integer, public ::index_x2l_Sa_v            ! bottom atm level mer wind
-  integer, public ::index_x2l_Sa_ptem         ! bottom atm level pot temp
-  integer, public ::index_x2l_Sa_shum         ! bottom atm level spec hum
-  integer, public ::index_x2l_Sa_pbot         ! bottom atm level pressure
-  integer, public ::index_x2l_Sa_tbot         ! bottom atm level temp
-  integer, public ::index_x2l_Faxa_lwdn       ! downward lw heat flux
-  integer, public ::index_x2l_Faxa_rainc      ! prec: liquid "convective"
-  integer, public ::index_x2l_Faxa_rainl      ! prec: liquid "large scale"
-  integer, public ::index_x2l_Faxa_snowc      ! prec: frozen "convective"
-  integer, public ::index_x2l_Faxa_snowl      ! prec: frozen "large scale"
-  integer, public ::index_x2l_Faxa_swndr      ! sw: nir direct  downward
-  integer, public ::index_x2l_Faxa_swvdr      ! sw: vis direct  downward
-  integer, public ::index_x2l_Faxa_swndf      ! sw: nir diffuse downward
-  integer, public ::index_x2l_Faxa_swvdf      ! sw: vis diffuse downward
-  integer, public ::index_x2l_Sa_co2prog      ! bottom atm level prognostic co2
-  integer, public ::index_x2l_Sa_co2diag      ! bottom atm level diagnostic co2
-  integer, public ::index_x2l_Faxa_bcphidry   ! flux: Black Carbon hydrophilic dry deposition
-  integer, public ::index_x2l_Faxa_bcphodry   ! flux: Black Carbon hydrophobic dry deposition
-  integer, public ::index_x2l_Faxa_bcphiwet   ! flux: Black Carbon hydrophilic wet deposition
-  integer, public ::index_x2l_Faxa_ocphidry   ! flux: Organic Carbon hydrophilic dry deposition
-  integer, public ::index_x2l_Faxa_ocphodry   ! flux: Organic Carbon hydrophobic dry deposition
-  integer, public ::index_x2l_Faxa_ocphiwet   ! flux: Organic Carbon hydrophilic dry deposition
-  integer, public ::index_x2l_Faxa_dstwet1    ! flux: Size 1 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstwet2    ! flux: Size 2 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstwet3    ! flux: Size 3 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstwet4    ! flux: Size 4 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstdry1    ! flux: Size 1 dust -- dry deposition
-  integer, public ::index_x2l_Faxa_dstdry2    ! flux: Size 2 dust -- dry deposition
-  integer, public ::index_x2l_Faxa_dstdry3    ! flux: Size 3 dust -- dry deposition
-  integer, public ::index_x2l_Faxa_dstdry4    ! flux: Size 4 dust -- dry deposition
-
-  integer, public ::index_x2l_Faxa_nhx        ! flux nhx from atm
-  integer, public ::index_x2l_Faxa_noy        ! flux noy from atm
-
-  integer, public ::index_x2l_Flrr_flood      ! rtm->lnd rof flood flux
-  integer, public ::index_x2l_Flrr_volr       ! rtm->lnd rof volr total volume
-  integer, public ::index_x2l_Flrr_volrmch    ! rtm->lnd rof volr main channel volume
-
-  ! In the following, index 0 is bare land, other indices are glc elevation classes
-  integer, allocatable, public ::index_x2l_Sg_ice_covered(:) ! Fraction of glacier from glc model
-  integer, allocatable, public ::index_x2l_Sg_topo(:)        ! Topo height from glc model
-  integer, allocatable, public ::index_x2l_Flgg_hflx(:)      ! Heat flux from glc model
-
-  integer, public ::index_x2l_Sg_icemask
-  integer, public ::index_x2l_Sg_icemask_coupled_fluxes
-
-  integer, public :: nflds_x2l = 0
-
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine clm_cpl_indices_set( )
-    !
-    ! !DESCRIPTION:
-    ! Set the coupler indices needed by the land model coupler
-    ! interface.
-    !
-    ! !USES:
-    use seq_flds_mod   , only: seq_flds_x2l_fields, seq_flds_l2x_fields
-    use mct_mod        , only: mct_aVect, mct_aVect_init, mct_avect_indexra
-    use mct_mod        , only: mct_aVect_clean, mct_avect_nRattr
-    use shr_drydep_mod , only: drydep_fields_token, n_drydep
-    use shr_megan_mod  , only: shr_megan_fields_token, shr_megan_mechcomps_n
-    use shr_fire_emis_mod,only: shr_fire_emis_fields_token, shr_fire_emis_ztop_token, shr_fire_emis_mechcomps_n
-    use clm_varctl     , only:  ndep_from_cpl
-    use glc_elevclass_mod, only: glc_get_num_elevation_classes, glc_elevclass_as_string
-    !
-    ! !ARGUMENTS:
-    implicit none
-    !
-    ! !REVISION HISTORY:
-    ! Author: Mariana Vertenstein
-    ! 01/2011, Erik Kluzek:         Added protex headers
-    !
-    ! !LOCAL VARIABLES:
-    type(mct_aVect)   :: l2x      ! temporary, land to coupler
-    type(mct_aVect)   :: x2l      ! temporary, coupler to land
-    integer           :: num
-    character(len=:), allocatable :: nec_str  ! string version of glc elev. class number
-    character(len=64) :: name
-    character(len=32) :: subname = 'clm_cpl_indices_set'  ! subroutine name
-    !-----------------------------------------------------------------------
-
-    ! Determine attribute vector indices
-
-    ! create temporary attribute vectors
-    call mct_aVect_init(x2l, rList=seq_flds_x2l_fields, lsize=1)
-    nflds_x2l = mct_avect_nRattr(x2l)
-
-    call mct_aVect_init(l2x, rList=seq_flds_l2x_fields, lsize=1)
-    nflds_l2x = mct_avect_nRattr(l2x)
-
-    !-------------------------------------------------------------
-    ! clm -> drv
-    !-------------------------------------------------------------
-
-    index_l2x_Flrl_rofsur   = mct_avect_indexra(l2x,'Flrl_rofsur')
-    index_l2x_Flrl_rofgwl   = mct_avect_indexra(l2x,'Flrl_rofgwl')
-    index_l2x_Flrl_rofsub   = mct_avect_indexra(l2x,'Flrl_rofsub')
-    index_l2x_Flrl_rofi     = mct_avect_indexra(l2x,'Flrl_rofi')
-    index_l2x_Flrl_irrig    = mct_avect_indexra(l2x,'Flrl_irrig')
-
-    index_l2x_Sl_t          = mct_avect_indexra(l2x,'Sl_t')
-    index_l2x_Sl_snowh      = mct_avect_indexra(l2x,'Sl_snowh')
-    index_l2x_Sl_avsdr      = mct_avect_indexra(l2x,'Sl_avsdr')
-    index_l2x_Sl_anidr      = mct_avect_indexra(l2x,'Sl_anidr')
-    index_l2x_Sl_avsdf      = mct_avect_indexra(l2x,'Sl_avsdf')
-    index_l2x_Sl_anidf      = mct_avect_indexra(l2x,'Sl_anidf')
-    index_l2x_Sl_tref       = mct_avect_indexra(l2x,'Sl_tref')
-    index_l2x_Sl_qref       = mct_avect_indexra(l2x,'Sl_qref')
-    index_l2x_Sl_u10        = mct_avect_indexra(l2x,'Sl_u10')
-    index_l2x_Sl_ram1       = mct_avect_indexra(l2x,'Sl_ram1')
-    index_l2x_Sl_fv         = mct_avect_indexra(l2x,'Sl_fv')
-    index_l2x_Sl_soilw      = mct_avect_indexra(l2x,'Sl_soilw',perrwith='quiet')
-
-    if ( n_drydep>0 )then
-       index_l2x_Sl_ddvel = mct_avect_indexra(l2x, trim(drydep_fields_token))
-    else
-       index_l2x_Sl_ddvel = 0
-    end if
-
-    index_l2x_Fall_taux     = mct_avect_indexra(l2x,'Fall_taux')
-    index_l2x_Fall_tauy     = mct_avect_indexra(l2x,'Fall_tauy')
-    index_l2x_Fall_lat      = mct_avect_indexra(l2x,'Fall_lat')
-    index_l2x_Fall_sen      = mct_avect_indexra(l2x,'Fall_sen')
-    index_l2x_Fall_lwup     = mct_avect_indexra(l2x,'Fall_lwup')
-    index_l2x_Fall_evap     = mct_avect_indexra(l2x,'Fall_evap')
-    index_l2x_Fall_swnet    = mct_avect_indexra(l2x,'Fall_swnet')
-    index_l2x_Fall_flxdst1  = mct_avect_indexra(l2x,'Fall_flxdst1')
-    index_l2x_Fall_flxdst2  = mct_avect_indexra(l2x,'Fall_flxdst2')
-    index_l2x_Fall_flxdst3  = mct_avect_indexra(l2x,'Fall_flxdst3')
-    index_l2x_Fall_flxdst4  = mct_avect_indexra(l2x,'Fall_flxdst4')
-
-    index_l2x_Fall_fco2_lnd = mct_avect_indexra(l2x,'Fall_fco2_lnd',perrwith='quiet')
-
-    index_l2x_Fall_methane  = mct_avect_indexra(l2x,'Fall_methane',perrWith='quiet')
-
-    ! MEGAN fluxes
-    if (shr_megan_mechcomps_n>0) then
-       index_l2x_Fall_flxvoc = mct_avect_indexra(l2x,trim(shr_megan_fields_token))
-    else
-       index_l2x_Fall_flxvoc = 0
-    endif
-
-    ! Fire fluxes
-    if (shr_fire_emis_mechcomps_n>0) then
-       index_l2x_Fall_flxfire = mct_avect_indexra(l2x,trim(shr_fire_emis_fields_token))
-       index_l2x_Sl_ztopfire = mct_avect_indexra(l2x,trim(shr_fire_emis_ztop_token))
-    else
-       index_l2x_Fall_flxfire = 0
-       index_l2x_Sl_ztopfire = 0
-    endif
-
-    !-------------------------------------------------------------
-    ! drv -> clm
-    !-------------------------------------------------------------
-
-    index_x2l_Sa_z          = mct_avect_indexra(x2l,'Sa_z')
-    index_x2l_Sa_topo       = mct_avect_indexra(x2l,'Sa_topo')
-    index_x2l_Sa_u          = mct_avect_indexra(x2l,'Sa_u')
-    index_x2l_Sa_v          = mct_avect_indexra(x2l,'Sa_v')
-    index_x2l_Sa_ptem       = mct_avect_indexra(x2l,'Sa_ptem')
-    index_x2l_Sa_pbot       = mct_avect_indexra(x2l,'Sa_pbot')
-    index_x2l_Sa_tbot       = mct_avect_indexra(x2l,'Sa_tbot')
-    index_x2l_Sa_shum       = mct_avect_indexra(x2l,'Sa_shum')
-    index_x2l_Sa_co2prog    = mct_avect_indexra(x2l,'Sa_co2prog',perrwith='quiet')
-    index_x2l_Sa_co2diag    = mct_avect_indexra(x2l,'Sa_co2diag',perrwith='quiet')
-
-    index_x2l_Sa_methane    = mct_avect_indexra(x2l,'Sa_methane',perrWith='quiet')
-
-    index_x2l_Flrr_volr     = mct_avect_indexra(x2l,'Flrr_volr')
-    index_x2l_Flrr_volrmch  = mct_avect_indexra(x2l,'Flrr_volrmch')
-
-    index_x2l_Faxa_lwdn     = mct_avect_indexra(x2l,'Faxa_lwdn')
-    index_x2l_Faxa_rainc    = mct_avect_indexra(x2l,'Faxa_rainc')
-    index_x2l_Faxa_rainl    = mct_avect_indexra(x2l,'Faxa_rainl')
-    index_x2l_Faxa_snowc    = mct_avect_indexra(x2l,'Faxa_snowc')
-    index_x2l_Faxa_snowl    = mct_avect_indexra(x2l,'Faxa_snowl')
-    index_x2l_Faxa_swndr    = mct_avect_indexra(x2l,'Faxa_swndr')
-    index_x2l_Faxa_swvdr    = mct_avect_indexra(x2l,'Faxa_swvdr')
-    index_x2l_Faxa_swndf    = mct_avect_indexra(x2l,'Faxa_swndf')
-    index_x2l_Faxa_swvdf    = mct_avect_indexra(x2l,'Faxa_swvdf')
-    index_x2l_Faxa_bcphidry = mct_avect_indexra(x2l,'Faxa_bcphidry')
-    index_x2l_Faxa_bcphodry = mct_avect_indexra(x2l,'Faxa_bcphodry')
-    index_x2l_Faxa_bcphiwet = mct_avect_indexra(x2l,'Faxa_bcphiwet')
-    index_x2l_Faxa_ocphidry = mct_avect_indexra(x2l,'Faxa_ocphidry')
-    index_x2l_Faxa_ocphodry = mct_avect_indexra(x2l,'Faxa_ocphodry')
-    index_x2l_Faxa_ocphiwet = mct_avect_indexra(x2l,'Faxa_ocphiwet')
-    index_x2l_Faxa_dstdry1  = mct_avect_indexra(x2l,'Faxa_dstdry1')
-    index_x2l_Faxa_dstdry2  = mct_avect_indexra(x2l,'Faxa_dstdry2')
-    index_x2l_Faxa_dstdry3  = mct_avect_indexra(x2l,'Faxa_dstdry3')
-    index_x2l_Faxa_dstdry4  = mct_avect_indexra(x2l,'Faxa_dstdry4')
-    index_x2l_Faxa_dstwet1  = mct_avect_indexra(x2l,'Faxa_dstwet1')
-    index_x2l_Faxa_dstwet2  = mct_avect_indexra(x2l,'Faxa_dstwet2')
-    index_x2l_Faxa_dstwet3  = mct_avect_indexra(x2l,'Faxa_dstwet3')
-    index_x2l_Faxa_dstwet4  = mct_avect_indexra(x2l,'Faxa_dstwet4')
-
-    index_x2l_Faxa_nhx      = mct_avect_indexra(x2l,'Faxa_nhx', perrWith='quiet')
-    index_x2l_Faxa_noy      = mct_avect_indexra(x2l,'Faxa_noy', perrWith='quiet')
-
-    if (index_x2l_Faxa_nhx > 0 .and. index_x2l_Faxa_noy > 0) then
-       ndep_from_cpl = .true.
-    end if
-
-    index_x2l_Flrr_flood    = mct_avect_indexra(x2l,'Flrr_flood')
-
-    !-------------------------------------------------------------
-    ! glc coupling
-    !-------------------------------------------------------------
-
-    index_x2l_Sg_icemask = mct_avect_indexra(x2l,'Sg_icemask')
-    index_x2l_Sg_icemask_coupled_fluxes = mct_avect_indexra(x2l,'Sg_icemask_coupled_fluxes')
-
-    glc_nec = glc_get_num_elevation_classes()
-    if (glc_nec < 1) then
-       call shr_sys_abort('ERROR: In CLM4.5 and later, glc_nec must be at least 1.')
-    end if
-
-    ! Create coupling fields for all glc elevation classes (1:glc_nec) plus bare land
-    ! (index 0).
-    allocate(index_l2x_Sl_tsrf(0:glc_nec))
-    allocate(index_l2x_Sl_topo(0:glc_nec))
-    allocate(index_l2x_Flgl_qice(0:glc_nec))
-    allocate(index_x2l_Sg_ice_covered(0:glc_nec))
-    allocate(index_x2l_Sg_topo(0:glc_nec))
-    allocate(index_x2l_Flgg_hflx(0:glc_nec))
-
-    do num = 0,glc_nec
-       nec_str = glc_elevclass_as_string(num)
-
-       name = 'Sg_ice_covered' // nec_str
-       index_x2l_Sg_ice_covered(num) = mct_avect_indexra(x2l,trim(name))
-       name = 'Sg_topo' // nec_str
-       index_x2l_Sg_topo(num)   = mct_avect_indexra(x2l,trim(name))
-       name = 'Flgg_hflx' // nec_str
-       index_x2l_Flgg_hflx(num) = mct_avect_indexra(x2l,trim(name))
-
-       name = 'Sl_tsrf' // nec_str
-       index_l2x_Sl_tsrf(num)   = mct_avect_indexra(l2x,trim(name))
-       name = 'Sl_topo' // nec_str
-       index_l2x_Sl_topo(num)   = mct_avect_indexra(l2x,trim(name))
-       name = 'Flgl_qice' // nec_str
-       index_l2x_Flgl_qice(num) = mct_avect_indexra(l2x,trim(name))
-    end do
-
-    call mct_aVect_clean(x2l)
-    call mct_aVect_clean(l2x)
-
-  end subroutine clm_cpl_indices_set
-
-!=======================================================================
-
-end module clm_cpl_indices
diff --git a/src/cpl/mct/laiStreamMod.F90 b/src/cpl/mct/laiStreamMod.F90
deleted file mode 100644
index 47d25287b7..0000000000
--- a/src/cpl/mct/laiStreamMod.F90
+++ /dev/null
@@ -1,241 +0,0 @@
-module laiStreamMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Read LAI from stream
-  !
-  ! !USES:
-  use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create
-  use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance
-  use shr_kind_mod    , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use decompMod       , only : bounds_type
-  use abortutils      , only : endrun
-  use clm_varctl      , only : iulog, inst_name
-  use perf_mod        , only : t_startf, t_stopf
-  use spmdMod         , only : masterproc, mpicom, comp_id
-  use ncdio_pio
-  use mct_mod
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: lai_init    ! position datasets for LAI
-  public :: lai_advance ! Advance the LAI streams (outside of a Open-MP threading loop)
-  public :: lai_interp  ! interpolates between two years of LAI data (when LAI streams
-
-  ! !PRIVATE MEMBER DATA:
-  integer, allocatable    :: g_to_ig(:)         ! Array matching gridcell index to data index
-  type(shr_strdata_type)  :: sdat_lai           ! LAI input data stream
-
-  character(len=*), parameter :: sourcefile = &
-       __FILE__
-
-!==============================================================================
-contains
-!==============================================================================
-
-  subroutine lai_init(bounds)
-    !
-    ! Initialize data stream information for LAI.
-    !
-    ! !USES:
-    use clm_time_manager , only : get_calendar
-    use ncdio_pio        , only : pio_subsystem
-    use shr_pio_mod      , only : shr_pio_getiotype
-    use shr_stream_mod   , only : shr_stream_file_null
-    use shr_string_mod   , only : shr_string_listCreateField
-    use clm_nlUtilsMod   , only : find_nlgroup_name
-    use ndepStreamMod    , only : clm_domain_mct
-    use histFileMod      , only : hist_addfld1d
-    use domainMod        , only : ldomain
-    use controlMod       , only : NLFilename
-    use lnd_set_decomp_and_domain , only : gsmap_global
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds          ! bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: stream_year_first_lai      ! first year in Lai stream to use
-    integer            :: stream_year_last_lai       ! last year in Lai stream to use
-    integer            :: model_year_align_lai       ! align stream_year_first_lai with
-    integer            :: nu_nml                     ! unit for namelist file
-    integer            :: nml_error                  ! namelist i/o error flag
-    type(mct_ggrid)    :: dom_clm                    ! domain information
-    character(len=CL)  :: stream_fldFileName_lai     ! lai stream filename to read
-    character(len=CL)  :: lai_mapalgo = 'bilinear'   ! Mapping alogrithm
-    character(len=CL)  :: lai_tintalgo = 'linear'    ! Time interpolation alogrithm
-    character(len=CXX) :: fldList                    ! field string
-    character(*), parameter :: laiString = "LAI"     ! base string for field string
-    integer     , parameter :: numLaiFields = 16     ! number of fields to build field string
-    character(*), parameter :: subName = "('laidyn_init')"
-    !-----------------------------------------------------------------------
-    !
-    ! deal with namelist variables here in init
-    !
-    namelist /lai_streams/         &
-         stream_year_first_lai,    &
-         stream_year_last_lai,     &
-         model_year_align_lai,     &
-         lai_mapalgo,              &
-         stream_fldFileName_lai,   &
-         lai_tintalgo
-
-    ! Default values for namelist
-    stream_year_first_lai     = 1      ! first year in stream to use
-    stream_year_last_lai      = 1      ! last  year in stream to use
-    model_year_align_lai      = 1      ! align stream_year_first_lai with this model year
-    stream_fldFileName_lai    = shr_stream_file_null
-
-    ! Read lai_streams namelist
-    if (masterproc) then
-       open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-       call find_nlgroup_name(nu_nml, 'lai_streams', status=nml_error)
-       if (nml_error == 0) then
-          read(nu_nml, nml=lai_streams,iostat=nml_error)
-          if (nml_error /= 0) then
-             call endrun(subname // ':: ERROR reading lai_streams namelist')
-          end if
-       else
-          call endrun(subname // ':: ERROR finding lai_streams namelist')
-       end if
-       close(nu_nml)
-    endif
-    call shr_mpi_bcast(stream_year_first_lai  , mpicom)
-    call shr_mpi_bcast(stream_year_last_lai   , mpicom)
-    call shr_mpi_bcast(model_year_align_lai   , mpicom)
-    call shr_mpi_bcast(stream_fldFileName_lai , mpicom)
-    call shr_mpi_bcast(lai_tintalgo           , mpicom)
-
-    if (masterproc) then
-       write(iulog,*) ' '
-       write(iulog,*) 'lai_stream settings:'
-       write(iulog,*) '  stream_year_first_lai  = ',stream_year_first_lai
-       write(iulog,*) '  stream_year_last_lai   = ',stream_year_last_lai
-       write(iulog,*) '  model_year_align_lai   = ',model_year_align_lai
-       write(iulog,*) '  stream_fldFileName_lai = ',trim(stream_fldFileName_lai)
-       write(iulog,*) '  lai_tintalgo           = ',trim(lai_tintalgo)
-    endif
-
-    call clm_domain_mct (bounds, dom_clm)
-
-    ! create the field list for these lai fields...use in shr_strdata_create
-    fldList = shr_string_listCreateField( numLaiFields, laiString )
-
-    call shr_strdata_create(sdat_lai,name="laidyn",    &
-         pio_subsystem=pio_subsystem,                  &
-         pio_iotype=shr_pio_getiotype(inst_name),      &
-         mpicom=mpicom, compid=comp_id,                &
-         gsmap=gsmap_global, ggrid=dom_clm,            &
-         nxg=ldomain%ni, nyg=ldomain%nj,               &
-         yearFirst=stream_year_first_lai,              &
-         yearLast=stream_year_last_lai,                &
-         yearAlign=model_year_align_lai,               &
-         offset=0,                                     &
-         domFilePath='',                               &
-         domFileName=trim(stream_fldFileName_lai),     &
-         domTvarName='time',                           &
-         domXvarName='lon' ,                           &
-         domYvarName='lat' ,                           &
-         domAreaName='area',                           &
-         domMaskName='mask',                           &
-         filePath='',                                  &
-         filename=(/stream_fldFileName_lai/),          &
-         fldListFile=fldList,                          &
-         fldListModel=fldList,                         &
-         fillalgo='none',                              &
-         mapalgo=lai_mapalgo,                          &
-         tintalgo=lai_tintalgo,                        &
-         calendar=get_calendar(),                      &
-         taxmode='cycle'                               )
-
-    if (masterproc) then
-       call shr_strdata_print(sdat_lai,'LAI data')
-    endif
-
-  end subroutine lai_init
-
-  !==============================================================================
-  subroutine lai_advance( bounds )
-    !
-    ! Advance LAI streams
-    !
-    ! !USES:
-    use clm_time_manager, only : get_curr_date
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)      , intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g, ig   ! Indices
-    integer :: year    ! year (0, ...) for nstep+1
-    integer :: mon     ! month (1, ..., 12) for nstep+1
-    integer :: day     ! day of month (1, ..., 31) for nstep+1
-    integer :: sec     ! seconds into current date for nstep+1
-    integer :: mcdate  ! Current model date (yyyymmdd)
-    !-----------------------------------------------------------------------
-
-    call get_curr_date(year, mon, day, sec)
-    mcdate = year*10000 + mon*100 + day
-
-    call shr_strdata_advance(sdat_lai, mcdate, sec, mpicom, 'laidyn')
-    if ( .not. allocated(g_to_ig) )then
-       allocate (g_to_ig(bounds%begg:bounds%endg) )
-       ig = 0
-       do g = bounds%begg,bounds%endg
-          ig = ig+1
-          g_to_ig(g) = ig
-       end do
-    end if
-
-  end subroutine lai_advance
-
-  !==============================================================================
-  subroutine lai_interp(bounds, canopystate_inst)
-    !
-    ! Interpolate data stream information for Lai.
-    !
-    ! !USES:
-    use pftconMod       , only : noveg
-    use CanopyStateType , only : canopystate_type
-    use PatchType       , only : patch
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)      , intent(in)    :: bounds
-    type(canopystate_type) , intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ivt, p, ip, ig
-    character(len=CL)  :: stream_var_name
-    !-----------------------------------------------------------------------
-    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (lbound(sdat_lai%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(sdat_lai%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__)
-
-    do p = bounds%begp, bounds%endp
-       ivt = patch%itype(p)
-       ! Set lai for each gridcell/patch combination
-       if (ivt /= noveg) then
-          ! vegetated pft
-          write(stream_var_name,"(i6)") ivt
-          stream_var_name = 'LAI_'//trim(adjustl(stream_var_name))
-          ip = mct_aVect_indexRA(sdat_lai%avs(1),trim(stream_var_name))
-          ig = g_to_ig(patch%gridcell(p))
-          canopystate_inst%tlai_patch(p) = sdat_lai%avs(1)%rAttr(ip,ig)
-       else                       
-          ! non-vegetated pft
-          canopystate_inst%tlai_patch(p) = 0._r8
-       endif
-    end do
-
-  end subroutine lai_interp
-
-end module LaiStreamMod
diff --git a/src/cpl/mct/lnd_comp_mct.F90 b/src/cpl/mct/lnd_comp_mct.F90
deleted file mode 100644
index e50602a378..0000000000
--- a/src/cpl/mct/lnd_comp_mct.F90
+++ /dev/null
@@ -1,632 +0,0 @@
-module lnd_comp_mct
-
-  !---------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  !  Interface of the active land model component of CESM the CLM (Community Land Model)
-  !  with the main CESM driver. This is a thin interface taking CESM driver information
-  !  in MCT (Model Coupling Toolkit) format and converting it to use by CLM.
-  !
-  ! !uses:
-  use shr_kind_mod     , only : r8 => shr_kind_r8
-  use shr_sys_mod      , only : shr_sys_flush
-  use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use mct_mod          , only : mct_avect, mct_gsmap, mct_gGrid
-  use decompmod        , only : bounds_type
-  use lnd_import_export, only : lnd_import, lnd_export
-  !
-  ! !public member functions:
-  implicit none
-  private                     ! by default make data private
-  !
-  ! !public member functions:
-  public :: lnd_init_mct      ! clm initialization
-  public :: lnd_run_mct       ! clm run phase
-  public :: lnd_final_mct     ! clm finalization/cleanup
-  !
-  ! !private member functions:
-  private :: lnd_domain_mct    ! set the land model domain information
-  private :: lnd_handle_resume ! handle pause/resume signals from the coupler
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-!====================================================================================
-contains
-!====================================================================================
-
-  subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Initialize land surface model and obtain relevant atmospheric model arrays
-    ! back from (i.e. albedos, surface temperature and snow cover over land).
-    !
-    ! !USES:
-    use shr_kind_mod     , only : shr_kind_cl
-    use abortutils       , only : endrun
-    use clm_time_manager , only : get_nstep, set_timemgr_init
-    use clm_initializeMod, only : initialize1, initialize2
-    use clm_instMod      , only : water_inst, lnd2atm_inst, lnd2glc_inst
-    use clm_varctl       , only : finidat, single_column, clm_varctl_set, iulog
-    use clm_varctl       , only : inst_index, inst_suffix, inst_name
-    use clm_varorb       , only : eccen, obliqr, lambm0, mvelpp
-    use controlMod       , only : control_setNL
-    use decompMod        , only : get_proc_bounds
-    use domainMod        , only : ldomain
-    use shr_file_mod     , only : shr_file_setLogUnit, shr_file_setLogLevel
-    use shr_file_mod     , only : shr_file_getLogUnit, shr_file_getLogLevel
-    use shr_file_mod     , only : shr_file_getUnit, shr_file_setIO
-    use seq_cdata_mod    , only : seq_cdata, seq_cdata_setptrs
-    use seq_timemgr_mod  , only : seq_timemgr_EClockGetData
-    use seq_infodata_mod , only : seq_infodata_type, seq_infodata_GetData, seq_infodata_PutData, &
-                                  seq_infodata_start_type_start, seq_infodata_start_type_cont,   &
-                                  seq_infodata_start_type_brnch
-    use seq_comm_mct     , only : seq_comm_suffix, seq_comm_inst, seq_comm_name
-    use seq_flds_mod     , only : seq_flds_x2l_fields, seq_flds_l2x_fields
-    use spmdMod          , only : masterproc, spmd_init
-    use clm_varctl       , only : nsrStartup, nsrContinue, nsrBranch
-    use clm_cpl_indices  , only : clm_cpl_indices_set
-    use mct_mod          , only : mct_aVect_init, mct_aVect_zero, mct_gsMap, mct_gsMap_init
-    use decompMod        , only : gindex_global
-    use lnd_set_decomp_and_domain, only : lnd_set_decomp_and_domain_from_surfrd, gsmap_global
-    use ESMF
-    !
-    ! !ARGUMENTS:
-    type(ESMF_Clock),           intent(inout) :: EClock           ! Input synchronization clock
-    type(seq_cdata),            intent(inout) :: cdata_l          ! Input land-model driver data
-    type(mct_aVect),            intent(inout) :: x2l_l, l2x_l     ! land model import and export states
-    character(len=*), optional, intent(in)    :: NLFilename       ! Namelist filename to read
-    !
-    ! !LOCAL VARIABLES:
-    integer                          :: LNDID        ! Land identifyer
-    integer                          :: mpicom_lnd   ! MPI communicator
-    type(mct_gsMap),         pointer :: GSMap_lnd    ! Land model MCT GS map
-    type(mct_gGrid),         pointer :: dom_l        ! Land model domain
-    type(seq_infodata_type), pointer :: infodata     ! CESM driver level info data
-    integer  :: lsize                                ! size of attribute vector
-    integer  :: gsize                                ! global size 
-    integer  :: g,i,j                                ! indices
-    integer  :: dtime_sync                           ! coupling time-step from the input synchronization clock
-    logical  :: exists                               ! true if file exists
-    logical  :: atm_aero                             ! Flag if aerosol data sent from atm model
-    real(r8) :: scmlat                               ! single-column latitude
-    real(r8) :: scmlon                               ! single-column longitude
-    character(len=SHR_KIND_CL) :: caseid             ! case identifier name
-    character(len=SHR_KIND_CL) :: ctitle             ! case description title
-    character(len=SHR_KIND_CL) :: starttype          ! start-type (startup, continue, branch, hybrid)
-    character(len=SHR_KIND_CL) :: calendar           ! calendar type name
-    character(len=SHR_KIND_CL) :: hostname           ! hostname of machine running on
-    character(len=SHR_KIND_CL) :: version            ! Model version
-    character(len=SHR_KIND_CL) :: username           ! user running the model
-    integer :: nsrest                                ! clm restart type
-    integer :: ref_ymd                               ! reference date (YYYYMMDD)
-    integer :: ref_tod                               ! reference time of day (sec)
-    integer :: start_ymd                             ! start date (YYYYMMDD)
-    integer :: start_tod                             ! start time of day (sec)
-    logical :: brnch_retain_casename                 ! flag if should retain the case name on a branch start type
-    integer :: lbnum                                 ! input to memory diagnostic
-    integer :: shrlogunit,shrloglev                  ! old values for log unit and log level
-    type(bounds_type) :: bounds                      ! bounds
-    logical :: noland
-    integer :: ni,nj
-    real(r8)         , parameter :: rundef = -9999999._r8
-    character(len=32), parameter :: sub = 'lnd_init_mct'
-    character(len=*),  parameter :: format = "('("//trim(sub)//") :',A)"
-    !-----------------------------------------------------------------------
-
-    ! Set cdata data
-    call seq_cdata_setptrs(cdata_l, ID=LNDID, mpicom=mpicom_lnd, &
-         gsMap=GSMap_lnd, dom=dom_l, infodata=infodata)
-
-    ! Determine attriute vector indices
-    call clm_cpl_indices_set()
-
-    ! Initialize clm MPI communicator
-    call spmd_init( mpicom_lnd, LNDID )
-
-#if (defined _MEMTRACE)
-    if(masterproc) then
-       lbnum=1
-       call memmon_dump_fort('memmon.out','lnd_init_mct:start::',lbnum)
-    endif
-#endif
-
-    inst_name   = seq_comm_name(LNDID)
-    inst_index  = seq_comm_inst(LNDID)
-    inst_suffix = seq_comm_suffix(LNDID)
-    ! Initialize io log unit
-
-    call shr_file_getLogUnit (shrlogunit)
-    if (masterproc) then
-       inquire(file='lnd_modelio.nml'//trim(inst_suffix),exist=exists)
-       if (exists) then
-          iulog = shr_file_getUnit()
-          call shr_file_setIO('lnd_modelio.nml'//trim(inst_suffix),iulog)
-       end if
-       write(iulog,format) "CLM land model initialization"
-    else
-       iulog = shrlogunit
-    end if
-
-    call shr_file_getLogLevel(shrloglev)
-    call shr_file_setLogUnit (iulog)
-
-    ! Use infodata to set orbital values
-    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
-         orb_lambm0=lambm0, orb_obliqr=obliqr )
-
-    ! Consistency check on namelist filename
-    call control_setNL("lnd_in"//trim(inst_suffix))
-
-    ! Initialize clm
-    ! initialize1 reads namelists
-    ! decomp and domain are set in lnd_set_decomp_and_domain_from_surfrd
-    ! initialize2 performs the rest of initialization
-    call seq_timemgr_EClockGetData(EClock,                               &
-                                   start_ymd=start_ymd,                  &
-                                   start_tod=start_tod, ref_ymd=ref_ymd, &
-                                   ref_tod=ref_tod, &
-                                   calendar=calendar, &
-                                   dtime=dtime_sync)
-    if (masterproc) then
-       write(iulog,*)'dtime = ',dtime_sync
-    end if
-    call seq_infodata_GetData(infodata, case_name=caseid,    &
-                              case_desc=ctitle, single_column=single_column,    &
-                              scmlat=scmlat, scmlon=scmlon,                     &
-                              brnch_retain_casename=brnch_retain_casename,      &
-                              start_type=starttype, model_version=version,      &
-                              hostname=hostname, username=username )
-
-    ! Single Column
-    if ( single_column .and. (scmlat == rundef  .or. scmlon == rundef ) ) then
-       call endrun(msg=' ERROR:: single column mode on -- but scmlat and scmlon are NOT set'//&
-            errMsg(sourcefile, __LINE__))
-    end if
-
-    ! Note that we assume that CTSM's internal dtime matches the coupling time step.
-    ! i.e., we currently do NOT allow sub-cycling within a coupling time step.
-    call set_timemgr_init( calendar_in=calendar, start_ymd_in=start_ymd, start_tod_in=start_tod, &
-         ref_ymd_in=ref_ymd, ref_tod_in=ref_tod, dtime_in=dtime_sync)
-
-    if (     trim(starttype) == trim(seq_infodata_start_type_start)) then
-       nsrest = nsrStartup
-    else if (trim(starttype) == trim(seq_infodata_start_type_cont) ) then
-       nsrest = nsrContinue
-    else if (trim(starttype) == trim(seq_infodata_start_type_brnch)) then
-       nsrest = nsrBranch
-    else
-       call endrun( sub//' ERROR: unknown starttype' )
-    end if
-
-    ! set default values for run control variables
-    call clm_varctl_set(caseid_in=caseid, ctitle_in=ctitle,                     &
-                        brnch_retain_casename_in=brnch_retain_casename,         &
-                        single_column_in=single_column, scmlat_in=scmlat,       &
-                        scmlon_in=scmlon, nsrest_in=nsrest, version_in=version, &
-                        hostname_in=hostname, username_in=username)
-
-    ! Read namelists
-    call initialize1(dtime=dtime_sync)
-
-    ! Initialize decomposition and domain (ldomain) type
-    call lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj)
-
-    ! If no land then exit out of initialization
-    if ( noland ) then
-
-       call seq_infodata_PutData( infodata, lnd_present   =.false.)
-       call seq_infodata_PutData( infodata, lnd_prognostic=.false.)
-
-    else
-
-       ! Determine if aerosol and dust deposition come from atmosphere component
-       call seq_infodata_GetData(infodata, atm_aero=atm_aero )
-       if ( .not. atm_aero )then
-          call endrun( sub//' ERROR: atmosphere model MUST send aerosols to CLM' )
-       end if
-
-       ! Initialize clm gsMap, clm domain and clm attribute vectors
-       call get_proc_bounds( bounds )
-       lsize = bounds%endg - bounds%begg + 1
-       gsize = ldomain%ni * ldomain%nj
-       call mct_gsMap_init( gsMap_lnd, gindex_global, mpicom_lnd, LNDID, lsize, gsize )
-       gsmap_global => gsmap_lnd ! module variable in lnd_set_decomp_and_domain
-       call lnd_domain_mct( bounds, lsize, gsMap_lnd, dom_l )
-       call mct_aVect_init(x2l_l, rList=seq_flds_x2l_fields, lsize=lsize)
-       call mct_aVect_zero(x2l_l)
-       call mct_aVect_init(l2x_l, rList=seq_flds_l2x_fields, lsize=lsize)
-       call mct_aVect_zero(l2x_l)
-
-       ! Finish initializing clm
-       call initialize2(ni,nj)
-
-       ! Create land export state
-       call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
-
-       ! Fill in infodata settings
-       call seq_infodata_PutData(infodata, lnd_prognostic=.true.)
-       call seq_infodata_PutData(infodata, lnd_nx=ldomain%ni, lnd_ny=ldomain%nj)
-       call lnd_handle_resume( cdata_l )
-
-       ! Reset shr logging to original values
-       call shr_file_setLogUnit (shrlogunit)
-       call shr_file_setLogLevel(shrloglev)
-
-#if (defined _MEMTRACE)
-       if(masterproc) then
-          write(iulog,*) TRIM(Sub) // ':end::'
-          lbnum=1
-          call memmon_dump_fort('memmon.out','lnd_int_mct:end::',lbnum)
-          call memmon_reset_addr()
-       endif
-#endif
-    end if
-
-  end subroutine lnd_init_mct
-
-  !====================================================================================
-  subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
-    !
-    ! !DESCRIPTION:
-    ! Run clm model
-    !
-    ! !USES:
-    use shr_kind_mod    ,  only : r8 => shr_kind_r8
-    use clm_instMod     ,  only : water_inst, lnd2atm_inst, atm2lnd_inst, lnd2glc_inst, glc2lnd_inst
-    use clm_driver      ,  only : clm_drv
-    use clm_time_manager,  only : get_curr_date, get_nstep, get_curr_calday, get_step_size
-    use clm_time_manager,  only : advance_timestep, update_rad_dtime
-    use decompMod       ,  only : get_proc_bounds
-    use abortutils      ,  only : endrun
-    use clm_varctl      ,  only : iulog
-    use clm_varorb      ,  only : eccen, obliqr, lambm0, mvelpp
-    use shr_file_mod    ,  only : shr_file_setLogUnit, shr_file_setLogLevel
-    use shr_file_mod    ,  only : shr_file_getLogUnit, shr_file_getLogLevel
-    use seq_cdata_mod   ,  only : seq_cdata, seq_cdata_setptrs
-    use seq_timemgr_mod ,  only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn
-    use seq_timemgr_mod ,  only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync
-    use seq_infodata_mod,  only : seq_infodata_type, seq_infodata_GetData
-    use spmdMod         ,  only : masterproc, mpicom
-    use perf_mod        ,  only : t_startf, t_stopf, t_barrierf
-    use shr_orb_mod     ,  only : shr_orb_decl
-    use ESMF
-    !
-    ! !ARGUMENTS:
-    type(ESMF_Clock) , intent(inout) :: EClock    ! Input synchronization clock from driver
-    type(seq_cdata)  , intent(inout) :: cdata_l   ! Input driver data for land model
-    type(mct_aVect)  , intent(inout) :: x2l_l     ! Import state to land model
-    type(mct_aVect)  , intent(inout) :: l2x_l     ! Export state from land model
-    !
-    ! !LOCAL VARIABLES:
-    integer      :: ymd_sync             ! Sync date (YYYYMMDD)
-    integer      :: yr_sync              ! Sync current year
-    integer      :: mon_sync             ! Sync current month
-    integer      :: day_sync             ! Sync current day
-    integer      :: tod_sync             ! Sync current time of day (sec)
-    integer      :: ymd                  ! CLM current date (YYYYMMDD)
-    integer      :: yr                   ! CLM current year
-    integer      :: mon                  ! CLM current month
-    integer      :: day                  ! CLM current day
-    integer      :: tod                  ! CLM current time of day (sec)
-    integer      :: dtime                ! time step increment (sec)
-    integer      :: nstep                ! time step index
-    logical      :: rstwr_sync           ! .true. ==> write restart file before returning
-    logical      :: rstwr                ! .true. ==> write restart file before returning
-    logical      :: nlend_sync           ! Flag signaling last time-step
-    logical      :: nlend                ! .true. ==> last time-step
-    logical      :: dosend               ! true => send data back to driver
-    logical      :: doalb                ! .true. ==> do albedo calculation on this time step
-    logical      :: rof_prognostic       ! .true. => running with a prognostic ROF model
-    logical      :: glc_present          ! .true. => running with a non-stub GLC model
-    real(r8)     :: nextsw_cday          ! calday from clock of next radiation computation
-    real(r8)     :: caldayp1             ! clm calday plus dtime offset
-    integer      :: shrlogunit,shrloglev ! old values for share log unit and log level
-    integer      :: lbnum                ! input to memory diagnostic
-    integer      :: g,i,lsize            ! counters
-    real(r8)     :: calday               ! calendar day for nstep
-    real(r8)     :: declin               ! solar declination angle in radians for nstep
-    real(r8)     :: declinp1             ! solar declination angle in radians for nstep+1
-    real(r8)     :: eccf                 ! earth orbit eccentricity factor
-    real(r8)     :: recip                ! reciprical
-    logical,save :: first_call = .true.  ! first call work
-    type(seq_infodata_type),pointer :: infodata             ! CESM information from the driver
-    type(mct_gGrid),        pointer :: dom_l                ! Land model domain data
-    type(bounds_type)               :: bounds               ! bounds
-    character(len=32)               :: rdate                ! date char string for restart file names
-    character(len=32), parameter    :: sub = "lnd_run_mct"
-    !---------------------------------------------------------------------------
-
-    ! Determine processor bounds
-
-    call get_proc_bounds(bounds)
-
-#if (defined _MEMTRACE)
-    if(masterproc) then
-       lbnum=1
-       call memmon_dump_fort('memmon.out','lnd_run_mct:start::',lbnum)
-    endif
-#endif
-
-    ! Reset shr logging to my log file
-    call shr_file_getLogUnit (shrlogunit)
-    call shr_file_getLogLevel(shrloglev)
-    call shr_file_setLogUnit (iulog)
-
-    ! Determine time of next atmospheric shortwave calculation
-    call seq_cdata_setptrs(cdata_l, infodata=infodata, dom=dom_l)
-    call seq_timemgr_EClockGetData(EClock, &
-         curr_ymd=ymd, curr_tod=tod_sync,  &
-         curr_yr=yr_sync, curr_mon=mon_sync, curr_day=day_sync)
-    call seq_infodata_GetData(infodata, nextsw_cday=nextsw_cday )
-
-    dtime = get_step_size()
-
-    ! Handle pause/resume signals from coupler
-    call lnd_handle_resume( cdata_l )
-
-    write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync,mon_sync,day_sync,tod_sync
-    nlend_sync = seq_timemgr_StopAlarmIsOn( EClock )
-    rstwr_sync = seq_timemgr_RestartAlarmIsOn( EClock )
-
-    ! Determine if we're running with a prognostic ROF model, and if we're running with a
-    ! non-stub GLC model. These won't change throughout the run, but we can't count on
-    ! their being set in initialization, so need to get them in the run method.
-
-    call seq_infodata_GetData( infodata, &
-         rof_prognostic=rof_prognostic, &
-         glc_present=glc_present)
-
-    ! Map MCT to land data type
-    ! Perform downscaling if appropriate
-
-
-    ! Map to clm (only when state and/or fluxes need to be updated)
-
-    call t_startf ('lc_lnd_import')
-    call lnd_import( bounds, &
-         x2l = x2l_l%rattr, &
-         glc_present = glc_present, &
-         atm2lnd_inst = atm2lnd_inst, &
-         glc2lnd_inst = glc2lnd_inst, &
-         wateratm2lndbulk_inst = water_inst%wateratm2lndbulk_inst)
-    call t_stopf ('lc_lnd_import')
-
-    ! Use infodata to set orbital values if updated mid-run
-
-    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
-         orb_lambm0=lambm0, orb_obliqr=obliqr )
-
-    ! Loop over time steps in coupling interval
-
-    dosend = .false.
-    do while(.not. dosend)
-
-       ! Determine if dosend
-       ! When time is not updated at the beginning of the loop - then return only if
-       ! are in sync with clock before time is updated
-       !
-       ! NOTE(wjs, 2020-03-09) I think the do while (.not. dosend) loop only is important
-       ! for the first time step (when we run 2 steps). After that, we now assume that we
-       ! run one time step per coupling interval (based on setting the model's dtime from
-       ! the driver). (According to Mariana Vertenstein, sub-cycling (running multiple
-       ! land model time steps per coupling interval) used to be supported, but hasn't
-       ! been fully supported for a long time.) We may want to rework this logic to make
-       ! this more explicit, or - ideally - get rid of this extra time step at the start
-       ! of the run, at which point I think we could do away with this looping entirely.
-
-       call get_curr_date( yr, mon, day, tod )
-       ymd = yr*10000 + mon*100 + day
-       tod = tod
-       dosend = (seq_timemgr_EClockDateInSync( EClock, ymd, tod))
-
-       ! Determine doalb based on nextsw_cday sent from atm model
-
-       nstep = get_nstep()
-       caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.)
-       if (nstep == 0) then
-          doalb = .false.
-       else if (nstep == 1) then
-          doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8)
-       else
-          doalb = (nextsw_cday >= -0.5_r8)
-       end if
-       call update_rad_dtime(doalb)
-
-       ! Determine if time to write restart and stop
-
-       rstwr = .false.
-       if (rstwr_sync .and. dosend) rstwr = .true.
-       nlend = .false.
-       if (nlend_sync .and. dosend) nlend = .true.
-
-       ! Run clm
-
-       call t_barrierf('sync_clm_run1', mpicom)
-       call t_startf ('clm_run')
-       call t_startf ('shr_orb_decl')
-       calday = get_curr_calday(reuse_day_365_for_day_366=.true.)
-       call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
-       call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
-       call t_stopf ('shr_orb_decl')
-       call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic)
-       call t_stopf ('clm_run')
-
-       ! Create l2x_l export state - add river runoff input to l2x_l if appropriate
-
-       call t_startf ('lc_lnd_export')
-       call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
-       call t_stopf ('lc_lnd_export')
-
-       ! Advance clm time step
-
-       call t_startf ('lc_clm2_adv_timestep')
-       call advance_timestep()
-       call t_stopf ('lc_clm2_adv_timestep')
-
-    end do
-
-    ! Check that internal clock is in sync with master clock
-
-    call get_curr_date( yr, mon, day, tod, offset=-dtime )
-    ymd = yr*10000 + mon*100 + day
-    tod = tod
-    if ( .not. seq_timemgr_EClockDateInSync( EClock, ymd, tod ) )then
-       call seq_timemgr_EclockGetData( EClock, curr_ymd=ymd_sync, curr_tod=tod_sync )
-       write(iulog,*)' clm ymd=',ymd     ,'  clm tod= ',tod
-       write(iulog,*)'sync ymd=',ymd_sync,' sync tod= ',tod_sync
-       call endrun( sub//":: CLM clock not in sync with Master Sync clock" )
-    end if
-
-    ! Reset shr logging to my original values
-
-    call shr_file_setLogUnit (shrlogunit)
-    call shr_file_setLogLevel(shrloglev)
-
-#if (defined _MEMTRACE)
-    if(masterproc) then
-       lbnum=1
-       call memmon_dump_fort('memmon.out','lnd_run_mct:end::',lbnum)
-       call memmon_reset_addr()
-    endif
-#endif
-
-    first_call  = .false.
-
-  end subroutine lnd_run_mct
-
-  !====================================================================================
-  subroutine lnd_final_mct( EClock, cdata_l, x2l_l, l2x_l)
-    !
-    ! !DESCRIPTION:
-    ! Finalize land surface model
-
-    use seq_cdata_mod   ,only : seq_cdata, seq_cdata_setptrs
-    use seq_timemgr_mod ,only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn
-    use seq_timemgr_mod ,only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync
-    use esmf
-    !
-    ! !ARGUMENTS:
-    type(ESMF_Clock) , intent(inout) :: EClock    ! Input synchronization clock from driver
-    type(seq_cdata)  , intent(inout) :: cdata_l   ! Input driver data for land model
-    type(mct_aVect)  , intent(inout) :: x2l_l     ! Import state to land model
-    type(mct_aVect)  , intent(inout) :: l2x_l     ! Export state from land model
-    !---------------------------------------------------------------------------
-
-    ! fill this in
-  end subroutine lnd_final_mct
-
-  !====================================================================================
-  subroutine lnd_domain_mct( bounds, lsize, gsMap_l, dom_l )
-    !
-    ! !DESCRIPTION:
-    ! Send the land model domain information to the coupler
-    !
-    ! !USES:
-    use clm_varcon  , only: re
-    use domainMod   , only: ldomain
-    use spmdMod     , only: iam
-    use mct_mod     , only: mct_gGrid_importIAttr
-    use mct_mod     , only: mct_gGrid_importRAttr, mct_gGrid_init, mct_gsMap_orderedPoints
-    use seq_flds_mod, only: seq_flds_dom_coord, seq_flds_dom_other
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in)  :: bounds  ! bounds
-    integer        , intent(in)    :: lsize   ! land model domain data size
-    type(mct_gsMap), intent(inout) :: gsMap_l ! Output land model MCT GS map
-    type(mct_ggrid), intent(out)   :: dom_l   ! Output domain information for land model
-    !
-    ! Local Variables
-    integer :: g,i,j              ! index
-    real(r8), pointer :: data(:)  ! temporary
-    integer , pointer :: idata(:) ! temporary
-    !---------------------------------------------------------------------------
-    !
-    ! Initialize mct domain type
-    ! lat/lon in degrees,  area in radians^2, mask is 1 (land), 0 (non-land)
-    ! Note that in addition land carries around landfrac for the purposes of domain checking
-    !
-    call mct_gGrid_init( GGrid=dom_l, CoordChars=trim(seq_flds_dom_coord), &
-       OtherChars=trim(seq_flds_dom_other), lsize=lsize )
-    !
-    ! Allocate memory
-    !
-    allocate(data(lsize))
-    !
-    ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT
-    !
-    call mct_gsMap_orderedPoints(gsMap_l, iam, idata)
-    call mct_gGrid_importIAttr(dom_l,'GlobGridNum',idata,lsize)
-    !
-    ! Determine domain (numbering scheme is: West to East and South to North to South pole)
-    ! Initialize attribute vector with special value
-    !
-    data(:) = -9999.0_R8
-    call mct_gGrid_importRAttr(dom_l,"lat"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_l,"lon"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_l,"area" ,data,lsize)
-    call mct_gGrid_importRAttr(dom_l,"aream",data,lsize)
-    data(:) = 0.0_R8
-    call mct_gGrid_importRAttr(dom_l,"mask" ,data,lsize)
-    !
-    ! Fill in correct values for domain components
-    ! Note aream will be filled in in the atm-lnd mapper
-    !
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%lonc(g)
-    end do
-    call mct_gGrid_importRattr(dom_l,"lon",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%latc(g)
-    end do
-    call mct_gGrid_importRattr(dom_l,"lat",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%area(g)/(re*re)
-    end do
-    call mct_gGrid_importRattr(dom_l,"area",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%mask(g), r8)
-    end do
-    call mct_gGrid_importRattr(dom_l,"mask",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%frac(g), r8)
-    end do
-    call mct_gGrid_importRattr(dom_l,"frac",data,lsize)
-
-    deallocate(data)
-    deallocate(idata)
-
-  end subroutine lnd_domain_mct
-
-  !====================================================================================
-  subroutine lnd_handle_resume( cdata_l )
-    !
-    ! !DESCRIPTION:
-    ! Handle resume signals for Data Assimilation (DA)
-    !
-    ! !USES:
-    use clm_time_manager , only : update_DA_nstep
-    use seq_cdata_mod    , only : seq_cdata, seq_cdata_setptrs
-    implicit none
-    ! !ARGUMENTS:
-    type(seq_cdata),            intent(inout) :: cdata_l          ! Input land-model driver data
-    ! !LOCAL VARIABLES:
-    logical :: resume_from_data_assim                      ! flag if we are resuming after data assimulation was done
-    !---------------------------------------------------------------------------
-
-    ! Check to see if restart was modified and we are resuming from data
-    ! assimilation
-    call seq_cdata_setptrs(cdata_l, post_assimilation=resume_from_data_assim)
-    if ( resume_from_data_assim ) call update_DA_nstep()
-
-  end subroutine lnd_handle_resume
-
-end module lnd_comp_mct
diff --git a/src/cpl/mct/lnd_import_export.F90 b/src/cpl/mct/lnd_import_export.F90
deleted file mode 100644
index 537abd49d9..0000000000
--- a/src/cpl/mct/lnd_import_export.F90
+++ /dev/null
@@ -1,354 +0,0 @@
-module lnd_import_export
-
-  use shr_kind_mod , only: r8 => shr_kind_r8, cl=>shr_kind_cl
-  use abortutils   , only: endrun
-  use decompmod    , only: bounds_type, subgrid_level_gridcell
-  use lnd2atmType  , only: lnd2atm_type
-  use lnd2glcMod   , only: lnd2glc_type
-  use atm2lndType  , only: atm2lnd_type
-  use glc2lndMod   , only: glc2lnd_type 
-  use Waterlnd2atmBulkType , only: waterlnd2atmbulk_type
-  use Wateratm2lndBulkType , only: wateratm2lndbulk_type
-  use clm_cpl_indices
-  use GridcellType      , only : grc
-  !
-  implicit none
-  !===============================================================================
-
-contains
-
-  !===============================================================================
-  subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst, wateratm2lndbulk_inst)
-
-    !---------------------------------------------------------------------------
-    ! !DESCRIPTION:
-    ! Convert the input data from the coupler to the land model 
-    !
-    ! !USES:
-    use seq_flds_mod    , only: seq_flds_x2l_fields
-    use clm_varctl      , only: co2_type, co2_ppmv, iulog, use_c13
-    use clm_varctl      , only: ndep_from_cpl 
-    use clm_varcon      , only: c13ratio
-    use domainMod       , only: ldomain
-    use lnd_import_export_utils, only : derive_quantities, check_for_errors, check_for_nans
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)  , intent(in)    :: bounds   ! bounds
-    real(r8)           , intent(in)    :: x2l(:,:) ! driver import state to land model
-    logical            , intent(in)    :: glc_present       ! .true. => running with a non-stub GLC model
-    type(atm2lnd_type) , intent(inout) :: atm2lnd_inst      ! clm internal input data type
-    type(glc2lnd_type) , intent(inout) :: glc2lnd_inst      ! clm internal input data type
-    type(wateratm2lndbulk_type), intent(inout) :: wateratm2lndbulk_inst   ! clm internal input data type
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begg, endg           ! bounds
-    integer  :: g,i,k,nstep,ier      ! indices, number of steps, and error code
-    real(r8) :: qsat_kg_kg           ! saturation specific humidity (kg/kg)
-    real(r8) :: forc_pbot            ! atmospheric pressure (Pa)
-    real(r8) :: forc_rainc(bounds%begg:bounds%endg)  ! rainxy Atm flux mm/s
-    real(r8) :: forc_rainl(bounds%begg:bounds%endg)  ! rainxy Atm flux mm/s
-    real(r8) :: forc_snowc(bounds%begg:bounds%endg)  ! snowfxy Atm flux  mm/s
-    real(r8) :: forc_snowl(bounds%begg:bounds%endg)  ! snowfxl Atm flux  mm/s
-    real(r8) :: co2_ppmv_diag        ! temporary
-    real(r8) :: co2_ppmv_prog        ! temporary
-    real(r8) :: co2_ppmv_val         ! temporary
-    integer  :: co2_type_idx         ! integer flag for co2_type options
-    character(len=32) :: fname       ! name of field that is NaN
-    character(len=32), parameter :: sub = 'lnd_import'
-
-    !---------------------------------------------------------------------------
-
-    ! Set bounds
-    begg = bounds%begg; endg = bounds%endg
-
-    co2_type_idx = 0
-    if (co2_type == 'prognostic') then
-       co2_type_idx = 1
-    else if (co2_type == 'diagnostic') then
-       co2_type_idx = 2
-    end if
-    if (co2_type == 'prognostic' .and. index_x2l_Sa_co2prog == 0) then
-       call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2prog for co2_type equal to prognostic' )
-    else if (co2_type == 'diagnostic' .and. index_x2l_Sa_co2diag == 0) then
-       call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2diag for co2_type equal to diagnostic' )
-    end if
-
-    ! Note that the precipitation fluxes received  from the coupler
-    ! are in units of kg/s/m^2. To convert these precipitation rates
-    ! in units of mm/sec, one must divide by 1000 kg/m^3 and multiply
-    ! by 1000 mm/m resulting in an overall factor of unity.
-    ! Below the units are therefore given in mm/s.
-
-    do g = begg,endg
-       i = 1 + (g - begg)
-
-       ! Determine flooding input, sign convention is positive downward and
-       ! hierarchy is atm/glc/lnd/rof/ice/ocn.  so water sent from rof to land is negative,
-       ! change the sign to indicate addition of water to system.
-
-       wateratm2lndbulk_inst%forc_flood_grc(g)   = -x2l(index_x2l_Flrr_flood,i)  
-
-       wateratm2lndbulk_inst%volr_grc(g)   = x2l(index_x2l_Flrr_volr,i) * (ldomain%area(g) * 1.e6_r8)
-       wateratm2lndbulk_inst%volrmch_grc(g)= x2l(index_x2l_Flrr_volrmch,i) * (ldomain%area(g) * 1.e6_r8)
-
-       ! Determine required receive fields
-
-       atm2lnd_inst%forc_hgt_grc(g)                  = x2l(index_x2l_Sa_z,i)         ! zgcmxy  Atm state m
-       atm2lnd_inst%forc_topo_grc(g)                 = x2l(index_x2l_Sa_topo,i)      ! Atm surface height (m)
-       atm2lnd_inst%forc_u_grc(g)                    = x2l(index_x2l_Sa_u,i)         ! forc_uxy  Atm state m/s
-       atm2lnd_inst%forc_v_grc(g)                    = x2l(index_x2l_Sa_v,i)         ! forc_vxy  Atm state m/s
-       atm2lnd_inst%forc_solad_not_downscaled_grc(g,2) = x2l(index_x2l_Faxa_swndr,i)   ! forc_sollxy  Atm flux  W/m^2
-       atm2lnd_inst%forc_solad_not_downscaled_grc(g,1) = x2l(index_x2l_Faxa_swvdr,i)   ! forc_solsxy  Atm flux  W/m^2
-       atm2lnd_inst%forc_solai_grc(g,2)              = x2l(index_x2l_Faxa_swndf,i)   ! forc_solldxy Atm flux  W/m^2
-       atm2lnd_inst%forc_solai_grc(g,1)              = x2l(index_x2l_Faxa_swvdf,i)   ! forc_solsdxy Atm flux  W/m^2
-
-       atm2lnd_inst%forc_th_not_downscaled_grc(g)    = x2l(index_x2l_Sa_ptem,i)      ! forc_thxy Atm state K
-       wateratm2lndbulk_inst%forc_q_not_downscaled_grc(g)     = x2l(index_x2l_Sa_shum,i)      ! forc_qxy  Atm state kg/kg
-       atm2lnd_inst%forc_pbot_not_downscaled_grc(g)  = x2l(index_x2l_Sa_pbot,i)      ! ptcmxy  Atm state Pa
-       atm2lnd_inst%forc_t_not_downscaled_grc(g)     = x2l(index_x2l_Sa_tbot,i)      ! forc_txy  Atm state K
-       atm2lnd_inst%forc_lwrad_not_downscaled_grc(g) = x2l(index_x2l_Faxa_lwdn,i)    ! flwdsxy Atm flux  W/m^2
-
-       forc_rainc(g)                                 = x2l(index_x2l_Faxa_rainc,i)   ! mm/s
-       forc_rainl(g)                                 = x2l(index_x2l_Faxa_rainl,i)   ! mm/s
-       forc_snowc(g)                                 = x2l(index_x2l_Faxa_snowc,i)   ! mm/s
-       forc_snowl(g)                                 = x2l(index_x2l_Faxa_snowl,i)   ! mm/s
-
-       ! atmosphere coupling, for prognostic/prescribed aerosols
-       atm2lnd_inst%forc_aer_grc(g,1)                = x2l(index_x2l_Faxa_bcphidry,i)
-       atm2lnd_inst%forc_aer_grc(g,2)                = x2l(index_x2l_Faxa_bcphodry,i)
-       atm2lnd_inst%forc_aer_grc(g,3)                = x2l(index_x2l_Faxa_bcphiwet,i)
-       atm2lnd_inst%forc_aer_grc(g,4)                = x2l(index_x2l_Faxa_ocphidry,i)
-       atm2lnd_inst%forc_aer_grc(g,5)                = x2l(index_x2l_Faxa_ocphodry,i)
-       atm2lnd_inst%forc_aer_grc(g,6)                = x2l(index_x2l_Faxa_ocphiwet,i)
-       atm2lnd_inst%forc_aer_grc(g,7)                = x2l(index_x2l_Faxa_dstwet1,i)
-       atm2lnd_inst%forc_aer_grc(g,8)                = x2l(index_x2l_Faxa_dstdry1,i)
-       atm2lnd_inst%forc_aer_grc(g,9)                = x2l(index_x2l_Faxa_dstwet2,i)
-       atm2lnd_inst%forc_aer_grc(g,10)               = x2l(index_x2l_Faxa_dstdry2,i)
-       atm2lnd_inst%forc_aer_grc(g,11)               = x2l(index_x2l_Faxa_dstwet3,i)
-       atm2lnd_inst%forc_aer_grc(g,12)               = x2l(index_x2l_Faxa_dstdry3,i)
-       atm2lnd_inst%forc_aer_grc(g,13)               = x2l(index_x2l_Faxa_dstwet4,i)
-       atm2lnd_inst%forc_aer_grc(g,14)               = x2l(index_x2l_Faxa_dstdry4,i)
-
-       if (index_x2l_Sa_methane /= 0) then
-          atm2lnd_inst%forc_pch4_grc(g) = x2l(index_x2l_Sa_methane,i)
-       endif
-
-       !--------------------------
-       ! Check for nans from coupler
-       !--------------------------
-
-       call check_for_nans(x2l(:,i), fname, begg, "x2l")
-
-    end do
-
-    !--------------------------
-    ! Derived quantities for required fields
-    ! and corresponding error checks
-    !--------------------------
-
-    call derive_quantities(bounds, atm2lnd_inst, wateratm2lndbulk_inst, &
-       forc_rainc, forc_rainl, forc_snowc, forc_snowl)
-
-    call check_for_errors(bounds, atm2lnd_inst, wateratm2lndbulk_inst)
-
-    ! Determine derived quantities for optional fields
-    ! Note that the following does unit conversions from ppmv to partial pressures (Pa)
-    ! Note that forc_pbot is in Pa
-
-    do g = begg,endg
-       i = 1 + (g - begg)
-
-       forc_pbot = atm2lnd_inst%forc_pbot_not_downscaled_grc(g)
-
-       ! Determine optional receive fields
-       if (index_x2l_Sa_co2prog /= 0) then
-          co2_ppmv_prog = x2l(index_x2l_Sa_co2prog,i)   ! co2 atm state prognostic
-       else
-          co2_ppmv_prog = co2_ppmv
-       end if
-       if (index_x2l_Sa_co2diag /= 0) then
-          co2_ppmv_diag = x2l(index_x2l_Sa_co2diag,i)   ! co2 atm state diagnostic
-       else
-          co2_ppmv_diag = co2_ppmv
-       end if
-
-       if (co2_type_idx == 1) then
-          co2_ppmv_val = co2_ppmv_prog
-       else if (co2_type_idx == 2) then
-          co2_ppmv_val = co2_ppmv_diag 
-       else
-          co2_ppmv_val = co2_ppmv
-       end if
-       if ( (co2_ppmv_val < 10.0_r8) .or. (co2_ppmv_val > 15000.0_r8) )then
-          call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, &
-               msg = sub//' ERROR: CO2 is outside of an expected range' )
-       end if
-       atm2lnd_inst%forc_pco2_grc(g) = co2_ppmv_val * 1.e-6_r8 * forc_pbot 
-       if (use_c13) then
-          atm2lnd_inst%forc_pc13o2_grc(g) = co2_ppmv_val * c13ratio * 1.e-6_r8 * forc_pbot
-       end if
-
-       if (ndep_from_cpl) then
-          ! The coupler is sending ndep in units if kgN/m2/s - and clm uses units of gN/m2/sec - so the
-          ! following conversion needs to happen
-          atm2lnd_inst%forc_ndep_grc(g) = (x2l(index_x2l_Faxa_nhx, i) + x2l(index_x2l_faxa_noy, i))*1000._r8
-       end if
-
-    end do
-
-    call glc2lnd_inst%set_glc2lnd_fields_mct( &
-         bounds = bounds, &
-         glc_present = glc_present, &
-         ! NOTE(wjs, 2017-12-13) the x2l argument doesn't have the typical bounds
-         ! subsetting (bounds%begg:bounds%endg). This mirrors the lack of these bounds in
-         ! the call to lnd_import from lnd_run_mct. This is okay as long as this code is
-         ! outside a clump loop.
-         x2l = x2l, &
-         index_x2l_Sg_ice_covered = index_x2l_Sg_ice_covered, &
-         index_x2l_Sg_topo = index_x2l_Sg_topo, &
-         index_x2l_Flgg_hflx = index_x2l_Flgg_hflx, &
-         index_x2l_Sg_icemask = index_x2l_Sg_icemask, &
-         index_x2l_Sg_icemask_coupled_fluxes = index_x2l_Sg_icemask_coupled_fluxes)
-
-  end subroutine lnd_import
-
-  !===============================================================================
-
-  subroutine lnd_export( bounds, waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x)
-
-    !---------------------------------------------------------------------------
-    ! !DESCRIPTION:
-    ! Convert the data to be sent from the clm model to the coupler 
-    ! 
-    ! !USES:
-    use shr_kind_mod       , only : r8 => shr_kind_r8
-    use seq_flds_mod       , only : seq_flds_l2x_fields
-    use clm_varctl         , only : iulog
-    use shr_drydep_mod     , only : n_drydep
-    use shr_megan_mod      , only : shr_megan_mechcomps_n
-    use shr_fire_emis_mod  , only : shr_fire_emis_mechcomps_n
-    use lnd_import_export_utils, only : check_for_nans
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type) , intent(in)    :: bounds  ! bounds
-    type(lnd2atm_type), intent(inout) :: lnd2atm_inst ! clm land to atmosphere exchange data type
-    type(lnd2glc_type), intent(inout) :: lnd2glc_inst ! clm land to atmosphere exchange data type
-    type(waterlnd2atmbulk_type), intent(in) :: waterlnd2atmbulk_inst
-    real(r8)          , intent(out)   :: l2x(:,:)! land to coupler export state on land grid
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begg, endg  ! bounds
-    integer  :: g,i,k ! indices
-    integer  :: ier   ! error status
-    integer  :: nstep ! time step index
-    integer  :: dtime ! time step   
-    integer  :: num   ! counter
-    character(len=32) :: fname       ! name of field that is NaN
-    character(len=32), parameter :: sub = 'lnd_export'
-    !---------------------------------------------------------------------------
-
-    ! Set bounds
-    begg = bounds%begg; endg = bounds%endg
-
-    ! cesm sign convention is that fluxes are positive downward
-
-    l2x(:,:) = 0.0_r8
-
-    do g = begg,endg
-       i = 1 + (g-begg)
-       l2x(index_l2x_Sl_t,i)        =  lnd2atm_inst%t_rad_grc(g)
-       l2x(index_l2x_Sl_snowh,i)    =  waterlnd2atmbulk_inst%h2osno_grc(g)
-       l2x(index_l2x_Sl_avsdr,i)    =  lnd2atm_inst%albd_grc(g,1)
-       l2x(index_l2x_Sl_anidr,i)    =  lnd2atm_inst%albd_grc(g,2)
-       l2x(index_l2x_Sl_avsdf,i)    =  lnd2atm_inst%albi_grc(g,1)
-       l2x(index_l2x_Sl_anidf,i)    =  lnd2atm_inst%albi_grc(g,2)
-       l2x(index_l2x_Sl_tref,i)     =  lnd2atm_inst%t_ref2m_grc(g)
-       l2x(index_l2x_Sl_qref,i)     =  waterlnd2atmbulk_inst%q_ref2m_grc(g)
-       l2x(index_l2x_Sl_u10,i)      =  lnd2atm_inst%u_ref10m_grc(g)
-       l2x(index_l2x_Fall_taux,i)   = -lnd2atm_inst%taux_grc(g)
-       l2x(index_l2x_Fall_tauy,i)   = -lnd2atm_inst%tauy_grc(g)
-       l2x(index_l2x_Fall_lat,i)    = -lnd2atm_inst%eflx_lh_tot_grc(g)
-       l2x(index_l2x_Fall_sen,i)    = -lnd2atm_inst%eflx_sh_tot_grc(g)
-       l2x(index_l2x_Fall_lwup,i)   = -lnd2atm_inst%eflx_lwrad_out_grc(g)
-       l2x(index_l2x_Fall_evap,i)   = -waterlnd2atmbulk_inst%qflx_evap_tot_grc(g)
-       l2x(index_l2x_Fall_swnet,i)  =  lnd2atm_inst%fsa_grc(g)
-       if (index_l2x_Fall_fco2_lnd /= 0) then
-          l2x(index_l2x_Fall_fco2_lnd,i) = -lnd2atm_inst%net_carbon_exchange_grc(g)  
-       end if
-
-       ! Additional fields for DUST, PROGSSLT, dry-deposition and VOC
-       ! These are now standard fields, but the check on the index makes sure the driver handles them
-       if (index_l2x_Sl_ram1      /= 0 )  l2x(index_l2x_Sl_ram1,i)     =  lnd2atm_inst%ram1_grc(g)
-       if (index_l2x_Sl_fv        /= 0 )  l2x(index_l2x_Sl_fv,i)       =  lnd2atm_inst%fv_grc(g)
-       if (index_l2x_Sl_soilw     /= 0 )  l2x(index_l2x_Sl_soilw,i)    =  waterlnd2atmbulk_inst%h2osoi_vol_grc(g,1)
-       if (index_l2x_Fall_flxdst1 /= 0 )  l2x(index_l2x_Fall_flxdst1,i)= -lnd2atm_inst%flxdst_grc(g,1)
-       if (index_l2x_Fall_flxdst2 /= 0 )  l2x(index_l2x_Fall_flxdst2,i)= -lnd2atm_inst%flxdst_grc(g,2)
-       if (index_l2x_Fall_flxdst3 /= 0 )  l2x(index_l2x_Fall_flxdst3,i)= -lnd2atm_inst%flxdst_grc(g,3)
-       if (index_l2x_Fall_flxdst4 /= 0 )  l2x(index_l2x_Fall_flxdst4,i)= -lnd2atm_inst%flxdst_grc(g,4)
-
-
-       ! for dry dep velocities
-       if (index_l2x_Sl_ddvel     /= 0 )  then
-          l2x(index_l2x_Sl_ddvel:index_l2x_Sl_ddvel+n_drydep-1,i) = &
-               lnd2atm_inst%ddvel_grc(g,:n_drydep)
-       end if
-
-       ! for MEGAN VOC emis fluxes
-       if (index_l2x_Fall_flxvoc  /= 0 ) then
-          l2x(index_l2x_Fall_flxvoc:index_l2x_Fall_flxvoc+shr_megan_mechcomps_n-1,i) = &
-               -lnd2atm_inst%flxvoc_grc(g,:shr_megan_mechcomps_n)
-       end if
-
-
-       ! for fire emis fluxes
-       if (index_l2x_Fall_flxfire  /= 0 ) then
-          l2x(index_l2x_Fall_flxfire:index_l2x_Fall_flxfire+shr_fire_emis_mechcomps_n-1,i) = &
-               -lnd2atm_inst%fireflx_grc(g,:shr_fire_emis_mechcomps_n)
-          l2x(index_l2x_Sl_ztopfire,i) = lnd2atm_inst%fireztop_grc(g)
-       end if
-
-       if (index_l2x_Fall_methane /= 0) then
-          l2x(index_l2x_Fall_methane,i) = -lnd2atm_inst%ch4_surf_flux_tot_grc(g)
-       endif
-
-       ! sign convention is positive downward with 
-       ! hierarchy of atm/glc/lnd/rof/ice/ocn.  
-       ! I.e. water sent from land to rof is positive
-
-       l2x(index_l2x_Flrl_rofsur,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsur_grc(g)
-
-       !  subsurface runoff is the sum of qflx_drain and qflx_perched_drain
-       l2x(index_l2x_Flrl_rofsub,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsub_grc(g) &
-            + waterlnd2atmbulk_inst%qflx_rofliq_drain_perched_grc(g)
-
-       !  qgwl sent individually to coupler
-       l2x(index_l2x_Flrl_rofgwl,i) = waterlnd2atmbulk_inst%qflx_rofliq_qgwl_grc(g)
-
-       ! ice  sent individually to coupler
-       l2x(index_l2x_Flrl_rofi,i) = waterlnd2atmbulk_inst%qflx_rofice_grc(g)
-
-       ! irrigation flux to be removed from main channel storage (negative)
-       l2x(index_l2x_Flrl_irrig,i) = - waterlnd2atmbulk_inst%qirrig_grc(g)
-
-       ! glc coupling
-       ! We could avoid setting these fields if glc_present is .false., if that would
-       ! help with performance. (The downside would be that we wouldn't have these fields
-       ! available for diagnostic purposes or to force a later T compset with dlnd.)
-       do num = 0,glc_nec
-          l2x(index_l2x_Sl_tsrf(num),i)   = lnd2glc_inst%tsrf_grc(g,num)
-          l2x(index_l2x_Sl_topo(num),i)   = lnd2glc_inst%topo_grc(g,num)
-          l2x(index_l2x_Flgl_qice(num),i) = lnd2glc_inst%qice_grc(g,num)
-       end do
-
-       !--------------------------
-       ! Check for nans to coupler
-       !--------------------------
-
-       call check_for_nans(l2x(:,i), fname, begg, "l2x")
-
-    end do
-
-  end subroutine lnd_export
-
-end module lnd_import_export
diff --git a/src/cpl/mct/lnd_set_decomp_and_domain.F90 b/src/cpl/mct/lnd_set_decomp_and_domain.F90
deleted file mode 100644
index 0a37554313..0000000000
--- a/src/cpl/mct/lnd_set_decomp_and_domain.F90
+++ /dev/null
@@ -1,352 +0,0 @@
-module lnd_set_decomp_and_domain
-
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use spmdMod      , only : masterproc
-  use clm_varctl   , only : iulog
-  use mct_mod      , only : mct_gsMap
-
-  implicit none
-  private ! except
-
-  ! public member routines
-  public :: lnd_set_decomp_and_domain_from_surfrd
-
-  ! private member routines
-  private :: surfrd_get_globmask  ! Reads global land mask (needed for setting domain decomp)
-  private :: surfrd_get_grid      ! Read grid/ladnfrac data into domain (after domain decomp)
-
-  ! translation between local and global indices at gridcell level
-  type(mct_gsmap), pointer, public :: gsmap_global           
-
-  ! translation between local and global indices at gridcell level for multiple levels
-  ! needed for 3d soil moisture stream
-  type(mct_gsmap), target , public :: gsMap_lnd2Dsoi_gdc2glo 
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-!===============================================================================
-contains
-!===============================================================================
-
-  subroutine lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj)
-
-    ! Initialize ldomain data types
-
-    use clm_varpar    , only: nlevsoi
-    use clm_varctl    , only: fatmlndfrc, use_soil_moisture_streams
-    use decompInitMod , only: decompInit_lnd
-    use decompMod     , only: bounds_type, get_proc_bounds
-    use domainMod     , only: ldomain, domain_check
-
-    ! input/output variables
-    logical, intent(out) :: noland
-    integer, intent(out) :: ni, nj ! global grid sizes
-
-    ! local variables
-    integer ,pointer  :: amask(:)   ! global land mask
-    integer           :: begg, endg ! processor bounds
-    type(bounds_type) :: bounds     ! bounds
-    character(len=32) :: subname = 'lnd_set_decomp_and_domain_from_surfrd'
-    !-----------------------------------------------------------------------
-
-    ! Read in global land grid and land mask (amask)- needed to set decomposition
-    ! global memory for amask is allocate in surfrd_get_glomask - must be deallocated below
-    if (masterproc) then
-       write(iulog,*) 'Attempting to read global land mask from ',trim(fatmlndfrc)
-    endif
-
-    ! Get global mask, ni and nj
-    call surfrd_get_globmask(filename=fatmlndfrc, mask=amask, ni=ni, nj=nj)
-
-    ! Exit early if no valid land points
-    if ( all(amask == 0) )then
-       if (masterproc) write(iulog,*) trim(subname)//': no valid land points do NOT run clm'
-       noland = .true.
-       return
-    else
-       noland = .false.
-    end if
-
-    ! Determine ctsm gridcell decomposition and processor bounds for gridcells
-    call decompInit_lnd(ni, nj, amask)
-    deallocate(amask)
-    if (use_soil_moisture_streams) call decompInit_lnd3D(ni, nj, nlevsoi)
-
-    ! Initialize bounds for just gridcells
-    ! Remaining bounds (landunits, columns, patches) will be determined
-    ! after the call to decompInit_glcp - so get_proc_bounds is called
-    ! twice and the gridcell information is just filled in twice
-    call get_proc_bounds(bounds)
-
-    ! Get grid cell bounds values
-    begg = bounds%begg
-    endg = bounds%endg
-
-    ! Initialize ldomain data type
-    if (masterproc) then
-       write(iulog,*) 'Attempting to read ldomain from ',trim(fatmlndfrc)
-    endif
-    call surfrd_get_grid(begg, endg, ldomain, fatmlndfrc)
-    if (masterproc) then
-       call domain_check(ldomain)
-    endif
-    ldomain%mask = 1  !!! TODO - is this needed?
-
-  end subroutine lnd_set_decomp_and_domain_from_surfrd
-
-  !-----------------------------------------------------------------------
-  subroutine surfrd_get_globmask(filename, mask, ni, nj)
-
-    ! Read the surface dataset grid related information
-    ! This is used to set the domain decomposition - so global data is read here
-
-    use fileutils  , only : getfil
-    use ncdio_pio  , only : ncd_io, ncd_pio_openfile, ncd_pio_closefile, ncd_inqfdims, file_desc_t
-    use abortutils , only : endrun
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-
-    ! input/output variables
-    character(len=*), intent(in)    :: filename  ! grid filename
-    integer         , pointer       :: mask(:)   ! grid mask
-    integer         , intent(out)   :: ni, nj    ! global grid sizes
-
-    ! local variables
-    logical               :: isgrid2d
-    integer               :: dimid,varid ! netCDF id's
-    integer               :: ns          ! size of grid on file
-    integer               :: n,i,j       ! index
-    integer               :: ier         ! error status
-    type(file_desc_t)     :: ncid        ! netcdf id
-    character(len=256)    :: locfn       ! local file name
-    logical               :: readvar     ! read variable in or not
-    integer , allocatable :: idata2d(:,:)
-    character(len=32) :: subname = 'surfrd_get_globmask' ! subroutine name
-    !-----------------------------------------------------------------------
-
-    if (filename == ' ') then
-       mask(:) = 1
-    else
-       ! Check if file exists
-       if (masterproc) then
-          if (filename == ' ') then
-             write(iulog,*) trim(subname),' ERROR: filename must be specified '
-             call endrun(msg=errMsg(sourcefile, __LINE__))
-          endif
-       end if
-
-       ! Open file
-       call getfil( filename, locfn, 0 )
-       call ncd_pio_openfile (ncid, trim(locfn), 0)
-
-       ! Determine dimensions and if grid file is 2d or 1d
-       call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
-       if (masterproc) then
-          write(iulog,*)'lat/lon grid flag (isgrid2d) is ',isgrid2d
-       end if
-       allocate(mask(ns))
-       mask(:) = 1
-       if (isgrid2d) then
-          ! Grid is 2d
-          allocate(idata2d(ni,nj))
-          idata2d(:,:) = 1
-          call ncd_io(ncid=ncid, varname='LANDMASK', data=idata2d, flag='read', readvar=readvar)
-          if (.not. readvar) then
-             call ncd_io(ncid=ncid, varname='mask', data=idata2d, flag='read', readvar=readvar)
-          end if
-          if (readvar) then
-             do j = 1,nj
-                do i = 1,ni
-                   n = (j-1)*ni + i
-                   mask(n) = idata2d(i,j)
-                enddo
-             enddo
-          end if
-          deallocate(idata2d)
-       else
-          ! Grid is not 2d
-          call ncd_io(ncid=ncid, varname='LANDMASK', data=mask, flag='read', readvar=readvar)
-          if (.not. readvar) then
-             call ncd_io(ncid=ncid, varname='mask', data=mask, flag='read', readvar=readvar)
-          end if
-       end if
-       if (.not. readvar) call endrun( msg=' ERROR: landmask not on fatmlndfrc file'//errMsg(sourcefile, __LINE__))
-
-       ! Close file
-       call ncd_pio_closefile(ncid)
-    end if
-
-  end subroutine surfrd_get_globmask
-
-  !-----------------------------------------------------------------------
-  subroutine surfrd_get_grid(begg, endg, ldomain, filename)
-
-    ! Read the surface dataset grid related information:
-    ! This is called after the domain decomposition has been created
-    ! - real latitude  of grid cell (degrees)
-    ! - real longitude of grid cell (degrees)
-
-    use clm_varcon   , only : spval, re, grlnd
-    use domainMod    , only : domain_type, lon1d, lat1d, domain_init
-    use fileutils    , only : getfil
-    use abortutils   , only : endrun
-    use shr_log_mod  , only : errMsg => shr_log_errMsg
-    use ncdio_pio    , only : file_desc_t, ncd_pio_openfile, ncd_pio_closefile
-    use ncdio_pio    , only : ncd_io, check_var, ncd_inqfdims, check_dim_size
-    use pio
-
-    ! input/output variables
-    integer                    , intent(in)    :: begg, endg
-    type(domain_type)          , intent(inout) :: ldomain     ! domain to init
-    character(len=*)           , intent(in)    :: filename    ! grid filename
-
-    ! local variables
-    type(file_desc_t)     :: ncid               ! netcdf id
-    integer               :: beg                ! local beg index
-    integer               :: end                ! local end index
-    integer               :: ni,nj,ns           ! size of grid on file
-    logical               :: readvar            ! true => variable is on input file
-    logical               :: isgrid2d           ! true => file is 2d lat/lon
-    logical               :: istype_domain      ! true => input file is of type domain
-    real(r8), allocatable :: rdata2d(:,:)       ! temporary
-    character(len=16)     :: vname              ! temporary
-    character(len=256)    :: locfn              ! local file name
-    integer               :: n                  ! indices
-    character(len=32) :: subname = 'surfrd_get_grid'     ! subroutine name
-    !-----------------------------------------------------------------------
-
-    if (masterproc) then
-       if (filename == ' ') then
-          write(iulog,*) trim(subname),' ERROR: filename must be specified '
-          call endrun(msg=errMsg(sourcefile, __LINE__))
-       endif
-    end if
-
-    call getfil( filename, locfn, 0 )
-    call ncd_pio_openfile (ncid, trim(locfn), 0)
-
-    ! Determine dimensions
-    call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
-
-    ! Determine isgrid2d flag for domain
-    call domain_init(ldomain, isgrid2d=isgrid2d, ni=ni, nj=nj, nbeg=begg, nend=endg)
-
-    ! Determine type of file - old style grid file or new style domain file
-    call check_var(ncid=ncid, varname='xc', readvar=readvar)
-    if (readvar)then
-        istype_domain = .true.
-    else
-        istype_domain = .false.
-    end if
-
-    ! Read in area, lon, lat
-    if (istype_domain) then
-       call ncd_io(ncid=ncid, varname= 'area', flag='read', data=ldomain%area, &
-            dim1name=grlnd, readvar=readvar)
-       ! convert from radians**2 to km**2
-       ldomain%area = ldomain%area * (re**2)
-       if (.not. readvar) call endrun( msg=' ERROR: area NOT on file'//errMsg(sourcefile, __LINE__))
-       call ncd_io(ncid=ncid, varname= 'xc', flag='read', data=ldomain%lonc, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) call endrun( msg=' ERROR: xc NOT on file'//errMsg(sourcefile, __LINE__))
-       call ncd_io(ncid=ncid, varname= 'yc', flag='read', data=ldomain%latc, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) call endrun( msg=' ERROR: yc NOT on file'//errMsg(sourcefile, __LINE__))
-    else
-       call endrun( msg=" ERROR: can no longer read non domain files" )
-    end if
-
-    if (isgrid2d) then
-       allocate(rdata2d(ni,nj), lon1d(ni), lat1d(nj))
-       if (istype_domain) vname = 'xc'
-       call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar)
-       lon1d(:) = rdata2d(:,1)
-       if (istype_domain) vname = 'yc'
-       call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar)
-       lat1d(:) = rdata2d(1,:)
-       deallocate(rdata2d)
-    end if
-
-    ! Check lat limited to -90,90
-    if (minval(ldomain%latc) < -90.0_r8 .or. &
-        maxval(ldomain%latc) >  90.0_r8) then
-       write(iulog,*) trim(subname),' WARNING: lat/lon min/max is ', &
-            minval(ldomain%latc),maxval(ldomain%latc)
-    endif
-    if ( any(ldomain%lonc < 0.0_r8) )then
-       call endrun( msg=' ERROR: lonc is negative (see https://github.com/ESCOMP/ctsm/issues/507)' &
-            //errMsg(sourcefile, __LINE__))
-    endif
-    call ncd_io(ncid=ncid, varname='mask', flag='read', data=ldomain%mask, &
-         dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun( msg=' ERROR: LANDMASK NOT on fracdata file'//errMsg(sourcefile, __LINE__))
-    end if
-    call ncd_io(ncid=ncid, varname='frac', flag='read', data=ldomain%frac, &
-         dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun( msg=' ERROR: LANDFRAC NOT on fracdata file'//errMsg(sourcefile, __LINE__))
-    end if
-
-    call ncd_pio_closefile(ncid)
-
-  end subroutine surfrd_get_grid
-
-  !------------------------------------------------------------------------------
-  subroutine decompInit_lnd3D(lni,lnj,lnk)
-    !
-    ! !DESCRIPTION:
-    !  Create a 3D decomposition gsmap for the global 2D grid with soil levels
-    !  as the 3rd dimesnion.
-    !
-    ! !USES:
-    use decompMod, only : gindex_global, bounds_type, get_proc_bounds
-    use spmdMod  , only : comp_id, mpicom
-    use mct_mod  , only : mct_gsmap_init 
-    !
-    ! !ARGUMENTS:
-    integer , intent(in) :: lni,lnj,lnk   ! domain global size
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: m,n,k                 ! indices
-    integer           :: begg,endg,lsize,gsize ! used for gsmap init
-    integer           :: begg3d,endg3d
-    integer, pointer  :: gindex(:)             ! global index for gsmap init
-    type(bounds_type) :: bounds
-    !------------------------------------------------------------------------------
-
-    ! Initialize gsmap_lnd2dsoi_gdc2glo
-    call get_proc_bounds(bounds)
-    begg = bounds%begg; endg=bounds%endg
-
-    begg3d = (begg-1)*lnk + 1
-    endg3d = endg*lnk
-    lsize = (endg3d - begg3d + 1 )
-    allocate(gindex(begg3d:endg3d))
-    do k = 1, lnk
-       do n = begg,endg
-          m = (begg-1)*lnk + (k-1)*(endg-begg+1) + (n-begg+1)
-          gindex(m) = gindex_global(n-begg+1) + (k-1)*(lni*lnj)
-       enddo
-    enddo
-    gsize = lni * lnj * lnk
-    call mct_gsMap_init(gsMap_lnd2Dsoi_gdc2glo, gindex, mpicom, comp_id, lsize, gsize)
-
-    ! Diagnostic output
-
-    if (masterproc) then
-       write(iulog,*)' 3D GSMap'
-       write(iulog,*)'   longitude points               = ',lni
-       write(iulog,*)'   latitude points                = ',lnj
-       write(iulog,*)'   soil levels                    = ',lnk
-       write(iulog,*)'   gsize                          = ',gsize
-       write(iulog,*)'   lsize                          = ',lsize
-       write(iulog,*)'   bounds(gindex)                 = ',size(gindex)
-       write(iulog,*)
-    end if
-
-    deallocate(gindex)
-
-  end subroutine decompInit_lnd3D
-
-end module lnd_set_decomp_and_domain
diff --git a/src/cpl/mct/ndepStreamMod.F90 b/src/cpl/mct/ndepStreamMod.F90
deleted file mode 100644
index d26ff7c95e..0000000000
--- a/src/cpl/mct/ndepStreamMod.F90
+++ /dev/null
@@ -1,376 +0,0 @@
-module ndepStreamMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Contains methods for reading in nitrogen deposition data file
-  ! Also includes functions for dynamic ndep file handling and
-  ! interpolation.
-  !
-  ! !USES
-  use shr_kind_mod, only: r8 => shr_kind_r8, CL => shr_kind_cl
-  use shr_strdata_mod, only: shr_strdata_type, shr_strdata_create
-  use shr_strdata_mod, only: shr_strdata_print, shr_strdata_advance
-  use mct_mod     , only: mct_ggrid
-  use spmdMod     , only: mpicom, masterproc, comp_id, iam
-  use clm_varctl  , only: iulog, inst_name
-  use abortutils  , only: endrun
-  use decompMod   , only: bounds_type
-  use domainMod   , only: ldomain
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: ndep_init      ! position datasets for dynamic ndep
-  public :: ndep_interp    ! interpolates between two years of ndep file data
-  public :: clm_domain_mct ! Sets up MCT domain for this resolution
-
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: check_units   ! Check the units and make sure they can be used
-
-  ! ! PRIVATE TYPES
-  type(shr_strdata_type)  :: sdat           ! input data stream
-  integer :: stream_year_first_ndep         ! first year in stream to use
-  integer :: stream_year_last_ndep          ! last year in stream to use
-  integer :: model_year_align_ndep          ! align stream_year_firstndep with
-  logical :: divide_by_secs_per_yr = .true. ! divide by the number of seconds per year
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !==============================================================================
-
-contains
-
-  !==============================================================================
-
-  subroutine ndep_init(bounds, NLFilename)
-   !
-   ! Initialize data stream information.
-   !
-   ! Uses:
-   use shr_kind_mod     , only : CS => shr_kind_cs
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use shr_nl_mod       , only : shr_nl_find_group_name
-   use shr_log_mod      , only : errMsg => shr_log_errMsg
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global
-   !
-   ! arguments
-   implicit none
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! local variables
-   integer            :: nu_nml    ! unit for namelist file
-   integer            :: nml_error ! namelist i/o error flag
-   type(mct_ggrid)    :: dom_clm   ! domain information
-   character(len=CL)  :: stream_fldFileName_ndep
-   character(len=CL)  :: ndepmapalgo = 'bilinear'
-   character(len=CL)  :: ndep_tintalgo = 'linear'
-   character(len=CS)  :: ndep_taxmode = 'extend'
-   character(len=CL)  :: ndep_varlist = 'NDEP_year'
-   character(*), parameter :: shr_strdata_unset = 'NOT_SET'
-   character(*), parameter :: subName = "('ndepdyn_init')"
-   character(*), parameter :: F00 = "('(ndepdyn_init) ',4a)"
-   !-----------------------------------------------------------------------
-
-   namelist /ndepdyn_nml/          &
-        stream_year_first_ndep,    &
-        stream_year_last_ndep,     &
-        model_year_align_ndep,     &
-        ndepmapalgo, ndep_taxmode, &
-        ndep_varlist,              &
-        stream_fldFileName_ndep,   &
-        ndep_tintalgo
-
-   ! Default values for namelist
-    stream_year_first_ndep  = 1                ! first year in stream to use
-    stream_year_last_ndep   = 1                ! last  year in stream to use
-    model_year_align_ndep   = 1                ! align stream_year_first_ndep with this model year
-    stream_fldFileName_ndep = ' '
-
-   ! Read ndepdyn_nml namelist
-   if (masterproc) then
-      open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call shr_nl_find_group_name(nu_nml, 'ndepdyn_nml', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=ndepdyn_nml,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg=' ERROR reading ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      else
-         call endrun(msg=' ERROR finding ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__))
-      end if
-      close(nu_nml)
-   endif
-
-   call shr_mpi_bcast(stream_year_first_ndep , mpicom)
-   call shr_mpi_bcast(stream_year_last_ndep  , mpicom)
-   call shr_mpi_bcast(model_year_align_ndep  , mpicom)
-   call shr_mpi_bcast(stream_fldFileName_ndep, mpicom)
-   call shr_mpi_bcast(ndep_varlist           , mpicom)
-   call shr_mpi_bcast(ndep_taxmode           , mpicom)
-   call shr_mpi_bcast(ndep_tintalgo          , mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'ndepdyn stream settings:'
-      write(iulog,*) '  stream_year_first_ndep  = ',stream_year_first_ndep
-      write(iulog,*) '  stream_year_last_ndep   = ',stream_year_last_ndep
-      write(iulog,*) '  model_year_align_ndep   = ',model_year_align_ndep
-      write(iulog,*) '  stream_fldFileName_ndep = ',stream_fldFileName_ndep
-      write(iulog,*) '  ndep_varList            = ',ndep_varList
-      write(iulog,*) '  ndep_taxmode            = ',ndep_taxmode
-      write(iulog,*) '  ndep_tintalgo           = ',ndep_tintalgo
-      write(iulog,*) ' '
-   endif
-   ! Read in units
-   call check_units( stream_fldFileName_ndep, ndep_varList )
-
-   ! Set domain and create streams
-   call clm_domain_mct (bounds, dom_clm)
-
-   call shr_strdata_create(sdat,name="clmndep",    &
-        pio_subsystem=pio_subsystem,               &
-        pio_iotype=shr_pio_getiotype(inst_name),   &
-        mpicom=mpicom, compid=comp_id,             &
-        gsmap=gsmap_global, ggrid=dom_clm,         &
-        nxg=ldomain%ni, nyg=ldomain%nj,            &
-        yearFirst=stream_year_first_ndep,          &
-        yearLast=stream_year_last_ndep,            &
-        yearAlign=model_year_align_ndep,           &
-        offset=0,                                  &
-        domFilePath='',                            &
-        domFileName=trim(stream_fldFileName_ndep), &
-        domTvarName='time',                        &
-        domXvarName='lon' ,                        &
-        domYvarName='lat' ,                        &
-        domAreaName='area',                        &
-        domMaskName='mask',                        &
-        filePath='',                               &
-        filename=(/trim(stream_fldFileName_ndep)/),&
-        fldListFile=ndep_varlist,                  &
-        fldListModel=ndep_varlist,                 &
-        fillalgo='none',                           &
-        mapalgo=ndepmapalgo,                       &
-        tintalgo=ndep_tintalgo,                    &
-        calendar=get_calendar(),                   &
-        taxmode=ndep_taxmode                       )
-
-
-   if (masterproc) then
-      call shr_strdata_print(sdat,'CLMNDEP data')
-   endif
-
- end subroutine ndep_init
- !================================================================
-
- subroutine check_units( stream_fldFileName_ndep, ndep_varList )
-   !-------------------------------------------------------------------
-   ! Check that units are correct on the file and if need any conversion
-   use ncdio_pio     , only : ncd_pio_openfile, ncd_inqvid, ncd_getatt, ncd_pio_closefile, ncd_nowrite
-   use ncdio_pio     , only : file_desc_t, var_desc_t
-   use shr_kind_mod  , only : CS => shr_kind_cs
-   use shr_log_mod   , only : errMsg => shr_log_errMsg
-   use shr_string_mod, only : shr_string_listGetName
-   implicit none
-
-   !-----------------------------------------------------------------------
-   !
-   ! Arguments
-   character(len=*), intent(IN)  :: stream_fldFileName_ndep  ! ndep filename
-   character(len=*), intent(IN)  :: ndep_varList             ! ndep variable list to examine
-   !
-   ! Local variables
-   type(file_desc_t) :: ncid     ! NetCDF filehandle for ndep file
-   type(var_desc_t)  :: vardesc  ! variable descriptor
-   integer           :: varid    ! variable index
-   logical           :: readvar  ! If variable was read
-   character(len=CS) :: ndepunits! ndep units
-   character(len=CS) :: fname    ! ndep field name
-   !-----------------------------------------------------------------------
-   call ncd_pio_openfile( ncid, trim(stream_fldFileName_ndep), ncd_nowrite )
-   call shr_string_listGetName( ndep_varList, 1, fname )
-   call ncd_inqvid(       ncid, fname, varid, vardesc, readvar=readvar )
-   if ( readvar ) then
-      call ncd_getatt(    ncid, varid, "units", ndepunits )
-   else
-      call endrun(msg=' ERROR finding variable: '//trim(fname)//" in file: "// &
-                      trim(stream_fldFileName_ndep)//errMsg(sourcefile, __LINE__))
-   end if
-   call ncd_pio_closefile( ncid )
-
-   ! Now check to make sure they are correct
-   if (      trim(ndepunits) == "g(N)/m2/s"  )then
-      divide_by_secs_per_yr = .false.
-   else if ( trim(ndepunits) == "g(N)/m2/yr" )then
-      divide_by_secs_per_yr = .true.
-   else
-      call endrun(msg=' ERROR in units for nitrogen deposition equal to: '//trim(ndepunits)//" not units expected"// &
-                      errMsg(sourcefile, __LINE__))
-   end if
-
- end subroutine check_units
-
- !================================================================
- subroutine ndep_interp(bounds, atm2lnd_inst)
-
-   !-----------------------------------------------------------------------
-   use clm_time_manager, only : get_curr_date, get_curr_days_per_year
-   use clm_varcon      , only : secspday
-   use atm2lndType     , only : atm2lnd_type
-   !
-   ! Arguments
-   type(bounds_type) , intent(in)    :: bounds
-   type(atm2lnd_type), intent(inout) :: atm2lnd_inst
-   !
-   ! Local variables
-   integer :: g, ig
-   integer :: year    ! year (0, ...) for nstep+1
-   integer :: mon     ! month (1, ..., 12) for nstep+1
-   integer :: day     ! day of month (1, ..., 31) for nstep+1
-   integer :: sec     ! seconds into current date for nstep+1
-   integer :: mcdate  ! Current model date (yyyymmdd)
-   integer :: dayspyr ! days per year
-   !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ndepdyn')
-
-   if ( divide_by_secs_per_yr )then
-      ig = 0
-      dayspyr = get_curr_days_per_year( )
-      do g = bounds%begg,bounds%endg
-         ig = ig+1
-         atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) / (secspday * dayspyr)
-      end do
-   else
-      ig = 0
-      do g = bounds%begg,bounds%endg
-         ig = ig+1
-         atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig)
-      end do
-   end if
-
- end subroutine ndep_interp
-
- !==============================================================================
-  subroutine clm_domain_mct(bounds, dom_clm, nlevels)
-
-    !-------------------------------------------------------------------
-    ! Set domain data type for internal clm grid
-    use clm_varcon                , only : re
-    use domainMod                 , only : ldomain
-    use mct_mod                   , only : mct_ggrid, mct_gsMap_lsize, mct_gGrid_init
-    use mct_mod                   , only : mct_gsMap_orderedPoints, mct_gGrid_importIAttr
-    use mct_mod                   , only : mct_gGrid_importRAttr, mct_gsMap
-    use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global
-    implicit none
-    !
-    ! arguments
-    type(bounds_type), intent(in) :: bounds
-    type(mct_ggrid), intent(out)   :: dom_clm     ! Output domain information for land model
-    integer, intent(in), optional :: nlevels      ! Number of levels if this is a 3D field
-    !
-    ! local variables
-    integer :: g,i,j,k            ! index
-    integer :: lsize              ! land model domain data size
-    real(r8), pointer :: data(:)  ! temporary
-    integer , pointer :: idata(:) ! temporary
-    integer :: nlevs              ! Number of vertical levels
-    type(mct_gsMap), pointer :: gsmap => null() ! MCT GS map
-    !-------------------------------------------------------------------
-    ! SEt number of levels, and get the GS map for either the 2D or 3D grid
-    nlevs = 1
-    if ( present(nlevels) ) nlevs = nlevels
-    if ( nlevs == 1 ) then
-       gsmap => gsmap_global
-    else
-       gsmap => gsMap_lnd2Dsoi_gdc2glo
-    end if
-    !
-    ! Initialize mct domain type
-    ! lat/lon in degrees,  area in radians^2, mask is 1 (land), 0 (non-land)
-    ! Note that in addition land carries around landfrac for the purposes of domain checking
-    !
-    lsize = mct_gsMap_lsize(gsmap, mpicom)
-    call mct_gGrid_init( GGrid=dom_clm, &
-         CoordChars='lat:lon:hgt', OtherChars='area:aream:mask:frac', lsize=lsize )
-    !
-    ! Allocate memory
-    !
-    allocate(data(lsize))
-    !
-    ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT
-    !
-    call mct_gsMap_orderedPoints(gsmap, iam, idata)
-    gsmap => null()
-    call mct_gGrid_importIAttr(dom_clm,'GlobGridNum',idata,lsize)
-    !
-    ! Determine domain (numbering scheme is: West to East and South to North to South pole)
-    ! Initialize attribute vector with special value
-    !
-    data(:) = -9999.0_R8
-    call mct_gGrid_importRAttr(dom_clm,"lat"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_clm,"lon"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_clm,"area" ,data,lsize)
-    call mct_gGrid_importRAttr(dom_clm,"aream",data,lsize)
-    data(:) = 0.0_R8
-    call mct_gGrid_importRAttr(dom_clm,"mask" ,data,lsize)
-    !
-    ! Determine bounds
-    !
-    ! Fill in correct values for domain components
-    ! Note aream will be filled in in the atm-lnd mapper
-    !
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%lonc(g)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"lon",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%latc(g)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"lat",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%area(g)/(re*re)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"area",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%mask(g), r8)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"mask",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%frac(g), r8)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"frac",data,lsize)
-
-    deallocate(data)
-    deallocate(idata)
-
-  end subroutine clm_domain_mct
-
-end module ndepStreamMod

From 788f4996c12dda3873af80d9875c4a6feda340c9 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 16:35:53 -0600
Subject: [PATCH 0229/1248] Remove a couple more references to MCT

---
 .../customizing-the-clm-configuration.rst                       | 2 +-
 src/main/clm_varctl.F90                                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index f8b5fee002..e76a9cc6f0 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -638,7 +638,7 @@ The output to the above command is as follows:
      -vichydro <name>       Turn VIC hydrologic parameterizations : [on | off] (default is off)
      -crop <name>           Toggle for prognostic crop model. [on | off] (default is off)
                             (can ONLY be turned on when BGC type is CN or CNDV)
-     -comp_intf <name>      Component interface to use (ESMF or MCT) (default MCT)
+     -comp_intf <name>      Component interface to use (default ESMF, currently no other option)
      -defaults <file>       Specify full path to a configuration file which will be used
                             to supply defaults instead of the defaults in bld/config_files.
                             This file is used to specify model configuration parameters only.
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 7d0b2b55ad..0daedbbb1f 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -115,7 +115,7 @@ module clm_varctl
   character(len=fname_len), public :: fsnowaging   = ' '      ! snow aging parameters file name
 
   character(len=fname_len), public :: fatmlndfrc = ' '        ! lnd frac file on atm grid
-                                                              ! only needed for LILAC and MCT drivers
+                                                              ! only needed for LILAC
 
   !----------------------------------------------------------
   ! Flag to read ndep rather than obtain it from coupler

From cc0e04dafe87cb878a8d3333c7a16d1b41a8c7e0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 10 May 2024 17:21:55 -0600
Subject: [PATCH 0230/1248] Update ntests in build-namelist_test.pl

---
 bld/unit_testers/build-namelist_test.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 12a5f4bd38..ec370749bb 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 2513;
+my $ntests = 2454;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1545;
+   $ntests += 1486;
 }
 plan( tests=>$ntests );
 

From 2b8c042973bd383d986c64dda73b11ab9350d2d7 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 10 May 2024 18:05:52 -0600
Subject: [PATCH 0231/1248] Fix the tests so expected fails, actually fail

---
 bld/unit_testers/build-namelist_test.pl | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 25545dcf8a..b0ddb1e448 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1480,57 +1480,73 @@ sub cat_and_create_namelistinfile {
                                      atm_forc=>"GSWP3v1",
                                      res => "0.9x1.25",
                                      bgc => "bgc",
+                                     crop => "--no-crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=T",
                                    },
      "f091850Clm45BgcCRU"        =>{ phys =>"clm4_5",
                                      atm_forc=>"CRUv7",
                                      res => "0.9x1.25",
                                      bgc => "bgc",
+                                     crop => "--no-crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=T",
                                    },
      "f091850Clm45BgcCAM6"       =>{ phys =>"clm4_5",
                                      atm_forc=>"cam6.0",
                                      res => "0.9x1.25",
                                      bgc => "bgc",
+                                     crop => "--crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=F",
                                    },
      "f091850Clm50BgcGSW"        =>{ phys =>"clm5_0",
                                      atm_forc=>"GSWP3v1",
                                      res => "0.9x1.25",
                                      bgc => "bgc",
+                                     crop => "--crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=F",
                                    },
      "f091850Clm50SpGSW"         =>{ phys =>"clm5_0",
                                      atm_forc=>"GSWP3v1",
                                      res => "0.9x1.25",
                                      bgc => "sp",
+                                     crop => "--no-crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=T",
                                    },
      "f091850Clm50BgcCRU"        =>{ phys =>"clm5_0",
                                      atm_forc=>"CRUv7",
                                      res => "0.9x1.25",
                                      bgc => "bgc",
+                                     crop => "--crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=F",
                                    },
      "f091850Clm50SpCRU"         =>{ phys =>"clm5_0",
                                      atm_forc=>"CRUv7",
                                      res => "0.9x1.25",
                                      bgc => "sp",
+                                     crop => "--no-crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=T",
                                    },
      "f091850Clm50BgcCAM6"       =>{ phys =>"clm5_0",
                                      atm_forc=>"cam6.0",
                                      res => "0.9x1.25",
                                      bgc => "bgc",
+                                     crop => "--crop",
                                      use_case => "1850_control",
                                      start_ymd => "18500101",
+                                     namelist => "irrigate=F",
                                    },
    );
 
@@ -1542,9 +1558,12 @@ sub cat_and_create_namelistinfile {
    my $usecase = $finidat_files{$key}{'use_case'};
    my $bgc = $finidat_files{$key}{'bgc'};
    my $res = $finidat_files{$key}{'res'};
+   my $crop = $finidat_files{$key}{'crop'};
+   my $namelist = $finidat_files{$key}{'namelist'};
    my $start_ymd = $finidat_files{$key}{'start_ymd'};
    my $lnd_tuning_mode = "${phys}_" . $finidat_files{$key}{'atm_forc'};
-   $options = "-bgc $bgc -res $res -use_case $usecase -envxml_dir . --lnd_tuning_mode $lnd_tuning_mode -namelist '&a start_ymd=$start_ymd/'";
+   $options = "-bgc $bgc -res $res -use_case $usecase -envxml_dir . $crop --lnd_tuning_mode $lnd_tuning_mode " . 
+              "-namelist '&a start_ymd=$start_ymd, $namelist/'";
    &make_env_run();
    eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
    is( $@, '', "options: $options" );
@@ -1552,7 +1571,7 @@ sub cat_and_create_namelistinfile {
    if ( $finidat =~ /initdata_map/ ) {
       my $result;
       eval( $result = `grep use_init_interp lnd_in` );
-      isnt( $#, 0, "use_init_interp needs to be set here and was not: $result")
+      is ( $result =~ /.true./, 1, "use_init_interp needs to be true here: $result");
    }
    $cfiles->checkfilesexist( "$options", $mode );
    $cfiles->shownmldiff( "default", "standard" );

From 8c109657651315ff83b98561108c6ac71a7f6b29 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 10 May 2024 21:05:33 -0600
Subject: [PATCH 0232/1248] Set use_init_interp=T for finidat files that are
 older than ctsm5.2

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 70 +++++++++----------
 1 file changed, 35 insertions(+), 35 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 6f2f265da4..c99700289e 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -970,21 +970,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm4_5_GSWP3v1"
+         lnd_tuning_mode="clm4_5_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm45BgcGs.0901-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm4_5_CRUv7"
+         lnd_tuning_mode="clm4_5_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm45BgcCruGs.1101-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm4_5_cam6.0"
+         lnd_tuning_mode="clm4_5_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm45BgcGs.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
@@ -992,7 +992,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_GSWP3v1"
+         lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
@@ -1016,14 +1016,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_CRUv7"
+         lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
@@ -1031,7 +1031,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_GSWP3v1"
+         lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
@@ -1045,7 +1045,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
 </finidat>
 
@@ -1053,7 +1053,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_GSWP3v1"
+         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
@@ -1067,7 +1067,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
 </finidat>
 
@@ -1125,7 +1125,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm4_5_cam6.0"
+         lnd_tuning_mode="clm4_5_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
@@ -1136,14 +1136,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
 </finidat>
 
@@ -1151,7 +1151,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
 </finidat>
 
@@ -1159,7 +1159,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
 </finidat>
 
@@ -1167,7 +1167,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
@@ -1175,7 +1175,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
@@ -1197,7 +1197,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
 </finidat>
 
@@ -1206,21 +1206,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_0_cam6.0"
+         lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm5_1 -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
 </finidat>
 
@@ -1228,7 +1228,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
 </finidat>
 
@@ -1236,7 +1236,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
 </finidat>
 
@@ -1244,7 +1244,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
@@ -1252,7 +1252,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
@@ -1260,7 +1260,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
 </finidat>
 
@@ -1269,21 +1269,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
+         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm6_0 -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
 </finidat>
 
@@ -1291,7 +1291,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
 </finidat>
 
@@ -1299,7 +1299,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
 </finidat>
 
@@ -1307,7 +1307,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
@@ -1315,7 +1315,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
@@ -1323,7 +1323,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
 </finidat>
 
@@ -1332,7 +1332,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 

From e14303f9ac6bb7a8f36dfebec2ab73d0a6e20151 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 12 May 2024 20:21:29 -0600
Subject: [PATCH 0233/1248] Fix irrigate for two use-cases so namelists all
 agree with the ctsm5.1.dev176 version

---
 bld/namelist_files/use_cases/2010_control.xml    | 6 +++---
 bld/namelist_files/use_cases/20thC_transient.xml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/bld/namelist_files/use_cases/2010_control.xml b/bld/namelist_files/use_cases/2010_control.xml
index d16177301c..2f72624077 100644
--- a/bld/namelist_files/use_cases/2010_control.xml
+++ b/bld/namelist_files/use_cases/2010_control.xml
@@ -8,9 +8,9 @@
 
 <sim_year_range>constant</sim_year_range>
 
-<irrigate use_crop=".true." =".false."    >.true.</irrigate>
-<irrigate use_crop=".true." =".false."    >.true.</irrigate>
-<irrigate use_crop=".true." phys="clm4_5" >.false.</irrigate>
+<irrigate use_crop=".true." use_cndv=".false."               >.true.</irrigate>
+<irrigate use_crop=".true." use_cndv=".true."                >.false.</irrigate>
+<irrigate use_crop=".true." use_cndv=".false." phys="clm4_5" >.false.</irrigate>
 
 <stream_year_first_ndep bgc="cn" use_cn=".true." >2010</stream_year_first_ndep>
 <stream_year_last_ndep  bgc="cn" use_cn=".true." >2010</stream_year_last_ndep>
diff --git a/bld/namelist_files/use_cases/20thC_transient.xml b/bld/namelist_files/use_cases/20thC_transient.xml
index b88ca3d3b1..6cbf9e0d38 100644
--- a/bld/namelist_files/use_cases/20thC_transient.xml
+++ b/bld/namelist_files/use_cases/20thC_transient.xml
@@ -20,7 +20,7 @@
 
 <irrigate use_crop=".true."               use_cndv=".false.">.true.</irrigate>
 <irrigate use_crop=".true."               use_cndv=".true." >.false.</irrigate>
-<irrigate use_crop=".true." phys="clm4_5"                   >.false.</irrigate>
+<irrigate use_crop=".true." phys="clm4_5" use_cndv=".false.">.false.</irrigate>
 
 <stream_year_first_ndep use_cn=".true."   >1850</stream_year_first_ndep>
 <stream_year_last_ndep  use_cn=".true."   >2015</stream_year_last_ndep>

From 9fa2841b8ed6ad0d0696969ee3ea9d4b5627aec7 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 00:56:57 -0600
Subject: [PATCH 0234/1248] New finidat files for clm5_1/clm6_0 for 1850

Use ne30np4.pg3_gx1v7 BgcCrop GSWP3v1
finidat file for 1850 clm5_1 and clm6_0.
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 57 ++++---------------
 1 file changed, 11 insertions(+), 46 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 40ba339d65..fff414d82e 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -758,34 +758,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
-<!-- 1850 for CTSM5.1 -->
-<!-- These two needs to specify use_cn=F/T since there is a version for both, other files just use the BGC version -->
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_GSWP3v1" use_cn=".false."
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+<!-- 1850 for CLM5.1/CLM6.0 -->
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm5_1"
+>hgrid=ne30np4.pg3 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. lnd_tuning_mode=clm6_0_GSWP3v1
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_GSWP3v1" use_cn=".true."
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
-</init_interp_attributes>
-
-<!-- 1850 spinup for CESM3 development for CLM5.1-->
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
-</init_interp_attributes>
-
-<!-- 1850 for CTSM6.0 -->
-<!-- These two needs to specify use_cn=F/T since there is a version for both, other files just use the BGC version -->
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_GSWP3v1" use_cn=".false."
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
-</init_interp_attributes>
-
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_GSWP3v1" use_cn=".true."
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
-</init_interp_attributes>
-
-<!-- 1850 spinup for CESM3 development for CLM6.0-->
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
+>hgrid=ne30np4.pg3 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. lnd_tuning_mode=clm6_0_GSWP3v1
 </init_interp_attributes>
 
 <!-- present day -->
@@ -1049,26 +1028,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
 </finidat>
 
-<!-- CTSM6_0 -->
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
-</finidat>
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm6_0_GSWP3v1"
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
-</finidat>
-<!-- From the clm5_0_cam6.0 setting above...-->
-<!-- Use f09 clm5_0 cam6 spinup file for clm6_0 cam6-->
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
+<!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at ne30pg3_mg17 for all clm5_1/clm6_0 options -->
+<!-- use_init_interp true because even though this is a ctsm5.2 dataset it was with early fsurfdat files -->
+<finidat hgrid="ne30np4.pg3" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="18500101" do_transient_pfts=".false."
+         use_crop=".true." irrigate=".false." lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm60BgcCrop-ciso.1361-01-01.ne30pg3_mg17_c240317.nc
 </finidat>
 
 <!--

From 0b41efe4cc507c3cf880501fcfc976b71661a23d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 01:08:49 -0600
Subject: [PATCH 0235/1248] Change name to remove shell type extension

---
 .../{cmp_baseline_lnd_in_files.sh => cmp_baseline_lnd_in_files} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename bld/unit_testers/{cmp_baseline_lnd_in_files.sh => cmp_baseline_lnd_in_files} (95%)

diff --git a/bld/unit_testers/cmp_baseline_lnd_in_files.sh b/bld/unit_testers/cmp_baseline_lnd_in_files
similarity index 95%
rename from bld/unit_testers/cmp_baseline_lnd_in_files.sh
rename to bld/unit_testers/cmp_baseline_lnd_in_files
index ebeeffc72a..3c6d84954c 100755
--- a/bld/unit_testers/cmp_baseline_lnd_in_files.sh
+++ b/bld/unit_testers/cmp_baseline_lnd_in_files
@@ -9,7 +9,7 @@ usage() {
   echo ""
   echo "***********************************************************************"
   echo "usage:"
-  echo "./cmp_baseline_lnd_in_files.sh <baseline> <comparison-baseline>"
+  echo "./cmp_baseline_lnd_in_files <baseline> <comparison-baseline>"
   echo "  "
   echo "Compares lnd_in files between two baselines on Derecho"
   echo "***********************************************************************"

From ac3cb735edc0febde700ec737886a65803e703f0 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 01:51:42 -0600
Subject: [PATCH 0236/1248] Reverse comparision so agrees with how documented

---
 bld/unit_testers/compare_namelists | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/bld/unit_testers/compare_namelists b/bld/unit_testers/compare_namelists
index 7a8badc288..0d0168b316 100755
--- a/bld/unit_testers/compare_namelists
+++ b/bld/unit_testers/compare_namelists
@@ -18,10 +18,10 @@ usage() {
   echo "     Run in verbose mode"
   echo "[-pa|--physicsA <physics-version>]  "
   echo "     Namelists of first physics version for comparison"
-  echo "     (in current directory)"
+  echo "     (in baseline directory)"
   echo "[-pb|--physicsB <physics-version>]  "
   echo "     Namelists of second physics version to compare to the first one"
-  echo "     (in baseline directory)"
+  echo "     (in current directory)"
   echo "[-b|--baseline <baseline>]  "
   echo "     Baseline directory to compare to (default current directory)"
   echo "  "
@@ -90,8 +90,8 @@ if [ "${filenames[*]}" = "$filepat" ]; then
 fi
 for file in ${filenames[*]}
 do
-   fileA="./$file"
-   fileB="$baseline/$file"
+   fileA="$baseline/$file"
+   fileB="./$file"
    # If physicsA option used and the file matches the physics input
    if [[ "$fileA" =~ "-phys+$PHYSA" ]] || [ "$PHYSA" = "all" ]; then
       # Replace physicsB for fileB

From 942fee9c6385ffc6b8888d98c05bb0119981736e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 01:52:44 -0600
Subject: [PATCH 0237/1248] remove clm5_1 old finidat file so will always use
 the ne30 new one

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index fff414d82e..59a0d9ee75 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1013,12 +1013,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_1_GSWP3v1"
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
-</finidat>
 <!-- From the clm5_0_cam6.0 setting above...-->
 <!-- Use f09 clm5_0 cam6 spinup file for clm5_1 cam6-->
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."

From 77690ed048713474d4bef2277c9b3734448a23a8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 02:44:47 -0600
Subject: [PATCH 0238/1248] Start on Change files

---
 doc/ChangeLog | 117 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 118 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 3307c8df88..172c203e7f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,121 @@
 ===============================================================
+Tag name: ctsm5.2.005
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Mon 13 May 2024 02:44:33 AM MDT
+One-line Summary: Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems
+
+Purpose and description of changes
+----------------------------------
+
+Fix the clm6_0 defaults that were incorrect in ctsm5.2.0. The use-cases needed to be changed to handle clm6_0.
+And clm6_0 wasn't handled in the merge of ctsm5.1.dev174 for the two new settings. Simplified the use-cases which
+should help prevent these problems in the future. use_init_interp will be set for ctsm5.1 finidat files.
+
+Fix some testing. mksurfdata_esmf and the MKSUIRFDATA test didn't work in a CESM checkout. build-namelist unit tests
+weren't going over the use-cases. Also started adding some tests to go over finidat files, but didn't yet capture all of them.
+Add some scripts to compare namelists in order to detect namelist issues for physics
+version updates, and more easily see namelist changes in one place (bld/unit_testers/cmp_baseline_lnd_in_files,
+bld/unit_testers/compare_namelists).
+
+Add some tests to detect issues in CESM and CAM testing (add more tests for cam6.0 forcing, add new IHistClm60BgcCropG
+compset). Add a NoAnthro compset to the ctsm_sci testing. Add I1850Clm60Sp test for f09 and f19 to ctsm_sci.
+
+Change NoAnthro compsets to use RTM rather than MOSART. Add science support to some clm6_0 compsets, as was obvious.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[X] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes #2492 -- Fix clm6_0 defaults
+   Fixes #2504 -- build-namelist unit tests for use-cases
+   Fixes #2519 -- MKSURFDATAESMF for CESM checkout
+   Fixes #2520 -- B1850 compsets are failing
+   One tick box in #2403 (new initial conditions)
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes made to namelist defaults (e.g., changed parameter values):
+  Fixes: snow_thermal_cond_method, irrigate and snicar_snobc_intmix for clm6_0
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+  New initial conditions for clm5_1/clm6_0 for 1850 from ne30pg3_g17 GSWP3v1 forcing for BgcCrop with ciso
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   build-namelist unit tester started to add some finidat tests, but only some of them were added to the list
+
+Changes to tests or testing: Add some tests to detect the CESM test issues
+
+
+Testing summary: regular ctsm_sci
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS (except
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS (except
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ---- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes!
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: clm6_0 (some clm4_5 see below)
+    - what platforms/compilers: All
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+      new climate so agrees with clm5_1 namelists, and fixes irrigate for clm4_5
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+   #2501 -- Fix clm6_0 defaults
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.004
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu 09 May 2024 03:10:52 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 17ad670f17..0edccb3a18 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems
        ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes
        ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev
        ctsm5.2.002 glemieux 04/26/2024 FATES default allometry parameter file update

From d66ddff54439bd192b9ed8b07419a17cd3282656 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 13 May 2024 11:21:08 -0700
Subject: [PATCH 0239/1248] update fates_harvest_mode to use chars to set
 namelist options

initial commit
---
 src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 10 ++++++----
 src/main/clm_varctl.F90                      |  2 +-
 src/main/controlMod.F90                      |  2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
index 4f326d82a5..d9bd0352ca 100644
--- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
+++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
@@ -171,13 +171,14 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename)
        end do
 
        ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled
-       if (fates_harvest_mode .ge. fates_harvest_luh_area ) then
+       if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. &
+           trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then
 
           ! change the harvest varnames being used depending on the mode selected
-          if (fates_harvest_mode .eq. fates_harvest_luh_area ) then
+          if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area ) then
              landuse_harvest_varnames => landuse_harvest_area_varnames
              landuse_harvest_units = landuse_harvest_area_units
-          elseif (fates_harvest_mode .eq. fates_harvest_luh_mass ) then
+          elseif (trim(fates_harvest_mode) .eq. fates_harvest_luh_mass ) then
              landuse_harvest_varnames => landuse_harvest_mass_varnames
              landuse_harvest_units = landuse_harvest_mass_units
           else
@@ -256,7 +257,8 @@ subroutine dynFatesLandUseInterp(bounds, init_state)
           call landuse_state_vars(varnum)%get_current_data(this_data)
           landuse_states(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg)
        end do
-       if (fates_harvest_mode .ge. fates_harvest_luh_area ) then
+       if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. &
+           trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then
           do varnum = 1, num_landuse_harvest_vars
              call landuse_harvest_vars(varnum)%get_current_data(this_data)
              landuse_harvest(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg)
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 64d6e15747..59b72c8e74 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -302,7 +302,7 @@ module clm_varctl
                                                                         ! > 1 for external data (lightning and/or anthropogenic ignitions)
                                                                         ! see bld/namelist_files/namelist_definition_clm4_5.xml for details
   logical, public            :: use_fates_tree_damage = .false.         ! true => turn on tree damage module
-  integer, public            :: fates_harvest_mode = 0                  ! 0 for no harvest/logging; 1-4 for harvest mode options
+  character(len=256), public :: fates_harvest_mode = ''                 ! five different harvest modes; see namelist definition
   logical, public            :: use_fates_planthydro = .false.          ! true => turn on fates hydro
   logical, public            :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking
   logical, public            :: use_fates_ed_st3   = .false.            ! true => static stand structure
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 55dd92305d..1dd432bb7e 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -775,7 +775,7 @@ subroutine control_spmd()
     call mpi_bcast (for_testing_allow_interp_non_ciso_to_ciso, 1, MPI_LOGICAL, 0, mpicom, ier)
 
     call mpi_bcast (fates_spitfire_mode, 1, MPI_INTEGER, 0, mpicom, ier)
-    call mpi_bcast (fates_harvest_mode, 1, MPI_INTEGER, 0, mpicom, ier)
+    call mpi_bcast (fates_harvest_mode, len(fates_harvest_mode) , MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_tree_damage, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_cohort_age_tracking, 1, MPI_LOGICAL, 0, mpicom, ier)

From a09d22376f704ea37c30b19e6978f6fa19a261bf Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 13:44:35 -0600
Subject: [PATCH 0240/1248] Some tests were failing to find the 1850 finidat
 file, more changes to match how the finidat matching is done so that it now
 works

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 25 ++++---------------
 1 file changed, 5 insertions(+), 20 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 59a0d9ee75..655e97c47c 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -760,11 +760,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 1850 for CLM5.1/CLM6.0 -->
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm5_1"
->hgrid=ne30np4.pg3 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. lnd_tuning_mode=clm6_0_GSWP3v1
+>hgrid=ne30np4.pg3 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
->hgrid=ne30np4.pg3 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. lnd_tuning_mode=clm6_0_GSWP3v1
+>hgrid=ne30np4.pg3 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1
 </init_interp_attributes>
 
 <!-- present day -->
@@ -1006,27 +1006,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
-<!-- CTSM5_1 -->
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
-</finidat>
-<!-- From the clm5_0_cam6.0 setting above...-->
-<!-- Use f09 clm5_0 cam6 spinup file for clm5_1 cam6-->
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
-</finidat>
-
 <!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at ne30pg3_mg17 for all clm5_1/clm6_0 options -->
 <!-- use_init_interp true because even though this is a ctsm5.2 dataset it was with early fsurfdat files -->
 <finidat hgrid="ne30np4.pg3" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" do_transient_pfts=".false."
-         use_crop=".true." irrigate=".false." lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm60BgcCrop-ciso.1361-01-01.ne30pg3_mg17_c240317.nc
 </finidat>
 

From 458c788eb6b7ca8b6351a5c3e4ebfae7d8364e21 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 13 May 2024 15:07:05 -0700
Subject: [PATCH 0241/1248] add default pass values for logging and harvest

---
 src/utils/clmfates_interfaceMod.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 5c23f1c1dc..ba6c59143f 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -511,6 +511,9 @@ subroutine CLMFatesGlobals2()
         call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking)
 
         ! FATES logging and harvest modes
+        pass_logging = 0
+        pass_lu_harvest = 0
+        pass_num_lu_harvest_cats = 0
         if (fates_harvest_mode > fates_harvest_no_logging) then
            pass_logging = 1 ! Time driven logging, without landuse harvest
            ! CLM landuse timeseries driven harvest rates
@@ -522,9 +525,6 @@ subroutine CLMFatesGlobals2()
            else if (fates_harvest_mode >= fates_harvest_luh_area) then
               pass_lu_harvest = 1
               pass_num_lu_harvest_cats = num_landuse_harvest_vars
-           else
-              pass_lu_harvest = 0
-              pass_num_lu_harvest_cats = 0
            end if
         end if
 

From 9ecc1bc79a1dd66a138fd398872ef8fa55e09fbf Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 16:10:43 -0600
Subject: [PATCH 0242/1248] Fix a resoplution name in a test

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index da38a4e27d..9cfba6f5b3 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -576,7 +576,7 @@
       <option name="comment"  >cism is not answer preserving across processor changes, but short test length should be ok.</option>
     </options>
   </test>
-  <test name="SMS" grid="f09_mg17" compset="I1850Clm50BgcCropG" testmods="clm/default">
+  <test name="SMS" grid="f09_g17" compset="I1850Clm50BgcCropG" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>

From 28f5bc36108af5281f3fdfd286b43bac5a849786 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 13 May 2024 15:25:00 -0700
Subject: [PATCH 0243/1248] update fates_harvest_mode to accept strings

---
 bld/CLMBuildNamelist.pm                       |  4 +--
 bld/namelist_files/namelist_defaults_ctsm.xml |  6 ++---
 .../namelist_definition_ctsm.xml              | 17 ++++++------
 bld/unit_testers/build-namelist_test.pl       |  6 ++---
 .../clm/FatesColdLUH2Mode0/user_nl_clm        |  2 +-
 .../clm/FatesColdLUH2Mode1/user_nl_clm        |  2 +-
 .../clm/FatesColdLUH2Mode2/user_nl_clm        |  2 +-
 .../clm/FatesColdLUH2Mode3/user_nl_clm        |  2 +-
 .../clm/FatesColdLUH2Mode4/user_nl_clm        |  2 +-
 src/dyn_subgrid/dynSubgridDriverMod.F90       |  2 +-
 src/utils/clmfates_interfaceMod.F90           | 27 ++++++++++---------
 11 files changed, 37 insertions(+), 35 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index aafc7739a3..456447925c 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4478,7 +4478,7 @@ sub setup_logic_fates {
             if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
               $log->fatal_error("use_fates_luh must be true when $var is true" );
             }
-            if ( $nl->get_value('fates_harvest_mode') > 0) {
+            if ( $nl->get_value('fates_harvest_mode') ne 'no_harvest') {
               $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" );
             }
           }
@@ -4487,7 +4487,7 @@ sub setup_logic_fates {
         my $var = "fates_harvest_mode";
         if ( defined($nl->get_value($var))  ) {
            # using fates_harvest mode with raw luh2 harvest data
-           if ( $nl->get_value($var) > 2) {
+           if ( $nl->get_value($var) eq 'luhdata_area' || $nl->get_value($var) eq 'luhdata_mass' ) {
               # Make sure that use_fates_luh is true when using raw fates luh2 harvest data
               if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
                 $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" );
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 9d2a34b7bf..5da9cb22bf 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2759,7 +2759,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 
 <!-- ===== FATES DEFAULTS =========== -->
 <fates_spitfire_mode           use_fates=".true.">0</fates_spitfire_mode>
-<fates_harvest_mode            use_fates=".true.">0</fates_harvest_mode>
+<fates_harvest_mode            use_fates=".true.">no_harvest</fates_harvest_mode>
 <use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
 <use_fates_tree_damage         use_fates=".true.">.false.</use_fates_tree_damage>
 <use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
@@ -2769,8 +2769,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="3"  >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="4"  >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="luhdata_area"  >.true.</use_fates_luh>
+<use_fates_luh                 use_fates=".true." fates_harvest_mode="luhdata_mass"  >.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
 <use_fates_luh                 use_fates=".true."                                >.false.</use_fates_luh>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index edcfa36d27..03b1e9e64d 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -735,14 +735,14 @@ Toggle to turn on FATES satellite phenology mode (only relevant if FATES is bein
 </entry>
 
 <entry id="fates_harvest_mode" type="integer" category="physics"
-        group="clm_inparm" valid_values="0,1,2,3,4", value="0" >
-Set FATES harvesting mode by setting fates_harvest_mode > 0.
+        group="clm_inparm" valid_values="no_harvest_event_code,surfdata_file,luhdata_area,luhdata_mass">
+Set FATES harvesting mode by setting fates_harvest_mode to a valid string option.
 Allowed values are:
- 0 : no fates harvesting of any kind
- 1 : fates logging via fates logging event codes (see fates parameter file) only
- 2 : fates harvest driven by CLM landuse timeseries data (dynHarvestMod)
- 3 : fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
- 4 : fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
+ no_harvest: no fates harvesting of any kind
+ event_code: fates logging via fates logging event codes (see fates parameter file) only
+ surfdata_file: fates harvest driven by CLM landuse timeseries data (dynHarvestMod)
+ luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
+ luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
 </entry>
 
 <entry id="use_fates_planthydro" type="logical" category="physics"
@@ -786,8 +786,7 @@ Full pathname to the inventory initialization control file.
 <entry id="use_fates_luh" type="logical" category="physics"
        group="clm_inparm" valid_values="" >
 If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file.
-This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harvest
-data (fates_harvest_mode >= 3)
+This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harvest data
 (Also, only valid for use_fates = true and is incompatible with transient runs currently.)
 </entry>
 
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index f674849b6f..973fdffd16 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1047,7 +1047,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm4_5",
                                    },
      "useloggingButNOTFATES"     =>{ options=>"-envxml_dir . -no-megan",
-                                     namelst=>"fates_harvest_mode=1",
+                                     namelst=>"fates_harvest_mode=event_code",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
@@ -1102,12 +1102,12 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan",
-                                     namelst=>"use_fates_potentialveg=T,fates_harvest_mode=1",
+                                     namelst=>"use_fates_potentialveg=T,fates_harvest_mode=event_code",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useFATESHARVEST3WOLUH"     =>{ options=>"-bgc fates -envxml_dir . -no-megan",
-                                     namelst=>"use_fates_luh=F,fates_harvest_mode=3",
+                                     namelst=>"use_fates_luh=F,fates_harvest_mode=luhdata_area",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm
index 929a8e6e14..b3b338e232 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = 0
+fates_harvest_mode = no_harvest
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm
index dea75b71e7..c0e1c476be 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = 1
+fates_harvest_mode = event_code
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm
index fd4c74fe57..61e1daaa93 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = 2
+fates_harvest_mode = surfdata_file
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm
index 3332e9e526..d760105e68 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = 3
+fates_harvest_mode = luhdata_area
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm
index 13dae9efee..bb5f30f75d 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = 4
+fates_harvest_mode = luhdata_mass
diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90
index 162247a0ff..faef029b40 100644
--- a/src/dyn_subgrid/dynSubgridDriverMod.F90
+++ b/src/dyn_subgrid/dynSubgridDriverMod.F90
@@ -128,7 +128,7 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst)
     ! flanduse_timeseries file. However, this could theoretically be changed so that the
     ! harvest data were separated from the pftdyn data, allowing them to differ in the
     ! years over which they apply.
-    if (get_do_harvest() .or. fates_harvest_mode == fates_harvest_clmlanduse) then
+    if (get_do_harvest() .or. trim(fates_harvest_mode) == fates_harvest_clmlanduse) then
        call dynHarvest_init(bounds_proc, harvest_filename=get_flanduse_timeseries())
     end if
 
diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index ba6c59143f..4205802088 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -186,6 +186,7 @@ module CLMFatesInterfaceMod
    use dynFATESLandUseChangeMod, only : fates_harvest_no_logging
    use dynFATESLandUseChangeMod, only : fates_harvest_clmlanduse
    use dynFATESLandUseChangeMod, only : fates_harvest_luh_area
+   use dynFATESLandUseChangeMod, only : fates_harvest_luh_mass
    use dynFATESLandUseChangeMod, only : landuse_harvest
    use dynFATESLandUseChangeMod, only : landuse_harvest_units
    use dynFATESLandUseChangeMod, only : landuse_harvest_varnames
@@ -514,20 +515,25 @@ subroutine CLMFatesGlobals2()
         pass_logging = 0
         pass_lu_harvest = 0
         pass_num_lu_harvest_cats = 0
-        if (fates_harvest_mode > fates_harvest_no_logging) then
+        if (trim(fates_harvest_mode) /= fates_harvest_no_logging) then
            pass_logging = 1 ! Time driven logging, without landuse harvest
            ! CLM landuse timeseries driven harvest rates
-           if (fates_harvest_mode == fates_harvest_clmlanduse) then
+           if (trim(fates_harvest_mode) == fates_harvest_clmlanduse) then
               pass_num_lu_harvest_cats = num_harvest_inst
               pass_lu_harvest = 1
 
            ! LUH2 landuse timeseries driven  harvest rates
-           else if (fates_harvest_mode >= fates_harvest_luh_area) then
+           else if (trim(fates_harvest_mode)== fates_harvest_luh_area .or. &
+                    trim(fates_harvest_mode)== fates_harvest_luh_mass) then
               pass_lu_harvest = 1
               pass_num_lu_harvest_cats = num_landuse_harvest_vars
            end if
         end if
 
+        call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest)
+        call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats)
+        call set_fates_ctrlparms('use_logging',ival=pass_logging)
+
         ! FATES landuse modes
         if(use_fates_luh) then
            pass_use_luh = 1
@@ -550,11 +556,6 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg)
 
-        ! Wait to set the harvest and logging variables after checking fates_harvest_modes
-        call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest)
-        call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats)
-        call set_fates_ctrlparms('use_logging',ival=pass_logging)
-
         if(use_fates_inventory_init) then
            pass_inventory_init = 1
         else
@@ -979,7 +980,7 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
       call GetAndSetTime
 
       ! Get harvest rates for CLM landuse timeseries driven rates
-      if (fates_harvest_mode == fates_harvest_clmlanduse) then
+      if (trim(fates_harvest_mode) == fates_harvest_clmlanduse) then
          call dynHarvest_interp_resolve_harvesttypes(bounds_clump, &
               harvest_rates=harvest_rates(begg:endg,1:num_harvest_inst), &
               after_start_of_harvest_ts=after_start_of_harvest_ts)
@@ -1105,7 +1106,7 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
          ! for now there is one veg column per gridcell, so store all harvest data in each site
          ! this will eventually change
          ! today's hlm harvest flag needs to be set no matter what
-         if (fates_harvest_mode == fates_harvest_clmlanduse) then
+         if (trim(fates_harvest_mode) == fates_harvest_clmlanduse) then
             if (after_start_of_harvest_ts) then
                this%fates(nc)%bc_in(s)%hlm_harvest_rates(1:num_harvest_inst) = harvest_rates(g,1:num_harvest_inst)
             else
@@ -1124,7 +1125,8 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
                call endrun(msg=errMsg(sourcefile, __LINE__))
            end if
 
-         else if (fates_harvest_mode >= fates_harvest_luh_area) then
+         else if (trim(fates_harvest_mode) == fates_harvest_luh_area .or. &
+                  trim(fates_harvest_mode) == fates_harvest_luh_mass) then
               this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g)
               this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames
               this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units
@@ -2082,7 +2084,8 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, &
                     this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g)
                     this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames
 
-                    if (fates_harvest_mode >= fates_harvest_luh_area ) then
+                    if (trim(fates_harvest_mode) == fates_harvest_luh_area .or. &
+                        trim(fates_harvest_mode) == fates_harvest_luh_mass) then
                        this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g)
                        this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames
                        this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units

From 8bf5f5abd69b4ccfe590b1b42ddebc1a91c8c2c1 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 16:32:08 -0600
Subject: [PATCH 0244/1248] Add test to expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 8ee60cf4b8..9da502fd54 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -51,6 +51,13 @@
     </phase>
   </test>
 
+  <test name="PEM_D_Ld3.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam6LndTuningMode">
+    <phase name="COMPARE_base_modpes">
+      <status>FAIL</status>
+      <issue>#2542</issue>
+    </phase>
+  </test>
+
   <test name="SMS_D_Ld1_Mmpi-serial_Vmct.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsRLA">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>

From 672da6de229e5a1acb166adf33375d772615de44 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 13 May 2024 16:46:38 -0600
Subject: [PATCH 0245/1248] Update change log a bit

---
 doc/ChangeLog | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 172c203e7f..de37d4934c 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.005
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
-Date: Mon 13 May 2024 02:44:33 AM MDT
+Date: Mon 13 May 2024 04:46:10 PM MDT
 One-line Summary: Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems
 
 Purpose and description of changes
@@ -76,11 +76,11 @@ Testing summary: regular ctsm_sci
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho - PASS (except
+    derecho - PASS (737 compare different to baseline)
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
-    derecho - PASS (except
+    derecho - PASS
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 

From 8aa0a708ca8751aa770ccc40a66fb962d26f5acc Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Apr 2024 13:56:24 -0600
Subject: [PATCH 0246/1248] Update cmeps to the branch

---
 Externals.cfg | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 185f412cab..1aa8991883 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -48,9 +48,12 @@ tag = cime6.0.217_httpsbranch03
 required = True
 
 [cmeps]
-tag = cmeps0.14.50
+#tag = cmeps0.14.50
+#branch = dust_emis_mod
+hash = d79e34f67df825f9265bdaaf3091f8995d5df1a2
 protocol = git
-repo_url = https://github.com/ESCOMP/CMEPS.git
+#repo_url = https://github.com/ESCOMP/CMEPS.git
+repo_url = https://github.com/ekluzek/CMEPS.git
 local_path = components/cmeps
 required = True
 

From 603d2677f85eff3a15a284ded3d89722371b81be Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Apr 2024 15:02:04 -0600
Subject: [PATCH 0247/1248] Add shr_dust_emis_mod.F90 to the files needed for
 unit testing, fails, because ESMF is currently needed and not available

---
 src/CMakeLists.txt | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 568b53cd15..9d2e6041b5 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -20,9 +20,11 @@ add_subdirectory(${CLM_ROOT}/share/src csm_share)
 add_subdirectory(${CLM_ROOT}/share/unit_test_stubs/util csm_share_stubs)
 add_subdirectory(${CLM_ROOT}/share/src/esmf_wrf_timemgr esmf_wrf_timemgr)
 
-# Add the single file we need from CMEPS
-set (drv_sources_needed
-  ${CLM_ROOT}/components/cmeps/cesm/nuopc_cap_share/glc_elevclass_mod.F90)
+# Add files needed from CMEPS
+list ( APPEND drv_sources_needed
+  ${CLM_ROOT}/components/cmeps/cesm/nuopc_cap_share/glc_elevclass_mod.F90
+  ${CLM_ROOT}/components/cmeps/cesm/nuopc_cap_share/shr_dust_emis_mod.F90
+  )
 
 # Add CLM source directories
 add_subdirectory(${CLM_ROOT}/src/utils clm_utils)

From 0b48097c502c98521b8014171a2d4f3cdaa5dec2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Apr 2024 18:59:30 -0600
Subject: [PATCH 0248/1248] Start adding the unit testing for dust emission in
 cmeps

---
 Externals.cfg                                 |  2 +-
 src/CMakeLists.txt                            |  4 ++
 src/drv_test/CMakeLists.txt                   |  1 +
 .../shr_dust_emis_test/CMakeLists.txt         |  3 ++
 .../shr_dust_emis_test/test_shr_dust_emis.pf  | 50 +++++++++++++++++++
 5 files changed, 59 insertions(+), 1 deletion(-)
 create mode 100644 src/drv_test/CMakeLists.txt
 create mode 100644 src/drv_test/shr_dust_emis_test/CMakeLists.txt
 create mode 100644 src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf

diff --git a/Externals.cfg b/Externals.cfg
index 1aa8991883..70c0bd6124 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -50,7 +50,7 @@ required = True
 [cmeps]
 #tag = cmeps0.14.50
 #branch = dust_emis_mod
-hash = d79e34f67df825f9265bdaaf3091f8995d5df1a2
+hash = 492faf0014ad9d91c22bb92e2570e558a76093fe
 protocol = git
 #repo_url = https://github.com/ESCOMP/CMEPS.git
 repo_url = https://github.com/ekluzek/CMEPS.git
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9d2e6041b5..9388e65bc2 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -105,3 +105,7 @@ add_subdirectory(${CLM_ROOT}/src/dyn_subgrid/test clm_dyn_subgrid_test)
 add_subdirectory(${CLM_ROOT}/src/main/test clm_main_test)
 add_subdirectory(${CLM_ROOT}/src/init_interp/test clm_init_interp_test)
 add_subdirectory(${CLM_ROOT}/src/self_tests/test clm_self_tests_test)
+
+# Add driver unit test directories
+add_subdirectory(${CLM_ROOT}/src/drv_test drv_test)
+
diff --git a/src/drv_test/CMakeLists.txt b/src/drv_test/CMakeLists.txt
new file mode 100644
index 0000000000..adf66b8b92
--- /dev/null
+++ b/src/drv_test/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(shr_dust_emis_test)
diff --git a/src/drv_test/shr_dust_emis_test/CMakeLists.txt b/src/drv_test/shr_dust_emis_test/CMakeLists.txt
new file mode 100644
index 0000000000..21fb9c8d47
--- /dev/null
+++ b/src/drv_test/shr_dust_emis_test/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_pfunit_ctest(dust_emis
+  TEST_SOURCES "test_shr_dust_emis.pf"
+  LINK_LIBRARIES clm csm_share)
diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
new file mode 100644
index 0000000000..aa60427eac
--- /dev/null
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -0,0 +1,50 @@
+module test_shr_dust_emis
+
+  ! Tests of shr_dust_emis_mod.F90 from CMEPS nuopc_cap_share
+
+  use funit
+  use shr_dust_emis_mod, only : check_if_initialized
+  use unittestUtils, only : endrun_msg
+
+  implicit none
+
+  @TestCase
+  type, extends(TestCase) :: TestDustEmis
+   contains
+     procedure :: setUp
+     procedure :: tearDown
+  end type TestDustEmis
+
+contains
+
+  ! ========================================================================
+  ! Helper routines
+  ! ========================================================================
+
+  subroutine setUp(this)
+    class(TestDustEmis), intent(inout) :: this
+  end subroutine setUp
+
+  subroutine tearDown(this)
+    class(TestDustEmis), intent(inout) :: this
+
+  end subroutine tearDown
+
+
+
+  ! ========================================================================
+  ! Begin tests
+  ! ========================================================================
+
+   @Test
+  subroutine check_if_initialized_aborts(this)
+    ! Test that the check_if_initialized check aborts when called initially
+    class(TestDustEmis), intent(inout) :: this
+
+    call check_if_initialized()
+    @assertExceptionRaised(endrun_msg('ERROR: dust emission namelist has NOT been read in yet, shr_dust_emis_mod is NOT initialized') )
+
+  end subroutine check_if_initialized_aborts
+
+ 
+end module test_shr_dust_emis

From d2d2da45ec2662c404424096b03a9b32debd9e01 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 09:21:16 -0600
Subject: [PATCH 0249/1248] Change call to is_NOT_initialized function, unit
 test works

---
 src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index aa60427eac..a619618e1d 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -3,7 +3,7 @@ module test_shr_dust_emis
   ! Tests of shr_dust_emis_mod.F90 from CMEPS nuopc_cap_share
 
   use funit
-  use shr_dust_emis_mod, only : check_if_initialized
+  use shr_dust_emis_mod, only : is_NOT_initialized
   use unittestUtils, only : endrun_msg
 
   implicit none
@@ -40,9 +40,11 @@ contains
   subroutine check_if_initialized_aborts(this)
     ! Test that the check_if_initialized check aborts when called initially
     class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
 
-    call check_if_initialized()
+    not_init = is_NOT_initialized()
     @assertExceptionRaised(endrun_msg('ERROR: dust emission namelist has NOT been read in yet, shr_dust_emis_mod is NOT initialized') )
+    @assertTrue(not_init)
 
   end subroutine check_if_initialized_aborts
 

From 66578f0efd1f575b3adfe49bf1682e9c6fe703cb Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 10:51:45 -0600
Subject: [PATCH 0250/1248] add a test that is expected to fail

---
 .../shr_dust_emis_test/test_shr_dust_emis.pf      | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index a619618e1d..646b3cfce1 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -3,8 +3,8 @@ module test_shr_dust_emis
   ! Tests of shr_dust_emis_mod.F90 from CMEPS nuopc_cap_share
 
   use funit
-  use shr_dust_emis_mod, only : is_NOT_initialized
-  use unittestUtils, only : endrun_msg
+  use shr_dust_emis_mod
+  use unittestUtils    , only : endrun_msg
 
   implicit none
 
@@ -48,5 +48,16 @@ contains
 
   end subroutine check_if_initialized_aborts
 
+   @Test
+  subroutine check_when_initialized_runs(this)
+    ! Test that the initializiation check runs when it is initialized
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'Zender_2003', 'lnd')
+    not_init = is_NOT_initialized()
+    @assertFalse(not_init)
+
+  end subroutine check_when_initialized_runs
  
 end module test_shr_dust_emis

From a6927691757bdb91dc4d911461446a4e0746c3aa Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 11:10:03 -0600
Subject: [PATCH 0251/1248] Update cmeps version so will work

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index 70c0bd6124..3753aac874 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -50,7 +50,7 @@ required = True
 [cmeps]
 #tag = cmeps0.14.50
 #branch = dust_emis_mod
-hash = 492faf0014ad9d91c22bb92e2570e558a76093fe
+hash = ecb6d45aa00a4960564ea963b00754fb4c3b7d2c
 protocol = git
 #repo_url = https://github.com/ESCOMP/CMEPS.git
 repo_url = https://github.com/ekluzek/CMEPS.git

From a65752d3d1abfc626631390c6b2378a5813e079f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Apr 2024 14:31:23 -0600
Subject: [PATCH 0252/1248] Add more tests that pass

---
 .../shr_dust_emis_test/test_shr_dust_emis.pf  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index 646b3cfce1..efe6a5c2a8 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -60,4 +60,35 @@ contains
 
   end subroutine check_when_initialized_runs
  
+   @Test
+  subroutine check_dust_emis(this)
+    ! Test that the dust_emis logical functions work as expected
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'Zender_2003', 'lnd')
+    @assertTrue( is_dust_emis_zender() )
+    @assertFalse( is_dust_emis_leung() )
+    call dust_emis_set_options( 'Leung_2023', 'lnd')
+    @assertFalse( is_dust_emis_zender() )
+    @assertTrue( is_dust_emis_leung() )
+
+  end subroutine check_dust_emis
+
+   
+  @Test
+  subroutine check_zender_soil(this)
+    ! Test that the dust_emis_Zender logical functions work as expected
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'Zender_2003', 'lnd')
+    @assertTrue( is_zender_soil_erod_from_land() )
+    @assertFalse( is_zender_soil_erod_from_atm() )
+    call dust_emis_set_options( 'Zender_2003', 'atm')
+    @assertFalse( is_zender_soil_erod_from_land() )
+    @assertTrue( is_zender_soil_erod_from_atm() )
+
+  end subroutine check_zender_soil
+ 
 end module test_shr_dust_emis

From dd73ca699a83c80f5d2dc36fb9fa7482b4eec5eb Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 1 May 2024 13:50:29 -0600
Subject: [PATCH 0253/1248] Add new tests and get working again

---
 .../shr_dust_emis_test/test_shr_dust_emis.pf  | 22 ++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index efe6a5c2a8..467d00de59 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -69,7 +69,7 @@ contains
     call dust_emis_set_options( 'Zender_2003', 'lnd')
     @assertTrue( is_dust_emis_zender() )
     @assertFalse( is_dust_emis_leung() )
-    call dust_emis_set_options( 'Leung_2023', 'lnd')
+    call dust_emis_set_options( 'Leung_2023', 'none')
     @assertFalse( is_dust_emis_zender() )
     @assertTrue( is_dust_emis_leung() )
 
@@ -90,5 +90,25 @@ contains
     @assertTrue( is_zender_soil_erod_from_atm() )
 
   end subroutine check_zender_soil
+
+     
+  @Test
+  subroutine check_options(this)
+    ! Test that the check_options subroutine catches errors that should die
+    class(TestDustEmis), intent(inout) :: this
+    logical :: not_init
+
+    call dust_emis_set_options( 'zztop', 'zztop')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: dust_emis_method namelist item is not valid'))
+    call dust_emis_set_options( 'Leung_2023', 'lnd')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source should NOT be set, when dust_emis_method=Leung_2023'))
+    call dust_emis_set_options( 'Leung_2023', 'atm')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source should NOT be set, when dust_emis_method=Leung_2023'))
+    call dust_emis_set_options( 'Zender_2003', 'none')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source can only be lnd or atm'))
+    call dust_emis_set_options( 'Zender_2003', 'zztop')
+    @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source can only be lnd or atm'))
+
+  end subroutine check_options
  
 end module test_shr_dust_emis

From ccd976af2ace8896eef72013d80ba3bccd8684af Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 1 May 2024 14:05:25 -0600
Subject: [PATCH 0254/1248] Update cmeps with unit-testing completed

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index 3753aac874..39818b0fdc 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -50,7 +50,7 @@ required = True
 [cmeps]
 #tag = cmeps0.14.50
 #branch = dust_emis_mod
-hash = ecb6d45aa00a4960564ea963b00754fb4c3b7d2c
+hash = 0285eeb59605df44bc3abf38a61e8436361e7e8c
 protocol = git
 #repo_url = https://github.com/ESCOMP/CMEPS.git
 repo_url = https://github.com/ekluzek/CMEPS.git

From 65fc5536bd17b81f3b532ac764e15991b61a1e41 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 4 May 2024 11:08:24 -0600
Subject: [PATCH 0255/1248] Add LND_SETS_DUST_EMIS_DRV_FLDS which will be used
 to NOT set dust_emis drv_flds_in settings when CAM is going to set them

---
 cime_config/config_component.xml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index f7adab268f..c474b7e0c1 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -162,6 +162,20 @@
     This is typically set by the compset.</desc>
   </entry>
 
+  <entry id="LND_SETS_DUST_EMIS_DRV_FLDS">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>TRUE</default_value>
+    <values>
+      <!-- Until CAM sets dust settings in drv_flds_in this should only be TRUE
+      <value compset="CAM"  >FALSE</value>
+      -->
+    </values>
+    <group>run_component_cpl</group>
+    <file>env_run.xml</file>
+    <desc>If CTSM will set the dust settings in drv_flds_in (TRUE), or if ATM (i.e. CAM) will - DO NOT EDIT (set by compset name)</desc>
+  </entry>
+
   <entry id="CLM_CONFIGURATION">
     <type>char</type>
     <valid_values>clm,nwp</valid_values>

From d9c94eb04ebbf31ef4d5441d26eb59d360b2251d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 4 May 2024 11:17:34 -0600
Subject: [PATCH 0256/1248] Move dust_emis and soil_erod namelist items to the
 drv_fld_in namelist file in CMEPS

---
 bld/CLMBuildNamelist.pm                            | 13 ++++++++-----
 bld/namelist_files/namelist_defaults_ctsm.xml      |  2 --
 bld/namelist_files/namelist_definition_ctsm.xml    | 14 --------------
 .../namelist_definition_drv_flds.xml               | 13 +++++++++++++
 bld/unit_testers/build-namelist_test.pl            | 14 +++++++++++++-
 5 files changed, 34 insertions(+), 22 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fb44023cd5..ce2c2a81d2 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -517,6 +517,7 @@ sub read_namelist_defaults {
                             "$cfgdir/namelist_files/namelist_defaults_ctsm.xml",
                             "$cfgdir/namelist_files/namelist_defaults_drv.xml",
                             "$cfgdir/namelist_files/namelist_defaults_fire_emis.xml",
+                            "$cfgdir/namelist_files/namelist_defaults_dust_emis.xml",
                             "$cfgdir/namelist_files/namelist_defaults_drydep.xml" );
 
   # Add the location of the use case defaults files to the options hash
@@ -3988,7 +3989,7 @@ sub setup_logic_fire_emis {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_dust_emis {
-  # Logic to handle the dust emissions
+  # Logic to handle the dust emissions namelists, both drv_flds_in and lnd_in files
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   # First get the dust emission method
@@ -4011,14 +4012,16 @@ sub setup_logic_dust_emis {
                        'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source,
                        'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} );
         }
-     } else {
+     } elsif ( $zender_source eq "atm" ) {
         foreach my $option ( @zender_files_in_lnd_opts ) {
            if ( defined($nl->get_value($option)) ) {
-             $log->fatal_error("zender_soil_erod_source is NOT lnd, but the file option $option is being set" .
-                               " and should NOT be unless you want it handled here in the LAND model, " .
+             $log->fatal_error("zender_soil_erod_source is atm, and the file option $option is being set" .
+                               " which should NOT be unless you want it handled here in the LAND model, " .
                                "otherwise the equivalent option is set in CAM" );
            }
         }
+     } elsif ( $zender_source eq "none" ) {
+        $log->fatal_error("zender_soil_erod_source is set to none and only atm or lnd should be used when $var is Zender_2002" );
      }
   } else {
      # Verify that NONE of the Zender options are being set if Zender is NOT being used
@@ -4736,7 +4739,7 @@ sub write_output_files {
   $log->verbose_message("Writing clm namelist to $outfile");
 
   # Drydep, fire-emission or MEGAN namelist for driver
-  @groups = qw(drydep_inparm megan_emis_nl fire_emis_nl carma_inparm);
+  @groups = qw(drydep_inparm megan_emis_nl fire_emis_nl carma_inparm dust_emis_inparm);
   $outfile = "$opts->{'dir'}/drv_flds_in";
   $nl->write($outfile, 'groups'=>\@groups, 'note'=>"$note" );
   $log->verbose_message("Writing @groups namelists to $outfile");
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index cc407961ff..b232c865cb 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1993,8 +1993,6 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- Defaults for Zender's soil erodibility data  -->
 <!-- ===========================================  -->
 
-<dust_emis_method>Zender_2003</dust_emis_method>
-<zender_soil_erod_source dust_emis_method="Zender_2003">atm</zender_soil_erod_source>
 <zendersoilerod_mapalgo>bilinear</zendersoilerod_mapalgo>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 37c457141c..e730082e90 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1612,20 +1612,6 @@ Mapping method from Nitrogen deposition input file to the model resolution
 <!-- Dust namelist and Zender soil erodibility stream                                          -->
 <!-- ========================================================================================  -->
 
-<entry id="dust_emis_method" type="char*12" category="physics"
-       group="clm_inparm" valid_values="Zender_2003,Leung_2023" >
-Which dust emission method is going to be used. Either the Zender 2003 scheme or the Leung 2023
-scheme.
-(NOTE: The Leung 2023 method is NOT currently available)
-</entry>
-
-<entry id="zender_soil_erod_source" type="char*3" category="physics"
-       group="zendersoilerod" valid_values="lnd,atm" >
-Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
-here in CTSM, or in the ATM model.
-(only used when dust_emis_method is Zender_2003)
-</entry>
-
 <entry id="zendersoilerod_mapalgo" type="char*256" category="physics"
        group="zendersoilerod" valid_values="bilinear,nn,nnoni,nnonj,spval,copy" >
 Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
diff --git a/bld/namelist_files/namelist_definition_drv_flds.xml b/bld/namelist_files/namelist_definition_drv_flds.xml
index 088f5c5fa9..89bab07f4f 100644
--- a/bld/namelist_files/namelist_definition_drv_flds.xml
+++ b/bld/namelist_files/namelist_definition_drv_flds.xml
@@ -123,4 +123,17 @@
     List of fluxes needed by the CARMA model, from CLM to CAM.
   </entry>
 
+  <entry id="dust_emis_method" type="char*80" category="dust_emissions"
+    group="dust_emis_inparm" valid_values="Zender_2003,Leung_2023" >
+     Which dust emission method is going to be used. Either the Zender 2003 scheme or the Leung 2023 scheme.
+     (NOTE: The Leung 2023 method is NOT currently available)
+  </entry>
+
+  <entry id="zender_soil_erod_source" type="char*80" category="dust_emissions"
+    group="dust_emis_inparm" valid_values="none,lnd,atm" >
+     Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
+     in the active LAND model or in the ATM model.
+     (only used when dust_emis_method is Zender_2003)
+  </entry>
+
 </namelist_definition>
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 7b654337af..114fb0c36c 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 2513;
+my $ntests = 2515;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 1545;
@@ -1255,6 +1255,18 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                      },
+     "soil_erod_none_w_Zender"  =>{ options=>"--envxml_dir .",
+                                     namelst=>"dust_emis_method='Zender_2003', " .
+                                     "zender_soil_erod_source='none'",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                     },
+     "soil_erod_bad_w_Zender"   =>{ options=>"--envxml_dir .",
+                                     namelst=>"dust_emis_method='Zender_2003', " .
+                                     "zender_soil_erod_source='zztop'",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                     },
                );
 foreach my $key ( keys(%failtest) ) {
    print( "$key\n" );

From 0c23d08c2bad4677b70afe22640e2a8bb5f4543a Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 2 May 2024 14:26:53 -0600
Subject: [PATCH 0257/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 82 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e5c2466085..e0a5e45cb6 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,85 @@
 ===============================================================
+Tag name: ctsm5.2.003
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Thu May  2 14:06:54 MDT 2024
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+Brings in 4 PRs from b4b-dev to master:
+- Regional CTSM Simulations and Capability of Creating Mesh Files (ESCOMP/CTSM#1892; Negin Sobhani and Adrianna Foster)
+- Add line about documentation in PR template (ESCOMP/CTSM#2488; Sam Rabin)
+- CTSM5.2 2000 fsurdat T42 64x128 file (ESCOMP/CTSM#2495; Sam Levis)
+- Move plumber2 scripts to python directory (ESCOMP/CTSM#2505; Teagan King)
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description):
+- Resolves ESCOMP/CTSM#1513: Need a process to subset ESMF mesh files from global ones for regional grids
+- Resolves ESCOMP/CTSM#1773: High resolution regional simulations
+- Resolves ESCOMP/CTSM#2187: Move new PLUMBER2 scripts to python directory to enable python testing
+- Resolves ESCOMP/CTSM#2486: Temporarily add back a T42 dataset for CAM
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to documentation:
+- Adds documentation for making mesh files
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+- Adds testing for mesh-making Python scripts
+- Adds testing for plumber2_surf_wrapper
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2513: Merge b4b-dev 2024-05-02
+- Constituent PRs:
+  - ESCOMP/CTSM#1892: Regional CTSM Simulations and Capability of Creating Mesh Files (https://github.com/ESCOMP/CTSM/pull/1892)
+  - ESCOMP/CTSM#2488: Add line about documentation in PR template (https://github.com/ESCOMP/CTSM/pull/2488)
+  - ESCOMP/CTSM#2495: CTSM5.2 2000 fsurdat T42 64x128 file (https://github.com/ESCOMP/CTSM/pull/2495)
+  - ESCOMP/CTSM#2505: Move plumber2 scripts to python directory (https://github.com/ESCOMP/CTSM/pull/2505)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.002
 Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
 Date: Fri 26 Apr 2024 11:13:46 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 40033a7d6f..b48e04889d 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev
        ctsm5.2.002 glemieux 04/26/2024 FATES default allometry parameter file update
        ctsm5.2.001     erik 04/22/2024 Merge b4b-dev
          ctsm5.2.0     many 04/20/2024 New mksurfdata_esmf tool to create new surface datasets that are in place

From 747d104c156733f520008819359612c0b8b1dd83 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 7 May 2024 03:30:20 -0600
Subject: [PATCH 0258/1248] Start adding reference for
 LND_SETS_DUST_EMIS_DRV_FLDS in unit tester

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 114fb0c36c..30110d92f7 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -42,7 +42,7 @@ sub make_env_run {
     my %settings = @_;
 
     # Set default settings
-    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" );
+    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE",  LND_SETS_DUST_EMIS_DRV_FLDS=>"TRUE", NEONSITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
        $env_vars{$item} = $settings{$item};

From c36f3a9e6aa9e58f8ff05d4db7ee7349690841f5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 7 May 2024 03:31:04 -0600
Subject: [PATCH 0259/1248] Add dust emis namelist default for drv_flds_in

---
 .../namelist_defaults_dust_emis.xml           | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 bld/namelist_files/namelist_defaults_dust_emis.xml

diff --git a/bld/namelist_files/namelist_defaults_dust_emis.xml b/bld/namelist_files/namelist_defaults_dust_emis.xml
new file mode 100644
index 0000000000..40bf3d9078
--- /dev/null
+++ b/bld/namelist_files/namelist_defaults_dust_emis.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+
+<?xml-stylesheet type="text/xsl" href="namelist_defaults.xsl"?>
+
+<namelist_defaults>
+
+<!--
+Values to use by default for creation of CLM model driver namelists.
+The element names are the same as the corresponding namelist
+variables.  Values that depend on the model configuration use
+attributes to express the dependency.  The recognized attributes
+are: RESOLUTION, defaults, mask, ic_ymd, ic_tod, sim_year and all configuration
+attributes from the config_cache.xml file (with keys converted to upper-case).
+-->
+
+<!-- Defaults for dust_emis_inparm namelist  -->
+<dust_emis_method>Zender_2003</dust_emis_method>
+
+<zender_soil_erod_source>atm</zender_soil_erod_source>
+
+</namelist_defaults>

From 8ab4063d65dff584758d054c05287e49a00d9130 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 15 May 2024 11:14:02 -0600
Subject: [PATCH 0260/1248] Git rebase didn't correct the change files for some
 reason, so going back to the b4b-dev version of those

---
 doc/ChangeLog | 81 ---------------------------------------------------
 doc/ChangeSum |  1 -
 2 files changed, 82 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e0a5e45cb6..e5c2466085 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,85 +1,4 @@
 ===============================================================
-Tag name: ctsm5.2.003
-Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
-Date: Thu May  2 14:06:54 MDT 2024
-One-line Summary: Merge b4b-dev
-
-Purpose and description of changes
-----------------------------------
-
-Brings in 4 PRs from b4b-dev to master:
-- Regional CTSM Simulations and Capability of Creating Mesh Files (ESCOMP/CTSM#1892; Negin Sobhani and Adrianna Foster)
-- Add line about documentation in PR template (ESCOMP/CTSM#2488; Sam Rabin)
-- CTSM5.2 2000 fsurdat T42 64x128 file (ESCOMP/CTSM#2495; Sam Levis)
-- Move plumber2 scripts to python directory (ESCOMP/CTSM#2505; Teagan King)
-
-
-Significant changes to scientifically-supported configurations
---------------------------------------------------------------
-
-Does this tag change answers significantly for any of the following physics configurations?
-(Details of any changes will be given in the "Answer changes" section below.)
-
-    [Put an [X] in the box for any configuration with significant answer changes.]
-
-[ ] clm6_0
-
-[ ] clm5_1
-
-[ ] clm5_0
-
-[ ] ctsm5_0-nwp
-
-[ ] clm4_5
-
-
-Bugs fixed
-----------
-
-List of CTSM issues fixed (include CTSM Issue # and description):
-- Resolves ESCOMP/CTSM#1513: Need a process to subset ESMF mesh files from global ones for regional grids
-- Resolves ESCOMP/CTSM#1773: High resolution regional simulations
-- Resolves ESCOMP/CTSM#2187: Move new PLUMBER2 scripts to python directory to enable python testing
-- Resolves ESCOMP/CTSM#2486: Temporarily add back a T42 dataset for CAM
-
-
-Notes of particular relevance for users
----------------------------------------
-
-Changes to documentation:
-- Adds documentation for making mesh files
-
-
-Notes of particular relevance for developers:
----------------------------------------------
-
-Changes to tests or testing:
-- Adds testing for mesh-making Python scripts
-- Adds testing for plumber2_surf_wrapper
-
-
-Testing summary:
-----------------
-
-  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
-
-    derecho ----- OK
-    izumi ------- OK
-
-
-Other details
--------------
-
-Pull Requests that document the changes (include PR ids):
-- ESCOMP/CTSM#2513: Merge b4b-dev 2024-05-02
-- Constituent PRs:
-  - ESCOMP/CTSM#1892: Regional CTSM Simulations and Capability of Creating Mesh Files (https://github.com/ESCOMP/CTSM/pull/1892)
-  - ESCOMP/CTSM#2488: Add line about documentation in PR template (https://github.com/ESCOMP/CTSM/pull/2488)
-  - ESCOMP/CTSM#2495: CTSM5.2 2000 fsurdat T42 64x128 file (https://github.com/ESCOMP/CTSM/pull/2495)
-  - ESCOMP/CTSM#2505: Move plumber2 scripts to python directory (https://github.com/ESCOMP/CTSM/pull/2505)
-
-===============================================================
-===============================================================
 Tag name: ctsm5.2.002
 Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
 Date: Fri 26 Apr 2024 11:13:46 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index b48e04889d..40033a7d6f 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,5 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev
        ctsm5.2.002 glemieux 04/26/2024 FATES default allometry parameter file update
        ctsm5.2.001     erik 04/22/2024 Merge b4b-dev
          ctsm5.2.0     many 04/20/2024 New mksurfdata_esmf tool to create new surface datasets that are in place

From 4715afef8db5cade7e3a2835ee6044bd711b21e3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 15 May 2024 14:33:34 -0600
Subject: [PATCH 0261/1248] Bring back
 src/unit_test_stubs/csm_share/CMakeLists.txt for FUNIT test

---
 src/unit_test_stubs/csm_share/CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 src/unit_test_stubs/csm_share/CMakeLists.txt

diff --git a/src/unit_test_stubs/csm_share/CMakeLists.txt b/src/unit_test_stubs/csm_share/CMakeLists.txt
new file mode 100644
index 0000000000..33ddbfb342
--- /dev/null
+++ b/src/unit_test_stubs/csm_share/CMakeLists.txt
@@ -0,0 +1,5 @@
+list(APPEND share_sources
+  shr_mpi_mod_stub.F90
+  )
+
+sourcelist_to_parent(share_sources)

From f19a080721f5fffa96b580da51a170cbe80d4244 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 15 May 2024 17:59:34 -0600
Subject: [PATCH 0262/1248] add more landuse graceful failures

If luh + fbg are present fail if flandusepftdat isn't valid.
Don't allow fluh_timeseries to be defined if in potential veg mode
to avoid confusing users that it is needed.
---
 bld/CLMBuildNamelist.pm | 71 ++++++++++++++++++++++++-----------------
 1 file changed, 42 insertions(+), 29 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index aafc7739a3..0d8ca732b4 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4433,21 +4433,9 @@ sub setup_logic_fates {
            }
         }
         # make sure that fates landuse x pft mode has the necessary run mode configurations
-        # and add the necessary landuse x pft static mapping data default if not defined
         my $var = "use_fates_lupft";
         if ( defined($nl->get_value($var))  ) {
           if ( &value_is_true($nl->get_value($var)) ) {
-            $var = "flandusepftdat";
-            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                        'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
-            my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
-            if ( ! defined($nl->get_value($var))  ) {
-              $log->fatal_error("$var is required when use_fates_lupft is set" );
-            } elsif ( ! -f "$fname" ) {
-              $log->fatal_error("$fname does NOT point to a valid filename" );
-            }
-
-            # make sure that nocomp and fbg mode are enabled as well as use_fates_luh
             my @list = ( "use_fates_luh", "use_fates_nocomp", "use_fates_fixed_biogeog" );
             foreach my $var ( @list ) {
               if ( ! &value_is_true($nl->get_value($var)) ) {
@@ -4457,31 +4445,56 @@ sub setup_logic_fates {
           }
         }
         # check that fates landuse change mode has the necessary luh2 landuse timeseries data
-        # and add the default if not defined
+        # and add the default if not defined.  Do not add default if use_fates_potentialveg is true.
+        # If fixed biogeography is on, make sure that flandusepftdat is avilable.
         my $var = "use_fates_luh";
         if ( defined($nl->get_value($var))  ) {
            if ( &value_is_true($nl->get_value($var)) ) {
-              $var = "fluh_timeseries";
-              add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
-              my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
-              if ( ! defined($nl->get_value($var))  ) {
-                 $log->fatal_error("$var is required when use_fates_luh is set" );
-              } elsif ( ! -f "$fname" ) {
-                 $log->fatal_error("$fname does NOT point to a valid filename" );
-              }
+              $var = "use_fates_potentialveg";
+              if ( defined($nl->get_value($var))  ) {
+                 if ( ! &value_is_true($nl->get_value($var)) ) {
+                    $var = "fluh_timeseries";
+                    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 
+           			'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
+                    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+                    if ( ! defined($nl->get_value($var))  ) {
+                       $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" );
+                    } elsif ( ! -f "$fname" ) {
+                       $log->fatal_error("$var does NOT point to a valid filename" );
+                    }
+                 }
+	      }
+              $var = "use_fates_fixed_biogeog";
+              if ( defined($nl->get_value($var))  ) {
+                 if ( &value_is_true($nl->get_value($var)) ) {
+            	    $var = "flandusepftdat";
+            	    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
+            	                'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
+            	    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+            	    if ( ! defined($nl->get_value($var))  ) {
+            	      $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
+            	    } elsif ( ! -f "$fname" ) {
+            	      $log->fatal_error("$var does NOT point to a valid filename" );
+            	    }
+		 }
+	      }
            }
         }
         # check that fates landuse is on and harvest mode is off when potential veg switch is true
         my $var = "use_fates_potentialveg";
         if ( defined($nl->get_value($var))  ) {
-          if ( &value_is_true($nl->get_value($var)) ) {
-            if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
-              $log->fatal_error("use_fates_luh must be true when $var is true" );
-            }
-            if ( $nl->get_value('fates_harvest_mode') > 0) {
-              $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" );
-            }
-          }
+           if ( &value_is_true($nl->get_value($var)) ) {
+              if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
+                $log->fatal_error("use_fates_luh must be true when $var is true" );
+              }
+              if ( $nl->get_value('fates_harvest_mode') > 0) {
+                $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" );
+              }
+              my $var = "fluh_timeseries";
+              if ( defined($nl->get_value($var))  ) {
+                 $log->fatal_error("fluh_timeseries can not be defined when use_fates_potentialveg is true" );
+                 }
+           }
         }
         # Check fates_harvest_mode compatibility
         my $var = "fates_harvest_mode";

From 39dc01e6f31f72246a5c3c781b5c83ab6e2a2598 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 16 May 2024 11:39:30 -0600
Subject: [PATCH 0263/1248] Revert "Remove the src/cpl/mct directory"

This reverts commit 371f093e02a7820e8beec823c97dd23b94277c05.

Jim Edwards posted the following in my PR:
"although you can remove cpl7 you cannot yet remove mct. However I don't
 expect you to remove any externals in this tag, I will remove them in
 the next tag."
---
 src/cpl/mct/ExcessIceStreamType.F90       | 144 +++++
 src/cpl/mct/FireDataBaseType.F90          | 561 +++++++++++++++++++
 src/cpl/mct/SoilMoistureStreamMod.F90     | 418 ++++++++++++++
 src/cpl/mct/UrbanTimeVarType.F90          | 314 +++++++++++
 src/cpl/mct/ch4FInundatedStreamType.F90   | 389 +++++++++++++
 src/cpl/mct/clm_cpl_indices.F90           | 330 +++++++++++
 src/cpl/mct/laiStreamMod.F90              | 241 +++++++++
 src/cpl/mct/lnd_comp_mct.F90              | 632 ++++++++++++++++++++++
 src/cpl/mct/lnd_import_export.F90         | 354 ++++++++++++
 src/cpl/mct/lnd_set_decomp_and_domain.F90 | 352 ++++++++++++
 src/cpl/mct/ndepStreamMod.F90             | 376 +++++++++++++
 11 files changed, 4111 insertions(+)
 create mode 100644 src/cpl/mct/ExcessIceStreamType.F90
 create mode 100644 src/cpl/mct/FireDataBaseType.F90
 create mode 100644 src/cpl/mct/SoilMoistureStreamMod.F90
 create mode 100644 src/cpl/mct/UrbanTimeVarType.F90
 create mode 100644 src/cpl/mct/ch4FInundatedStreamType.F90
 create mode 100644 src/cpl/mct/clm_cpl_indices.F90
 create mode 100644 src/cpl/mct/laiStreamMod.F90
 create mode 100644 src/cpl/mct/lnd_comp_mct.F90
 create mode 100644 src/cpl/mct/lnd_import_export.F90
 create mode 100644 src/cpl/mct/lnd_set_decomp_and_domain.F90
 create mode 100644 src/cpl/mct/ndepStreamMod.F90

diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90
new file mode 100644
index 0000000000..5c5394233c
--- /dev/null
+++ b/src/cpl/mct/ExcessIceStreamType.F90
@@ -0,0 +1,144 @@
+module ExcessIceStreamType
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Stub for ExcessIceStreams for the MCT driver. So that MCT can be used
+  ! without excess ice streams.
+  !
+  ! !USES
+  use shr_kind_mod     , only : r8 => shr_kind_r8, CL => shr_kind_CL
+  use shr_log_mod      , only : errMsg => shr_log_errMsg
+  use spmdMod          , only : mpicom, masterproc
+  use clm_varctl       , only : iulog
+  use abortutils       , only : endrun
+  use decompMod        , only : bounds_type
+
+  ! !PUBLIC TYPES:
+  implicit none
+  private
+
+  public  :: UseExcessIceStreams      ! If streams will be used
+
+  type, public :: excessicestream_type
+  contains
+
+      ! !PUBLIC MEMBER FUNCTIONS:
+      procedure, public  :: Init            ! Initialize and read data in
+      procedure, public  :: CalcExcessIce   ! Calculate excess ice ammount
+
+      ! !PRIVATE MEMBER FUNCTIONS:
+      procedure, private :: ReadNML     ! Read in namelist
+
+  end type excessicestream_type
+  ! ! PRIVATE DATA:
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+!==============================================================================
+contains
+!==============================================================================
+
+  subroutine Init(this, bounds, NLFilename)
+    !
+    !
+    ! arguments
+    implicit none
+    class(excessicestream_type) :: this
+    type(bounds_type), intent(in)   :: bounds
+    character(len=*),  intent(in)   :: NLFilename   ! Namelist filename
+
+    !
+    ! local variables
+
+    call this%ReadNML( bounds, NLFileName )
+  end subroutine Init
+
+  subroutine CalcExcessIce(this,bounds,exice_bulk_init)
+  
+  ! only transfers grid values to columns
+   implicit none
+   class(excessicestream_type)        :: this
+   type(bounds_type),  intent(in)     :: bounds
+   real(r8)         ,  intent(inout)  :: exice_bulk_init(bounds%begc:bounds%endc) 
+   !
+   ! !LOCAL VARIABLES:
+   
+  end subroutine CalcExcessIce
+
+  logical function UseExcessIceStreams()
+  !
+  ! !DESCRIPTION:
+  ! Return true if
+  !
+  ! !USES:
+  !
+  ! !ARGUMENTS:
+  implicit none
+  !
+  ! !LOCAL VARIABLES:
+  UseExcessIceStreams = .false.
+end function UseExcessIceStreams
+
+subroutine ReadNML(this, bounds, NLFilename)
+  !
+  ! Read the namelist data stream information.
+  !
+  ! Uses:
+  use shr_nl_mod       , only : shr_nl_find_group_name
+  use shr_log_mod      , only : errMsg => shr_log_errMsg
+  use shr_mpi_mod      , only : shr_mpi_bcast
+  !
+  ! arguments
+  implicit none
+  class(excessicestream_type)   :: this
+  type(bounds_type), intent(in) :: bounds
+  character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+  !
+  ! local variables
+  integer            :: nu_nml    ! unit for namelist file
+  integer            :: nml_error ! namelist i/o error flag
+  logical            :: use_excess_ice_streams = .false.         ! logical to turn on use of excess ice streams
+  character(len=CL)  :: stream_fldFileName_exice = ' '
+  character(len=CL)  :: stream_mapalgo_exice = 'none'
+  character(len=*), parameter :: namelist_name = 'exice_streams'    ! MUST agree with name in namelist and read
+  character(len=*), parameter :: subName = "('exice_streams::ReadNML')"
+  !-----------------------------------------------------------------------
+
+  namelist /exice_streams/ &               ! MUST agree with namelist_name above
+       stream_mapalgo_exice,  stream_fldFileName_exice, use_excess_ice_streams
+  !-----------------------------------------------------------------------
+  ! Default values for namelist
+
+  ! Read excess ice namelist
+  if (masterproc) then
+     open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+     call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error)
+     if (nml_error == 0) then
+        read(nu_nml, nml=exice_streams,iostat=nml_error)   ! MUST agree with namelist_name above
+        if (nml_error /= 0) then
+           call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
+        end if
+     else
+        call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
+     end if
+     close(nu_nml)
+  endif
+
+  call shr_mpi_bcast(use_excess_ice_streams   , mpicom)
+
+  if (masterproc) then
+     if ( use_excess_ice_streams ) then
+        call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__))
+     end if
+     if ( trim(stream_fldFileName_exice) /= ''  ) then
+        call endrun(msg=' ERROR stream_fldFileName_exice can NOT be set for the MCT driver'//errMsg(sourcefile, __LINE__))
+     end if
+     if ( trim(stream_mapalgo_exice) /= 'none'  ) then
+        call endrun(msg=' ERROR stream_mapalgo_exice can only be none for the MCT driver'//errMsg(sourcefile, __LINE__))
+     end if
+  endif
+
+end subroutine ReadNML
+
+end module ExcessIceStreamType
diff --git a/src/cpl/mct/FireDataBaseType.F90 b/src/cpl/mct/FireDataBaseType.F90
new file mode 100644
index 0000000000..0ee635b2fa
--- /dev/null
+++ b/src/cpl/mct/FireDataBaseType.F90
@@ -0,0 +1,561 @@
+module FireDataBaseType
+
+#include "shr_assert.h"
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! module for handling of fire data
+  !
+  ! !USES:
+  use shr_kind_mod    , only : r8 => shr_kind_r8, CL => shr_kind_CL
+  use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create, shr_strdata_print
+  use shr_strdata_mod , only : shr_strdata_advance
+  use shr_log_mod     , only : errMsg => shr_log_errMsg
+  use clm_varctl      , only : iulog, inst_name
+  use spmdMod         , only : masterproc, mpicom, comp_id
+  use fileutils       , only : getavu, relavu
+  use domainMod       , only : ldomain
+  use abortutils      , only : endrun
+  use decompMod       , only : bounds_type
+  use FireMethodType  , only : fire_method_type
+  use lnd_set_decomp_and_domain, only : gsmap_global
+  use mct_mod
+  !
+  implicit none
+  private
+  !
+  ! !PUBLIC TYPES:
+  public :: fire_base_type
+
+  !
+  type, abstract, extends(fire_method_type) :: fire_base_type
+    private
+      ! !PRIVATE MEMBER DATA:
+
+      real(r8), public, pointer :: forc_lnfm(:)    ! Lightning frequency
+      real(r8), public, pointer :: forc_hdm(:)     ! Human population density
+      
+      real(r8), public, pointer :: gdp_lf_col(:)   ! col global real gdp data (k US$/capita)
+      real(r8), public, pointer :: peatf_lf_col(:) ! col global peatland fraction data (0-1)
+      integer , public, pointer :: abm_lf_col(:)   ! col global peak month of crop fire emissions
+
+      type(shr_strdata_type) :: sdat_hdm    ! Human population density input data stream
+      type(shr_strdata_type) :: sdat_lnfm   ! Lightning input data stream
+
+    contains
+      !
+      ! !PUBLIC MEMBER FUNCTIONS:
+      procedure, public :: FireInit => BaseFireInit     ! Initialization of Fire
+      procedure, public :: BaseFireInit                 ! Initialization of Fire
+      procedure(FireReadNML_interface), public, deferred :: FireReadNML       ! Read in namelist for Fire
+      procedure, public :: FireInterp        ! Interpolate fire data
+      procedure(need_lightning_and_popdens_interface), public, deferred :: &
+           need_lightning_and_popdens ! Returns true if need lightning & popdens
+      !
+      ! !PRIVATE MEMBER FUNCTIONS:
+      procedure, private :: hdm_init     ! position datasets for dynamic human population density
+      procedure, private :: hdm_interp   ! interpolates between two years of human pop. density file data
+      procedure, private :: lnfm_init    ! position datasets for Lightning
+      procedure, private :: lnfm_interp  ! interpolates between two years of Lightning file data
+      procedure, private :: surfdataread ! read fire related data from surface data set
+  end type fire_base_type
+  !-----------------------------------------------------------------------
+
+  abstract interface
+     !-----------------------------------------------------------------------
+     function need_lightning_and_popdens_interface(this) result(need_lightning_and_popdens)
+       !
+       ! !DESCRIPTION:
+       ! Returns true if need lightning and popdens, false otherwise
+       !
+       ! USES
+       import :: fire_base_type
+       !
+       ! !ARGUMENTS:
+       class(fire_base_type), intent(in) :: this
+       logical :: need_lightning_and_popdens  ! function result
+       !-----------------------------------------------------------------------
+     end function need_lightning_and_popdens_interface
+  end interface
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+contains
+
+  !-----------------------------------------------------------------------
+  subroutine FireReadNML_interface( this, NLFilename )
+    !
+    ! !DESCRIPTION:
+    ! Read the namelist for Fire
+    !
+    ! !USES:
+    !
+    ! !ARGUMENTS:
+    class(fire_base_type) :: this
+    character(len=*), intent(in) :: NLFilename ! Namelist filename
+  end subroutine FireReadNML_interface
+
+  !-----------------------------------------------------------------------
+  subroutine BaseFireInit( this, bounds, NLFilename )
+    !
+    ! !DESCRIPTION:
+    ! Initialize CN Fire module
+    ! !USES:
+    use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
+    !
+    ! !ARGUMENTS:
+    class(fire_base_type) :: this
+    type(bounds_type), intent(in) :: bounds
+    character(len=*),  intent(in) :: NLFilename
+    !-----------------------------------------------------------------------
+
+    if ( this%need_lightning_and_popdens() ) then
+       ! Allocate lightning forcing data
+       allocate( this%forc_lnfm(bounds%begg:bounds%endg) )
+       this%forc_lnfm(bounds%begg:) = nan
+       ! Allocate pop dens forcing data
+       allocate( this%forc_hdm(bounds%begg:bounds%endg) )
+       this%forc_hdm(bounds%begg:) = nan
+       
+       ! Allocate real gdp data
+       allocate(this%gdp_lf_col(bounds%begc:bounds%endc))
+       ! Allocate peatland fraction data
+       allocate(this%peatf_lf_col(bounds%begc:bounds%endc))
+       ! Allocates peak month of crop fire emissions
+       allocate(this%abm_lf_col(bounds%begc:bounds%endc))
+   
+
+       call this%hdm_init(bounds, NLFilename)
+       call this%hdm_interp(bounds)
+       call this%lnfm_init(bounds, NLFilename)
+       call this%lnfm_interp(bounds)
+       call this%surfdataread(bounds)
+    end if
+
+  end subroutine BaseFireInit
+
+  !-----------------------------------------------------------------------
+  subroutine FireInterp(this,bounds)
+    !
+    ! !DESCRIPTION:
+    ! Interpolate CN Fire datasets
+    !
+    ! !ARGUMENTS:
+    class(fire_base_type) :: this
+    type(bounds_type), intent(in) :: bounds
+    !-----------------------------------------------------------------------
+
+    if ( this%need_lightning_and_popdens() ) then
+       call this%hdm_interp(bounds)
+       call this%lnfm_interp(bounds)
+    end if
+
+  end subroutine FireInterp
+
+  !-----------------------------------------------------------------------
+  subroutine hdm_init( this, bounds, NLFilename )
+   !
+   ! !DESCRIPTION:
+   ! Initialize data stream information for population density.
+   !
+   ! !USES:
+   use clm_time_manager , only : get_calendar
+   use ncdio_pio        , only : pio_subsystem
+   use shr_pio_mod      , only : shr_pio_getiotype
+   use clm_nlUtilsMod   , only : find_nlgroup_name
+   use ndepStreamMod    , only : clm_domain_mct
+   use histFileMod      , only : hist_addfld1d
+   !
+   ! !ARGUMENTS:
+   implicit none
+   class(fire_base_type)         :: this
+   type(bounds_type), intent(in) :: bounds
+   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+   !
+   ! !LOCAL VARIABLES:
+   integer            :: stream_year_first_popdens   ! first year in pop. dens. stream to use
+   integer            :: stream_year_last_popdens    ! last year in pop. dens. stream to use
+   integer            :: model_year_align_popdens    ! align stream_year_first_hdm with
+   integer            :: nu_nml                      ! unit for namelist file
+   integer            :: nml_error                   ! namelist i/o error flag
+   type(mct_ggrid)    :: dom_clm                     ! domain information
+   character(len=CL)  :: stream_fldFileName_popdens  ! population density streams filename
+   character(len=CL)  :: popdensmapalgo = 'bilinear' ! mapping alogrithm for population density
+   character(len=CL)  :: popdens_tintalgo = 'nearest'! time interpolation alogrithm for population density
+   character(len=CL)  :: stream_meshfile_popdens     ! not used
+   character(*), parameter :: subName = "('hdmdyn_init')"
+   character(*), parameter :: F00 = "('(hdmdyn_init) ',4a)"
+   !-----------------------------------------------------------------------
+
+   namelist /popd_streams/          &
+        stream_year_first_popdens,  &
+        stream_year_last_popdens,   &
+        model_year_align_popdens,   &
+        popdensmapalgo,             &
+        stream_fldFileName_popdens, &
+        stream_meshfile_popdens   , &
+        popdens_tintalgo
+
+   ! Default values for namelist
+   stream_year_first_popdens  = 1       ! first year in stream to use
+   stream_year_last_popdens   = 1       ! last  year in stream to use
+   model_year_align_popdens   = 1       ! align stream_year_first_popdens with this model year
+   stream_fldFileName_popdens = ' '
+
+   ! Read popd_streams namelist
+   if (masterproc) then
+      nu_nml = getavu()
+      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+      call find_nlgroup_name(nu_nml, 'popd_streams', status=nml_error)
+      if (nml_error == 0) then
+         read(nu_nml, nml=popd_streams,iostat=nml_error)
+         if (nml_error /= 0) then
+            call endrun(msg='ERROR reading popd_streams namelist'//errMsg(sourcefile, __LINE__))
+         end if
+      end if
+      close(nu_nml)
+      call relavu( nu_nml )
+   endif
+
+   call shr_mpi_bcast(stream_year_first_popdens, mpicom)
+   call shr_mpi_bcast(stream_year_last_popdens, mpicom)
+   call shr_mpi_bcast(model_year_align_popdens, mpicom)
+   call shr_mpi_bcast(stream_fldFileName_popdens, mpicom)
+   call shr_mpi_bcast(popdens_tintalgo, mpicom)
+
+   if (masterproc) then
+      write(iulog,*) ' '
+      write(iulog,*) 'popdens_streams settings:'
+      write(iulog,*) '  stream_year_first_popdens  = ',stream_year_first_popdens
+      write(iulog,*) '  stream_year_last_popdens   = ',stream_year_last_popdens
+      write(iulog,*) '  model_year_align_popdens   = ',model_year_align_popdens
+      write(iulog,*) '  stream_fldFileName_popdens = ',stream_fldFileName_popdens
+      write(iulog,*) '  popdens_tintalgo           = ',popdens_tintalgo
+      write(iulog,*) ' '
+   endif
+
+   call clm_domain_mct (bounds, dom_clm)
+
+   call shr_strdata_create(this%sdat_hdm,name="clmhdm", &
+        pio_subsystem=pio_subsystem,                    &
+        pio_iotype=shr_pio_getiotype(inst_name),        &
+        mpicom=mpicom, compid=comp_id,                  &
+        gsmap=gsmap_global, ggrid=dom_clm,              &
+        nxg=ldomain%ni, nyg=ldomain%nj,                 &
+        yearFirst=stream_year_first_popdens,            &
+        yearLast=stream_year_last_popdens,              &
+        yearAlign=model_year_align_popdens,             &
+        offset=0,                                       &
+        domFilePath='',                                 &
+        domFileName=trim(stream_fldFileName_popdens),   &
+        domTvarName='time',                             &
+        domXvarName='lon' ,                             &
+        domYvarName='lat' ,                             &
+        domAreaName='area',                             &
+        domMaskName='mask',                             &
+        filePath='',                                    &
+        filename=(/trim(stream_fldFileName_popdens)/) , &
+        fldListFile='hdm',                              &
+        fldListModel='hdm',                             &
+        fillalgo='none',                                &
+        mapalgo=popdensmapalgo,                         &
+        calendar=get_calendar(),                        &
+        tintalgo=popdens_tintalgo,                      &
+        taxmode='extend'                           )
+
+   if (masterproc) then
+      call shr_strdata_print(this%sdat_hdm,'population density data')
+   endif
+
+   ! Add history fields
+   call hist_addfld1d (fname='HDM', units='counts/km^2',      &
+         avgflag='A', long_name='human population density',   &
+         ptr_lnd=this%forc_hdm, default='inactive')
+
+  end subroutine hdm_init
+
+  !-----------------------------------------------------------------------
+  subroutine hdm_interp( this, bounds)
+  !
+  ! !DESCRIPTION:
+  ! Interpolate data stream information for population density.
+  !
+  ! !USES:
+  use clm_time_manager, only : get_curr_date
+  !
+  ! !ARGUMENTS:
+  class(fire_base_type)       :: this
+  type(bounds_type), intent(in) :: bounds
+  !
+  ! !LOCAL VARIABLES:
+  integer :: g, ig
+  integer :: year    ! year (0, ...) for nstep+1
+  integer :: mon     ! month (1, ..., 12) for nstep+1
+  integer :: day     ! day of month (1, ..., 31) for nstep+1
+  integer :: sec     ! seconds into current date for nstep+1
+  integer :: mcdate  ! Current model date (yyyymmdd)
+  !-----------------------------------------------------------------------
+
+   call get_curr_date(year, mon, day, sec)
+   mcdate = year*10000 + mon*100 + day
+
+   call shr_strdata_advance(this%sdat_hdm, mcdate, sec, mpicom, 'hdmdyn')
+
+   ig = 0
+   do g = bounds%begg,bounds%endg
+      ig = ig+1
+      this%forc_hdm(g) = this%sdat_hdm%avs(1)%rAttr(1,ig)
+   end do
+
+  end subroutine hdm_interp
+
+  !-----------------------------------------------------------------------
+  subroutine lnfm_init( this, bounds, NLFilename )
+  !
+  ! !DESCRIPTION:
+  !
+  ! Initialize data stream information for Lightning.
+  !
+  ! !USES:
+  use clm_time_manager , only : get_calendar
+  use ncdio_pio        , only : pio_subsystem
+  use shr_pio_mod      , only : shr_pio_getiotype
+  use clm_nlUtilsMod   , only : find_nlgroup_name
+  use ndepStreamMod    , only : clm_domain_mct
+  use histFileMod      , only : hist_addfld1d
+  !
+  ! !ARGUMENTS:
+  implicit none
+  class(fire_base_type)       :: this
+  type(bounds_type), intent(in) :: bounds
+  character(len=*),  intent(in) :: NLFilename
+  !
+  ! !LOCAL VARIABLES:
+  integer            :: stream_year_first_lightng  ! first year in Lightning stream to use
+  integer            :: stream_year_last_lightng   ! last year in Lightning stream to use
+  integer            :: model_year_align_lightng   ! align stream_year_first_lnfm with
+  integer            :: nu_nml                     ! unit for namelist file
+  integer            :: nml_error                  ! namelist i/o error flag
+  type(mct_ggrid)    :: dom_clm                    ! domain information
+  character(len=CL)  :: stream_fldFileName_lightng ! lightning stream filename to read
+  character(len=CL)  :: lightng_tintalgo = 'linear'! time interpolation alogrithm
+  character(len=CL)  :: lightngmapalgo = 'bilinear'! Mapping alogrithm
+  character(*), parameter :: subName = "('lnfmdyn_init')"
+  character(*), parameter :: F00 = "('(lnfmdyn_init) ',4a)"
+  !-----------------------------------------------------------------------
+
+   namelist /light_streams/         &
+        stream_year_first_lightng,  &
+        stream_year_last_lightng,   &
+        model_year_align_lightng,   &
+        lightngmapalgo,             &
+        stream_fldFileName_lightng, &
+        lightng_tintalgo
+
+   ! Default values for namelist
+    stream_year_first_lightng  = 1      ! first year in stream to use
+    stream_year_last_lightng   = 1      ! last  year in stream to use
+    model_year_align_lightng   = 1      ! align stream_year_first_lnfm with this model year
+    stream_fldFileName_lightng = ' '
+
+   ! Read light_streams namelist
+   if (masterproc) then
+      nu_nml = getavu()
+      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+      call find_nlgroup_name(nu_nml, 'light_streams', status=nml_error)
+      if (nml_error == 0) then
+         read(nu_nml, nml=light_streams,iostat=nml_error)
+         if (nml_error /= 0) then
+            call endrun(msg='ERROR reading light_streams namelist'//errMsg(sourcefile, __LINE__))
+         end if
+      end if
+      close(nu_nml)
+      call relavu( nu_nml )
+   endif
+
+   call shr_mpi_bcast(stream_year_first_lightng, mpicom)
+   call shr_mpi_bcast(stream_year_last_lightng, mpicom)
+   call shr_mpi_bcast(model_year_align_lightng, mpicom)
+   call shr_mpi_bcast(stream_fldFileName_lightng, mpicom)
+   call shr_mpi_bcast(lightng_tintalgo, mpicom)
+
+   if (masterproc) then
+      write(iulog,*) ' '
+      write(iulog,*) 'light_stream settings:'
+      write(iulog,*) '  stream_year_first_lightng  = ',stream_year_first_lightng
+      write(iulog,*) '  stream_year_last_lightng   = ',stream_year_last_lightng
+      write(iulog,*) '  model_year_align_lightng   = ',model_year_align_lightng
+      write(iulog,*) '  stream_fldFileName_lightng = ',stream_fldFileName_lightng
+      write(iulog,*) '  lightng_tintalgo           = ',lightng_tintalgo
+      write(iulog,*) ' '
+   endif
+
+   call clm_domain_mct (bounds, dom_clm)
+
+   call shr_strdata_create(this%sdat_lnfm,name="clmlnfm", &
+        pio_subsystem=pio_subsystem,                      &
+        pio_iotype=shr_pio_getiotype(inst_name),          &
+        mpicom=mpicom, compid=comp_id,                    &
+        gsmap=gsmap_global, ggrid=dom_clm,                &
+        nxg=ldomain%ni, nyg=ldomain%nj,                   &
+        yearFirst=stream_year_first_lightng,              &
+        yearLast=stream_year_last_lightng,                &
+        yearAlign=model_year_align_lightng,               &
+        offset=0,                                         &
+        domFilePath='',                                   &
+        domFileName=trim(stream_fldFileName_lightng),     &
+        domTvarName='time',                               &
+        domXvarName='lon' ,                               &
+        domYvarName='lat' ,                               &
+        domAreaName='area',                               &
+        domMaskName='mask',                               &
+        filePath='',                                      &
+        filename=(/trim(stream_fldFileName_lightng)/),    &
+        fldListFile='lnfm',                               &
+        fldListModel='lnfm',                              &
+        fillalgo='none',                                  &
+        tintalgo=lightng_tintalgo,                        &
+        mapalgo=lightngmapalgo,                           &
+        calendar=get_calendar(),                          &
+        taxmode='cycle'                            )
+
+   if (masterproc) then
+      call shr_strdata_print(this%sdat_lnfm,'Lightning data')
+   endif
+
+   ! Add history fields
+   call hist_addfld1d (fname='LNFM', units='counts/km^2/hr',  &
+         avgflag='A', long_name='Lightning frequency',        &
+         ptr_lnd=this%forc_lnfm, default='inactive')
+
+  end subroutine lnfm_init
+
+  !-----------------------------------------------------------------------
+  subroutine lnfm_interp(this, bounds )
+  !
+  ! !DESCRIPTION:
+  ! Interpolate data stream information for Lightning.
+  !
+  ! !USES:
+  use clm_time_manager, only : get_curr_date
+  !
+  ! !ARGUMENTS:
+  class(fire_base_type)       :: this
+  type(bounds_type), intent(in) :: bounds
+  !
+  ! !LOCAL VARIABLES:
+  integer :: g, ig
+  integer :: year    ! year (0, ...) for nstep+1
+  integer :: mon     ! month (1, ..., 12) for nstep+1
+  integer :: day     ! day of month (1, ..., 31) for nstep+1
+  integer :: sec     ! seconds into current date for nstep+1
+  integer :: mcdate  ! Current model date (yyyymmdd)
+  !-----------------------------------------------------------------------
+
+   call get_curr_date(year, mon, day, sec)
+   mcdate = year*10000 + mon*100 + day
+
+   call shr_strdata_advance(this%sdat_lnfm, mcdate, sec, mpicom, 'lnfmdyn')
+
+   ig = 0
+   do g = bounds%begg,bounds%endg
+      ig = ig+1
+      this%forc_lnfm(g) = this%sdat_lnfm%avs(1)%rAttr(1,ig)
+   end do
+
+  end subroutine lnfm_interp
+
+  !-----------------------------------------------------------------------
+  subroutine surfdataread(this, bounds)
+  !
+  ! !DESCRIPTION:
+  ! Read surface data set to populate relevant fire-related variables
+  !
+  ! !USES:
+  use spmdMod    , only : masterproc
+  use clm_varctl , only : nsrest, nsrStartup, fsurdat
+  use clm_varcon , only : grlnd
+  use ColumnType , only : col
+  use fileutils  , only : getfil
+  use ncdio_pio
+  !
+  ! !ARGUMENTS:
+  class(fire_base_type) :: this
+  type(bounds_type), intent(in) :: bounds
+  !
+  ! !LOCAL VARIABLES:
+  integer               :: g,c       ! indices
+  type(file_desc_t)     :: ncid      ! netcdf id
+  logical               :: readvar   ! true => variable is on initial dataset
+  character(len=256)    :: locfn     ! local filename
+  real(r8), pointer     :: gdp(:)    ! global gdp data (needs to be a pointer for use in ncdio)
+  real(r8), pointer     :: peatf(:)  ! global peatf data (needs to be a pointer for use in ncdio)
+  integer,  pointer     :: abm(:)    ! global abm data (needs to be a pointer for use in ncdio)
+  !-----------------------------------------------------------------------
+
+   ! --------------------------------------------------------------------
+   ! Open surface dataset
+   ! --------------------------------------------------------------------
+
+   call getfil (fsurdat, locfn, 0)
+   call ncd_pio_openfile (ncid, locfn, 0)
+
+   ! --------------------------------------------------------------------
+   ! Read in GDP data
+   ! --------------------------------------------------------------------
+
+   allocate(gdp(bounds%begg:bounds%endg))
+   call ncd_io(ncid=ncid, varname='gdp', flag='read', data=gdp, dim1name=grlnd, readvar=readvar)
+   if (.not. readvar) then
+      call endrun(msg=' ERROR: gdp NOT on surfdata file'//errMsg(sourcefile, __LINE__))
+   end if
+   do c = bounds%begc, bounds%endc
+      g = col%gridcell(c)
+      this%gdp_lf_col(c) = gdp(g)
+   end do
+   deallocate(gdp)
+
+   ! --------------------------------------------------------------------
+   ! Read in peatf data
+   ! --------------------------------------------------------------------
+
+   allocate(peatf(bounds%begg:bounds%endg))
+   call ncd_io(ncid=ncid, varname='peatf', flag='read', data=peatf, dim1name=grlnd, readvar=readvar)
+   if (.not. readvar) then
+      call endrun(msg=' ERROR: peatf NOT on surfdata file'//errMsg(sourcefile, __LINE__))
+   end if
+   do c = bounds%begc, bounds%endc
+      g = col%gridcell(c)
+      this%peatf_lf_col(c) = peatf(g)
+   end do
+   deallocate(peatf)
+
+   ! --------------------------------------------------------------------
+   ! Read in ABM data
+   ! --------------------------------------------------------------------
+
+   allocate(abm(bounds%begg:bounds%endg))
+   call ncd_io(ncid=ncid, varname='abm', flag='read', data=abm, dim1name=grlnd, readvar=readvar)
+   if (.not. readvar) then
+      call endrun(msg=' ERROR: abm NOT on surfdata file'//errMsg(sourcefile, __LINE__))
+   end if
+   do c = bounds%begc, bounds%endc
+      g = col%gridcell(c)
+      this%abm_lf_col(c) = abm(g)
+   end do
+   deallocate(abm)
+
+   ! Close file
+
+   call ncd_pio_closefile(ncid)
+
+   if (masterproc) then
+      write(iulog,*) 'Successfully read fmax, soil color, sand and clay boundary data'
+      write(iulog,*)
+   endif
+   
+  end subroutine surfdataread
+  
+  
+end module FireDataBaseType
diff --git a/src/cpl/mct/SoilMoistureStreamMod.F90 b/src/cpl/mct/SoilMoistureStreamMod.F90
new file mode 100644
index 0000000000..8b366d6c8e
--- /dev/null
+++ b/src/cpl/mct/SoilMoistureStreamMod.F90
@@ -0,0 +1,418 @@
+module SoilMoistureStreamMod
+
+  ! **********************************************************************
+  ! --------------------------- IMPORTANT NOTE ---------------------------
+  !
+  ! In cases using the NUOPC driver/mediator, we use a different version of this module,
+  ! based on CDEPS, which resides in src/cpl/nuopc/. Changes to the science here should
+  ! also be made in the similar file in src/cpl/nuopc. Once we start using CDEPS by
+  ! default, we can remove this version and move the CDEPS-based version into its place.
+  ! **********************************************************************
+
+#include "shr_assert.h"
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Read in soil moisture from data stream
+  !
+  ! !USES:
+  use shr_strdata_mod           , only : shr_strdata_type, shr_strdata_create
+  use shr_strdata_mod           , only : shr_strdata_print, shr_strdata_advance
+  use shr_kind_mod              , only : r8 => shr_kind_r8
+  use shr_kind_mod              , only : CL => shr_kind_CL, CXX => shr_kind_CXX
+  use shr_log_mod               , only : errMsg => shr_log_errMsg
+  use decompMod                 , only : bounds_type, subgrid_level_column
+  use abortutils                , only : endrun
+  use clm_varctl                , only : iulog, use_soil_moisture_streams, inst_name
+  use clm_varcon                , only : grlnd
+  use controlMod                , only : NLFilename
+  use domainMod                 , only : ldomain
+  use LandunitType              , only : lun
+  use ColumnType                , only : col
+  use SoilStateType             , only : soilstate_type
+  use WaterStateBulkType        , only : waterstatebulk_type
+  use perf_mod                  , only : t_startf, t_stopf
+  use spmdMod                   , only : masterproc, mpicom, comp_id
+  use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo
+  use mct_mod
+  use ncdio_pio
+  !
+  ! !PUBLIC TYPES:
+  implicit none
+  private
+  !
+  ! !PUBLIC MEMBER FUNCTIONS:
+  public :: PrescribedSoilMoistureInit    ! position datasets for soil moisture
+  public :: PrescribedSoilMoistureAdvance ! Advance the soil moisture stream (outside of Open-MP loops)
+  public :: PrescribedSoilMoistureInterp  ! interpolates between two periods of soil moisture data
+
+  ! !PRIVATE MEMBER DATA:
+  type(shr_strdata_type) :: sdat_soilm    ! soil moisture input data stream
+  integer :: ism                          ! Soil moisture steram index
+  integer, allocatable :: g_to_ig(:)      ! Array matching gridcell index to data index
+  logical :: soilm_ignore_data_if_missing ! If should ignore overridding a point with soil moisture data
+                                          ! from the streams file, if the streams file shows that point
+                                          ! as missing (namelist item)
+  !
+  ! !PRIVATE TYPES:
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+  !-----------------------------------------------------------------------
+
+contains
+
+  !-----------------------------------------------------------------------
+  !
+  ! soil_moisture_init
+  !
+  !-----------------------------------------------------------------------
+  subroutine PrescribedSoilMoistureInit(bounds)
+    !
+    ! Initialize data stream information for soil moisture.
+    !
+    !
+    ! !USES:
+    use clm_time_manager , only : get_calendar
+    use ncdio_pio        , only : pio_subsystem
+    use shr_pio_mod      , only : shr_pio_getiotype
+    use clm_nlUtilsMod   , only : find_nlgroup_name
+    use ndepStreamMod    , only : clm_domain_mct
+    use shr_stream_mod   , only : shr_stream_file_null
+    use shr_string_mod   , only : shr_string_listCreateField
+    use clm_varpar       , only : nlevsoi
+    !
+    ! !ARGUMENTS:
+    implicit none
+    type(bounds_type), intent(in) :: bounds          ! bounds
+    !
+    ! !LOCAL VARIABLES:
+    integer            :: i                          ! index
+    integer            :: stream_year_first_soilm    ! first year in Ustar stream to use
+    integer            :: stream_year_last_soilm     ! last year in Ustar stream to use
+    integer            :: model_year_align_soilm     ! align stream_year_first_soilm with
+    integer            :: nu_nml                     ! unit for namelist file
+    integer            :: nml_error                  ! namelist i/o error flag
+    integer            :: soilm_offset               ! Offset in time for dataset (sec)
+    type(mct_ggrid)    :: dom_clm                    ! domain information
+    character(len=CL)  :: stream_fldfilename_soilm   ! ustar stream filename to read
+    character(len=CL)  :: soilm_tintalgo = 'linear'  ! Time interpolation alogrithm
+
+    character(*), parameter    :: subName = "('PrescribedSoilMoistureInit')"
+    character(*), parameter    :: F00 = "('(PrescribedSoilMoistureInit) ',4a)"
+    character(*), parameter    :: soilmString = "H2OSOI"  ! base string for field string
+    character(CXX)             :: fldList            ! field string
+    !-----------------------------------------------------------------------
+    !
+    ! deal with namelist variables here in init
+    !
+    namelist /soil_moisture_streams/   &
+         stream_year_first_soilm,      &
+         stream_year_last_soilm,       &
+         model_year_align_soilm,       &
+         soilm_tintalgo,               &
+         soilm_offset,                 &
+         soilm_ignore_data_if_missing, &
+         stream_fldfilename_soilm
+
+    ! Default values for namelist
+    stream_year_first_soilm      = 1      ! first year in stream to use
+    stream_year_last_soilm       = 1      ! last  year in stream to use
+    model_year_align_soilm       = 1      ! align stream_year_first_soilm with this model year
+    stream_fldfilename_soilm     = shr_stream_file_null
+    soilm_offset                 = 0
+    soilm_ignore_data_if_missing = .false.
+
+    ! Read soilm_streams namelist
+    if (masterproc) then
+       open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+       call find_nlgroup_name(nu_nml, 'soil_moisture_streams', status=nml_error)
+       if (nml_error == 0) then
+          read(nu_nml, nml=soil_moisture_streams,iostat=nml_error)
+          if (nml_error /= 0) then
+             call endrun(subname // ':: ERROR reading soil_moisture_streams namelist')
+          end if
+       else
+          call endrun(subname // ':: ERROR finding soilm_streams namelist')
+       end if
+       close(nu_nml)
+    endif
+
+    call shr_mpi_bcast(stream_year_first_soilm, mpicom)
+    call shr_mpi_bcast(stream_year_last_soilm, mpicom)
+    call shr_mpi_bcast(model_year_align_soilm, mpicom)
+    call shr_mpi_bcast(stream_fldfilename_soilm, mpicom)
+    call shr_mpi_bcast(soilm_tintalgo, mpicom)
+    call shr_mpi_bcast(soilm_offset, mpicom)
+    call shr_mpi_bcast(soilm_ignore_data_if_missing, mpicom)
+
+    if (masterproc) then
+
+       write(iulog,*) ' '
+       write(iulog,*) 'soil_moisture_stream settings:'
+       write(iulog,*) '  stream_year_first_soilm  = ',stream_year_first_soilm
+       write(iulog,*) '  stream_year_last_soilm   = ',stream_year_last_soilm
+       write(iulog,*) '  model_year_align_soilm   = ',model_year_align_soilm
+       write(iulog,*) '  stream_fldfilename_soilm = ',trim(stream_fldfilename_soilm)
+       write(iulog,*) '  soilm_tintalgo = ',trim(soilm_tintalgo)
+       write(iulog,*) '  soilm_offset = ',soilm_offset
+       if ( soilm_ignore_data_if_missing )then
+          write(iulog,*) '  Do NOT override a point with streams data if the streams data is missing'
+       else
+          write(iulog,*) '  Abort, if you find a model point where the input streams data is set to missing value'
+       end if
+
+    endif
+
+    call clm_domain_mct (bounds, dom_clm, nlevels=nlevsoi)
+
+    ! create the field list for these fields...use in shr_strdata_create
+    fldList = trim(soilmString)
+    if (masterproc) write(iulog,*) 'fieldlist: ', trim(fldList)
+
+    call shr_strdata_create(sdat_soilm,name="soil_moisture",    &
+         pio_subsystem=pio_subsystem,                  &
+         pio_iotype=shr_pio_getiotype(inst_name),          &
+         mpicom=mpicom, compid=comp_id,                &
+         gsmap=gsMap_lnd2Dsoi_gdc2glo, ggrid=dom_clm,  &
+         nxg=ldomain%ni, nyg=ldomain%nj,               &
+         nzg=nlevsoi,                                  &
+         yearFirst=stream_year_first_soilm,            &
+         yearLast=stream_year_last_soilm,              &
+         yearAlign=model_year_align_soilm,             &
+         offset=soilm_offset,                          &
+         domFilePath='',                               &
+         domFileName=trim(stream_fldFileName_soilm),   &
+         domTvarName='time',                           &
+         domXvarName='lon' ,                           &
+         domYvarName='lat' ,                           &
+         domZvarName='levsoi' ,                        &
+         domAreaName='area',                           &
+         domMaskName='mask',                           &
+         filePath='',                                  &
+         filename=(/stream_fldFileName_soilm/),        &
+         fldListFile=fldList,                          &
+         fldListModel=fldList,                         &
+         fillalgo='none',                              &
+         mapalgo='none',                               &
+         tintalgo=soilm_tintalgo,                      &
+         calendar=get_calendar(),                      &
+         dtlimit = 15._r8,                             &
+         taxmode='cycle'                               )
+
+    if (masterproc) then
+       call shr_strdata_print(sdat_soilm,'soil moisture data')
+    endif
+
+  end subroutine PrescribedSoilMoistureInit
+
+
+  !-----------------------------------------------------------------------
+  !
+  ! PrescribedSoilMoistureAdvance
+  !
+  !-----------------------------------------------------------------------
+  subroutine PrescribedSoilMoistureAdvance( bounds )
+    !
+    ! Advanace the prescribed soil moisture stream
+    !
+    ! !USES:
+    use clm_time_manager, only : get_curr_date
+    !
+    ! !ARGUMENTS:
+    type(bounds_type)         , intent(in)    :: bounds
+    !
+    ! !LOCAL VARIABLES:
+    character(len=CL)  :: stream_var_name
+    integer :: g, ig
+    integer :: ier    ! error code
+    integer :: year    ! year (0, ...) for nstep+1
+    integer :: mon     ! month (1, ..., 12) for nstep+1
+    integer :: day     ! day of month (1, ..., 31) for nstep+1
+    integer :: sec     ! seconds into current date for nstep+1
+    integer :: mcdate  ! Current model date (yyyymmdd)
+
+    call get_curr_date(year, mon, day, sec)
+    mcdate = year*10000 + mon*100 + day
+
+    stream_var_name = 'H2OSOI'
+
+    ! Determine variable index
+    ism = mct_aVect_indexRA(sdat_soilm%avs(1),trim(stream_var_name))
+
+    call shr_strdata_advance(sdat_soilm, mcdate, sec, mpicom, trim(stream_var_name))
+
+    ! Map gridcell to AV index
+    ier = 0
+    if ( .not. allocated(g_to_ig) )then
+       allocate (g_to_ig(bounds%begg:bounds%endg), stat=ier)
+       if (ier /= 0) then
+          write(iulog,*) 'Prescribed soil moisture allocation error'
+          call endrun(msg=errMsg(sourcefile, __LINE__))
+       end if
+
+       ig = 0
+       do g = bounds%begg,bounds%endg
+          ig = ig+1
+          g_to_ig(g) = ig
+       end do
+    end if
+
+  end subroutine PrescribedSoilMoistureAdvance
+
+  !-----------------------------------------------------------------------
+  !
+  ! PrescribedSoilMoistureInterp
+  !
+  !-----------------------------------------------------------------------
+  subroutine PrescribedSoilMoistureInterp(bounds, soilstate_inst, &
+       waterstatebulk_inst)
+    !
+    ! Assign data stream information for prescribed soil moisture.
+    !
+    ! !USES:
+    use clm_time_manager, only : get_curr_date
+    use clm_varpar      , only : nlevsoi
+    use clm_varcon      , only : denh2o, denice, watmin, spval
+    use landunit_varcon , only : istsoil, istcrop
+    !
+    ! !ARGUMENTS:
+    implicit none
+    type(bounds_type)         , intent(in)    :: bounds
+    type(soilstate_type)      , intent(in)    :: soilstate_inst
+    type(waterstatebulk_type) , intent(inout) :: waterstatebulk_inst
+    !
+    ! !LOCAL VARIABLES:
+    integer :: c, g, j, ig, n
+    real(r8) :: soilm_liq_frac            ! liquid fraction of soil moisture
+    real(r8) :: soilm_ice_frac            ! ice fraction of soil moisture
+    real(r8) :: moisture_increment        ! soil moisture adjustment increment
+    real(r8) :: h2osoi_vol_initial        ! initial vwc value
+    character(*), parameter    :: subName = "('PrescribedSoilMoistureInterp')"
+
+    !-----------------------------------------------------------------------
+
+    SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,2) >= g_to_ig(bounds%endg)+(nlevsoi-1)*size(g_to_ig) ), sourcefile, __LINE__)
+    associate( &
+         dz               =>    col%dz                                , & ! Input:  [real(r8) (:,:) ]  layer depth (m)
+         watsat           =>    soilstate_inst%watsat_col             , & ! Input:  [real(r8) (:,:) ]  volumetric soil water at saturation (porosity)
+         h2osoi_liq       =>    waterstatebulk_inst%h2osoi_liq_col        , & ! Input/Output:  [real(r8) (:,:) ]  liquid water (kg/m2)
+         h2osoi_ice       =>    waterstatebulk_inst%h2osoi_ice_col        , & ! Input/Output:  [real(r8) (:,:) ]  ice water (kg/m2)
+         h2osoi_vol       =>    waterstatebulk_inst%h2osoi_vol_col        , & ! Output: volumetric soil water (m3/m3)
+         h2osoi_vol_prs   =>    waterstatebulk_inst%h2osoi_vol_prs_grc      & ! Output: prescribed volumetric soil water (m3/m3)
+         )
+      SHR_ASSERT_FL( (lbound(h2osoi_vol,1) <= bounds%begc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_vol,1) >= bounds%endc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(h2osoi_vol,2) == 1 ),           sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_vol,2) >= nlevsoi ),     sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(dz,1) <= bounds%begc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(dz,1) >= bounds%endc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(dz,2) <= 1 ),           sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(dz,2) >= nlevsoi ),     sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(watsat,1) <= bounds%begc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(watsat,1) >= bounds%endc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(watsat,2) <= 1 ),           sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(watsat,2) >= nlevsoi ),     sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(h2osoi_liq,1) <= bounds%begc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_liq,1) >= bounds%endc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(h2osoi_liq,2) <= 1 ),           sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_liq,2) >= nlevsoi ),     sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(h2osoi_ice,1) <= bounds%begc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_ice,1) >= bounds%endc ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(h2osoi_ice,2) <= 1 ),           sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_ice,2) >= nlevsoi ),     sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,1) <= bounds%begg ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,1) >= bounds%endg ), sourcefile, __LINE__)
+      SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,2) == 1 ),           sourcefile, __LINE__)
+      SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,2) >= nlevsoi ),     sourcefile, __LINE__)
+      !
+      ! Set the prescribed soil moisture read from the file everywhere
+      !
+      do g = bounds%begg, bounds%endg
+         ig = g_to_ig(g)
+         do j = 1, nlevsoi
+
+             !n = ig + (j-1)*size(g_to_ig)
+             n = ig + (j-1)*size(g_to_ig)
+
+             h2osoi_vol_prs(g,j) = sdat_soilm%avs(1)%rAttr(ism,n)
+
+             ! If soil moiture is being interpolated in time and the result is
+             ! large that probably means one of the two data points is missing (set to spval)
+             if ( h2osoi_vol_prs(g,j) > 10.0_r8 .and. (h2osoi_vol_prs(g,j) /= spval) )then
+                h2osoi_vol_prs(g,j) = spval
+             end if
+
+         end do
+      end do
+
+      do c = bounds%begc, bounds%endc
+         !
+         ! Set variable for each gridcell/column combination
+         !
+         g = col%gridcell(c)
+         ig = g_to_ig(g)
+
+         ! EBK Jan/2020, also check weights on gridcell (See https://github.com/ESCOMP/CTSM/issues/847)
+         if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) .and. &
+              (col%wtgcell(c) /= 0._r8) ) then
+            !       this is a 2d field (gridcell/nlevsoi) !
+            do j = 1, nlevsoi
+
+               n = ig + (j-1)*size(g_to_ig)
+
+               ! if soil water is zero, liq/ice fractions cannot be calculated
+               if((h2osoi_liq(c, j) + h2osoi_ice(c, j)) > 0._r8) then
+
+                  ! save original soil moisture value
+                  h2osoi_vol_initial = h2osoi_vol(c,j)
+
+                  ! Check if the vegetated land mask from the dataset on the
+                  ! file is different
+                  if ( (h2osoi_vol_prs(g,j) == spval) .and. (h2osoi_vol_initial /= spval) )then
+                     if ( soilm_ignore_data_if_missing )then
+                        cycle
+                     else
+                        write(iulog,*) 'Input soil moisture dataset is not vegetated as expected: gridcell=', &
+                                        g, ' active = ', col%active(c)
+                        call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, &
+                             msg = subname // &
+                             ' ERROR:: The input soil moisture stream is NOT vegetated for one of the land points' )
+                     end if
+                  end if
+
+                  ! update volumetric soil moisture from data prescribed from the file
+                  h2osoi_vol(c,j) = h2osoi_vol_prs(g,j)
+
+
+                  ! calculate liq/ice mass fractions
+                  soilm_liq_frac  = h2osoi_liq(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j))
+                  soilm_ice_frac  = h2osoi_ice(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j))
+
+                  ! calculate moisture increment
+                  moisture_increment = h2osoi_vol(c,j) - h2osoi_vol_initial
+                  ! add limitation check
+                  moisture_increment = min((watsat(c,j) - h2osoi_vol_initial),max(-(h2osoi_vol_initial-watmin),moisture_increment))
+
+                  ! update liq/ice water mass due to (volumetric) moisture increment
+                  h2osoi_liq(c,j) = h2osoi_liq(c,j) + (soilm_liq_frac * moisture_increment * dz(c, j) * denh2o)
+                  h2osoi_ice(c,j) = h2osoi_ice(c,j) + (soilm_ice_frac * moisture_increment * dz(c, j) * denice)
+
+               else
+                  call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, &
+                       msg = subname // ':: ERROR h2osoil liquid plus ice is zero')
+               endif
+            enddo
+         endif
+      end do
+
+    end associate
+
+  end subroutine PrescribedSoilMoistureInterp
+
+end module SoilMoistureStreamMod
diff --git a/src/cpl/mct/UrbanTimeVarType.F90 b/src/cpl/mct/UrbanTimeVarType.F90
new file mode 100644
index 0000000000..805ac47fbf
--- /dev/null
+++ b/src/cpl/mct/UrbanTimeVarType.F90
@@ -0,0 +1,314 @@
+module UrbanTimeVarType
+
+  !------------------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Urban Time Varying Data
+  !
+  ! !USES:
+  use shr_kind_mod    , only : r8 => shr_kind_r8, CL => shr_kind_CL
+  use shr_log_mod     , only : errMsg => shr_log_errMsg
+  use abortutils      , only : endrun
+  use decompMod       , only : bounds_type, subgrid_level_landunit
+  use clm_varctl      , only : iulog, inst_name
+  use landunit_varcon , only : isturb_MIN, isturb_MAX
+  use clm_varcon      , only : spval
+  use LandunitType    , only : lun
+  use GridcellType    , only : grc
+  use mct_mod
+  use shr_strdata_mod , only : shr_strdata_type
+  !
+  implicit none
+  save
+  private
+  !
+  !
+
+  ! !PUBLIC TYPE
+  type, public :: urbantv_type
+
+     real(r8), public, pointer     :: t_building_max(:)    ! lun maximum internal building air temperature (K)
+     type(shr_strdata_type)        :: sdat_urbantv         ! urban time varying input data stream
+   contains
+
+     ! !PUBLIC MEMBER FUNCTIONS:
+     procedure, public :: Init              ! Allocate and initialize urbantv
+     procedure, public :: urbantv_init      ! Initialize urban time varying stream
+     procedure, public :: urbantv_interp    ! Interpolate urban time varying stream
+
+  end type urbantv_type
+
+  !-----------------------------------------------------------------------
+  character(15), private :: stream_var_name(isturb_MIN:isturb_MAX)
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+contains
+
+  !-----------------------------------------------------------------------
+  subroutine Init(this, bounds, NLFilename)
+    !
+    ! Allocate module variables and data structures
+    !
+    ! !USES:
+    use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
+    use histFileMod     , only : hist_addfld1d
+    !
+    ! !ARGUMENTS:
+    class(urbantv_type) :: this
+    type(bounds_type) , intent(in) :: bounds
+    character(len=*)  , intent(in) :: NLFilename   ! Namelist filename
+    !
+    ! !LOCAL VARIABLES:
+    integer		:: begl, endl
+    !---------------------------------------------------------------------
+
+    begl = bounds%begl; endl = bounds%endl
+
+    ! Allocate urbantv data structure
+
+    allocate(this%t_building_max      (begl:endl))          ; this%t_building_max      (:)   = nan
+
+    call this%urbantv_init(bounds, NLFilename)
+    call this%urbantv_interp(bounds)
+
+    ! Add history fields
+    call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
+          avgflag='A', long_name='prescribed maximum interior building temperature',   &
+          ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
+          l2g_scale_type='unity')
+
+
+  end subroutine Init
+
+  !-----------------------------------------------------------------------
+
+  !-----------------------------------------------------------------------
+  subroutine urbantv_init(this, bounds, NLFilename)
+   !
+   ! !DESCRIPTION:
+   ! Initialize data stream information for urban time varying data
+   !
+   ! !USES:
+   use clm_time_manager , only : get_calendar
+   use ncdio_pio        , only : pio_subsystem
+   use shr_pio_mod      , only : shr_pio_getiotype
+   use clm_nlUtilsMod   , only : find_nlgroup_name
+   use ndepStreamMod    , only : clm_domain_mct
+   use spmdMod          , only : masterproc, mpicom, comp_id
+   use fileutils        , only : getavu, relavu
+   use shr_mpi_mod      , only : shr_mpi_bcast
+   use shr_string_mod   , only : shr_string_listAppend
+   use shr_strdata_mod  , only : shr_strdata_create, shr_strdata_print
+   use domainMod        , only : ldomain
+   use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
+   use landunit_varcon  , only : isturb_TBD, isturb_HD, isturb_MD
+   use lnd_set_decomp_and_domain , only : gsmap_global
+   !
+   ! !ARGUMENTS:
+   implicit none
+   class(urbantv_type)           :: this
+   type(bounds_type), intent(in) :: bounds
+   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+   !
+   ! !LOCAL VARIABLES:
+   integer            :: begl, endl                           ! landunits
+   integer            :: ifield                               ! field index
+   integer            :: stream_year_first_urbantv            ! first year in urban tv stream to use
+   integer            :: stream_year_last_urbantv             ! last year in urban tv stream to use
+   integer            :: model_year_align_urbantv             ! align stream_year_first_urbantv
+                                                              !  with this model year
+   integer            :: nu_nml                               ! unit for namelist file
+   integer            :: nml_error                            ! namelist i/o error flag
+   type(mct_ggrid)    :: dom_clm                              ! domain information
+   character(len=CL)  :: stream_fldFileName_urbantv           ! urban tv streams filename
+   character(len=CL)  :: urbantvmapalgo = 'nn'                ! mapping alogrithm for urban ac
+   character(len=CL)  :: urbantv_tintalgo = 'linear'          ! time interpolation alogrithm
+   character(len=CL)  :: fldList                              ! field string
+   character(*), parameter :: urbantvString = "tbuildmax_"    ! base string for field string
+   character(*), parameter :: subName = "('urbantv_init')"
+   character(*), parameter :: F00 = "('(urbantv_init) ',4a)"
+   !-----------------------------------------------------------------------
+   namelist /urbantv_streams/       &
+        stream_year_first_urbantv,  &
+        stream_year_last_urbantv,   &
+        model_year_align_urbantv,   &
+        urbantvmapalgo,             &
+        stream_fldFileName_urbantv, &
+        urbantv_tintalgo
+   !-----------------------------------------------------------------------
+
+   begl = bounds%begl; endl = bounds%endl
+
+   ! Default values for namelist
+   stream_year_first_urbantv  = 1       ! first year in stream to use
+   stream_year_last_urbantv   = 1       ! last  year in stream to use
+   model_year_align_urbantv   = 1       ! align stream_year_first_urbantv with this model year
+   stream_fldFileName_urbantv = ' '
+
+   ! Read urbantv_streams namelist
+   if (masterproc) then
+      nu_nml = getavu()
+      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+      call find_nlgroup_name(nu_nml, 'urbantv_streams', status=nml_error)
+      if (nml_error == 0) then
+         read(nu_nml, nml=urbantv_streams,iostat=nml_error)
+         if (nml_error /= 0) then
+            call endrun(msg='ERROR reading urbantv_streams namelist'//errMsg(sourcefile, __LINE__))
+         end if
+      end if
+      close(nu_nml)
+      call relavu( nu_nml )
+   endif
+
+   call shr_mpi_bcast(stream_year_first_urbantv, mpicom)
+   call shr_mpi_bcast(stream_year_last_urbantv, mpicom)
+   call shr_mpi_bcast(model_year_align_urbantv, mpicom)
+   call shr_mpi_bcast(stream_fldFileName_urbantv, mpicom)
+   call shr_mpi_bcast(urbantv_tintalgo, mpicom)
+
+   if (masterproc) then
+      write(iulog,*) ' '
+      write(iulog,*) 'urbantv_streams settings:'
+      write(iulog,*) '  stream_year_first_urbantv  = ',stream_year_first_urbantv
+      write(iulog,*) '  stream_year_last_urbantv   = ',stream_year_last_urbantv
+      write(iulog,*) '  model_year_align_urbantv   = ',model_year_align_urbantv
+      write(iulog,*) '  stream_fldFileName_urbantv = ',stream_fldFileName_urbantv
+      write(iulog,*) '  urbantv_tintalgo           = ',urbantv_tintalgo
+      write(iulog,*) ' '
+   endif
+
+   call clm_domain_mct (bounds, dom_clm)
+
+   ! create the field list for these urbantv fields...use in shr_strdata_create
+   stream_var_name(:)          = "NOT_SET"
+   stream_var_name(isturb_TBD) = urbantvString//"TBD"
+   stream_var_name(isturb_HD)  = urbantvString//"HD"
+   stream_var_name(isturb_MD)  = urbantvString//"MD"
+   fldList = ""
+   do ifield = isturb_MIN, isturb_MAX
+      call shr_string_listAppend( fldList, stream_var_name(ifield) )
+   end do
+
+   call shr_strdata_create(this%sdat_urbantv,name="clmurbantv", &
+        pio_subsystem=pio_subsystem,                            &
+        pio_iotype=shr_pio_getiotype(inst_name),                &
+        mpicom=mpicom, compid=comp_id,                          &
+        gsmap=gsmap_global, ggrid=dom_clm,                      &
+        nxg=ldomain%ni, nyg=ldomain%nj,                         &
+        yearFirst=stream_year_first_urbantv,                    &
+        yearLast=stream_year_last_urbantv,                      &
+        yearAlign=model_year_align_urbantv,                     &
+        offset=0,                                               &
+        domFilePath='',                                         &
+        domFileName=trim(stream_fldFileName_urbantv),           &
+        domTvarName='time',                                     &
+        domXvarName='lon' ,                                     &
+        domYvarName='lat' ,                                     &
+        domAreaName='area',                                     &
+        domMaskName='LANDMASK',                                 &
+        filePath='',                                            &
+        filename=(/trim(stream_fldFileName_urbantv)/) ,         &
+        fldListFile=fldList,                                    &
+        fldListModel=fldList,                                   &
+        fillalgo='none',                                        &
+        mapalgo=urbantvmapalgo,                                 &
+        calendar=get_calendar(),                                &
+        tintalgo=urbantv_tintalgo,                              &
+        taxmode='extend'                                 )
+
+   if (masterproc) then
+      call shr_strdata_print(this%sdat_urbantv,'urban time varying data')
+   endif
+
+
+  end subroutine urbantv_init
+
+  !-----------------------------------------------------------------------
+  subroutine urbantv_interp(this, bounds)
+  !
+  ! !DESCRIPTION:
+  ! Interpolate data stream information for urban time varying data.
+  !
+  ! !USES:
+  use clm_time_manager, only : get_curr_date
+  use spmdMod         , only : mpicom
+  use shr_strdata_mod , only : shr_strdata_advance
+  use clm_instur      , only : urban_valid
+  !
+  ! !ARGUMENTS:
+  class(urbantv_type)           :: this
+  type(bounds_type), intent(in) :: bounds
+  !
+  ! !LOCAL VARIABLES:
+  logical :: found
+  integer :: l, glun, ig, g, ip
+  integer :: year    ! year (0, ...) for nstep+1
+  integer :: mon     ! month (1, ..., 12) for nstep+1
+  integer :: day     ! day of month (1, ..., 31) for nstep+1
+  integer :: sec     ! seconds into current date for nstep+1
+  integer :: mcdate  ! Current model date (yyyymmdd)
+  integer :: lindx   ! landunit index
+  integer :: gindx   ! gridcell index
+  !-----------------------------------------------------------------------
+
+   call get_curr_date(year, mon, day, sec)
+   mcdate = year*10000 + mon*100 + day
+
+   call shr_strdata_advance(this%sdat_urbantv, mcdate, sec, mpicom, 'urbantvdyn')
+
+   do l = bounds%begl,bounds%endl
+      if (lun%urbpoi(l)) then
+         glun  = lun%gridcell(l)
+         ip = mct_aVect_indexRA(this%sdat_urbantv%avs(1),trim(stream_var_name(lun%itype(l))))
+         !
+         ! Determine vector index corresponding to glun
+         !
+         ig = 0
+         do g = bounds%begg,bounds%endg
+            ig = ig+1
+            if (g == glun) exit
+         end do
+
+         this%t_building_max(l) = this%sdat_urbantv%avs(1)%rAttr(ip,ig)
+      else
+         this%t_building_max(l) = spval
+      end if
+   end do
+
+   found = .false.
+   do l = bounds%begl,bounds%endl
+      if (lun%urbpoi(l)) then
+         glun  = lun%gridcell(l)
+         !
+         ! Determine vector index corresponding to glun
+         !
+         ig = 0
+         do g = bounds%begg,bounds%endg
+            ig = ig+1
+            if (g == glun) exit
+         end do
+
+         if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
+            found = .true.
+            gindx = g
+            lindx = l
+            exit
+         end if
+      end if
+   end do
+   if ( found ) then
+      write(iulog,*)'ERROR: no valid urban data for g= ',gindx
+      write(iulog,*)'landunit type:   ',lun%itype(lindx)
+      write(iulog,*)'urban_valid:     ',urban_valid(gindx)
+      write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
+      call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, &
+           msg=errmsg(sourcefile, __LINE__))
+   end if
+
+
+  end subroutine urbantv_interp
+
+  !-----------------------------------------------------------------------
+
+end module UrbanTimeVarType
diff --git a/src/cpl/mct/ch4FInundatedStreamType.F90 b/src/cpl/mct/ch4FInundatedStreamType.F90
new file mode 100644
index 0000000000..3c26f4d109
--- /dev/null
+++ b/src/cpl/mct/ch4FInundatedStreamType.F90
@@ -0,0 +1,389 @@
+module ch4FInundatedStreamType
+
+#include "shr_assert.h"
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Contains methods for reading in finundated streams file for methane code.
+  !
+  ! !USES
+  use shr_kind_mod   , only: r8 => shr_kind_r8, CL => shr_kind_cl
+  use spmdMod        , only: mpicom, masterproc
+  use clm_varctl     , only: iulog, inst_name
+  use abortutils     , only: endrun
+  use decompMod      , only: bounds_type
+  use ch4varcon      , only: finundation_mtd
+
+  ! !PUBLIC TYPES:
+  implicit none
+  private
+  save
+
+  type, public :: ch4finundatedstream_type
+     real(r8), pointer, private :: zwt0_gdc  (:)         ! col coefficient for determining finundated (m)
+     real(r8), pointer, private :: f0_gdc    (:)         ! col maximum inundated fraction for a gridcell (for methane code)
+     real(r8), pointer, private :: p3_gdc    (:)         ! col coefficient for determining finundated (m)
+     real(r8), pointer, private :: fws_slope_gdc     (:) ! col slope in fws = slope * tws + intercept (A coefficient)
+     real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient)
+  contains
+
+      ! !PUBLIC MEMBER FUNCTIONS:
+      procedure, public :: Init            ! Initialize and read data in
+      procedure, public :: CalcFinundated  ! Calculate finundated based on input streams
+      procedure, public :: UseStreams      ! If streams will be used
+
+      ! !PRIVATE MEMBER FUNCTIONS:
+      procedure, private :: InitAllocate   ! Allocate data
+
+  end type ch4finundatedstream_type
+
+
+  ! ! PRIVATE DATA:
+
+  type, private :: streamcontrol_type
+     character(len=CL)  :: stream_fldFileName_ch4finundated   ! Filename
+     character(len=CL)  :: ch4finundatedmapalgo               ! map algo
+     character(len=CL)  :: fldList                            ! List of fields to read
+  contains
+     procedure, private :: ReadNML     ! Read in namelist
+  end type streamcontrol_type
+
+  type(streamcontrol_type), private :: control        ! Stream control data
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+  !==============================================================================
+
+contains
+
+  !==============================================================================
+
+  subroutine Init(this, bounds, NLFilename)
+   !
+   ! Initialize the ch4 finundated stream object
+   !
+   ! Uses:
+   use clm_time_manager , only : get_calendar, get_curr_date
+   use ncdio_pio        , only : pio_subsystem
+   use shr_pio_mod      , only : shr_pio_getiotype
+   use shr_nl_mod       , only : shr_nl_find_group_name
+   use shr_mpi_mod      , only : shr_mpi_bcast
+   use ndepStreamMod    , only : clm_domain_mct
+   use domainMod        , only : ldomain
+   use decompMod        , only : bounds_type
+   use mct_mod          , only : mct_ggrid, mct_avect_indexra
+   use shr_strdata_mod  , only : shr_strdata_type, shr_strdata_create
+   use shr_strdata_mod  , only : shr_strdata_print, shr_strdata_advance
+   use spmdMod          , only : comp_id, iam
+   use ch4varcon        , only : finundation_mtd_h2osfc
+   use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+   use lnd_set_decomp_and_domain , only : gsmap_global
+   !
+   ! arguments
+   implicit none
+   class(ch4finundatedstream_type) :: this
+   type(bounds_type), intent(in) :: bounds
+   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+   !
+   ! local variables
+   integer            :: ig, g            ! Indices
+   type(mct_ggrid)    :: dom_clm          ! domain information
+   type(shr_strdata_type) :: sdat         ! input data stream
+   integer            :: index_ZWT0       = 0 ! Index of ZWT0 field
+   integer            :: index_F0         = 0 ! Index of F0 field
+   integer            :: index_P3         = 0 ! Index of P3 field
+   integer            :: index_FWS_TWS_A  = 0 ! Index of FWS_TWS_A field
+   integer            :: index_FWS_TWS_B  = 0 ! Index of FWS_TWS_B field
+   integer            :: year                 ! year (0, ...) for nstep+1
+   integer            :: mon                  ! month (1, ..., 12) for nstep+1
+   integer            :: day                  ! day of month (1, ..., 31) for nstep+1
+   integer            :: sec                  ! seconds into current date for nstep+1
+   integer            :: mcdate               ! Current model date (yyyymmdd)
+   character(len=*), parameter :: stream_name = 'ch4finundated'
+   character(*), parameter :: subName = "('ch4finundatedstream::Init')"
+   !-----------------------------------------------------------------------
+   if ( finundation_mtd /= finundation_mtd_h2osfc )then
+      call this%InitAllocate( bounds )
+      call control%ReadNML( bounds, NLFileName )
+
+      if ( this%useStreams() )then
+         call clm_domain_mct (bounds, dom_clm)
+
+         call shr_strdata_create(sdat,name=stream_name,                 &
+           pio_subsystem=pio_subsystem,                                 &
+           pio_iotype=shr_pio_getiotype(inst_name),                     &
+           mpicom=mpicom, compid=comp_id,                               &
+           gsmap=gsmap_global, ggrid=dom_clm,                           &
+           nxg=ldomain%ni, nyg=ldomain%nj,                              &
+           yearFirst=1996,                                              &
+           yearLast=1996,                                               &
+           yearAlign=1,                                                 &
+           offset=0,                                                    &
+           domFilePath='',                                              &
+           domFileName=trim(control%stream_fldFileName_ch4finundated),  &
+           domTvarName='time',                                          &
+           domXvarName='LONGXY' ,                                       &
+           domYvarName='LATIXY' ,                                       &
+           domAreaName='AREA',                                          &
+           domMaskName='LANDMASK',                                      &
+           filePath='',                                                 &
+           filename=(/trim(control%stream_fldFileName_ch4finundated)/), &
+           fldListFile=control%fldList,                                 &
+           fldListModel=control%fldList,                                &
+           fillalgo='none',                                             &
+           mapalgo=control%ch4finundatedmapalgo,                        &
+           calendar=get_calendar(),                                     &
+           taxmode='extend'                           )
+
+         if (masterproc) then
+            call shr_strdata_print(sdat,'CLM '//stream_name//' data')
+         endif
+
+         if( finundation_mtd == finundation_mtd_ZWT_inversion )then
+            index_ZWT0      = mct_avect_indexra(sdat%avs(1),'ZWT0')
+            index_F0        = mct_avect_indexra(sdat%avs(1),'F0' )
+            index_P3        = mct_avect_indexra(sdat%avs(1),'P3' )
+         else if( finundation_mtd == finundation_mtd_TWS_inversion )then
+            index_FWS_TWS_A = mct_avect_indexra(sdat%avs(1),'FWS_TWS_A')
+            index_FWS_TWS_B = mct_avect_indexra(sdat%avs(1),'FWS_TWS_B')
+         end if
+
+
+         ! Explicitly set current date to a hardcoded constant value. Otherwise
+         ! using the real date can cause roundoff differences that are
+         ! detrected as issues with exact restart.  EBK M05/20/2017
+         !call get_curr_date(year, mon, day, sec)
+         year = 1996
+         mon  = 12
+         day  = 31
+         sec  = 0
+         mcdate = year*10000 + mon*100 + day
+
+         call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ch4finundated')
+
+         ! Get the data
+         ig = 0
+         do g = bounds%begg,bounds%endg
+            ig = ig+1
+            if ( index_ZWT0 > 0 )then
+               this%zwt0_gdc(g) = sdat%avs(1)%rAttr(index_ZWT0,ig)
+            end if
+            if ( index_F0 > 0 )then
+               this%f0_gdc(g) = sdat%avs(1)%rAttr(index_F0,ig)
+            end if
+            if ( index_P3 > 0 )then
+               this%p3_gdc(g) = sdat%avs(1)%rAttr(index_P3,ig)
+            end if
+            if ( index_FWS_TWS_A > 0 )then
+               this%fws_slope_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_A,ig)
+            end if
+            if ( index_FWS_TWS_B > 0 )then
+               this%fws_intercept_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_B,ig)
+            end if
+         end do
+      end if
+   end if
+
+  end subroutine Init
+
+  !-----------------------------------------------------------------------
+  logical function UseStreams(this)
+    !
+    ! !DESCRIPTION:
+    ! Return true if
+    !
+    ! !USES:
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(ch4finundatedstream_type) :: this
+    !
+    ! !LOCAL VARIABLES:
+    if ( trim(control%stream_fldFileName_ch4finundated) == '' )then
+       UseStreams = .false.
+    else
+       UseStreams = .true.
+    end if
+  end function UseStreams
+
+  !-----------------------------------------------------------------------
+  subroutine InitAllocate(this, bounds)
+    !
+    ! !DESCRIPTION:
+    ! Allocate module variables and data structures
+    !
+    ! !USES:
+    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
+    use ch4varcon     , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(ch4finundatedstream_type) :: this
+    type(bounds_type), intent(in) :: bounds
+    !
+    ! !LOCAL VARIABLES:
+    integer  :: begc, endc
+    integer  :: begg, endg
+    !---------------------------------------------------------------------
+
+    begc = bounds%begc; endc = bounds%endc
+    begg = bounds%begg; endg = bounds%endg
+
+    if( finundation_mtd == finundation_mtd_ZWT_inversion )then
+       allocate(this%zwt0_gdc         (begg:endg))            ;  this%zwt0_gdc         (:)   = nan
+       allocate(this%f0_gdc           (begg:endg))            ;  this%f0_gdc           (:)   = nan
+       allocate(this%p3_gdc           (begg:endg))            ;  this%p3_gdc           (:)   = nan
+    else if( finundation_mtd == finundation_mtd_TWS_inversion )then
+       allocate(this%fws_slope_gdc    (begg:endg))            ;  this%fws_slope_gdc    (:)   = nan
+       allocate(this%fws_intercept_gdc(begg:endg))            ;  this%fws_intercept_gdc(:)   = nan
+    end if
+
+  end subroutine InitAllocate
+
+  !-----------------------------------------------------------------------
+  subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, &
+                            waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated )
+    !
+    ! !DESCRIPTION:
+    !
+    ! Calculate finundated according to the appropriate methodology
+    !
+    ! !USES:
+    use ColumnType       , only : col
+    use ch4varcon        , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion
+    use ch4varcon        , only : finundation_mtd_TWS_inversion
+    use clm_varpar       , only : nlevsoi
+    use SoilHydrologyType, only : soilhydrology_type
+    use WaterDiagnosticBulkType   , only : waterdiagnosticbulk_type
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(ch4finundatedstream_type)                        :: this
+    type(bounds_type)                      , intent(in)    :: bounds
+    integer                                , intent(in)    :: num_soilc          ! number of column soil points in column filter
+    integer                                , intent(in)    :: filter_soilc(:)    ! column filter for soil points
+    type(soilhydrology_type)               , intent(in)    :: soilhydrology_inst
+    type(waterdiagnosticbulk_type)                  , intent(in)    :: waterdiagnosticbulk_inst
+    real(r8)                               , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
+    real(r8)                               , intent(inout) :: finundated(bounds%begc:)        ! fractional inundated area in soil column (excluding dedicated wetland columns)
+    !
+    ! !LOCAL VARIABLES:
+    integer  :: g, c, fc    ! Indices
+    real(r8) :: zwt_actual  ! Total water storage (ZWT) to use either perched or total depending on conditions
+
+    SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__)
+    SHR_ASSERT_ALL_FL((ubound(finundated)        == (/bounds%endc/)), sourcefile, __LINE__)
+
+    associate(                                                                 &
+         z                    =>   col%z                                     , & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
+         zwt                  =>   soilhydrology_inst%zwt_col                , & ! Input:  [real(r8) (:)   ]  water table depth (m)
+         zwt_perched          =>   soilhydrology_inst%zwt_perched_col        , & ! Input:  [real(r8) (:)   ]  perched water table depth (m)
+         tws                  =>   waterdiagnosticbulk_inst%tws_grc                   , & ! Input:  [real(r8) (:)   ]  total water storage (kg m-2)
+         frac_h2osfc          =>   waterdiagnosticbulk_inst%frac_h2osfc_col             & ! Input:  [real(r8) (:)   ]  fraction of ground covered by surface water (0 to 1)
+    )
+
+    ! Calculate finundated
+    do fc = 1, num_soilc
+       c = filter_soilc(fc)
+       g = col%gridcell(c)
+       select case( finundation_mtd )
+          case ( finundation_mtd_h2osfc )
+             finundated(c) = frac_h2osfc(c)
+          case ( finundation_mtd_ZWT_inversion )
+             if (this%zwt0_gdc(g) > 0._r8) then
+                if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then
+                   zwt_actual = zwt_perched(c)
+                else
+                   zwt_actual = zwt(c)
+                end if
+                finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c)
+             else
+                finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c)
+             end if
+          case ( finundation_mtd_TWS_inversion )
+             finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g)
+       end select
+       finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) )
+    end do
+    end associate
+
+  end subroutine CalcFinundated
+  !==============================================================================
+
+  subroutine ReadNML(this, bounds, NLFilename)
+   !
+   ! Read the namelist data stream information.
+   !
+   ! Uses:
+   use clm_time_manager , only : get_calendar
+   use ncdio_pio        , only : pio_subsystem
+   use shr_pio_mod      , only : shr_pio_getiotype
+   use shr_nl_mod       , only : shr_nl_find_group_name
+   use shr_log_mod      , only : errMsg => shr_log_errMsg
+   use shr_mpi_mod      , only : shr_mpi_bcast
+   use fileutils        , only : getavu, relavu
+   use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
+   !
+   ! arguments
+   implicit none
+   class(streamcontrol_type)    :: this
+   type(bounds_type), intent(in) :: bounds
+   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+   !
+   ! local variables
+   integer            :: nu_nml    ! unit for namelist file
+   integer            :: nml_error ! namelist i/o error flag
+   character(len=CL)  :: stream_fldFileName_ch4finundated = ' '
+   character(len=CL)  :: ch4finundatedmapalgo = 'bilinear'
+   character(len=*), parameter :: namelist_name = 'ch4finundated'    ! MUST agree with name in namelist and read
+   character(len=*), parameter :: shr_strdata_unset = 'NOT_SET'
+   character(len=*), parameter :: subName = "('ch4finundated::ReadNML')"
+   character(len=*), parameter :: F00 = "('(ch4finundated_readnml) ',4a)"
+   !-----------------------------------------------------------------------
+
+   namelist /ch4finundated/        &               ! MUST agree with namelist_name above
+        ch4finundatedmapalgo,  stream_fldFileName_ch4finundated
+
+   ! Default values for namelist
+
+   ! Read ch4finundated namelist
+   if (masterproc) then
+      nu_nml = getavu()
+      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+      call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error)
+      if (nml_error == 0) then
+         read(nu_nml, nml=ch4finundated,iostat=nml_error)   ! MUST agree with namelist_name above
+         if (nml_error /= 0) then
+            call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
+         end if
+      else
+         call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
+      end if
+      close(nu_nml)
+      call relavu( nu_nml )
+   endif
+
+   call shr_mpi_bcast(stream_fldFileName_ch4finundated, mpicom)
+   call shr_mpi_bcast(ch4finundatedmapalgo            , mpicom)
+
+   if (masterproc) then
+      write(iulog,*) ' '
+      write(iulog,*) namelist_name, ' stream settings:'
+      write(iulog,*) '  stream_fldFileName_ch4finundated = ',stream_fldFileName_ch4finundated
+      write(iulog,*) '  ch4finundatedmapalgo             = ',ch4finundatedmapalgo
+      write(iulog,*) ' '
+   endif
+   this%stream_fldFileName_ch4finundated = stream_fldFileName_ch4finundated
+   this%ch4finundatedmapalgo             = ch4finundatedmapalgo
+   if (      finundation_mtd == finundation_mtd_ZWT_inversion  )then
+       this%fldList = "ZWT0:F0:P3"
+   else if ( finundation_mtd == finundation_mtd_TWS_inversion  )then
+       this%fldList = "FWS_TWS_A:FWS_TWS_B"
+   else
+       call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// &
+                   errMsg(sourcefile, __LINE__))
+   end if
+
+ end subroutine ReadNML
+
+end module ch4FInundatedStreamType
diff --git a/src/cpl/mct/clm_cpl_indices.F90 b/src/cpl/mct/clm_cpl_indices.F90
new file mode 100644
index 0000000000..09ed89e92d
--- /dev/null
+++ b/src/cpl/mct/clm_cpl_indices.F90
@@ -0,0 +1,330 @@
+module clm_cpl_indices
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  !    Module containing the indices for the fields passed between CLM and
+  !    the driver. Includes the River Transport Model fields (RTM) and the
+  !    fields needed by the land-ice component (sno).
+  !
+  ! !USES:
+
+  use shr_sys_mod,    only : shr_sys_abort
+  implicit none
+
+  SAVE
+  private                              ! By default make data private
+  !
+  ! !PUBLIC MEMBER FUNCTIONS:
+  public :: clm_cpl_indices_set        ! Set the coupler indices
+  !
+  ! !PUBLIC DATA MEMBERS:
+  !
+  integer , public :: glc_nec     ! number of elevation classes for glacier_mec landunits
+                                  ! (from coupler) - must equal maxpatch_glc from namelist
+
+  ! lnd -> drv (required)
+
+  integer, public ::index_l2x_Flrl_rofsur     ! lnd->rtm input liquid surface fluxes
+  integer, public ::index_l2x_Flrl_rofgwl     ! lnd->rtm input liquid gwl fluxes
+  integer, public ::index_l2x_Flrl_rofsub     ! lnd->rtm input liquid subsurface fluxes
+  integer, public ::index_l2x_Flrl_rofi       ! lnd->rtm input frozen fluxes
+  integer, public ::index_l2x_Flrl_irrig      ! irrigation withdrawal
+
+  integer, public ::index_l2x_Sl_t            ! temperature
+  integer, public ::index_l2x_Sl_tref         ! 2m reference temperature
+  integer, public ::index_l2x_Sl_qref         ! 2m reference specific humidity
+  integer, public ::index_l2x_Sl_avsdr        ! albedo: direct , visible
+  integer, public ::index_l2x_Sl_anidr        ! albedo: direct , near-ir
+  integer, public ::index_l2x_Sl_avsdf        ! albedo: diffuse, visible
+  integer, public ::index_l2x_Sl_anidf        ! albedo: diffuse, near-ir
+  integer, public ::index_l2x_Sl_snowh        ! snow height
+  integer, public ::index_l2x_Sl_u10          ! 10m wind
+  integer, public ::index_l2x_Sl_ddvel        ! dry deposition velocities (optional)
+  integer, public ::index_l2x_Sl_fv           ! friction velocity
+  integer, public ::index_l2x_Sl_ram1         ! aerodynamical resistance
+  integer, public ::index_l2x_Sl_soilw        ! volumetric soil water
+  integer, public ::index_l2x_Fall_taux       ! wind stress, zonal
+  integer, public ::index_l2x_Fall_tauy       ! wind stress, meridional
+  integer, public ::index_l2x_Fall_lat        ! latent          heat flux
+  integer, public ::index_l2x_Fall_sen        ! sensible        heat flux
+  integer, public ::index_l2x_Fall_lwup       ! upward longwave heat flux
+  integer, public ::index_l2x_Fall_evap       ! evaporation     water flux
+  integer, public ::index_l2x_Fall_swnet      ! heat flux       shortwave net
+  integer, public ::index_l2x_Fall_fco2_lnd   ! co2 flux **For testing set to 0
+  integer, public ::index_l2x_Fall_flxdst1    ! dust flux size bin 1
+  integer, public ::index_l2x_Fall_flxdst2    ! dust flux size bin 2
+  integer, public ::index_l2x_Fall_flxdst3    ! dust flux size bin 3
+  integer, public ::index_l2x_Fall_flxdst4    ! dust flux size bin 4
+  integer, public ::index_l2x_Fall_flxvoc     ! MEGAN fluxes
+  integer, public ::index_l2x_Fall_flxfire    ! Fire fluxes
+  integer, public ::index_l2x_Sl_ztopfire     ! Top of fire emissions (m)
+
+  ! In the following, index 0 is bare land, other indices are glc elevation classes
+  integer, allocatable, public ::index_l2x_Sl_tsrf(:)   ! glc MEC temperature
+  integer, allocatable, public ::index_l2x_Sl_topo(:)   ! glc MEC topo height
+  integer, allocatable, public ::index_l2x_Flgl_qice(:) ! glc MEC ice flux
+
+  integer, public ::index_x2l_Sa_methane
+  integer, public ::index_l2x_Fall_methane
+
+  integer, public :: nflds_l2x = 0
+
+  ! drv -> lnd (required)
+
+  integer, public ::index_x2l_Sa_z            ! bottom atm level height
+  integer, public ::index_x2l_Sa_topo         ! atm surface height (m)
+  integer, public ::index_x2l_Sa_u            ! bottom atm level zon wind
+  integer, public ::index_x2l_Sa_v            ! bottom atm level mer wind
+  integer, public ::index_x2l_Sa_ptem         ! bottom atm level pot temp
+  integer, public ::index_x2l_Sa_shum         ! bottom atm level spec hum
+  integer, public ::index_x2l_Sa_pbot         ! bottom atm level pressure
+  integer, public ::index_x2l_Sa_tbot         ! bottom atm level temp
+  integer, public ::index_x2l_Faxa_lwdn       ! downward lw heat flux
+  integer, public ::index_x2l_Faxa_rainc      ! prec: liquid "convective"
+  integer, public ::index_x2l_Faxa_rainl      ! prec: liquid "large scale"
+  integer, public ::index_x2l_Faxa_snowc      ! prec: frozen "convective"
+  integer, public ::index_x2l_Faxa_snowl      ! prec: frozen "large scale"
+  integer, public ::index_x2l_Faxa_swndr      ! sw: nir direct  downward
+  integer, public ::index_x2l_Faxa_swvdr      ! sw: vis direct  downward
+  integer, public ::index_x2l_Faxa_swndf      ! sw: nir diffuse downward
+  integer, public ::index_x2l_Faxa_swvdf      ! sw: vis diffuse downward
+  integer, public ::index_x2l_Sa_co2prog      ! bottom atm level prognostic co2
+  integer, public ::index_x2l_Sa_co2diag      ! bottom atm level diagnostic co2
+  integer, public ::index_x2l_Faxa_bcphidry   ! flux: Black Carbon hydrophilic dry deposition
+  integer, public ::index_x2l_Faxa_bcphodry   ! flux: Black Carbon hydrophobic dry deposition
+  integer, public ::index_x2l_Faxa_bcphiwet   ! flux: Black Carbon hydrophilic wet deposition
+  integer, public ::index_x2l_Faxa_ocphidry   ! flux: Organic Carbon hydrophilic dry deposition
+  integer, public ::index_x2l_Faxa_ocphodry   ! flux: Organic Carbon hydrophobic dry deposition
+  integer, public ::index_x2l_Faxa_ocphiwet   ! flux: Organic Carbon hydrophilic dry deposition
+  integer, public ::index_x2l_Faxa_dstwet1    ! flux: Size 1 dust -- wet deposition
+  integer, public ::index_x2l_Faxa_dstwet2    ! flux: Size 2 dust -- wet deposition
+  integer, public ::index_x2l_Faxa_dstwet3    ! flux: Size 3 dust -- wet deposition
+  integer, public ::index_x2l_Faxa_dstwet4    ! flux: Size 4 dust -- wet deposition
+  integer, public ::index_x2l_Faxa_dstdry1    ! flux: Size 1 dust -- dry deposition
+  integer, public ::index_x2l_Faxa_dstdry2    ! flux: Size 2 dust -- dry deposition
+  integer, public ::index_x2l_Faxa_dstdry3    ! flux: Size 3 dust -- dry deposition
+  integer, public ::index_x2l_Faxa_dstdry4    ! flux: Size 4 dust -- dry deposition
+
+  integer, public ::index_x2l_Faxa_nhx        ! flux nhx from atm
+  integer, public ::index_x2l_Faxa_noy        ! flux noy from atm
+
+  integer, public ::index_x2l_Flrr_flood      ! rtm->lnd rof flood flux
+  integer, public ::index_x2l_Flrr_volr       ! rtm->lnd rof volr total volume
+  integer, public ::index_x2l_Flrr_volrmch    ! rtm->lnd rof volr main channel volume
+
+  ! In the following, index 0 is bare land, other indices are glc elevation classes
+  integer, allocatable, public ::index_x2l_Sg_ice_covered(:) ! Fraction of glacier from glc model
+  integer, allocatable, public ::index_x2l_Sg_topo(:)        ! Topo height from glc model
+  integer, allocatable, public ::index_x2l_Flgg_hflx(:)      ! Heat flux from glc model
+
+  integer, public ::index_x2l_Sg_icemask
+  integer, public ::index_x2l_Sg_icemask_coupled_fluxes
+
+  integer, public :: nflds_x2l = 0
+
+  !-----------------------------------------------------------------------
+
+contains
+
+  !-----------------------------------------------------------------------
+  subroutine clm_cpl_indices_set( )
+    !
+    ! !DESCRIPTION:
+    ! Set the coupler indices needed by the land model coupler
+    ! interface.
+    !
+    ! !USES:
+    use seq_flds_mod   , only: seq_flds_x2l_fields, seq_flds_l2x_fields
+    use mct_mod        , only: mct_aVect, mct_aVect_init, mct_avect_indexra
+    use mct_mod        , only: mct_aVect_clean, mct_avect_nRattr
+    use shr_drydep_mod , only: drydep_fields_token, n_drydep
+    use shr_megan_mod  , only: shr_megan_fields_token, shr_megan_mechcomps_n
+    use shr_fire_emis_mod,only: shr_fire_emis_fields_token, shr_fire_emis_ztop_token, shr_fire_emis_mechcomps_n
+    use clm_varctl     , only:  ndep_from_cpl
+    use glc_elevclass_mod, only: glc_get_num_elevation_classes, glc_elevclass_as_string
+    !
+    ! !ARGUMENTS:
+    implicit none
+    !
+    ! !REVISION HISTORY:
+    ! Author: Mariana Vertenstein
+    ! 01/2011, Erik Kluzek:         Added protex headers
+    !
+    ! !LOCAL VARIABLES:
+    type(mct_aVect)   :: l2x      ! temporary, land to coupler
+    type(mct_aVect)   :: x2l      ! temporary, coupler to land
+    integer           :: num
+    character(len=:), allocatable :: nec_str  ! string version of glc elev. class number
+    character(len=64) :: name
+    character(len=32) :: subname = 'clm_cpl_indices_set'  ! subroutine name
+    !-----------------------------------------------------------------------
+
+    ! Determine attribute vector indices
+
+    ! create temporary attribute vectors
+    call mct_aVect_init(x2l, rList=seq_flds_x2l_fields, lsize=1)
+    nflds_x2l = mct_avect_nRattr(x2l)
+
+    call mct_aVect_init(l2x, rList=seq_flds_l2x_fields, lsize=1)
+    nflds_l2x = mct_avect_nRattr(l2x)
+
+    !-------------------------------------------------------------
+    ! clm -> drv
+    !-------------------------------------------------------------
+
+    index_l2x_Flrl_rofsur   = mct_avect_indexra(l2x,'Flrl_rofsur')
+    index_l2x_Flrl_rofgwl   = mct_avect_indexra(l2x,'Flrl_rofgwl')
+    index_l2x_Flrl_rofsub   = mct_avect_indexra(l2x,'Flrl_rofsub')
+    index_l2x_Flrl_rofi     = mct_avect_indexra(l2x,'Flrl_rofi')
+    index_l2x_Flrl_irrig    = mct_avect_indexra(l2x,'Flrl_irrig')
+
+    index_l2x_Sl_t          = mct_avect_indexra(l2x,'Sl_t')
+    index_l2x_Sl_snowh      = mct_avect_indexra(l2x,'Sl_snowh')
+    index_l2x_Sl_avsdr      = mct_avect_indexra(l2x,'Sl_avsdr')
+    index_l2x_Sl_anidr      = mct_avect_indexra(l2x,'Sl_anidr')
+    index_l2x_Sl_avsdf      = mct_avect_indexra(l2x,'Sl_avsdf')
+    index_l2x_Sl_anidf      = mct_avect_indexra(l2x,'Sl_anidf')
+    index_l2x_Sl_tref       = mct_avect_indexra(l2x,'Sl_tref')
+    index_l2x_Sl_qref       = mct_avect_indexra(l2x,'Sl_qref')
+    index_l2x_Sl_u10        = mct_avect_indexra(l2x,'Sl_u10')
+    index_l2x_Sl_ram1       = mct_avect_indexra(l2x,'Sl_ram1')
+    index_l2x_Sl_fv         = mct_avect_indexra(l2x,'Sl_fv')
+    index_l2x_Sl_soilw      = mct_avect_indexra(l2x,'Sl_soilw',perrwith='quiet')
+
+    if ( n_drydep>0 )then
+       index_l2x_Sl_ddvel = mct_avect_indexra(l2x, trim(drydep_fields_token))
+    else
+       index_l2x_Sl_ddvel = 0
+    end if
+
+    index_l2x_Fall_taux     = mct_avect_indexra(l2x,'Fall_taux')
+    index_l2x_Fall_tauy     = mct_avect_indexra(l2x,'Fall_tauy')
+    index_l2x_Fall_lat      = mct_avect_indexra(l2x,'Fall_lat')
+    index_l2x_Fall_sen      = mct_avect_indexra(l2x,'Fall_sen')
+    index_l2x_Fall_lwup     = mct_avect_indexra(l2x,'Fall_lwup')
+    index_l2x_Fall_evap     = mct_avect_indexra(l2x,'Fall_evap')
+    index_l2x_Fall_swnet    = mct_avect_indexra(l2x,'Fall_swnet')
+    index_l2x_Fall_flxdst1  = mct_avect_indexra(l2x,'Fall_flxdst1')
+    index_l2x_Fall_flxdst2  = mct_avect_indexra(l2x,'Fall_flxdst2')
+    index_l2x_Fall_flxdst3  = mct_avect_indexra(l2x,'Fall_flxdst3')
+    index_l2x_Fall_flxdst4  = mct_avect_indexra(l2x,'Fall_flxdst4')
+
+    index_l2x_Fall_fco2_lnd = mct_avect_indexra(l2x,'Fall_fco2_lnd',perrwith='quiet')
+
+    index_l2x_Fall_methane  = mct_avect_indexra(l2x,'Fall_methane',perrWith='quiet')
+
+    ! MEGAN fluxes
+    if (shr_megan_mechcomps_n>0) then
+       index_l2x_Fall_flxvoc = mct_avect_indexra(l2x,trim(shr_megan_fields_token))
+    else
+       index_l2x_Fall_flxvoc = 0
+    endif
+
+    ! Fire fluxes
+    if (shr_fire_emis_mechcomps_n>0) then
+       index_l2x_Fall_flxfire = mct_avect_indexra(l2x,trim(shr_fire_emis_fields_token))
+       index_l2x_Sl_ztopfire = mct_avect_indexra(l2x,trim(shr_fire_emis_ztop_token))
+    else
+       index_l2x_Fall_flxfire = 0
+       index_l2x_Sl_ztopfire = 0
+    endif
+
+    !-------------------------------------------------------------
+    ! drv -> clm
+    !-------------------------------------------------------------
+
+    index_x2l_Sa_z          = mct_avect_indexra(x2l,'Sa_z')
+    index_x2l_Sa_topo       = mct_avect_indexra(x2l,'Sa_topo')
+    index_x2l_Sa_u          = mct_avect_indexra(x2l,'Sa_u')
+    index_x2l_Sa_v          = mct_avect_indexra(x2l,'Sa_v')
+    index_x2l_Sa_ptem       = mct_avect_indexra(x2l,'Sa_ptem')
+    index_x2l_Sa_pbot       = mct_avect_indexra(x2l,'Sa_pbot')
+    index_x2l_Sa_tbot       = mct_avect_indexra(x2l,'Sa_tbot')
+    index_x2l_Sa_shum       = mct_avect_indexra(x2l,'Sa_shum')
+    index_x2l_Sa_co2prog    = mct_avect_indexra(x2l,'Sa_co2prog',perrwith='quiet')
+    index_x2l_Sa_co2diag    = mct_avect_indexra(x2l,'Sa_co2diag',perrwith='quiet')
+
+    index_x2l_Sa_methane    = mct_avect_indexra(x2l,'Sa_methane',perrWith='quiet')
+
+    index_x2l_Flrr_volr     = mct_avect_indexra(x2l,'Flrr_volr')
+    index_x2l_Flrr_volrmch  = mct_avect_indexra(x2l,'Flrr_volrmch')
+
+    index_x2l_Faxa_lwdn     = mct_avect_indexra(x2l,'Faxa_lwdn')
+    index_x2l_Faxa_rainc    = mct_avect_indexra(x2l,'Faxa_rainc')
+    index_x2l_Faxa_rainl    = mct_avect_indexra(x2l,'Faxa_rainl')
+    index_x2l_Faxa_snowc    = mct_avect_indexra(x2l,'Faxa_snowc')
+    index_x2l_Faxa_snowl    = mct_avect_indexra(x2l,'Faxa_snowl')
+    index_x2l_Faxa_swndr    = mct_avect_indexra(x2l,'Faxa_swndr')
+    index_x2l_Faxa_swvdr    = mct_avect_indexra(x2l,'Faxa_swvdr')
+    index_x2l_Faxa_swndf    = mct_avect_indexra(x2l,'Faxa_swndf')
+    index_x2l_Faxa_swvdf    = mct_avect_indexra(x2l,'Faxa_swvdf')
+    index_x2l_Faxa_bcphidry = mct_avect_indexra(x2l,'Faxa_bcphidry')
+    index_x2l_Faxa_bcphodry = mct_avect_indexra(x2l,'Faxa_bcphodry')
+    index_x2l_Faxa_bcphiwet = mct_avect_indexra(x2l,'Faxa_bcphiwet')
+    index_x2l_Faxa_ocphidry = mct_avect_indexra(x2l,'Faxa_ocphidry')
+    index_x2l_Faxa_ocphodry = mct_avect_indexra(x2l,'Faxa_ocphodry')
+    index_x2l_Faxa_ocphiwet = mct_avect_indexra(x2l,'Faxa_ocphiwet')
+    index_x2l_Faxa_dstdry1  = mct_avect_indexra(x2l,'Faxa_dstdry1')
+    index_x2l_Faxa_dstdry2  = mct_avect_indexra(x2l,'Faxa_dstdry2')
+    index_x2l_Faxa_dstdry3  = mct_avect_indexra(x2l,'Faxa_dstdry3')
+    index_x2l_Faxa_dstdry4  = mct_avect_indexra(x2l,'Faxa_dstdry4')
+    index_x2l_Faxa_dstwet1  = mct_avect_indexra(x2l,'Faxa_dstwet1')
+    index_x2l_Faxa_dstwet2  = mct_avect_indexra(x2l,'Faxa_dstwet2')
+    index_x2l_Faxa_dstwet3  = mct_avect_indexra(x2l,'Faxa_dstwet3')
+    index_x2l_Faxa_dstwet4  = mct_avect_indexra(x2l,'Faxa_dstwet4')
+
+    index_x2l_Faxa_nhx      = mct_avect_indexra(x2l,'Faxa_nhx', perrWith='quiet')
+    index_x2l_Faxa_noy      = mct_avect_indexra(x2l,'Faxa_noy', perrWith='quiet')
+
+    if (index_x2l_Faxa_nhx > 0 .and. index_x2l_Faxa_noy > 0) then
+       ndep_from_cpl = .true.
+    end if
+
+    index_x2l_Flrr_flood    = mct_avect_indexra(x2l,'Flrr_flood')
+
+    !-------------------------------------------------------------
+    ! glc coupling
+    !-------------------------------------------------------------
+
+    index_x2l_Sg_icemask = mct_avect_indexra(x2l,'Sg_icemask')
+    index_x2l_Sg_icemask_coupled_fluxes = mct_avect_indexra(x2l,'Sg_icemask_coupled_fluxes')
+
+    glc_nec = glc_get_num_elevation_classes()
+    if (glc_nec < 1) then
+       call shr_sys_abort('ERROR: In CLM4.5 and later, glc_nec must be at least 1.')
+    end if
+
+    ! Create coupling fields for all glc elevation classes (1:glc_nec) plus bare land
+    ! (index 0).
+    allocate(index_l2x_Sl_tsrf(0:glc_nec))
+    allocate(index_l2x_Sl_topo(0:glc_nec))
+    allocate(index_l2x_Flgl_qice(0:glc_nec))
+    allocate(index_x2l_Sg_ice_covered(0:glc_nec))
+    allocate(index_x2l_Sg_topo(0:glc_nec))
+    allocate(index_x2l_Flgg_hflx(0:glc_nec))
+
+    do num = 0,glc_nec
+       nec_str = glc_elevclass_as_string(num)
+
+       name = 'Sg_ice_covered' // nec_str
+       index_x2l_Sg_ice_covered(num) = mct_avect_indexra(x2l,trim(name))
+       name = 'Sg_topo' // nec_str
+       index_x2l_Sg_topo(num)   = mct_avect_indexra(x2l,trim(name))
+       name = 'Flgg_hflx' // nec_str
+       index_x2l_Flgg_hflx(num) = mct_avect_indexra(x2l,trim(name))
+
+       name = 'Sl_tsrf' // nec_str
+       index_l2x_Sl_tsrf(num)   = mct_avect_indexra(l2x,trim(name))
+       name = 'Sl_topo' // nec_str
+       index_l2x_Sl_topo(num)   = mct_avect_indexra(l2x,trim(name))
+       name = 'Flgl_qice' // nec_str
+       index_l2x_Flgl_qice(num) = mct_avect_indexra(l2x,trim(name))
+    end do
+
+    call mct_aVect_clean(x2l)
+    call mct_aVect_clean(l2x)
+
+  end subroutine clm_cpl_indices_set
+
+!=======================================================================
+
+end module clm_cpl_indices
diff --git a/src/cpl/mct/laiStreamMod.F90 b/src/cpl/mct/laiStreamMod.F90
new file mode 100644
index 0000000000..47d25287b7
--- /dev/null
+++ b/src/cpl/mct/laiStreamMod.F90
@@ -0,0 +1,241 @@
+module laiStreamMod
+
+#include "shr_assert.h"
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Read LAI from stream
+  !
+  ! !USES:
+  use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create
+  use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance
+  use shr_kind_mod    , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX
+  use shr_log_mod     , only : errMsg => shr_log_errMsg
+  use decompMod       , only : bounds_type
+  use abortutils      , only : endrun
+  use clm_varctl      , only : iulog, inst_name
+  use perf_mod        , only : t_startf, t_stopf
+  use spmdMod         , only : masterproc, mpicom, comp_id
+  use ncdio_pio
+  use mct_mod
+  !
+  ! !PUBLIC TYPES:
+  implicit none
+  private
+
+  ! !PUBLIC MEMBER FUNCTIONS:
+  public :: lai_init    ! position datasets for LAI
+  public :: lai_advance ! Advance the LAI streams (outside of a Open-MP threading loop)
+  public :: lai_interp  ! interpolates between two years of LAI data (when LAI streams
+
+  ! !PRIVATE MEMBER DATA:
+  integer, allocatable    :: g_to_ig(:)         ! Array matching gridcell index to data index
+  type(shr_strdata_type)  :: sdat_lai           ! LAI input data stream
+
+  character(len=*), parameter :: sourcefile = &
+       __FILE__
+
+!==============================================================================
+contains
+!==============================================================================
+
+  subroutine lai_init(bounds)
+    !
+    ! Initialize data stream information for LAI.
+    !
+    ! !USES:
+    use clm_time_manager , only : get_calendar
+    use ncdio_pio        , only : pio_subsystem
+    use shr_pio_mod      , only : shr_pio_getiotype
+    use shr_stream_mod   , only : shr_stream_file_null
+    use shr_string_mod   , only : shr_string_listCreateField
+    use clm_nlUtilsMod   , only : find_nlgroup_name
+    use ndepStreamMod    , only : clm_domain_mct
+    use histFileMod      , only : hist_addfld1d
+    use domainMod        , only : ldomain
+    use controlMod       , only : NLFilename
+    use lnd_set_decomp_and_domain , only : gsmap_global
+    !
+    ! !ARGUMENTS:
+    implicit none
+    type(bounds_type), intent(in) :: bounds          ! bounds
+    !
+    ! !LOCAL VARIABLES:
+    integer            :: stream_year_first_lai      ! first year in Lai stream to use
+    integer            :: stream_year_last_lai       ! last year in Lai stream to use
+    integer            :: model_year_align_lai       ! align stream_year_first_lai with
+    integer            :: nu_nml                     ! unit for namelist file
+    integer            :: nml_error                  ! namelist i/o error flag
+    type(mct_ggrid)    :: dom_clm                    ! domain information
+    character(len=CL)  :: stream_fldFileName_lai     ! lai stream filename to read
+    character(len=CL)  :: lai_mapalgo = 'bilinear'   ! Mapping alogrithm
+    character(len=CL)  :: lai_tintalgo = 'linear'    ! Time interpolation alogrithm
+    character(len=CXX) :: fldList                    ! field string
+    character(*), parameter :: laiString = "LAI"     ! base string for field string
+    integer     , parameter :: numLaiFields = 16     ! number of fields to build field string
+    character(*), parameter :: subName = "('laidyn_init')"
+    !-----------------------------------------------------------------------
+    !
+    ! deal with namelist variables here in init
+    !
+    namelist /lai_streams/         &
+         stream_year_first_lai,    &
+         stream_year_last_lai,     &
+         model_year_align_lai,     &
+         lai_mapalgo,              &
+         stream_fldFileName_lai,   &
+         lai_tintalgo
+
+    ! Default values for namelist
+    stream_year_first_lai     = 1      ! first year in stream to use
+    stream_year_last_lai      = 1      ! last  year in stream to use
+    model_year_align_lai      = 1      ! align stream_year_first_lai with this model year
+    stream_fldFileName_lai    = shr_stream_file_null
+
+    ! Read lai_streams namelist
+    if (masterproc) then
+       open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+       call find_nlgroup_name(nu_nml, 'lai_streams', status=nml_error)
+       if (nml_error == 0) then
+          read(nu_nml, nml=lai_streams,iostat=nml_error)
+          if (nml_error /= 0) then
+             call endrun(subname // ':: ERROR reading lai_streams namelist')
+          end if
+       else
+          call endrun(subname // ':: ERROR finding lai_streams namelist')
+       end if
+       close(nu_nml)
+    endif
+    call shr_mpi_bcast(stream_year_first_lai  , mpicom)
+    call shr_mpi_bcast(stream_year_last_lai   , mpicom)
+    call shr_mpi_bcast(model_year_align_lai   , mpicom)
+    call shr_mpi_bcast(stream_fldFileName_lai , mpicom)
+    call shr_mpi_bcast(lai_tintalgo           , mpicom)
+
+    if (masterproc) then
+       write(iulog,*) ' '
+       write(iulog,*) 'lai_stream settings:'
+       write(iulog,*) '  stream_year_first_lai  = ',stream_year_first_lai
+       write(iulog,*) '  stream_year_last_lai   = ',stream_year_last_lai
+       write(iulog,*) '  model_year_align_lai   = ',model_year_align_lai
+       write(iulog,*) '  stream_fldFileName_lai = ',trim(stream_fldFileName_lai)
+       write(iulog,*) '  lai_tintalgo           = ',trim(lai_tintalgo)
+    endif
+
+    call clm_domain_mct (bounds, dom_clm)
+
+    ! create the field list for these lai fields...use in shr_strdata_create
+    fldList = shr_string_listCreateField( numLaiFields, laiString )
+
+    call shr_strdata_create(sdat_lai,name="laidyn",    &
+         pio_subsystem=pio_subsystem,                  &
+         pio_iotype=shr_pio_getiotype(inst_name),      &
+         mpicom=mpicom, compid=comp_id,                &
+         gsmap=gsmap_global, ggrid=dom_clm,            &
+         nxg=ldomain%ni, nyg=ldomain%nj,               &
+         yearFirst=stream_year_first_lai,              &
+         yearLast=stream_year_last_lai,                &
+         yearAlign=model_year_align_lai,               &
+         offset=0,                                     &
+         domFilePath='',                               &
+         domFileName=trim(stream_fldFileName_lai),     &
+         domTvarName='time',                           &
+         domXvarName='lon' ,                           &
+         domYvarName='lat' ,                           &
+         domAreaName='area',                           &
+         domMaskName='mask',                           &
+         filePath='',                                  &
+         filename=(/stream_fldFileName_lai/),          &
+         fldListFile=fldList,                          &
+         fldListModel=fldList,                         &
+         fillalgo='none',                              &
+         mapalgo=lai_mapalgo,                          &
+         tintalgo=lai_tintalgo,                        &
+         calendar=get_calendar(),                      &
+         taxmode='cycle'                               )
+
+    if (masterproc) then
+       call shr_strdata_print(sdat_lai,'LAI data')
+    endif
+
+  end subroutine lai_init
+
+  !==============================================================================
+  subroutine lai_advance( bounds )
+    !
+    ! Advance LAI streams
+    !
+    ! !USES:
+    use clm_time_manager, only : get_curr_date
+    !
+    ! !ARGUMENTS:
+    implicit none
+    type(bounds_type)      , intent(in)    :: bounds
+    !
+    ! !LOCAL VARIABLES:
+    integer :: g, ig   ! Indices
+    integer :: year    ! year (0, ...) for nstep+1
+    integer :: mon     ! month (1, ..., 12) for nstep+1
+    integer :: day     ! day of month (1, ..., 31) for nstep+1
+    integer :: sec     ! seconds into current date for nstep+1
+    integer :: mcdate  ! Current model date (yyyymmdd)
+    !-----------------------------------------------------------------------
+
+    call get_curr_date(year, mon, day, sec)
+    mcdate = year*10000 + mon*100 + day
+
+    call shr_strdata_advance(sdat_lai, mcdate, sec, mpicom, 'laidyn')
+    if ( .not. allocated(g_to_ig) )then
+       allocate (g_to_ig(bounds%begg:bounds%endg) )
+       ig = 0
+       do g = bounds%begg,bounds%endg
+          ig = ig+1
+          g_to_ig(g) = ig
+       end do
+    end if
+
+  end subroutine lai_advance
+
+  !==============================================================================
+  subroutine lai_interp(bounds, canopystate_inst)
+    !
+    ! Interpolate data stream information for Lai.
+    !
+    ! !USES:
+    use pftconMod       , only : noveg
+    use CanopyStateType , only : canopystate_type
+    use PatchType       , only : patch
+    !
+    ! !ARGUMENTS:
+    implicit none
+    type(bounds_type)      , intent(in)    :: bounds
+    type(canopystate_type) , intent(inout) :: canopystate_inst
+    !
+    ! !LOCAL VARIABLES:
+    integer :: ivt, p, ip, ig
+    character(len=CL)  :: stream_var_name
+    !-----------------------------------------------------------------------
+    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (lbound(sdat_lai%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (ubound(sdat_lai%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__)
+
+    do p = bounds%begp, bounds%endp
+       ivt = patch%itype(p)
+       ! Set lai for each gridcell/patch combination
+       if (ivt /= noveg) then
+          ! vegetated pft
+          write(stream_var_name,"(i6)") ivt
+          stream_var_name = 'LAI_'//trim(adjustl(stream_var_name))
+          ip = mct_aVect_indexRA(sdat_lai%avs(1),trim(stream_var_name))
+          ig = g_to_ig(patch%gridcell(p))
+          canopystate_inst%tlai_patch(p) = sdat_lai%avs(1)%rAttr(ip,ig)
+       else                       
+          ! non-vegetated pft
+          canopystate_inst%tlai_patch(p) = 0._r8
+       endif
+    end do
+
+  end subroutine lai_interp
+
+end module LaiStreamMod
diff --git a/src/cpl/mct/lnd_comp_mct.F90 b/src/cpl/mct/lnd_comp_mct.F90
new file mode 100644
index 0000000000..e50602a378
--- /dev/null
+++ b/src/cpl/mct/lnd_comp_mct.F90
@@ -0,0 +1,632 @@
+module lnd_comp_mct
+
+  !---------------------------------------------------------------------------
+  ! !DESCRIPTION:
+  !  Interface of the active land model component of CESM the CLM (Community Land Model)
+  !  with the main CESM driver. This is a thin interface taking CESM driver information
+  !  in MCT (Model Coupling Toolkit) format and converting it to use by CLM.
+  !
+  ! !uses:
+  use shr_kind_mod     , only : r8 => shr_kind_r8
+  use shr_sys_mod      , only : shr_sys_flush
+  use shr_log_mod      , only : errMsg => shr_log_errMsg
+  use mct_mod          , only : mct_avect, mct_gsmap, mct_gGrid
+  use decompmod        , only : bounds_type
+  use lnd_import_export, only : lnd_import, lnd_export
+  !
+  ! !public member functions:
+  implicit none
+  private                     ! by default make data private
+  !
+  ! !public member functions:
+  public :: lnd_init_mct      ! clm initialization
+  public :: lnd_run_mct       ! clm run phase
+  public :: lnd_final_mct     ! clm finalization/cleanup
+  !
+  ! !private member functions:
+  private :: lnd_domain_mct    ! set the land model domain information
+  private :: lnd_handle_resume ! handle pause/resume signals from the coupler
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+!====================================================================================
+contains
+!====================================================================================
+
+  subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
+    !
+    ! !DESCRIPTION:
+    ! Initialize land surface model and obtain relevant atmospheric model arrays
+    ! back from (i.e. albedos, surface temperature and snow cover over land).
+    !
+    ! !USES:
+    use shr_kind_mod     , only : shr_kind_cl
+    use abortutils       , only : endrun
+    use clm_time_manager , only : get_nstep, set_timemgr_init
+    use clm_initializeMod, only : initialize1, initialize2
+    use clm_instMod      , only : water_inst, lnd2atm_inst, lnd2glc_inst
+    use clm_varctl       , only : finidat, single_column, clm_varctl_set, iulog
+    use clm_varctl       , only : inst_index, inst_suffix, inst_name
+    use clm_varorb       , only : eccen, obliqr, lambm0, mvelpp
+    use controlMod       , only : control_setNL
+    use decompMod        , only : get_proc_bounds
+    use domainMod        , only : ldomain
+    use shr_file_mod     , only : shr_file_setLogUnit, shr_file_setLogLevel
+    use shr_file_mod     , only : shr_file_getLogUnit, shr_file_getLogLevel
+    use shr_file_mod     , only : shr_file_getUnit, shr_file_setIO
+    use seq_cdata_mod    , only : seq_cdata, seq_cdata_setptrs
+    use seq_timemgr_mod  , only : seq_timemgr_EClockGetData
+    use seq_infodata_mod , only : seq_infodata_type, seq_infodata_GetData, seq_infodata_PutData, &
+                                  seq_infodata_start_type_start, seq_infodata_start_type_cont,   &
+                                  seq_infodata_start_type_brnch
+    use seq_comm_mct     , only : seq_comm_suffix, seq_comm_inst, seq_comm_name
+    use seq_flds_mod     , only : seq_flds_x2l_fields, seq_flds_l2x_fields
+    use spmdMod          , only : masterproc, spmd_init
+    use clm_varctl       , only : nsrStartup, nsrContinue, nsrBranch
+    use clm_cpl_indices  , only : clm_cpl_indices_set
+    use mct_mod          , only : mct_aVect_init, mct_aVect_zero, mct_gsMap, mct_gsMap_init
+    use decompMod        , only : gindex_global
+    use lnd_set_decomp_and_domain, only : lnd_set_decomp_and_domain_from_surfrd, gsmap_global
+    use ESMF
+    !
+    ! !ARGUMENTS:
+    type(ESMF_Clock),           intent(inout) :: EClock           ! Input synchronization clock
+    type(seq_cdata),            intent(inout) :: cdata_l          ! Input land-model driver data
+    type(mct_aVect),            intent(inout) :: x2l_l, l2x_l     ! land model import and export states
+    character(len=*), optional, intent(in)    :: NLFilename       ! Namelist filename to read
+    !
+    ! !LOCAL VARIABLES:
+    integer                          :: LNDID        ! Land identifyer
+    integer                          :: mpicom_lnd   ! MPI communicator
+    type(mct_gsMap),         pointer :: GSMap_lnd    ! Land model MCT GS map
+    type(mct_gGrid),         pointer :: dom_l        ! Land model domain
+    type(seq_infodata_type), pointer :: infodata     ! CESM driver level info data
+    integer  :: lsize                                ! size of attribute vector
+    integer  :: gsize                                ! global size 
+    integer  :: g,i,j                                ! indices
+    integer  :: dtime_sync                           ! coupling time-step from the input synchronization clock
+    logical  :: exists                               ! true if file exists
+    logical  :: atm_aero                             ! Flag if aerosol data sent from atm model
+    real(r8) :: scmlat                               ! single-column latitude
+    real(r8) :: scmlon                               ! single-column longitude
+    character(len=SHR_KIND_CL) :: caseid             ! case identifier name
+    character(len=SHR_KIND_CL) :: ctitle             ! case description title
+    character(len=SHR_KIND_CL) :: starttype          ! start-type (startup, continue, branch, hybrid)
+    character(len=SHR_KIND_CL) :: calendar           ! calendar type name
+    character(len=SHR_KIND_CL) :: hostname           ! hostname of machine running on
+    character(len=SHR_KIND_CL) :: version            ! Model version
+    character(len=SHR_KIND_CL) :: username           ! user running the model
+    integer :: nsrest                                ! clm restart type
+    integer :: ref_ymd                               ! reference date (YYYYMMDD)
+    integer :: ref_tod                               ! reference time of day (sec)
+    integer :: start_ymd                             ! start date (YYYYMMDD)
+    integer :: start_tod                             ! start time of day (sec)
+    logical :: brnch_retain_casename                 ! flag if should retain the case name on a branch start type
+    integer :: lbnum                                 ! input to memory diagnostic
+    integer :: shrlogunit,shrloglev                  ! old values for log unit and log level
+    type(bounds_type) :: bounds                      ! bounds
+    logical :: noland
+    integer :: ni,nj
+    real(r8)         , parameter :: rundef = -9999999._r8
+    character(len=32), parameter :: sub = 'lnd_init_mct'
+    character(len=*),  parameter :: format = "('("//trim(sub)//") :',A)"
+    !-----------------------------------------------------------------------
+
+    ! Set cdata data
+    call seq_cdata_setptrs(cdata_l, ID=LNDID, mpicom=mpicom_lnd, &
+         gsMap=GSMap_lnd, dom=dom_l, infodata=infodata)
+
+    ! Determine attriute vector indices
+    call clm_cpl_indices_set()
+
+    ! Initialize clm MPI communicator
+    call spmd_init( mpicom_lnd, LNDID )
+
+#if (defined _MEMTRACE)
+    if(masterproc) then
+       lbnum=1
+       call memmon_dump_fort('memmon.out','lnd_init_mct:start::',lbnum)
+    endif
+#endif
+
+    inst_name   = seq_comm_name(LNDID)
+    inst_index  = seq_comm_inst(LNDID)
+    inst_suffix = seq_comm_suffix(LNDID)
+    ! Initialize io log unit
+
+    call shr_file_getLogUnit (shrlogunit)
+    if (masterproc) then
+       inquire(file='lnd_modelio.nml'//trim(inst_suffix),exist=exists)
+       if (exists) then
+          iulog = shr_file_getUnit()
+          call shr_file_setIO('lnd_modelio.nml'//trim(inst_suffix),iulog)
+       end if
+       write(iulog,format) "CLM land model initialization"
+    else
+       iulog = shrlogunit
+    end if
+
+    call shr_file_getLogLevel(shrloglev)
+    call shr_file_setLogUnit (iulog)
+
+    ! Use infodata to set orbital values
+    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
+         orb_lambm0=lambm0, orb_obliqr=obliqr )
+
+    ! Consistency check on namelist filename
+    call control_setNL("lnd_in"//trim(inst_suffix))
+
+    ! Initialize clm
+    ! initialize1 reads namelists
+    ! decomp and domain are set in lnd_set_decomp_and_domain_from_surfrd
+    ! initialize2 performs the rest of initialization
+    call seq_timemgr_EClockGetData(EClock,                               &
+                                   start_ymd=start_ymd,                  &
+                                   start_tod=start_tod, ref_ymd=ref_ymd, &
+                                   ref_tod=ref_tod, &
+                                   calendar=calendar, &
+                                   dtime=dtime_sync)
+    if (masterproc) then
+       write(iulog,*)'dtime = ',dtime_sync
+    end if
+    call seq_infodata_GetData(infodata, case_name=caseid,    &
+                              case_desc=ctitle, single_column=single_column,    &
+                              scmlat=scmlat, scmlon=scmlon,                     &
+                              brnch_retain_casename=brnch_retain_casename,      &
+                              start_type=starttype, model_version=version,      &
+                              hostname=hostname, username=username )
+
+    ! Single Column
+    if ( single_column .and. (scmlat == rundef  .or. scmlon == rundef ) ) then
+       call endrun(msg=' ERROR:: single column mode on -- but scmlat and scmlon are NOT set'//&
+            errMsg(sourcefile, __LINE__))
+    end if
+
+    ! Note that we assume that CTSM's internal dtime matches the coupling time step.
+    ! i.e., we currently do NOT allow sub-cycling within a coupling time step.
+    call set_timemgr_init( calendar_in=calendar, start_ymd_in=start_ymd, start_tod_in=start_tod, &
+         ref_ymd_in=ref_ymd, ref_tod_in=ref_tod, dtime_in=dtime_sync)
+
+    if (     trim(starttype) == trim(seq_infodata_start_type_start)) then
+       nsrest = nsrStartup
+    else if (trim(starttype) == trim(seq_infodata_start_type_cont) ) then
+       nsrest = nsrContinue
+    else if (trim(starttype) == trim(seq_infodata_start_type_brnch)) then
+       nsrest = nsrBranch
+    else
+       call endrun( sub//' ERROR: unknown starttype' )
+    end if
+
+    ! set default values for run control variables
+    call clm_varctl_set(caseid_in=caseid, ctitle_in=ctitle,                     &
+                        brnch_retain_casename_in=brnch_retain_casename,         &
+                        single_column_in=single_column, scmlat_in=scmlat,       &
+                        scmlon_in=scmlon, nsrest_in=nsrest, version_in=version, &
+                        hostname_in=hostname, username_in=username)
+
+    ! Read namelists
+    call initialize1(dtime=dtime_sync)
+
+    ! Initialize decomposition and domain (ldomain) type
+    call lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj)
+
+    ! If no land then exit out of initialization
+    if ( noland ) then
+
+       call seq_infodata_PutData( infodata, lnd_present   =.false.)
+       call seq_infodata_PutData( infodata, lnd_prognostic=.false.)
+
+    else
+
+       ! Determine if aerosol and dust deposition come from atmosphere component
+       call seq_infodata_GetData(infodata, atm_aero=atm_aero )
+       if ( .not. atm_aero )then
+          call endrun( sub//' ERROR: atmosphere model MUST send aerosols to CLM' )
+       end if
+
+       ! Initialize clm gsMap, clm domain and clm attribute vectors
+       call get_proc_bounds( bounds )
+       lsize = bounds%endg - bounds%begg + 1
+       gsize = ldomain%ni * ldomain%nj
+       call mct_gsMap_init( gsMap_lnd, gindex_global, mpicom_lnd, LNDID, lsize, gsize )
+       gsmap_global => gsmap_lnd ! module variable in lnd_set_decomp_and_domain
+       call lnd_domain_mct( bounds, lsize, gsMap_lnd, dom_l )
+       call mct_aVect_init(x2l_l, rList=seq_flds_x2l_fields, lsize=lsize)
+       call mct_aVect_zero(x2l_l)
+       call mct_aVect_init(l2x_l, rList=seq_flds_l2x_fields, lsize=lsize)
+       call mct_aVect_zero(l2x_l)
+
+       ! Finish initializing clm
+       call initialize2(ni,nj)
+
+       ! Create land export state
+       call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
+
+       ! Fill in infodata settings
+       call seq_infodata_PutData(infodata, lnd_prognostic=.true.)
+       call seq_infodata_PutData(infodata, lnd_nx=ldomain%ni, lnd_ny=ldomain%nj)
+       call lnd_handle_resume( cdata_l )
+
+       ! Reset shr logging to original values
+       call shr_file_setLogUnit (shrlogunit)
+       call shr_file_setLogLevel(shrloglev)
+
+#if (defined _MEMTRACE)
+       if(masterproc) then
+          write(iulog,*) TRIM(Sub) // ':end::'
+          lbnum=1
+          call memmon_dump_fort('memmon.out','lnd_int_mct:end::',lbnum)
+          call memmon_reset_addr()
+       endif
+#endif
+    end if
+
+  end subroutine lnd_init_mct
+
+  !====================================================================================
+  subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
+    !
+    ! !DESCRIPTION:
+    ! Run clm model
+    !
+    ! !USES:
+    use shr_kind_mod    ,  only : r8 => shr_kind_r8
+    use clm_instMod     ,  only : water_inst, lnd2atm_inst, atm2lnd_inst, lnd2glc_inst, glc2lnd_inst
+    use clm_driver      ,  only : clm_drv
+    use clm_time_manager,  only : get_curr_date, get_nstep, get_curr_calday, get_step_size
+    use clm_time_manager,  only : advance_timestep, update_rad_dtime
+    use decompMod       ,  only : get_proc_bounds
+    use abortutils      ,  only : endrun
+    use clm_varctl      ,  only : iulog
+    use clm_varorb      ,  only : eccen, obliqr, lambm0, mvelpp
+    use shr_file_mod    ,  only : shr_file_setLogUnit, shr_file_setLogLevel
+    use shr_file_mod    ,  only : shr_file_getLogUnit, shr_file_getLogLevel
+    use seq_cdata_mod   ,  only : seq_cdata, seq_cdata_setptrs
+    use seq_timemgr_mod ,  only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn
+    use seq_timemgr_mod ,  only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync
+    use seq_infodata_mod,  only : seq_infodata_type, seq_infodata_GetData
+    use spmdMod         ,  only : masterproc, mpicom
+    use perf_mod        ,  only : t_startf, t_stopf, t_barrierf
+    use shr_orb_mod     ,  only : shr_orb_decl
+    use ESMF
+    !
+    ! !ARGUMENTS:
+    type(ESMF_Clock) , intent(inout) :: EClock    ! Input synchronization clock from driver
+    type(seq_cdata)  , intent(inout) :: cdata_l   ! Input driver data for land model
+    type(mct_aVect)  , intent(inout) :: x2l_l     ! Import state to land model
+    type(mct_aVect)  , intent(inout) :: l2x_l     ! Export state from land model
+    !
+    ! !LOCAL VARIABLES:
+    integer      :: ymd_sync             ! Sync date (YYYYMMDD)
+    integer      :: yr_sync              ! Sync current year
+    integer      :: mon_sync             ! Sync current month
+    integer      :: day_sync             ! Sync current day
+    integer      :: tod_sync             ! Sync current time of day (sec)
+    integer      :: ymd                  ! CLM current date (YYYYMMDD)
+    integer      :: yr                   ! CLM current year
+    integer      :: mon                  ! CLM current month
+    integer      :: day                  ! CLM current day
+    integer      :: tod                  ! CLM current time of day (sec)
+    integer      :: dtime                ! time step increment (sec)
+    integer      :: nstep                ! time step index
+    logical      :: rstwr_sync           ! .true. ==> write restart file before returning
+    logical      :: rstwr                ! .true. ==> write restart file before returning
+    logical      :: nlend_sync           ! Flag signaling last time-step
+    logical      :: nlend                ! .true. ==> last time-step
+    logical      :: dosend               ! true => send data back to driver
+    logical      :: doalb                ! .true. ==> do albedo calculation on this time step
+    logical      :: rof_prognostic       ! .true. => running with a prognostic ROF model
+    logical      :: glc_present          ! .true. => running with a non-stub GLC model
+    real(r8)     :: nextsw_cday          ! calday from clock of next radiation computation
+    real(r8)     :: caldayp1             ! clm calday plus dtime offset
+    integer      :: shrlogunit,shrloglev ! old values for share log unit and log level
+    integer      :: lbnum                ! input to memory diagnostic
+    integer      :: g,i,lsize            ! counters
+    real(r8)     :: calday               ! calendar day for nstep
+    real(r8)     :: declin               ! solar declination angle in radians for nstep
+    real(r8)     :: declinp1             ! solar declination angle in radians for nstep+1
+    real(r8)     :: eccf                 ! earth orbit eccentricity factor
+    real(r8)     :: recip                ! reciprical
+    logical,save :: first_call = .true.  ! first call work
+    type(seq_infodata_type),pointer :: infodata             ! CESM information from the driver
+    type(mct_gGrid),        pointer :: dom_l                ! Land model domain data
+    type(bounds_type)               :: bounds               ! bounds
+    character(len=32)               :: rdate                ! date char string for restart file names
+    character(len=32), parameter    :: sub = "lnd_run_mct"
+    !---------------------------------------------------------------------------
+
+    ! Determine processor bounds
+
+    call get_proc_bounds(bounds)
+
+#if (defined _MEMTRACE)
+    if(masterproc) then
+       lbnum=1
+       call memmon_dump_fort('memmon.out','lnd_run_mct:start::',lbnum)
+    endif
+#endif
+
+    ! Reset shr logging to my log file
+    call shr_file_getLogUnit (shrlogunit)
+    call shr_file_getLogLevel(shrloglev)
+    call shr_file_setLogUnit (iulog)
+
+    ! Determine time of next atmospheric shortwave calculation
+    call seq_cdata_setptrs(cdata_l, infodata=infodata, dom=dom_l)
+    call seq_timemgr_EClockGetData(EClock, &
+         curr_ymd=ymd, curr_tod=tod_sync,  &
+         curr_yr=yr_sync, curr_mon=mon_sync, curr_day=day_sync)
+    call seq_infodata_GetData(infodata, nextsw_cday=nextsw_cday )
+
+    dtime = get_step_size()
+
+    ! Handle pause/resume signals from coupler
+    call lnd_handle_resume( cdata_l )
+
+    write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync,mon_sync,day_sync,tod_sync
+    nlend_sync = seq_timemgr_StopAlarmIsOn( EClock )
+    rstwr_sync = seq_timemgr_RestartAlarmIsOn( EClock )
+
+    ! Determine if we're running with a prognostic ROF model, and if we're running with a
+    ! non-stub GLC model. These won't change throughout the run, but we can't count on
+    ! their being set in initialization, so need to get them in the run method.
+
+    call seq_infodata_GetData( infodata, &
+         rof_prognostic=rof_prognostic, &
+         glc_present=glc_present)
+
+    ! Map MCT to land data type
+    ! Perform downscaling if appropriate
+
+
+    ! Map to clm (only when state and/or fluxes need to be updated)
+
+    call t_startf ('lc_lnd_import')
+    call lnd_import( bounds, &
+         x2l = x2l_l%rattr, &
+         glc_present = glc_present, &
+         atm2lnd_inst = atm2lnd_inst, &
+         glc2lnd_inst = glc2lnd_inst, &
+         wateratm2lndbulk_inst = water_inst%wateratm2lndbulk_inst)
+    call t_stopf ('lc_lnd_import')
+
+    ! Use infodata to set orbital values if updated mid-run
+
+    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
+         orb_lambm0=lambm0, orb_obliqr=obliqr )
+
+    ! Loop over time steps in coupling interval
+
+    dosend = .false.
+    do while(.not. dosend)
+
+       ! Determine if dosend
+       ! When time is not updated at the beginning of the loop - then return only if
+       ! are in sync with clock before time is updated
+       !
+       ! NOTE(wjs, 2020-03-09) I think the do while (.not. dosend) loop only is important
+       ! for the first time step (when we run 2 steps). After that, we now assume that we
+       ! run one time step per coupling interval (based on setting the model's dtime from
+       ! the driver). (According to Mariana Vertenstein, sub-cycling (running multiple
+       ! land model time steps per coupling interval) used to be supported, but hasn't
+       ! been fully supported for a long time.) We may want to rework this logic to make
+       ! this more explicit, or - ideally - get rid of this extra time step at the start
+       ! of the run, at which point I think we could do away with this looping entirely.
+
+       call get_curr_date( yr, mon, day, tod )
+       ymd = yr*10000 + mon*100 + day
+       tod = tod
+       dosend = (seq_timemgr_EClockDateInSync( EClock, ymd, tod))
+
+       ! Determine doalb based on nextsw_cday sent from atm model
+
+       nstep = get_nstep()
+       caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.)
+       if (nstep == 0) then
+          doalb = .false.
+       else if (nstep == 1) then
+          doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8)
+       else
+          doalb = (nextsw_cday >= -0.5_r8)
+       end if
+       call update_rad_dtime(doalb)
+
+       ! Determine if time to write restart and stop
+
+       rstwr = .false.
+       if (rstwr_sync .and. dosend) rstwr = .true.
+       nlend = .false.
+       if (nlend_sync .and. dosend) nlend = .true.
+
+       ! Run clm
+
+       call t_barrierf('sync_clm_run1', mpicom)
+       call t_startf ('clm_run')
+       call t_startf ('shr_orb_decl')
+       calday = get_curr_calday(reuse_day_365_for_day_366=.true.)
+       call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
+       call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
+       call t_stopf ('shr_orb_decl')
+       call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic)
+       call t_stopf ('clm_run')
+
+       ! Create l2x_l export state - add river runoff input to l2x_l if appropriate
+
+       call t_startf ('lc_lnd_export')
+       call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
+       call t_stopf ('lc_lnd_export')
+
+       ! Advance clm time step
+
+       call t_startf ('lc_clm2_adv_timestep')
+       call advance_timestep()
+       call t_stopf ('lc_clm2_adv_timestep')
+
+    end do
+
+    ! Check that internal clock is in sync with master clock
+
+    call get_curr_date( yr, mon, day, tod, offset=-dtime )
+    ymd = yr*10000 + mon*100 + day
+    tod = tod
+    if ( .not. seq_timemgr_EClockDateInSync( EClock, ymd, tod ) )then
+       call seq_timemgr_EclockGetData( EClock, curr_ymd=ymd_sync, curr_tod=tod_sync )
+       write(iulog,*)' clm ymd=',ymd     ,'  clm tod= ',tod
+       write(iulog,*)'sync ymd=',ymd_sync,' sync tod= ',tod_sync
+       call endrun( sub//":: CLM clock not in sync with Master Sync clock" )
+    end if
+
+    ! Reset shr logging to my original values
+
+    call shr_file_setLogUnit (shrlogunit)
+    call shr_file_setLogLevel(shrloglev)
+
+#if (defined _MEMTRACE)
+    if(masterproc) then
+       lbnum=1
+       call memmon_dump_fort('memmon.out','lnd_run_mct:end::',lbnum)
+       call memmon_reset_addr()
+    endif
+#endif
+
+    first_call  = .false.
+
+  end subroutine lnd_run_mct
+
+  !====================================================================================
+  subroutine lnd_final_mct( EClock, cdata_l, x2l_l, l2x_l)
+    !
+    ! !DESCRIPTION:
+    ! Finalize land surface model
+
+    use seq_cdata_mod   ,only : seq_cdata, seq_cdata_setptrs
+    use seq_timemgr_mod ,only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn
+    use seq_timemgr_mod ,only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync
+    use esmf
+    !
+    ! !ARGUMENTS:
+    type(ESMF_Clock) , intent(inout) :: EClock    ! Input synchronization clock from driver
+    type(seq_cdata)  , intent(inout) :: cdata_l   ! Input driver data for land model
+    type(mct_aVect)  , intent(inout) :: x2l_l     ! Import state to land model
+    type(mct_aVect)  , intent(inout) :: l2x_l     ! Export state from land model
+    !---------------------------------------------------------------------------
+
+    ! fill this in
+  end subroutine lnd_final_mct
+
+  !====================================================================================
+  subroutine lnd_domain_mct( bounds, lsize, gsMap_l, dom_l )
+    !
+    ! !DESCRIPTION:
+    ! Send the land model domain information to the coupler
+    !
+    ! !USES:
+    use clm_varcon  , only: re
+    use domainMod   , only: ldomain
+    use spmdMod     , only: iam
+    use mct_mod     , only: mct_gGrid_importIAttr
+    use mct_mod     , only: mct_gGrid_importRAttr, mct_gGrid_init, mct_gsMap_orderedPoints
+    use seq_flds_mod, only: seq_flds_dom_coord, seq_flds_dom_other
+    !
+    ! !ARGUMENTS:
+    type(bounds_type), intent(in)  :: bounds  ! bounds
+    integer        , intent(in)    :: lsize   ! land model domain data size
+    type(mct_gsMap), intent(inout) :: gsMap_l ! Output land model MCT GS map
+    type(mct_ggrid), intent(out)   :: dom_l   ! Output domain information for land model
+    !
+    ! Local Variables
+    integer :: g,i,j              ! index
+    real(r8), pointer :: data(:)  ! temporary
+    integer , pointer :: idata(:) ! temporary
+    !---------------------------------------------------------------------------
+    !
+    ! Initialize mct domain type
+    ! lat/lon in degrees,  area in radians^2, mask is 1 (land), 0 (non-land)
+    ! Note that in addition land carries around landfrac for the purposes of domain checking
+    !
+    call mct_gGrid_init( GGrid=dom_l, CoordChars=trim(seq_flds_dom_coord), &
+       OtherChars=trim(seq_flds_dom_other), lsize=lsize )
+    !
+    ! Allocate memory
+    !
+    allocate(data(lsize))
+    !
+    ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT
+    !
+    call mct_gsMap_orderedPoints(gsMap_l, iam, idata)
+    call mct_gGrid_importIAttr(dom_l,'GlobGridNum',idata,lsize)
+    !
+    ! Determine domain (numbering scheme is: West to East and South to North to South pole)
+    ! Initialize attribute vector with special value
+    !
+    data(:) = -9999.0_R8
+    call mct_gGrid_importRAttr(dom_l,"lat"  ,data,lsize)
+    call mct_gGrid_importRAttr(dom_l,"lon"  ,data,lsize)
+    call mct_gGrid_importRAttr(dom_l,"area" ,data,lsize)
+    call mct_gGrid_importRAttr(dom_l,"aream",data,lsize)
+    data(:) = 0.0_R8
+    call mct_gGrid_importRAttr(dom_l,"mask" ,data,lsize)
+    !
+    ! Fill in correct values for domain components
+    ! Note aream will be filled in in the atm-lnd mapper
+    !
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = ldomain%lonc(g)
+    end do
+    call mct_gGrid_importRattr(dom_l,"lon",data,lsize)
+
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = ldomain%latc(g)
+    end do
+    call mct_gGrid_importRattr(dom_l,"lat",data,lsize)
+
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = ldomain%area(g)/(re*re)
+    end do
+    call mct_gGrid_importRattr(dom_l,"area",data,lsize)
+
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = real(ldomain%mask(g), r8)
+    end do
+    call mct_gGrid_importRattr(dom_l,"mask",data,lsize)
+
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = real(ldomain%frac(g), r8)
+    end do
+    call mct_gGrid_importRattr(dom_l,"frac",data,lsize)
+
+    deallocate(data)
+    deallocate(idata)
+
+  end subroutine lnd_domain_mct
+
+  !====================================================================================
+  subroutine lnd_handle_resume( cdata_l )
+    !
+    ! !DESCRIPTION:
+    ! Handle resume signals for Data Assimilation (DA)
+    !
+    ! !USES:
+    use clm_time_manager , only : update_DA_nstep
+    use seq_cdata_mod    , only : seq_cdata, seq_cdata_setptrs
+    implicit none
+    ! !ARGUMENTS:
+    type(seq_cdata),            intent(inout) :: cdata_l          ! Input land-model driver data
+    ! !LOCAL VARIABLES:
+    logical :: resume_from_data_assim                      ! flag if we are resuming after data assimulation was done
+    !---------------------------------------------------------------------------
+
+    ! Check to see if restart was modified and we are resuming from data
+    ! assimilation
+    call seq_cdata_setptrs(cdata_l, post_assimilation=resume_from_data_assim)
+    if ( resume_from_data_assim ) call update_DA_nstep()
+
+  end subroutine lnd_handle_resume
+
+end module lnd_comp_mct
diff --git a/src/cpl/mct/lnd_import_export.F90 b/src/cpl/mct/lnd_import_export.F90
new file mode 100644
index 0000000000..537abd49d9
--- /dev/null
+++ b/src/cpl/mct/lnd_import_export.F90
@@ -0,0 +1,354 @@
+module lnd_import_export
+
+  use shr_kind_mod , only: r8 => shr_kind_r8, cl=>shr_kind_cl
+  use abortutils   , only: endrun
+  use decompmod    , only: bounds_type, subgrid_level_gridcell
+  use lnd2atmType  , only: lnd2atm_type
+  use lnd2glcMod   , only: lnd2glc_type
+  use atm2lndType  , only: atm2lnd_type
+  use glc2lndMod   , only: glc2lnd_type 
+  use Waterlnd2atmBulkType , only: waterlnd2atmbulk_type
+  use Wateratm2lndBulkType , only: wateratm2lndbulk_type
+  use clm_cpl_indices
+  use GridcellType      , only : grc
+  !
+  implicit none
+  !===============================================================================
+
+contains
+
+  !===============================================================================
+  subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst, wateratm2lndbulk_inst)
+
+    !---------------------------------------------------------------------------
+    ! !DESCRIPTION:
+    ! Convert the input data from the coupler to the land model 
+    !
+    ! !USES:
+    use seq_flds_mod    , only: seq_flds_x2l_fields
+    use clm_varctl      , only: co2_type, co2_ppmv, iulog, use_c13
+    use clm_varctl      , only: ndep_from_cpl 
+    use clm_varcon      , only: c13ratio
+    use domainMod       , only: ldomain
+    use lnd_import_export_utils, only : derive_quantities, check_for_errors, check_for_nans
+    !
+    ! !ARGUMENTS:
+    type(bounds_type)  , intent(in)    :: bounds   ! bounds
+    real(r8)           , intent(in)    :: x2l(:,:) ! driver import state to land model
+    logical            , intent(in)    :: glc_present       ! .true. => running with a non-stub GLC model
+    type(atm2lnd_type) , intent(inout) :: atm2lnd_inst      ! clm internal input data type
+    type(glc2lnd_type) , intent(inout) :: glc2lnd_inst      ! clm internal input data type
+    type(wateratm2lndbulk_type), intent(inout) :: wateratm2lndbulk_inst   ! clm internal input data type
+    !
+    ! !LOCAL VARIABLES:
+    integer  :: begg, endg           ! bounds
+    integer  :: g,i,k,nstep,ier      ! indices, number of steps, and error code
+    real(r8) :: qsat_kg_kg           ! saturation specific humidity (kg/kg)
+    real(r8) :: forc_pbot            ! atmospheric pressure (Pa)
+    real(r8) :: forc_rainc(bounds%begg:bounds%endg)  ! rainxy Atm flux mm/s
+    real(r8) :: forc_rainl(bounds%begg:bounds%endg)  ! rainxy Atm flux mm/s
+    real(r8) :: forc_snowc(bounds%begg:bounds%endg)  ! snowfxy Atm flux  mm/s
+    real(r8) :: forc_snowl(bounds%begg:bounds%endg)  ! snowfxl Atm flux  mm/s
+    real(r8) :: co2_ppmv_diag        ! temporary
+    real(r8) :: co2_ppmv_prog        ! temporary
+    real(r8) :: co2_ppmv_val         ! temporary
+    integer  :: co2_type_idx         ! integer flag for co2_type options
+    character(len=32) :: fname       ! name of field that is NaN
+    character(len=32), parameter :: sub = 'lnd_import'
+
+    !---------------------------------------------------------------------------
+
+    ! Set bounds
+    begg = bounds%begg; endg = bounds%endg
+
+    co2_type_idx = 0
+    if (co2_type == 'prognostic') then
+       co2_type_idx = 1
+    else if (co2_type == 'diagnostic') then
+       co2_type_idx = 2
+    end if
+    if (co2_type == 'prognostic' .and. index_x2l_Sa_co2prog == 0) then
+       call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2prog for co2_type equal to prognostic' )
+    else if (co2_type == 'diagnostic' .and. index_x2l_Sa_co2diag == 0) then
+       call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2diag for co2_type equal to diagnostic' )
+    end if
+
+    ! Note that the precipitation fluxes received  from the coupler
+    ! are in units of kg/s/m^2. To convert these precipitation rates
+    ! in units of mm/sec, one must divide by 1000 kg/m^3 and multiply
+    ! by 1000 mm/m resulting in an overall factor of unity.
+    ! Below the units are therefore given in mm/s.
+
+    do g = begg,endg
+       i = 1 + (g - begg)
+
+       ! Determine flooding input, sign convention is positive downward and
+       ! hierarchy is atm/glc/lnd/rof/ice/ocn.  so water sent from rof to land is negative,
+       ! change the sign to indicate addition of water to system.
+
+       wateratm2lndbulk_inst%forc_flood_grc(g)   = -x2l(index_x2l_Flrr_flood,i)  
+
+       wateratm2lndbulk_inst%volr_grc(g)   = x2l(index_x2l_Flrr_volr,i) * (ldomain%area(g) * 1.e6_r8)
+       wateratm2lndbulk_inst%volrmch_grc(g)= x2l(index_x2l_Flrr_volrmch,i) * (ldomain%area(g) * 1.e6_r8)
+
+       ! Determine required receive fields
+
+       atm2lnd_inst%forc_hgt_grc(g)                  = x2l(index_x2l_Sa_z,i)         ! zgcmxy  Atm state m
+       atm2lnd_inst%forc_topo_grc(g)                 = x2l(index_x2l_Sa_topo,i)      ! Atm surface height (m)
+       atm2lnd_inst%forc_u_grc(g)                    = x2l(index_x2l_Sa_u,i)         ! forc_uxy  Atm state m/s
+       atm2lnd_inst%forc_v_grc(g)                    = x2l(index_x2l_Sa_v,i)         ! forc_vxy  Atm state m/s
+       atm2lnd_inst%forc_solad_not_downscaled_grc(g,2) = x2l(index_x2l_Faxa_swndr,i)   ! forc_sollxy  Atm flux  W/m^2
+       atm2lnd_inst%forc_solad_not_downscaled_grc(g,1) = x2l(index_x2l_Faxa_swvdr,i)   ! forc_solsxy  Atm flux  W/m^2
+       atm2lnd_inst%forc_solai_grc(g,2)              = x2l(index_x2l_Faxa_swndf,i)   ! forc_solldxy Atm flux  W/m^2
+       atm2lnd_inst%forc_solai_grc(g,1)              = x2l(index_x2l_Faxa_swvdf,i)   ! forc_solsdxy Atm flux  W/m^2
+
+       atm2lnd_inst%forc_th_not_downscaled_grc(g)    = x2l(index_x2l_Sa_ptem,i)      ! forc_thxy Atm state K
+       wateratm2lndbulk_inst%forc_q_not_downscaled_grc(g)     = x2l(index_x2l_Sa_shum,i)      ! forc_qxy  Atm state kg/kg
+       atm2lnd_inst%forc_pbot_not_downscaled_grc(g)  = x2l(index_x2l_Sa_pbot,i)      ! ptcmxy  Atm state Pa
+       atm2lnd_inst%forc_t_not_downscaled_grc(g)     = x2l(index_x2l_Sa_tbot,i)      ! forc_txy  Atm state K
+       atm2lnd_inst%forc_lwrad_not_downscaled_grc(g) = x2l(index_x2l_Faxa_lwdn,i)    ! flwdsxy Atm flux  W/m^2
+
+       forc_rainc(g)                                 = x2l(index_x2l_Faxa_rainc,i)   ! mm/s
+       forc_rainl(g)                                 = x2l(index_x2l_Faxa_rainl,i)   ! mm/s
+       forc_snowc(g)                                 = x2l(index_x2l_Faxa_snowc,i)   ! mm/s
+       forc_snowl(g)                                 = x2l(index_x2l_Faxa_snowl,i)   ! mm/s
+
+       ! atmosphere coupling, for prognostic/prescribed aerosols
+       atm2lnd_inst%forc_aer_grc(g,1)                = x2l(index_x2l_Faxa_bcphidry,i)
+       atm2lnd_inst%forc_aer_grc(g,2)                = x2l(index_x2l_Faxa_bcphodry,i)
+       atm2lnd_inst%forc_aer_grc(g,3)                = x2l(index_x2l_Faxa_bcphiwet,i)
+       atm2lnd_inst%forc_aer_grc(g,4)                = x2l(index_x2l_Faxa_ocphidry,i)
+       atm2lnd_inst%forc_aer_grc(g,5)                = x2l(index_x2l_Faxa_ocphodry,i)
+       atm2lnd_inst%forc_aer_grc(g,6)                = x2l(index_x2l_Faxa_ocphiwet,i)
+       atm2lnd_inst%forc_aer_grc(g,7)                = x2l(index_x2l_Faxa_dstwet1,i)
+       atm2lnd_inst%forc_aer_grc(g,8)                = x2l(index_x2l_Faxa_dstdry1,i)
+       atm2lnd_inst%forc_aer_grc(g,9)                = x2l(index_x2l_Faxa_dstwet2,i)
+       atm2lnd_inst%forc_aer_grc(g,10)               = x2l(index_x2l_Faxa_dstdry2,i)
+       atm2lnd_inst%forc_aer_grc(g,11)               = x2l(index_x2l_Faxa_dstwet3,i)
+       atm2lnd_inst%forc_aer_grc(g,12)               = x2l(index_x2l_Faxa_dstdry3,i)
+       atm2lnd_inst%forc_aer_grc(g,13)               = x2l(index_x2l_Faxa_dstwet4,i)
+       atm2lnd_inst%forc_aer_grc(g,14)               = x2l(index_x2l_Faxa_dstdry4,i)
+
+       if (index_x2l_Sa_methane /= 0) then
+          atm2lnd_inst%forc_pch4_grc(g) = x2l(index_x2l_Sa_methane,i)
+       endif
+
+       !--------------------------
+       ! Check for nans from coupler
+       !--------------------------
+
+       call check_for_nans(x2l(:,i), fname, begg, "x2l")
+
+    end do
+
+    !--------------------------
+    ! Derived quantities for required fields
+    ! and corresponding error checks
+    !--------------------------
+
+    call derive_quantities(bounds, atm2lnd_inst, wateratm2lndbulk_inst, &
+       forc_rainc, forc_rainl, forc_snowc, forc_snowl)
+
+    call check_for_errors(bounds, atm2lnd_inst, wateratm2lndbulk_inst)
+
+    ! Determine derived quantities for optional fields
+    ! Note that the following does unit conversions from ppmv to partial pressures (Pa)
+    ! Note that forc_pbot is in Pa
+
+    do g = begg,endg
+       i = 1 + (g - begg)
+
+       forc_pbot = atm2lnd_inst%forc_pbot_not_downscaled_grc(g)
+
+       ! Determine optional receive fields
+       if (index_x2l_Sa_co2prog /= 0) then
+          co2_ppmv_prog = x2l(index_x2l_Sa_co2prog,i)   ! co2 atm state prognostic
+       else
+          co2_ppmv_prog = co2_ppmv
+       end if
+       if (index_x2l_Sa_co2diag /= 0) then
+          co2_ppmv_diag = x2l(index_x2l_Sa_co2diag,i)   ! co2 atm state diagnostic
+       else
+          co2_ppmv_diag = co2_ppmv
+       end if
+
+       if (co2_type_idx == 1) then
+          co2_ppmv_val = co2_ppmv_prog
+       else if (co2_type_idx == 2) then
+          co2_ppmv_val = co2_ppmv_diag 
+       else
+          co2_ppmv_val = co2_ppmv
+       end if
+       if ( (co2_ppmv_val < 10.0_r8) .or. (co2_ppmv_val > 15000.0_r8) )then
+          call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, &
+               msg = sub//' ERROR: CO2 is outside of an expected range' )
+       end if
+       atm2lnd_inst%forc_pco2_grc(g) = co2_ppmv_val * 1.e-6_r8 * forc_pbot 
+       if (use_c13) then
+          atm2lnd_inst%forc_pc13o2_grc(g) = co2_ppmv_val * c13ratio * 1.e-6_r8 * forc_pbot
+       end if
+
+       if (ndep_from_cpl) then
+          ! The coupler is sending ndep in units if kgN/m2/s - and clm uses units of gN/m2/sec - so the
+          ! following conversion needs to happen
+          atm2lnd_inst%forc_ndep_grc(g) = (x2l(index_x2l_Faxa_nhx, i) + x2l(index_x2l_faxa_noy, i))*1000._r8
+       end if
+
+    end do
+
+    call glc2lnd_inst%set_glc2lnd_fields_mct( &
+         bounds = bounds, &
+         glc_present = glc_present, &
+         ! NOTE(wjs, 2017-12-13) the x2l argument doesn't have the typical bounds
+         ! subsetting (bounds%begg:bounds%endg). This mirrors the lack of these bounds in
+         ! the call to lnd_import from lnd_run_mct. This is okay as long as this code is
+         ! outside a clump loop.
+         x2l = x2l, &
+         index_x2l_Sg_ice_covered = index_x2l_Sg_ice_covered, &
+         index_x2l_Sg_topo = index_x2l_Sg_topo, &
+         index_x2l_Flgg_hflx = index_x2l_Flgg_hflx, &
+         index_x2l_Sg_icemask = index_x2l_Sg_icemask, &
+         index_x2l_Sg_icemask_coupled_fluxes = index_x2l_Sg_icemask_coupled_fluxes)
+
+  end subroutine lnd_import
+
+  !===============================================================================
+
+  subroutine lnd_export( bounds, waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x)
+
+    !---------------------------------------------------------------------------
+    ! !DESCRIPTION:
+    ! Convert the data to be sent from the clm model to the coupler 
+    ! 
+    ! !USES:
+    use shr_kind_mod       , only : r8 => shr_kind_r8
+    use seq_flds_mod       , only : seq_flds_l2x_fields
+    use clm_varctl         , only : iulog
+    use shr_drydep_mod     , only : n_drydep
+    use shr_megan_mod      , only : shr_megan_mechcomps_n
+    use shr_fire_emis_mod  , only : shr_fire_emis_mechcomps_n
+    use lnd_import_export_utils, only : check_for_nans
+    !
+    ! !ARGUMENTS:
+    implicit none
+    type(bounds_type) , intent(in)    :: bounds  ! bounds
+    type(lnd2atm_type), intent(inout) :: lnd2atm_inst ! clm land to atmosphere exchange data type
+    type(lnd2glc_type), intent(inout) :: lnd2glc_inst ! clm land to atmosphere exchange data type
+    type(waterlnd2atmbulk_type), intent(in) :: waterlnd2atmbulk_inst
+    real(r8)          , intent(out)   :: l2x(:,:)! land to coupler export state on land grid
+    !
+    ! !LOCAL VARIABLES:
+    integer  :: begg, endg  ! bounds
+    integer  :: g,i,k ! indices
+    integer  :: ier   ! error status
+    integer  :: nstep ! time step index
+    integer  :: dtime ! time step   
+    integer  :: num   ! counter
+    character(len=32) :: fname       ! name of field that is NaN
+    character(len=32), parameter :: sub = 'lnd_export'
+    !---------------------------------------------------------------------------
+
+    ! Set bounds
+    begg = bounds%begg; endg = bounds%endg
+
+    ! cesm sign convention is that fluxes are positive downward
+
+    l2x(:,:) = 0.0_r8
+
+    do g = begg,endg
+       i = 1 + (g-begg)
+       l2x(index_l2x_Sl_t,i)        =  lnd2atm_inst%t_rad_grc(g)
+       l2x(index_l2x_Sl_snowh,i)    =  waterlnd2atmbulk_inst%h2osno_grc(g)
+       l2x(index_l2x_Sl_avsdr,i)    =  lnd2atm_inst%albd_grc(g,1)
+       l2x(index_l2x_Sl_anidr,i)    =  lnd2atm_inst%albd_grc(g,2)
+       l2x(index_l2x_Sl_avsdf,i)    =  lnd2atm_inst%albi_grc(g,1)
+       l2x(index_l2x_Sl_anidf,i)    =  lnd2atm_inst%albi_grc(g,2)
+       l2x(index_l2x_Sl_tref,i)     =  lnd2atm_inst%t_ref2m_grc(g)
+       l2x(index_l2x_Sl_qref,i)     =  waterlnd2atmbulk_inst%q_ref2m_grc(g)
+       l2x(index_l2x_Sl_u10,i)      =  lnd2atm_inst%u_ref10m_grc(g)
+       l2x(index_l2x_Fall_taux,i)   = -lnd2atm_inst%taux_grc(g)
+       l2x(index_l2x_Fall_tauy,i)   = -lnd2atm_inst%tauy_grc(g)
+       l2x(index_l2x_Fall_lat,i)    = -lnd2atm_inst%eflx_lh_tot_grc(g)
+       l2x(index_l2x_Fall_sen,i)    = -lnd2atm_inst%eflx_sh_tot_grc(g)
+       l2x(index_l2x_Fall_lwup,i)   = -lnd2atm_inst%eflx_lwrad_out_grc(g)
+       l2x(index_l2x_Fall_evap,i)   = -waterlnd2atmbulk_inst%qflx_evap_tot_grc(g)
+       l2x(index_l2x_Fall_swnet,i)  =  lnd2atm_inst%fsa_grc(g)
+       if (index_l2x_Fall_fco2_lnd /= 0) then
+          l2x(index_l2x_Fall_fco2_lnd,i) = -lnd2atm_inst%net_carbon_exchange_grc(g)  
+       end if
+
+       ! Additional fields for DUST, PROGSSLT, dry-deposition and VOC
+       ! These are now standard fields, but the check on the index makes sure the driver handles them
+       if (index_l2x_Sl_ram1      /= 0 )  l2x(index_l2x_Sl_ram1,i)     =  lnd2atm_inst%ram1_grc(g)
+       if (index_l2x_Sl_fv        /= 0 )  l2x(index_l2x_Sl_fv,i)       =  lnd2atm_inst%fv_grc(g)
+       if (index_l2x_Sl_soilw     /= 0 )  l2x(index_l2x_Sl_soilw,i)    =  waterlnd2atmbulk_inst%h2osoi_vol_grc(g,1)
+       if (index_l2x_Fall_flxdst1 /= 0 )  l2x(index_l2x_Fall_flxdst1,i)= -lnd2atm_inst%flxdst_grc(g,1)
+       if (index_l2x_Fall_flxdst2 /= 0 )  l2x(index_l2x_Fall_flxdst2,i)= -lnd2atm_inst%flxdst_grc(g,2)
+       if (index_l2x_Fall_flxdst3 /= 0 )  l2x(index_l2x_Fall_flxdst3,i)= -lnd2atm_inst%flxdst_grc(g,3)
+       if (index_l2x_Fall_flxdst4 /= 0 )  l2x(index_l2x_Fall_flxdst4,i)= -lnd2atm_inst%flxdst_grc(g,4)
+
+
+       ! for dry dep velocities
+       if (index_l2x_Sl_ddvel     /= 0 )  then
+          l2x(index_l2x_Sl_ddvel:index_l2x_Sl_ddvel+n_drydep-1,i) = &
+               lnd2atm_inst%ddvel_grc(g,:n_drydep)
+       end if
+
+       ! for MEGAN VOC emis fluxes
+       if (index_l2x_Fall_flxvoc  /= 0 ) then
+          l2x(index_l2x_Fall_flxvoc:index_l2x_Fall_flxvoc+shr_megan_mechcomps_n-1,i) = &
+               -lnd2atm_inst%flxvoc_grc(g,:shr_megan_mechcomps_n)
+       end if
+
+
+       ! for fire emis fluxes
+       if (index_l2x_Fall_flxfire  /= 0 ) then
+          l2x(index_l2x_Fall_flxfire:index_l2x_Fall_flxfire+shr_fire_emis_mechcomps_n-1,i) = &
+               -lnd2atm_inst%fireflx_grc(g,:shr_fire_emis_mechcomps_n)
+          l2x(index_l2x_Sl_ztopfire,i) = lnd2atm_inst%fireztop_grc(g)
+       end if
+
+       if (index_l2x_Fall_methane /= 0) then
+          l2x(index_l2x_Fall_methane,i) = -lnd2atm_inst%ch4_surf_flux_tot_grc(g)
+       endif
+
+       ! sign convention is positive downward with 
+       ! hierarchy of atm/glc/lnd/rof/ice/ocn.  
+       ! I.e. water sent from land to rof is positive
+
+       l2x(index_l2x_Flrl_rofsur,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsur_grc(g)
+
+       !  subsurface runoff is the sum of qflx_drain and qflx_perched_drain
+       l2x(index_l2x_Flrl_rofsub,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsub_grc(g) &
+            + waterlnd2atmbulk_inst%qflx_rofliq_drain_perched_grc(g)
+
+       !  qgwl sent individually to coupler
+       l2x(index_l2x_Flrl_rofgwl,i) = waterlnd2atmbulk_inst%qflx_rofliq_qgwl_grc(g)
+
+       ! ice  sent individually to coupler
+       l2x(index_l2x_Flrl_rofi,i) = waterlnd2atmbulk_inst%qflx_rofice_grc(g)
+
+       ! irrigation flux to be removed from main channel storage (negative)
+       l2x(index_l2x_Flrl_irrig,i) = - waterlnd2atmbulk_inst%qirrig_grc(g)
+
+       ! glc coupling
+       ! We could avoid setting these fields if glc_present is .false., if that would
+       ! help with performance. (The downside would be that we wouldn't have these fields
+       ! available for diagnostic purposes or to force a later T compset with dlnd.)
+       do num = 0,glc_nec
+          l2x(index_l2x_Sl_tsrf(num),i)   = lnd2glc_inst%tsrf_grc(g,num)
+          l2x(index_l2x_Sl_topo(num),i)   = lnd2glc_inst%topo_grc(g,num)
+          l2x(index_l2x_Flgl_qice(num),i) = lnd2glc_inst%qice_grc(g,num)
+       end do
+
+       !--------------------------
+       ! Check for nans to coupler
+       !--------------------------
+
+       call check_for_nans(l2x(:,i), fname, begg, "l2x")
+
+    end do
+
+  end subroutine lnd_export
+
+end module lnd_import_export
diff --git a/src/cpl/mct/lnd_set_decomp_and_domain.F90 b/src/cpl/mct/lnd_set_decomp_and_domain.F90
new file mode 100644
index 0000000000..0a37554313
--- /dev/null
+++ b/src/cpl/mct/lnd_set_decomp_and_domain.F90
@@ -0,0 +1,352 @@
+module lnd_set_decomp_and_domain
+
+  use shr_kind_mod , only : r8 => shr_kind_r8
+  use spmdMod      , only : masterproc
+  use clm_varctl   , only : iulog
+  use mct_mod      , only : mct_gsMap
+
+  implicit none
+  private ! except
+
+  ! public member routines
+  public :: lnd_set_decomp_and_domain_from_surfrd
+
+  ! private member routines
+  private :: surfrd_get_globmask  ! Reads global land mask (needed for setting domain decomp)
+  private :: surfrd_get_grid      ! Read grid/ladnfrac data into domain (after domain decomp)
+
+  ! translation between local and global indices at gridcell level
+  type(mct_gsmap), pointer, public :: gsmap_global           
+
+  ! translation between local and global indices at gridcell level for multiple levels
+  ! needed for 3d soil moisture stream
+  type(mct_gsmap), target , public :: gsMap_lnd2Dsoi_gdc2glo 
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+!===============================================================================
+contains
+!===============================================================================
+
+  subroutine lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj)
+
+    ! Initialize ldomain data types
+
+    use clm_varpar    , only: nlevsoi
+    use clm_varctl    , only: fatmlndfrc, use_soil_moisture_streams
+    use decompInitMod , only: decompInit_lnd
+    use decompMod     , only: bounds_type, get_proc_bounds
+    use domainMod     , only: ldomain, domain_check
+
+    ! input/output variables
+    logical, intent(out) :: noland
+    integer, intent(out) :: ni, nj ! global grid sizes
+
+    ! local variables
+    integer ,pointer  :: amask(:)   ! global land mask
+    integer           :: begg, endg ! processor bounds
+    type(bounds_type) :: bounds     ! bounds
+    character(len=32) :: subname = 'lnd_set_decomp_and_domain_from_surfrd'
+    !-----------------------------------------------------------------------
+
+    ! Read in global land grid and land mask (amask)- needed to set decomposition
+    ! global memory for amask is allocate in surfrd_get_glomask - must be deallocated below
+    if (masterproc) then
+       write(iulog,*) 'Attempting to read global land mask from ',trim(fatmlndfrc)
+    endif
+
+    ! Get global mask, ni and nj
+    call surfrd_get_globmask(filename=fatmlndfrc, mask=amask, ni=ni, nj=nj)
+
+    ! Exit early if no valid land points
+    if ( all(amask == 0) )then
+       if (masterproc) write(iulog,*) trim(subname)//': no valid land points do NOT run clm'
+       noland = .true.
+       return
+    else
+       noland = .false.
+    end if
+
+    ! Determine ctsm gridcell decomposition and processor bounds for gridcells
+    call decompInit_lnd(ni, nj, amask)
+    deallocate(amask)
+    if (use_soil_moisture_streams) call decompInit_lnd3D(ni, nj, nlevsoi)
+
+    ! Initialize bounds for just gridcells
+    ! Remaining bounds (landunits, columns, patches) will be determined
+    ! after the call to decompInit_glcp - so get_proc_bounds is called
+    ! twice and the gridcell information is just filled in twice
+    call get_proc_bounds(bounds)
+
+    ! Get grid cell bounds values
+    begg = bounds%begg
+    endg = bounds%endg
+
+    ! Initialize ldomain data type
+    if (masterproc) then
+       write(iulog,*) 'Attempting to read ldomain from ',trim(fatmlndfrc)
+    endif
+    call surfrd_get_grid(begg, endg, ldomain, fatmlndfrc)
+    if (masterproc) then
+       call domain_check(ldomain)
+    endif
+    ldomain%mask = 1  !!! TODO - is this needed?
+
+  end subroutine lnd_set_decomp_and_domain_from_surfrd
+
+  !-----------------------------------------------------------------------
+  subroutine surfrd_get_globmask(filename, mask, ni, nj)
+
+    ! Read the surface dataset grid related information
+    ! This is used to set the domain decomposition - so global data is read here
+
+    use fileutils  , only : getfil
+    use ncdio_pio  , only : ncd_io, ncd_pio_openfile, ncd_pio_closefile, ncd_inqfdims, file_desc_t
+    use abortutils , only : endrun
+    use shr_log_mod, only : errMsg => shr_log_errMsg
+
+    ! input/output variables
+    character(len=*), intent(in)    :: filename  ! grid filename
+    integer         , pointer       :: mask(:)   ! grid mask
+    integer         , intent(out)   :: ni, nj    ! global grid sizes
+
+    ! local variables
+    logical               :: isgrid2d
+    integer               :: dimid,varid ! netCDF id's
+    integer               :: ns          ! size of grid on file
+    integer               :: n,i,j       ! index
+    integer               :: ier         ! error status
+    type(file_desc_t)     :: ncid        ! netcdf id
+    character(len=256)    :: locfn       ! local file name
+    logical               :: readvar     ! read variable in or not
+    integer , allocatable :: idata2d(:,:)
+    character(len=32) :: subname = 'surfrd_get_globmask' ! subroutine name
+    !-----------------------------------------------------------------------
+
+    if (filename == ' ') then
+       mask(:) = 1
+    else
+       ! Check if file exists
+       if (masterproc) then
+          if (filename == ' ') then
+             write(iulog,*) trim(subname),' ERROR: filename must be specified '
+             call endrun(msg=errMsg(sourcefile, __LINE__))
+          endif
+       end if
+
+       ! Open file
+       call getfil( filename, locfn, 0 )
+       call ncd_pio_openfile (ncid, trim(locfn), 0)
+
+       ! Determine dimensions and if grid file is 2d or 1d
+       call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
+       if (masterproc) then
+          write(iulog,*)'lat/lon grid flag (isgrid2d) is ',isgrid2d
+       end if
+       allocate(mask(ns))
+       mask(:) = 1
+       if (isgrid2d) then
+          ! Grid is 2d
+          allocate(idata2d(ni,nj))
+          idata2d(:,:) = 1
+          call ncd_io(ncid=ncid, varname='LANDMASK', data=idata2d, flag='read', readvar=readvar)
+          if (.not. readvar) then
+             call ncd_io(ncid=ncid, varname='mask', data=idata2d, flag='read', readvar=readvar)
+          end if
+          if (readvar) then
+             do j = 1,nj
+                do i = 1,ni
+                   n = (j-1)*ni + i
+                   mask(n) = idata2d(i,j)
+                enddo
+             enddo
+          end if
+          deallocate(idata2d)
+       else
+          ! Grid is not 2d
+          call ncd_io(ncid=ncid, varname='LANDMASK', data=mask, flag='read', readvar=readvar)
+          if (.not. readvar) then
+             call ncd_io(ncid=ncid, varname='mask', data=mask, flag='read', readvar=readvar)
+          end if
+       end if
+       if (.not. readvar) call endrun( msg=' ERROR: landmask not on fatmlndfrc file'//errMsg(sourcefile, __LINE__))
+
+       ! Close file
+       call ncd_pio_closefile(ncid)
+    end if
+
+  end subroutine surfrd_get_globmask
+
+  !-----------------------------------------------------------------------
+  subroutine surfrd_get_grid(begg, endg, ldomain, filename)
+
+    ! Read the surface dataset grid related information:
+    ! This is called after the domain decomposition has been created
+    ! - real latitude  of grid cell (degrees)
+    ! - real longitude of grid cell (degrees)
+
+    use clm_varcon   , only : spval, re, grlnd
+    use domainMod    , only : domain_type, lon1d, lat1d, domain_init
+    use fileutils    , only : getfil
+    use abortutils   , only : endrun
+    use shr_log_mod  , only : errMsg => shr_log_errMsg
+    use ncdio_pio    , only : file_desc_t, ncd_pio_openfile, ncd_pio_closefile
+    use ncdio_pio    , only : ncd_io, check_var, ncd_inqfdims, check_dim_size
+    use pio
+
+    ! input/output variables
+    integer                    , intent(in)    :: begg, endg
+    type(domain_type)          , intent(inout) :: ldomain     ! domain to init
+    character(len=*)           , intent(in)    :: filename    ! grid filename
+
+    ! local variables
+    type(file_desc_t)     :: ncid               ! netcdf id
+    integer               :: beg                ! local beg index
+    integer               :: end                ! local end index
+    integer               :: ni,nj,ns           ! size of grid on file
+    logical               :: readvar            ! true => variable is on input file
+    logical               :: isgrid2d           ! true => file is 2d lat/lon
+    logical               :: istype_domain      ! true => input file is of type domain
+    real(r8), allocatable :: rdata2d(:,:)       ! temporary
+    character(len=16)     :: vname              ! temporary
+    character(len=256)    :: locfn              ! local file name
+    integer               :: n                  ! indices
+    character(len=32) :: subname = 'surfrd_get_grid'     ! subroutine name
+    !-----------------------------------------------------------------------
+
+    if (masterproc) then
+       if (filename == ' ') then
+          write(iulog,*) trim(subname),' ERROR: filename must be specified '
+          call endrun(msg=errMsg(sourcefile, __LINE__))
+       endif
+    end if
+
+    call getfil( filename, locfn, 0 )
+    call ncd_pio_openfile (ncid, trim(locfn), 0)
+
+    ! Determine dimensions
+    call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
+
+    ! Determine isgrid2d flag for domain
+    call domain_init(ldomain, isgrid2d=isgrid2d, ni=ni, nj=nj, nbeg=begg, nend=endg)
+
+    ! Determine type of file - old style grid file or new style domain file
+    call check_var(ncid=ncid, varname='xc', readvar=readvar)
+    if (readvar)then
+        istype_domain = .true.
+    else
+        istype_domain = .false.
+    end if
+
+    ! Read in area, lon, lat
+    if (istype_domain) then
+       call ncd_io(ncid=ncid, varname= 'area', flag='read', data=ldomain%area, &
+            dim1name=grlnd, readvar=readvar)
+       ! convert from radians**2 to km**2
+       ldomain%area = ldomain%area * (re**2)
+       if (.not. readvar) call endrun( msg=' ERROR: area NOT on file'//errMsg(sourcefile, __LINE__))
+       call ncd_io(ncid=ncid, varname= 'xc', flag='read', data=ldomain%lonc, &
+            dim1name=grlnd, readvar=readvar)
+       if (.not. readvar) call endrun( msg=' ERROR: xc NOT on file'//errMsg(sourcefile, __LINE__))
+       call ncd_io(ncid=ncid, varname= 'yc', flag='read', data=ldomain%latc, &
+            dim1name=grlnd, readvar=readvar)
+       if (.not. readvar) call endrun( msg=' ERROR: yc NOT on file'//errMsg(sourcefile, __LINE__))
+    else
+       call endrun( msg=" ERROR: can no longer read non domain files" )
+    end if
+
+    if (isgrid2d) then
+       allocate(rdata2d(ni,nj), lon1d(ni), lat1d(nj))
+       if (istype_domain) vname = 'xc'
+       call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar)
+       lon1d(:) = rdata2d(:,1)
+       if (istype_domain) vname = 'yc'
+       call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar)
+       lat1d(:) = rdata2d(1,:)
+       deallocate(rdata2d)
+    end if
+
+    ! Check lat limited to -90,90
+    if (minval(ldomain%latc) < -90.0_r8 .or. &
+        maxval(ldomain%latc) >  90.0_r8) then
+       write(iulog,*) trim(subname),' WARNING: lat/lon min/max is ', &
+            minval(ldomain%latc),maxval(ldomain%latc)
+    endif
+    if ( any(ldomain%lonc < 0.0_r8) )then
+       call endrun( msg=' ERROR: lonc is negative (see https://github.com/ESCOMP/ctsm/issues/507)' &
+            //errMsg(sourcefile, __LINE__))
+    endif
+    call ncd_io(ncid=ncid, varname='mask', flag='read', data=ldomain%mask, &
+         dim1name=grlnd, readvar=readvar)
+    if (.not. readvar) then
+       call endrun( msg=' ERROR: LANDMASK NOT on fracdata file'//errMsg(sourcefile, __LINE__))
+    end if
+    call ncd_io(ncid=ncid, varname='frac', flag='read', data=ldomain%frac, &
+         dim1name=grlnd, readvar=readvar)
+    if (.not. readvar) then
+       call endrun( msg=' ERROR: LANDFRAC NOT on fracdata file'//errMsg(sourcefile, __LINE__))
+    end if
+
+    call ncd_pio_closefile(ncid)
+
+  end subroutine surfrd_get_grid
+
+  !------------------------------------------------------------------------------
+  subroutine decompInit_lnd3D(lni,lnj,lnk)
+    !
+    ! !DESCRIPTION:
+    !  Create a 3D decomposition gsmap for the global 2D grid with soil levels
+    !  as the 3rd dimesnion.
+    !
+    ! !USES:
+    use decompMod, only : gindex_global, bounds_type, get_proc_bounds
+    use spmdMod  , only : comp_id, mpicom
+    use mct_mod  , only : mct_gsmap_init 
+    !
+    ! !ARGUMENTS:
+    integer , intent(in) :: lni,lnj,lnk   ! domain global size
+    !
+    ! !LOCAL VARIABLES:
+    integer           :: m,n,k                 ! indices
+    integer           :: begg,endg,lsize,gsize ! used for gsmap init
+    integer           :: begg3d,endg3d
+    integer, pointer  :: gindex(:)             ! global index for gsmap init
+    type(bounds_type) :: bounds
+    !------------------------------------------------------------------------------
+
+    ! Initialize gsmap_lnd2dsoi_gdc2glo
+    call get_proc_bounds(bounds)
+    begg = bounds%begg; endg=bounds%endg
+
+    begg3d = (begg-1)*lnk + 1
+    endg3d = endg*lnk
+    lsize = (endg3d - begg3d + 1 )
+    allocate(gindex(begg3d:endg3d))
+    do k = 1, lnk
+       do n = begg,endg
+          m = (begg-1)*lnk + (k-1)*(endg-begg+1) + (n-begg+1)
+          gindex(m) = gindex_global(n-begg+1) + (k-1)*(lni*lnj)
+       enddo
+    enddo
+    gsize = lni * lnj * lnk
+    call mct_gsMap_init(gsMap_lnd2Dsoi_gdc2glo, gindex, mpicom, comp_id, lsize, gsize)
+
+    ! Diagnostic output
+
+    if (masterproc) then
+       write(iulog,*)' 3D GSMap'
+       write(iulog,*)'   longitude points               = ',lni
+       write(iulog,*)'   latitude points                = ',lnj
+       write(iulog,*)'   soil levels                    = ',lnk
+       write(iulog,*)'   gsize                          = ',gsize
+       write(iulog,*)'   lsize                          = ',lsize
+       write(iulog,*)'   bounds(gindex)                 = ',size(gindex)
+       write(iulog,*)
+    end if
+
+    deallocate(gindex)
+
+  end subroutine decompInit_lnd3D
+
+end module lnd_set_decomp_and_domain
diff --git a/src/cpl/mct/ndepStreamMod.F90 b/src/cpl/mct/ndepStreamMod.F90
new file mode 100644
index 0000000000..d26ff7c95e
--- /dev/null
+++ b/src/cpl/mct/ndepStreamMod.F90
@@ -0,0 +1,376 @@
+module ndepStreamMod
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Contains methods for reading in nitrogen deposition data file
+  ! Also includes functions for dynamic ndep file handling and
+  ! interpolation.
+  !
+  ! !USES
+  use shr_kind_mod, only: r8 => shr_kind_r8, CL => shr_kind_cl
+  use shr_strdata_mod, only: shr_strdata_type, shr_strdata_create
+  use shr_strdata_mod, only: shr_strdata_print, shr_strdata_advance
+  use mct_mod     , only: mct_ggrid
+  use spmdMod     , only: mpicom, masterproc, comp_id, iam
+  use clm_varctl  , only: iulog, inst_name
+  use abortutils  , only: endrun
+  use decompMod   , only: bounds_type
+  use domainMod   , only: ldomain
+
+  ! !PUBLIC TYPES:
+  implicit none
+  private
+
+  ! !PUBLIC MEMBER FUNCTIONS:
+  public :: ndep_init      ! position datasets for dynamic ndep
+  public :: ndep_interp    ! interpolates between two years of ndep file data
+  public :: clm_domain_mct ! Sets up MCT domain for this resolution
+
+  ! !PRIVATE MEMBER FUNCTIONS:
+  private :: check_units   ! Check the units and make sure they can be used
+
+  ! ! PRIVATE TYPES
+  type(shr_strdata_type)  :: sdat           ! input data stream
+  integer :: stream_year_first_ndep         ! first year in stream to use
+  integer :: stream_year_last_ndep          ! last year in stream to use
+  integer :: model_year_align_ndep          ! align stream_year_firstndep with
+  logical :: divide_by_secs_per_yr = .true. ! divide by the number of seconds per year
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+  !==============================================================================
+
+contains
+
+  !==============================================================================
+
+  subroutine ndep_init(bounds, NLFilename)
+   !
+   ! Initialize data stream information.
+   !
+   ! Uses:
+   use shr_kind_mod     , only : CS => shr_kind_cs
+   use clm_time_manager , only : get_calendar
+   use ncdio_pio        , only : pio_subsystem
+   use shr_pio_mod      , only : shr_pio_getiotype
+   use shr_nl_mod       , only : shr_nl_find_group_name
+   use shr_log_mod      , only : errMsg => shr_log_errMsg
+   use shr_mpi_mod      , only : shr_mpi_bcast
+   use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global
+   !
+   ! arguments
+   implicit none
+   type(bounds_type), intent(in) :: bounds
+   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
+   !
+   ! local variables
+   integer            :: nu_nml    ! unit for namelist file
+   integer            :: nml_error ! namelist i/o error flag
+   type(mct_ggrid)    :: dom_clm   ! domain information
+   character(len=CL)  :: stream_fldFileName_ndep
+   character(len=CL)  :: ndepmapalgo = 'bilinear'
+   character(len=CL)  :: ndep_tintalgo = 'linear'
+   character(len=CS)  :: ndep_taxmode = 'extend'
+   character(len=CL)  :: ndep_varlist = 'NDEP_year'
+   character(*), parameter :: shr_strdata_unset = 'NOT_SET'
+   character(*), parameter :: subName = "('ndepdyn_init')"
+   character(*), parameter :: F00 = "('(ndepdyn_init) ',4a)"
+   !-----------------------------------------------------------------------
+
+   namelist /ndepdyn_nml/          &
+        stream_year_first_ndep,    &
+        stream_year_last_ndep,     &
+        model_year_align_ndep,     &
+        ndepmapalgo, ndep_taxmode, &
+        ndep_varlist,              &
+        stream_fldFileName_ndep,   &
+        ndep_tintalgo
+
+   ! Default values for namelist
+    stream_year_first_ndep  = 1                ! first year in stream to use
+    stream_year_last_ndep   = 1                ! last  year in stream to use
+    model_year_align_ndep   = 1                ! align stream_year_first_ndep with this model year
+    stream_fldFileName_ndep = ' '
+
+   ! Read ndepdyn_nml namelist
+   if (masterproc) then
+      open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
+      call shr_nl_find_group_name(nu_nml, 'ndepdyn_nml', status=nml_error)
+      if (nml_error == 0) then
+         read(nu_nml, nml=ndepdyn_nml,iostat=nml_error)
+         if (nml_error /= 0) then
+            call endrun(msg=' ERROR reading ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__))
+         end if
+      else
+         call endrun(msg=' ERROR finding ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__))
+      end if
+      close(nu_nml)
+   endif
+
+   call shr_mpi_bcast(stream_year_first_ndep , mpicom)
+   call shr_mpi_bcast(stream_year_last_ndep  , mpicom)
+   call shr_mpi_bcast(model_year_align_ndep  , mpicom)
+   call shr_mpi_bcast(stream_fldFileName_ndep, mpicom)
+   call shr_mpi_bcast(ndep_varlist           , mpicom)
+   call shr_mpi_bcast(ndep_taxmode           , mpicom)
+   call shr_mpi_bcast(ndep_tintalgo          , mpicom)
+
+   if (masterproc) then
+      write(iulog,*) ' '
+      write(iulog,*) 'ndepdyn stream settings:'
+      write(iulog,*) '  stream_year_first_ndep  = ',stream_year_first_ndep
+      write(iulog,*) '  stream_year_last_ndep   = ',stream_year_last_ndep
+      write(iulog,*) '  model_year_align_ndep   = ',model_year_align_ndep
+      write(iulog,*) '  stream_fldFileName_ndep = ',stream_fldFileName_ndep
+      write(iulog,*) '  ndep_varList            = ',ndep_varList
+      write(iulog,*) '  ndep_taxmode            = ',ndep_taxmode
+      write(iulog,*) '  ndep_tintalgo           = ',ndep_tintalgo
+      write(iulog,*) ' '
+   endif
+   ! Read in units
+   call check_units( stream_fldFileName_ndep, ndep_varList )
+
+   ! Set domain and create streams
+   call clm_domain_mct (bounds, dom_clm)
+
+   call shr_strdata_create(sdat,name="clmndep",    &
+        pio_subsystem=pio_subsystem,               &
+        pio_iotype=shr_pio_getiotype(inst_name),   &
+        mpicom=mpicom, compid=comp_id,             &
+        gsmap=gsmap_global, ggrid=dom_clm,         &
+        nxg=ldomain%ni, nyg=ldomain%nj,            &
+        yearFirst=stream_year_first_ndep,          &
+        yearLast=stream_year_last_ndep,            &
+        yearAlign=model_year_align_ndep,           &
+        offset=0,                                  &
+        domFilePath='',                            &
+        domFileName=trim(stream_fldFileName_ndep), &
+        domTvarName='time',                        &
+        domXvarName='lon' ,                        &
+        domYvarName='lat' ,                        &
+        domAreaName='area',                        &
+        domMaskName='mask',                        &
+        filePath='',                               &
+        filename=(/trim(stream_fldFileName_ndep)/),&
+        fldListFile=ndep_varlist,                  &
+        fldListModel=ndep_varlist,                 &
+        fillalgo='none',                           &
+        mapalgo=ndepmapalgo,                       &
+        tintalgo=ndep_tintalgo,                    &
+        calendar=get_calendar(),                   &
+        taxmode=ndep_taxmode                       )
+
+
+   if (masterproc) then
+      call shr_strdata_print(sdat,'CLMNDEP data')
+   endif
+
+ end subroutine ndep_init
+ !================================================================
+
+ subroutine check_units( stream_fldFileName_ndep, ndep_varList )
+   !-------------------------------------------------------------------
+   ! Check that units are correct on the file and if need any conversion
+   use ncdio_pio     , only : ncd_pio_openfile, ncd_inqvid, ncd_getatt, ncd_pio_closefile, ncd_nowrite
+   use ncdio_pio     , only : file_desc_t, var_desc_t
+   use shr_kind_mod  , only : CS => shr_kind_cs
+   use shr_log_mod   , only : errMsg => shr_log_errMsg
+   use shr_string_mod, only : shr_string_listGetName
+   implicit none
+
+   !-----------------------------------------------------------------------
+   !
+   ! Arguments
+   character(len=*), intent(IN)  :: stream_fldFileName_ndep  ! ndep filename
+   character(len=*), intent(IN)  :: ndep_varList             ! ndep variable list to examine
+   !
+   ! Local variables
+   type(file_desc_t) :: ncid     ! NetCDF filehandle for ndep file
+   type(var_desc_t)  :: vardesc  ! variable descriptor
+   integer           :: varid    ! variable index
+   logical           :: readvar  ! If variable was read
+   character(len=CS) :: ndepunits! ndep units
+   character(len=CS) :: fname    ! ndep field name
+   !-----------------------------------------------------------------------
+   call ncd_pio_openfile( ncid, trim(stream_fldFileName_ndep), ncd_nowrite )
+   call shr_string_listGetName( ndep_varList, 1, fname )
+   call ncd_inqvid(       ncid, fname, varid, vardesc, readvar=readvar )
+   if ( readvar ) then
+      call ncd_getatt(    ncid, varid, "units", ndepunits )
+   else
+      call endrun(msg=' ERROR finding variable: '//trim(fname)//" in file: "// &
+                      trim(stream_fldFileName_ndep)//errMsg(sourcefile, __LINE__))
+   end if
+   call ncd_pio_closefile( ncid )
+
+   ! Now check to make sure they are correct
+   if (      trim(ndepunits) == "g(N)/m2/s"  )then
+      divide_by_secs_per_yr = .false.
+   else if ( trim(ndepunits) == "g(N)/m2/yr" )then
+      divide_by_secs_per_yr = .true.
+   else
+      call endrun(msg=' ERROR in units for nitrogen deposition equal to: '//trim(ndepunits)//" not units expected"// &
+                      errMsg(sourcefile, __LINE__))
+   end if
+
+ end subroutine check_units
+
+ !================================================================
+ subroutine ndep_interp(bounds, atm2lnd_inst)
+
+   !-----------------------------------------------------------------------
+   use clm_time_manager, only : get_curr_date, get_curr_days_per_year
+   use clm_varcon      , only : secspday
+   use atm2lndType     , only : atm2lnd_type
+   !
+   ! Arguments
+   type(bounds_type) , intent(in)    :: bounds
+   type(atm2lnd_type), intent(inout) :: atm2lnd_inst
+   !
+   ! Local variables
+   integer :: g, ig
+   integer :: year    ! year (0, ...) for nstep+1
+   integer :: mon     ! month (1, ..., 12) for nstep+1
+   integer :: day     ! day of month (1, ..., 31) for nstep+1
+   integer :: sec     ! seconds into current date for nstep+1
+   integer :: mcdate  ! Current model date (yyyymmdd)
+   integer :: dayspyr ! days per year
+   !-----------------------------------------------------------------------
+
+   call get_curr_date(year, mon, day, sec)
+   mcdate = year*10000 + mon*100 + day
+
+   call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ndepdyn')
+
+   if ( divide_by_secs_per_yr )then
+      ig = 0
+      dayspyr = get_curr_days_per_year( )
+      do g = bounds%begg,bounds%endg
+         ig = ig+1
+         atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) / (secspday * dayspyr)
+      end do
+   else
+      ig = 0
+      do g = bounds%begg,bounds%endg
+         ig = ig+1
+         atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig)
+      end do
+   end if
+
+ end subroutine ndep_interp
+
+ !==============================================================================
+  subroutine clm_domain_mct(bounds, dom_clm, nlevels)
+
+    !-------------------------------------------------------------------
+    ! Set domain data type for internal clm grid
+    use clm_varcon                , only : re
+    use domainMod                 , only : ldomain
+    use mct_mod                   , only : mct_ggrid, mct_gsMap_lsize, mct_gGrid_init
+    use mct_mod                   , only : mct_gsMap_orderedPoints, mct_gGrid_importIAttr
+    use mct_mod                   , only : mct_gGrid_importRAttr, mct_gsMap
+    use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global
+    implicit none
+    !
+    ! arguments
+    type(bounds_type), intent(in) :: bounds
+    type(mct_ggrid), intent(out)   :: dom_clm     ! Output domain information for land model
+    integer, intent(in), optional :: nlevels      ! Number of levels if this is a 3D field
+    !
+    ! local variables
+    integer :: g,i,j,k            ! index
+    integer :: lsize              ! land model domain data size
+    real(r8), pointer :: data(:)  ! temporary
+    integer , pointer :: idata(:) ! temporary
+    integer :: nlevs              ! Number of vertical levels
+    type(mct_gsMap), pointer :: gsmap => null() ! MCT GS map
+    !-------------------------------------------------------------------
+    ! SEt number of levels, and get the GS map for either the 2D or 3D grid
+    nlevs = 1
+    if ( present(nlevels) ) nlevs = nlevels
+    if ( nlevs == 1 ) then
+       gsmap => gsmap_global
+    else
+       gsmap => gsMap_lnd2Dsoi_gdc2glo
+    end if
+    !
+    ! Initialize mct domain type
+    ! lat/lon in degrees,  area in radians^2, mask is 1 (land), 0 (non-land)
+    ! Note that in addition land carries around landfrac for the purposes of domain checking
+    !
+    lsize = mct_gsMap_lsize(gsmap, mpicom)
+    call mct_gGrid_init( GGrid=dom_clm, &
+         CoordChars='lat:lon:hgt', OtherChars='area:aream:mask:frac', lsize=lsize )
+    !
+    ! Allocate memory
+    !
+    allocate(data(lsize))
+    !
+    ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT
+    !
+    call mct_gsMap_orderedPoints(gsmap, iam, idata)
+    gsmap => null()
+    call mct_gGrid_importIAttr(dom_clm,'GlobGridNum',idata,lsize)
+    !
+    ! Determine domain (numbering scheme is: West to East and South to North to South pole)
+    ! Initialize attribute vector with special value
+    !
+    data(:) = -9999.0_R8
+    call mct_gGrid_importRAttr(dom_clm,"lat"  ,data,lsize)
+    call mct_gGrid_importRAttr(dom_clm,"lon"  ,data,lsize)
+    call mct_gGrid_importRAttr(dom_clm,"area" ,data,lsize)
+    call mct_gGrid_importRAttr(dom_clm,"aream",data,lsize)
+    data(:) = 0.0_R8
+    call mct_gGrid_importRAttr(dom_clm,"mask" ,data,lsize)
+    !
+    ! Determine bounds
+    !
+    ! Fill in correct values for domain components
+    ! Note aream will be filled in in the atm-lnd mapper
+    !
+    do k = 1, nlevs
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = ldomain%lonc(g)
+    end do
+    end do
+    call mct_gGrid_importRattr(dom_clm,"lon",data,lsize)
+
+    do k = 1, nlevs
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = ldomain%latc(g)
+    end do
+    end do
+    call mct_gGrid_importRattr(dom_clm,"lat",data,lsize)
+
+    do k = 1, nlevs
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = ldomain%area(g)/(re*re)
+    end do
+    end do
+    call mct_gGrid_importRattr(dom_clm,"area",data,lsize)
+
+    do k = 1, nlevs
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = real(ldomain%mask(g), r8)
+    end do
+    end do
+    call mct_gGrid_importRattr(dom_clm,"mask",data,lsize)
+
+    do k = 1, nlevs
+    do g = bounds%begg,bounds%endg
+       i = 1 + (g - bounds%begg)
+       data(i) = real(ldomain%frac(g), r8)
+    end do
+    end do
+    call mct_gGrid_importRattr(dom_clm,"frac",data,lsize)
+
+    deallocate(data)
+    deallocate(idata)
+
+  end subroutine clm_domain_mct
+
+end module ndepStreamMod

From 7c295b84189ae3e2e62d369cc8e65fbac80406b5 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 16 May 2024 14:47:23 -0600
Subject: [PATCH 0264/1248] Remove test/tools/test_driver.sh, unrelated to this
 PR, good to clean up

---
 test/tools/test_driver.sh | 721 --------------------------------------
 1 file changed, 721 deletions(-)
 delete mode 100755 test/tools/test_driver.sh

diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh
deleted file mode 100755
index 307d1accf8..0000000000
--- a/test/tools/test_driver.sh
+++ /dev/null
@@ -1,721 +0,0 @@
-#!/bin/sh
-#
-# test_driver.sh:  driver script for the offline testing of CLM of tools
-#
-# interactive usage on all machines:
-#
-# env ./test_driver.sh -i
-#
-# valid arguments: 
-# -i    interactive usage
-# -d    debug usage -- display tests that will run -- but do NOT actually execute them
-# -f    force batch submission (avoids user prompt)
-# -h    displays this help message
-#
-#
-# **pass environment variables by preceding above commands 
-#   with 'env var1=setting var2=setting '
-# **more details in the CLM testing user's guide, accessible 
-#   from the CLM developers web page
-
-
-#will attach timestamp onto end of script name to prevent overwriting
-cur_time=`date '+%H:%M:%S'`
-
-hostname=`hostname`
-echo $hostname
-case $hostname in
-
-    ##Derecho
-     derecho* | dec*)
-    submit_script="test_driver_derecho${cur_time}.sh"
-
-##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv
-cat > ./${submit_script} << EOF
-#!/bin/sh
-#
-
-interactive="YES"
-input_file="tests_pretag_derecho_nompi"
-c_threads=128
-
-export INITMODULES="/glade/u/apps/derecho/23.06/spack/opt/spack/lmod/8.7.20/gcc/7.5.0/pdxb/lmod/lmod/init/sh"
-. \$INITMODULES
-
-module --force purge
-module load ncarenv
-module load craype
-module load intel
-module load mkl
-module load ncarcompilers
-module load netcdf
-module load nco
-module load ncl
-
-#omp threads
-if [ -z "\$CLM_THREADS" ]; then   #threads NOT set on command line
-  export CLM_THREADS=\$c_threads
-fi
-
-# Stop on first failed test
-if [ -z "\$CLM_SOFF" ]; then   #CLM_SOFF NOT set
-  export CLM_SOFF=FALSE
-fi
-
-export CESM_MACH="derecho"
-export CESM_COMP="intel"
-
-export NETCDF_DIR=\$NETCDF
-export INC_NETCDF=\$NETCDF/include
-export LIB_NETCDF=\$NETCDF/lib
-export MAKE_CMD="gmake -j "
-export CFG_STRING=""
-export TOOLS_MAKE_STRING="USER_FC=ifort USER_LINKER=ifort USER_CPPDEFS=-DLINUX"
-export MACH_WORKSPACE=\$SCRATCH
-export CPRNC_EXE="$CESMDATAROOT/cprnc/cprnc"
-dataroot="$CESMDATAROOT/inputdata"
-export TOOLSLIBS=""
-export REGRID_PROC=1
-export TOOLS_CONF_STRING="--mpilib mpi-serial"
-
-
-echo_arg=""
-
-EOF
-#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^
-   ;;
-
-   ##cheyenne
-    cheyenne* | r*i*n*)
-   submit_script="test_driver_cheyenne${cur_time}.sh"
-
-#vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv
-at > ./${submit_script} << EOF
-!/bin/sh
-
-
-interactive="YES"
-input_file="tests_pretag_cheyenne_nompi"
-c_threads=36
-
-
-export INITMODULES="/glade/u/apps/ch/opt/lmod/8.1.7/lmod/lmod/init/sh"
-. \$INITMODULES
-
-module purge
-module load ncarenv
-module load intel
-module load mkl
-module load ncarcompilers
-module load netcdf
-
-module load nco
-module load ncl
-
-module load conda
-
-
-##omp threads
-if [ -z "\$CLM_THREADS" ]; then   #threads NOT set on command line
-   export CLM_THREADS=\$c_threads
-fi
-
-# Stop on first failed test
-if [ -z "\$CLM_SOFF" ]; then   #CLM_SOFF NOT set
-   export CLM_SOFF=FALSE
-fi
-
-export CESM_MACH="cheyenne"
-export CESM_COMP="intel"
-
-export NETCDF_DIR=\$NETCDF
-export INC_NETCDF=\$NETCDF/include
-export LIB_NETCDF=\$NETCDF/lib
-export MAKE_CMD="gmake -j "
-export CFG_STRING=""
-export TOOLS_MAKE_STRING="USER_FC=ifort USER_LINKER=ifort USER_CPPDEFS=-DLINUX"
-export MACH_WORKSPACE="/glade/scratch"
-export CPRNC_EXE="$CESMDATAROOT/tools/cime/tools/cprnc/cprnc.cheyenne"
-dataroot="$CESMDATAROOT"
-export TOOLSLIBS=""
-export REGRID_PROC=1
-export TOOLS_CONF_STRING="--mpilib mpi-serial"
-
-
-echo_arg=""
-
-EOF
-##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^
-    ;;
-
-    ## DAV cluster
-     casper* | pronghorn*)
-    submit_script="test_driver_dav${cur_time}.sh"
-
-##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv
-cat > ./${submit_script} << EOF
-#!/bin/sh
-#
-
-interactive="YES"
-input_file="tests_posttag_dav_mpi"
-c_threads=36
-
-
-export INITMODULES="/glade/u/apps/ch/opt/lmod/8.1.7/lmod/lmod/init/sh"
-. \$INITMODULES
-
-module purge
-module load ncarenv
-module load intel
-module load mkl
-module load ncarcompilers
-module load netcdf
-module load openmpi
-
-module load nco
-module load conda
-module load ncl
-
-
-##omp threads
-if [ -z "\$CLM_THREADS" ]; then   #threads NOT set on command line
-   export CLM_THREADS=\$c_threads
-fi
-
-# Stop on first failed test
-if [ -z "\$CLM_SOFF" ]; then   #CLM_SOFF NOT set
-   export CLM_SOFF=FALSE
-fi
-
-export CESM_MACH="cheyenne"
-export CESM_COMP="intel"
-
-export NETCDF_DIR=\$NETCDF
-export INC_NETCDF=\$NETCDF/include
-export LIB_NETCDF=\$NETCDF/lib
-export MAKE_CMD="gmake -j "
-export CFG_STRING=""
-export TOOLS_MAKE_STRING="USER_FC=ifort USER_LINKER=ifort USER_CPPDEFS=-DLINUX"
-export MACH_WORKSPACE="/glade/scratch"
-export CPRNC_EXE="$CESMDATAROOT/tools/cime/tools/cprnc/cprnc.cheyenne"
-dataroot="$CESMDATAROOT"
-export TOOLSLIBS=""
-export TOOLS_CONF_STRING="--mpilib mpich"
-
-
-echo_arg=""
-
-EOF
-##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^
-    ;;
-
-    ## hobart
-    hobart* | h*.cgd.ucar.edu) 
-    submit_script="test_driver_hobart_${cur_time}.sh"
-    export PATH=/cluster/torque/bin:${PATH}
-
-##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv
-cat > ./${submit_script} << EOF
-#!/bin/sh
-#
-
-# Name of the queue (CHANGE THIS if needed)
-#PBS -q long
-# Number of nodes (CHANGE THIS if needed)
-#PBS -l nodes=1:ppn=24
-# output file base name
-#PBS -N test_dr
-# Put standard error and standard out in same file
-#PBS -j oe
-# Export all Environment variables
-#PBS -V
-# End of options
-
-if [ -n "\$PBS_JOBID" ]; then    #batch job
-    export JOBID=\`echo \${PBS_JOBID} | cut -f1 -d'.'\`
-    initdir=\${PBS_O_WORKDIR}
-fi
-
-if [ "\$PBS_ENVIRONMENT" = "PBS_BATCH" ]; then
-    interactive="NO"
-    input_file="tests_posttag_hobart"
-else
-    interactive="YES"
-    input_file="tests_posttag_hobart_nompi"
-fi
-
-##omp threads
-if [ -z "\$CLM_THREADS" ]; then   #threads NOT set on command line
-   export CLM_THREADS=2
-fi
-export CLM_RESTART_THREADS=1
-
-##mpi tasks
-export CLM_TASKS=24
-export CLM_RESTART_TASKS=20
-
-export P4_GLOBMEMSIZE=500000000
-
-
-export CESM_MACH="hobart"
-
-ulimit -s unlimited
-ulimit -c unlimited
-
-export CESM_COMP="intel"
-export TOOLS_MAKE_STRING="USER_FC=ifort USER_CC=icc "
-export TOOLS_CONF_STRING=" -mpilib mpi-serial"
-export CFG_STRING=""
-export INITMODULES="/usr/share/Modules/init/sh"
-
-. \$INITMODULES
-module purge
-module load compiler/intel
-module load tool/nco
-module load tool/netcdf
-module load lang/python
-
-export NETCDF_DIR=\$NETCDF_PATH
-export INC_NETCDF=\${NETCDF_PATH}/include
-export LIB_NETCDF=\${NETCDF_PATH}/lib
-export MAKE_CMD="gmake -j 5"   ##using hyper-threading on hobart
-export MACH_WORKSPACE="/scratch/cluster"
-export CPRNC_EXE=/fs/cgd/csm/tools/cprnc/cprnc
-export DATM_QIAN_DATA_DIR="/project/tss/atm_forcing.datm7.Qian.T62.c080727"
-dataroot="/fs/cgd/csm"
-export TOOLSSLIBS=""
-echo_arg="-e"
-
-EOF
-##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^
-    ;;
-
-    ## izumi
-    izumi* | i*.unified.ucar.edu) 
-    submit_script="test_driver_izumi_${cur_time}.sh"
-    export PATH=/cluster/torque/bin:${PATH}
-
-##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv
-cat > ./${submit_script} << EOF
-#!/bin/sh
-#
-
-# Name of the queue (CHANGE THIS if needed)
-#PBS -q long
-# Number of nodes (CHANGE THIS if needed)
-#PBS -l nodes=1:ppn=24
-# output file base name
-#PBS -N test_dr
-# Put standard error and standard out in same file
-#PBS -j oe
-# Export all Environment variables
-#PBS -V
-# End of options
-
-if [ -n "\$PBS_JOBID" ]; then    #batch job
-    export JOBID=\`echo \${PBS_JOBID} | cut -f1 -d'.'\`
-    initdir=\${PBS_O_WORKDIR}
-fi
-
-if [ "\$PBS_ENVIRONMENT" = "PBS_BATCH" ]; then
-    interactive="NO"
-    input_file="tests_posttag_izumi"
-else
-    interactive="YES"
-    input_file="tests_posttag_izumi_nompi"
-fi
-
-##omp threads
-if [ -z "\$CLM_THREADS" ]; then   #threads NOT set on command line
-   export CLM_THREADS=2
-fi
-export CLM_RESTART_THREADS=1
-
-##mpi tasks
-export CLM_TASKS=24
-export CLM_RESTART_TASKS=20
-
-export P4_GLOBMEMSIZE=500000000
-
-
-export CESM_MACH="izumi"
-
-ulimit -s unlimited
-ulimit -c unlimited
-
-export CESM_COMP="intel"
-export TOOLS_MAKE_STRING="USER_FC=ifort USER_CC=icc "
-export TOOLS_CONF_STRING=" -mpilib mpi-serial"
-export CFG_STRING=""
-export INITMODULES="/usr/share/Modules/init/sh"
-
-. \$INITMODULES
-module purge
-module load compiler/intel
-module load tool/nco
-module load tool/netcdf
-module load lang/python
-
-export NETCDF_DIR=\$NETCDF_PATH
-export INC_NETCDF=\${NETCDF_PATH}/include
-export LIB_NETCDF=\${NETCDF_PATH}/lib
-export MAKE_CMD="gmake -j 5"   ##using hyper-threading on izumi
-export MACH_WORKSPACE="/scratch/cluster"
-export CPRNC_EXE=/fs/cgd/csm/tools/cprnc/cprnc.izumi
-export DATM_QIAN_DATA_DIR="/project/tss/atm_forcing.datm7.Qian.T62.c080727"
-dataroot="/fs/cgd/csm"
-export TOOLSSLIBS=""
-echo_arg="-e"
-
-EOF
-##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^
-    ;;
-
-    * )
-    echo "Only setup to work on: derecho, cheyenne, hobart and izumi"
-    exit
- 
-
-esac
-
-##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv
-cat >> ./${submit_script} << EOF
-
-export CPRNC_OPT=""
-if [ -n "\${CLM_JOBID}" ]; then
-    export JOBID=\${CLM_JOBID}
-fi
-##check if interactive job
-
-if [ "\$interactive" = "YES" ]; then
-
-    if [ -z "\${JOBID}" ]; then
-       export JOBID=\$\$
-    fi
-    echo "test_driver.sh: interactive run - setting JOBID to \$JOBID"
-    if [ \$0 = "test_driver.sh" ]; then
-	initdir="."
-    else
-	initdir=\${0%/*}
-    fi
-else
-    echo "ERROR: you *always* need to use the interactive option (-i)"
-    echo "       currently doesn't work without it"
-    exit 3
-fi
-
-##establish script dir and clm_root
-if [ -f \${initdir}/test_driver.sh ]; then
-    export CLM_SCRIPTDIR=\`cd \${initdir}; pwd \`
-    export CLM_ROOT=\`cd \${CLM_SCRIPTDIR}/../..; pwd \`
-    export CTSM_ROOT=\${CLM_ROOT}
-    if [ -d \${CLM_ROOT}/cime ]; then
-       export CIME_ROOT=\${CLM_ROOT}/cime
-    else
-       export CIME_ROOT=\${CLM_ROOT}/../../cime
-    fi
-    if [ ! -d \${CIME_ROOT} ]; then
-       echo "ERROR: trouble finding the CIME_ROOT directory: \$CIME_ROOT"
-       exit 3
-    fi
-else
-    if [ -n "\${CLM_ROOT}" ] && [ -f \${CLM_ROOT}/test/tools/test_driver.sh ]; then
-	export CLM_SCRIPTDIR=\`cd \${CLM_ROOT}/test/tools; pwd \`
-    else
-	echo "ERROR: unable to determine script directory "
-	echo "       if initiating batch job from directory other than the one containing test_driver.sh, "
-	echo "       you must set the environment variable CLM_ROOT to the full path of directory containing "
-        echo "       <cime/scripts>. "
-	exit 3
-    fi
-fi
-
-# Setup conda environment
-conda activate ctsm_pylib
-if [ \$? -ne 0 ]; then
-   echo "ERROR: Trouble activating the ctsm_pylib conda environment, be sure it's setup with \$CLM_ROOT/py_env_create, then rerun"
-   exit 4
-fi
-
-##output files
-clm_log=\${initdir}/td.\${JOBID}.log
-if [ -f \$clm_log ]; then
-    rm \$clm_log
-fi
-clm_status=\${initdir}/td.\${JOBID}.status
-if [ -f \$clm_status ]; then
-    rm \$clm_status
-fi
-
-##setup test work directory
-if [ -z "\$CLM_TESTDIR" ]; then
-    export CLM_TESTDIR=\${MACH_WORKSPACE}/\$LOGNAME/clmTests/test-driver.\${JOBID}
-    if [ -d \$CLM_TESTDIR ] && [ \$CLM_RETAIN_FILES != "TRUE" ]; then
-        rm -r \$CLM_TESTDIR
-    fi
-fi
-if [ ! -d \$CLM_TESTDIR ]; then
-    mkdir -p \$CLM_TESTDIR
-    if [ \$? -ne 0 ]; then
-	echo "ERROR: unable to create work directory \$CLM_TESTDIR"
-	exit 4
-    fi
-fi
-
-## PIO build directory
-export PIO_LIBDIR=\$CLM_TESTDIR/pio
-
-##set our own environment vars
-export CSMDATA=\${dataroot}/inputdata
-export DIN_LOC_ROOT=\${CSMDATA}
-export MPI_TYPE_MAX=100000
-
-##process other env vars possibly coming in
-if [ -z "\$CLM_RETAIN_FILES" ]; then
-    export CLM_RETAIN_FILES=FALSE
-fi
-if [ -n "\${CLM_INPUT_TESTS}" ]; then
-    input_file=\$CLM_INPUT_TESTS
-else
-    input_file=\${CLM_SCRIPTDIR}/\${input_file}
-fi
-if [ ! -f \${input_file} ]; then
-    echo "ERROR: unable to locate input file \${input_file}"
-    exit 5
-fi
-
-if [ \$interactive = "YES" ]; then
-    echo "reading tests from \${input_file}"
-else
-    echo "reading tests from \${input_file}" >> \${clm_log}
-fi
-
-num_tests=\`wc -w < \${input_file}\`
-echo "STATUS OF CLM TESTING UNDER JOB \${JOBID};  scheduled to run \$num_tests tests from:" >> \${clm_status}
-echo "\$input_file" >> \${clm_status}
-echo "" >> \${clm_status}
-echo " on machine: $hostname" >> \${clm_status}
-if [ -n "${BL_ROOT}" ]; then
-   echo "tests of baseline will use source code from:" >> \${clm_status}
-   echo "\$BL_ROOT" >> \${clm_status}
-fi
-if [ \$interactive = "NO" ]; then
-    echo "see \${clm_log} for more detailed output" >> \${clm_status}
-fi
-echo "" >> \${clm_status}
-
-test_list=""
-while read input_line; do
-    test_list="\${test_list}\${input_line} "
-done < \${input_file}
-
-
-##initialize flags, counter
-skipped_tests="NO"
-pending_tests="NO"
-count=0
-
-##loop through the tests of input file
-for test_id in \${test_list}; do
-    count=\`expr \$count + 1\`
-    while [ \${#count} -lt 3 ]; do
-        count="0\${count}"
-    done
-
-    master_line=\`grep \$test_id \${CLM_SCRIPTDIR}/input_tests_master\`
-    status_out=""
-    for arg in \${master_line}; do
-        status_out="\${status_out}\${arg} "
-    done
-
-    if [ -z "\$status_out" ]; then
-	echo "No test matches \$test_id in \${CLM_SCRIPTDIR}/input_tests_master"
-        exit 3
-    fi
-
-    test_cmd=\${status_out#* }
-
-    status_out="\${count} \${status_out}"
-
-    if [ \$interactive = "YES" ]; then
-        echo ""
-        echo "***********************************************************************************"
-        echo "\${status_out}"
-        echo "***********************************************************************************"
-    else
-        echo "" >> \${clm_log}
-        echo "***********************************************************************************"\
-            >> \${clm_log}
-        echo "\$status_out" >> \${clm_log}
-        echo "***********************************************************************************"\
-            >> \${clm_log}
-    fi
-
-    if [ \${#status_out} -gt 94 ]; then
-        status_out=\`echo "\${status_out}" | cut -c1-100\`
-    fi
-    while [ \${#status_out} -lt 97 ]; do
-        status_out="\${status_out}."
-    done
-
-    echo \$echo_arg "\$status_out\c" >> \${clm_status}
-
-    if [   \$interactive = "YES" ]; then
-        \${CLM_SCRIPTDIR}/\${test_cmd}
-        rc=\$?
-    else
-        \${CLM_SCRIPTDIR}/\${test_cmd} >> \${clm_log} 2>&1
-        rc=\$?
-    fi
-    if [ \$rc -eq 0 ]; then
-        echo "PASS" >> \${clm_status}
-    elif [ \$rc -eq 255 ]; then
-        echo "SKIPPED*" >> \${clm_status}
-        skipped_tests="YES"
-    elif [ \$rc -eq 254 ]; then
-        echo "PENDING**" >> \${clm_status}
-        pending_tests="YES"
-    else
-        echo " rc=\$rc FAIL" >> \${clm_status}
-        if [ "\$CLM_SOFF" = "TRUE" ]; then
-           echo "stopping on first failure" >> \${clm_status}
-           echo "stopping on first failure" >> \${clm_log}
-           exit 6
-	fi
-    fi
-done
-
-echo "end of input" >> \${clm_status}
-if [ \$interactive = "YES" ]; then
-    echo "end of input"
-else
-    echo "end of input" >> \${clm_log}
-fi
-
-if [ \$skipped_tests = "YES" ]; then
-    echo "*  please verify that any skipped tests are not required of your clm commit" >> \${clm_status}
-fi
-if [ \$pending_tests = "YES" ]; then
-    echo "** tests that are pending must be checked manually for a successful completion" >> \${clm_status}
-    if [ \$interactive = "NO" ]; then
-	echo "   see the test's output in \${clm_log} " >> \${clm_status}
-	echo "   for the location of test results" >> \${clm_status}
-    fi
-fi
-
-if [ "\$interactive" = "YES" ]; then
-   passInt="test_driver.sh-i"
-else
-   passInt="test_driver.sh"
-fi
-
-../../bld/unit_testers/xFail/wrapClmTests.pl -statusFile "\${clm_status}" -numberOfTests "\${num_tests}" -callingScript "\${passInt}"
-
-exit 0
-
-EOF
-##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^
-
-
-chmod a+x $submit_script
-if [ ! -z "$CLM_RETAIN_FILES" ]; then
-   export CLM_RETAIN_FILES="FALSE"
-fi
-arg1=${1##*-}
-case $arg1 in
-    [iI]* )
-    debug="NO"
-    interactive="YES"
-    compile_only="NO"
-    export debug
-    export interactive
-    export compile_only
-    ./${submit_script}
-    exit 0
-    ;;
-
-    [cC]* )
-    debug="NO"
-    interactive="YES"
-    compile_only="YES"
-    export debug
-    export CLM_RETAIN_FILES="TRUE"
-    export interactive
-    export compile_only
-    export CLM_RETAIN_FILES="TRUE"
-    ./${submit_script}
-    exit 0
-    ;;
-
-    [dD]* )
-    debug="YES"
-    interactive="YES"
-    compile_only="NO"
-    export debug
-    export interactive
-    export compile_only
-    ./${submit_script}
-    exit 0
-    ;;
-
-    [fF]* )
-    debug="NO"
-    interactive="NO"
-    compile_only="NO"
-    export debug
-    export interactive
-    export compile_only
-    ;;
-
-    "" )
-    echo ""
-    echo "**********************"
-    echo "$submit_script has been created and will be submitted to the batch queue..."
-    echo "(ret) to continue, (a) to abort"
-    read ans
-    case $ans in
-	[aA]* ) 
-	echo "aborting...type ./test_driver.sh -h for help message"
-	exit 0
-	;;
-    esac
-    debug="NO"
-    interactive="NO"
-    compile_only="NO"
-    export debug
-    export interactive
-    export compile_only
-    ;;
-
-    * )
-    echo ""
-    echo "**********************"
-    echo "usage on derecho, cheyenne, hobart, and izumi: "
-    echo "./test_driver.sh -i"
-    echo ""
-    echo "valid arguments: "
-    echo "-i    interactive usage"
-    echo "-c    compile-only usage (run configure and compile do not run clm)"
-    echo "-d    debug-only  usage (run configure and build-namelist do NOT compile or run clm)"
-    echo "-f    force batch submission (avoids user prompt)"
-    echo "-h    displays this help message"
-    echo ""
-    echo "**pass environment variables by preceding above commands "
-    echo "  with 'env var1=setting var2=setting '"
-    echo ""
-    echo "**********************"
-    exit 0
-    ;;
-esac
-
-echo "submitting..."
-case $hostname in
-    #default
-    * )
-    echo "no submission capability on this machine use the interactive option: -i"
-    exit 0
-    ;;
-
-esac
-exit 0

From 7c5c632f02b54f2285bdfb3902834d78715077f7 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 16 May 2024 15:03:31 -0600
Subject: [PATCH 0265/1248] fix namelist definition

---
 bld/namelist_files/namelist_definition_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 03b1e9e64d..58e0aca3a6 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -734,8 +734,8 @@ Toggle to turn on no competition mode (only relevant if FATES is being used).
 Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used).                        
 </entry>
 
-<entry id="fates_harvest_mode" type="integer" category="physics"
-        group="clm_inparm" valid_values="no_harvest_event_code,surfdata_file,luhdata_area,luhdata_mass">
+<entry id="fates_harvest_mode" type="char*13" category="physics"
+        group="clm_inparm" valid_values="no_harvest,event_code,surfdata_file,luhdata_area,luhdata_mass">
 Set FATES harvesting mode by setting fates_harvest_mode to a valid string option.
 Allowed values are:
  no_harvest: no fates harvesting of any kind

From 5e9bc2e9a40987ff5477d0b3cdc742c3fbcf5f23 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 16 May 2024 15:04:39 -0600
Subject: [PATCH 0266/1248] Update finidat that previously failing test now
 picks up by default

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index c62df7d77b..90e397d544 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1097,7 +1097,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_GSWP3v1"
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
+>lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm52BgcCrop.2000-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240515.nc
 </finidat>
 
 

From 0266a70e98142750e6c34494740a8dd3e600a93c Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 16 May 2024 15:22:10 -0600
Subject: [PATCH 0267/1248] update landuse parameters from ints to chars

---
 src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
index d9bd0352ca..f330ee2b78 100644
--- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
+++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
@@ -35,11 +35,11 @@ module dynFATESLandUseChangeMod
   integer, public, parameter    :: num_landuse_harvest_vars = 5
 
   ! Define the fates landuse namelist mode switch values
-  integer, public, parameter    :: fates_harvest_no_logging   = 0
-  integer, public, parameter    :: fates_harvest_logging_only = 1
-  integer, public, parameter    :: fates_harvest_clmlanduse   = 2
-  integer, public, parameter    :: fates_harvest_luh_area     = 3
-  integer, public, parameter    :: fates_harvest_luh_mass     = 4
+  character(len=13), public, parameter    :: fates_harvest_no_logging   = 'no_harvest'
+  character(len=13), public, parameter    :: fates_harvest_logging_only = 'event_code'
+  character(len=13), public, parameter    :: fates_harvest_clmlanduse   = 'surfdata_file'
+  character(len=13), public, parameter    :: fates_harvest_luh_area     = 'luhdata_area'
+  character(len=13), public, parameter    :: fates_harvest_luh_mass     = 'luhdata_mass'
 
   ! Define landuse harvest unit integer representation
   integer, public, parameter    :: landuse_harvest_area_units = 1

From b706c5a717652f24ca30e7dd43285b9e527b0f16 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 16 May 2024 16:22:11 -0600
Subject: [PATCH 0268/1248] Have build-namelist not do the dust emission
 namelist settings, when the XML variable is set for CAM to do it, and add a
 test for this

---
 bld/CLMBuildNamelist.pm                 | 120 +++++++++--------
 bld/unit_testers/build-namelist_test.pl | 169 ++----------------------
 2 files changed, 80 insertions(+), 209 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index ce2c2a81d2..98fdd861a0 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -97,7 +97,7 @@ OPTIONS
 				        CENTURY or MIMICS decomposition
                                         This toggles on the namelist variables:
 				        use_fates. use_lch4 and use_nitrif_denitrif are optional
-				 
+
                               (Only for CLM4.5/CLM5.0)
      -[no-]chk_res            Also check [do NOT check] to make sure the resolution and
                               land-mask is valid.
@@ -1012,7 +1012,7 @@ sub setup_cmdl_fire_light_res {
      if ( ! &value_is_true($nl_flags->{'neon'}) ) {
          if ( defined($opts->{'clm_usr_name'}) ) {
             $log->warning("The NEON lightning dataset does NOT cover the entire globe, make sure it covers the region for your grid");
-         } else { 
+         } else {
             $log->fatal_error("The NEON lightning dataset can NOT be used for global grids or regions or points outside of its area as it does NOT cover the entire globe.");
          }
      }
@@ -1702,7 +1702,7 @@ sub process_namelist_inline_logic {
   ######################################
   # namelist options for dust emissions
   ######################################
-  setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl);
+  setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
 
   #################################
   # namelist group: megan_emis_nl #
@@ -2273,7 +2273,7 @@ sub setup_logic_crop_inparm {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting",
                  'use_crop'=>$nl->get_value('use_crop') );
-     
+
      my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac');
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_residue_removal_frac' );
      if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) {
@@ -2614,8 +2614,8 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
                 if ( defined($use_init_interp_default) ) {
                    $log->fatal_error($err_msg." but can't find one without $useinitvar being set to true, change it to true in your user_nl_clm file in your case");
                 } else {
-                   my $set = "Relevent settings: use_cndv = ". $nl_flags->{'use_cndv'} . " phys = " . 
-                              $physv->as_string() . " hgrid = " . $nl_flags->{'res'} . " sim_year = " . 
+                   my $set = "Relevent settings: use_cndv = ". $nl_flags->{'use_cndv'} . " phys = " .
+                              $physv->as_string() . " hgrid = " . $nl_flags->{'res'} . " sim_year = " .
                               $settings{'sim_year'} . " lnd_tuning_mode = " . $nl_flags->{'lnd_tuning_mode'} .
                               "use_fates = " . $nl_flags->{'use_fates'};
                    $log->fatal_error($err_msg." but the default setting of $useinitvar is false, so set both $var to a startup file and $useinitvar==TRUE, or developers should modify the namelist_defaults file".$set);
@@ -3158,7 +3158,6 @@ sub setup_logic_supplemental_nitrogen {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
 		  'suplnitro', 'use_fates'=>$nl_flags->{'use_fates'});
   }
-  
   #
   # Error checking for suplnitro
   #
@@ -3683,10 +3682,10 @@ sub setup_logic_nitrogen_deposition {
                 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'},
                 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'},
-		'use_cn'=>$nl_flags->{'use_cn'}, 
+		'use_cn'=>$nl_flags->{'use_cn'},
 		'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'},
-		'use_cn'=>$nl_flags->{'use_cn'}, 
+		'use_cn'=>$nl_flags->{'use_cn'},
 		'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'},
                 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'},
@@ -3990,51 +3989,64 @@ sub setup_logic_fire_emis {
 
 sub setup_logic_dust_emis {
   # Logic to handle the dust emissions namelists, both drv_flds_in and lnd_in files
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;
 
-  # First get the dust emission method
-  my $var = "dust_emis_method";
-  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var );
-
-  my $dust_emis_method = remove_leading_and_trailing_quotes( $nl->get_value($var) );
-
-  my @zender_files_in_lnd_opts = ( "stream_fldfilename_zendersoilerod", "stream_meshfile_zendersoilerod",
-                                   "zendersoilerod_mapalgo" );
-  if ( $dust_emis_method eq "Zender_2003" ) {
-     # get the zender_soil_erod_source
-     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-                 "zender_soil_erod_source", 'dust_emis_method'=>$dust_emis_method );
-
-     my $zender_source = remove_leading_and_trailing_quotes( $nl->get_value('zender_soil_erod_source') );
-     if ( $zender_source eq "lnd" ) {
-        foreach my $option ( @zender_files_in_lnd_opts ) {
-           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $option,
-                       'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source,
-                       'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} );
-        }
-     } elsif ( $zender_source eq "atm" ) {
-        foreach my $option ( @zender_files_in_lnd_opts ) {
-           if ( defined($nl->get_value($option)) ) {
-             $log->fatal_error("zender_soil_erod_source is atm, and the file option $option is being set" .
-                               " which should NOT be unless you want it handled here in the LAND model, " .
-                               "otherwise the equivalent option is set in CAM" );
-           }
-        }
-     } elsif ( $zender_source eq "none" ) {
-        $log->fatal_error("zender_soil_erod_source is set to none and only atm or lnd should be used when $var is Zender_2002" );
-     }
+  # Only set dust emission settings -- if not connected to CAM
+  my $lnd_sets_dust = logical_to_fortran($envxml_ref->{'LND_SETS_DUST_EMIS_DRV_FLDS'});
+  if ( &value_is_true( $lnd_sets_dust)) {
+
+      # First get the dust emission method
+      my $var = "dust_emis_method";
+      add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var );
+      my $dust_emis_method = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+
+      my @zender_files_in_lnd_opts = ( "stream_fldfilename_zendersoilerod", "stream_meshfile_zendersoilerod",
+                                       "zendersoilerod_mapalgo" );
+      if ( $dust_emis_method eq "Zender_2003" ) {
+         # get the zender_soil_erod_source
+         add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+                     "zender_soil_erod_source", 'dust_emis_method'=>$dust_emis_method );
+
+         my $zender_source = remove_leading_and_trailing_quotes( $nl->get_value('zender_soil_erod_source') );
+         if ( $zender_source eq "lnd" ) {
+            foreach my $option ( @zender_files_in_lnd_opts ) {
+               add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $option,
+                           'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source,
+                           'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} );
+            }
+         } elsif ( $zender_source eq "atm" ) {
+            foreach my $option ( @zender_files_in_lnd_opts ) {
+               if ( defined($nl->get_value($option)) ) {
+                  $log->fatal_error("zender_soil_erod_source is atm, and the file option $option is being set" .
+                                    " which should NOT be unless you want it handled here in the LAND model, " .
+                                    "otherwise the equivalent option is set in CAM" );
+               }
+            }
+         } elsif ( $zender_source eq "none" ) {
+            $log->fatal_error("zender_soil_erod_source is set to none and only atm or lnd should be used when $var is Zender_2002" );
+         }
+      } else {
+         # Verify that NONE of the Zender options are being set if Zender is NOT being used
+         push @zender_files_in_lnd_opts, "zender_soil_erod_source";
+         foreach my $option ( @zender_files_in_lnd_opts ) {
+            if ( defined($nl->get_value($option)) ) {
+               $log->fatal_error("dust_emis_method is NOT set to Zender_2003, but one of it's options " .
+                                 "$option is being set, need to change one or the other" );
+            }
+         }
+         if ( $dust_emis_method eq "Leung_2023" ) {
+            $log->warning("dust_emis_method is Leung_2023 and that option has NOT been brought into CTSM yet");
+         }
+      }
+  # Otherwise make sure dust settings are NOT being set in CLM
   } else {
-     # Verify that NONE of the Zender options are being set if Zender is NOT being used
-     push @zender_files_in_lnd_opts, "zender_soil_erod_source";
-     foreach my $option ( @zender_files_in_lnd_opts ) {
-        if ( defined($nl->get_value($option)) ) {
-          $log->fatal_error("dust_emis_method is NOT set to Zender_2003, but one of it's options " .
-                            "$option is being set, need to change one or the other" );
-        }
-     }
-     if ( $dust_emis_method eq "Leung_2023" ) {
-        $log->warning("dust_emis_method is Leung_2023 and that option has NOT been brought into CTSM yet");
-     }
+      my @vars = ( "dust_emis_method", "zender_soil_erod_source" );
+      foreach my $option ( @vars ) {
+         if ( defined($nl->get_value($option)) ) {
+            $log->fatal_error("Dust emission variable is being set in CTSM, which should NOT be done when" .
+                              " connected to CAM as CAM should set them");
+         }
+      }
   }
 }
 
@@ -4528,8 +4540,8 @@ sub setup_logic_fates {
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');
         if ( ($parteh_mode == 1) &&  ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
-          $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " . 
-                            "but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" . 
+          $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " .
+                            "but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" .
                             "Change suplnitro back to ALL");
         }
         #
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 30110d92f7..d017997c6a 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 2515;
+my $ntests = 2516;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 1545;
@@ -500,447 +500,358 @@ sub cat_and_create_namelistinfile {
 my %failtest = (
      "coldstart but with IC file"=>{ options=>"-clm_start_type cold -envxml_dir .",
                                      namelst=>"finidat='$finidat'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "clm_demand on finidat"     =>{ options=>"-clm_demand finidat -envxml_dir .",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "blank IC file, not cold"   =>{ options=>"-clm_start_type startup -envxml_dir .",
                                      namelst=>"finidat=' '",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "startup without interp"    =>{ options=>"-clm_start_type startup -envxml_dir . -bgc sp -sim_year 1850",
                                      namelst=>"use_init_interp=.false., start_ymd=19200901",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "use_crop without -crop"    =>{ options=>" -envxml_dir .",
                                      namelst=>"use_crop=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "soilm_stream off w file"      =>{ options=>"-res 0.9x1.25 -envxml_dir .",
                                      namelst=>"use_soil_moisture_streams = .false.,stream_fldfilename_soilm='file_provided_when_off'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "exice_stream off w file"  =>{ options=>"-res 0.9x1.25 -envxml_dir .",
                                      namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.,stream_fldfilename_exice='file_provided_when_off'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "exice_stream off w mesh"  =>{ options=>"-res 0.9x1.25 -envxml_dir .",
                                      namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.,stream_meshfile_exice='file_provided_when_off'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "exice off, but stream on"  =>{ options=>"-res 0.9x1.25 -envxml_dir .",
                                      namelst=>"use_excess_ice=.false., use_excess_ice_streams = .true.,stream_fldfilename_exice='file_provided', stream_meshfile_exice='file_provided'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "exice stream off, but setmap"=>{ options=>"-res 0.9x1.25 -envxml_dir .",
                                      namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.,stream_mapalgo_exice='bilinear'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "exice stream on, but mct"    =>{ options=>"--res 0.9x1.25 --envxml_dir . --driver mct --lnd_frac $DOMFILE ",
                                      namelst=>"use_excess_ice=.true., use_excess_ice_streams=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "clm50CNDVwtransient"       =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "decomp_without_cn"         =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"soil_decomp_method='CENTURYKoven2013'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "bgc_with_no_decomp"        =>{ options=>" -envxml_dir . -bgc bgc",
                                      namelst=>"soil_decomp_method='None'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "reseed without CN"         =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"reseed_dead_plants=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "onset_threh w SP"          =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"onset_thresh_depends_on_veg=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "dribble_crphrv w/o CN"     =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"dribble_crophrv_xsmrpool_2atm=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "dribble_crphrv w/o crop"   =>{ options=>" -envxml_dir . -bgc bgc -no-crop",
                                      namelst=>"dribble_crophrv_xsmrpool_2atm=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "CNDV with flanduse_timeseries - clm4_5"=>{ options=>"-bgc bgc -dynamic_vegetation -envxml_dir . -ignore_warnings",
                                      namelst=>"flanduse_timeseries='my_flanduse_timeseries_file.nc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "use_cndv=T without bldnml op"=>{ options=>"-bgc bgc -envxml_dir . -ignore_warnings",
                                      namelst=>"use_cndv=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "use_cndv=F with dyn_veg op"=>{ options=>"-bgc bgc -dynamic_vegetation -envxml_dir . -ignore_warnings",
                                      namelst=>"use_cndv=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "crop with use_crop false"  =>{ options=>"-crop -bgc bgc -envxml_dir .",
                                      namelst=>"use_crop=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "crop without CN"           =>{ options=>"-crop -bgc sp -envxml_dir .",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "toosmall soil w trans"     =>{ options=>"-envxml_dir .",
                                      namelst=>"toosmall_soil=10, dyn_transient_pfts=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "toosmall lake w trans"     =>{ options=>"-envxml_dir .",
                                      namelst=>"toosmall_lake=10, dyn_transient_pfts=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "toosmall crop w trans"     =>{ options=>"-bgc bgc -crop -envxml_dir .",
                                      namelst=>"toosmall_crop=10, dyn_transient_pfts=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "toosmall wetl w trans"     =>{ options=>"-bgc bgc -envxml_dir .",
                                      namelst=>"toosmall_wetland=10, dyn_transient_pfts=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "toosmall glc  w trans"     =>{ options=>"-bgc sp  -envxml_dir .",
                                      namelst=>"toosmall_glacier=10, dyn_transient_pfts=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "toosmall urban w trans"    =>{ options=>"-bgc sp  -envxml_dir .",
                                      namelst=>"toosmall_urban=10, dyn_transient_pfts=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "collapse_urban w trans"    =>{ options=>"-bgc sp  -envxml_dir .",
                                      namelst=>"collapse_urban=T, dyn_transient_crops=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "n_dom_landunits w trans"    =>{ options=>"-bgc sp  -envxml_dir .",
                                      namelst=>"n_dom_landunits=2, dyn_transient_crops=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "n_dom_pfts w trans"         =>{ options=>"-bgc sp  -envxml_dir .",
                                      namelst=>"n_dom_pfts=2, dyn_transient_crops=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "baset_map without crop"    =>{ options=>"-bgc bgc -envxml_dir . -no-crop",
                                      namelst=>"baset_mapping='constant'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "mapvary var w/o varymap"   =>{ options=>"-crop -bgc bgc -envxml_dir . -crop",
                                      namelst=>"baset_mapping='constant', baset_latvary_slope=1.0, baset_latvary_intercept=10.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "grainproductWOcrop"       =>{ options=>"-bgc bgc -no-crop -envxml_dir .",
                                     namelst=>"use_grainproduct=.true.",
-                                    GLC_TWO_WAY_COUPLING=>"FALSE",
                                     phys=>"clm4_5",
                                    },
      "interp without finidat"    =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"use_init_interp=.true. finidat=' '",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "sp and c13"                =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"use_c13=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "sp and c14"                =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"use_c14=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "bombspike no c14"          =>{ options=>"-bgc bgc -envxml_dir .",
                                      namelst=>"use_c14=.false. use_c14_bombspike=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "use c13 timeseries no cn"  =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"use_c13_timeseries=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "use c13 timeseries no c13"=>{ options=>"-bgc bgc -envxml_dir .",
                                      namelst=>"use_c13=.false. use_c13_timeseries=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "bombspike no cn"           =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"use_c14_bombspike=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lightres no cn"            =>{ options=>"-bgc sp -envxml_dir . -light_res 360x720",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "NEONlightresButGlobal"     =>{ options=>"--res 4x5 --bgc bgc --envxml_dir . --light_res 106x740",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "spno-fire"                 =>{ options=>"-bgc sp -envxml_dir . -use_case 2000_control",
                                      namelst=>"fire_method='nofire'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lightres no fire"          =>{ options=>"-bgc bgc -envxml_dir . -light_res 360x720",
                                      namelst=>"fire_method='nofire'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lightres none bgc"         =>{ options=>"-bgc bgc -envxml_dir . -light_res none",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lightresnotnone-nofire"    =>{ options=>"-bgc bgc -envxml_dir . -light_res 94x192",
                                      namelst=>"fire_method='nofire'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lightresnonenofirelightfil"=>{ options=>"-bgc bgc -envxml_dir . -light_res none",
                                      namelst=>"fire_method='nofire',stream_fldfilename_lightng='build-namelist_test.pl'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lightrescontradictlightfil"=>{ options=>"-bgc bgc -envxml_dir . -light_res 360x720",
                                      namelst=>"stream_fldfilename_lightng='build-namelist_test.pl'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "finundated and not methane"=>{ options=>"-bgc bgc -envxml_dir .",
                                      namelst=>"use_lch4=.false.,finundation_method='h2osfc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "use_cn=true bgc=sp"        =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"use_cn=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "freeliv wo fun"            =>{ options=>"-bgc bgc -envxml_dir .",
                                      namelst=>"freelivfix_intercept=9.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "use_cn=false bgc=bgc"      =>{ options=>"-bgc bgc -envxml_dir .",
                                      namelst=>"use_cn=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "lower=aqu-45 with/o Zeng"  =>{ options=>"-envxml_dir .",
                                      namelst=>"lower_boundary_condition=4,soilwater_movement_method=1,use_bedrock=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "Zeng w lower=flux"         =>{ options=>"-envxml_dir .",
                                      namelst=>"lower_boundary_condition=1,soilwater_movement_method=0,use_bedrock=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "Zeng w lower=zeroflux"     =>{ options=>"-envxml_dir .",
                                      namelst=>"lower_boundary_condition=2,soilwater_movement_method=0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "Zeng w lower=table"        =>{ options=>"-envxml_dir .",
                                      namelst=>"lower_boundary_condition=3,soilwater_movement_method=0,use_bedrock=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "use_vic=F with -vic op"    =>{ options=>"-vichydro -envxml_dir .",
                                      namelst=>"use_vichydro=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "-vic with l_bnd=flux"      =>{ options=>"-vichydro -envxml_dir .",
                                      namelst=>"lower_boundary_condition=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "-vic with l_bnd=zeroflux"  =>{ options=>"-vichydro -envxml_dir .",
                                      namelst=>"lower_boundary_condition=2",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "bedrock with l_bnc=flux"   =>{ options=>"-envxml_dir .",
                                      namelst=>"use_bedrock=.true., lower_boundary_condition=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "bedrock with l_bnc=tabl"   =>{ options=>"-envxml_dir .",
                                      namelst=>"use_bedrock=.true., lower_boundary_condition=3",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "bedrock with l_bnc=aqui"   =>{ options=>"-envxml_dir .",
                                      namelst=>"use_bedrock=.true., lower_boundary_condition=4",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "zengdeck with l_bnc=flux"  =>{ options=>"-envxml_dir .",
                                      namelst=>"soilwater_movement_method=0, lower_boundary_condition=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "zengdeck with l_bnc=z-flux"=>{ options=>"-envxml_dir .",
                                      namelst=>"soilwater_movement_method=0, lower_boundary_condition=2",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "zengdeck with l_bnc=tabl"  =>{ options=>"-envxml_dir .",
                                      namelst=>"soilwater_movement_method=0, lower_boundary_condition=3",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "l_bnd=tabl with h2osfcfl=0"=>{ options=>"-envxml_dir .",
                                      namelst=>"h2osfcflag=0, lower_boundary_condition=3",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "l_bnd=flux with h2osfcfl=0"=>{ options=>"-envxml_dir .",
                                      namelst=>"h2osfcflag=0, lower_boundary_condition=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "l_bnd=zflux with h2osfcfl=0"=>{ options=>"-envxml_dir .",
                                      namelst=>"h2osfcflag=0, lower_boundary_condition=2",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "h2osfcfl=0 with clm5.0"    =>{ options=>"-envxml_dir .",
                                      namelst=>"h2osfcflag=0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "45bad lnd_tuning_mode value" =>{ options=>"-lnd_tuning_mode clm5_0_GSWP3  -envxml_dir .",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "50bad lnd_tuning_mode value" =>{ options=>"-lnd_tuning_mode clm4_5_CRUNCEP  -envxml_dir .",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "bgc_spinup without cn"     =>{ options=>"-clm_accelerated_spinup on -bgc sp -envxml_dir .",
                                      namelst=>"spinup_state=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "spinup=1 without bldnml op"=>{ options=>"-clm_accelerated_spinup off -bgc bgc -envxml_dir .",
                                      namelst=>"spinup_state=1",,
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "bgc_spinup without cn"     =>{ options=>"-clm_accelerated_spinup on -bgc sp -envxml_dir .",
                                      namelst=>"spinup_state=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "baseflow w aquifer"        =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"baseflow_scalar=1.0, lower_boundary_condition=4,use_bedrock=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "baseflow w table"          =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"baseflow_scalar=1.0, lower_boundary_condition=3,use_bedrock=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "br_root and bgc=sp"        =>{ options=>"-bgc sp -envxml_dir .",
                                      namelst=>"br_root=1.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "both co2_type and on nml"  =>{ options=>"-co2_type constant -envxml_dir .",
                                      namelst=>"co2_type='prognostic'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "both lnd_frac and on nml"  =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .",
                                      namelst=>"fatmlndfrc='frac.nc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lnd_frac set to UNSET"     =>{ options=>"-driver mct -lnd_frac UNSET -envxml_dir .",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "lnd_frac set but nuopc"    =>{ options=>"-driver nuopc -lnd_frac $DOMFILE -envxml_dir .",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "lnd_frac not set but lilac"=>{ options=>"-driver nuopc -lilac -envxml_dir . -lnd_frac UNSET",
                                      namelst=>"fsurdat='surfdata.nc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "fatmlndfrc set but nuopc"  =>{ options=>"-driver nuopc -envxml_dir .",
                                      namelst=>"fatmlndfrc='frac.nc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "force_send but not nuopc"  =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .",
                                      namelst=>"force_send_to_atm = .false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "branch but NO nrevsn"      =>{ options=>"-clm_start_type branch -envxml_dir .",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "glc_nec inconsistent"      =>{ options=>"-envxml_dir .",
                                      namelst=>"maxpatch_glc=5",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "NoGLCMec"                  =>{ options=>"-envxml_dir . -glc_nec 0",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "UpdateGlcContradict"       =>{ options=>"-envxml_dir .",
@@ -950,321 +861,263 @@ sub cat_and_create_namelistinfile {
                                    },
      "useFATESContradict"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_fates=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "useFATESContradict2"       =>{ options=>"-envxml_dir . -no-megan",
                                      namelst=>"use_fates=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "useFATESWCN"               =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_cn=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useFATESWcrop"             =>{ options=>"-bgc fates -envxml_dir . -no-megan -crop",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "useFATESWcreatecrop"       =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"create_crop_landunit=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useFATESWn_dom_pft"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"n_dom_pfts = 1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useFATESWbMH"              =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_biomass_heat_storage=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "FireNoneButFATESfireon"    =>{ options=>"-bgc fates -envxml_dir . -no-megan -light_res none",
                                      namelst=>"fates_spitfire_mode=4",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "FATESwspitfireOffLigtOn"    =>{ options=>"-bgc fates -envxml_dir . -no-megan -light_res 360x720",
                                      namelst=>"fates_spitfire_mode=0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "useFATESWluna"             =>{ options=>"--bgc fates --envxml_dir . --no-megan",
                                      namelst=>"use_luna=TRUE",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "useFATESWfun"              =>{ options=>"--bgc fates --envxml_dir . --no-megan",
                                      namelst=>"use_fun=TRUE",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "useFATESWOsuplnitro"       =>{ options=>"--bgc fates --envxml_dir . --no-megan",
                                      namelst=>"suplnitro='NONE'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "FireNoneButBGCfireon"    =>{ options=>"-bgc bgc -envxml_dir . -light_res none",
                                      namelst=>"fire_method='li2021gswpfrc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "createcropFalse"           =>{ options=>"-bgc bgc -envxml_dir . -no-megan",
                                      namelst=>"create_crop_landunit=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "usespitfireButNOTFATES"    =>{ options=>"-envxml_dir . -no-megan",
                                      namelst=>"fates_spitfire_mode=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "usespitfireusefatessp"    =>{ options=>"-envxml_dir . --bgc fates",
                                      namelst=>"fates_spitfire_mode=1,use_fates_sp=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "usefatesspusefateshydro"   =>{ options=>"-envxml_dir . --bgc fates",
                                      namelst=>"use_fates_sp=.true.,use_fates_planthydro=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useloggingButNOTFATES"     =>{ options=>"-envxml_dir . -no-megan",
                                      namelst=>"use_fates_logging=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "useinventorybutnotfile"    =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_fates_inventory_init=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "inventoryfileDNE"          =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_fates_inventory_init=.true., fates_inventory_ctrl_filename='zztop'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "useinventorybutnotfile"    =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan",
                                      namelst=>"use_fates_luh=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "inventoryfileDNE"          =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_fates_luh=.true., fluh_timeseries='zztop'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "useMEGANwithFATES"         =>{ options=>"-bgc fates -envxml_dir . -megan",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "useFIREEMISwithFATES"      =>{ options=>"-bgc fates -envxml_dir . -fire_emis --no-megan",
                                     namelst=>"",
-                                    GLC_TWO_WAY_COUPLING=>"FALSE",
                                     phys=>"clm4_5",
                                  },
      "useDRYDEPwithFATES"        =>{ options=>"--bgc fates --envxml_dir . --no-megan --drydep",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
      "useFATESSPWONOCOMP"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_fates_sp=T,use_fates_nocomp=F",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useFATESTRANSWdynPFT"      =>{ options=>"-bgc fates -envxml_dir . -use_case 20thC_transient -no-megan",
                                      namelst=>"do_transient_pfts=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useHYDSTwithFATES"         =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_hydrstress=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useHYDSTwithdynroot"       =>{ options=>"-bgc bgc -envxml_dir . -megan",
                                      namelst=>"use_hydrstress=.true., use_dynroot=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "specWOfireemis"            =>{ options=>"-envxml_dir . -no-fire_emis",
                                      namelst=>"fire_emis_specifier='bc_a1 = BC'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "elevWOfireemis"            =>{ options=>"-envxml_dir . -no-fire_emis",
                                      namelst=>"fire_emis_elevated=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "noanthro_w_crop"            =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -crop -use_case 1850_noanthro_control",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "noanthro_w_irrig"           =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control",
                                      namelst=>"irrigate=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "spdotransconflict"          =>{ options=>"-envxml_dir . -bgc sp -use_case 20thC_transient",
                                      namelst=>"do_transient_pfts=T,do_transient_crops=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "dogrossandsp"               =>{ options=>"--envxml_dir . --bgc sp --use_case 20thC_transient",
                                      namelst=>"do_grossunrep=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "dogrossandfates"            =>{ options=>"--envxml_dir . --bgc fates --use_case 20thC_transient --no-megan",
                                      namelst=>"do_grossunrep=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "dogrossandnottrans"         =>{ options=>"--envxml_dir . --bgc bgc --use_case 2000_control",
                                      namelst=>"do_grossunrep=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "nocropwfert"                =>{ options=>"-envxml_dir . -bgc sp -no-crop",
                                      namelst=>"use_fertilizer=T",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lmr1WOcn"                   =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"leafresp_method=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lmr2WOcn"                   =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"leafresp_method=2",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lmr0Wcn"                    =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"leafresp_method=0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "nofireButSetcli_scale"     =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"fire_method='nofire', cli_scale=5.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "nocnButSetrh_low"          =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"rh_low=5.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "funWOcn"                   =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"use_fun=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "flexCNWOcn"                =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"use_flexibleCN=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "flexCNFUNwcarbonresp"      =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"use_flexibleCN=.true.,use_FUN=.true.,carbon_resp_opt=1",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "funWOnitrif"               =>{ options=>"-envxml_dir .",
                                      namelst=>"use_fun=.true., use_nitrif_denitrif=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "SPModeWNitrifNMethane"     =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"use_lch4=.true., use_nitrif_denitrif=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "knitrmaxWOnitrif"          =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"use_nitrif_denitrif=.false., k_nitr_max=1.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "respcoefWOnitrif"          =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"use_nitrif_denitrif=.false., denitrif_respiration_coefficient=1.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "respexpWOnitrif"           =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"use_nitrif_denitrif=.false., denitrif_respiration_exponent=1.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "lunaWSPandlnctrue"         =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"use_luna=.true., lnc_opt=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "NOlunabutsetJmaxb1"        =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"use_luna=.false., jmaxb1=1.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "envxml_not_dir"            =>{ options=>"-envxml_dir myuser_nl_clm",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "envxml_emptydir"           =>{ options=>"-envxml_dir xFail",
                                      namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "fates_non_sp_laistreams"   =>{ options=>"--envxml_dir . --bgc fates",
                                      namelst=>"use_lai_streams=.true., use_fates_sp=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                      },
      "bgc_non_sp_laistreams"     =>{ options=>"--envxml_dir . -bgc bgc",
                                      namelst=>"use_lai_streams=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                      },
      "bgc_laistreams_input"     =>{ options=>"--envxml_dir . --bgc bgc",
                                      namelst=>"stream_year_first_lai=1999",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                      },
      "crop_laistreams_input"     =>{ options=>"--envxml_dir . --bgc sp --crop",
                                      namelst=>"use_lai_streams=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                      },
      "soil_erod_wo_Zender"      =>{ options=>"--envxml_dir . --ignore_warnings",
                                      namelst=>"dust_emis_method='Leung_2023', " .
                                      "stream_meshfile_zendersoilerod = '/dev/null'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                      },
      "soil_erod_wo_lnd_source"  =>{ options=>"--envxml_dir .",
                                      namelst=>"dust_emis_method='Zender_2003', " .
                                      "stream_fldfilename_zendersoilerod = '/dev/null', zender_soil_erod_source='atm'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                      },
      "soil_erod_none_w_Zender"  =>{ options=>"--envxml_dir .",
                                      namelst=>"dust_emis_method='Zender_2003', " .
                                      "zender_soil_erod_source='none'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                      },
      "soil_erod_bad_w_Zender"   =>{ options=>"--envxml_dir .",
                                      namelst=>"dust_emis_method='Zender_2003', " .
                                      "zender_soil_erod_source='zztop'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                     },
+     "Set_Dust_When_CAM_Sets"   =>{ options=>"--envxml_dir .",
+                                     namelst=>"dust_emis_method='Zender_2003'",
+                                     LND_SETS_DUST_EMIS_DRV_FLDS=>"FALSE",
                                      phys=>"clm5_1",
                                      },
                );
@@ -1273,7 +1126,13 @@ sub cat_and_create_namelistinfile {
    &make_config_cache($failtest{$key}{"phys"});
    my $options  = $failtest{$key}{"options"};
    my $namelist = $failtest{$key}{"namelst"};
-   &make_env_run( GLC_TWO_WAY_COUPLING=>$failtest{$key}{"GLC_TWO_WAY_COUPLING"} );
+   my %settings;
+   foreach my $xmlvar ( "GLC_TWO_WAY_COUPLING", "LND_SETS_DUST_EMIS_DRV_FLDS") {
+      if ( defined($failtest{$key}{$xmlvar}) ) {
+         $settings{$xmlvar} = $failtest{$key}{$xmlvar};
+      }
+   }
+   &make_env_run( %settings );
    eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
    isnt( $?, 0, $key );
    system( "cat $tempfile" );
@@ -1515,7 +1374,7 @@ sub cat_and_create_namelistinfile {
 # cases; I'm not sure if it's actually important to test this with all
 # of the different use cases.
 my @glc_res = ( "0.9x1.25", "1.9x2.5" );
-my @use_cases = ( 
+my @use_cases = (
                   "1850-2100_SSP2-4.5_transient",
                   "1850_control",
                   "2000_control",

From 0a08723cfe7365a7fb639513232bbeb1c12716c9 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 16 May 2024 16:38:06 -0600
Subject: [PATCH 0269/1248] Fix for issue #2546

---
 cime_config/config_component.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index be6916ae0c..d69bdbc302 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -78,7 +78,7 @@
     </desc>
     <default_value>UNSET</default_value>
     <!-- 10 forcing options for each CLM physics option: CRUv7, GSWP3, cam7.0, cam6.0, cam5.0, cam4.0, QIAN, 1PT, NLDAS2, ERA5 -->
-    <valid_values>clm5_0_cam6.0,clm5_0_cam7.0,clm5.0_cam5.0,clm5.0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm5_1_CRUv7,clm5_1_GSWP3v1,clm5_1_cam6.0,clm5_1_QIAN,clm5_1_1PT,clm5_1_NLDAS2,clm5_1_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5</valid_values>
+    <valid_values>clm5_0_cam6.0,clm5_0_cam7.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm5_1_CRUv7,clm5_1_GSWP3v1,clm5_1_cam6.0,clm5_1_QIAN,clm5_1_1PT,clm5_1_NLDAS2,clm5_1_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5</valid_values>
     <values match="last">
       <!-- Options for atm forcing are: CRU, CRUv7, GSWP3, cam6.0 (also used for DATM%CPLHIST), cam5.0, cam4.0, QIAN, WISOQIA, 1PT, NLDAS2, and ERA5) -->
       <!-- All the clm4_5 physics options -->

From 438d85a58b120a1329db4c47520ff473a40bcc5b Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Fri, 17 May 2024 09:27:55 -0600
Subject: [PATCH 0270/1248] Added a missing bracket

---
 bld/CLMBuildNamelist.pm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index ad378ffc6d..3658f681af 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -785,7 +785,7 @@ sub setup_cmdl_fates_mode {
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
                       "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries",
-                      "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel");
+                      "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel" );
 
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
@@ -4517,7 +4517,7 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","fates_seeddisp_cadence","fates_history_dimlevel",
-                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage");
+                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" );
 
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
@@ -4564,12 +4564,12 @@ sub setup_logic_fates {
 
               # fates landuse can't be on with FATES SP mode is active
               if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
-                    $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
+		  $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
+	      }
 
               # hydro isn't currently supported to work when FATES SP mode is active
               if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
                     $log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
-
               }
            }
         }

From 21f38b4701491c98281f2accdcb6d878c3d1fa67 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 17 May 2024 11:43:26 -0600
Subject: [PATCH 0271/1248] Add an empty unit tester for DUSTMod

---
 .../test/DustEmis_test/CMakeLists.txt         |  6 ++
 .../test/DustEmis_test/test_DustEmis.pf       | 34 +++++++
 .../share_esmf/ZenderSoilErodStreamType.F90   | 88 +++++++++++++++++++
 3 files changed, 128 insertions(+)
 create mode 100644 src/biogeochem/test/DustEmis_test/CMakeLists.txt
 create mode 100644 src/biogeochem/test/DustEmis_test/test_DustEmis.pf
 create mode 100644 src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90

diff --git a/src/biogeochem/test/DustEmis_test/CMakeLists.txt b/src/biogeochem/test/DustEmis_test/CMakeLists.txt
new file mode 100644
index 0000000000..a618489386
--- /dev/null
+++ b/src/biogeochem/test/DustEmis_test/CMakeLists.txt
@@ -0,0 +1,6 @@
+set (pfunit_sources
+  test_DustEmis.pf)
+
+add_pfunit_ctest(DustEmis
+  TEST_SOURCES "${pfunit_sources}"
+  LINK_LIBRARIES clm csm_share esmf_wrf_timemgr)
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
new file mode 100644
index 0000000000..e0e668ea67
--- /dev/null
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -0,0 +1,34 @@
+module test_DustEmis
+
+  ! Tests of DustEmis
+
+  use funit
+  use DUSTMod
+  use shr_kind_mod , only : r8 => shr_kind_r8
+
+  implicit none
+
+  @TestCase
+  type, extends(TestCase) :: TestDustEmis
+   contains
+     procedure :: setUp
+     procedure :: tearDown
+  end type TestDustEmis
+
+contains
+
+  subroutine setUp(this)
+    class(TestDustEmis), intent(inout) :: this
+  end subroutine setUp
+
+  subroutine tearDown(this)
+    class(TestDustEmis), intent(inout) :: this
+  end subroutine tearDown
+
+  @Test
+  subroutine check_dust_emis(this)
+    class(TestDustEmis), intent(inout) :: this
+
+  end subroutine check_dust_emis
+
+end module test_DustEmis
\ No newline at end of file
diff --git a/src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90 b/src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90
new file mode 100644
index 0000000000..570fcec05f
--- /dev/null
+++ b/src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90
@@ -0,0 +1,88 @@
+module ZenderSoilErodStreamType
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! UNIT-TEST STUB for ZenderSoilErodStreamType
+  !
+  ! !USES
+  use shr_kind_mod     , only : r8 => shr_kind_r8, CL => shr_kind_cl
+  use shr_log_mod      , only : errMsg => shr_log_errMsg
+  use abortutils       , only : endrun
+  use decompMod        , only : bounds_type
+
+  ! !PUBLIC TYPES:
+  implicit none
+  private
+
+  type, public :: soil_erod_stream_type
+  contains
+
+      ! !PUBLIC MEMBER FUNCTIONS:
+      procedure, public :: Init            ! Initialize and read data in
+      procedure, public :: CalcDustSource ! Calculate dust source spatial filter (basically truncating stream data value smaller than 0.1 following CAM's practice) based on input streams
+      procedure, public :: UseStreams      ! If streams will be used
+
+  end type soil_erod_stream_type
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+!==============================================================================
+contains
+!==============================================================================
+
+  subroutine Init(this, bounds, NLFilename)
+   !
+   ! Initialize the Zender soil eroditability stream object
+   !
+   ! Uses:
+   !
+   ! arguments
+   implicit none
+   class(soil_erod_stream_type) :: this
+   type(bounds_type), intent(in)   :: bounds
+   character(len=*),  intent(in)   :: NLFilename   ! Namelist filename
+   !
+   ! local variables
+   !-----------------------------------------------------------------------
+
+  end subroutine Init
+
+  !==============================================================================
+  logical function UseStreams(this)
+    !
+    ! !DESCRIPTION:
+    ! Return true if the Zender method is being used and the soil erodability
+    ! file is being used with it
+    !
+    ! !USES:
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(soil_erod_stream_type) :: this
+    !
+    ! !LOCAL VARIABLES:
+    UseStreams = .false.
+  end function UseStreams
+
+  !==============================================================================
+  subroutine CalcDustSource(this, bounds, soil_erod)
+    !
+    ! !DESCRIPTION:
+    !  Calculate the soil eroditability for the Zender dust method.
+    !
+    ! !USES:
+    !USES
+    !
+    ! !ARGUMENTS:
+    implicit none
+    class(soil_erod_stream_type)             :: this
+    type(bounds_type)              , intent(in)    :: bounds
+    real(r8)                       , intent(inout) :: soil_erod(bounds%begc:)      ! [fraction] rock drag partition factor (roughness effect)
+    !
+    ! !LOCAL VARIABLES:
+    !---------------------------------------------------------------------
+
+  end subroutine CalcDustSource
+
+end module ZenderSoilErodStreamType

From 7d8213bc814be0b9274feea0c4d0472b8f96bf07 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 17 May 2024 11:43:37 -0600
Subject: [PATCH 0272/1248] Add an empty unit tester for DUSTMod

---
 src/biogeochem/CMakeLists.txt                 | 1 +
 src/biogeochem/test/CMakeLists.txt            | 1 +
 src/biogeophys/CMakeLists.txt                 | 1 +
 src/unit_test_stubs/share_esmf/CMakeLists.txt | 1 +
 4 files changed, 4 insertions(+)

diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt
index e31bbc80f8..0f46dc665d 100644
--- a/src/biogeochem/CMakeLists.txt
+++ b/src/biogeochem/CMakeLists.txt
@@ -6,6 +6,7 @@ list(APPEND clm_sources
   CNPhenologyMod.F90
   CNSpeciesMod.F90
   CNDVType.F90
+  DUSTMod.F90
   CropReprPoolsMod.F90
   CropType.F90
   CNVegStateType.F90
diff --git a/src/biogeochem/test/CMakeLists.txt b/src/biogeochem/test/CMakeLists.txt
index 81fe9bbaf0..e22a720523 100644
--- a/src/biogeochem/test/CMakeLists.txt
+++ b/src/biogeochem/test/CMakeLists.txt
@@ -2,3 +2,4 @@ add_subdirectory(Species_test)
 add_subdirectory(CNVegComputeSeed_test)
 add_subdirectory(CNPhenology_test)
 add_subdirectory(Latbaset_test)
+add_subdirectory(DustEmis_test)
diff --git a/src/biogeophys/CMakeLists.txt b/src/biogeophys/CMakeLists.txt
index 2ffc346670..86edcca9f9 100644
--- a/src/biogeophys/CMakeLists.txt
+++ b/src/biogeophys/CMakeLists.txt
@@ -7,6 +7,7 @@ list(APPEND clm_sources
   BalanceCheckMod.F90
   CanopyStateType.F90
   EnergyFluxType.F90
+  FrictionVelocityMod.F90
   GlacierSurfaceMassBalanceMod.F90
   HillslopeHydrologyUtilsMod.F90
   HumanIndexMod.F90
diff --git a/src/unit_test_stubs/share_esmf/CMakeLists.txt b/src/unit_test_stubs/share_esmf/CMakeLists.txt
index 5eb2d42415..5ffce0ba94 100644
--- a/src/unit_test_stubs/share_esmf/CMakeLists.txt
+++ b/src/unit_test_stubs/share_esmf/CMakeLists.txt
@@ -1,5 +1,6 @@
 list(APPEND clm_sources
   ExcessIceStreamType.F90
+  ZenderSoilErodStreamType.F90
   )
 
 sourcelist_to_parent(clm_sources)

From 3254949e133f5fd42411a896690b256529ea150c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 17 May 2024 13:09:31 -0600
Subject: [PATCH 0273/1248] Add objects needed and a failing unit test that
 just runs the two main subroutines, needs to add initialization of the input
 objects

---
 .../test/DustEmis_test/test_DustEmis.pf       | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index e0e668ea67..ff4b69ab72 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -3,13 +3,31 @@ module test_DustEmis
   ! Tests of DustEmis
 
   use funit
+  use unittestSubgridMod
+  use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
   use DUSTMod
   use shr_kind_mod , only : r8 => shr_kind_r8
+  use unittestFilterBuilderMod, only : filter_from_range
+  use atm2lndType, only : atm2lnd_type
+  use SoilStateType, only : soilstate_type
+  use CanopyStateType, only : canopystate_type
+  use WaterStateBulkType, only : waterstatebulk_type
+  use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
+  use FrictionVelocityMod, only : frictionvel_type
 
   implicit none
 
   @TestCase
   type, extends(TestCase) :: TestDustEmis
+     type(dust_type) :: dust_emis
+     integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
+     integer :: num_nolakep              ! number of patches in non-lake filter
+     type(atm2lnd_type) :: atm2lnd_inst
+     type(soilstate_type) :: soilstate_inst
+     type(canopystate_type) :: canopystate_inst
+     type(WaterStateBulk_Type) :: waterstatebulk_inst
+     type(waterdiagnosticbulk_type) :: waterdiagnosticbulk_inst
+     type(frictionvel_type) :: frictionvel_inst
    contains
      procedure :: setUp
      procedure :: tearDown
@@ -19,16 +37,30 @@ contains
 
   subroutine setUp(this)
     class(TestDustEmis), intent(inout) :: this
+
+    character(len=5) :: NLFilename = 'none'
+
+     call setup_single_veg_patch( pft_type=0 )
+     call this%dust_emis%Init( bounds, NLFilename )
+     call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
   end subroutine setUp
 
   subroutine tearDown(this)
     class(TestDustEmis), intent(inout) :: this
+
+    call unittest_subgrid_teardown()
+    deallocate( this%filter_nolakep )
   end subroutine tearDown
 
   @Test
   subroutine check_dust_emis(this)
     class(TestDustEmis), intent(inout) :: this
 
+    call DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                      this%soilstate_inst, this%canopystate_inst, this%waterstatebulk_inst, &
+                      this%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis)
+    call DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst, this%dust_emis)
+
   end subroutine check_dust_emis
 
 end module test_DustEmis
\ No newline at end of file

From e4544510e23abf8a9a68e8dd143840742eb8b2fc Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 17 May 2024 13:55:46 -0600
Subject: [PATCH 0274/1248] Add izumi nag debug tests to ExpectedTestFails as
 per ESCOMP/CMEPS#460

---
 cime_config/testdefs/ExpectedTestFails.xml | 85 ++++++++++++++++++++++
 1 file changed, 85 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index f600444547..09a425ed9e 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -44,6 +44,91 @@
   </test>
 
   <!-- aux_clm test suite failures -->
+  <test name="ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-reduceOutput">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-reduceOutput">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-SNICARFRC">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm50Bgc.izumi_nag.clm-ciso">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-flexCN_FUN">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-luna">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-noFUN_flexCN">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-reduceOutput">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-o3lombardozzi2015">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Ld9.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-clm60cam6LndTuningModeZDustSoilErod">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_P48x1.f10_f10_mg37.IHistClm60Bgc.izumi_nag.clm-decStart">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERS_D.f10_f10_mg37.I1850Clm60Sp.izumi_nag.clm-ExcessIceStreams">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+  <test name="ERS_D_Ld5.f10_f10_mg37.I2000Clm50Fates.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
+    </phase>
+  </test>
+
   <test name="SMS_D_Ld10.f10_f10_mg37.I2000Clm50BgcCrop.izumi_intel.clm-tracer_consistency">
     <phase name="RUN">
       <status>FAIL</status>

From e6f62c431b05460f62c6549e464797df7a7ebf58 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 17 May 2024 15:56:00 -0600
Subject: [PATCH 0275/1248] fix reading of fates_harvest_modes during namelist
 build checks

---
 bld/CLMBuildNamelist.pm | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 01f7918d62..c1ec60fb33 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4487,8 +4487,9 @@ sub setup_logic_fates {
               if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
                 $log->fatal_error("use_fates_luh must be true when $var is true" );
               }
-              if ( $nl->get_value('fates_harvest_mode') ne 'no_harvest') {
-                $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" );
+              my $var = remove_leading_and_trailing_quotes($nl->get_value('fates_harvest_mode'));
+              if ( $var ne 'no_harvest') {
+                $log->fatal_error("fates_harvest_mode set to $var.  It must set to no_harvest when use_potential_veg is true." );
               }
               my $var = "fluh_timeseries";
               if ( defined($nl->get_value($var))  ) {
@@ -4500,10 +4501,22 @@ sub setup_logic_fates {
         my $var = "fates_harvest_mode";
         if ( defined($nl->get_value($var))  ) {
            # using fates_harvest mode with raw luh2 harvest data
-           if ( $nl->get_value($var) eq 'luhdata_area' || $nl->get_value($var) eq 'luhdata_mass' ) {
+           my $mode = remove_leading_and_trailing_quotes($nl->get_value($var));
+           if ( $mode eq 'luhdata_area' || $mode  eq 'luhdata_mass' ) {
               # Make sure that use_fates_luh is true when using raw fates luh2 harvest data
               if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
-                $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" );
+                $log->fatal_error("use_fates_luh is required to be true when $var is luhdata_mass or luhdata_area" );
+              }
+           } elsif ( $mode  eq 'surfdata_file' ) {
+              # Check to make sure that the user set the flanduse_timeseries file
+              # Since the flanduse_timeseries logic checking is upstream of the fates logic,
+              # don't try and add the default here
+              my $var = "flanduse_timeseries";
+              my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+              if ( ! defined($nl->get_value($var))  ) {
+                $log->fatal_error("$var is required when fates_harvest_mode is surfdata_file" );
+              } elsif ( ! -f "$fname" ) {
+                $log->fatal_error("$var does NOT point to a valid filename" );
               }
            }
         }

From 093f0666b9b1d78701240a2036e1efca8e073133 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 17 May 2024 16:18:20 -0600
Subject: [PATCH 0276/1248] minor comment update

---
 bld/CLMBuildNamelist.pm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index c1ec60fb33..e563bdffa8 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4510,7 +4510,8 @@ sub setup_logic_fates {
            } elsif ( $mode  eq 'surfdata_file' ) {
               # Check to make sure that the user set the flanduse_timeseries file
               # Since the flanduse_timeseries logic checking is upstream of the fates logic,
-              # don't try and add the default here
+              # don't add the default here.  The onus is on the user to match the correct timeseries
+              # data to the correct surface dataset resolution
               my $var = "flanduse_timeseries";
               my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
               if ( ! defined($nl->get_value($var))  ) {

From 9397431486d17cfdda6267c6eca77d2f65a888ae Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Fri, 17 May 2024 16:46:18 -0600
Subject: [PATCH 0277/1248] First draft ChangeLog/ChangeSum

---
 doc/ChangeLog | 106 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 107 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index de37d4934c..e4af944b8f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,110 @@
 ===============================================================
+Tag name: ctsm5.2.006
+Originator(s): slevis (Samuel Levis)
+Date: Fri May 17 16:17:54 MDT 2024
+One-line Summary: Update externals to cesm2_3_beta17
+
+Purpose and description of changes
+----------------------------------
+
+#2493 update externals to beta17
+#2294 remove references to mct but do not remove /src/mct
+
+Changes unrelated to the tag's title:
+#2546 fix error in cam4/cam5 test
+Remove /test/tools/test_driver.sh
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+Fixes #2493 update externals to beta17
+Fixes #2546 fix error in cam4/cam5 test (unrelated)
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to documentation: Remove references to mct and cpl7
+
+Substantial timing or memory changes: Not considered
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+I added a long list of izumi nag debug tests to ExpectedFailures as per
+https://github.com/ESCOMP/CMEPS/pull/460
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho -
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    (any machine) -
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho -----
+    izumi ------- IN PROGRESS
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ----
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  [ If a tag changes answers relative to baseline comparison the
+    following should be filled in (otherwise remove this section).
+    And always remove these three lines and parts that don't apply. ]
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations:
+    - what platforms/compilers:
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+
+   If bitwise differences were observed, how did you show they were no worse
+   than roundoff? Roundoff differences means one or more lines of code change results
+   only by roundoff level (because order of operation changes for example). Roundoff
+   changes to state fields usually grow to greater than roundoff as the simulation progresses.
+
+Other details
+-------------
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+cism, ccs_config, cime, cmeps, cdeps
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2539
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.005
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Mon 13 May 2024 04:46:10 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 0edccb3a18..c73cb19309 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.006   slevis 05/17/2024 Update externals to cesm2_3_beta17
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems
        ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes
        ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev

From 6b460a21afc98134f330a37f9a6cda837f364aee Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 17 May 2024 18:40:30 -0600
Subject: [PATCH 0278/1248] Update ntests in build-namelist_test.pl

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 doc/ChangeLog                           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index aa579cf908..53c71ae0e9 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3313;
+my $ntests = 3254;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2001;
diff --git a/doc/ChangeLog b/doc/ChangeLog
index e4af944b8f..5644ed295d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -11,7 +11,7 @@ Purpose and description of changes
 #2294 remove references to mct but do not remove /src/mct
 
 Changes unrelated to the tag's title:
-#2546 fix error in cam4/cam5 test
+#2546 fix error in cam4/cam5 test (ekluzek)
 Remove /test/tools/test_driver.sh
 
 Significant changes to scientifically-supported configurations

From 5244813b54835ba58582afcc17b5b02d80ad442e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 18 May 2024 16:25:32 -0600
Subject: [PATCH 0279/1248] Initialize input fields needed for unit-testing of
 dust emissions and get the unit tester to PASS!

---
 .../test/DustEmis_test/test_DustEmis.pf       | 205 +++++++++++++++++-
 src/biogeophys/CanopyStateType.F90            |  17 ++
 src/biogeophys/FrictionVelocityMod.F90        |  18 ++
 src/main/clm_instMod.F90                      |  10 +-
 4 files changed, 235 insertions(+), 15 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index ff4b69ab72..b7ea76df9c 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -5,15 +5,20 @@ module test_DustEmis
   use funit
   use unittestSubgridMod
   use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
+  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init
+  use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
+  use clm_varcon, only : clm_varcon_init, clm_varcon_clean
+  use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting
   use DUSTMod
   use shr_kind_mod , only : r8 => shr_kind_r8
   use unittestFilterBuilderMod, only : filter_from_range
-  use atm2lndType, only : atm2lnd_type
+  use atm2lndType, only : atm2lnd_type, atm2lnd_params_type
   use SoilStateType, only : soilstate_type
   use CanopyStateType, only : canopystate_type
-  use WaterStateBulkType, only : waterstatebulk_type
-  use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
+  use TemperatureType, only : temperature_type
+  use WaterType, only : water_type 
   use FrictionVelocityMod, only : frictionvel_type
+  use unittestWaterTypeFactory, only : unittest_water_type_factory_type
 
   implicit none
 
@@ -25,42 +30,222 @@ module test_DustEmis
      type(atm2lnd_type) :: atm2lnd_inst
      type(soilstate_type) :: soilstate_inst
      type(canopystate_type) :: canopystate_inst
-     type(WaterStateBulk_Type) :: waterstatebulk_inst
-     type(waterdiagnosticbulk_type) :: waterdiagnosticbulk_inst
+     type(temperature_type) :: temperature_inst
+     type(unittest_water_type_factory_type) :: water_factory
+     type(water_type) :: water_inst
      type(frictionvel_type) :: frictionvel_inst
    contains
      procedure :: setUp
      procedure :: tearDown
+     procedure :: setupEnvironment
+     procedure :: create_atm2lnd
+     procedure :: create_fv
   end type TestDustEmis
 
 contains
 
+  !-----------------------------------------------------------------------
+
   subroutine setUp(this)
+    use ColumnType, only : col
     class(TestDustEmis), intent(inout) :: this
 
     character(len=5) :: NLFilename = 'none'
+    real(r8), allocatable :: snow_depth_col(:)
+    real(r8), allocatable :: urb_em(:)
+    integer :: begl, endl, begc, endc
+    integer :: c
+    type(atm2lnd_params_type) :: atm2lnd_params
+
+    soil_layerstruct_predefined = '20SL_8.5m'
+    create_crop_landunit = .true.
+    use_crop = .false.
+    call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
+    call clm_varcon_init( is_simple_buildtemp=.true.)
+    call this%water_factory%init()
+    call this%water_factory%setup_before_subgrid( &
+        my_nlevsoi = nlevsoi, &
+        nlevgrnd_additional = nlevgrnd - nlevsoi, &
+        my_nlevsno = 3)
+    call setup_single_veg_patch( pft_type=0 )
+    begl = bounds%begl
+    endl = bounds%endl
+    begc = bounds%begc
+    endc = bounds%endc
+    allocate( urb_em(begl:endl) )
 
-     call setup_single_veg_patch( pft_type=0 )
-     call this%dust_emis%Init( bounds, NLFilename )
-     call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
+    call this%dust_emis%Init( bounds, NLFilename )
+    call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
+    atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
+                                          glcmec_downscale_longwave = .false., &
+                                          lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
+    )
+    allocate (snow_depth_col(begc:endc))
+    snow_depth_col(begc:endc) = 0.0_r8
+    call SnowHydrologySetControlForTesting()
+    call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc))
+    call this%water_factory%setup_after_subgrid(snl = 3)
+    call this%soilstate_inst%Init(bounds)
+    do c = begc, endc
+       this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1)
+    end do
+    call this%setupEnvironment( )
+    call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
+    call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
+    call this%canopystate_inst%SetNMLForTesting()
+    call this%canopystate_inst%Init(bounds)
+    call this%frictionvel_inst%InitForTesting(bounds)
+    urb_em(begl:endl) = 0.99_r8
+    call this%temperature_inst%Init(bounds,           &
+                               em_roof_lun=urb_em(begl:endl), &
+                               em_wall_lun=urb_em(begl:endl), &
+                               em_improad_lun=urb_em(begl:endl), &
+                               em_perroad_lun=urb_em(begl:endl), &
+                               is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
+    deallocate (snow_depth_col )
+    deallocate( urb_em )
   end subroutine setUp
 
+  !-----------------------------------------------------------------------
+
   subroutine tearDown(this)
     class(TestDustEmis), intent(inout) :: this
 
+    call this%water_factory%teardown(this%water_inst)
     call unittest_subgrid_teardown()
+    call this%atm2lnd_inst%Clean()
+    call clm_varcon_clean()
     deallocate( this%filter_nolakep )
   end subroutine tearDown
 
+  !-----------------------------------------------------------------------
+
+  subroutine setupEnvironment(this)
+    !
+    ! !DESCRIPTION:
+    ! Sets up the external environment used by Dust emissions - i.e., things accessed via
+    ! 'use' statements.
+    !
+    ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has
+    ! been completed.
+    !
+    use ColumnType, only : col
+    use GridcellType, only : grc
+    class(TestDustEmis), intent(in) :: this
+    !
+    integer :: c,j
+    real(r8), parameter :: clay = 10.0_r8
+
+    !-----------------------------------------------------------------------
+    col%dz(:,1:nlevgrnd) = 1.0_r8
+    do j = 1, nlevgrnd
+       do c = bounds%begc, bounds%endc
+          col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j)
+       end do
+    end do
+
+    do c = bounds%begc, bounds%endc
+       ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are
+       ! considered bedrock
+       col%nbedrock(c) = nlevsoi
+
+       this%soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
+       this%soilstate_inst%mss_frc_cly_vld_col(c) = 0.17_r8
+    end do
+
+
+    ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager)
+    grc%londeg(:) = 0.0_r8
+
+    grc%area(:) = 10.0_r8
+    
+  end subroutine setupEnvironment
+
+  !-----------------------------------------------------------------------
+
+  subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho )
+    ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets
+    ! forcing fields based on inputs. Excluded inputs are given a default value
+    class(TestDustEmis), intent(inout) :: this
+    real(r8), intent(in), optional :: forc_t(:)
+    real(r8), intent(in), optional :: forc_pbot(:)
+    real(r8), intent(in), optional :: forc_rho(:)
+
+    real(r8), parameter :: forc_t_default = 301._r8
+    real(r8), parameter :: forc_pbot_default = 100000._r8
+    real(r8), parameter :: forc_rho_default = 1.1_r8
+    ! ------------------------------------------------------------------------
+
+    if (present(forc_t)) then
+       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:)
+    else
+       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default
+    end if
+
+    if (present(forc_pbot)) then
+       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:)
+    else
+       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default
+    end if
+
+    if (present(forc_rho)) then
+       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:)
+    else
+       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default
+    end if
+
+  end subroutine create_atm2lnd
+
+  !-----------------------------------------------------------------------
+
+  subroutine create_fv(this, fv, u10, ram1)
+    ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
+    ! fields based on inputs. Excluded inputs are given a default value
+    class(TestDustEmis), intent(inout) :: this
+    real(r8), intent(in), optional :: fv(:)
+    real(r8), intent(in), optional :: u10(:)
+    real(r8), intent(in), optional :: ram1(:)
+
+    real(r8), parameter :: fv_default = 0.2_r8
+    real(r8), parameter :: u10_default = 4._r8
+    real(r8), parameter :: ram1_default = 200._r8
+    ! ------------------------------------------------------------------------
+
+    if (present(fv)) then
+       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv(:)
+    else
+       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default
+    end if
+
+    if (present(u10)) then
+       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10(:)
+    else
+       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default
+    end if
+
+    if (present(ram1)) then
+       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1(:)
+    else
+       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default
+    end if
+
+  end subroutine create_fv
+
+  !-----------------------------------------------------------------------
+
   @Test
   subroutine check_dust_emis(this)
     class(TestDustEmis), intent(inout) :: this
 
+    call this%create_atm2lnd()
+    call this%create_fv()
     call DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                      this%soilstate_inst, this%canopystate_inst, this%waterstatebulk_inst, &
-                      this%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis)
+                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis)
     call DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst, this%dust_emis)
 
+  !-----------------------------------------------------------------------
+
   end subroutine check_dust_emis
 
 end module test_DustEmis
\ No newline at end of file
diff --git a/src/biogeophys/CanopyStateType.F90 b/src/biogeophys/CanopyStateType.F90
index 313f7a83f3..4bfc08fc80 100644
--- a/src/biogeophys/CanopyStateType.F90
+++ b/src/biogeophys/CanopyStateType.F90
@@ -72,6 +72,8 @@ module CanopyStateType
      procedure, public  :: UpdateAccVars
      procedure, public  :: Restart
 
+     procedure, public  :: SetNMLForTesting ! Set namelist for unit-testing
+
   end type CanopyState_type
 
   character(len=*), parameter, private :: sourcefile = &
@@ -442,6 +444,21 @@ subroutine ReadNML( this, NLFilename )
 
   end subroutine ReadNML
 
+ !-----------------------------------------------------------------------
+
+  subroutine SetNMLForTesting( this )
+     !
+     ! Set canopy parameter namelist control settings for unit-testing
+     !
+     class(canopystate_type)      :: this
+     ! LOCAL VARIABLES:
+     !-----------------------------------------------------------------------
+ 
+     
+     this%leaf_mr_vcm = 0.015_r8
+   
+   end subroutine SetNMLForTesting
+
   !-----------------------------------------------------------------------
   subroutine UpdateAccVars (this, bounds)
     !
diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90
index 7cea2a22f9..042415f545 100644
--- a/src/biogeophys/FrictionVelocityMod.F90
+++ b/src/biogeophys/FrictionVelocityMod.F90
@@ -89,6 +89,8 @@ module FrictionVelocityMod
      procedure, public :: FrictionVelocity       ! Calculate friction velocity
      procedure, public :: MoninObukIni           ! Initialization of the Monin-Obukhov length
 
+     procedure, public  :: InitForTesting        ! version of Init meant for unit testing
+
      ! Private procedures
      procedure, private :: InitAllocate
      procedure, private :: InitHistory
@@ -122,6 +124,22 @@ subroutine Init(this, bounds, NLFilename, params_ncid)
 
   end subroutine Init
 
+  !------------------------------------------------------------------------
+  subroutine InitForTesting(this, bounds)
+    ! Initialization for unit testing, hardcodes namelist and parameter file settings
+    class(frictionvel_type) :: this
+    type(bounds_type), intent(in) :: bounds
+
+    call this%InitAllocate(bounds)
+    call this%InitHistory(bounds)
+    call this%InitCold(bounds)
+    this%zetamaxstable = 0.5_r8
+    this%zsno = 0.00085_r8
+    this%zlnd = 0.000775_r8
+    this%zglc = 0.00230000005_r8
+
+  end subroutine InitForTesting
+
   !------------------------------------------------------------------------
   subroutine InitAllocate(this, bounds)
     !
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index b9d74c418a..a24e05b27c 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -296,11 +296,11 @@ subroutine clm_instInit(bounds)
     ! Initialization of public data types
 
     call temperature_inst%Init(bounds,           &
-         urbanparams_inst%em_roof(begl:endl),    &
-         urbanparams_inst%em_wall(begl:endl),    &
-         urbanparams_inst%em_improad(begl:endl), &
-         urbanparams_inst%em_perroad(begl:endl), &
-         IsSimpleBuildTemp(), IsProgBuildTemp() )
+         em_roof_lun=urbanparams_inst%em_roof(begl:endl),    &
+         em_wall_lun=urbanparams_inst%em_wall(begl:endl),    &
+         em_improad_lun=urbanparams_inst%em_improad(begl:endl), &
+         em_perroad_lun=urbanparams_inst%em_perroad(begl:endl), &
+         is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp() )
 
     call active_layer_inst%Init(bounds)
 

From 9bf2ad13acdca56437392b0e80e715320c3a7eb5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 18 May 2024 22:17:39 -0600
Subject: [PATCH 0280/1248] Put DustEmission and DustDryDep as methods inside
 of the dust_type

---
 src/biogeochem/DUSTMod.F90                    | 39 +++++++++----------
 .../test/DustEmis_test/test_DustEmis.pf       | 10 ++---
 2 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index ffa2bfe6f0..e0e4e469a1 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -37,11 +37,6 @@ module DUSTMod
   implicit none
   private
   !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  !
-  public DustEmission   ! Dust mobilization 
-  public DustDryDep     ! Turbulent dry deposition for dust
-  !
   ! !PUBLIC DATA:
   !
   real(r8) , allocatable :: ovr_src_snk_mss(:,:)
@@ -61,16 +56,18 @@ module DUSTMod
      real(r8), pointer, private :: vlc_trb_2_patch           (:)   ! turbulent deposition velocity 2(m/s)
      real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
      real(r8), pointer, private :: vlc_trb_4_patch           (:)   ! turbulent deposition velocity 4(m/s)
-     type(soil_erod_stream_type), private :: soil_erod_stream ! Zender soil erodibility stream data
+     type(soil_erod_stream_type), private :: soil_erod_stream      ! Zender soil erodibility stream data
      real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! [dimensionless] basin factor, or soil erodibility, time-constant
 
    contains
 
      procedure , public  :: Init
+     procedure , public  :: DustEmission   ! Dust mobilization 
+     procedure , public  :: DustDryDep     ! Turbulent dry deposition for dust
      procedure , private :: InitAllocate 
      procedure , private :: InitHistory  
      procedure , private :: InitCold     
-     procedure , private :: InitDustVars ! Initialize variables used in subroutine Dust
+     procedure , private :: InitDustVars   ! Initialize variables used in DustEmission method
 
   end type dust_type
   !------------------------------------------------------------------------
@@ -213,10 +210,10 @@ subroutine InitCold(this, bounds)
   end subroutine InitCold
 
   !------------------------------------------------------------------------
-  subroutine DustEmission (bounds, &
+  subroutine DustEmission (this, bounds, &
        num_nolakep, filter_nolakep, &
        atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, &
-       frictionvel_inst, dust_inst)
+       frictionvel_inst)
     !
     ! !DESCRIPTION: 
     ! Dust mobilization. This code simulates dust mobilization due to wind
@@ -230,6 +227,7 @@ subroutine DustEmission (bounds, &
     use subgridaveMod, only : p2g
     !
     ! !ARGUMENTS:
+    class (dust_type)                      :: this
     type(bounds_type)      , intent(in)    :: bounds                      
     integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
     integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
@@ -239,7 +237,6 @@ subroutine DustEmission (bounds, &
     type(waterstatebulk_type)  , intent(in)    :: waterstatebulk_inst
     type(waterdiagnosticbulk_type)  , intent(in)    :: waterdiagnosticbulk_inst
     type(frictionvel_type) , intent(in)    :: frictionvel_inst
-    type(dust_type)        , intent(inout) :: dust_inst
 
     !
     ! !LOCAL VARIABLES
@@ -291,9 +288,9 @@ subroutine DustEmission (bounds, &
          fv                  => frictionvel_inst%fv_patch            , & ! Input:  [real(r8) (:)   ]  friction velocity (m/s) (for dust model)          
          u10                 => frictionvel_inst%u10_patch           , & ! Input:  [real(r8) (:)   ]  10-m wind (m/s) (created for dust model)          
          
-         mbl_bsn_fct         => dust_inst%mbl_bsn_fct_col            , & ! Input:  [real(r8) (:)   ]  basin factor
-         flx_mss_vrt_dst     => dust_inst%flx_mss_vrt_dst_patch      , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
-         flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch    & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
+         mbl_bsn_fct         => this%mbl_bsn_fct_col                 , & ! Input:  [real(r8) (:)   ]  basin factor
+         flx_mss_vrt_dst     => this%flx_mss_vrt_dst_patch           , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
+         flx_mss_vrt_dst_tot => this%flx_mss_vrt_dst_tot_patch         & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -498,8 +495,8 @@ subroutine DustEmission (bounds, &
   end subroutine DustEmission
 
    !------------------------------------------------------------------------
-  subroutine DustDryDep (bounds, &
-       atm2lnd_inst, frictionvel_inst, dust_inst)
+  subroutine DustDryDep (this, bounds, &
+       atm2lnd_inst, frictionvel_inst)
     !
     ! !DESCRIPTION: 
     !
@@ -520,10 +517,10 @@ subroutine DustDryDep (bounds, &
     use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ
     !
     ! !ARGUMENTS:
+    class (dust_type)                      :: this
     type(bounds_type)      , intent(in)    :: bounds 
     type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
     type(frictionvel_type) , intent(in)    :: frictionvel_inst
-    type(dust_type)        , intent(inout) :: dust_inst
     !
     ! !LOCAL VARIABLES
     integer  :: p,c,g,m,n                             ! indices
@@ -550,11 +547,11 @@ subroutine DustDryDep (bounds, &
          ram1      =>    frictionvel_inst%ram1_patch           , & ! Input:  [real(r8)  (:)   ]  aerodynamical resistance (s/m)                    
          fv        =>    frictionvel_inst%fv_patch             , & ! Input:  [real(r8)  (:)   ]  friction velocity (m/s)                           
          
-         vlc_trb   =>    dust_inst%vlc_trb_patch               , & ! Output:  [real(r8) (:,:) ]  Turbulent deposn velocity (m/s)                 
-         vlc_trb_1 =>    dust_inst%vlc_trb_1_patch             , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 1                   
-         vlc_trb_2 =>    dust_inst%vlc_trb_2_patch             , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 2                   
-         vlc_trb_3 =>    dust_inst%vlc_trb_3_patch             , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 3                   
-         vlc_trb_4 =>    dust_inst%vlc_trb_4_patch               & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 4                   
+         vlc_trb   =>    this%vlc_trb_patch                   , & ! Output:  [real(r8) (:,:) ]  Turbulent deposn velocity (m/s)                 
+         vlc_trb_1 =>    this%vlc_trb_1_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 1                   
+         vlc_trb_2 =>    this%vlc_trb_2_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 2                   
+         vlc_trb_3 =>    this%vlc_trb_3_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 3                   
+         vlc_trb_4 =>    this%vlc_trb_4_patch                   & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 4                   
          )
 
       do p = bounds%begp,bounds%endp
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index b7ea76df9c..9be97453b0 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -239,13 +239,13 @@ contains
 
     call this%create_atm2lnd()
     call this%create_fv()
-    call DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
                       this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis)
-    call DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst, this%dust_emis)
-
-  !-----------------------------------------------------------------------
+                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
 
   end subroutine check_dust_emis
 
+  !-----------------------------------------------------------------------
+
 end module test_DustEmis
\ No newline at end of file

From 7072f7aa8e1e44a5af15b5c82c4634268b5dc50b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 20 May 2024 11:29:08 -0600
Subject: [PATCH 0281/1248] Resolve the mizuRoute issue

---
 Externals.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index a8a77a40f1..cb2622dedf 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -27,10 +27,10 @@ tag = mosart1_0_49
 required = True
 
 [mizuRoute]
-local_path = components/mizuRoute
+tag = cesm-coupling.n02_v2.1.2
 protocol = git
+local_path = components/mizuroute
 repo_url = https://github.com/ESCOMP/mizuRoute
-hash = 81c720c
 required = True
 
 [ccs_config]

From ff4d35f2607bb637e37baaca0109d4d189efe0fd Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 10:30:14 -0600
Subject: [PATCH 0282/1248] Remove set_glc2lnd_fields_mct (not tested, yet)

---
 src/main/glc2lndMod.F90 | 56 -----------------------------------------
 1 file changed, 56 deletions(-)

diff --git a/src/main/glc2lndMod.F90 b/src/main/glc2lndMod.F90
index ecd6818210..2d0dbb5791 100644
--- a/src/main/glc2lndMod.F90
+++ b/src/main/glc2lndMod.F90
@@ -78,7 +78,6 @@ module glc2lndMod
      ! - set_glc2lnd_fields
      ! - update_glc2lnd_fracs
      ! - update_glc2lnd_topo
-     procedure, public  :: set_glc2lnd_fields_mct   ! set coupling fields sent from glc to lnd
      procedure, public  :: set_glc2lnd_fields_nuopc ! set coupling fields sent from glc to lnd
      procedure, public  :: update_glc2lnd_fracs     ! update subgrid fractions based on input from GLC
      procedure, public  :: update_glc2lnd_topo      ! update topographic heights
@@ -242,61 +241,6 @@ subroutine Clean(this)
 
   end subroutine Clean
 
-  !-----------------------------------------------------------------------
-  subroutine set_glc2lnd_fields_mct(this, bounds, glc_present, x2l, &
-       index_x2l_Sg_ice_covered, index_x2l_Sg_topo, index_x2l_Flgg_hflx, &
-       index_x2l_Sg_icemask, index_x2l_Sg_icemask_coupled_fluxes)
-    !
-    ! !DESCRIPTION:
-    ! Set coupling fields sent from glc to lnd
-    !
-    ! If glc_present is true, then the given fields are all assumed to be valid; if
-    ! glc_present is false, then these fields are ignored.
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type), intent(inout) :: this
-    type(bounds_type)  , intent(in)    :: bounds
-    logical  , intent(in) :: glc_present                         ! true if running with a non-stub glc model
-    real(r8) , intent(in) :: x2l(:, bounds%begg: )               ! driver import state to land model [field, gridcell]
-    integer  , intent(in) :: index_x2l_Sg_ice_covered( 0: )      ! indices of ice-covered field in x2l, for each elevation class
-    integer  , intent(in) :: index_x2l_Sg_topo( 0: )             ! indices of topo field in x2l, for each elevation class
-    integer  , intent(in) :: index_x2l_Flgg_hflx( 0: )           ! indices of heat flux field in x2l, for each elevation class
-    integer  , intent(in) :: index_x2l_Sg_icemask                ! index of icemask field in x2l
-    integer  , intent(in) :: index_x2l_Sg_icemask_coupled_fluxes ! index of icemask_coupled_fluxes field in x2l
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g
-    integer :: ice_class
-
-    character(len=*), parameter :: subname = 'set_glc2lnd_fields_mct'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_FL((ubound(x2l, 2) == bounds%endg), sourcefile, __LINE__)
-    SHR_ASSERT_ALL_FL((ubound(index_x2l_Sg_ice_covered) == (/maxpatch_glc/)), sourcefile, __LINE__)
-    SHR_ASSERT_ALL_FL((ubound(index_x2l_Sg_topo) == (/maxpatch_glc/)), sourcefile, __LINE__)
-    SHR_ASSERT_ALL_FL((ubound(index_x2l_Flgg_hflx) == (/maxpatch_glc/)), sourcefile, __LINE__)
-
-    if (glc_present) then
-       do g = bounds%begg, bounds%endg
-          do ice_class = 0, maxpatch_glc
-             this%frac_grc(g,ice_class)  = x2l(index_x2l_Sg_ice_covered(ice_class),g)
-             this%topo_grc(g,ice_class)  = x2l(index_x2l_Sg_topo(ice_class),g)
-             this%hflx_grc(g,ice_class)  = x2l(index_x2l_Flgg_hflx(ice_class),g)
-          end do
-          this%icemask_grc(g)  = x2l(index_x2l_Sg_icemask,g)
-          this%icemask_coupled_fluxes_grc(g)  = x2l(index_x2l_Sg_icemask_coupled_fluxes,g)
-       end do
-
-       call this%set_glc2lnd_fields_wrapup(bounds)
-    else
-       if (glc_do_dynglacier) then
-          call endrun(' ERROR: With glc_present false (e.g., a stub glc model), glc_do_dynglacier must be false '// &
-               errMsg(sourcefile, __LINE__))
-       end if
-    end if
-
-  end subroutine set_glc2lnd_fields_mct
-
   !-----------------------------------------------------------------------
   subroutine set_glc2lnd_fields_nuopc(this, bounds, glc_present, &
        frac_grc, topo_grc, hflx_grc, icemask_grc, icemask_coupled_fluxes_grc)

From 4d62578a920eae09f482776576a30e9750e1e8e1 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 10:47:56 -0600
Subject: [PATCH 0283/1248] Remove /src/cpl/mct again; I was right the first
 time

---
 src/cpl/mct/ExcessIceStreamType.F90       | 144 -----
 src/cpl/mct/FireDataBaseType.F90          | 561 -------------------
 src/cpl/mct/SoilMoistureStreamMod.F90     | 418 --------------
 src/cpl/mct/UrbanTimeVarType.F90          | 314 -----------
 src/cpl/mct/ch4FInundatedStreamType.F90   | 389 -------------
 src/cpl/mct/clm_cpl_indices.F90           | 330 -----------
 src/cpl/mct/laiStreamMod.F90              | 241 ---------
 src/cpl/mct/lnd_comp_mct.F90              | 632 ----------------------
 src/cpl/mct/lnd_import_export.F90         | 354 ------------
 src/cpl/mct/lnd_set_decomp_and_domain.F90 | 352 ------------
 src/cpl/mct/ndepStreamMod.F90             | 376 -------------
 11 files changed, 4111 deletions(-)
 delete mode 100644 src/cpl/mct/ExcessIceStreamType.F90
 delete mode 100644 src/cpl/mct/FireDataBaseType.F90
 delete mode 100644 src/cpl/mct/SoilMoistureStreamMod.F90
 delete mode 100644 src/cpl/mct/UrbanTimeVarType.F90
 delete mode 100644 src/cpl/mct/ch4FInundatedStreamType.F90
 delete mode 100644 src/cpl/mct/clm_cpl_indices.F90
 delete mode 100644 src/cpl/mct/laiStreamMod.F90
 delete mode 100644 src/cpl/mct/lnd_comp_mct.F90
 delete mode 100644 src/cpl/mct/lnd_import_export.F90
 delete mode 100644 src/cpl/mct/lnd_set_decomp_and_domain.F90
 delete mode 100644 src/cpl/mct/ndepStreamMod.F90

diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90
deleted file mode 100644
index 5c5394233c..0000000000
--- a/src/cpl/mct/ExcessIceStreamType.F90
+++ /dev/null
@@ -1,144 +0,0 @@
-module ExcessIceStreamType
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Stub for ExcessIceStreams for the MCT driver. So that MCT can be used
-  ! without excess ice streams.
-  !
-  ! !USES
-  use shr_kind_mod     , only : r8 => shr_kind_r8, CL => shr_kind_CL
-  use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use spmdMod          , only : mpicom, masterproc
-  use clm_varctl       , only : iulog
-  use abortutils       , only : endrun
-  use decompMod        , only : bounds_type
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-
-  public  :: UseExcessIceStreams      ! If streams will be used
-
-  type, public :: excessicestream_type
-  contains
-
-      ! !PUBLIC MEMBER FUNCTIONS:
-      procedure, public  :: Init            ! Initialize and read data in
-      procedure, public  :: CalcExcessIce   ! Calculate excess ice ammount
-
-      ! !PRIVATE MEMBER FUNCTIONS:
-      procedure, private :: ReadNML     ! Read in namelist
-
-  end type excessicestream_type
-  ! ! PRIVATE DATA:
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-!==============================================================================
-contains
-!==============================================================================
-
-  subroutine Init(this, bounds, NLFilename)
-    !
-    !
-    ! arguments
-    implicit none
-    class(excessicestream_type) :: this
-    type(bounds_type), intent(in)   :: bounds
-    character(len=*),  intent(in)   :: NLFilename   ! Namelist filename
-
-    !
-    ! local variables
-
-    call this%ReadNML( bounds, NLFileName )
-  end subroutine Init
-
-  subroutine CalcExcessIce(this,bounds,exice_bulk_init)
-  
-  ! only transfers grid values to columns
-   implicit none
-   class(excessicestream_type)        :: this
-   type(bounds_type),  intent(in)     :: bounds
-   real(r8)         ,  intent(inout)  :: exice_bulk_init(bounds%begc:bounds%endc) 
-   !
-   ! !LOCAL VARIABLES:
-   
-  end subroutine CalcExcessIce
-
-  logical function UseExcessIceStreams()
-  !
-  ! !DESCRIPTION:
-  ! Return true if
-  !
-  ! !USES:
-  !
-  ! !ARGUMENTS:
-  implicit none
-  !
-  ! !LOCAL VARIABLES:
-  UseExcessIceStreams = .false.
-end function UseExcessIceStreams
-
-subroutine ReadNML(this, bounds, NLFilename)
-  !
-  ! Read the namelist data stream information.
-  !
-  ! Uses:
-  use shr_nl_mod       , only : shr_nl_find_group_name
-  use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use shr_mpi_mod      , only : shr_mpi_bcast
-  !
-  ! arguments
-  implicit none
-  class(excessicestream_type)   :: this
-  type(bounds_type), intent(in) :: bounds
-  character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-  !
-  ! local variables
-  integer            :: nu_nml    ! unit for namelist file
-  integer            :: nml_error ! namelist i/o error flag
-  logical            :: use_excess_ice_streams = .false.         ! logical to turn on use of excess ice streams
-  character(len=CL)  :: stream_fldFileName_exice = ' '
-  character(len=CL)  :: stream_mapalgo_exice = 'none'
-  character(len=*), parameter :: namelist_name = 'exice_streams'    ! MUST agree with name in namelist and read
-  character(len=*), parameter :: subName = "('exice_streams::ReadNML')"
-  !-----------------------------------------------------------------------
-
-  namelist /exice_streams/ &               ! MUST agree with namelist_name above
-       stream_mapalgo_exice,  stream_fldFileName_exice, use_excess_ice_streams
-  !-----------------------------------------------------------------------
-  ! Default values for namelist
-
-  ! Read excess ice namelist
-  if (masterproc) then
-     open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-     call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error)
-     if (nml_error == 0) then
-        read(nu_nml, nml=exice_streams,iostat=nml_error)   ! MUST agree with namelist_name above
-        if (nml_error /= 0) then
-           call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-        end if
-     else
-        call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-     end if
-     close(nu_nml)
-  endif
-
-  call shr_mpi_bcast(use_excess_ice_streams   , mpicom)
-
-  if (masterproc) then
-     if ( use_excess_ice_streams ) then
-        call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__))
-     end if
-     if ( trim(stream_fldFileName_exice) /= ''  ) then
-        call endrun(msg=' ERROR stream_fldFileName_exice can NOT be set for the MCT driver'//errMsg(sourcefile, __LINE__))
-     end if
-     if ( trim(stream_mapalgo_exice) /= 'none'  ) then
-        call endrun(msg=' ERROR stream_mapalgo_exice can only be none for the MCT driver'//errMsg(sourcefile, __LINE__))
-     end if
-  endif
-
-end subroutine ReadNML
-
-end module ExcessIceStreamType
diff --git a/src/cpl/mct/FireDataBaseType.F90 b/src/cpl/mct/FireDataBaseType.F90
deleted file mode 100644
index 0ee635b2fa..0000000000
--- a/src/cpl/mct/FireDataBaseType.F90
+++ /dev/null
@@ -1,561 +0,0 @@
-module FireDataBaseType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! module for handling of fire data
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8, CL => shr_kind_CL
-  use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create, shr_strdata_print
-  use shr_strdata_mod , only : shr_strdata_advance
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use clm_varctl      , only : iulog, inst_name
-  use spmdMod         , only : masterproc, mpicom, comp_id
-  use fileutils       , only : getavu, relavu
-  use domainMod       , only : ldomain
-  use abortutils      , only : endrun
-  use decompMod       , only : bounds_type
-  use FireMethodType  , only : fire_method_type
-  use lnd_set_decomp_and_domain, only : gsmap_global
-  use mct_mod
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC TYPES:
-  public :: fire_base_type
-
-  !
-  type, abstract, extends(fire_method_type) :: fire_base_type
-    private
-      ! !PRIVATE MEMBER DATA:
-
-      real(r8), public, pointer :: forc_lnfm(:)    ! Lightning frequency
-      real(r8), public, pointer :: forc_hdm(:)     ! Human population density
-      
-      real(r8), public, pointer :: gdp_lf_col(:)   ! col global real gdp data (k US$/capita)
-      real(r8), public, pointer :: peatf_lf_col(:) ! col global peatland fraction data (0-1)
-      integer , public, pointer :: abm_lf_col(:)   ! col global peak month of crop fire emissions
-
-      type(shr_strdata_type) :: sdat_hdm    ! Human population density input data stream
-      type(shr_strdata_type) :: sdat_lnfm   ! Lightning input data stream
-
-    contains
-      !
-      ! !PUBLIC MEMBER FUNCTIONS:
-      procedure, public :: FireInit => BaseFireInit     ! Initialization of Fire
-      procedure, public :: BaseFireInit                 ! Initialization of Fire
-      procedure(FireReadNML_interface), public, deferred :: FireReadNML       ! Read in namelist for Fire
-      procedure, public :: FireInterp        ! Interpolate fire data
-      procedure(need_lightning_and_popdens_interface), public, deferred :: &
-           need_lightning_and_popdens ! Returns true if need lightning & popdens
-      !
-      ! !PRIVATE MEMBER FUNCTIONS:
-      procedure, private :: hdm_init     ! position datasets for dynamic human population density
-      procedure, private :: hdm_interp   ! interpolates between two years of human pop. density file data
-      procedure, private :: lnfm_init    ! position datasets for Lightning
-      procedure, private :: lnfm_interp  ! interpolates between two years of Lightning file data
-      procedure, private :: surfdataread ! read fire related data from surface data set
-  end type fire_base_type
-  !-----------------------------------------------------------------------
-
-  abstract interface
-     !-----------------------------------------------------------------------
-     function need_lightning_and_popdens_interface(this) result(need_lightning_and_popdens)
-       !
-       ! !DESCRIPTION:
-       ! Returns true if need lightning and popdens, false otherwise
-       !
-       ! USES
-       import :: fire_base_type
-       !
-       ! !ARGUMENTS:
-       class(fire_base_type), intent(in) :: this
-       logical :: need_lightning_and_popdens  ! function result
-       !-----------------------------------------------------------------------
-     end function need_lightning_and_popdens_interface
-  end interface
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine FireReadNML_interface( this, NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Read the namelist for Fire
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(fire_base_type) :: this
-    character(len=*), intent(in) :: NLFilename ! Namelist filename
-  end subroutine FireReadNML_interface
-
-  !-----------------------------------------------------------------------
-  subroutine BaseFireInit( this, bounds, NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Initialize CN Fire module
-    ! !USES:
-    use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(fire_base_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    character(len=*),  intent(in) :: NLFilename
-    !-----------------------------------------------------------------------
-
-    if ( this%need_lightning_and_popdens() ) then
-       ! Allocate lightning forcing data
-       allocate( this%forc_lnfm(bounds%begg:bounds%endg) )
-       this%forc_lnfm(bounds%begg:) = nan
-       ! Allocate pop dens forcing data
-       allocate( this%forc_hdm(bounds%begg:bounds%endg) )
-       this%forc_hdm(bounds%begg:) = nan
-       
-       ! Allocate real gdp data
-       allocate(this%gdp_lf_col(bounds%begc:bounds%endc))
-       ! Allocate peatland fraction data
-       allocate(this%peatf_lf_col(bounds%begc:bounds%endc))
-       ! Allocates peak month of crop fire emissions
-       allocate(this%abm_lf_col(bounds%begc:bounds%endc))
-   
-
-       call this%hdm_init(bounds, NLFilename)
-       call this%hdm_interp(bounds)
-       call this%lnfm_init(bounds, NLFilename)
-       call this%lnfm_interp(bounds)
-       call this%surfdataread(bounds)
-    end if
-
-  end subroutine BaseFireInit
-
-  !-----------------------------------------------------------------------
-  subroutine FireInterp(this,bounds)
-    !
-    ! !DESCRIPTION:
-    ! Interpolate CN Fire datasets
-    !
-    ! !ARGUMENTS:
-    class(fire_base_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !-----------------------------------------------------------------------
-
-    if ( this%need_lightning_and_popdens() ) then
-       call this%hdm_interp(bounds)
-       call this%lnfm_interp(bounds)
-    end if
-
-  end subroutine FireInterp
-
-  !-----------------------------------------------------------------------
-  subroutine hdm_init( this, bounds, NLFilename )
-   !
-   ! !DESCRIPTION:
-   ! Initialize data stream information for population density.
-   !
-   ! !USES:
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use clm_nlUtilsMod   , only : find_nlgroup_name
-   use ndepStreamMod    , only : clm_domain_mct
-   use histFileMod      , only : hist_addfld1d
-   !
-   ! !ARGUMENTS:
-   implicit none
-   class(fire_base_type)         :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! !LOCAL VARIABLES:
-   integer            :: stream_year_first_popdens   ! first year in pop. dens. stream to use
-   integer            :: stream_year_last_popdens    ! last year in pop. dens. stream to use
-   integer            :: model_year_align_popdens    ! align stream_year_first_hdm with
-   integer            :: nu_nml                      ! unit for namelist file
-   integer            :: nml_error                   ! namelist i/o error flag
-   type(mct_ggrid)    :: dom_clm                     ! domain information
-   character(len=CL)  :: stream_fldFileName_popdens  ! population density streams filename
-   character(len=CL)  :: popdensmapalgo = 'bilinear' ! mapping alogrithm for population density
-   character(len=CL)  :: popdens_tintalgo = 'nearest'! time interpolation alogrithm for population density
-   character(len=CL)  :: stream_meshfile_popdens     ! not used
-   character(*), parameter :: subName = "('hdmdyn_init')"
-   character(*), parameter :: F00 = "('(hdmdyn_init) ',4a)"
-   !-----------------------------------------------------------------------
-
-   namelist /popd_streams/          &
-        stream_year_first_popdens,  &
-        stream_year_last_popdens,   &
-        model_year_align_popdens,   &
-        popdensmapalgo,             &
-        stream_fldFileName_popdens, &
-        stream_meshfile_popdens   , &
-        popdens_tintalgo
-
-   ! Default values for namelist
-   stream_year_first_popdens  = 1       ! first year in stream to use
-   stream_year_last_popdens   = 1       ! last  year in stream to use
-   model_year_align_popdens   = 1       ! align stream_year_first_popdens with this model year
-   stream_fldFileName_popdens = ' '
-
-   ! Read popd_streams namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call find_nlgroup_name(nu_nml, 'popd_streams', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=popd_streams,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg='ERROR reading popd_streams namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_year_first_popdens, mpicom)
-   call shr_mpi_bcast(stream_year_last_popdens, mpicom)
-   call shr_mpi_bcast(model_year_align_popdens, mpicom)
-   call shr_mpi_bcast(stream_fldFileName_popdens, mpicom)
-   call shr_mpi_bcast(popdens_tintalgo, mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'popdens_streams settings:'
-      write(iulog,*) '  stream_year_first_popdens  = ',stream_year_first_popdens
-      write(iulog,*) '  stream_year_last_popdens   = ',stream_year_last_popdens
-      write(iulog,*) '  model_year_align_popdens   = ',model_year_align_popdens
-      write(iulog,*) '  stream_fldFileName_popdens = ',stream_fldFileName_popdens
-      write(iulog,*) '  popdens_tintalgo           = ',popdens_tintalgo
-      write(iulog,*) ' '
-   endif
-
-   call clm_domain_mct (bounds, dom_clm)
-
-   call shr_strdata_create(this%sdat_hdm,name="clmhdm", &
-        pio_subsystem=pio_subsystem,                    &
-        pio_iotype=shr_pio_getiotype(inst_name),        &
-        mpicom=mpicom, compid=comp_id,                  &
-        gsmap=gsmap_global, ggrid=dom_clm,              &
-        nxg=ldomain%ni, nyg=ldomain%nj,                 &
-        yearFirst=stream_year_first_popdens,            &
-        yearLast=stream_year_last_popdens,              &
-        yearAlign=model_year_align_popdens,             &
-        offset=0,                                       &
-        domFilePath='',                                 &
-        domFileName=trim(stream_fldFileName_popdens),   &
-        domTvarName='time',                             &
-        domXvarName='lon' ,                             &
-        domYvarName='lat' ,                             &
-        domAreaName='area',                             &
-        domMaskName='mask',                             &
-        filePath='',                                    &
-        filename=(/trim(stream_fldFileName_popdens)/) , &
-        fldListFile='hdm',                              &
-        fldListModel='hdm',                             &
-        fillalgo='none',                                &
-        mapalgo=popdensmapalgo,                         &
-        calendar=get_calendar(),                        &
-        tintalgo=popdens_tintalgo,                      &
-        taxmode='extend'                           )
-
-   if (masterproc) then
-      call shr_strdata_print(this%sdat_hdm,'population density data')
-   endif
-
-   ! Add history fields
-   call hist_addfld1d (fname='HDM', units='counts/km^2',      &
-         avgflag='A', long_name='human population density',   &
-         ptr_lnd=this%forc_hdm, default='inactive')
-
-  end subroutine hdm_init
-
-  !-----------------------------------------------------------------------
-  subroutine hdm_interp( this, bounds)
-  !
-  ! !DESCRIPTION:
-  ! Interpolate data stream information for population density.
-  !
-  ! !USES:
-  use clm_time_manager, only : get_curr_date
-  !
-  ! !ARGUMENTS:
-  class(fire_base_type)       :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  integer :: g, ig
-  integer :: year    ! year (0, ...) for nstep+1
-  integer :: mon     ! month (1, ..., 12) for nstep+1
-  integer :: day     ! day of month (1, ..., 31) for nstep+1
-  integer :: sec     ! seconds into current date for nstep+1
-  integer :: mcdate  ! Current model date (yyyymmdd)
-  !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(this%sdat_hdm, mcdate, sec, mpicom, 'hdmdyn')
-
-   ig = 0
-   do g = bounds%begg,bounds%endg
-      ig = ig+1
-      this%forc_hdm(g) = this%sdat_hdm%avs(1)%rAttr(1,ig)
-   end do
-
-  end subroutine hdm_interp
-
-  !-----------------------------------------------------------------------
-  subroutine lnfm_init( this, bounds, NLFilename )
-  !
-  ! !DESCRIPTION:
-  !
-  ! Initialize data stream information for Lightning.
-  !
-  ! !USES:
-  use clm_time_manager , only : get_calendar
-  use ncdio_pio        , only : pio_subsystem
-  use shr_pio_mod      , only : shr_pio_getiotype
-  use clm_nlUtilsMod   , only : find_nlgroup_name
-  use ndepStreamMod    , only : clm_domain_mct
-  use histFileMod      , only : hist_addfld1d
-  !
-  ! !ARGUMENTS:
-  implicit none
-  class(fire_base_type)       :: this
-  type(bounds_type), intent(in) :: bounds
-  character(len=*),  intent(in) :: NLFilename
-  !
-  ! !LOCAL VARIABLES:
-  integer            :: stream_year_first_lightng  ! first year in Lightning stream to use
-  integer            :: stream_year_last_lightng   ! last year in Lightning stream to use
-  integer            :: model_year_align_lightng   ! align stream_year_first_lnfm with
-  integer            :: nu_nml                     ! unit for namelist file
-  integer            :: nml_error                  ! namelist i/o error flag
-  type(mct_ggrid)    :: dom_clm                    ! domain information
-  character(len=CL)  :: stream_fldFileName_lightng ! lightning stream filename to read
-  character(len=CL)  :: lightng_tintalgo = 'linear'! time interpolation alogrithm
-  character(len=CL)  :: lightngmapalgo = 'bilinear'! Mapping alogrithm
-  character(*), parameter :: subName = "('lnfmdyn_init')"
-  character(*), parameter :: F00 = "('(lnfmdyn_init) ',4a)"
-  !-----------------------------------------------------------------------
-
-   namelist /light_streams/         &
-        stream_year_first_lightng,  &
-        stream_year_last_lightng,   &
-        model_year_align_lightng,   &
-        lightngmapalgo,             &
-        stream_fldFileName_lightng, &
-        lightng_tintalgo
-
-   ! Default values for namelist
-    stream_year_first_lightng  = 1      ! first year in stream to use
-    stream_year_last_lightng   = 1      ! last  year in stream to use
-    model_year_align_lightng   = 1      ! align stream_year_first_lnfm with this model year
-    stream_fldFileName_lightng = ' '
-
-   ! Read light_streams namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call find_nlgroup_name(nu_nml, 'light_streams', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=light_streams,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg='ERROR reading light_streams namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_year_first_lightng, mpicom)
-   call shr_mpi_bcast(stream_year_last_lightng, mpicom)
-   call shr_mpi_bcast(model_year_align_lightng, mpicom)
-   call shr_mpi_bcast(stream_fldFileName_lightng, mpicom)
-   call shr_mpi_bcast(lightng_tintalgo, mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'light_stream settings:'
-      write(iulog,*) '  stream_year_first_lightng  = ',stream_year_first_lightng
-      write(iulog,*) '  stream_year_last_lightng   = ',stream_year_last_lightng
-      write(iulog,*) '  model_year_align_lightng   = ',model_year_align_lightng
-      write(iulog,*) '  stream_fldFileName_lightng = ',stream_fldFileName_lightng
-      write(iulog,*) '  lightng_tintalgo           = ',lightng_tintalgo
-      write(iulog,*) ' '
-   endif
-
-   call clm_domain_mct (bounds, dom_clm)
-
-   call shr_strdata_create(this%sdat_lnfm,name="clmlnfm", &
-        pio_subsystem=pio_subsystem,                      &
-        pio_iotype=shr_pio_getiotype(inst_name),          &
-        mpicom=mpicom, compid=comp_id,                    &
-        gsmap=gsmap_global, ggrid=dom_clm,                &
-        nxg=ldomain%ni, nyg=ldomain%nj,                   &
-        yearFirst=stream_year_first_lightng,              &
-        yearLast=stream_year_last_lightng,                &
-        yearAlign=model_year_align_lightng,               &
-        offset=0,                                         &
-        domFilePath='',                                   &
-        domFileName=trim(stream_fldFileName_lightng),     &
-        domTvarName='time',                               &
-        domXvarName='lon' ,                               &
-        domYvarName='lat' ,                               &
-        domAreaName='area',                               &
-        domMaskName='mask',                               &
-        filePath='',                                      &
-        filename=(/trim(stream_fldFileName_lightng)/),    &
-        fldListFile='lnfm',                               &
-        fldListModel='lnfm',                              &
-        fillalgo='none',                                  &
-        tintalgo=lightng_tintalgo,                        &
-        mapalgo=lightngmapalgo,                           &
-        calendar=get_calendar(),                          &
-        taxmode='cycle'                            )
-
-   if (masterproc) then
-      call shr_strdata_print(this%sdat_lnfm,'Lightning data')
-   endif
-
-   ! Add history fields
-   call hist_addfld1d (fname='LNFM', units='counts/km^2/hr',  &
-         avgflag='A', long_name='Lightning frequency',        &
-         ptr_lnd=this%forc_lnfm, default='inactive')
-
-  end subroutine lnfm_init
-
-  !-----------------------------------------------------------------------
-  subroutine lnfm_interp(this, bounds )
-  !
-  ! !DESCRIPTION:
-  ! Interpolate data stream information for Lightning.
-  !
-  ! !USES:
-  use clm_time_manager, only : get_curr_date
-  !
-  ! !ARGUMENTS:
-  class(fire_base_type)       :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  integer :: g, ig
-  integer :: year    ! year (0, ...) for nstep+1
-  integer :: mon     ! month (1, ..., 12) for nstep+1
-  integer :: day     ! day of month (1, ..., 31) for nstep+1
-  integer :: sec     ! seconds into current date for nstep+1
-  integer :: mcdate  ! Current model date (yyyymmdd)
-  !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(this%sdat_lnfm, mcdate, sec, mpicom, 'lnfmdyn')
-
-   ig = 0
-   do g = bounds%begg,bounds%endg
-      ig = ig+1
-      this%forc_lnfm(g) = this%sdat_lnfm%avs(1)%rAttr(1,ig)
-   end do
-
-  end subroutine lnfm_interp
-
-  !-----------------------------------------------------------------------
-  subroutine surfdataread(this, bounds)
-  !
-  ! !DESCRIPTION:
-  ! Read surface data set to populate relevant fire-related variables
-  !
-  ! !USES:
-  use spmdMod    , only : masterproc
-  use clm_varctl , only : nsrest, nsrStartup, fsurdat
-  use clm_varcon , only : grlnd
-  use ColumnType , only : col
-  use fileutils  , only : getfil
-  use ncdio_pio
-  !
-  ! !ARGUMENTS:
-  class(fire_base_type) :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  integer               :: g,c       ! indices
-  type(file_desc_t)     :: ncid      ! netcdf id
-  logical               :: readvar   ! true => variable is on initial dataset
-  character(len=256)    :: locfn     ! local filename
-  real(r8), pointer     :: gdp(:)    ! global gdp data (needs to be a pointer for use in ncdio)
-  real(r8), pointer     :: peatf(:)  ! global peatf data (needs to be a pointer for use in ncdio)
-  integer,  pointer     :: abm(:)    ! global abm data (needs to be a pointer for use in ncdio)
-  !-----------------------------------------------------------------------
-
-   ! --------------------------------------------------------------------
-   ! Open surface dataset
-   ! --------------------------------------------------------------------
-
-   call getfil (fsurdat, locfn, 0)
-   call ncd_pio_openfile (ncid, locfn, 0)
-
-   ! --------------------------------------------------------------------
-   ! Read in GDP data
-   ! --------------------------------------------------------------------
-
-   allocate(gdp(bounds%begg:bounds%endg))
-   call ncd_io(ncid=ncid, varname='gdp', flag='read', data=gdp, dim1name=grlnd, readvar=readvar)
-   if (.not. readvar) then
-      call endrun(msg=' ERROR: gdp NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-   end if
-   do c = bounds%begc, bounds%endc
-      g = col%gridcell(c)
-      this%gdp_lf_col(c) = gdp(g)
-   end do
-   deallocate(gdp)
-
-   ! --------------------------------------------------------------------
-   ! Read in peatf data
-   ! --------------------------------------------------------------------
-
-   allocate(peatf(bounds%begg:bounds%endg))
-   call ncd_io(ncid=ncid, varname='peatf', flag='read', data=peatf, dim1name=grlnd, readvar=readvar)
-   if (.not. readvar) then
-      call endrun(msg=' ERROR: peatf NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-   end if
-   do c = bounds%begc, bounds%endc
-      g = col%gridcell(c)
-      this%peatf_lf_col(c) = peatf(g)
-   end do
-   deallocate(peatf)
-
-   ! --------------------------------------------------------------------
-   ! Read in ABM data
-   ! --------------------------------------------------------------------
-
-   allocate(abm(bounds%begg:bounds%endg))
-   call ncd_io(ncid=ncid, varname='abm', flag='read', data=abm, dim1name=grlnd, readvar=readvar)
-   if (.not. readvar) then
-      call endrun(msg=' ERROR: abm NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-   end if
-   do c = bounds%begc, bounds%endc
-      g = col%gridcell(c)
-      this%abm_lf_col(c) = abm(g)
-   end do
-   deallocate(abm)
-
-   ! Close file
-
-   call ncd_pio_closefile(ncid)
-
-   if (masterproc) then
-      write(iulog,*) 'Successfully read fmax, soil color, sand and clay boundary data'
-      write(iulog,*)
-   endif
-   
-  end subroutine surfdataread
-  
-  
-end module FireDataBaseType
diff --git a/src/cpl/mct/SoilMoistureStreamMod.F90 b/src/cpl/mct/SoilMoistureStreamMod.F90
deleted file mode 100644
index 8b366d6c8e..0000000000
--- a/src/cpl/mct/SoilMoistureStreamMod.F90
+++ /dev/null
@@ -1,418 +0,0 @@
-module SoilMoistureStreamMod
-
-  ! **********************************************************************
-  ! --------------------------- IMPORTANT NOTE ---------------------------
-  !
-  ! In cases using the NUOPC driver/mediator, we use a different version of this module,
-  ! based on CDEPS, which resides in src/cpl/nuopc/. Changes to the science here should
-  ! also be made in the similar file in src/cpl/nuopc. Once we start using CDEPS by
-  ! default, we can remove this version and move the CDEPS-based version into its place.
-  ! **********************************************************************
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Read in soil moisture from data stream
-  !
-  ! !USES:
-  use shr_strdata_mod           , only : shr_strdata_type, shr_strdata_create
-  use shr_strdata_mod           , only : shr_strdata_print, shr_strdata_advance
-  use shr_kind_mod              , only : r8 => shr_kind_r8
-  use shr_kind_mod              , only : CL => shr_kind_CL, CXX => shr_kind_CXX
-  use shr_log_mod               , only : errMsg => shr_log_errMsg
-  use decompMod                 , only : bounds_type, subgrid_level_column
-  use abortutils                , only : endrun
-  use clm_varctl                , only : iulog, use_soil_moisture_streams, inst_name
-  use clm_varcon                , only : grlnd
-  use controlMod                , only : NLFilename
-  use domainMod                 , only : ldomain
-  use LandunitType              , only : lun
-  use ColumnType                , only : col
-  use SoilStateType             , only : soilstate_type
-  use WaterStateBulkType        , only : waterstatebulk_type
-  use perf_mod                  , only : t_startf, t_stopf
-  use spmdMod                   , only : masterproc, mpicom, comp_id
-  use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo
-  use mct_mod
-  use ncdio_pio
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: PrescribedSoilMoistureInit    ! position datasets for soil moisture
-  public :: PrescribedSoilMoistureAdvance ! Advance the soil moisture stream (outside of Open-MP loops)
-  public :: PrescribedSoilMoistureInterp  ! interpolates between two periods of soil moisture data
-
-  ! !PRIVATE MEMBER DATA:
-  type(shr_strdata_type) :: sdat_soilm    ! soil moisture input data stream
-  integer :: ism                          ! Soil moisture steram index
-  integer, allocatable :: g_to_ig(:)      ! Array matching gridcell index to data index
-  logical :: soilm_ignore_data_if_missing ! If should ignore overridding a point with soil moisture data
-                                          ! from the streams file, if the streams file shows that point
-                                          ! as missing (namelist item)
-  !
-  ! !PRIVATE TYPES:
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  !
-  ! soil_moisture_init
-  !
-  !-----------------------------------------------------------------------
-  subroutine PrescribedSoilMoistureInit(bounds)
-    !
-    ! Initialize data stream information for soil moisture.
-    !
-    !
-    ! !USES:
-    use clm_time_manager , only : get_calendar
-    use ncdio_pio        , only : pio_subsystem
-    use shr_pio_mod      , only : shr_pio_getiotype
-    use clm_nlUtilsMod   , only : find_nlgroup_name
-    use ndepStreamMod    , only : clm_domain_mct
-    use shr_stream_mod   , only : shr_stream_file_null
-    use shr_string_mod   , only : shr_string_listCreateField
-    use clm_varpar       , only : nlevsoi
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds          ! bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: i                          ! index
-    integer            :: stream_year_first_soilm    ! first year in Ustar stream to use
-    integer            :: stream_year_last_soilm     ! last year in Ustar stream to use
-    integer            :: model_year_align_soilm     ! align stream_year_first_soilm with
-    integer            :: nu_nml                     ! unit for namelist file
-    integer            :: nml_error                  ! namelist i/o error flag
-    integer            :: soilm_offset               ! Offset in time for dataset (sec)
-    type(mct_ggrid)    :: dom_clm                    ! domain information
-    character(len=CL)  :: stream_fldfilename_soilm   ! ustar stream filename to read
-    character(len=CL)  :: soilm_tintalgo = 'linear'  ! Time interpolation alogrithm
-
-    character(*), parameter    :: subName = "('PrescribedSoilMoistureInit')"
-    character(*), parameter    :: F00 = "('(PrescribedSoilMoistureInit) ',4a)"
-    character(*), parameter    :: soilmString = "H2OSOI"  ! base string for field string
-    character(CXX)             :: fldList            ! field string
-    !-----------------------------------------------------------------------
-    !
-    ! deal with namelist variables here in init
-    !
-    namelist /soil_moisture_streams/   &
-         stream_year_first_soilm,      &
-         stream_year_last_soilm,       &
-         model_year_align_soilm,       &
-         soilm_tintalgo,               &
-         soilm_offset,                 &
-         soilm_ignore_data_if_missing, &
-         stream_fldfilename_soilm
-
-    ! Default values for namelist
-    stream_year_first_soilm      = 1      ! first year in stream to use
-    stream_year_last_soilm       = 1      ! last  year in stream to use
-    model_year_align_soilm       = 1      ! align stream_year_first_soilm with this model year
-    stream_fldfilename_soilm     = shr_stream_file_null
-    soilm_offset                 = 0
-    soilm_ignore_data_if_missing = .false.
-
-    ! Read soilm_streams namelist
-    if (masterproc) then
-       open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-       call find_nlgroup_name(nu_nml, 'soil_moisture_streams', status=nml_error)
-       if (nml_error == 0) then
-          read(nu_nml, nml=soil_moisture_streams,iostat=nml_error)
-          if (nml_error /= 0) then
-             call endrun(subname // ':: ERROR reading soil_moisture_streams namelist')
-          end if
-       else
-          call endrun(subname // ':: ERROR finding soilm_streams namelist')
-       end if
-       close(nu_nml)
-    endif
-
-    call shr_mpi_bcast(stream_year_first_soilm, mpicom)
-    call shr_mpi_bcast(stream_year_last_soilm, mpicom)
-    call shr_mpi_bcast(model_year_align_soilm, mpicom)
-    call shr_mpi_bcast(stream_fldfilename_soilm, mpicom)
-    call shr_mpi_bcast(soilm_tintalgo, mpicom)
-    call shr_mpi_bcast(soilm_offset, mpicom)
-    call shr_mpi_bcast(soilm_ignore_data_if_missing, mpicom)
-
-    if (masterproc) then
-
-       write(iulog,*) ' '
-       write(iulog,*) 'soil_moisture_stream settings:'
-       write(iulog,*) '  stream_year_first_soilm  = ',stream_year_first_soilm
-       write(iulog,*) '  stream_year_last_soilm   = ',stream_year_last_soilm
-       write(iulog,*) '  model_year_align_soilm   = ',model_year_align_soilm
-       write(iulog,*) '  stream_fldfilename_soilm = ',trim(stream_fldfilename_soilm)
-       write(iulog,*) '  soilm_tintalgo = ',trim(soilm_tintalgo)
-       write(iulog,*) '  soilm_offset = ',soilm_offset
-       if ( soilm_ignore_data_if_missing )then
-          write(iulog,*) '  Do NOT override a point with streams data if the streams data is missing'
-       else
-          write(iulog,*) '  Abort, if you find a model point where the input streams data is set to missing value'
-       end if
-
-    endif
-
-    call clm_domain_mct (bounds, dom_clm, nlevels=nlevsoi)
-
-    ! create the field list for these fields...use in shr_strdata_create
-    fldList = trim(soilmString)
-    if (masterproc) write(iulog,*) 'fieldlist: ', trim(fldList)
-
-    call shr_strdata_create(sdat_soilm,name="soil_moisture",    &
-         pio_subsystem=pio_subsystem,                  &
-         pio_iotype=shr_pio_getiotype(inst_name),          &
-         mpicom=mpicom, compid=comp_id,                &
-         gsmap=gsMap_lnd2Dsoi_gdc2glo, ggrid=dom_clm,  &
-         nxg=ldomain%ni, nyg=ldomain%nj,               &
-         nzg=nlevsoi,                                  &
-         yearFirst=stream_year_first_soilm,            &
-         yearLast=stream_year_last_soilm,              &
-         yearAlign=model_year_align_soilm,             &
-         offset=soilm_offset,                          &
-         domFilePath='',                               &
-         domFileName=trim(stream_fldFileName_soilm),   &
-         domTvarName='time',                           &
-         domXvarName='lon' ,                           &
-         domYvarName='lat' ,                           &
-         domZvarName='levsoi' ,                        &
-         domAreaName='area',                           &
-         domMaskName='mask',                           &
-         filePath='',                                  &
-         filename=(/stream_fldFileName_soilm/),        &
-         fldListFile=fldList,                          &
-         fldListModel=fldList,                         &
-         fillalgo='none',                              &
-         mapalgo='none',                               &
-         tintalgo=soilm_tintalgo,                      &
-         calendar=get_calendar(),                      &
-         dtlimit = 15._r8,                             &
-         taxmode='cycle'                               )
-
-    if (masterproc) then
-       call shr_strdata_print(sdat_soilm,'soil moisture data')
-    endif
-
-  end subroutine PrescribedSoilMoistureInit
-
-
-  !-----------------------------------------------------------------------
-  !
-  ! PrescribedSoilMoistureAdvance
-  !
-  !-----------------------------------------------------------------------
-  subroutine PrescribedSoilMoistureAdvance( bounds )
-    !
-    ! Advanace the prescribed soil moisture stream
-    !
-    ! !USES:
-    use clm_time_manager, only : get_curr_date
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)         , intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    character(len=CL)  :: stream_var_name
-    integer :: g, ig
-    integer :: ier    ! error code
-    integer :: year    ! year (0, ...) for nstep+1
-    integer :: mon     ! month (1, ..., 12) for nstep+1
-    integer :: day     ! day of month (1, ..., 31) for nstep+1
-    integer :: sec     ! seconds into current date for nstep+1
-    integer :: mcdate  ! Current model date (yyyymmdd)
-
-    call get_curr_date(year, mon, day, sec)
-    mcdate = year*10000 + mon*100 + day
-
-    stream_var_name = 'H2OSOI'
-
-    ! Determine variable index
-    ism = mct_aVect_indexRA(sdat_soilm%avs(1),trim(stream_var_name))
-
-    call shr_strdata_advance(sdat_soilm, mcdate, sec, mpicom, trim(stream_var_name))
-
-    ! Map gridcell to AV index
-    ier = 0
-    if ( .not. allocated(g_to_ig) )then
-       allocate (g_to_ig(bounds%begg:bounds%endg), stat=ier)
-       if (ier /= 0) then
-          write(iulog,*) 'Prescribed soil moisture allocation error'
-          call endrun(msg=errMsg(sourcefile, __LINE__))
-       end if
-
-       ig = 0
-       do g = bounds%begg,bounds%endg
-          ig = ig+1
-          g_to_ig(g) = ig
-       end do
-    end if
-
-  end subroutine PrescribedSoilMoistureAdvance
-
-  !-----------------------------------------------------------------------
-  !
-  ! PrescribedSoilMoistureInterp
-  !
-  !-----------------------------------------------------------------------
-  subroutine PrescribedSoilMoistureInterp(bounds, soilstate_inst, &
-       waterstatebulk_inst)
-    !
-    ! Assign data stream information for prescribed soil moisture.
-    !
-    ! !USES:
-    use clm_time_manager, only : get_curr_date
-    use clm_varpar      , only : nlevsoi
-    use clm_varcon      , only : denh2o, denice, watmin, spval
-    use landunit_varcon , only : istsoil, istcrop
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)         , intent(in)    :: bounds
-    type(soilstate_type)      , intent(in)    :: soilstate_inst
-    type(waterstatebulk_type) , intent(inout) :: waterstatebulk_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c, g, j, ig, n
-    real(r8) :: soilm_liq_frac            ! liquid fraction of soil moisture
-    real(r8) :: soilm_ice_frac            ! ice fraction of soil moisture
-    real(r8) :: moisture_increment        ! soil moisture adjustment increment
-    real(r8) :: h2osoi_vol_initial        ! initial vwc value
-    character(*), parameter    :: subName = "('PrescribedSoilMoistureInterp')"
-
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,2) >= g_to_ig(bounds%endg)+(nlevsoi-1)*size(g_to_ig) ), sourcefile, __LINE__)
-    associate( &
-         dz               =>    col%dz                                , & ! Input:  [real(r8) (:,:) ]  layer depth (m)
-         watsat           =>    soilstate_inst%watsat_col             , & ! Input:  [real(r8) (:,:) ]  volumetric soil water at saturation (porosity)
-         h2osoi_liq       =>    waterstatebulk_inst%h2osoi_liq_col        , & ! Input/Output:  [real(r8) (:,:) ]  liquid water (kg/m2)
-         h2osoi_ice       =>    waterstatebulk_inst%h2osoi_ice_col        , & ! Input/Output:  [real(r8) (:,:) ]  ice water (kg/m2)
-         h2osoi_vol       =>    waterstatebulk_inst%h2osoi_vol_col        , & ! Output: volumetric soil water (m3/m3)
-         h2osoi_vol_prs   =>    waterstatebulk_inst%h2osoi_vol_prs_grc      & ! Output: prescribed volumetric soil water (m3/m3)
-         )
-      SHR_ASSERT_FL( (lbound(h2osoi_vol,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_vol,2) == 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(dz,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(dz,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(dz,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(dz,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(watsat,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(watsat,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(watsat,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(watsat,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_liq,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_liq,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_liq,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_liq,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_ice,1) <= bounds%begc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_ice,1) >= bounds%endc ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_ice,2) <= 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_ice,2) >= nlevsoi ),     sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,1) <= bounds%begg ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,1) >= bounds%endg ), sourcefile, __LINE__)
-      SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,2) == 1 ),           sourcefile, __LINE__)
-      SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,2) >= nlevsoi ),     sourcefile, __LINE__)
-      !
-      ! Set the prescribed soil moisture read from the file everywhere
-      !
-      do g = bounds%begg, bounds%endg
-         ig = g_to_ig(g)
-         do j = 1, nlevsoi
-
-             !n = ig + (j-1)*size(g_to_ig)
-             n = ig + (j-1)*size(g_to_ig)
-
-             h2osoi_vol_prs(g,j) = sdat_soilm%avs(1)%rAttr(ism,n)
-
-             ! If soil moiture is being interpolated in time and the result is
-             ! large that probably means one of the two data points is missing (set to spval)
-             if ( h2osoi_vol_prs(g,j) > 10.0_r8 .and. (h2osoi_vol_prs(g,j) /= spval) )then
-                h2osoi_vol_prs(g,j) = spval
-             end if
-
-         end do
-      end do
-
-      do c = bounds%begc, bounds%endc
-         !
-         ! Set variable for each gridcell/column combination
-         !
-         g = col%gridcell(c)
-         ig = g_to_ig(g)
-
-         ! EBK Jan/2020, also check weights on gridcell (See https://github.com/ESCOMP/CTSM/issues/847)
-         if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) .and. &
-              (col%wtgcell(c) /= 0._r8) ) then
-            !       this is a 2d field (gridcell/nlevsoi) !
-            do j = 1, nlevsoi
-
-               n = ig + (j-1)*size(g_to_ig)
-
-               ! if soil water is zero, liq/ice fractions cannot be calculated
-               if((h2osoi_liq(c, j) + h2osoi_ice(c, j)) > 0._r8) then
-
-                  ! save original soil moisture value
-                  h2osoi_vol_initial = h2osoi_vol(c,j)
-
-                  ! Check if the vegetated land mask from the dataset on the
-                  ! file is different
-                  if ( (h2osoi_vol_prs(g,j) == spval) .and. (h2osoi_vol_initial /= spval) )then
-                     if ( soilm_ignore_data_if_missing )then
-                        cycle
-                     else
-                        write(iulog,*) 'Input soil moisture dataset is not vegetated as expected: gridcell=', &
-                                        g, ' active = ', col%active(c)
-                        call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, &
-                             msg = subname // &
-                             ' ERROR:: The input soil moisture stream is NOT vegetated for one of the land points' )
-                     end if
-                  end if
-
-                  ! update volumetric soil moisture from data prescribed from the file
-                  h2osoi_vol(c,j) = h2osoi_vol_prs(g,j)
-
-
-                  ! calculate liq/ice mass fractions
-                  soilm_liq_frac  = h2osoi_liq(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j))
-                  soilm_ice_frac  = h2osoi_ice(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j))
-
-                  ! calculate moisture increment
-                  moisture_increment = h2osoi_vol(c,j) - h2osoi_vol_initial
-                  ! add limitation check
-                  moisture_increment = min((watsat(c,j) - h2osoi_vol_initial),max(-(h2osoi_vol_initial-watmin),moisture_increment))
-
-                  ! update liq/ice water mass due to (volumetric) moisture increment
-                  h2osoi_liq(c,j) = h2osoi_liq(c,j) + (soilm_liq_frac * moisture_increment * dz(c, j) * denh2o)
-                  h2osoi_ice(c,j) = h2osoi_ice(c,j) + (soilm_ice_frac * moisture_increment * dz(c, j) * denice)
-
-               else
-                  call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, &
-                       msg = subname // ':: ERROR h2osoil liquid plus ice is zero')
-               endif
-            enddo
-         endif
-      end do
-
-    end associate
-
-  end subroutine PrescribedSoilMoistureInterp
-
-end module SoilMoistureStreamMod
diff --git a/src/cpl/mct/UrbanTimeVarType.F90 b/src/cpl/mct/UrbanTimeVarType.F90
deleted file mode 100644
index 805ac47fbf..0000000000
--- a/src/cpl/mct/UrbanTimeVarType.F90
+++ /dev/null
@@ -1,314 +0,0 @@
-module UrbanTimeVarType
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Urban Time Varying Data
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8, CL => shr_kind_CL
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use abortutils      , only : endrun
-  use decompMod       , only : bounds_type, subgrid_level_landunit
-  use clm_varctl      , only : iulog, inst_name
-  use landunit_varcon , only : isturb_MIN, isturb_MAX
-  use clm_varcon      , only : spval
-  use LandunitType    , only : lun
-  use GridcellType    , only : grc
-  use mct_mod
-  use shr_strdata_mod , only : shr_strdata_type
-  !
-  implicit none
-  save
-  private
-  !
-  !
-
-  ! !PUBLIC TYPE
-  type, public :: urbantv_type
-
-     real(r8), public, pointer     :: t_building_max(:)    ! lun maximum internal building air temperature (K)
-     type(shr_strdata_type)        :: sdat_urbantv         ! urban time varying input data stream
-   contains
-
-     ! !PUBLIC MEMBER FUNCTIONS:
-     procedure, public :: Init              ! Allocate and initialize urbantv
-     procedure, public :: urbantv_init      ! Initialize urban time varying stream
-     procedure, public :: urbantv_interp    ! Interpolate urban time varying stream
-
-  end type urbantv_type
-
-  !-----------------------------------------------------------------------
-  character(15), private :: stream_var_name(isturb_MIN:isturb_MAX)
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
-    !
-    ! Allocate module variables and data structures
-    !
-    ! !USES:
-    use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-    use histFileMod     , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(urbantv_type) :: this
-    type(bounds_type) , intent(in) :: bounds
-    character(len=*)  , intent(in) :: NLFilename   ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer		:: begl, endl
-    !---------------------------------------------------------------------
-
-    begl = bounds%begl; endl = bounds%endl
-
-    ! Allocate urbantv data structure
-
-    allocate(this%t_building_max      (begl:endl))          ; this%t_building_max      (:)   = nan
-
-    call this%urbantv_init(bounds, NLFilename)
-    call this%urbantv_interp(bounds)
-
-    ! Add history fields
-    call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
-          avgflag='A', long_name='prescribed maximum interior building temperature',   &
-          ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
-          l2g_scale_type='unity')
-
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  subroutine urbantv_init(this, bounds, NLFilename)
-   !
-   ! !DESCRIPTION:
-   ! Initialize data stream information for urban time varying data
-   !
-   ! !USES:
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use clm_nlUtilsMod   , only : find_nlgroup_name
-   use ndepStreamMod    , only : clm_domain_mct
-   use spmdMod          , only : masterproc, mpicom, comp_id
-   use fileutils        , only : getavu, relavu
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use shr_string_mod   , only : shr_string_listAppend
-   use shr_strdata_mod  , only : shr_strdata_create, shr_strdata_print
-   use domainMod        , only : ldomain
-   use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
-   use landunit_varcon  , only : isturb_TBD, isturb_HD, isturb_MD
-   use lnd_set_decomp_and_domain , only : gsmap_global
-   !
-   ! !ARGUMENTS:
-   implicit none
-   class(urbantv_type)           :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! !LOCAL VARIABLES:
-   integer            :: begl, endl                           ! landunits
-   integer            :: ifield                               ! field index
-   integer            :: stream_year_first_urbantv            ! first year in urban tv stream to use
-   integer            :: stream_year_last_urbantv             ! last year in urban tv stream to use
-   integer            :: model_year_align_urbantv             ! align stream_year_first_urbantv
-                                                              !  with this model year
-   integer            :: nu_nml                               ! unit for namelist file
-   integer            :: nml_error                            ! namelist i/o error flag
-   type(mct_ggrid)    :: dom_clm                              ! domain information
-   character(len=CL)  :: stream_fldFileName_urbantv           ! urban tv streams filename
-   character(len=CL)  :: urbantvmapalgo = 'nn'                ! mapping alogrithm for urban ac
-   character(len=CL)  :: urbantv_tintalgo = 'linear'          ! time interpolation alogrithm
-   character(len=CL)  :: fldList                              ! field string
-   character(*), parameter :: urbantvString = "tbuildmax_"    ! base string for field string
-   character(*), parameter :: subName = "('urbantv_init')"
-   character(*), parameter :: F00 = "('(urbantv_init) ',4a)"
-   !-----------------------------------------------------------------------
-   namelist /urbantv_streams/       &
-        stream_year_first_urbantv,  &
-        stream_year_last_urbantv,   &
-        model_year_align_urbantv,   &
-        urbantvmapalgo,             &
-        stream_fldFileName_urbantv, &
-        urbantv_tintalgo
-   !-----------------------------------------------------------------------
-
-   begl = bounds%begl; endl = bounds%endl
-
-   ! Default values for namelist
-   stream_year_first_urbantv  = 1       ! first year in stream to use
-   stream_year_last_urbantv   = 1       ! last  year in stream to use
-   model_year_align_urbantv   = 1       ! align stream_year_first_urbantv with this model year
-   stream_fldFileName_urbantv = ' '
-
-   ! Read urbantv_streams namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call find_nlgroup_name(nu_nml, 'urbantv_streams', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=urbantv_streams,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg='ERROR reading urbantv_streams namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_year_first_urbantv, mpicom)
-   call shr_mpi_bcast(stream_year_last_urbantv, mpicom)
-   call shr_mpi_bcast(model_year_align_urbantv, mpicom)
-   call shr_mpi_bcast(stream_fldFileName_urbantv, mpicom)
-   call shr_mpi_bcast(urbantv_tintalgo, mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'urbantv_streams settings:'
-      write(iulog,*) '  stream_year_first_urbantv  = ',stream_year_first_urbantv
-      write(iulog,*) '  stream_year_last_urbantv   = ',stream_year_last_urbantv
-      write(iulog,*) '  model_year_align_urbantv   = ',model_year_align_urbantv
-      write(iulog,*) '  stream_fldFileName_urbantv = ',stream_fldFileName_urbantv
-      write(iulog,*) '  urbantv_tintalgo           = ',urbantv_tintalgo
-      write(iulog,*) ' '
-   endif
-
-   call clm_domain_mct (bounds, dom_clm)
-
-   ! create the field list for these urbantv fields...use in shr_strdata_create
-   stream_var_name(:)          = "NOT_SET"
-   stream_var_name(isturb_TBD) = urbantvString//"TBD"
-   stream_var_name(isturb_HD)  = urbantvString//"HD"
-   stream_var_name(isturb_MD)  = urbantvString//"MD"
-   fldList = ""
-   do ifield = isturb_MIN, isturb_MAX
-      call shr_string_listAppend( fldList, stream_var_name(ifield) )
-   end do
-
-   call shr_strdata_create(this%sdat_urbantv,name="clmurbantv", &
-        pio_subsystem=pio_subsystem,                            &
-        pio_iotype=shr_pio_getiotype(inst_name),                &
-        mpicom=mpicom, compid=comp_id,                          &
-        gsmap=gsmap_global, ggrid=dom_clm,                      &
-        nxg=ldomain%ni, nyg=ldomain%nj,                         &
-        yearFirst=stream_year_first_urbantv,                    &
-        yearLast=stream_year_last_urbantv,                      &
-        yearAlign=model_year_align_urbantv,                     &
-        offset=0,                                               &
-        domFilePath='',                                         &
-        domFileName=trim(stream_fldFileName_urbantv),           &
-        domTvarName='time',                                     &
-        domXvarName='lon' ,                                     &
-        domYvarName='lat' ,                                     &
-        domAreaName='area',                                     &
-        domMaskName='LANDMASK',                                 &
-        filePath='',                                            &
-        filename=(/trim(stream_fldFileName_urbantv)/) ,         &
-        fldListFile=fldList,                                    &
-        fldListModel=fldList,                                   &
-        fillalgo='none',                                        &
-        mapalgo=urbantvmapalgo,                                 &
-        calendar=get_calendar(),                                &
-        tintalgo=urbantv_tintalgo,                              &
-        taxmode='extend'                                 )
-
-   if (masterproc) then
-      call shr_strdata_print(this%sdat_urbantv,'urban time varying data')
-   endif
-
-
-  end subroutine urbantv_init
-
-  !-----------------------------------------------------------------------
-  subroutine urbantv_interp(this, bounds)
-  !
-  ! !DESCRIPTION:
-  ! Interpolate data stream information for urban time varying data.
-  !
-  ! !USES:
-  use clm_time_manager, only : get_curr_date
-  use spmdMod         , only : mpicom
-  use shr_strdata_mod , only : shr_strdata_advance
-  use clm_instur      , only : urban_valid
-  !
-  ! !ARGUMENTS:
-  class(urbantv_type)           :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  logical :: found
-  integer :: l, glun, ig, g, ip
-  integer :: year    ! year (0, ...) for nstep+1
-  integer :: mon     ! month (1, ..., 12) for nstep+1
-  integer :: day     ! day of month (1, ..., 31) for nstep+1
-  integer :: sec     ! seconds into current date for nstep+1
-  integer :: mcdate  ! Current model date (yyyymmdd)
-  integer :: lindx   ! landunit index
-  integer :: gindx   ! gridcell index
-  !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(this%sdat_urbantv, mcdate, sec, mpicom, 'urbantvdyn')
-
-   do l = bounds%begl,bounds%endl
-      if (lun%urbpoi(l)) then
-         glun  = lun%gridcell(l)
-         ip = mct_aVect_indexRA(this%sdat_urbantv%avs(1),trim(stream_var_name(lun%itype(l))))
-         !
-         ! Determine vector index corresponding to glun
-         !
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if (g == glun) exit
-         end do
-
-         this%t_building_max(l) = this%sdat_urbantv%avs(1)%rAttr(ip,ig)
-      else
-         this%t_building_max(l) = spval
-      end if
-   end do
-
-   found = .false.
-   do l = bounds%begl,bounds%endl
-      if (lun%urbpoi(l)) then
-         glun  = lun%gridcell(l)
-         !
-         ! Determine vector index corresponding to glun
-         !
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if (g == glun) exit
-         end do
-
-         if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
-            found = .true.
-            gindx = g
-            lindx = l
-            exit
-         end if
-      end if
-   end do
-   if ( found ) then
-      write(iulog,*)'ERROR: no valid urban data for g= ',gindx
-      write(iulog,*)'landunit type:   ',lun%itype(lindx)
-      write(iulog,*)'urban_valid:     ',urban_valid(gindx)
-      write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
-      call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, &
-           msg=errmsg(sourcefile, __LINE__))
-   end if
-
-
-  end subroutine urbantv_interp
-
-  !-----------------------------------------------------------------------
-
-end module UrbanTimeVarType
diff --git a/src/cpl/mct/ch4FInundatedStreamType.F90 b/src/cpl/mct/ch4FInundatedStreamType.F90
deleted file mode 100644
index 3c26f4d109..0000000000
--- a/src/cpl/mct/ch4FInundatedStreamType.F90
+++ /dev/null
@@ -1,389 +0,0 @@
-module ch4FInundatedStreamType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Contains methods for reading in finundated streams file for methane code.
-  !
-  ! !USES
-  use shr_kind_mod   , only: r8 => shr_kind_r8, CL => shr_kind_cl
-  use spmdMod        , only: mpicom, masterproc
-  use clm_varctl     , only: iulog, inst_name
-  use abortutils     , only: endrun
-  use decompMod      , only: bounds_type
-  use ch4varcon      , only: finundation_mtd
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-
-  type, public :: ch4finundatedstream_type
-     real(r8), pointer, private :: zwt0_gdc  (:)         ! col coefficient for determining finundated (m)
-     real(r8), pointer, private :: f0_gdc    (:)         ! col maximum inundated fraction for a gridcell (for methane code)
-     real(r8), pointer, private :: p3_gdc    (:)         ! col coefficient for determining finundated (m)
-     real(r8), pointer, private :: fws_slope_gdc     (:) ! col slope in fws = slope * tws + intercept (A coefficient)
-     real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient)
-  contains
-
-      ! !PUBLIC MEMBER FUNCTIONS:
-      procedure, public :: Init            ! Initialize and read data in
-      procedure, public :: CalcFinundated  ! Calculate finundated based on input streams
-      procedure, public :: UseStreams      ! If streams will be used
-
-      ! !PRIVATE MEMBER FUNCTIONS:
-      procedure, private :: InitAllocate   ! Allocate data
-
-  end type ch4finundatedstream_type
-
-
-  ! ! PRIVATE DATA:
-
-  type, private :: streamcontrol_type
-     character(len=CL)  :: stream_fldFileName_ch4finundated   ! Filename
-     character(len=CL)  :: ch4finundatedmapalgo               ! map algo
-     character(len=CL)  :: fldList                            ! List of fields to read
-  contains
-     procedure, private :: ReadNML     ! Read in namelist
-  end type streamcontrol_type
-
-  type(streamcontrol_type), private :: control        ! Stream control data
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !==============================================================================
-
-contains
-
-  !==============================================================================
-
-  subroutine Init(this, bounds, NLFilename)
-   !
-   ! Initialize the ch4 finundated stream object
-   !
-   ! Uses:
-   use clm_time_manager , only : get_calendar, get_curr_date
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use shr_nl_mod       , only : shr_nl_find_group_name
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use ndepStreamMod    , only : clm_domain_mct
-   use domainMod        , only : ldomain
-   use decompMod        , only : bounds_type
-   use mct_mod          , only : mct_ggrid, mct_avect_indexra
-   use shr_strdata_mod  , only : shr_strdata_type, shr_strdata_create
-   use shr_strdata_mod  , only : shr_strdata_print, shr_strdata_advance
-   use spmdMod          , only : comp_id, iam
-   use ch4varcon        , only : finundation_mtd_h2osfc
-   use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
-   use lnd_set_decomp_and_domain , only : gsmap_global
-   !
-   ! arguments
-   implicit none
-   class(ch4finundatedstream_type) :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! local variables
-   integer            :: ig, g            ! Indices
-   type(mct_ggrid)    :: dom_clm          ! domain information
-   type(shr_strdata_type) :: sdat         ! input data stream
-   integer            :: index_ZWT0       = 0 ! Index of ZWT0 field
-   integer            :: index_F0         = 0 ! Index of F0 field
-   integer            :: index_P3         = 0 ! Index of P3 field
-   integer            :: index_FWS_TWS_A  = 0 ! Index of FWS_TWS_A field
-   integer            :: index_FWS_TWS_B  = 0 ! Index of FWS_TWS_B field
-   integer            :: year                 ! year (0, ...) for nstep+1
-   integer            :: mon                  ! month (1, ..., 12) for nstep+1
-   integer            :: day                  ! day of month (1, ..., 31) for nstep+1
-   integer            :: sec                  ! seconds into current date for nstep+1
-   integer            :: mcdate               ! Current model date (yyyymmdd)
-   character(len=*), parameter :: stream_name = 'ch4finundated'
-   character(*), parameter :: subName = "('ch4finundatedstream::Init')"
-   !-----------------------------------------------------------------------
-   if ( finundation_mtd /= finundation_mtd_h2osfc )then
-      call this%InitAllocate( bounds )
-      call control%ReadNML( bounds, NLFileName )
-
-      if ( this%useStreams() )then
-         call clm_domain_mct (bounds, dom_clm)
-
-         call shr_strdata_create(sdat,name=stream_name,                 &
-           pio_subsystem=pio_subsystem,                                 &
-           pio_iotype=shr_pio_getiotype(inst_name),                     &
-           mpicom=mpicom, compid=comp_id,                               &
-           gsmap=gsmap_global, ggrid=dom_clm,                           &
-           nxg=ldomain%ni, nyg=ldomain%nj,                              &
-           yearFirst=1996,                                              &
-           yearLast=1996,                                               &
-           yearAlign=1,                                                 &
-           offset=0,                                                    &
-           domFilePath='',                                              &
-           domFileName=trim(control%stream_fldFileName_ch4finundated),  &
-           domTvarName='time',                                          &
-           domXvarName='LONGXY' ,                                       &
-           domYvarName='LATIXY' ,                                       &
-           domAreaName='AREA',                                          &
-           domMaskName='LANDMASK',                                      &
-           filePath='',                                                 &
-           filename=(/trim(control%stream_fldFileName_ch4finundated)/), &
-           fldListFile=control%fldList,                                 &
-           fldListModel=control%fldList,                                &
-           fillalgo='none',                                             &
-           mapalgo=control%ch4finundatedmapalgo,                        &
-           calendar=get_calendar(),                                     &
-           taxmode='extend'                           )
-
-         if (masterproc) then
-            call shr_strdata_print(sdat,'CLM '//stream_name//' data')
-         endif
-
-         if( finundation_mtd == finundation_mtd_ZWT_inversion )then
-            index_ZWT0      = mct_avect_indexra(sdat%avs(1),'ZWT0')
-            index_F0        = mct_avect_indexra(sdat%avs(1),'F0' )
-            index_P3        = mct_avect_indexra(sdat%avs(1),'P3' )
-         else if( finundation_mtd == finundation_mtd_TWS_inversion )then
-            index_FWS_TWS_A = mct_avect_indexra(sdat%avs(1),'FWS_TWS_A')
-            index_FWS_TWS_B = mct_avect_indexra(sdat%avs(1),'FWS_TWS_B')
-         end if
-
-
-         ! Explicitly set current date to a hardcoded constant value. Otherwise
-         ! using the real date can cause roundoff differences that are
-         ! detrected as issues with exact restart.  EBK M05/20/2017
-         !call get_curr_date(year, mon, day, sec)
-         year = 1996
-         mon  = 12
-         day  = 31
-         sec  = 0
-         mcdate = year*10000 + mon*100 + day
-
-         call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ch4finundated')
-
-         ! Get the data
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if ( index_ZWT0 > 0 )then
-               this%zwt0_gdc(g) = sdat%avs(1)%rAttr(index_ZWT0,ig)
-            end if
-            if ( index_F0 > 0 )then
-               this%f0_gdc(g) = sdat%avs(1)%rAttr(index_F0,ig)
-            end if
-            if ( index_P3 > 0 )then
-               this%p3_gdc(g) = sdat%avs(1)%rAttr(index_P3,ig)
-            end if
-            if ( index_FWS_TWS_A > 0 )then
-               this%fws_slope_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_A,ig)
-            end if
-            if ( index_FWS_TWS_B > 0 )then
-               this%fws_intercept_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_B,ig)
-            end if
-         end do
-      end if
-   end if
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  logical function UseStreams(this)
-    !
-    ! !DESCRIPTION:
-    ! Return true if
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(ch4finundatedstream_type) :: this
-    !
-    ! !LOCAL VARIABLES:
-    if ( trim(control%stream_fldFileName_ch4finundated) == '' )then
-       UseStreams = .false.
-    else
-       UseStreams = .true.
-    end if
-  end function UseStreams
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Allocate module variables and data structures
-    !
-    ! !USES:
-    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    use ch4varcon     , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(ch4finundatedstream_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begc, endc
-    integer  :: begg, endg
-    !---------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    if( finundation_mtd == finundation_mtd_ZWT_inversion )then
-       allocate(this%zwt0_gdc         (begg:endg))            ;  this%zwt0_gdc         (:)   = nan
-       allocate(this%f0_gdc           (begg:endg))            ;  this%f0_gdc           (:)   = nan
-       allocate(this%p3_gdc           (begg:endg))            ;  this%p3_gdc           (:)   = nan
-    else if( finundation_mtd == finundation_mtd_TWS_inversion )then
-       allocate(this%fws_slope_gdc    (begg:endg))            ;  this%fws_slope_gdc    (:)   = nan
-       allocate(this%fws_intercept_gdc(begg:endg))            ;  this%fws_intercept_gdc(:)   = nan
-    end if
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, &
-                            waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated )
-    !
-    ! !DESCRIPTION:
-    !
-    ! Calculate finundated according to the appropriate methodology
-    !
-    ! !USES:
-    use ColumnType       , only : col
-    use ch4varcon        , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion
-    use ch4varcon        , only : finundation_mtd_TWS_inversion
-    use clm_varpar       , only : nlevsoi
-    use SoilHydrologyType, only : soilhydrology_type
-    use WaterDiagnosticBulkType   , only : waterdiagnosticbulk_type
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(ch4finundatedstream_type)                        :: this
-    type(bounds_type)                      , intent(in)    :: bounds
-    integer                                , intent(in)    :: num_soilc          ! number of column soil points in column filter
-    integer                                , intent(in)    :: filter_soilc(:)    ! column filter for soil points
-    type(soilhydrology_type)               , intent(in)    :: soilhydrology_inst
-    type(waterdiagnosticbulk_type)                  , intent(in)    :: waterdiagnosticbulk_inst
-    real(r8)                               , intent(in)    :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s)
-    real(r8)                               , intent(inout) :: finundated(bounds%begc:)        ! fractional inundated area in soil column (excluding dedicated wetland columns)
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: g, c, fc    ! Indices
-    real(r8) :: zwt_actual  ! Total water storage (ZWT) to use either perched or total depending on conditions
-
-    SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__)
-    SHR_ASSERT_ALL_FL((ubound(finundated)        == (/bounds%endc/)), sourcefile, __LINE__)
-
-    associate(                                                                 &
-         z                    =>   col%z                                     , & ! Input:  [real(r8) (:,:) ]  layer depth (m) (-nlevsno+1:nlevsoi)
-         zwt                  =>   soilhydrology_inst%zwt_col                , & ! Input:  [real(r8) (:)   ]  water table depth (m)
-         zwt_perched          =>   soilhydrology_inst%zwt_perched_col        , & ! Input:  [real(r8) (:)   ]  perched water table depth (m)
-         tws                  =>   waterdiagnosticbulk_inst%tws_grc                   , & ! Input:  [real(r8) (:)   ]  total water storage (kg m-2)
-         frac_h2osfc          =>   waterdiagnosticbulk_inst%frac_h2osfc_col             & ! Input:  [real(r8) (:)   ]  fraction of ground covered by surface water (0 to 1)
-    )
-
-    ! Calculate finundated
-    do fc = 1, num_soilc
-       c = filter_soilc(fc)
-       g = col%gridcell(c)
-       select case( finundation_mtd )
-          case ( finundation_mtd_h2osfc )
-             finundated(c) = frac_h2osfc(c)
-          case ( finundation_mtd_ZWT_inversion )
-             if (this%zwt0_gdc(g) > 0._r8) then
-                if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then
-                   zwt_actual = zwt_perched(c)
-                else
-                   zwt_actual = zwt(c)
-                end if
-                finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c)
-             else
-                finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c)
-             end if
-          case ( finundation_mtd_TWS_inversion )
-             finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g)
-       end select
-       finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) )
-    end do
-    end associate
-
-  end subroutine CalcFinundated
-  !==============================================================================
-
-  subroutine ReadNML(this, bounds, NLFilename)
-   !
-   ! Read the namelist data stream information.
-   !
-   ! Uses:
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use shr_nl_mod       , only : shr_nl_find_group_name
-   use shr_log_mod      , only : errMsg => shr_log_errMsg
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use fileutils        , only : getavu, relavu
-   use ch4varcon        , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion
-   !
-   ! arguments
-   implicit none
-   class(streamcontrol_type)    :: this
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! local variables
-   integer            :: nu_nml    ! unit for namelist file
-   integer            :: nml_error ! namelist i/o error flag
-   character(len=CL)  :: stream_fldFileName_ch4finundated = ' '
-   character(len=CL)  :: ch4finundatedmapalgo = 'bilinear'
-   character(len=*), parameter :: namelist_name = 'ch4finundated'    ! MUST agree with name in namelist and read
-   character(len=*), parameter :: shr_strdata_unset = 'NOT_SET'
-   character(len=*), parameter :: subName = "('ch4finundated::ReadNML')"
-   character(len=*), parameter :: F00 = "('(ch4finundated_readnml) ',4a)"
-   !-----------------------------------------------------------------------
-
-   namelist /ch4finundated/        &               ! MUST agree with namelist_name above
-        ch4finundatedmapalgo,  stream_fldFileName_ch4finundated
-
-   ! Default values for namelist
-
-   ! Read ch4finundated namelist
-   if (masterproc) then
-      nu_nml = getavu()
-      open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=ch4finundated,iostat=nml_error)   ! MUST agree with namelist_name above
-         if (nml_error /= 0) then
-            call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      else
-         call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__))
-      end if
-      close(nu_nml)
-      call relavu( nu_nml )
-   endif
-
-   call shr_mpi_bcast(stream_fldFileName_ch4finundated, mpicom)
-   call shr_mpi_bcast(ch4finundatedmapalgo            , mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) namelist_name, ' stream settings:'
-      write(iulog,*) '  stream_fldFileName_ch4finundated = ',stream_fldFileName_ch4finundated
-      write(iulog,*) '  ch4finundatedmapalgo             = ',ch4finundatedmapalgo
-      write(iulog,*) ' '
-   endif
-   this%stream_fldFileName_ch4finundated = stream_fldFileName_ch4finundated
-   this%ch4finundatedmapalgo             = ch4finundatedmapalgo
-   if (      finundation_mtd == finundation_mtd_ZWT_inversion  )then
-       this%fldList = "ZWT0:F0:P3"
-   else if ( finundation_mtd == finundation_mtd_TWS_inversion  )then
-       this%fldList = "FWS_TWS_A:FWS_TWS_B"
-   else
-       call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// &
-                   errMsg(sourcefile, __LINE__))
-   end if
-
- end subroutine ReadNML
-
-end module ch4FInundatedStreamType
diff --git a/src/cpl/mct/clm_cpl_indices.F90 b/src/cpl/mct/clm_cpl_indices.F90
deleted file mode 100644
index 09ed89e92d..0000000000
--- a/src/cpl/mct/clm_cpl_indices.F90
+++ /dev/null
@@ -1,330 +0,0 @@
-module clm_cpl_indices
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  !    Module containing the indices for the fields passed between CLM and
-  !    the driver. Includes the River Transport Model fields (RTM) and the
-  !    fields needed by the land-ice component (sno).
-  !
-  ! !USES:
-
-  use shr_sys_mod,    only : shr_sys_abort
-  implicit none
-
-  SAVE
-  private                              ! By default make data private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: clm_cpl_indices_set        ! Set the coupler indices
-  !
-  ! !PUBLIC DATA MEMBERS:
-  !
-  integer , public :: glc_nec     ! number of elevation classes for glacier_mec landunits
-                                  ! (from coupler) - must equal maxpatch_glc from namelist
-
-  ! lnd -> drv (required)
-
-  integer, public ::index_l2x_Flrl_rofsur     ! lnd->rtm input liquid surface fluxes
-  integer, public ::index_l2x_Flrl_rofgwl     ! lnd->rtm input liquid gwl fluxes
-  integer, public ::index_l2x_Flrl_rofsub     ! lnd->rtm input liquid subsurface fluxes
-  integer, public ::index_l2x_Flrl_rofi       ! lnd->rtm input frozen fluxes
-  integer, public ::index_l2x_Flrl_irrig      ! irrigation withdrawal
-
-  integer, public ::index_l2x_Sl_t            ! temperature
-  integer, public ::index_l2x_Sl_tref         ! 2m reference temperature
-  integer, public ::index_l2x_Sl_qref         ! 2m reference specific humidity
-  integer, public ::index_l2x_Sl_avsdr        ! albedo: direct , visible
-  integer, public ::index_l2x_Sl_anidr        ! albedo: direct , near-ir
-  integer, public ::index_l2x_Sl_avsdf        ! albedo: diffuse, visible
-  integer, public ::index_l2x_Sl_anidf        ! albedo: diffuse, near-ir
-  integer, public ::index_l2x_Sl_snowh        ! snow height
-  integer, public ::index_l2x_Sl_u10          ! 10m wind
-  integer, public ::index_l2x_Sl_ddvel        ! dry deposition velocities (optional)
-  integer, public ::index_l2x_Sl_fv           ! friction velocity
-  integer, public ::index_l2x_Sl_ram1         ! aerodynamical resistance
-  integer, public ::index_l2x_Sl_soilw        ! volumetric soil water
-  integer, public ::index_l2x_Fall_taux       ! wind stress, zonal
-  integer, public ::index_l2x_Fall_tauy       ! wind stress, meridional
-  integer, public ::index_l2x_Fall_lat        ! latent          heat flux
-  integer, public ::index_l2x_Fall_sen        ! sensible        heat flux
-  integer, public ::index_l2x_Fall_lwup       ! upward longwave heat flux
-  integer, public ::index_l2x_Fall_evap       ! evaporation     water flux
-  integer, public ::index_l2x_Fall_swnet      ! heat flux       shortwave net
-  integer, public ::index_l2x_Fall_fco2_lnd   ! co2 flux **For testing set to 0
-  integer, public ::index_l2x_Fall_flxdst1    ! dust flux size bin 1
-  integer, public ::index_l2x_Fall_flxdst2    ! dust flux size bin 2
-  integer, public ::index_l2x_Fall_flxdst3    ! dust flux size bin 3
-  integer, public ::index_l2x_Fall_flxdst4    ! dust flux size bin 4
-  integer, public ::index_l2x_Fall_flxvoc     ! MEGAN fluxes
-  integer, public ::index_l2x_Fall_flxfire    ! Fire fluxes
-  integer, public ::index_l2x_Sl_ztopfire     ! Top of fire emissions (m)
-
-  ! In the following, index 0 is bare land, other indices are glc elevation classes
-  integer, allocatable, public ::index_l2x_Sl_tsrf(:)   ! glc MEC temperature
-  integer, allocatable, public ::index_l2x_Sl_topo(:)   ! glc MEC topo height
-  integer, allocatable, public ::index_l2x_Flgl_qice(:) ! glc MEC ice flux
-
-  integer, public ::index_x2l_Sa_methane
-  integer, public ::index_l2x_Fall_methane
-
-  integer, public :: nflds_l2x = 0
-
-  ! drv -> lnd (required)
-
-  integer, public ::index_x2l_Sa_z            ! bottom atm level height
-  integer, public ::index_x2l_Sa_topo         ! atm surface height (m)
-  integer, public ::index_x2l_Sa_u            ! bottom atm level zon wind
-  integer, public ::index_x2l_Sa_v            ! bottom atm level mer wind
-  integer, public ::index_x2l_Sa_ptem         ! bottom atm level pot temp
-  integer, public ::index_x2l_Sa_shum         ! bottom atm level spec hum
-  integer, public ::index_x2l_Sa_pbot         ! bottom atm level pressure
-  integer, public ::index_x2l_Sa_tbot         ! bottom atm level temp
-  integer, public ::index_x2l_Faxa_lwdn       ! downward lw heat flux
-  integer, public ::index_x2l_Faxa_rainc      ! prec: liquid "convective"
-  integer, public ::index_x2l_Faxa_rainl      ! prec: liquid "large scale"
-  integer, public ::index_x2l_Faxa_snowc      ! prec: frozen "convective"
-  integer, public ::index_x2l_Faxa_snowl      ! prec: frozen "large scale"
-  integer, public ::index_x2l_Faxa_swndr      ! sw: nir direct  downward
-  integer, public ::index_x2l_Faxa_swvdr      ! sw: vis direct  downward
-  integer, public ::index_x2l_Faxa_swndf      ! sw: nir diffuse downward
-  integer, public ::index_x2l_Faxa_swvdf      ! sw: vis diffuse downward
-  integer, public ::index_x2l_Sa_co2prog      ! bottom atm level prognostic co2
-  integer, public ::index_x2l_Sa_co2diag      ! bottom atm level diagnostic co2
-  integer, public ::index_x2l_Faxa_bcphidry   ! flux: Black Carbon hydrophilic dry deposition
-  integer, public ::index_x2l_Faxa_bcphodry   ! flux: Black Carbon hydrophobic dry deposition
-  integer, public ::index_x2l_Faxa_bcphiwet   ! flux: Black Carbon hydrophilic wet deposition
-  integer, public ::index_x2l_Faxa_ocphidry   ! flux: Organic Carbon hydrophilic dry deposition
-  integer, public ::index_x2l_Faxa_ocphodry   ! flux: Organic Carbon hydrophobic dry deposition
-  integer, public ::index_x2l_Faxa_ocphiwet   ! flux: Organic Carbon hydrophilic dry deposition
-  integer, public ::index_x2l_Faxa_dstwet1    ! flux: Size 1 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstwet2    ! flux: Size 2 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstwet3    ! flux: Size 3 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstwet4    ! flux: Size 4 dust -- wet deposition
-  integer, public ::index_x2l_Faxa_dstdry1    ! flux: Size 1 dust -- dry deposition
-  integer, public ::index_x2l_Faxa_dstdry2    ! flux: Size 2 dust -- dry deposition
-  integer, public ::index_x2l_Faxa_dstdry3    ! flux: Size 3 dust -- dry deposition
-  integer, public ::index_x2l_Faxa_dstdry4    ! flux: Size 4 dust -- dry deposition
-
-  integer, public ::index_x2l_Faxa_nhx        ! flux nhx from atm
-  integer, public ::index_x2l_Faxa_noy        ! flux noy from atm
-
-  integer, public ::index_x2l_Flrr_flood      ! rtm->lnd rof flood flux
-  integer, public ::index_x2l_Flrr_volr       ! rtm->lnd rof volr total volume
-  integer, public ::index_x2l_Flrr_volrmch    ! rtm->lnd rof volr main channel volume
-
-  ! In the following, index 0 is bare land, other indices are glc elevation classes
-  integer, allocatable, public ::index_x2l_Sg_ice_covered(:) ! Fraction of glacier from glc model
-  integer, allocatable, public ::index_x2l_Sg_topo(:)        ! Topo height from glc model
-  integer, allocatable, public ::index_x2l_Flgg_hflx(:)      ! Heat flux from glc model
-
-  integer, public ::index_x2l_Sg_icemask
-  integer, public ::index_x2l_Sg_icemask_coupled_fluxes
-
-  integer, public :: nflds_x2l = 0
-
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine clm_cpl_indices_set( )
-    !
-    ! !DESCRIPTION:
-    ! Set the coupler indices needed by the land model coupler
-    ! interface.
-    !
-    ! !USES:
-    use seq_flds_mod   , only: seq_flds_x2l_fields, seq_flds_l2x_fields
-    use mct_mod        , only: mct_aVect, mct_aVect_init, mct_avect_indexra
-    use mct_mod        , only: mct_aVect_clean, mct_avect_nRattr
-    use shr_drydep_mod , only: drydep_fields_token, n_drydep
-    use shr_megan_mod  , only: shr_megan_fields_token, shr_megan_mechcomps_n
-    use shr_fire_emis_mod,only: shr_fire_emis_fields_token, shr_fire_emis_ztop_token, shr_fire_emis_mechcomps_n
-    use clm_varctl     , only:  ndep_from_cpl
-    use glc_elevclass_mod, only: glc_get_num_elevation_classes, glc_elevclass_as_string
-    !
-    ! !ARGUMENTS:
-    implicit none
-    !
-    ! !REVISION HISTORY:
-    ! Author: Mariana Vertenstein
-    ! 01/2011, Erik Kluzek:         Added protex headers
-    !
-    ! !LOCAL VARIABLES:
-    type(mct_aVect)   :: l2x      ! temporary, land to coupler
-    type(mct_aVect)   :: x2l      ! temporary, coupler to land
-    integer           :: num
-    character(len=:), allocatable :: nec_str  ! string version of glc elev. class number
-    character(len=64) :: name
-    character(len=32) :: subname = 'clm_cpl_indices_set'  ! subroutine name
-    !-----------------------------------------------------------------------
-
-    ! Determine attribute vector indices
-
-    ! create temporary attribute vectors
-    call mct_aVect_init(x2l, rList=seq_flds_x2l_fields, lsize=1)
-    nflds_x2l = mct_avect_nRattr(x2l)
-
-    call mct_aVect_init(l2x, rList=seq_flds_l2x_fields, lsize=1)
-    nflds_l2x = mct_avect_nRattr(l2x)
-
-    !-------------------------------------------------------------
-    ! clm -> drv
-    !-------------------------------------------------------------
-
-    index_l2x_Flrl_rofsur   = mct_avect_indexra(l2x,'Flrl_rofsur')
-    index_l2x_Flrl_rofgwl   = mct_avect_indexra(l2x,'Flrl_rofgwl')
-    index_l2x_Flrl_rofsub   = mct_avect_indexra(l2x,'Flrl_rofsub')
-    index_l2x_Flrl_rofi     = mct_avect_indexra(l2x,'Flrl_rofi')
-    index_l2x_Flrl_irrig    = mct_avect_indexra(l2x,'Flrl_irrig')
-
-    index_l2x_Sl_t          = mct_avect_indexra(l2x,'Sl_t')
-    index_l2x_Sl_snowh      = mct_avect_indexra(l2x,'Sl_snowh')
-    index_l2x_Sl_avsdr      = mct_avect_indexra(l2x,'Sl_avsdr')
-    index_l2x_Sl_anidr      = mct_avect_indexra(l2x,'Sl_anidr')
-    index_l2x_Sl_avsdf      = mct_avect_indexra(l2x,'Sl_avsdf')
-    index_l2x_Sl_anidf      = mct_avect_indexra(l2x,'Sl_anidf')
-    index_l2x_Sl_tref       = mct_avect_indexra(l2x,'Sl_tref')
-    index_l2x_Sl_qref       = mct_avect_indexra(l2x,'Sl_qref')
-    index_l2x_Sl_u10        = mct_avect_indexra(l2x,'Sl_u10')
-    index_l2x_Sl_ram1       = mct_avect_indexra(l2x,'Sl_ram1')
-    index_l2x_Sl_fv         = mct_avect_indexra(l2x,'Sl_fv')
-    index_l2x_Sl_soilw      = mct_avect_indexra(l2x,'Sl_soilw',perrwith='quiet')
-
-    if ( n_drydep>0 )then
-       index_l2x_Sl_ddvel = mct_avect_indexra(l2x, trim(drydep_fields_token))
-    else
-       index_l2x_Sl_ddvel = 0
-    end if
-
-    index_l2x_Fall_taux     = mct_avect_indexra(l2x,'Fall_taux')
-    index_l2x_Fall_tauy     = mct_avect_indexra(l2x,'Fall_tauy')
-    index_l2x_Fall_lat      = mct_avect_indexra(l2x,'Fall_lat')
-    index_l2x_Fall_sen      = mct_avect_indexra(l2x,'Fall_sen')
-    index_l2x_Fall_lwup     = mct_avect_indexra(l2x,'Fall_lwup')
-    index_l2x_Fall_evap     = mct_avect_indexra(l2x,'Fall_evap')
-    index_l2x_Fall_swnet    = mct_avect_indexra(l2x,'Fall_swnet')
-    index_l2x_Fall_flxdst1  = mct_avect_indexra(l2x,'Fall_flxdst1')
-    index_l2x_Fall_flxdst2  = mct_avect_indexra(l2x,'Fall_flxdst2')
-    index_l2x_Fall_flxdst3  = mct_avect_indexra(l2x,'Fall_flxdst3')
-    index_l2x_Fall_flxdst4  = mct_avect_indexra(l2x,'Fall_flxdst4')
-
-    index_l2x_Fall_fco2_lnd = mct_avect_indexra(l2x,'Fall_fco2_lnd',perrwith='quiet')
-
-    index_l2x_Fall_methane  = mct_avect_indexra(l2x,'Fall_methane',perrWith='quiet')
-
-    ! MEGAN fluxes
-    if (shr_megan_mechcomps_n>0) then
-       index_l2x_Fall_flxvoc = mct_avect_indexra(l2x,trim(shr_megan_fields_token))
-    else
-       index_l2x_Fall_flxvoc = 0
-    endif
-
-    ! Fire fluxes
-    if (shr_fire_emis_mechcomps_n>0) then
-       index_l2x_Fall_flxfire = mct_avect_indexra(l2x,trim(shr_fire_emis_fields_token))
-       index_l2x_Sl_ztopfire = mct_avect_indexra(l2x,trim(shr_fire_emis_ztop_token))
-    else
-       index_l2x_Fall_flxfire = 0
-       index_l2x_Sl_ztopfire = 0
-    endif
-
-    !-------------------------------------------------------------
-    ! drv -> clm
-    !-------------------------------------------------------------
-
-    index_x2l_Sa_z          = mct_avect_indexra(x2l,'Sa_z')
-    index_x2l_Sa_topo       = mct_avect_indexra(x2l,'Sa_topo')
-    index_x2l_Sa_u          = mct_avect_indexra(x2l,'Sa_u')
-    index_x2l_Sa_v          = mct_avect_indexra(x2l,'Sa_v')
-    index_x2l_Sa_ptem       = mct_avect_indexra(x2l,'Sa_ptem')
-    index_x2l_Sa_pbot       = mct_avect_indexra(x2l,'Sa_pbot')
-    index_x2l_Sa_tbot       = mct_avect_indexra(x2l,'Sa_tbot')
-    index_x2l_Sa_shum       = mct_avect_indexra(x2l,'Sa_shum')
-    index_x2l_Sa_co2prog    = mct_avect_indexra(x2l,'Sa_co2prog',perrwith='quiet')
-    index_x2l_Sa_co2diag    = mct_avect_indexra(x2l,'Sa_co2diag',perrwith='quiet')
-
-    index_x2l_Sa_methane    = mct_avect_indexra(x2l,'Sa_methane',perrWith='quiet')
-
-    index_x2l_Flrr_volr     = mct_avect_indexra(x2l,'Flrr_volr')
-    index_x2l_Flrr_volrmch  = mct_avect_indexra(x2l,'Flrr_volrmch')
-
-    index_x2l_Faxa_lwdn     = mct_avect_indexra(x2l,'Faxa_lwdn')
-    index_x2l_Faxa_rainc    = mct_avect_indexra(x2l,'Faxa_rainc')
-    index_x2l_Faxa_rainl    = mct_avect_indexra(x2l,'Faxa_rainl')
-    index_x2l_Faxa_snowc    = mct_avect_indexra(x2l,'Faxa_snowc')
-    index_x2l_Faxa_snowl    = mct_avect_indexra(x2l,'Faxa_snowl')
-    index_x2l_Faxa_swndr    = mct_avect_indexra(x2l,'Faxa_swndr')
-    index_x2l_Faxa_swvdr    = mct_avect_indexra(x2l,'Faxa_swvdr')
-    index_x2l_Faxa_swndf    = mct_avect_indexra(x2l,'Faxa_swndf')
-    index_x2l_Faxa_swvdf    = mct_avect_indexra(x2l,'Faxa_swvdf')
-    index_x2l_Faxa_bcphidry = mct_avect_indexra(x2l,'Faxa_bcphidry')
-    index_x2l_Faxa_bcphodry = mct_avect_indexra(x2l,'Faxa_bcphodry')
-    index_x2l_Faxa_bcphiwet = mct_avect_indexra(x2l,'Faxa_bcphiwet')
-    index_x2l_Faxa_ocphidry = mct_avect_indexra(x2l,'Faxa_ocphidry')
-    index_x2l_Faxa_ocphodry = mct_avect_indexra(x2l,'Faxa_ocphodry')
-    index_x2l_Faxa_ocphiwet = mct_avect_indexra(x2l,'Faxa_ocphiwet')
-    index_x2l_Faxa_dstdry1  = mct_avect_indexra(x2l,'Faxa_dstdry1')
-    index_x2l_Faxa_dstdry2  = mct_avect_indexra(x2l,'Faxa_dstdry2')
-    index_x2l_Faxa_dstdry3  = mct_avect_indexra(x2l,'Faxa_dstdry3')
-    index_x2l_Faxa_dstdry4  = mct_avect_indexra(x2l,'Faxa_dstdry4')
-    index_x2l_Faxa_dstwet1  = mct_avect_indexra(x2l,'Faxa_dstwet1')
-    index_x2l_Faxa_dstwet2  = mct_avect_indexra(x2l,'Faxa_dstwet2')
-    index_x2l_Faxa_dstwet3  = mct_avect_indexra(x2l,'Faxa_dstwet3')
-    index_x2l_Faxa_dstwet4  = mct_avect_indexra(x2l,'Faxa_dstwet4')
-
-    index_x2l_Faxa_nhx      = mct_avect_indexra(x2l,'Faxa_nhx', perrWith='quiet')
-    index_x2l_Faxa_noy      = mct_avect_indexra(x2l,'Faxa_noy', perrWith='quiet')
-
-    if (index_x2l_Faxa_nhx > 0 .and. index_x2l_Faxa_noy > 0) then
-       ndep_from_cpl = .true.
-    end if
-
-    index_x2l_Flrr_flood    = mct_avect_indexra(x2l,'Flrr_flood')
-
-    !-------------------------------------------------------------
-    ! glc coupling
-    !-------------------------------------------------------------
-
-    index_x2l_Sg_icemask = mct_avect_indexra(x2l,'Sg_icemask')
-    index_x2l_Sg_icemask_coupled_fluxes = mct_avect_indexra(x2l,'Sg_icemask_coupled_fluxes')
-
-    glc_nec = glc_get_num_elevation_classes()
-    if (glc_nec < 1) then
-       call shr_sys_abort('ERROR: In CLM4.5 and later, glc_nec must be at least 1.')
-    end if
-
-    ! Create coupling fields for all glc elevation classes (1:glc_nec) plus bare land
-    ! (index 0).
-    allocate(index_l2x_Sl_tsrf(0:glc_nec))
-    allocate(index_l2x_Sl_topo(0:glc_nec))
-    allocate(index_l2x_Flgl_qice(0:glc_nec))
-    allocate(index_x2l_Sg_ice_covered(0:glc_nec))
-    allocate(index_x2l_Sg_topo(0:glc_nec))
-    allocate(index_x2l_Flgg_hflx(0:glc_nec))
-
-    do num = 0,glc_nec
-       nec_str = glc_elevclass_as_string(num)
-
-       name = 'Sg_ice_covered' // nec_str
-       index_x2l_Sg_ice_covered(num) = mct_avect_indexra(x2l,trim(name))
-       name = 'Sg_topo' // nec_str
-       index_x2l_Sg_topo(num)   = mct_avect_indexra(x2l,trim(name))
-       name = 'Flgg_hflx' // nec_str
-       index_x2l_Flgg_hflx(num) = mct_avect_indexra(x2l,trim(name))
-
-       name = 'Sl_tsrf' // nec_str
-       index_l2x_Sl_tsrf(num)   = mct_avect_indexra(l2x,trim(name))
-       name = 'Sl_topo' // nec_str
-       index_l2x_Sl_topo(num)   = mct_avect_indexra(l2x,trim(name))
-       name = 'Flgl_qice' // nec_str
-       index_l2x_Flgl_qice(num) = mct_avect_indexra(l2x,trim(name))
-    end do
-
-    call mct_aVect_clean(x2l)
-    call mct_aVect_clean(l2x)
-
-  end subroutine clm_cpl_indices_set
-
-!=======================================================================
-
-end module clm_cpl_indices
diff --git a/src/cpl/mct/laiStreamMod.F90 b/src/cpl/mct/laiStreamMod.F90
deleted file mode 100644
index 47d25287b7..0000000000
--- a/src/cpl/mct/laiStreamMod.F90
+++ /dev/null
@@ -1,241 +0,0 @@
-module laiStreamMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Read LAI from stream
-  !
-  ! !USES:
-  use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create
-  use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance
-  use shr_kind_mod    , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use decompMod       , only : bounds_type
-  use abortutils      , only : endrun
-  use clm_varctl      , only : iulog, inst_name
-  use perf_mod        , only : t_startf, t_stopf
-  use spmdMod         , only : masterproc, mpicom, comp_id
-  use ncdio_pio
-  use mct_mod
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: lai_init    ! position datasets for LAI
-  public :: lai_advance ! Advance the LAI streams (outside of a Open-MP threading loop)
-  public :: lai_interp  ! interpolates between two years of LAI data (when LAI streams
-
-  ! !PRIVATE MEMBER DATA:
-  integer, allocatable    :: g_to_ig(:)         ! Array matching gridcell index to data index
-  type(shr_strdata_type)  :: sdat_lai           ! LAI input data stream
-
-  character(len=*), parameter :: sourcefile = &
-       __FILE__
-
-!==============================================================================
-contains
-!==============================================================================
-
-  subroutine lai_init(bounds)
-    !
-    ! Initialize data stream information for LAI.
-    !
-    ! !USES:
-    use clm_time_manager , only : get_calendar
-    use ncdio_pio        , only : pio_subsystem
-    use shr_pio_mod      , only : shr_pio_getiotype
-    use shr_stream_mod   , only : shr_stream_file_null
-    use shr_string_mod   , only : shr_string_listCreateField
-    use clm_nlUtilsMod   , only : find_nlgroup_name
-    use ndepStreamMod    , only : clm_domain_mct
-    use histFileMod      , only : hist_addfld1d
-    use domainMod        , only : ldomain
-    use controlMod       , only : NLFilename
-    use lnd_set_decomp_and_domain , only : gsmap_global
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds          ! bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: stream_year_first_lai      ! first year in Lai stream to use
-    integer            :: stream_year_last_lai       ! last year in Lai stream to use
-    integer            :: model_year_align_lai       ! align stream_year_first_lai with
-    integer            :: nu_nml                     ! unit for namelist file
-    integer            :: nml_error                  ! namelist i/o error flag
-    type(mct_ggrid)    :: dom_clm                    ! domain information
-    character(len=CL)  :: stream_fldFileName_lai     ! lai stream filename to read
-    character(len=CL)  :: lai_mapalgo = 'bilinear'   ! Mapping alogrithm
-    character(len=CL)  :: lai_tintalgo = 'linear'    ! Time interpolation alogrithm
-    character(len=CXX) :: fldList                    ! field string
-    character(*), parameter :: laiString = "LAI"     ! base string for field string
-    integer     , parameter :: numLaiFields = 16     ! number of fields to build field string
-    character(*), parameter :: subName = "('laidyn_init')"
-    !-----------------------------------------------------------------------
-    !
-    ! deal with namelist variables here in init
-    !
-    namelist /lai_streams/         &
-         stream_year_first_lai,    &
-         stream_year_last_lai,     &
-         model_year_align_lai,     &
-         lai_mapalgo,              &
-         stream_fldFileName_lai,   &
-         lai_tintalgo
-
-    ! Default values for namelist
-    stream_year_first_lai     = 1      ! first year in stream to use
-    stream_year_last_lai      = 1      ! last  year in stream to use
-    model_year_align_lai      = 1      ! align stream_year_first_lai with this model year
-    stream_fldFileName_lai    = shr_stream_file_null
-
-    ! Read lai_streams namelist
-    if (masterproc) then
-       open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-       call find_nlgroup_name(nu_nml, 'lai_streams', status=nml_error)
-       if (nml_error == 0) then
-          read(nu_nml, nml=lai_streams,iostat=nml_error)
-          if (nml_error /= 0) then
-             call endrun(subname // ':: ERROR reading lai_streams namelist')
-          end if
-       else
-          call endrun(subname // ':: ERROR finding lai_streams namelist')
-       end if
-       close(nu_nml)
-    endif
-    call shr_mpi_bcast(stream_year_first_lai  , mpicom)
-    call shr_mpi_bcast(stream_year_last_lai   , mpicom)
-    call shr_mpi_bcast(model_year_align_lai   , mpicom)
-    call shr_mpi_bcast(stream_fldFileName_lai , mpicom)
-    call shr_mpi_bcast(lai_tintalgo           , mpicom)
-
-    if (masterproc) then
-       write(iulog,*) ' '
-       write(iulog,*) 'lai_stream settings:'
-       write(iulog,*) '  stream_year_first_lai  = ',stream_year_first_lai
-       write(iulog,*) '  stream_year_last_lai   = ',stream_year_last_lai
-       write(iulog,*) '  model_year_align_lai   = ',model_year_align_lai
-       write(iulog,*) '  stream_fldFileName_lai = ',trim(stream_fldFileName_lai)
-       write(iulog,*) '  lai_tintalgo           = ',trim(lai_tintalgo)
-    endif
-
-    call clm_domain_mct (bounds, dom_clm)
-
-    ! create the field list for these lai fields...use in shr_strdata_create
-    fldList = shr_string_listCreateField( numLaiFields, laiString )
-
-    call shr_strdata_create(sdat_lai,name="laidyn",    &
-         pio_subsystem=pio_subsystem,                  &
-         pio_iotype=shr_pio_getiotype(inst_name),      &
-         mpicom=mpicom, compid=comp_id,                &
-         gsmap=gsmap_global, ggrid=dom_clm,            &
-         nxg=ldomain%ni, nyg=ldomain%nj,               &
-         yearFirst=stream_year_first_lai,              &
-         yearLast=stream_year_last_lai,                &
-         yearAlign=model_year_align_lai,               &
-         offset=0,                                     &
-         domFilePath='',                               &
-         domFileName=trim(stream_fldFileName_lai),     &
-         domTvarName='time',                           &
-         domXvarName='lon' ,                           &
-         domYvarName='lat' ,                           &
-         domAreaName='area',                           &
-         domMaskName='mask',                           &
-         filePath='',                                  &
-         filename=(/stream_fldFileName_lai/),          &
-         fldListFile=fldList,                          &
-         fldListModel=fldList,                         &
-         fillalgo='none',                              &
-         mapalgo=lai_mapalgo,                          &
-         tintalgo=lai_tintalgo,                        &
-         calendar=get_calendar(),                      &
-         taxmode='cycle'                               )
-
-    if (masterproc) then
-       call shr_strdata_print(sdat_lai,'LAI data')
-    endif
-
-  end subroutine lai_init
-
-  !==============================================================================
-  subroutine lai_advance( bounds )
-    !
-    ! Advance LAI streams
-    !
-    ! !USES:
-    use clm_time_manager, only : get_curr_date
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)      , intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g, ig   ! Indices
-    integer :: year    ! year (0, ...) for nstep+1
-    integer :: mon     ! month (1, ..., 12) for nstep+1
-    integer :: day     ! day of month (1, ..., 31) for nstep+1
-    integer :: sec     ! seconds into current date for nstep+1
-    integer :: mcdate  ! Current model date (yyyymmdd)
-    !-----------------------------------------------------------------------
-
-    call get_curr_date(year, mon, day, sec)
-    mcdate = year*10000 + mon*100 + day
-
-    call shr_strdata_advance(sdat_lai, mcdate, sec, mpicom, 'laidyn')
-    if ( .not. allocated(g_to_ig) )then
-       allocate (g_to_ig(bounds%begg:bounds%endg) )
-       ig = 0
-       do g = bounds%begg,bounds%endg
-          ig = ig+1
-          g_to_ig(g) = ig
-       end do
-    end if
-
-  end subroutine lai_advance
-
-  !==============================================================================
-  subroutine lai_interp(bounds, canopystate_inst)
-    !
-    ! Interpolate data stream information for Lai.
-    !
-    ! !USES:
-    use pftconMod       , only : noveg
-    use CanopyStateType , only : canopystate_type
-    use PatchType       , only : patch
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)      , intent(in)    :: bounds
-    type(canopystate_type) , intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ivt, p, ip, ig
-    character(len=CL)  :: stream_var_name
-    !-----------------------------------------------------------------------
-    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (lbound(sdat_lai%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(sdat_lai%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__)
-
-    do p = bounds%begp, bounds%endp
-       ivt = patch%itype(p)
-       ! Set lai for each gridcell/patch combination
-       if (ivt /= noveg) then
-          ! vegetated pft
-          write(stream_var_name,"(i6)") ivt
-          stream_var_name = 'LAI_'//trim(adjustl(stream_var_name))
-          ip = mct_aVect_indexRA(sdat_lai%avs(1),trim(stream_var_name))
-          ig = g_to_ig(patch%gridcell(p))
-          canopystate_inst%tlai_patch(p) = sdat_lai%avs(1)%rAttr(ip,ig)
-       else                       
-          ! non-vegetated pft
-          canopystate_inst%tlai_patch(p) = 0._r8
-       endif
-    end do
-
-  end subroutine lai_interp
-
-end module LaiStreamMod
diff --git a/src/cpl/mct/lnd_comp_mct.F90 b/src/cpl/mct/lnd_comp_mct.F90
deleted file mode 100644
index e50602a378..0000000000
--- a/src/cpl/mct/lnd_comp_mct.F90
+++ /dev/null
@@ -1,632 +0,0 @@
-module lnd_comp_mct
-
-  !---------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  !  Interface of the active land model component of CESM the CLM (Community Land Model)
-  !  with the main CESM driver. This is a thin interface taking CESM driver information
-  !  in MCT (Model Coupling Toolkit) format and converting it to use by CLM.
-  !
-  ! !uses:
-  use shr_kind_mod     , only : r8 => shr_kind_r8
-  use shr_sys_mod      , only : shr_sys_flush
-  use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use mct_mod          , only : mct_avect, mct_gsmap, mct_gGrid
-  use decompmod        , only : bounds_type
-  use lnd_import_export, only : lnd_import, lnd_export
-  !
-  ! !public member functions:
-  implicit none
-  private                     ! by default make data private
-  !
-  ! !public member functions:
-  public :: lnd_init_mct      ! clm initialization
-  public :: lnd_run_mct       ! clm run phase
-  public :: lnd_final_mct     ! clm finalization/cleanup
-  !
-  ! !private member functions:
-  private :: lnd_domain_mct    ! set the land model domain information
-  private :: lnd_handle_resume ! handle pause/resume signals from the coupler
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-!====================================================================================
-contains
-!====================================================================================
-
-  subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Initialize land surface model and obtain relevant atmospheric model arrays
-    ! back from (i.e. albedos, surface temperature and snow cover over land).
-    !
-    ! !USES:
-    use shr_kind_mod     , only : shr_kind_cl
-    use abortutils       , only : endrun
-    use clm_time_manager , only : get_nstep, set_timemgr_init
-    use clm_initializeMod, only : initialize1, initialize2
-    use clm_instMod      , only : water_inst, lnd2atm_inst, lnd2glc_inst
-    use clm_varctl       , only : finidat, single_column, clm_varctl_set, iulog
-    use clm_varctl       , only : inst_index, inst_suffix, inst_name
-    use clm_varorb       , only : eccen, obliqr, lambm0, mvelpp
-    use controlMod       , only : control_setNL
-    use decompMod        , only : get_proc_bounds
-    use domainMod        , only : ldomain
-    use shr_file_mod     , only : shr_file_setLogUnit, shr_file_setLogLevel
-    use shr_file_mod     , only : shr_file_getLogUnit, shr_file_getLogLevel
-    use shr_file_mod     , only : shr_file_getUnit, shr_file_setIO
-    use seq_cdata_mod    , only : seq_cdata, seq_cdata_setptrs
-    use seq_timemgr_mod  , only : seq_timemgr_EClockGetData
-    use seq_infodata_mod , only : seq_infodata_type, seq_infodata_GetData, seq_infodata_PutData, &
-                                  seq_infodata_start_type_start, seq_infodata_start_type_cont,   &
-                                  seq_infodata_start_type_brnch
-    use seq_comm_mct     , only : seq_comm_suffix, seq_comm_inst, seq_comm_name
-    use seq_flds_mod     , only : seq_flds_x2l_fields, seq_flds_l2x_fields
-    use spmdMod          , only : masterproc, spmd_init
-    use clm_varctl       , only : nsrStartup, nsrContinue, nsrBranch
-    use clm_cpl_indices  , only : clm_cpl_indices_set
-    use mct_mod          , only : mct_aVect_init, mct_aVect_zero, mct_gsMap, mct_gsMap_init
-    use decompMod        , only : gindex_global
-    use lnd_set_decomp_and_domain, only : lnd_set_decomp_and_domain_from_surfrd, gsmap_global
-    use ESMF
-    !
-    ! !ARGUMENTS:
-    type(ESMF_Clock),           intent(inout) :: EClock           ! Input synchronization clock
-    type(seq_cdata),            intent(inout) :: cdata_l          ! Input land-model driver data
-    type(mct_aVect),            intent(inout) :: x2l_l, l2x_l     ! land model import and export states
-    character(len=*), optional, intent(in)    :: NLFilename       ! Namelist filename to read
-    !
-    ! !LOCAL VARIABLES:
-    integer                          :: LNDID        ! Land identifyer
-    integer                          :: mpicom_lnd   ! MPI communicator
-    type(mct_gsMap),         pointer :: GSMap_lnd    ! Land model MCT GS map
-    type(mct_gGrid),         pointer :: dom_l        ! Land model domain
-    type(seq_infodata_type), pointer :: infodata     ! CESM driver level info data
-    integer  :: lsize                                ! size of attribute vector
-    integer  :: gsize                                ! global size 
-    integer  :: g,i,j                                ! indices
-    integer  :: dtime_sync                           ! coupling time-step from the input synchronization clock
-    logical  :: exists                               ! true if file exists
-    logical  :: atm_aero                             ! Flag if aerosol data sent from atm model
-    real(r8) :: scmlat                               ! single-column latitude
-    real(r8) :: scmlon                               ! single-column longitude
-    character(len=SHR_KIND_CL) :: caseid             ! case identifier name
-    character(len=SHR_KIND_CL) :: ctitle             ! case description title
-    character(len=SHR_KIND_CL) :: starttype          ! start-type (startup, continue, branch, hybrid)
-    character(len=SHR_KIND_CL) :: calendar           ! calendar type name
-    character(len=SHR_KIND_CL) :: hostname           ! hostname of machine running on
-    character(len=SHR_KIND_CL) :: version            ! Model version
-    character(len=SHR_KIND_CL) :: username           ! user running the model
-    integer :: nsrest                                ! clm restart type
-    integer :: ref_ymd                               ! reference date (YYYYMMDD)
-    integer :: ref_tod                               ! reference time of day (sec)
-    integer :: start_ymd                             ! start date (YYYYMMDD)
-    integer :: start_tod                             ! start time of day (sec)
-    logical :: brnch_retain_casename                 ! flag if should retain the case name on a branch start type
-    integer :: lbnum                                 ! input to memory diagnostic
-    integer :: shrlogunit,shrloglev                  ! old values for log unit and log level
-    type(bounds_type) :: bounds                      ! bounds
-    logical :: noland
-    integer :: ni,nj
-    real(r8)         , parameter :: rundef = -9999999._r8
-    character(len=32), parameter :: sub = 'lnd_init_mct'
-    character(len=*),  parameter :: format = "('("//trim(sub)//") :',A)"
-    !-----------------------------------------------------------------------
-
-    ! Set cdata data
-    call seq_cdata_setptrs(cdata_l, ID=LNDID, mpicom=mpicom_lnd, &
-         gsMap=GSMap_lnd, dom=dom_l, infodata=infodata)
-
-    ! Determine attriute vector indices
-    call clm_cpl_indices_set()
-
-    ! Initialize clm MPI communicator
-    call spmd_init( mpicom_lnd, LNDID )
-
-#if (defined _MEMTRACE)
-    if(masterproc) then
-       lbnum=1
-       call memmon_dump_fort('memmon.out','lnd_init_mct:start::',lbnum)
-    endif
-#endif
-
-    inst_name   = seq_comm_name(LNDID)
-    inst_index  = seq_comm_inst(LNDID)
-    inst_suffix = seq_comm_suffix(LNDID)
-    ! Initialize io log unit
-
-    call shr_file_getLogUnit (shrlogunit)
-    if (masterproc) then
-       inquire(file='lnd_modelio.nml'//trim(inst_suffix),exist=exists)
-       if (exists) then
-          iulog = shr_file_getUnit()
-          call shr_file_setIO('lnd_modelio.nml'//trim(inst_suffix),iulog)
-       end if
-       write(iulog,format) "CLM land model initialization"
-    else
-       iulog = shrlogunit
-    end if
-
-    call shr_file_getLogLevel(shrloglev)
-    call shr_file_setLogUnit (iulog)
-
-    ! Use infodata to set orbital values
-    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
-         orb_lambm0=lambm0, orb_obliqr=obliqr )
-
-    ! Consistency check on namelist filename
-    call control_setNL("lnd_in"//trim(inst_suffix))
-
-    ! Initialize clm
-    ! initialize1 reads namelists
-    ! decomp and domain are set in lnd_set_decomp_and_domain_from_surfrd
-    ! initialize2 performs the rest of initialization
-    call seq_timemgr_EClockGetData(EClock,                               &
-                                   start_ymd=start_ymd,                  &
-                                   start_tod=start_tod, ref_ymd=ref_ymd, &
-                                   ref_tod=ref_tod, &
-                                   calendar=calendar, &
-                                   dtime=dtime_sync)
-    if (masterproc) then
-       write(iulog,*)'dtime = ',dtime_sync
-    end if
-    call seq_infodata_GetData(infodata, case_name=caseid,    &
-                              case_desc=ctitle, single_column=single_column,    &
-                              scmlat=scmlat, scmlon=scmlon,                     &
-                              brnch_retain_casename=brnch_retain_casename,      &
-                              start_type=starttype, model_version=version,      &
-                              hostname=hostname, username=username )
-
-    ! Single Column
-    if ( single_column .and. (scmlat == rundef  .or. scmlon == rundef ) ) then
-       call endrun(msg=' ERROR:: single column mode on -- but scmlat and scmlon are NOT set'//&
-            errMsg(sourcefile, __LINE__))
-    end if
-
-    ! Note that we assume that CTSM's internal dtime matches the coupling time step.
-    ! i.e., we currently do NOT allow sub-cycling within a coupling time step.
-    call set_timemgr_init( calendar_in=calendar, start_ymd_in=start_ymd, start_tod_in=start_tod, &
-         ref_ymd_in=ref_ymd, ref_tod_in=ref_tod, dtime_in=dtime_sync)
-
-    if (     trim(starttype) == trim(seq_infodata_start_type_start)) then
-       nsrest = nsrStartup
-    else if (trim(starttype) == trim(seq_infodata_start_type_cont) ) then
-       nsrest = nsrContinue
-    else if (trim(starttype) == trim(seq_infodata_start_type_brnch)) then
-       nsrest = nsrBranch
-    else
-       call endrun( sub//' ERROR: unknown starttype' )
-    end if
-
-    ! set default values for run control variables
-    call clm_varctl_set(caseid_in=caseid, ctitle_in=ctitle,                     &
-                        brnch_retain_casename_in=brnch_retain_casename,         &
-                        single_column_in=single_column, scmlat_in=scmlat,       &
-                        scmlon_in=scmlon, nsrest_in=nsrest, version_in=version, &
-                        hostname_in=hostname, username_in=username)
-
-    ! Read namelists
-    call initialize1(dtime=dtime_sync)
-
-    ! Initialize decomposition and domain (ldomain) type
-    call lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj)
-
-    ! If no land then exit out of initialization
-    if ( noland ) then
-
-       call seq_infodata_PutData( infodata, lnd_present   =.false.)
-       call seq_infodata_PutData( infodata, lnd_prognostic=.false.)
-
-    else
-
-       ! Determine if aerosol and dust deposition come from atmosphere component
-       call seq_infodata_GetData(infodata, atm_aero=atm_aero )
-       if ( .not. atm_aero )then
-          call endrun( sub//' ERROR: atmosphere model MUST send aerosols to CLM' )
-       end if
-
-       ! Initialize clm gsMap, clm domain and clm attribute vectors
-       call get_proc_bounds( bounds )
-       lsize = bounds%endg - bounds%begg + 1
-       gsize = ldomain%ni * ldomain%nj
-       call mct_gsMap_init( gsMap_lnd, gindex_global, mpicom_lnd, LNDID, lsize, gsize )
-       gsmap_global => gsmap_lnd ! module variable in lnd_set_decomp_and_domain
-       call lnd_domain_mct( bounds, lsize, gsMap_lnd, dom_l )
-       call mct_aVect_init(x2l_l, rList=seq_flds_x2l_fields, lsize=lsize)
-       call mct_aVect_zero(x2l_l)
-       call mct_aVect_init(l2x_l, rList=seq_flds_l2x_fields, lsize=lsize)
-       call mct_aVect_zero(l2x_l)
-
-       ! Finish initializing clm
-       call initialize2(ni,nj)
-
-       ! Create land export state
-       call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
-
-       ! Fill in infodata settings
-       call seq_infodata_PutData(infodata, lnd_prognostic=.true.)
-       call seq_infodata_PutData(infodata, lnd_nx=ldomain%ni, lnd_ny=ldomain%nj)
-       call lnd_handle_resume( cdata_l )
-
-       ! Reset shr logging to original values
-       call shr_file_setLogUnit (shrlogunit)
-       call shr_file_setLogLevel(shrloglev)
-
-#if (defined _MEMTRACE)
-       if(masterproc) then
-          write(iulog,*) TRIM(Sub) // ':end::'
-          lbnum=1
-          call memmon_dump_fort('memmon.out','lnd_int_mct:end::',lbnum)
-          call memmon_reset_addr()
-       endif
-#endif
-    end if
-
-  end subroutine lnd_init_mct
-
-  !====================================================================================
-  subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
-    !
-    ! !DESCRIPTION:
-    ! Run clm model
-    !
-    ! !USES:
-    use shr_kind_mod    ,  only : r8 => shr_kind_r8
-    use clm_instMod     ,  only : water_inst, lnd2atm_inst, atm2lnd_inst, lnd2glc_inst, glc2lnd_inst
-    use clm_driver      ,  only : clm_drv
-    use clm_time_manager,  only : get_curr_date, get_nstep, get_curr_calday, get_step_size
-    use clm_time_manager,  only : advance_timestep, update_rad_dtime
-    use decompMod       ,  only : get_proc_bounds
-    use abortutils      ,  only : endrun
-    use clm_varctl      ,  only : iulog
-    use clm_varorb      ,  only : eccen, obliqr, lambm0, mvelpp
-    use shr_file_mod    ,  only : shr_file_setLogUnit, shr_file_setLogLevel
-    use shr_file_mod    ,  only : shr_file_getLogUnit, shr_file_getLogLevel
-    use seq_cdata_mod   ,  only : seq_cdata, seq_cdata_setptrs
-    use seq_timemgr_mod ,  only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn
-    use seq_timemgr_mod ,  only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync
-    use seq_infodata_mod,  only : seq_infodata_type, seq_infodata_GetData
-    use spmdMod         ,  only : masterproc, mpicom
-    use perf_mod        ,  only : t_startf, t_stopf, t_barrierf
-    use shr_orb_mod     ,  only : shr_orb_decl
-    use ESMF
-    !
-    ! !ARGUMENTS:
-    type(ESMF_Clock) , intent(inout) :: EClock    ! Input synchronization clock from driver
-    type(seq_cdata)  , intent(inout) :: cdata_l   ! Input driver data for land model
-    type(mct_aVect)  , intent(inout) :: x2l_l     ! Import state to land model
-    type(mct_aVect)  , intent(inout) :: l2x_l     ! Export state from land model
-    !
-    ! !LOCAL VARIABLES:
-    integer      :: ymd_sync             ! Sync date (YYYYMMDD)
-    integer      :: yr_sync              ! Sync current year
-    integer      :: mon_sync             ! Sync current month
-    integer      :: day_sync             ! Sync current day
-    integer      :: tod_sync             ! Sync current time of day (sec)
-    integer      :: ymd                  ! CLM current date (YYYYMMDD)
-    integer      :: yr                   ! CLM current year
-    integer      :: mon                  ! CLM current month
-    integer      :: day                  ! CLM current day
-    integer      :: tod                  ! CLM current time of day (sec)
-    integer      :: dtime                ! time step increment (sec)
-    integer      :: nstep                ! time step index
-    logical      :: rstwr_sync           ! .true. ==> write restart file before returning
-    logical      :: rstwr                ! .true. ==> write restart file before returning
-    logical      :: nlend_sync           ! Flag signaling last time-step
-    logical      :: nlend                ! .true. ==> last time-step
-    logical      :: dosend               ! true => send data back to driver
-    logical      :: doalb                ! .true. ==> do albedo calculation on this time step
-    logical      :: rof_prognostic       ! .true. => running with a prognostic ROF model
-    logical      :: glc_present          ! .true. => running with a non-stub GLC model
-    real(r8)     :: nextsw_cday          ! calday from clock of next radiation computation
-    real(r8)     :: caldayp1             ! clm calday plus dtime offset
-    integer      :: shrlogunit,shrloglev ! old values for share log unit and log level
-    integer      :: lbnum                ! input to memory diagnostic
-    integer      :: g,i,lsize            ! counters
-    real(r8)     :: calday               ! calendar day for nstep
-    real(r8)     :: declin               ! solar declination angle in radians for nstep
-    real(r8)     :: declinp1             ! solar declination angle in radians for nstep+1
-    real(r8)     :: eccf                 ! earth orbit eccentricity factor
-    real(r8)     :: recip                ! reciprical
-    logical,save :: first_call = .true.  ! first call work
-    type(seq_infodata_type),pointer :: infodata             ! CESM information from the driver
-    type(mct_gGrid),        pointer :: dom_l                ! Land model domain data
-    type(bounds_type)               :: bounds               ! bounds
-    character(len=32)               :: rdate                ! date char string for restart file names
-    character(len=32), parameter    :: sub = "lnd_run_mct"
-    !---------------------------------------------------------------------------
-
-    ! Determine processor bounds
-
-    call get_proc_bounds(bounds)
-
-#if (defined _MEMTRACE)
-    if(masterproc) then
-       lbnum=1
-       call memmon_dump_fort('memmon.out','lnd_run_mct:start::',lbnum)
-    endif
-#endif
-
-    ! Reset shr logging to my log file
-    call shr_file_getLogUnit (shrlogunit)
-    call shr_file_getLogLevel(shrloglev)
-    call shr_file_setLogUnit (iulog)
-
-    ! Determine time of next atmospheric shortwave calculation
-    call seq_cdata_setptrs(cdata_l, infodata=infodata, dom=dom_l)
-    call seq_timemgr_EClockGetData(EClock, &
-         curr_ymd=ymd, curr_tod=tod_sync,  &
-         curr_yr=yr_sync, curr_mon=mon_sync, curr_day=day_sync)
-    call seq_infodata_GetData(infodata, nextsw_cday=nextsw_cday )
-
-    dtime = get_step_size()
-
-    ! Handle pause/resume signals from coupler
-    call lnd_handle_resume( cdata_l )
-
-    write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync,mon_sync,day_sync,tod_sync
-    nlend_sync = seq_timemgr_StopAlarmIsOn( EClock )
-    rstwr_sync = seq_timemgr_RestartAlarmIsOn( EClock )
-
-    ! Determine if we're running with a prognostic ROF model, and if we're running with a
-    ! non-stub GLC model. These won't change throughout the run, but we can't count on
-    ! their being set in initialization, so need to get them in the run method.
-
-    call seq_infodata_GetData( infodata, &
-         rof_prognostic=rof_prognostic, &
-         glc_present=glc_present)
-
-    ! Map MCT to land data type
-    ! Perform downscaling if appropriate
-
-
-    ! Map to clm (only when state and/or fluxes need to be updated)
-
-    call t_startf ('lc_lnd_import')
-    call lnd_import( bounds, &
-         x2l = x2l_l%rattr, &
-         glc_present = glc_present, &
-         atm2lnd_inst = atm2lnd_inst, &
-         glc2lnd_inst = glc2lnd_inst, &
-         wateratm2lndbulk_inst = water_inst%wateratm2lndbulk_inst)
-    call t_stopf ('lc_lnd_import')
-
-    ! Use infodata to set orbital values if updated mid-run
-
-    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
-         orb_lambm0=lambm0, orb_obliqr=obliqr )
-
-    ! Loop over time steps in coupling interval
-
-    dosend = .false.
-    do while(.not. dosend)
-
-       ! Determine if dosend
-       ! When time is not updated at the beginning of the loop - then return only if
-       ! are in sync with clock before time is updated
-       !
-       ! NOTE(wjs, 2020-03-09) I think the do while (.not. dosend) loop only is important
-       ! for the first time step (when we run 2 steps). After that, we now assume that we
-       ! run one time step per coupling interval (based on setting the model's dtime from
-       ! the driver). (According to Mariana Vertenstein, sub-cycling (running multiple
-       ! land model time steps per coupling interval) used to be supported, but hasn't
-       ! been fully supported for a long time.) We may want to rework this logic to make
-       ! this more explicit, or - ideally - get rid of this extra time step at the start
-       ! of the run, at which point I think we could do away with this looping entirely.
-
-       call get_curr_date( yr, mon, day, tod )
-       ymd = yr*10000 + mon*100 + day
-       tod = tod
-       dosend = (seq_timemgr_EClockDateInSync( EClock, ymd, tod))
-
-       ! Determine doalb based on nextsw_cday sent from atm model
-
-       nstep = get_nstep()
-       caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.)
-       if (nstep == 0) then
-          doalb = .false.
-       else if (nstep == 1) then
-          doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8)
-       else
-          doalb = (nextsw_cday >= -0.5_r8)
-       end if
-       call update_rad_dtime(doalb)
-
-       ! Determine if time to write restart and stop
-
-       rstwr = .false.
-       if (rstwr_sync .and. dosend) rstwr = .true.
-       nlend = .false.
-       if (nlend_sync .and. dosend) nlend = .true.
-
-       ! Run clm
-
-       call t_barrierf('sync_clm_run1', mpicom)
-       call t_startf ('clm_run')
-       call t_startf ('shr_orb_decl')
-       calday = get_curr_calday(reuse_day_365_for_day_366=.true.)
-       call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
-       call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
-       call t_stopf ('shr_orb_decl')
-       call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic)
-       call t_stopf ('clm_run')
-
-       ! Create l2x_l export state - add river runoff input to l2x_l if appropriate
-
-       call t_startf ('lc_lnd_export')
-       call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
-       call t_stopf ('lc_lnd_export')
-
-       ! Advance clm time step
-
-       call t_startf ('lc_clm2_adv_timestep')
-       call advance_timestep()
-       call t_stopf ('lc_clm2_adv_timestep')
-
-    end do
-
-    ! Check that internal clock is in sync with master clock
-
-    call get_curr_date( yr, mon, day, tod, offset=-dtime )
-    ymd = yr*10000 + mon*100 + day
-    tod = tod
-    if ( .not. seq_timemgr_EClockDateInSync( EClock, ymd, tod ) )then
-       call seq_timemgr_EclockGetData( EClock, curr_ymd=ymd_sync, curr_tod=tod_sync )
-       write(iulog,*)' clm ymd=',ymd     ,'  clm tod= ',tod
-       write(iulog,*)'sync ymd=',ymd_sync,' sync tod= ',tod_sync
-       call endrun( sub//":: CLM clock not in sync with Master Sync clock" )
-    end if
-
-    ! Reset shr logging to my original values
-
-    call shr_file_setLogUnit (shrlogunit)
-    call shr_file_setLogLevel(shrloglev)
-
-#if (defined _MEMTRACE)
-    if(masterproc) then
-       lbnum=1
-       call memmon_dump_fort('memmon.out','lnd_run_mct:end::',lbnum)
-       call memmon_reset_addr()
-    endif
-#endif
-
-    first_call  = .false.
-
-  end subroutine lnd_run_mct
-
-  !====================================================================================
-  subroutine lnd_final_mct( EClock, cdata_l, x2l_l, l2x_l)
-    !
-    ! !DESCRIPTION:
-    ! Finalize land surface model
-
-    use seq_cdata_mod   ,only : seq_cdata, seq_cdata_setptrs
-    use seq_timemgr_mod ,only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn
-    use seq_timemgr_mod ,only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync
-    use esmf
-    !
-    ! !ARGUMENTS:
-    type(ESMF_Clock) , intent(inout) :: EClock    ! Input synchronization clock from driver
-    type(seq_cdata)  , intent(inout) :: cdata_l   ! Input driver data for land model
-    type(mct_aVect)  , intent(inout) :: x2l_l     ! Import state to land model
-    type(mct_aVect)  , intent(inout) :: l2x_l     ! Export state from land model
-    !---------------------------------------------------------------------------
-
-    ! fill this in
-  end subroutine lnd_final_mct
-
-  !====================================================================================
-  subroutine lnd_domain_mct( bounds, lsize, gsMap_l, dom_l )
-    !
-    ! !DESCRIPTION:
-    ! Send the land model domain information to the coupler
-    !
-    ! !USES:
-    use clm_varcon  , only: re
-    use domainMod   , only: ldomain
-    use spmdMod     , only: iam
-    use mct_mod     , only: mct_gGrid_importIAttr
-    use mct_mod     , only: mct_gGrid_importRAttr, mct_gGrid_init, mct_gsMap_orderedPoints
-    use seq_flds_mod, only: seq_flds_dom_coord, seq_flds_dom_other
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in)  :: bounds  ! bounds
-    integer        , intent(in)    :: lsize   ! land model domain data size
-    type(mct_gsMap), intent(inout) :: gsMap_l ! Output land model MCT GS map
-    type(mct_ggrid), intent(out)   :: dom_l   ! Output domain information for land model
-    !
-    ! Local Variables
-    integer :: g,i,j              ! index
-    real(r8), pointer :: data(:)  ! temporary
-    integer , pointer :: idata(:) ! temporary
-    !---------------------------------------------------------------------------
-    !
-    ! Initialize mct domain type
-    ! lat/lon in degrees,  area in radians^2, mask is 1 (land), 0 (non-land)
-    ! Note that in addition land carries around landfrac for the purposes of domain checking
-    !
-    call mct_gGrid_init( GGrid=dom_l, CoordChars=trim(seq_flds_dom_coord), &
-       OtherChars=trim(seq_flds_dom_other), lsize=lsize )
-    !
-    ! Allocate memory
-    !
-    allocate(data(lsize))
-    !
-    ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT
-    !
-    call mct_gsMap_orderedPoints(gsMap_l, iam, idata)
-    call mct_gGrid_importIAttr(dom_l,'GlobGridNum',idata,lsize)
-    !
-    ! Determine domain (numbering scheme is: West to East and South to North to South pole)
-    ! Initialize attribute vector with special value
-    !
-    data(:) = -9999.0_R8
-    call mct_gGrid_importRAttr(dom_l,"lat"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_l,"lon"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_l,"area" ,data,lsize)
-    call mct_gGrid_importRAttr(dom_l,"aream",data,lsize)
-    data(:) = 0.0_R8
-    call mct_gGrid_importRAttr(dom_l,"mask" ,data,lsize)
-    !
-    ! Fill in correct values for domain components
-    ! Note aream will be filled in in the atm-lnd mapper
-    !
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%lonc(g)
-    end do
-    call mct_gGrid_importRattr(dom_l,"lon",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%latc(g)
-    end do
-    call mct_gGrid_importRattr(dom_l,"lat",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%area(g)/(re*re)
-    end do
-    call mct_gGrid_importRattr(dom_l,"area",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%mask(g), r8)
-    end do
-    call mct_gGrid_importRattr(dom_l,"mask",data,lsize)
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%frac(g), r8)
-    end do
-    call mct_gGrid_importRattr(dom_l,"frac",data,lsize)
-
-    deallocate(data)
-    deallocate(idata)
-
-  end subroutine lnd_domain_mct
-
-  !====================================================================================
-  subroutine lnd_handle_resume( cdata_l )
-    !
-    ! !DESCRIPTION:
-    ! Handle resume signals for Data Assimilation (DA)
-    !
-    ! !USES:
-    use clm_time_manager , only : update_DA_nstep
-    use seq_cdata_mod    , only : seq_cdata, seq_cdata_setptrs
-    implicit none
-    ! !ARGUMENTS:
-    type(seq_cdata),            intent(inout) :: cdata_l          ! Input land-model driver data
-    ! !LOCAL VARIABLES:
-    logical :: resume_from_data_assim                      ! flag if we are resuming after data assimulation was done
-    !---------------------------------------------------------------------------
-
-    ! Check to see if restart was modified and we are resuming from data
-    ! assimilation
-    call seq_cdata_setptrs(cdata_l, post_assimilation=resume_from_data_assim)
-    if ( resume_from_data_assim ) call update_DA_nstep()
-
-  end subroutine lnd_handle_resume
-
-end module lnd_comp_mct
diff --git a/src/cpl/mct/lnd_import_export.F90 b/src/cpl/mct/lnd_import_export.F90
deleted file mode 100644
index 537abd49d9..0000000000
--- a/src/cpl/mct/lnd_import_export.F90
+++ /dev/null
@@ -1,354 +0,0 @@
-module lnd_import_export
-
-  use shr_kind_mod , only: r8 => shr_kind_r8, cl=>shr_kind_cl
-  use abortutils   , only: endrun
-  use decompmod    , only: bounds_type, subgrid_level_gridcell
-  use lnd2atmType  , only: lnd2atm_type
-  use lnd2glcMod   , only: lnd2glc_type
-  use atm2lndType  , only: atm2lnd_type
-  use glc2lndMod   , only: glc2lnd_type 
-  use Waterlnd2atmBulkType , only: waterlnd2atmbulk_type
-  use Wateratm2lndBulkType , only: wateratm2lndbulk_type
-  use clm_cpl_indices
-  use GridcellType      , only : grc
-  !
-  implicit none
-  !===============================================================================
-
-contains
-
-  !===============================================================================
-  subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst, wateratm2lndbulk_inst)
-
-    !---------------------------------------------------------------------------
-    ! !DESCRIPTION:
-    ! Convert the input data from the coupler to the land model 
-    !
-    ! !USES:
-    use seq_flds_mod    , only: seq_flds_x2l_fields
-    use clm_varctl      , only: co2_type, co2_ppmv, iulog, use_c13
-    use clm_varctl      , only: ndep_from_cpl 
-    use clm_varcon      , only: c13ratio
-    use domainMod       , only: ldomain
-    use lnd_import_export_utils, only : derive_quantities, check_for_errors, check_for_nans
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)  , intent(in)    :: bounds   ! bounds
-    real(r8)           , intent(in)    :: x2l(:,:) ! driver import state to land model
-    logical            , intent(in)    :: glc_present       ! .true. => running with a non-stub GLC model
-    type(atm2lnd_type) , intent(inout) :: atm2lnd_inst      ! clm internal input data type
-    type(glc2lnd_type) , intent(inout) :: glc2lnd_inst      ! clm internal input data type
-    type(wateratm2lndbulk_type), intent(inout) :: wateratm2lndbulk_inst   ! clm internal input data type
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begg, endg           ! bounds
-    integer  :: g,i,k,nstep,ier      ! indices, number of steps, and error code
-    real(r8) :: qsat_kg_kg           ! saturation specific humidity (kg/kg)
-    real(r8) :: forc_pbot            ! atmospheric pressure (Pa)
-    real(r8) :: forc_rainc(bounds%begg:bounds%endg)  ! rainxy Atm flux mm/s
-    real(r8) :: forc_rainl(bounds%begg:bounds%endg)  ! rainxy Atm flux mm/s
-    real(r8) :: forc_snowc(bounds%begg:bounds%endg)  ! snowfxy Atm flux  mm/s
-    real(r8) :: forc_snowl(bounds%begg:bounds%endg)  ! snowfxl Atm flux  mm/s
-    real(r8) :: co2_ppmv_diag        ! temporary
-    real(r8) :: co2_ppmv_prog        ! temporary
-    real(r8) :: co2_ppmv_val         ! temporary
-    integer  :: co2_type_idx         ! integer flag for co2_type options
-    character(len=32) :: fname       ! name of field that is NaN
-    character(len=32), parameter :: sub = 'lnd_import'
-
-    !---------------------------------------------------------------------------
-
-    ! Set bounds
-    begg = bounds%begg; endg = bounds%endg
-
-    co2_type_idx = 0
-    if (co2_type == 'prognostic') then
-       co2_type_idx = 1
-    else if (co2_type == 'diagnostic') then
-       co2_type_idx = 2
-    end if
-    if (co2_type == 'prognostic' .and. index_x2l_Sa_co2prog == 0) then
-       call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2prog for co2_type equal to prognostic' )
-    else if (co2_type == 'diagnostic' .and. index_x2l_Sa_co2diag == 0) then
-       call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2diag for co2_type equal to diagnostic' )
-    end if
-
-    ! Note that the precipitation fluxes received  from the coupler
-    ! are in units of kg/s/m^2. To convert these precipitation rates
-    ! in units of mm/sec, one must divide by 1000 kg/m^3 and multiply
-    ! by 1000 mm/m resulting in an overall factor of unity.
-    ! Below the units are therefore given in mm/s.
-
-    do g = begg,endg
-       i = 1 + (g - begg)
-
-       ! Determine flooding input, sign convention is positive downward and
-       ! hierarchy is atm/glc/lnd/rof/ice/ocn.  so water sent from rof to land is negative,
-       ! change the sign to indicate addition of water to system.
-
-       wateratm2lndbulk_inst%forc_flood_grc(g)   = -x2l(index_x2l_Flrr_flood,i)  
-
-       wateratm2lndbulk_inst%volr_grc(g)   = x2l(index_x2l_Flrr_volr,i) * (ldomain%area(g) * 1.e6_r8)
-       wateratm2lndbulk_inst%volrmch_grc(g)= x2l(index_x2l_Flrr_volrmch,i) * (ldomain%area(g) * 1.e6_r8)
-
-       ! Determine required receive fields
-
-       atm2lnd_inst%forc_hgt_grc(g)                  = x2l(index_x2l_Sa_z,i)         ! zgcmxy  Atm state m
-       atm2lnd_inst%forc_topo_grc(g)                 = x2l(index_x2l_Sa_topo,i)      ! Atm surface height (m)
-       atm2lnd_inst%forc_u_grc(g)                    = x2l(index_x2l_Sa_u,i)         ! forc_uxy  Atm state m/s
-       atm2lnd_inst%forc_v_grc(g)                    = x2l(index_x2l_Sa_v,i)         ! forc_vxy  Atm state m/s
-       atm2lnd_inst%forc_solad_not_downscaled_grc(g,2) = x2l(index_x2l_Faxa_swndr,i)   ! forc_sollxy  Atm flux  W/m^2
-       atm2lnd_inst%forc_solad_not_downscaled_grc(g,1) = x2l(index_x2l_Faxa_swvdr,i)   ! forc_solsxy  Atm flux  W/m^2
-       atm2lnd_inst%forc_solai_grc(g,2)              = x2l(index_x2l_Faxa_swndf,i)   ! forc_solldxy Atm flux  W/m^2
-       atm2lnd_inst%forc_solai_grc(g,1)              = x2l(index_x2l_Faxa_swvdf,i)   ! forc_solsdxy Atm flux  W/m^2
-
-       atm2lnd_inst%forc_th_not_downscaled_grc(g)    = x2l(index_x2l_Sa_ptem,i)      ! forc_thxy Atm state K
-       wateratm2lndbulk_inst%forc_q_not_downscaled_grc(g)     = x2l(index_x2l_Sa_shum,i)      ! forc_qxy  Atm state kg/kg
-       atm2lnd_inst%forc_pbot_not_downscaled_grc(g)  = x2l(index_x2l_Sa_pbot,i)      ! ptcmxy  Atm state Pa
-       atm2lnd_inst%forc_t_not_downscaled_grc(g)     = x2l(index_x2l_Sa_tbot,i)      ! forc_txy  Atm state K
-       atm2lnd_inst%forc_lwrad_not_downscaled_grc(g) = x2l(index_x2l_Faxa_lwdn,i)    ! flwdsxy Atm flux  W/m^2
-
-       forc_rainc(g)                                 = x2l(index_x2l_Faxa_rainc,i)   ! mm/s
-       forc_rainl(g)                                 = x2l(index_x2l_Faxa_rainl,i)   ! mm/s
-       forc_snowc(g)                                 = x2l(index_x2l_Faxa_snowc,i)   ! mm/s
-       forc_snowl(g)                                 = x2l(index_x2l_Faxa_snowl,i)   ! mm/s
-
-       ! atmosphere coupling, for prognostic/prescribed aerosols
-       atm2lnd_inst%forc_aer_grc(g,1)                = x2l(index_x2l_Faxa_bcphidry,i)
-       atm2lnd_inst%forc_aer_grc(g,2)                = x2l(index_x2l_Faxa_bcphodry,i)
-       atm2lnd_inst%forc_aer_grc(g,3)                = x2l(index_x2l_Faxa_bcphiwet,i)
-       atm2lnd_inst%forc_aer_grc(g,4)                = x2l(index_x2l_Faxa_ocphidry,i)
-       atm2lnd_inst%forc_aer_grc(g,5)                = x2l(index_x2l_Faxa_ocphodry,i)
-       atm2lnd_inst%forc_aer_grc(g,6)                = x2l(index_x2l_Faxa_ocphiwet,i)
-       atm2lnd_inst%forc_aer_grc(g,7)                = x2l(index_x2l_Faxa_dstwet1,i)
-       atm2lnd_inst%forc_aer_grc(g,8)                = x2l(index_x2l_Faxa_dstdry1,i)
-       atm2lnd_inst%forc_aer_grc(g,9)                = x2l(index_x2l_Faxa_dstwet2,i)
-       atm2lnd_inst%forc_aer_grc(g,10)               = x2l(index_x2l_Faxa_dstdry2,i)
-       atm2lnd_inst%forc_aer_grc(g,11)               = x2l(index_x2l_Faxa_dstwet3,i)
-       atm2lnd_inst%forc_aer_grc(g,12)               = x2l(index_x2l_Faxa_dstdry3,i)
-       atm2lnd_inst%forc_aer_grc(g,13)               = x2l(index_x2l_Faxa_dstwet4,i)
-       atm2lnd_inst%forc_aer_grc(g,14)               = x2l(index_x2l_Faxa_dstdry4,i)
-
-       if (index_x2l_Sa_methane /= 0) then
-          atm2lnd_inst%forc_pch4_grc(g) = x2l(index_x2l_Sa_methane,i)
-       endif
-
-       !--------------------------
-       ! Check for nans from coupler
-       !--------------------------
-
-       call check_for_nans(x2l(:,i), fname, begg, "x2l")
-
-    end do
-
-    !--------------------------
-    ! Derived quantities for required fields
-    ! and corresponding error checks
-    !--------------------------
-
-    call derive_quantities(bounds, atm2lnd_inst, wateratm2lndbulk_inst, &
-       forc_rainc, forc_rainl, forc_snowc, forc_snowl)
-
-    call check_for_errors(bounds, atm2lnd_inst, wateratm2lndbulk_inst)
-
-    ! Determine derived quantities for optional fields
-    ! Note that the following does unit conversions from ppmv to partial pressures (Pa)
-    ! Note that forc_pbot is in Pa
-
-    do g = begg,endg
-       i = 1 + (g - begg)
-
-       forc_pbot = atm2lnd_inst%forc_pbot_not_downscaled_grc(g)
-
-       ! Determine optional receive fields
-       if (index_x2l_Sa_co2prog /= 0) then
-          co2_ppmv_prog = x2l(index_x2l_Sa_co2prog,i)   ! co2 atm state prognostic
-       else
-          co2_ppmv_prog = co2_ppmv
-       end if
-       if (index_x2l_Sa_co2diag /= 0) then
-          co2_ppmv_diag = x2l(index_x2l_Sa_co2diag,i)   ! co2 atm state diagnostic
-       else
-          co2_ppmv_diag = co2_ppmv
-       end if
-
-       if (co2_type_idx == 1) then
-          co2_ppmv_val = co2_ppmv_prog
-       else if (co2_type_idx == 2) then
-          co2_ppmv_val = co2_ppmv_diag 
-       else
-          co2_ppmv_val = co2_ppmv
-       end if
-       if ( (co2_ppmv_val < 10.0_r8) .or. (co2_ppmv_val > 15000.0_r8) )then
-          call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, &
-               msg = sub//' ERROR: CO2 is outside of an expected range' )
-       end if
-       atm2lnd_inst%forc_pco2_grc(g) = co2_ppmv_val * 1.e-6_r8 * forc_pbot 
-       if (use_c13) then
-          atm2lnd_inst%forc_pc13o2_grc(g) = co2_ppmv_val * c13ratio * 1.e-6_r8 * forc_pbot
-       end if
-
-       if (ndep_from_cpl) then
-          ! The coupler is sending ndep in units if kgN/m2/s - and clm uses units of gN/m2/sec - so the
-          ! following conversion needs to happen
-          atm2lnd_inst%forc_ndep_grc(g) = (x2l(index_x2l_Faxa_nhx, i) + x2l(index_x2l_faxa_noy, i))*1000._r8
-       end if
-
-    end do
-
-    call glc2lnd_inst%set_glc2lnd_fields_mct( &
-         bounds = bounds, &
-         glc_present = glc_present, &
-         ! NOTE(wjs, 2017-12-13) the x2l argument doesn't have the typical bounds
-         ! subsetting (bounds%begg:bounds%endg). This mirrors the lack of these bounds in
-         ! the call to lnd_import from lnd_run_mct. This is okay as long as this code is
-         ! outside a clump loop.
-         x2l = x2l, &
-         index_x2l_Sg_ice_covered = index_x2l_Sg_ice_covered, &
-         index_x2l_Sg_topo = index_x2l_Sg_topo, &
-         index_x2l_Flgg_hflx = index_x2l_Flgg_hflx, &
-         index_x2l_Sg_icemask = index_x2l_Sg_icemask, &
-         index_x2l_Sg_icemask_coupled_fluxes = index_x2l_Sg_icemask_coupled_fluxes)
-
-  end subroutine lnd_import
-
-  !===============================================================================
-
-  subroutine lnd_export( bounds, waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x)
-
-    !---------------------------------------------------------------------------
-    ! !DESCRIPTION:
-    ! Convert the data to be sent from the clm model to the coupler 
-    ! 
-    ! !USES:
-    use shr_kind_mod       , only : r8 => shr_kind_r8
-    use seq_flds_mod       , only : seq_flds_l2x_fields
-    use clm_varctl         , only : iulog
-    use shr_drydep_mod     , only : n_drydep
-    use shr_megan_mod      , only : shr_megan_mechcomps_n
-    use shr_fire_emis_mod  , only : shr_fire_emis_mechcomps_n
-    use lnd_import_export_utils, only : check_for_nans
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type) , intent(in)    :: bounds  ! bounds
-    type(lnd2atm_type), intent(inout) :: lnd2atm_inst ! clm land to atmosphere exchange data type
-    type(lnd2glc_type), intent(inout) :: lnd2glc_inst ! clm land to atmosphere exchange data type
-    type(waterlnd2atmbulk_type), intent(in) :: waterlnd2atmbulk_inst
-    real(r8)          , intent(out)   :: l2x(:,:)! land to coupler export state on land grid
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begg, endg  ! bounds
-    integer  :: g,i,k ! indices
-    integer  :: ier   ! error status
-    integer  :: nstep ! time step index
-    integer  :: dtime ! time step   
-    integer  :: num   ! counter
-    character(len=32) :: fname       ! name of field that is NaN
-    character(len=32), parameter :: sub = 'lnd_export'
-    !---------------------------------------------------------------------------
-
-    ! Set bounds
-    begg = bounds%begg; endg = bounds%endg
-
-    ! cesm sign convention is that fluxes are positive downward
-
-    l2x(:,:) = 0.0_r8
-
-    do g = begg,endg
-       i = 1 + (g-begg)
-       l2x(index_l2x_Sl_t,i)        =  lnd2atm_inst%t_rad_grc(g)
-       l2x(index_l2x_Sl_snowh,i)    =  waterlnd2atmbulk_inst%h2osno_grc(g)
-       l2x(index_l2x_Sl_avsdr,i)    =  lnd2atm_inst%albd_grc(g,1)
-       l2x(index_l2x_Sl_anidr,i)    =  lnd2atm_inst%albd_grc(g,2)
-       l2x(index_l2x_Sl_avsdf,i)    =  lnd2atm_inst%albi_grc(g,1)
-       l2x(index_l2x_Sl_anidf,i)    =  lnd2atm_inst%albi_grc(g,2)
-       l2x(index_l2x_Sl_tref,i)     =  lnd2atm_inst%t_ref2m_grc(g)
-       l2x(index_l2x_Sl_qref,i)     =  waterlnd2atmbulk_inst%q_ref2m_grc(g)
-       l2x(index_l2x_Sl_u10,i)      =  lnd2atm_inst%u_ref10m_grc(g)
-       l2x(index_l2x_Fall_taux,i)   = -lnd2atm_inst%taux_grc(g)
-       l2x(index_l2x_Fall_tauy,i)   = -lnd2atm_inst%tauy_grc(g)
-       l2x(index_l2x_Fall_lat,i)    = -lnd2atm_inst%eflx_lh_tot_grc(g)
-       l2x(index_l2x_Fall_sen,i)    = -lnd2atm_inst%eflx_sh_tot_grc(g)
-       l2x(index_l2x_Fall_lwup,i)   = -lnd2atm_inst%eflx_lwrad_out_grc(g)
-       l2x(index_l2x_Fall_evap,i)   = -waterlnd2atmbulk_inst%qflx_evap_tot_grc(g)
-       l2x(index_l2x_Fall_swnet,i)  =  lnd2atm_inst%fsa_grc(g)
-       if (index_l2x_Fall_fco2_lnd /= 0) then
-          l2x(index_l2x_Fall_fco2_lnd,i) = -lnd2atm_inst%net_carbon_exchange_grc(g)  
-       end if
-
-       ! Additional fields for DUST, PROGSSLT, dry-deposition and VOC
-       ! These are now standard fields, but the check on the index makes sure the driver handles them
-       if (index_l2x_Sl_ram1      /= 0 )  l2x(index_l2x_Sl_ram1,i)     =  lnd2atm_inst%ram1_grc(g)
-       if (index_l2x_Sl_fv        /= 0 )  l2x(index_l2x_Sl_fv,i)       =  lnd2atm_inst%fv_grc(g)
-       if (index_l2x_Sl_soilw     /= 0 )  l2x(index_l2x_Sl_soilw,i)    =  waterlnd2atmbulk_inst%h2osoi_vol_grc(g,1)
-       if (index_l2x_Fall_flxdst1 /= 0 )  l2x(index_l2x_Fall_flxdst1,i)= -lnd2atm_inst%flxdst_grc(g,1)
-       if (index_l2x_Fall_flxdst2 /= 0 )  l2x(index_l2x_Fall_flxdst2,i)= -lnd2atm_inst%flxdst_grc(g,2)
-       if (index_l2x_Fall_flxdst3 /= 0 )  l2x(index_l2x_Fall_flxdst3,i)= -lnd2atm_inst%flxdst_grc(g,3)
-       if (index_l2x_Fall_flxdst4 /= 0 )  l2x(index_l2x_Fall_flxdst4,i)= -lnd2atm_inst%flxdst_grc(g,4)
-
-
-       ! for dry dep velocities
-       if (index_l2x_Sl_ddvel     /= 0 )  then
-          l2x(index_l2x_Sl_ddvel:index_l2x_Sl_ddvel+n_drydep-1,i) = &
-               lnd2atm_inst%ddvel_grc(g,:n_drydep)
-       end if
-
-       ! for MEGAN VOC emis fluxes
-       if (index_l2x_Fall_flxvoc  /= 0 ) then
-          l2x(index_l2x_Fall_flxvoc:index_l2x_Fall_flxvoc+shr_megan_mechcomps_n-1,i) = &
-               -lnd2atm_inst%flxvoc_grc(g,:shr_megan_mechcomps_n)
-       end if
-
-
-       ! for fire emis fluxes
-       if (index_l2x_Fall_flxfire  /= 0 ) then
-          l2x(index_l2x_Fall_flxfire:index_l2x_Fall_flxfire+shr_fire_emis_mechcomps_n-1,i) = &
-               -lnd2atm_inst%fireflx_grc(g,:shr_fire_emis_mechcomps_n)
-          l2x(index_l2x_Sl_ztopfire,i) = lnd2atm_inst%fireztop_grc(g)
-       end if
-
-       if (index_l2x_Fall_methane /= 0) then
-          l2x(index_l2x_Fall_methane,i) = -lnd2atm_inst%ch4_surf_flux_tot_grc(g)
-       endif
-
-       ! sign convention is positive downward with 
-       ! hierarchy of atm/glc/lnd/rof/ice/ocn.  
-       ! I.e. water sent from land to rof is positive
-
-       l2x(index_l2x_Flrl_rofsur,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsur_grc(g)
-
-       !  subsurface runoff is the sum of qflx_drain and qflx_perched_drain
-       l2x(index_l2x_Flrl_rofsub,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsub_grc(g) &
-            + waterlnd2atmbulk_inst%qflx_rofliq_drain_perched_grc(g)
-
-       !  qgwl sent individually to coupler
-       l2x(index_l2x_Flrl_rofgwl,i) = waterlnd2atmbulk_inst%qflx_rofliq_qgwl_grc(g)
-
-       ! ice  sent individually to coupler
-       l2x(index_l2x_Flrl_rofi,i) = waterlnd2atmbulk_inst%qflx_rofice_grc(g)
-
-       ! irrigation flux to be removed from main channel storage (negative)
-       l2x(index_l2x_Flrl_irrig,i) = - waterlnd2atmbulk_inst%qirrig_grc(g)
-
-       ! glc coupling
-       ! We could avoid setting these fields if glc_present is .false., if that would
-       ! help with performance. (The downside would be that we wouldn't have these fields
-       ! available for diagnostic purposes or to force a later T compset with dlnd.)
-       do num = 0,glc_nec
-          l2x(index_l2x_Sl_tsrf(num),i)   = lnd2glc_inst%tsrf_grc(g,num)
-          l2x(index_l2x_Sl_topo(num),i)   = lnd2glc_inst%topo_grc(g,num)
-          l2x(index_l2x_Flgl_qice(num),i) = lnd2glc_inst%qice_grc(g,num)
-       end do
-
-       !--------------------------
-       ! Check for nans to coupler
-       !--------------------------
-
-       call check_for_nans(l2x(:,i), fname, begg, "l2x")
-
-    end do
-
-  end subroutine lnd_export
-
-end module lnd_import_export
diff --git a/src/cpl/mct/lnd_set_decomp_and_domain.F90 b/src/cpl/mct/lnd_set_decomp_and_domain.F90
deleted file mode 100644
index 0a37554313..0000000000
--- a/src/cpl/mct/lnd_set_decomp_and_domain.F90
+++ /dev/null
@@ -1,352 +0,0 @@
-module lnd_set_decomp_and_domain
-
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use spmdMod      , only : masterproc
-  use clm_varctl   , only : iulog
-  use mct_mod      , only : mct_gsMap
-
-  implicit none
-  private ! except
-
-  ! public member routines
-  public :: lnd_set_decomp_and_domain_from_surfrd
-
-  ! private member routines
-  private :: surfrd_get_globmask  ! Reads global land mask (needed for setting domain decomp)
-  private :: surfrd_get_grid      ! Read grid/ladnfrac data into domain (after domain decomp)
-
-  ! translation between local and global indices at gridcell level
-  type(mct_gsmap), pointer, public :: gsmap_global           
-
-  ! translation between local and global indices at gridcell level for multiple levels
-  ! needed for 3d soil moisture stream
-  type(mct_gsmap), target , public :: gsMap_lnd2Dsoi_gdc2glo 
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-!===============================================================================
-contains
-!===============================================================================
-
-  subroutine lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj)
-
-    ! Initialize ldomain data types
-
-    use clm_varpar    , only: nlevsoi
-    use clm_varctl    , only: fatmlndfrc, use_soil_moisture_streams
-    use decompInitMod , only: decompInit_lnd
-    use decompMod     , only: bounds_type, get_proc_bounds
-    use domainMod     , only: ldomain, domain_check
-
-    ! input/output variables
-    logical, intent(out) :: noland
-    integer, intent(out) :: ni, nj ! global grid sizes
-
-    ! local variables
-    integer ,pointer  :: amask(:)   ! global land mask
-    integer           :: begg, endg ! processor bounds
-    type(bounds_type) :: bounds     ! bounds
-    character(len=32) :: subname = 'lnd_set_decomp_and_domain_from_surfrd'
-    !-----------------------------------------------------------------------
-
-    ! Read in global land grid and land mask (amask)- needed to set decomposition
-    ! global memory for amask is allocate in surfrd_get_glomask - must be deallocated below
-    if (masterproc) then
-       write(iulog,*) 'Attempting to read global land mask from ',trim(fatmlndfrc)
-    endif
-
-    ! Get global mask, ni and nj
-    call surfrd_get_globmask(filename=fatmlndfrc, mask=amask, ni=ni, nj=nj)
-
-    ! Exit early if no valid land points
-    if ( all(amask == 0) )then
-       if (masterproc) write(iulog,*) trim(subname)//': no valid land points do NOT run clm'
-       noland = .true.
-       return
-    else
-       noland = .false.
-    end if
-
-    ! Determine ctsm gridcell decomposition and processor bounds for gridcells
-    call decompInit_lnd(ni, nj, amask)
-    deallocate(amask)
-    if (use_soil_moisture_streams) call decompInit_lnd3D(ni, nj, nlevsoi)
-
-    ! Initialize bounds for just gridcells
-    ! Remaining bounds (landunits, columns, patches) will be determined
-    ! after the call to decompInit_glcp - so get_proc_bounds is called
-    ! twice and the gridcell information is just filled in twice
-    call get_proc_bounds(bounds)
-
-    ! Get grid cell bounds values
-    begg = bounds%begg
-    endg = bounds%endg
-
-    ! Initialize ldomain data type
-    if (masterproc) then
-       write(iulog,*) 'Attempting to read ldomain from ',trim(fatmlndfrc)
-    endif
-    call surfrd_get_grid(begg, endg, ldomain, fatmlndfrc)
-    if (masterproc) then
-       call domain_check(ldomain)
-    endif
-    ldomain%mask = 1  !!! TODO - is this needed?
-
-  end subroutine lnd_set_decomp_and_domain_from_surfrd
-
-  !-----------------------------------------------------------------------
-  subroutine surfrd_get_globmask(filename, mask, ni, nj)
-
-    ! Read the surface dataset grid related information
-    ! This is used to set the domain decomposition - so global data is read here
-
-    use fileutils  , only : getfil
-    use ncdio_pio  , only : ncd_io, ncd_pio_openfile, ncd_pio_closefile, ncd_inqfdims, file_desc_t
-    use abortutils , only : endrun
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-
-    ! input/output variables
-    character(len=*), intent(in)    :: filename  ! grid filename
-    integer         , pointer       :: mask(:)   ! grid mask
-    integer         , intent(out)   :: ni, nj    ! global grid sizes
-
-    ! local variables
-    logical               :: isgrid2d
-    integer               :: dimid,varid ! netCDF id's
-    integer               :: ns          ! size of grid on file
-    integer               :: n,i,j       ! index
-    integer               :: ier         ! error status
-    type(file_desc_t)     :: ncid        ! netcdf id
-    character(len=256)    :: locfn       ! local file name
-    logical               :: readvar     ! read variable in or not
-    integer , allocatable :: idata2d(:,:)
-    character(len=32) :: subname = 'surfrd_get_globmask' ! subroutine name
-    !-----------------------------------------------------------------------
-
-    if (filename == ' ') then
-       mask(:) = 1
-    else
-       ! Check if file exists
-       if (masterproc) then
-          if (filename == ' ') then
-             write(iulog,*) trim(subname),' ERROR: filename must be specified '
-             call endrun(msg=errMsg(sourcefile, __LINE__))
-          endif
-       end if
-
-       ! Open file
-       call getfil( filename, locfn, 0 )
-       call ncd_pio_openfile (ncid, trim(locfn), 0)
-
-       ! Determine dimensions and if grid file is 2d or 1d
-       call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
-       if (masterproc) then
-          write(iulog,*)'lat/lon grid flag (isgrid2d) is ',isgrid2d
-       end if
-       allocate(mask(ns))
-       mask(:) = 1
-       if (isgrid2d) then
-          ! Grid is 2d
-          allocate(idata2d(ni,nj))
-          idata2d(:,:) = 1
-          call ncd_io(ncid=ncid, varname='LANDMASK', data=idata2d, flag='read', readvar=readvar)
-          if (.not. readvar) then
-             call ncd_io(ncid=ncid, varname='mask', data=idata2d, flag='read', readvar=readvar)
-          end if
-          if (readvar) then
-             do j = 1,nj
-                do i = 1,ni
-                   n = (j-1)*ni + i
-                   mask(n) = idata2d(i,j)
-                enddo
-             enddo
-          end if
-          deallocate(idata2d)
-       else
-          ! Grid is not 2d
-          call ncd_io(ncid=ncid, varname='LANDMASK', data=mask, flag='read', readvar=readvar)
-          if (.not. readvar) then
-             call ncd_io(ncid=ncid, varname='mask', data=mask, flag='read', readvar=readvar)
-          end if
-       end if
-       if (.not. readvar) call endrun( msg=' ERROR: landmask not on fatmlndfrc file'//errMsg(sourcefile, __LINE__))
-
-       ! Close file
-       call ncd_pio_closefile(ncid)
-    end if
-
-  end subroutine surfrd_get_globmask
-
-  !-----------------------------------------------------------------------
-  subroutine surfrd_get_grid(begg, endg, ldomain, filename)
-
-    ! Read the surface dataset grid related information:
-    ! This is called after the domain decomposition has been created
-    ! - real latitude  of grid cell (degrees)
-    ! - real longitude of grid cell (degrees)
-
-    use clm_varcon   , only : spval, re, grlnd
-    use domainMod    , only : domain_type, lon1d, lat1d, domain_init
-    use fileutils    , only : getfil
-    use abortutils   , only : endrun
-    use shr_log_mod  , only : errMsg => shr_log_errMsg
-    use ncdio_pio    , only : file_desc_t, ncd_pio_openfile, ncd_pio_closefile
-    use ncdio_pio    , only : ncd_io, check_var, ncd_inqfdims, check_dim_size
-    use pio
-
-    ! input/output variables
-    integer                    , intent(in)    :: begg, endg
-    type(domain_type)          , intent(inout) :: ldomain     ! domain to init
-    character(len=*)           , intent(in)    :: filename    ! grid filename
-
-    ! local variables
-    type(file_desc_t)     :: ncid               ! netcdf id
-    integer               :: beg                ! local beg index
-    integer               :: end                ! local end index
-    integer               :: ni,nj,ns           ! size of grid on file
-    logical               :: readvar            ! true => variable is on input file
-    logical               :: isgrid2d           ! true => file is 2d lat/lon
-    logical               :: istype_domain      ! true => input file is of type domain
-    real(r8), allocatable :: rdata2d(:,:)       ! temporary
-    character(len=16)     :: vname              ! temporary
-    character(len=256)    :: locfn              ! local file name
-    integer               :: n                  ! indices
-    character(len=32) :: subname = 'surfrd_get_grid'     ! subroutine name
-    !-----------------------------------------------------------------------
-
-    if (masterproc) then
-       if (filename == ' ') then
-          write(iulog,*) trim(subname),' ERROR: filename must be specified '
-          call endrun(msg=errMsg(sourcefile, __LINE__))
-       endif
-    end if
-
-    call getfil( filename, locfn, 0 )
-    call ncd_pio_openfile (ncid, trim(locfn), 0)
-
-    ! Determine dimensions
-    call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
-
-    ! Determine isgrid2d flag for domain
-    call domain_init(ldomain, isgrid2d=isgrid2d, ni=ni, nj=nj, nbeg=begg, nend=endg)
-
-    ! Determine type of file - old style grid file or new style domain file
-    call check_var(ncid=ncid, varname='xc', readvar=readvar)
-    if (readvar)then
-        istype_domain = .true.
-    else
-        istype_domain = .false.
-    end if
-
-    ! Read in area, lon, lat
-    if (istype_domain) then
-       call ncd_io(ncid=ncid, varname= 'area', flag='read', data=ldomain%area, &
-            dim1name=grlnd, readvar=readvar)
-       ! convert from radians**2 to km**2
-       ldomain%area = ldomain%area * (re**2)
-       if (.not. readvar) call endrun( msg=' ERROR: area NOT on file'//errMsg(sourcefile, __LINE__))
-       call ncd_io(ncid=ncid, varname= 'xc', flag='read', data=ldomain%lonc, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) call endrun( msg=' ERROR: xc NOT on file'//errMsg(sourcefile, __LINE__))
-       call ncd_io(ncid=ncid, varname= 'yc', flag='read', data=ldomain%latc, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) call endrun( msg=' ERROR: yc NOT on file'//errMsg(sourcefile, __LINE__))
-    else
-       call endrun( msg=" ERROR: can no longer read non domain files" )
-    end if
-
-    if (isgrid2d) then
-       allocate(rdata2d(ni,nj), lon1d(ni), lat1d(nj))
-       if (istype_domain) vname = 'xc'
-       call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar)
-       lon1d(:) = rdata2d(:,1)
-       if (istype_domain) vname = 'yc'
-       call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar)
-       lat1d(:) = rdata2d(1,:)
-       deallocate(rdata2d)
-    end if
-
-    ! Check lat limited to -90,90
-    if (minval(ldomain%latc) < -90.0_r8 .or. &
-        maxval(ldomain%latc) >  90.0_r8) then
-       write(iulog,*) trim(subname),' WARNING: lat/lon min/max is ', &
-            minval(ldomain%latc),maxval(ldomain%latc)
-    endif
-    if ( any(ldomain%lonc < 0.0_r8) )then
-       call endrun( msg=' ERROR: lonc is negative (see https://github.com/ESCOMP/ctsm/issues/507)' &
-            //errMsg(sourcefile, __LINE__))
-    endif
-    call ncd_io(ncid=ncid, varname='mask', flag='read', data=ldomain%mask, &
-         dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun( msg=' ERROR: LANDMASK NOT on fracdata file'//errMsg(sourcefile, __LINE__))
-    end if
-    call ncd_io(ncid=ncid, varname='frac', flag='read', data=ldomain%frac, &
-         dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun( msg=' ERROR: LANDFRAC NOT on fracdata file'//errMsg(sourcefile, __LINE__))
-    end if
-
-    call ncd_pio_closefile(ncid)
-
-  end subroutine surfrd_get_grid
-
-  !------------------------------------------------------------------------------
-  subroutine decompInit_lnd3D(lni,lnj,lnk)
-    !
-    ! !DESCRIPTION:
-    !  Create a 3D decomposition gsmap for the global 2D grid with soil levels
-    !  as the 3rd dimesnion.
-    !
-    ! !USES:
-    use decompMod, only : gindex_global, bounds_type, get_proc_bounds
-    use spmdMod  , only : comp_id, mpicom
-    use mct_mod  , only : mct_gsmap_init 
-    !
-    ! !ARGUMENTS:
-    integer , intent(in) :: lni,lnj,lnk   ! domain global size
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: m,n,k                 ! indices
-    integer           :: begg,endg,lsize,gsize ! used for gsmap init
-    integer           :: begg3d,endg3d
-    integer, pointer  :: gindex(:)             ! global index for gsmap init
-    type(bounds_type) :: bounds
-    !------------------------------------------------------------------------------
-
-    ! Initialize gsmap_lnd2dsoi_gdc2glo
-    call get_proc_bounds(bounds)
-    begg = bounds%begg; endg=bounds%endg
-
-    begg3d = (begg-1)*lnk + 1
-    endg3d = endg*lnk
-    lsize = (endg3d - begg3d + 1 )
-    allocate(gindex(begg3d:endg3d))
-    do k = 1, lnk
-       do n = begg,endg
-          m = (begg-1)*lnk + (k-1)*(endg-begg+1) + (n-begg+1)
-          gindex(m) = gindex_global(n-begg+1) + (k-1)*(lni*lnj)
-       enddo
-    enddo
-    gsize = lni * lnj * lnk
-    call mct_gsMap_init(gsMap_lnd2Dsoi_gdc2glo, gindex, mpicom, comp_id, lsize, gsize)
-
-    ! Diagnostic output
-
-    if (masterproc) then
-       write(iulog,*)' 3D GSMap'
-       write(iulog,*)'   longitude points               = ',lni
-       write(iulog,*)'   latitude points                = ',lnj
-       write(iulog,*)'   soil levels                    = ',lnk
-       write(iulog,*)'   gsize                          = ',gsize
-       write(iulog,*)'   lsize                          = ',lsize
-       write(iulog,*)'   bounds(gindex)                 = ',size(gindex)
-       write(iulog,*)
-    end if
-
-    deallocate(gindex)
-
-  end subroutine decompInit_lnd3D
-
-end module lnd_set_decomp_and_domain
diff --git a/src/cpl/mct/ndepStreamMod.F90 b/src/cpl/mct/ndepStreamMod.F90
deleted file mode 100644
index d26ff7c95e..0000000000
--- a/src/cpl/mct/ndepStreamMod.F90
+++ /dev/null
@@ -1,376 +0,0 @@
-module ndepStreamMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Contains methods for reading in nitrogen deposition data file
-  ! Also includes functions for dynamic ndep file handling and
-  ! interpolation.
-  !
-  ! !USES
-  use shr_kind_mod, only: r8 => shr_kind_r8, CL => shr_kind_cl
-  use shr_strdata_mod, only: shr_strdata_type, shr_strdata_create
-  use shr_strdata_mod, only: shr_strdata_print, shr_strdata_advance
-  use mct_mod     , only: mct_ggrid
-  use spmdMod     , only: mpicom, masterproc, comp_id, iam
-  use clm_varctl  , only: iulog, inst_name
-  use abortutils  , only: endrun
-  use decompMod   , only: bounds_type
-  use domainMod   , only: ldomain
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: ndep_init      ! position datasets for dynamic ndep
-  public :: ndep_interp    ! interpolates between two years of ndep file data
-  public :: clm_domain_mct ! Sets up MCT domain for this resolution
-
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: check_units   ! Check the units and make sure they can be used
-
-  ! ! PRIVATE TYPES
-  type(shr_strdata_type)  :: sdat           ! input data stream
-  integer :: stream_year_first_ndep         ! first year in stream to use
-  integer :: stream_year_last_ndep          ! last year in stream to use
-  integer :: model_year_align_ndep          ! align stream_year_firstndep with
-  logical :: divide_by_secs_per_yr = .true. ! divide by the number of seconds per year
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !==============================================================================
-
-contains
-
-  !==============================================================================
-
-  subroutine ndep_init(bounds, NLFilename)
-   !
-   ! Initialize data stream information.
-   !
-   ! Uses:
-   use shr_kind_mod     , only : CS => shr_kind_cs
-   use clm_time_manager , only : get_calendar
-   use ncdio_pio        , only : pio_subsystem
-   use shr_pio_mod      , only : shr_pio_getiotype
-   use shr_nl_mod       , only : shr_nl_find_group_name
-   use shr_log_mod      , only : errMsg => shr_log_errMsg
-   use shr_mpi_mod      , only : shr_mpi_bcast
-   use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global
-   !
-   ! arguments
-   implicit none
-   type(bounds_type), intent(in) :: bounds
-   character(len=*),  intent(in) :: NLFilename   ! Namelist filename
-   !
-   ! local variables
-   integer            :: nu_nml    ! unit for namelist file
-   integer            :: nml_error ! namelist i/o error flag
-   type(mct_ggrid)    :: dom_clm   ! domain information
-   character(len=CL)  :: stream_fldFileName_ndep
-   character(len=CL)  :: ndepmapalgo = 'bilinear'
-   character(len=CL)  :: ndep_tintalgo = 'linear'
-   character(len=CS)  :: ndep_taxmode = 'extend'
-   character(len=CL)  :: ndep_varlist = 'NDEP_year'
-   character(*), parameter :: shr_strdata_unset = 'NOT_SET'
-   character(*), parameter :: subName = "('ndepdyn_init')"
-   character(*), parameter :: F00 = "('(ndepdyn_init) ',4a)"
-   !-----------------------------------------------------------------------
-
-   namelist /ndepdyn_nml/          &
-        stream_year_first_ndep,    &
-        stream_year_last_ndep,     &
-        model_year_align_ndep,     &
-        ndepmapalgo, ndep_taxmode, &
-        ndep_varlist,              &
-        stream_fldFileName_ndep,   &
-        ndep_tintalgo
-
-   ! Default values for namelist
-    stream_year_first_ndep  = 1                ! first year in stream to use
-    stream_year_last_ndep   = 1                ! last  year in stream to use
-    model_year_align_ndep   = 1                ! align stream_year_first_ndep with this model year
-    stream_fldFileName_ndep = ' '
-
-   ! Read ndepdyn_nml namelist
-   if (masterproc) then
-      open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-      call shr_nl_find_group_name(nu_nml, 'ndepdyn_nml', status=nml_error)
-      if (nml_error == 0) then
-         read(nu_nml, nml=ndepdyn_nml,iostat=nml_error)
-         if (nml_error /= 0) then
-            call endrun(msg=' ERROR reading ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__))
-         end if
-      else
-         call endrun(msg=' ERROR finding ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__))
-      end if
-      close(nu_nml)
-   endif
-
-   call shr_mpi_bcast(stream_year_first_ndep , mpicom)
-   call shr_mpi_bcast(stream_year_last_ndep  , mpicom)
-   call shr_mpi_bcast(model_year_align_ndep  , mpicom)
-   call shr_mpi_bcast(stream_fldFileName_ndep, mpicom)
-   call shr_mpi_bcast(ndep_varlist           , mpicom)
-   call shr_mpi_bcast(ndep_taxmode           , mpicom)
-   call shr_mpi_bcast(ndep_tintalgo          , mpicom)
-
-   if (masterproc) then
-      write(iulog,*) ' '
-      write(iulog,*) 'ndepdyn stream settings:'
-      write(iulog,*) '  stream_year_first_ndep  = ',stream_year_first_ndep
-      write(iulog,*) '  stream_year_last_ndep   = ',stream_year_last_ndep
-      write(iulog,*) '  model_year_align_ndep   = ',model_year_align_ndep
-      write(iulog,*) '  stream_fldFileName_ndep = ',stream_fldFileName_ndep
-      write(iulog,*) '  ndep_varList            = ',ndep_varList
-      write(iulog,*) '  ndep_taxmode            = ',ndep_taxmode
-      write(iulog,*) '  ndep_tintalgo           = ',ndep_tintalgo
-      write(iulog,*) ' '
-   endif
-   ! Read in units
-   call check_units( stream_fldFileName_ndep, ndep_varList )
-
-   ! Set domain and create streams
-   call clm_domain_mct (bounds, dom_clm)
-
-   call shr_strdata_create(sdat,name="clmndep",    &
-        pio_subsystem=pio_subsystem,               &
-        pio_iotype=shr_pio_getiotype(inst_name),   &
-        mpicom=mpicom, compid=comp_id,             &
-        gsmap=gsmap_global, ggrid=dom_clm,         &
-        nxg=ldomain%ni, nyg=ldomain%nj,            &
-        yearFirst=stream_year_first_ndep,          &
-        yearLast=stream_year_last_ndep,            &
-        yearAlign=model_year_align_ndep,           &
-        offset=0,                                  &
-        domFilePath='',                            &
-        domFileName=trim(stream_fldFileName_ndep), &
-        domTvarName='time',                        &
-        domXvarName='lon' ,                        &
-        domYvarName='lat' ,                        &
-        domAreaName='area',                        &
-        domMaskName='mask',                        &
-        filePath='',                               &
-        filename=(/trim(stream_fldFileName_ndep)/),&
-        fldListFile=ndep_varlist,                  &
-        fldListModel=ndep_varlist,                 &
-        fillalgo='none',                           &
-        mapalgo=ndepmapalgo,                       &
-        tintalgo=ndep_tintalgo,                    &
-        calendar=get_calendar(),                   &
-        taxmode=ndep_taxmode                       )
-
-
-   if (masterproc) then
-      call shr_strdata_print(sdat,'CLMNDEP data')
-   endif
-
- end subroutine ndep_init
- !================================================================
-
- subroutine check_units( stream_fldFileName_ndep, ndep_varList )
-   !-------------------------------------------------------------------
-   ! Check that units are correct on the file and if need any conversion
-   use ncdio_pio     , only : ncd_pio_openfile, ncd_inqvid, ncd_getatt, ncd_pio_closefile, ncd_nowrite
-   use ncdio_pio     , only : file_desc_t, var_desc_t
-   use shr_kind_mod  , only : CS => shr_kind_cs
-   use shr_log_mod   , only : errMsg => shr_log_errMsg
-   use shr_string_mod, only : shr_string_listGetName
-   implicit none
-
-   !-----------------------------------------------------------------------
-   !
-   ! Arguments
-   character(len=*), intent(IN)  :: stream_fldFileName_ndep  ! ndep filename
-   character(len=*), intent(IN)  :: ndep_varList             ! ndep variable list to examine
-   !
-   ! Local variables
-   type(file_desc_t) :: ncid     ! NetCDF filehandle for ndep file
-   type(var_desc_t)  :: vardesc  ! variable descriptor
-   integer           :: varid    ! variable index
-   logical           :: readvar  ! If variable was read
-   character(len=CS) :: ndepunits! ndep units
-   character(len=CS) :: fname    ! ndep field name
-   !-----------------------------------------------------------------------
-   call ncd_pio_openfile( ncid, trim(stream_fldFileName_ndep), ncd_nowrite )
-   call shr_string_listGetName( ndep_varList, 1, fname )
-   call ncd_inqvid(       ncid, fname, varid, vardesc, readvar=readvar )
-   if ( readvar ) then
-      call ncd_getatt(    ncid, varid, "units", ndepunits )
-   else
-      call endrun(msg=' ERROR finding variable: '//trim(fname)//" in file: "// &
-                      trim(stream_fldFileName_ndep)//errMsg(sourcefile, __LINE__))
-   end if
-   call ncd_pio_closefile( ncid )
-
-   ! Now check to make sure they are correct
-   if (      trim(ndepunits) == "g(N)/m2/s"  )then
-      divide_by_secs_per_yr = .false.
-   else if ( trim(ndepunits) == "g(N)/m2/yr" )then
-      divide_by_secs_per_yr = .true.
-   else
-      call endrun(msg=' ERROR in units for nitrogen deposition equal to: '//trim(ndepunits)//" not units expected"// &
-                      errMsg(sourcefile, __LINE__))
-   end if
-
- end subroutine check_units
-
- !================================================================
- subroutine ndep_interp(bounds, atm2lnd_inst)
-
-   !-----------------------------------------------------------------------
-   use clm_time_manager, only : get_curr_date, get_curr_days_per_year
-   use clm_varcon      , only : secspday
-   use atm2lndType     , only : atm2lnd_type
-   !
-   ! Arguments
-   type(bounds_type) , intent(in)    :: bounds
-   type(atm2lnd_type), intent(inout) :: atm2lnd_inst
-   !
-   ! Local variables
-   integer :: g, ig
-   integer :: year    ! year (0, ...) for nstep+1
-   integer :: mon     ! month (1, ..., 12) for nstep+1
-   integer :: day     ! day of month (1, ..., 31) for nstep+1
-   integer :: sec     ! seconds into current date for nstep+1
-   integer :: mcdate  ! Current model date (yyyymmdd)
-   integer :: dayspyr ! days per year
-   !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ndepdyn')
-
-   if ( divide_by_secs_per_yr )then
-      ig = 0
-      dayspyr = get_curr_days_per_year( )
-      do g = bounds%begg,bounds%endg
-         ig = ig+1
-         atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) / (secspday * dayspyr)
-      end do
-   else
-      ig = 0
-      do g = bounds%begg,bounds%endg
-         ig = ig+1
-         atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig)
-      end do
-   end if
-
- end subroutine ndep_interp
-
- !==============================================================================
-  subroutine clm_domain_mct(bounds, dom_clm, nlevels)
-
-    !-------------------------------------------------------------------
-    ! Set domain data type for internal clm grid
-    use clm_varcon                , only : re
-    use domainMod                 , only : ldomain
-    use mct_mod                   , only : mct_ggrid, mct_gsMap_lsize, mct_gGrid_init
-    use mct_mod                   , only : mct_gsMap_orderedPoints, mct_gGrid_importIAttr
-    use mct_mod                   , only : mct_gGrid_importRAttr, mct_gsMap
-    use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global
-    implicit none
-    !
-    ! arguments
-    type(bounds_type), intent(in) :: bounds
-    type(mct_ggrid), intent(out)   :: dom_clm     ! Output domain information for land model
-    integer, intent(in), optional :: nlevels      ! Number of levels if this is a 3D field
-    !
-    ! local variables
-    integer :: g,i,j,k            ! index
-    integer :: lsize              ! land model domain data size
-    real(r8), pointer :: data(:)  ! temporary
-    integer , pointer :: idata(:) ! temporary
-    integer :: nlevs              ! Number of vertical levels
-    type(mct_gsMap), pointer :: gsmap => null() ! MCT GS map
-    !-------------------------------------------------------------------
-    ! SEt number of levels, and get the GS map for either the 2D or 3D grid
-    nlevs = 1
-    if ( present(nlevels) ) nlevs = nlevels
-    if ( nlevs == 1 ) then
-       gsmap => gsmap_global
-    else
-       gsmap => gsMap_lnd2Dsoi_gdc2glo
-    end if
-    !
-    ! Initialize mct domain type
-    ! lat/lon in degrees,  area in radians^2, mask is 1 (land), 0 (non-land)
-    ! Note that in addition land carries around landfrac for the purposes of domain checking
-    !
-    lsize = mct_gsMap_lsize(gsmap, mpicom)
-    call mct_gGrid_init( GGrid=dom_clm, &
-         CoordChars='lat:lon:hgt', OtherChars='area:aream:mask:frac', lsize=lsize )
-    !
-    ! Allocate memory
-    !
-    allocate(data(lsize))
-    !
-    ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT
-    !
-    call mct_gsMap_orderedPoints(gsmap, iam, idata)
-    gsmap => null()
-    call mct_gGrid_importIAttr(dom_clm,'GlobGridNum',idata,lsize)
-    !
-    ! Determine domain (numbering scheme is: West to East and South to North to South pole)
-    ! Initialize attribute vector with special value
-    !
-    data(:) = -9999.0_R8
-    call mct_gGrid_importRAttr(dom_clm,"lat"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_clm,"lon"  ,data,lsize)
-    call mct_gGrid_importRAttr(dom_clm,"area" ,data,lsize)
-    call mct_gGrid_importRAttr(dom_clm,"aream",data,lsize)
-    data(:) = 0.0_R8
-    call mct_gGrid_importRAttr(dom_clm,"mask" ,data,lsize)
-    !
-    ! Determine bounds
-    !
-    ! Fill in correct values for domain components
-    ! Note aream will be filled in in the atm-lnd mapper
-    !
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%lonc(g)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"lon",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%latc(g)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"lat",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%area(g)/(re*re)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"area",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%mask(g), r8)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"mask",data,lsize)
-
-    do k = 1, nlevs
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%frac(g), r8)
-    end do
-    end do
-    call mct_gGrid_importRattr(dom_clm,"frac",data,lsize)
-
-    deallocate(data)
-    deallocate(idata)
-
-  end subroutine clm_domain_mct
-
-end module ndepStreamMod

From 4cbc00d42ba54b07fd1992e7d574b94c29ae939b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 10:48:35 -0600
Subject: [PATCH 0284/1248] Remove another mct comment

---
 src/cpl/nuopc/lnd_import_export.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/cpl/nuopc/lnd_import_export.F90 b/src/cpl/nuopc/lnd_import_export.F90
index 11cc807640..b9966f81e9 100644
--- a/src/cpl/nuopc/lnd_import_export.F90
+++ b/src/cpl/nuopc/lnd_import_export.F90
@@ -248,7 +248,6 @@ subroutine advertise_fields(gcomp, flds_scalar_name, glc_present, cism_evolve, r
     if (shr_megan_mechcomps_n .ne. megan_nflds) call shr_sys_abort('ERROR: megan field count mismatch')
 
     ! CARMA volumetric soil water from land
-    ! TODO: is the following correct - the CARMA field exchange is very confusing in mct
     call shr_carma_readnl('drv_flds_in', carma_fields)
 
     ! export to atm

From 854ff9d438aa24edb644459f31c89494ed4ee983 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 10:50:43 -0600
Subject: [PATCH 0285/1248] Remove
 cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb directory

---
 .../testdefs/testmods_dirs/clm/nuopc_cap_bfb/README    | 10 ----------
 .../testmods_dirs/clm/nuopc_cap_bfb/include_user_mods  |  1 -
 .../testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl        |  4 ----
 3 files changed, 15 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl

diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README
deleted file mode 100644
index aefd8adee7..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README
+++ /dev/null
@@ -1,10 +0,0 @@
-This testmod directory currently isn't used in any tests, but is useful
-for the following reason:
-
-According to Mariana Vertenstein: At least at one point, you could get
-bit-for-bit answers when comparing the mct and nuopc versions of CTSM in
-an I compset with SROF and SGLC, if using the changes in this testmod in
-both the mct and nuopc runs.
-
-So we are keeping this around in case someone wants to reproduce that
-comparison.
diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods
deleted file mode 100644
index fe0e18cf88..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl
deleted file mode 100644
index 6bfefec90b..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl
+++ /dev/null
@@ -1,4 +0,0 @@
-orb_eccen = 0.
-orb_mvelp = 0.
-orb_obliq = 0.
-orb_mode = "fixed_parameters"

From 6b6ea52f5271866c525cef19c480c2c7bbc35031 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 10:55:30 -0600
Subject: [PATCH 0286/1248] Remove mention of mct in README.NUOPC_driver.md

---
 README.NUOPC_driver.md | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/README.NUOPC_driver.md b/README.NUOPC_driver.md
index 9eb5d5b2cb..6caf63a9bd 100644
--- a/README.NUOPC_driver.md
+++ b/README.NUOPC_driver.md
@@ -40,9 +40,3 @@ ESMF_PROFILING_LEVEL --- Verbosity level for ESMF profiling
 nuopc.runseq is a text file that determines how the driver operates. You can change the operation
 by having an updated copy in your case directory.
 
-
-## What if I want to use the MCT driver?
-
-The MCT driver is now removed. For more notes see:
-
-https://docs.google.com/presentation/d/1yjiKSEV53JDAJbYxhpY2T9GTxlWFzQAn

From 40367c56210797ae6fe27991be8cb82f9708894d Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 10:56:28 -0600
Subject: [PATCH 0287/1248] Remove an expected failure the mentions mct in
 ExpectedTestFails.xml

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index dc850d51ab..a29e55cc9e 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -143,13 +143,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld1_Mmpi-serial_Vmct.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsRLA">
-    <phase name="SHAREDLIB_BUILD">
-      <status>FAIL</status>
-      <issue>#1887</issue>
-    </phase>
-  </test>
-
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>

From e99eaeaba4a502277e4b2f99096b0e130cff46d8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 11:00:11 -0600
Subject: [PATCH 0288/1248] Add back mct to Externals.cfg

---
 Externals.cfg | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/Externals.cfg b/Externals.cfg
index cb2622dedf..8ef524bf24 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -69,6 +69,13 @@ repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
 required = True
 
+[mct]
+tag = MCT_2.11.0
+protocol = git
+repo_url = https://github.com/MCSclimate/MCT
+local_path = libraries/mct
+required = True
+
 [parallelio]
 tag = pio2_6_2
 protocol = git

From fed6805e85ca0c2ccb6eada9946f4c4f634f5e54 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 11:05:10 -0600
Subject: [PATCH 0289/1248] Remove /test subdirectory

---
 test/tools/CLM_compare.sh                     |  39 -----
 test/tools/Makefile                           |  12 --
 test/tools/README                             |  73 ----------
 test/tools/README.testnames                   |  69 ---------
 test/tools/TBLCFGtools.sh                     | 120 ----------------
 test/tools/TBLscript_tools.sh                 | 122 ----------------
 test/tools/TBLtools.sh                        | 119 ---------------
 test/tools/TCBCFGtools.sh                     | 135 ------------------
 test/tools/TCBtools.sh                        | 121 ----------------
 test/tools/TSMCFGtools.sh                     | 113 ---------------
 test/tools/TSMscript_tools.sh                 |  98 -------------
 test/tools/TSMtools.sh                        | 117 ---------------
 test/tools/config_files/CFGtools__ds          |   0
 test/tools/config_files/README                |   9 --
 test/tools/config_files/tools__do             |   1 -
 test/tools/config_files/tools__ds             |   1 -
 test/tools/config_files/tools__o              |   1 -
 test/tools/config_files/tools__s              |   1 -
 test/tools/gen_test_table.sh                  |  80 -----------
 test/tools/get_cprnc_diffs.sh                 |  56 --------
 test/tools/input_tests_master                 |  32 -----
 test/tools/nl_files/mesh_maker_fv09           |   1 -
 test/tools/nl_files/mkmapdata_if10            |   1 -
 test/tools/nl_files/mkmapdata_ne30np4         |   1 -
 .../nl_files/mkprocdata_ne30_to_f19_I2000     |   1 -
 test/tools/nl_files/modify_data_YELL          |   1 -
 test/tools/nl_files/run_neon_OSBS             |   1 -
 test/tools/nl_files/run_neon_YELL_PRISM       |   1 -
 test/tools/nl_files/subset_data_KONA          |   1 -
 test/tools/nl_files/subset_data_US-UMB        |   1 -
 test/tools/nl_files/subset_data_YELL          |   1 -
 .../nl_files/subset_data_f09_1x1pt_townshipSD |   1 -
 .../subset_data_f09_37x288pt_PanBoreal        |   1 -
 .../subset_data_f09_4x9pt_AlaskaTananaValley  |   1 -
 .../subset_data_f09_58x45pt_SouthAmerica      |   1 -
 .../subset_data_f09_90x288pt_1850PanTropics   |   1 -
 test/tools/show_var_diffs.sh                  |  79 ----------
 test/tools/tests_posttag_hobart_nompi         |   1 -
 test/tools/tests_posttag_nompi_regression     |   1 -
 test/tools/tests_pretag_cheyenne_nompi        |   3 -
 test/tools/tests_pretag_derecho_nompi         |   9 --
 test/tools/tests_pretag_nompi_neon            |   8 --
 42 files changed, 1435 deletions(-)
 delete mode 100755 test/tools/CLM_compare.sh
 delete mode 100644 test/tools/Makefile
 delete mode 100644 test/tools/README
 delete mode 100644 test/tools/README.testnames
 delete mode 100755 test/tools/TBLCFGtools.sh
 delete mode 100755 test/tools/TBLscript_tools.sh
 delete mode 100755 test/tools/TBLtools.sh
 delete mode 100755 test/tools/TCBCFGtools.sh
 delete mode 100755 test/tools/TCBtools.sh
 delete mode 100755 test/tools/TSMCFGtools.sh
 delete mode 100755 test/tools/TSMscript_tools.sh
 delete mode 100755 test/tools/TSMtools.sh
 delete mode 100644 test/tools/config_files/CFGtools__ds
 delete mode 100644 test/tools/config_files/README
 delete mode 100644 test/tools/config_files/tools__do
 delete mode 100644 test/tools/config_files/tools__ds
 delete mode 100644 test/tools/config_files/tools__o
 delete mode 100644 test/tools/config_files/tools__s
 delete mode 100755 test/tools/gen_test_table.sh
 delete mode 100755 test/tools/get_cprnc_diffs.sh
 delete mode 100644 test/tools/input_tests_master
 delete mode 100644 test/tools/nl_files/mesh_maker_fv09
 delete mode 100644 test/tools/nl_files/mkmapdata_if10
 delete mode 100644 test/tools/nl_files/mkmapdata_ne30np4
 delete mode 100644 test/tools/nl_files/mkprocdata_ne30_to_f19_I2000
 delete mode 100644 test/tools/nl_files/modify_data_YELL
 delete mode 100644 test/tools/nl_files/run_neon_OSBS
 delete mode 100644 test/tools/nl_files/run_neon_YELL_PRISM
 delete mode 100644 test/tools/nl_files/subset_data_KONA
 delete mode 100644 test/tools/nl_files/subset_data_US-UMB
 delete mode 100644 test/tools/nl_files/subset_data_YELL
 delete mode 100644 test/tools/nl_files/subset_data_f09_1x1pt_townshipSD
 delete mode 100644 test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal
 delete mode 100644 test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley
 delete mode 100644 test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica
 delete mode 100644 test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics
 delete mode 100755 test/tools/show_var_diffs.sh
 delete mode 100644 test/tools/tests_posttag_hobart_nompi
 delete mode 100644 test/tools/tests_posttag_nompi_regression
 delete mode 100644 test/tools/tests_pretag_cheyenne_nompi
 delete mode 100644 test/tools/tests_pretag_derecho_nompi
 delete mode 100644 test/tools/tests_pretag_nompi_neon

diff --git a/test/tools/CLM_compare.sh b/test/tools/CLM_compare.sh
deleted file mode 100755
index 38f547c3ab..0000000000
--- a/test/tools/CLM_compare.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 2 ]; then
-    echo "CLM_compare.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-echo "CLM_compare.sh: comparing $1 " 
-echo "                with      $2" 
-
-##note syntax here as stderr and stdout from cprnc command go 
-##to separate places!
-${CPRNC_EXE} ${CPRNC_OPT} $1 $2 2>&1 > cprnc.out
-rc=$?
-if [ $rc -ne 0 ]; then
-    echo "CLM_compare.sh: error doing comparison, cprnc error= $rc" 
-    exit 2
-fi
-
-result_old=`perl -e 'while (my $ll = <>) \
-    { if ($ll =~ /(\d+)[^0-9]+compared[^0-9]+(\d+)/) \
-    { print "PASS" if $1>0 && $2==0 }}' cprnc.out`
-if grep -c "the two files seem to be IDENTICAL" cprnc.out > /dev/null; then
-   result=PASS
-elif grep -c "the two files seem to be DIFFERENT" cprnc.out > /dev/null; then
-   result=FAIL
-else
-   result=$result_old
-fi
-
-if [ "$result" = "PASS" ]; then
-    echo "CLM_compare.sh: files are b4b" 
-else
-    echo "CLM_compare.sh: files are NOT b4b" 
-    exit 3
-fi
-
-exit 0
diff --git a/test/tools/Makefile b/test/tools/Makefile
deleted file mode 100644
index b5031abdba..0000000000
--- a/test/tools/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-#
-# Makefile to build clm testing documentation
-#
-
-# Get list of tests_ files
-SOURCES    = $(wildcard tests_*)
-
-all: test_table.html
-
-test_table.html: $(SOURCES)
-	gen_test_table.sh
-
diff --git a/test/tools/README b/test/tools/README
deleted file mode 100644
index c545f625b8..0000000000
--- a/test/tools/README
+++ /dev/null
@@ -1,73 +0,0 @@
-$CTSMROOT/clm/test/tools/README					06/08/2018
-
-Scripts for testing the CLM support tools with many different 
-configurations and run-time options.
-
-I.   MAIN SCRIPTS:
-
-test_driver.sh - Test the CLM offline tools
-
-To use...
-
-./test_driver.sh -i
-
-on Derecho
-
-qcmd -l walltime=08:00:00 -- ./test_driver.sh -i >& run.out &
-
-And to for example to compare to another baseline code (in this case ctsm5.1.dev066, which would need to be cloned at the given
-path) ...
-
-qcmd -l walltime=08:00:00 -- env BL_ROOT=/glade/scratch/erik/ctsm5.1.dev066 ./test_driver.sh -i >& run.out &
-
-on izumi
-
-nohup ./test_driver.sh -i >& run.out &
-
-release tests
-
-qcmd -l walltime=10:00:00 -- env CLM_INPUT_TESTS=`pwd`/tests_posttag_nompi_regression \
-./test_driver.sh -i >& run_regress.out &
-
-To run neon-specific tests, please use login nodes:
-env CLM_INPUT_TESTS=`pwd`/tests_pretag_nompi_neon ./test_driver.sh -i > & run_neon.out &
-
-
-Intended for use on NCAR machines Derecho, Casper (DAV) and izumi.
-
-II. RUNNING test_driver.sh TOOLS TESTING:
-
-Basic use:
-
-./test_driver.sh -i
-./test_driver.sh -h   # to get help on options
- 
-Important environment variables (just used by test_driver.sh)
-
-BL_ROOT ---------------- Root directory of CLM baseline code to compare to 
-                         (if not set BL test will not be performed)
-BL_TESTDIR ------------- Root directory of where to put baseline tests
-CLM_INPUT_TESTS -------- Filename of file with list of tests to perform
-CLM_TESTDIR ------------ Root directory of where to put most tests
-CLM_RETAIN_FILES ------- If set to TRUE -- don't cleanup files after testing
-CLM_FC ----------------- Use given compiler
-CLM_JOBID -------------- Job identification number to use (rather than process ID)
-CLM_THREADS ------------ Number of open-MP threads to use 
-                         (by default this is set differently by machine)
-CLM_SOFF --------------- If set to TRUE -- stop on first failed test (default FALSE)
-
-Important files for test_driver tools testing:
-
-test_driver.sh ------- Main test script for tools
-nl_files ------------- Directory with various namelists to test
-config_files --------- Directory with various configurations to test
-input_tests_master --- Master list of tests
-tests_pretag_* ------- Tests for specific machines to do by default before a tag is done
-tests_posttag_* ------ Tests for specific machines to do for more extensive testing 
-                       after a tag is done
-CLM_compare.sh ------- Compares output history files between two cases
-T*.sh ---------------- Basic test script to do a specific type of test
-gen_test_table.sh ---- Creates HTML table of tests
-Makefile ------------- Will build the HTML table of tests
-
-../../tools/README.testing - Information on how the testing works for the CLM tools
diff --git a/test/tools/README.testnames b/test/tools/README.testnames
deleted file mode 100644
index 74dbe8e5f3..0000000000
--- a/test/tools/README.testnames
+++ /dev/null
@@ -1,69 +0,0 @@
-Tests for test_driver are for the CLM tools only.
-
-Test naming conventions for the test_driver.sh script:
-
-Test names are:
-
-xxnmi
-
-Where: xx is the two-letter test type 
-       sm=smoke, br=branch, er=exact restart, bl=base-line comparision,
-       cb=configure-build, rp=reproducibility, op=OpenMP threading for tools
-
-n is the configuration type:
-
-1 -- unused
-2 -- unused
-3 -- unused
-4 -- unused
-5 -- unused
-6 -- unused
-7 -- unused
-8 -- unused
-9 -- mesh_maker
-0 -- run_neon
-a -- modify_data
-b -- subset_data
-c -- mkprocdata_map
-d -- mkmapgrids
-e -- unused
-f -- unused
-g -- unused
-h -- unused
-i -- tools scripts
-
-m is the resolution
-
-0 -- 0.9x1.25
-1 -- 48x96
-5 -- 10x15
-6 -- 5x5_amazon
-7 -- 1x1 brazil
-8 -- US-UMB
-9 -- 4x5
-a -- NEON YELL
-b -- NEON KONA
-c -- NEON OSBS
-d -- SouthAmerica
-e -- 1850PanTropics
-f -- PanBoreal
-g -- AlaskaTananaValley
-h -- single point from the 0.9x1.25 grid (Township SD)
-y -- 1.9x2.5 with transient 1850-2100 for rcp=2.6 and glacier-MEC on
-T -- 1x1_numaIA
-Z -- 10x15 with crop on
-@ -- ne120np4
-# -- ne30np4
-
-i is the specific test (usually this implies...)
-
-1 -- Serial  script
-2 -- Serial
-3 -- OpenMP only
-4 -- serial, DEBUG
-7 -- OpenMP only second test, DEBUG
-8 -- OpenMP only third test, DEBUG
-9 -- Serial Script
-0 -- Serial Script
-
-
diff --git a/test/tools/TBLCFGtools.sh b/test/tools/TBLCFGtools.sh
deleted file mode 100755
index 6276c885e2..0000000000
--- a/test/tools/TBLCFGtools.sh
+++ /dev/null
@@ -1,120 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 3 ]; then
-    echo "TBLCFGtools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-if [ -z "$BL_ROOT" ] && [ -z "$BL_TESTDIR" ]; then
-    echo "TBL.sh: no environment variables set for baseline test - will skip"
-    exit 255
-fi
-
-tool=$(basename $1)
-test_name=TBLCFGtools.$tool.$2.$3
-
-if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TBLCFGtools.sh: smoke test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TBLCFGtools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TBLCFGtools.sh: smoke test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TBLCFGtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-rundir=${CLM_TESTDIR}/${test_name}
-if [ -d ${rundir} ]; then
-    rm -r ${rundir}
-fi
-mkdir -p ${rundir} 
-if [ $? -ne 0 ]; then
-    echo "TBLCFGtools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${rundir}
-
-echo "TBLCFGtools.sh: calling TSMCFGtools.sh to run $tool executable" 
-${CLM_SCRIPTDIR}/TSMCFGtools.sh $1 $2 $3
-rc=$?
-if [ $rc -ne 0 ]; then
-    echo "TBLCFGtools.sh: error from TSMCFGtools.sh= $rc" 
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 4
-fi
-
-if [ -n "${BL_ROOT}" ]; then
-    if [ -z "$BL_TESTDIR" ]; then
-        BL_TESTDIR=${CLM_TESTDIR}.bl
-    fi
-    echo "TBLCFGtools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR"
-
-    echo "TBLCFGtools.sh: calling ****baseline**** TSMCFGtools.sh for smoke test"
-    bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools`
-    env CLM_TESTDIR=${BL_TESTDIR} \
-        CLM_ROOT=${BL_ROOT} \
-        CLM_SCRIPTDIR=$bl_dir \
-        $bl_dir/TSMCFGtools.sh $1 $2 $3
-    rc=$?
-    if [ $rc -ne 0 ]; then
-        echo "TBLCFGtools.sh: error from *baseline* TSMCFGtools.sh= $rc"
-        echo "FAIL.job${JOBID}" > TestStatus
-        exit 5
-    fi
-fi
-
-echo "TBLCFGtools.sh: starting b4b comparisons "
-files_to_compare=`cd ${CLM_TESTDIR}/TSMCFGtools.$tool.$2.$3; ls *.nc`
-if [ -z "${files_to_compare}" ] && [ "$debug" != "YES" ]; then
-    echo "TBLCFGtools.sh: error locating files to compare"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 6
-fi
-
-all_comparisons_good="TRUE"
-for compare_file in ${files_to_compare}; do
-
-    env CPRNC_OPT="-m" \
-        ${CLM_SCRIPTDIR}/CLM_compare.sh \
-        ${BL_TESTDIR}/TSMCFGtools.$tool.$2.$3/${compare_file} \
-        ${CLM_TESTDIR}/TSMCFGtools.$tool.$2.$3/${compare_file}
-    rc=$?
-    mv cprnc.out cprnc.${compare_file}.out
-    if [ $rc -eq 0 ]; then
-        echo "TBLCFGtools.sh: comparison successful; output in ${rundir}/cprnc.${compare_file}.out"
-    else
-        echo "TBLCFGtools.sh: error from CLM_compare.sh= $rc; see ${rundir}/cprnc.${compare_file}.out for details
-"
-        all_comparisons_good="FALSE"
-    fi
-done
-
-if [ ${all_comparisons_good} = "TRUE" ]; then
-    echo "TBLCFGtools.sh: baseline test passed"
-    echo "PASS" > TestStatus
-    if [ $CLM_RETAIN_FILES != "TRUE" ]; then
-        echo "TBLCFGtools.sh: removing some unneeded files to save disc space"
-        rm *.nc
-        rm *.r*
-    fi
-else
-    echo "TBLCFGtools.sh: at least one file comparison did not pass"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 7
-fi
-
-exit 0
diff --git a/test/tools/TBLscript_tools.sh b/test/tools/TBLscript_tools.sh
deleted file mode 100755
index d05492c687..0000000000
--- a/test/tools/TBLscript_tools.sh
+++ /dev/null
@@ -1,122 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 3 ]; then
-    echo "TBLscript_tools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-if [ -z "$BL_ROOT" ] && [ -z "$BL_TESTDIR" ]; then
-    echo "TBLscript_tools.sh: no environment variables set for baseline test - will skip"
-    exit 255
-fi
-
-test_name=TBLscript_tools.$1.$2.$3
-
-if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TBLscript_tools.sh: smoke test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TBLscript_tools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TBLscript_tools.sh: smoke test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TBLscript_tools.sh: this smoke test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-rundir=${CLM_TESTDIR}/${test_name}
-if [ -d ${rundir} ]; then
-    rm -r ${rundir}
-fi
-mkdir -p ${rundir} 
-if [ $? -ne 0 ]; then
-    echo "TBLscript_tools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${rundir}
-
-echo "TBLscript_tools.sh: calling TSMscript_tools.sh to run $1 executable" 
-${CLM_SCRIPTDIR}/TSMscript_tools.sh $1 $2 $3
-rc=$?
-if [ $rc -ne 0 ]; then
-    echo "TBLscript_tools.sh: error from TSMtools.sh= $rc" 
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 4
-fi
-
-if [ -n "${BL_ROOT}" ]; then
-    if [ -z "$BL_TESTDIR" ]; then
-        BL_TESTDIR=${CLM_TESTDIR}.bl
-    fi
-    echo "TBLscript_tools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR"
-
-    echo "TBLscript_tools.sh: calling ****baseline**** TSMtools.sh for smoke test"
-    bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools`
-    env CLM_TESTDIR=${BL_TESTDIR} \
-        CLM_SCRIPTDIR=$bl_dir \
-        CLM_ROOT=$BL_ROOT \
-        CTSM_ROOT=$BL_ROOT \
-        CIME_ROOT=$BL_ROOT/cime \
-        $bl_dir/TSMscript_tools.sh $1 $2 $3
-    rc=$?
-    if [ $rc -ne 0 ]; then
-        echo "TBLscript_tools.sh: error from *baseline* TSMscript_tools.sh= $rc"
-        echo "FAIL.job${JOBID}" > TestStatus
-        exit 5
-    fi
-fi
-
-echo "TBLscript_tools.sh: starting b4b comparisons "
-files_to_compare=`cd ${CLM_TESTDIR}/TSMscript_tools.$1.$2.$3; ls *.nc`
-if [ -z "${files_to_compare}" ] && [ "$debug" != "YES" ]; then
-    echo "TBLscript_tools.sh: error locating files to compare"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 6
-fi
-
-all_comparisons_good="TRUE"
-for compare_file in ${files_to_compare}; do
-
-    env CPRNC_OPT="-m" \
-        ${CLM_SCRIPTDIR}/CLM_compare.sh \
-        ${BL_TESTDIR}/TSMscript_tools.$1.$2.$3/${compare_file} \
-        ${CLM_TESTDIR}/TSMscript_tools.$1.$2.$3/${compare_file}
-    rc=$?
-    mv cprnc.out cprnc.${compare_file}.out
-    if [ $rc -eq 0 ]; then
-        echo "TBLscript_tools.sh: comparison successful; output in ${rundir}/cprnc.${compare_file}.out"
-    else
-        echo "TBLscript_tools.sh: error from CLM_compare.sh= $rc; see ${rundir}/cprnc.${compare_file}.out for details"
-        all_comparisons_good="FALSE"
-    fi
-done
-
-if [ ${all_comparisons_good} = "TRUE" ]; then
-    echo "TBLscript_tools.sh: baseline test passed"
-    echo "PASS" > TestStatus
-    if [ $CLM_RETAIN_FILES != "TRUE" ]; then
-        echo "TBLscript_tools.sh: removing some unneeded files to save disc space"
-        rm *.nc
-        rm *.r*
-    fi
-else
-    echo "TBLscript_tools.sh: at least one file comparison did not pass"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 7
-fi
-
-
-
-exit 0
diff --git a/test/tools/TBLtools.sh b/test/tools/TBLtools.sh
deleted file mode 100755
index 555ea7d1be..0000000000
--- a/test/tools/TBLtools.sh
+++ /dev/null
@@ -1,119 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 3 ]; then
-    echo "TBLtools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-if [ -z "$BL_ROOT" ] && [ -z "$BL_TESTDIR" ]; then
-    echo "TBL.sh: no environment variables set for baseline test - will skip"
-    exit 255
-fi
-
-test_name=TBLtools.$1.$2.$3
-
-if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TBLtools.sh: smoke test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TBLtools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TBLtools.sh: smoke test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TBLtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-rundir=${CLM_TESTDIR}/${test_name}
-if [ -d ${rundir} ]; then
-    rm -r ${rundir}
-fi
-mkdir -p ${rundir} 
-if [ $? -ne 0 ]; then
-    echo "TBLtools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${rundir}
-
-echo "TBLtools.sh: calling TSMtools.sh to run $1 executable" 
-${CLM_SCRIPTDIR}/TSMtools.sh $1 $2 $3
-rc=$?
-if [ $rc -ne 0 ]; then
-    echo "TBLtools.sh: error from TSMtools.sh= $rc" 
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 4
-fi
-
-if [ -n "${BL_ROOT}" ]; then
-    if [ -z "$BL_TESTDIR" ]; then
-        BL_TESTDIR=${CLM_TESTDIR}.bl
-    fi
-    echo "TBLtools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR"
-
-    echo "TBLtools.sh: calling ****baseline**** TSMtools.sh for smoke test"
-    bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools`
-    env CLM_TESTDIR=${BL_TESTDIR} \
-        CLM_ROOT=${BL_ROOT} \
-        CLM_SCRIPTDIR=$bl_dir \
-        $bl_dir/TSMtools.sh $1 $2 $3
-    rc=$?
-    if [ $rc -ne 0 ]; then
-        echo "TBLtools.sh: error from *baseline* TSMtools.sh= $rc"
-        echo "FAIL.job${JOBID}" > TestStatus
-        exit 5
-    fi
-fi
-
-echo "TBLtools.sh: starting b4b comparisons "
-files_to_compare=`cd ${CLM_TESTDIR}/TSMtools.$1.$2.$3; ls *.nc`
-if [ -z "${files_to_compare}" ] && [ "$debug" != "YES" ]; then
-    echo "TBLtools.sh: error locating files to compare"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 6
-fi
-
-all_comparisons_good="TRUE"
-for compare_file in ${files_to_compare}; do
-
-    env CPRNC_OPT="-m" \
-        ${CLM_SCRIPTDIR}/CLM_compare.sh \
-        ${BL_TESTDIR}/TSMtools.$1.$2.$3/${compare_file} \
-        ${CLM_TESTDIR}/TSMtools.$1.$2.$3/${compare_file}
-    rc=$?
-    mv cprnc.out cprnc.${compare_file}.out
-    if [ $rc -eq 0 ]; then
-        echo "TBLtools.sh: comparison successful; output in ${rundir}/cprnc.${compare_file}.out"
-    else
-        echo "TBLtools.sh: error from CLM_compare.sh= $rc; see ${rundir}/cprnc.${compare_file}.out for details
-"
-        all_comparisons_good="FALSE"
-    fi
-done
-
-if [ ${all_comparisons_good} = "TRUE" ]; then
-    echo "TBLtools.sh: baseline test passed"
-    echo "PASS" > TestStatus
-    if [ $CLM_RETAIN_FILES != "TRUE" ]; then
-        echo "TBLtools.sh: removing some unneeded files to save disc space"
-        rm *.nc
-        rm *.r*
-    fi
-else
-    echo "TBLtools.sh: at least one file comparison did not pass"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 7
-fi
-
-exit 0
diff --git a/test/tools/TCBCFGtools.sh b/test/tools/TCBCFGtools.sh
deleted file mode 100755
index 5c0b015123..0000000000
--- a/test/tools/TCBCFGtools.sh
+++ /dev/null
@@ -1,135 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 2 ]; then
-    echo "TCBCFGtools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-tool=$(basename $1)
-test_name=TCBCFGtools.$tool.$2
-
-if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TCBCFGtools.sh: build test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TCBCFGtools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TCBCFGtools.sh: build test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TCBCFGtools.sh: this build test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-cfgdir=`ls -1d ${CLM_ROOT}/tools/${1}`
-if [ $? -ne 0 ];then
-   cfgdir=`ls -1d ${CIME_ROOT}/tools/mapping/${1}*`
-   echo "use: $cfgdir"
-fi
-blddir=${CLM_TESTDIR}/${test_name}/src
-if [ -d ${blddir} ]; then
-    rm -r ${blddir}
-fi
-mkdir -p ${blddir}
-if [ $? -ne 0 ]; then
-    echo "TCBCFGtools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${blddir}
-
-echo "TCBCFGtools.sh: building $tool executable; output in ${blddir}/test.log" 
-#
-# Copy build files over
-#
-cp $cfgdir/src/Makefile .
-cp $cfgdir/src/Filepath .
-#
-# Add cfgdir path to beginning of each path in Filepath
-#
-touch Filepath
-while read filepath_arg; do
-    echo "${cfgdir}/src/${filepath_arg}" >> Filepath
-done < ${cfgdir}/src/Filepath
-
-#
-# Figure out configuration
-#
-if [ ! -f ${CLM_SCRIPTDIR}/config_files/$tool ]; then
-    echo "TCB.sh: configure options file ${CLM_SCRIPTDIR}/config_files/$tool not found"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 4
-fi
-
-##construct string of args to configure
-config_string=" "
-while read config_arg; do
-    config_string="${config_string}${config_arg} "
-done < ${CLM_SCRIPTDIR}/config_files/$tool
-
-if [ "$TOOLSLIBS" != "" ]; then
-   export SLIBS=$TOOLSLIBS
-fi
-echo "env CIMEROOT=$CLM_ROOT/cime COMPILER=$CESM_COMP $config_string $CLM_ROOT/cime/tools/configure --macros-format Makefile --machine $CESM_MACH $TOOLS_CONF_STRING"
-env       CIMEROOT=$CLM_ROOT/cime COMPILER=$CESM_COMP $config_string $CLM_ROOT/cime/tools/configure --macros-format Makefile --machine $CESM_MACH $TOOLS_CONF_STRING >> test.log 2>&1
-rc=$?
-if [ $rc -ne 0 ]; then
-   echo "TCBCFGtools.sh: configure failed, error from configure= $rc" 
-   echo "TCBCFGtools.sh: see ${blddir}/test.log for details"
-   echo "FAIL.job${JOBID}" > TestStatus
-   exit 5
-fi
-
-. $INITMODULES
-. ./.env_mach_specific.sh
-
-attempt=1
-still_compiling="TRUE"
-while [ $still_compiling = "TRUE" ]; do
-
-    echo "TCBCFGtools.sh: call to make:" 
-    echo "        ${MAKE_CMD} USER_CPPDEFS=-DLINUX"
-    if [ "$debug" != "YES" ]; then
-       ${MAKE_CMD} USER_CPPDEFS=-DLINUX >> test.log 2>&1
-       status="PASS"
-       rc=$?
-    else
-       status="GEN"
-       rc=0
-    fi
-    if [ $rc -eq 0 ]; then
-	echo "TCBCFGtools.sh: make was successful" 
-	echo "TCBCFGtools.sh: configure and build test passed"
-	echo "$status" > TestStatus
-	if [ $CLM_RETAIN_FILES != "TRUE" ]; then
-	    echo "TCBCFGtools.sh: removing some unneeded files to save disc space" 
-	    rm *.o
-	    rm *.mod
-	fi
-	still_compiling="FALSE"
-    elif [ $attempt -lt 10 ] && \
-        grep -c "LICENSE MANAGER PROBLEM" test.log > /dev/null; then
-        attempt=`expr $attempt + 1`
-        echo "TCBCFGtools.sh: encountered License Manager Problem; launching attempt #$attempt"
-    else
-	echo "TCBCFGtools.sh: clm build failed, error from make= $rc" 
-	echo "TCBCFGtools.sh: see ${blddir}/test.log for details"
-	echo "FAIL.job${JOBID}" > TestStatus
-	exit 6
-    fi
-done
-if [ "$TOOLSLIBS" != "" ]; then
-   export -n SLIBS
-fi
-
-exit 0
diff --git a/test/tools/TCBtools.sh b/test/tools/TCBtools.sh
deleted file mode 100755
index 205b2e9da0..0000000000
--- a/test/tools/TCBtools.sh
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 2 ]; then
-    echo "TCBtools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-test_name=TCBtools.$1.$2
-
-if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TCBtools.sh: build test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TCBtools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TCBtools.sh: build test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TCBtools.sh: this build test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-cfgdir=`ls -1d ${CLM_ROOT}/tools/$1`
-blddir=${CLM_TESTDIR}/${test_name}/src
-if [ -d ${blddir} ]; then
-    rm -r ${blddir}
-fi
-mkdir -p ${blddir}
-if [ $? -ne 0 ]; then
-    echo "TCBtools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${blddir}
-
-echo "TCBtools.sh: building $1 executable; output in ${blddir}/test.log" 
-#
-# Copy build files over
-#
-cp $cfgdir/src/Makefile      .
-cp $cfgdir/src/Srcfiles      .
-cp $cfgdir/src/Mkdepends     .
-cp $cfgdir/src/Makefile.common .
-#
-# Add cfgdir path to beginning of each path in Filepath
-#
-touch Filepath
-while read filepath_arg; do
-    echo "${cfgdir}/src/${filepath_arg}" >> Filepath
-done < ${cfgdir}/src/Filepath
-
-#
-# Figure out configuration
-#
-if [ ! -f ${CLM_SCRIPTDIR}/config_files/$2 ]; then
-    echo "TCB.sh: configure options file ${CLM_SCRIPTDIR}/config_files/$2 not found"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 4
-fi
-
-##construct string of args to configure
-config_string="$TOOLS_MAKE_STRING TOOLROOT=$cfgdir "
-while read config_arg; do
-    config_string="${config_string}${config_arg} "
-done < ${CLM_SCRIPTDIR}/config_files/$2
-
-attempt=1
-still_compiling="TRUE"
-if [ "$TOOLSLIBS" != "" ]; then
-   export SLIBS=$TOOLSLIBS
-fi
-while [ $still_compiling = "TRUE" ]; do
-
-    ln -s Macros.make Macros
-
-    echo "TCBtools.sh: call to make:" 
-    echo "        ${MAKE_CMD} ${config_string} "
-    if [ "$debug" != "YES" ]; then
-       ${MAKE_CMD} ${config_string} >> test.log 2>&1
-       status="PASS"
-       rc=$(( $rc + $? ))
-    else
-       status="GEN"
-       rc=0
-    fi
-    if [ $rc -eq 0 ]; then
-	echo "TCBtools.sh: make was successful" 
-	echo "TCBtools.sh: configure and build test passed"
-	echo "$status" > TestStatus
-	if [ $CLM_RETAIN_FILES != "TRUE" ]; then
-	    echo "TCBtools.sh: removing some unneeded files to save disc space" 
-	    rm *.o
-	    rm *.mod
-	fi
-	still_compiling="FALSE"
-    elif [ $attempt -lt 10 ] && \
-        grep -c "LICENSE MANAGER PROBLEM" test.log > /dev/null; then
-        attempt=`expr $attempt + 1`
-        echo "TCBtools.sh: encountered License Manager Problem; launching attempt #$attempt"
-    else
-	echo "TCBtools.sh: clm build failed, error from make= $rc" 
-	echo "TCBtools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details"
-	echo "FAIL.job${JOBID}" > TestStatus
-	exit 6
-    fi
-done
-if [ "$TOOLSLIBS" != "" ]; then
-   export -n SLIBS
-fi
-
-exit 0
diff --git a/test/tools/TSMCFGtools.sh b/test/tools/TSMCFGtools.sh
deleted file mode 100755
index b667a4c6ec..0000000000
--- a/test/tools/TSMCFGtools.sh
+++ /dev/null
@@ -1,113 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 3 ]; then
-    echo "TSMCFGtools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-tool=$(basename $1)
-test_name=TSMCFGtools.$tool.$2.$3
-
-
-if [ -z "$CLM_RERUN" ]; then
-  CLM_RERUN="no"
-fi
-
-if [ "$CLM_RERUN" != "yes" ] && [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TSMCFGtools.sh: smoke test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TSMCFGtools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TSMCFGtools.sh: smoke test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TSMCFGtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-cfgdir=`ls -1d ${CLM_ROOT}/tools/${1}*`
-rundir=${CLM_TESTDIR}/${test_name}
-if [ -d ${rundir} ]; then
-    rm -r ${rundir}
-fi
-mkdir -p ${rundir} 
-if [ $? -ne 0 ]; then
-    echo "TSMCFGtools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${rundir}
-
-echo "TSMCFGtools.sh: calling TCBCFGtools.sh to prepare $tool executable" 
-${CLM_SCRIPTDIR}/TCBCFGtools.sh $1 $2
-rc=$?
-if [ $rc -ne 0 ]; then
-    echo "TSMCFGtools.sh: error from TCBtools.sh= $rc" 
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 4
-fi
-
-echo "TSMCFGtools.sh: running $tool output in ${rundir}/test.log" 
-
-if [ "$2" = "CFGtools__o" ] || [ "$2" = "CFGtools__do" ]; then
-   toolrun="env OMP_NUM_THREADS=${CLM_THREADS} ${CLM_TESTDIR}/TCBCFGtools.$tool.$2/${tool}*"
-else
-   toolrun="${CLM_TESTDIR}/TCBCFGtools.$tool.$2/${tool}*"
-fi
-
-runfile="${CLM_SCRIPTDIR}/nl_files/$tool.$3"
-if [ ! -f "${runfile}" ]; then
-   echo "TSMCFGtools.sh: error ${runfile} input run file not found"
-   echo "FAIL.job${JOBID}" > TestStatus
-   exit 5
-fi
-
-echo "Run file type = ${3#*.}"
-if [ ${3#*.} == "runoptions" ]; then
-  runopts=`cat ${runfile} | sed -e "s|CSMDATA|$CSMDATA|g"`
-  echo "$toolrun $runopts"
-  cp $cfgdir/*.nc .
-  if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then
-     $toolrun  $runopts >> test.log 2>&1
-     rc=$?
-     status="PASS"
-  else
-     echo "Successfully created file" > test.log
-     status="GEN"
-     rc=0
-  fi
-else
-  echo "$toolrun < ${runfile}"
-  if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then
-     $toolrun < ${runfile} >> test.log 2>&1
-     rc=$?
-     status="PASS"
-  else
-     echo "Successfully created file" > test.log
-     status="GEN"
-     rc=0
-  fi
-fi
-
-if [ $rc -eq 0 ] && grep -ci "Successfully created " test.log > /dev/null; then
-    echo "TSMCFGtools.sh: smoke test passed" 
-    echo "$status" > TestStatus
-else
-    echo "TSMCFGtools.sh: error running $tool, error= $rc" 
-    echo "TSMCFGtools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 6
-fi
-
-exit 0
diff --git a/test/tools/TSMscript_tools.sh b/test/tools/TSMscript_tools.sh
deleted file mode 100755
index 943fec97f2..0000000000
--- a/test/tools/TSMscript_tools.sh
+++ /dev/null
@@ -1,98 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 3 ]; then
-    echo "TSMscript_tools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-test_name=TSMscript_tools.$1.$2.$3
-
-if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TSMscript_tools.sh: smoke test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TSMscript_tools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TSMscript_tools.sh: smoke test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TSMscript_tools.sh: this smoke test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-cfgdir=`ls -1d ${CLM_ROOT}/tools/$1`
-rundir=${CLM_TESTDIR}/${test_name}
-if [ -d ${rundir} ]; then
-    rm -r ${rundir}
-fi
-mkdir -p ${rundir} 
-if [ $? -ne 0 ]; then
-    echo "TSMscript_tools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${rundir}
-
-optfile=${3%^*}
-cfgfile=${3#*^}
-
-if [ "$optfile" != "$3" ]; then
-  echo "TSMscript_tools.sh: calling TCBtools.sh to prepare $1 executable"
-  ${CLM_SCRIPTDIR}/TCBtools.sh $1 $cfgfile
-  rc=$?
-  if [ $rc -ne 0 ]; then
-      echo "TSMscript_tools.sh: error from TCBtools.sh= $rc"
-      echo "FAIL.job${JOBID}" > TestStatus
-      exit 4
-  fi 
-  tcbtools=${CLM_TESTDIR}/TCBtools.$1.$cfgfile
-else
-  tcbtools="$rundir"
-fi
-
-scopts=`cat ${CLM_SCRIPTDIR}/nl_files/$optfile | sed -e "s|CSMDATA|$CSMDATA|g" | sed -e "s|EXEDIR|$tcbtools|g" | sed -e "s|CFGDIR|$cfgdir|g"`
-scopts=`echo $scopts | sed -e "s|CTSM_ROOT|$CTSM_ROOT|g" | sed -e "s|CIME_ROOT|$CIME_ROOT|g"`
-
-echo "TSMscript_tools.sh: running ${cfgdir}/$2 with $scopts; output in ${rundir}/test.log" 
-
-if [ ! -f "${cfgdir}/$2" ]; then
-    echo "TSMscript_tools.sh: error ${cfgdir}/$2 input script not found"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 5
-fi
-
-if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then
-   ${cfgdir}/$2 $scopts >> test.log 2>&1
-   rc=$?
-   status="PASS"
-else
-   echo "success" > test.log
-   status="GEN"
-   rc=0
-fi
-
-if [ $rc -eq 0 ] && grep -ci "Successfully " test.log > /dev/null; then
-    echo "TSMscript_tools.sh: smoke test passed" 
-    echo "$status" > TestStatus
-    # Copy files from subdirectories up...
-    # (use hard links rather than symbolic links because 'ln -s' does funny
-    # things when there are no matching files)
-    ln */*.nc */*/*.nc .
-else
-    echo "TSMscript_tools.sh: error running $2, error= $rc" 
-    echo "TSMscript_tools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 6
-fi
-
-exit 0
diff --git a/test/tools/TSMtools.sh b/test/tools/TSMtools.sh
deleted file mode 100755
index 33a2316973..0000000000
--- a/test/tools/TSMtools.sh
+++ /dev/null
@@ -1,117 +0,0 @@
-#!/bin/sh 
-#
-
-if [ $# -ne 3 ]; then
-    echo "TSMtools.sh: incorrect number of input arguments" 
-    exit 1
-fi
-
-test_name=TSMtools.$1.$2.$3
-
-if [ -z "$CLM_RERUN" ]; then
-  CLM_RERUN="no"
-fi
-
-if [ "$CLM_RERUN" != "yes" ] && [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then
-    if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TSMtools.sh: smoke test has already passed; results are in "
-	echo "        ${CLM_TESTDIR}/${test_name}" 
-        exit 0
-    elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then
-        echo "TSMtools.sh: test already generated"
-    else
-	read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus
-        prev_jobid=${fail_msg#*job}
-
-	if [ $JOBID = $prev_jobid ]; then
-            echo "TSMtools.sh: smoke test has already failed for this job - will not reattempt; "
-	    echo "        results are in: ${CLM_TESTDIR}/${test_name}" 
-	    exit 2
-	else
-	    echo "TSMtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to "
-	    echo "        ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again"
-            cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid
-        fi
-    fi
-fi
-
-cfgdir=`ls -1d ${CLM_ROOT}/tools/$1`
-rundir=${CLM_TESTDIR}/${test_name}
-if [ -d ${rundir} ]; then
-    rm -r ${rundir}
-fi
-mkdir -p ${rundir} 
-if [ $? -ne 0 ]; then
-    echo "TSMtools.sh: error, unable to create work subdirectory" 
-    exit 3
-fi
-cd ${rundir}
-
-echo "Copy any text files over"
-cp $cfgdir/*.txt $rundir
-
-echo "TSMtools.sh: calling TCBtools.sh to prepare $1 executable" 
-${CLM_SCRIPTDIR}/TCBtools.sh $1 $2
-rc=$?
-if [ $rc -ne 0 ]; then
-    echo "TSMtools.sh: error from TCBtools.sh= $rc" 
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 4
-fi
-
-echo "TSMtools.sh: running $1; output in ${rundir}/test.log" 
-
-if [ "$3" = "tools__o" ] || [ "$3" = "tools__do" ]; then
-   toolrun="env OMP_NUM_THREADS=${CLM_THREADS} ${CLM_TESTDIR}/TCBtools.$1.$2/$1"
-else
-   toolrun="${CLM_TESTDIR}/TCBtools.$1.$2/$1"
-fi
-
-runfile="${cfgdir}/$1.$3"
-
-if [ ! -f "${runfile}" ]; then
-    runfile="${CLM_SCRIPTDIR}/nl_files/$1.$3"
-    if [ ! -f "${runfile}" ]; then
-        echo "TSMtools.sh: error ${runfile} input run file not found"
-        echo "FAIL.job${JOBID}" > TestStatus
-        exit 5
-    fi
-fi
-
-echo "Run file type = ${3#*.}"
-if [ ${3#*.} == "runoptions" ]; then
-  echo "$toolrun "`cat ${runfile}`
-  cp $cfgdir/*.nc .
-  if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then
-     $toolrun  `cat ${runfile}` >> test.log 2>&1
-     rc=$?
-     status="PASS"
-  else
-     echo "Successfully created file" > test.log
-     status="GEN"
-     rc=0
-  fi
-else
-  echo "$toolrun < ${runfile}"
-  if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then
-     $toolrun < ${runfile} >> test.log 2>&1
-     rc=$?
-     status="PASS"
-  else
-     echo "Successfully created file" > test.log
-     status="GEN"
-     rc=0
-  fi
-fi
-
-if [ $rc -eq 0 ] && grep -ci "Successfully created " test.log > /dev/null; then
-    echo "TSMtools.sh: smoke test passed" 
-    echo "$status" > TestStatus
-else
-    echo "TSMtools.sh: error running $1, error= $rc" 
-    echo "TSMtools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details"
-    echo "FAIL.job${JOBID}" > TestStatus
-    exit 6
-fi
-
-exit 0
diff --git a/test/tools/config_files/CFGtools__ds b/test/tools/config_files/CFGtools__ds
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/test/tools/config_files/README b/test/tools/config_files/README
deleted file mode 100644
index bdfe5e0dd0..0000000000
--- a/test/tools/config_files/README
+++ /dev/null
@@ -1,9 +0,0 @@
-_do   => debug on, omp only on
-_ds   => debug on, serial mode (neither mpi nor omp)
-
-_o    => debug off, omp only on
-_s    => debug off, serial mode (neither mpi nor omp)
-
-tools__ds => options for tools, debug on, serial mode
-tools__do => options for tools, debug on, omp only on
-tools__o  => options for tools, debug off, omp only on
diff --git a/test/tools/config_files/tools__do b/test/tools/config_files/tools__do
deleted file mode 100644
index 7f061ed65d..0000000000
--- a/test/tools/config_files/tools__do
+++ /dev/null
@@ -1 +0,0 @@
-SMP=TRUE OPT=FALSE
diff --git a/test/tools/config_files/tools__ds b/test/tools/config_files/tools__ds
deleted file mode 100644
index cf2d414b28..0000000000
--- a/test/tools/config_files/tools__ds
+++ /dev/null
@@ -1 +0,0 @@
-OPT=FALSE
diff --git a/test/tools/config_files/tools__o b/test/tools/config_files/tools__o
deleted file mode 100644
index 8821e0bc5a..0000000000
--- a/test/tools/config_files/tools__o
+++ /dev/null
@@ -1 +0,0 @@
-SMP=TRUE OPT=TRUE
diff --git a/test/tools/config_files/tools__s b/test/tools/config_files/tools__s
deleted file mode 100644
index 507973f8be..0000000000
--- a/test/tools/config_files/tools__s
+++ /dev/null
@@ -1 +0,0 @@
-OPT=TRUE
diff --git a/test/tools/gen_test_table.sh b/test/tools/gen_test_table.sh
deleted file mode 100755
index 0791ad0447..0000000000
--- a/test/tools/gen_test_table.sh
+++ /dev/null
@@ -1,80 +0,0 @@
-#!/bin/sh 
-#
-
-# this script, when executed in the directory containing the test-driver 
-# scripts (~/test/system) will loop through the default test 
-# lists for pre and post tag testing of clm and create an html file 
-# (test_table.html) with the specifics of each test detailed
-
-outfile="./test_table.html"
-
-echo '<?xml version="1.0" encoding="UTF-8"?>' > $outfile
-echo '<!DOCTYPE html>' >> $outfile
-echo '<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">' >> $outfile
-echo '<head>' >> $outfile
-echo '<title>CLM Testing Information Page</title>' >> $outfile
-echo '</head>' >> $outfile
-echo '<body  bgcolor="666699" text="black" link="white" vlink="FF9933">' >> $outfile
-
-#########################################################################################
-for input_file in `ls tests_*` ; do
-    echo '<table border="2" width="750">' >> $outfile
-    echo "<caption>$input_file</caption>" >> $outfile
-    echo "<tr>" >> $outfile
-    echo "<th>test# </th>" >> $outfile
-    echo "<th>testid </th>" >> $outfile
-    echo "<th>test script </th>" >> $outfile
-    echo "<th>arg1 </th>" >> $outfile
-    echo "<th>arg2 </th>" >> $outfile
-    echo "<th>arg3 </th>" >> $outfile
-    echo "</tr>" >> $outfile
-
-    test_list=""
-    while read input_line; do
-	test_list="${test_list}${input_line} "
-    done < ./${input_file}
-
-    count=0
-    ##loop through the tests of input file
-    for test_id in ${test_list}; do
-	echo "<tr>" >> $outfile
-	count=`expr $count + 1`
-	while [ ${#count} -lt 3 ]; do
-		count="0${count}"
-	done
-	echo "<td> $count </td>" >> $outfile
-
-	master_line=`grep $test_id ./input_tests_master`
-        dir=""
-	for arg in ${master_line}; do
-            arg1=${arg%^*}
-            arg2=${arg#*^}
-            if [ -d ../../tools/$arg ]; then
-                dir=$arg
-	    elif [ -f ./nl_files/$arg ]; then
-		echo "<td><a href=\"./nl_files/$arg\">$arg </a></td>" >> $outfile
-	    elif [ -f ./config_files/$arg ]; then
-		echo "<td><a href=\"./config_files/$arg\">$arg </a></td>" >> $outfile
-	    elif [ -f ./nl_files/$arg1 ] && [ -f ./nl_files/$arg2 ]; then
-		echo  "<td><a href=\"./nl_files/$arg1\">$arg1</a>^" \
-                        "<a href=\"./nl_files/$arg2\">$arg2</a></td>" >> $outfile
-	    elif [ -f ./nl_files/$arg1 ] && [ -f ./config_files/$arg2 ]; then
-		echo "<td><a href=\"./nl_files/$arg1\">$arg1</a>^" \
-                        "<a href=\"./config_files/$arg2\">$arg2</a></td>" >> $outfile
-	    elif [ -f ../../tools/$dir/$dir.$arg ]; then
-		echo "<td><a href=\"../../tools/$dir/$dir.$arg\">$arg </a></td>" >> $outfile
-	    else
-		echo "<td>$arg </td>" >> $outfile
-	    fi
-	done
-	echo '</tr>' >> $outfile
-    done
-    echo '</table>' >> $outfile
-    echo '<pre>' >> $outfile
-    echo ' ' >> $outfile
-    echo '</pre>' >> $outfile
-done
-echo '</body>' >> $outfile
-echo '</html>' >> $outfile
-
-exit 0
diff --git a/test/tools/get_cprnc_diffs.sh b/test/tools/get_cprnc_diffs.sh
deleted file mode 100755
index 360220cb71..0000000000
--- a/test/tools/get_cprnc_diffs.sh
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/bin/bash
-
-# This script extracts lines from the output of cprnc that tell us
-# which variables differ between two files
-#
-# Usage: get_cprnc_diffs filename
-
-# ----------------------------------------------------------------------
-# SET PARAMETERS HERE
-# ----------------------------------------------------------------------
-
-# maximum number of differences to extract from the cprnc output
-maxdiffs=200
-
-# ----------------------------------------------------------------------
-# LOCAL FUNCTIONS DEFINED HERE
-# ----------------------------------------------------------------------
-
-# This function gets differences for one prefix (e.g., "RMS")
-# Usage: get_diffs prefix
-# (also uses $infile and $maxdiffs from the parent script)
-function get_diffs {
-    prefix=$1
-    outfile=${infile}.${prefix}.$$
-    grep "$prefix" $infile > $outfile
-    numlines=`wc -l $outfile | awk '{print $1}'`
-    if [ $numlines -gt $maxdiffs ]; then
-	echo "WARNING: Too many instances of $prefix - only printing last $maxdiffs"
-	tail -$maxdiffs $outfile
-    else
-	cat $outfile
-    fi
-    rm $outfile
-}
-
-# ----------------------------------------------------------------------
-# BEGIN MAIN SCRIPT
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Handle command-line arguments
-# ----------------------------------------------------------------------
-
-if [[ $# -ne 1 ]]; then
-    echo "Usage: get_cprnc_diffs filename"
-    exit 1
-fi
-
-infile=$1
-
-# ----------------------------------------------------------------------
-# Do the processing
-# ----------------------------------------------------------------------
-
-get_diffs RMS
-get_diffs FILLDIFF
diff --git a/test/tools/input_tests_master b/test/tools/input_tests_master
deleted file mode 100644
index 7da8c19803..0000000000
--- a/test/tools/input_tests_master
+++ /dev/null
@@ -1,32 +0,0 @@
-<id>  <run command>
-
-smc#4 TSMscript_tools.sh mkprocdata_map mkprocdata_map_wrap mkprocdata_ne30_to_f19_I2000^tools__ds
-blc#4 TBLscript_tools.sh mkprocdata_map mkprocdata_map_wrap mkprocdata_ne30_to_f19_I2000^tools__ds
-
-sm0c1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_OSBS
-bl0c1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_OSBS
-sm0a1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_YELL_PRISM
-bl0a1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_YELL_PRISM
-
-smba1 TSMscript_tools.sh site_and_regional subset_data subset_data_YELL
-blba1 TBLscript_tools.sh site_and_regional subset_data subset_data_YELL
-smbb1 TSMscript_tools.sh site_and_regional subset_data subset_data_KONA
-blbb1 TBLscript_tools.sh site_and_regional subset_data subset_data_KONA
-smb81 TSMscript_tools.sh site_and_regional subset_data subset_data_US-UMB
-blb81 TBLscript_tools.sh site_and_regional subset_data subset_data_US-UMB
-smbh1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_1x1pt_townshipSD
-blbh1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_1x1pt_townshipSD
-smbd1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_58x45pt_SouthAmerica
-blbd1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_58x45pt_SouthAmerica
-smbe1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_90x288pt_1850PanTropics
-blbe1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_90x288pt_1850PanTropics
-smbf1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_37x288pt_PanBoreal
-blbf1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_37x288pt_PanBoreal
-smbg1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_4x9pt_AlaskaTananaValley
-blbg1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_4x9pt_AlaskaTananaValley
-
-sm901 TSMscript_tools.sh site_and_regional mesh_maker mesh_maker_fv09
-bl901 TBLscript_tools.sh site_and_regional mesh_maker mesh_maker_fv09
-
-smaa2 TSMscript_tools.sh site_and_regional modify_singlept_site_neon.py modify_data_YELL
-blaa2 TBLscript_tools.sh site_and_regional modify_singlept_site_neon.py modify_data_YELL
diff --git a/test/tools/nl_files/mesh_maker_fv09 b/test/tools/nl_files/mesh_maker_fv09
deleted file mode 100644
index 7de951fee1..0000000000
--- a/test/tools/nl_files/mesh_maker_fv09
+++ /dev/null
@@ -1 +0,0 @@
- --input CSMDATA/atm/datm7/domain.lnd.fv0.9x1.25_gx1v6.090309.nc --lat yc --lon xc --overwrite --mask mask --area area --verbose
diff --git a/test/tools/nl_files/mkmapdata_if10 b/test/tools/nl_files/mkmapdata_if10
deleted file mode 100644
index f726ea34e7..0000000000
--- a/test/tools/nl_files/mkmapdata_if10
+++ /dev/null
@@ -1 +0,0 @@
--r 10x15 --fast --batch
diff --git a/test/tools/nl_files/mkmapdata_ne30np4 b/test/tools/nl_files/mkmapdata_ne30np4
deleted file mode 100644
index ae435ac2bc..0000000000
--- a/test/tools/nl_files/mkmapdata_ne30np4
+++ /dev/null
@@ -1 +0,0 @@
--r ne30np4 --fast --batch
diff --git a/test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 b/test/tools/nl_files/mkprocdata_ne30_to_f19_I2000
deleted file mode 100644
index af85dcf226..0000000000
--- a/test/tools/nl_files/mkprocdata_ne30_to_f19_I2000
+++ /dev/null
@@ -1 +0,0 @@
--i CSMDATA/lnd/clm2/test_mkprocdata_map/clm4054_ne30g16_I2000.clm2.h0.2000-01_c170430.nc -o ne30output_onf19grid.nc -m CSMDATA/lnd/clm2/test_mkprocdata_map/map_ne30np4_nomask_to_fv1.9x2.5_nomask_aave_da_c121107.nc -t CSMDATA/lnd/clm2/test_mkprocdata_map/clm4054_f19g16_I2000.clm2.h0.2000-01_c170430.nc -e EXEDIR
diff --git a/test/tools/nl_files/modify_data_YELL b/test/tools/nl_files/modify_data_YELL
deleted file mode 100644
index 0d180e8bf6..0000000000
--- a/test/tools/nl_files/modify_data_YELL
+++ /dev/null
@@ -1 +0,0 @@
---neon_site YELL --surf_dir CSMDATA/lnd/clm2/surfdata_esmf/NEON --out_dir EXEDIR --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/run_neon_OSBS b/test/tools/nl_files/run_neon_OSBS
deleted file mode 100644
index 0c274b13ad..0000000000
--- a/test/tools/nl_files/run_neon_OSBS
+++ /dev/null
@@ -1 +0,0 @@
---verbose --run-type ad --setup-only --neon-site OSBS
diff --git a/test/tools/nl_files/run_neon_YELL_PRISM b/test/tools/nl_files/run_neon_YELL_PRISM
deleted file mode 100644
index f5ebdf9fdf..0000000000
--- a/test/tools/nl_files/run_neon_YELL_PRISM
+++ /dev/null
@@ -1 +0,0 @@
---verbose --run-type transient --setup-only --neon-site YELL --prism --neon-version v2 --experiment toolstest
diff --git a/test/tools/nl_files/subset_data_KONA b/test/tools/nl_files/subset_data_KONA
deleted file mode 100644
index 0df59b1b17..0000000000
--- a/test/tools/nl_files/subset_data_KONA
+++ /dev/null
@@ -1 +0,0 @@
-point --lon 263.38956 --lat 39.1082 --site KONA --dompft 17 19 23 45 --pctpft 28 12 32 28 --crop --create-surface --outdir EXEDIR/KONA_user-mod_and_data --user-mods-dir EXEDIR/KONA_user-mod_and_data --verbose  --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/subset_data_US-UMB b/test/tools/nl_files/subset_data_US-UMB
deleted file mode 100644
index 935b0dc99d..0000000000
--- a/test/tools/nl_files/subset_data_US-UMB
+++ /dev/null
@@ -1 +0,0 @@
-point --lon 275.28626 --lat 45.5598 --site 1x1_US-UMB --dompft 7 --cap-saturation --uniform-snowpack --create-surface --outdir EXEDIR/US-UMB_user-mod_and_data --user-mods-dir EXEDIR/US-UMB_user-mod_and_data --verbose  --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/subset_data_YELL b/test/tools/nl_files/subset_data_YELL
deleted file mode 100644
index 0d6960e7f5..0000000000
--- a/test/tools/nl_files/subset_data_YELL
+++ /dev/null
@@ -1 +0,0 @@
-point --lon 250.45804 --lat 44.95597 --site YELL --dompft 1 --crop --uniform-snowpack --cap-saturation --create-surface --outdir EXEDIR/YELL_user-mod_and_data --user-mods-dir EXEDIR/YELL_user-mod_and_data --silent --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/subset_data_f09_1x1pt_townshipSD b/test/tools/nl_files/subset_data_f09_1x1pt_townshipSD
deleted file mode 100644
index aa25c07d1e..0000000000
--- a/test/tools/nl_files/subset_data_f09_1x1pt_townshipSD
+++ /dev/null
@@ -1 +0,0 @@
-point --lon 257.5 --lat 43.822 --site f09_1x1pt_townshipSD  --include-nonveg --crop --create-datm --create-user-mods --datm-syr 2000 --datm-eyr 2000 --create-surface --outdir EXEDIR/f09_US_pt_user-mod_and_data --user-mods-dir EXEDIR/f09_US_pt_user-mod_and_data --verbose --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal b/test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal
deleted file mode 100644
index 448b5052d6..0000000000
--- a/test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal
+++ /dev/null
@@ -1 +0,0 @@
-region --lat1 55 --lat2 89.1 --lon1 0 --lon2 360 --create-mesh --create-surface --create-domain --create-user-mods --verbose --overwrite --reg f09_37x288pt_PanBoreal --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley b/test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley
deleted file mode 100644
index 9928d78429..0000000000
--- a/test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley
+++ /dev/null
@@ -1 +0,0 @@
-region --lat1 62 --lat2 66 --lon1 -152 --lon2 -141 --create-mesh --create-domain --create-surface --create-user-mods --verbose --overwrite --reg f09_4x9pt_AlaskaTananaValley --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica b/test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica
deleted file mode 100644
index 201dd2c76c..0000000000
--- a/test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica
+++ /dev/null
@@ -1 +0,0 @@
-region --lat1 -40 --lat2 15 --lon1 275 --lon2 330 --create-mesh --create-surface --create-user-mods --create-domain --create-landuse --verbose --overwrite --reg f09_58x45_SouthAmerica --inputdata-dir CSMDATA
diff --git a/test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics b/test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics
deleted file mode 100644
index 1c9d5eace9..0000000000
--- a/test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics
+++ /dev/null
@@ -1 +0,0 @@
-region --lat1 -55 --lat2 30 --lon1 0 --lon2 360 --crop --create-surface --create-domain --create-mesh --overwrite --reg f09_90x288pt_1850PanTropics --inputdata-dir CSMDATA --cfg-file CTSM_ROOT/tools/mksurfdata_map/default_data_1850.cfg --verbose
diff --git a/test/tools/show_var_diffs.sh b/test/tools/show_var_diffs.sh
deleted file mode 100755
index f462d4ad0c..0000000000
--- a/test/tools/show_var_diffs.sh
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/bin/bash
-
-# This script processes a log file that was output by test_driver,
-# giving lists of all variables with differences in values (those with
-# RMS errors), and all variables with differences in fill patterns.
-#
-# This assumes that the log file contains output like:
-#  RMS foo
-#  RMS bar
-#  FILLDIFF foo
-#  FILLDIFF bar
-# Some characteristics of these output lines are:
-# - they begin with a leading space, followed by RMS or FILLDIFF
-# - the variable name is in the second column of the line
-#
-# Note that (as of 4-5-12) the log file only contains output from the
-# last file that didn't match, so this could potentially miss
-# something -- especially if there are both h0 and h1 files in the
-# comparison.
-
-# Usage: show_var_diffs logfile
-
-# ----------------------------------------------------------------------
-# LOCAL FUNCTIONS DEFINED HERE
-# ----------------------------------------------------------------------
-
-# This function shows the differences for one prefix (e.g., "RMS")
-# Usage: show_diffs prefix
-# (also uses $logfile from the parent script)
-# 
-# Matches lines that start with the regular expression "^ ${prefix}"
-# (note that one leading space is expected before the prefix)
-#
-# Assumes that the variable name is in the second column of matching lines
-function show_diffs {
-    prefix=$1
-
-    # first determine if there were warnings relating to this prefix
-    grep "WARNING: Too many instances of ${prefix}" $logfile > /dev/null
-    if [ $? -eq 0 ]; then  # found a warning
-	echo "WARNING: Some output was truncated; this may not be a complete list"
-    fi
-    
-    # now make a list of all variables matching this prefix
-    grep "^ ${prefix}" $logfile > $logfile.tmp.$$
-    if [ $? -eq 0 ]; then
-	awk '{print $2}' $logfile.tmp.$$ | sort | uniq
-    else
-	echo "(no differences)"
-    fi
-
-    rm $logfile.tmp.$$
-}
-
-# ----------------------------------------------------------------------
-# BEGIN MAIN SCRIPT
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Handle command-line arguments
-# ----------------------------------------------------------------------
-
-if [[ $# -ne 1 ]]; then
-    echo "Usage: show_var_diffs logfile"
-    exit 1
-fi
-
-logfile=$1
-
-# ----------------------------------------------------------------------
-# Do the processing
-# ----------------------------------------------------------------------
-
-echo "Variables with differences in values:"
-show_diffs "RMS"
-
-echo ""
-echo "Variables with differences in fill patterns:"
-show_diffs "FILLDIFF"
\ No newline at end of file
diff --git a/test/tools/tests_posttag_hobart_nompi b/test/tools/tests_posttag_hobart_nompi
deleted file mode 100644
index c185428868..0000000000
--- a/test/tools/tests_posttag_hobart_nompi
+++ /dev/null
@@ -1 +0,0 @@
-smc#4             blc#4
diff --git a/test/tools/tests_posttag_nompi_regression b/test/tools/tests_posttag_nompi_regression
deleted file mode 100644
index c185428868..0000000000
--- a/test/tools/tests_posttag_nompi_regression
+++ /dev/null
@@ -1 +0,0 @@
-smc#4             blc#4
diff --git a/test/tools/tests_pretag_cheyenne_nompi b/test/tools/tests_pretag_cheyenne_nompi
deleted file mode 100644
index e92ffaaaad..0000000000
--- a/test/tools/tests_pretag_cheyenne_nompi
+++ /dev/null
@@ -1,3 +0,0 @@
-smc#4             blc#4
-smba1             blba1
-smbd1             blbd1
diff --git a/test/tools/tests_pretag_derecho_nompi b/test/tools/tests_pretag_derecho_nompi
deleted file mode 100644
index 5fdaf335ae..0000000000
--- a/test/tools/tests_pretag_derecho_nompi
+++ /dev/null
@@ -1,9 +0,0 @@
-smba1             blba1
-smbd1             blbd1
-sm0a1             bl0a1
-sm0c1             bl0c1
-smaa2             blaa2
-smba1             blba1
-smb81             blb81
-smbc1             blbc1
-smbd1             blbd1
diff --git a/test/tools/tests_pretag_nompi_neon b/test/tools/tests_pretag_nompi_neon
deleted file mode 100644
index e5fa27e6c4..0000000000
--- a/test/tools/tests_pretag_nompi_neon
+++ /dev/null
@@ -1,8 +0,0 @@
-sm0a1             bl0a1
-sm0c1             bl0c1
-smaa2             blaa2
-smba1             blba1
-smbb1             blbb1
-smb81             blb81
-smbc1             blbc1
-smbd1             blbd1

From 69dbee8149945c173c66cfa8670adecccf333d16 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 11:08:53 -0600
Subject: [PATCH 0290/1248] Remove bld/unit_testers/xFail/wrapClmTests.pl

---
 bld/unit_testers/xFail/wrapClmTests.pl | 128 -------------------------
 1 file changed, 128 deletions(-)
 delete mode 100755 bld/unit_testers/xFail/wrapClmTests.pl

diff --git a/bld/unit_testers/xFail/wrapClmTests.pl b/bld/unit_testers/xFail/wrapClmTests.pl
deleted file mode 100755
index 28238b9d5d..0000000000
--- a/bld/unit_testers/xFail/wrapClmTests.pl
+++ /dev/null
@@ -1,128 +0,0 @@
-#!/usr/bin/env perl
-
-#-# =========================================================================================
-
-=head1 wrapClmTest.pl
-
-=head1 Overview
-
-This is a wrapper script that is called from test_driver.sh for either interactive or batch
-tests.  It calls the CTOR for the xFail::expectedFail.pm module and also parses the td*.status
-file to create a new file with xFails listed.
-
-It takes the following arguments:
-
-   numberOfTests ->  number of tests from test_driver.sh
-   statusFile    ->  name of the td.<pid>.status file
-   callingScript ->  name of script calling this.  For test_driver.sh it may be one of:
-                        1) test_driver.sh-i for interactive tests
-                        2) test_driver.sh   for batch tests
-
-=head1 Notes
-
-This script may be run standalone which is useful for testing purposes.
- 
-=cut
-
-#-# =========================================================================================
-
-use strict;
-use Getopt::Long;
-use English;
-use Cwd;
-use Scalar::Util qw(looks_like_number);
-
-my $DEBUG=0;
-
-sub usage {
-    die <<EOF;
-SYNOPSIS
-     wrapClmTests [options]
-
-     Usually called from test_driver.sh.  Scans the td.*.status file and checks for expected test failures.
-OPTIONS
-     -help [or -h]                        Print usage to STDOUT.                               
-     -numberOfTests "numberOfTests"
-     -statusFile    "statusFile"          Name of status file
-     -callingScript "callingScript"       Name of calling script
-
-EOF
-}
-
-#
-# Process command-line options.
-#
-my %opts = ( help        => 0,
-             numberOfTests  => undef,
-             statusFile     => undef,
-             callingScript  => undef,
-            );
-
-GetOptions(
-    "h|help"           => \$opts{'help'},
-    "numberOfTests=s"  => \$opts{'numberOfTests'},
-    "statusFile=s"     => \$opts{'statusFile'},
-    "callingScript=s"  => \$opts{'callingScript'},
-)  or usage();
-
-# Give usage message.
-usage() if $opts{'help'};
-
-my $statFoo = undef;
-my $nTests = undef;
-my $script= undef;
-
-if (defined($opts{'statusFile'})) {
-    $statFoo = $opts{'statusFile'};
-}
-if (defined($opts{'numberOfTests'})) {
-    $nTests = $opts{'numberOfTests'};
-}
-if (defined($opts{'callingScript'})) {
-    $script = $opts{'callingScript'};
-}
-
-my ( $self ) = @_;
- 
-#Figure out where configure directory is and where can use the XML/Lite module from
-my $ProgName;
-($ProgName = $PROGRAM_NAME) =~ s!(.*)/!!; # name of program
-my $ProgDir = $1;                         # name of directory where program lives
- 
-my $cwd = getcwd();  # current working directory
-my $cfgdir;
- 
-if ($ProgDir) { $cfgdir = $ProgDir; }
-else { $cfgdir = $cwd; }
- 
-#-----------------------------------------------------------------------------------------------
-# Add $cfgdir to the list of paths that Perl searches for modules
-#-----------------------------------------------------------------------------------------------
-my @dirs = ( $cfgdir,
-             "$cfgdir/../",
-             "$cfgdir/../../../../../cime/utils/perl5lib");
-unshift @INC, @dirs;
-my $result = eval "require expectedFail";
-if ( ! defined($result) ) {
-   die <<"EOF";
-** Cannot find perl module \"xFail/expectedFail.pm\" from directories: @dirs **
-EOF
-}
-
-#_# ====================================
-#_# setup work complete.  Now parse file
-#_# ====================================
-
-if ($DEBUG) {
-   print (" wrapClmTests.pl:: calling script $script \n");
-   print (" wrapClmTests.pl:: number of tests $nTests \n");
-   print (" wrapClmTests.pl:: processing $statFoo \n");
-}
-
-#_# compGen not used for CLM batch or interactive tests, but we use "compare" as the default in this case
-my $compGen="compare";  
-my $xFail = xFail::expectedFail->new($script,$compGen,$nTests);
-
-$xFail->parseOutputCLM($statFoo);
-
-exit(0);

From 8ef1ff4a3a4c2ca4c44c0d59bd654819b32edd62 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 11:19:49 -0600
Subject: [PATCH 0291/1248] Remove obsolete parts of
 bld/unit_testers/xFail/expectedFail.pm

---
 bld/unit_testers/xFail/expectedFail.pm | 119 +------------------------
 1 file changed, 2 insertions(+), 117 deletions(-)

diff --git a/bld/unit_testers/xFail/expectedFail.pm b/bld/unit_testers/xFail/expectedFail.pm
index 9feaa3e38b..067e3a51d8 100755
--- a/bld/unit_testers/xFail/expectedFail.pm
+++ b/bld/unit_testers/xFail/expectedFail.pm
@@ -5,7 +5,7 @@ Documentation for expectedFail.pm
 =head1 Overview
 
 The module expectedFail.pm supplies the capability of checking if a failed test is expected to fail.
-It is called directly from either test_driver.sh (for batch and interactive tests) or build-namelist_test.pl.  
+It is called directly from build-namelist_test.pl.  
 Future plans involve integrating this module into cesm tests.
 
 =head1 Use Case
@@ -112,7 +112,7 @@ sub new {
 
 =head1 parseOutput
 
-parseOutput parsese the output from the build-namelist_test.pl script.  It is similar
+parseOutput parses the output from the build-namelist_test.pl script.  It is similar
 to, but not interchangable with parseOutputCLM.
 
 The only argument is that of the reference variable that contains the information dumped
@@ -223,119 +223,6 @@ sub parseOutput
 #
 ##############################################################################
 
-=head1 parseOutputCLM
-
-parseOutputCLM parsese the output from the test_driver.sh script.  It is similar
-to, but not interchangable with parseOutput.
-
-parseOutputCLM takes one arguments:
-   $statFoo->     the name of the td.<pid>.status file 
-
-returns:  nothing
-
-=cut
-
-##############################################################################
-#
-##############################################################################
-sub parseOutputCLM
-{
-
-   my $report;
-   my $testId;
-   my @testName={};
-   my $testReason;
-
-   my ($self, $statFoo) = @_ ;
-    
-   open(FOO, "< $statFoo"); # open for input
-   open(FOO_OUT, "> $statFoo.xFail"); # open for input
-
-   my(@reportLines);
-
-   while (<FOO>) {
-
-      my($line) = $_;
-
-      my @outArr=split(/ /,$line);
-      if (looks_like_number(@outArr[0])) {
-
-         $self->{_numericalTestId}++;
-
-         my $num=sprintf("%03d", $self->{_numericalTestId});
-         my $totNum=sprintf("%03d", $self->{_totTests});
-
-         #_# last element has the pass/fail info.
-         chomp(@outArr[-1]);
-         my $repPass=substr(@outArr[-1], -4, 4);
-
-         if ($DEBUG) {
-            print ("xFail::expectedFail::parseOutput @outArr[0] \n");
-            print ("xFail::expectedFail::parseOutput @outArr[1] \n");
-            print ("xFail::expectedFail::parseOutput @outArr[2] \n");
-            print ("xFail::expectedFail::parseOutput @outArr[3] \n");
-            print ("xFail::expectedFail::parseOutput @outArr[4] \n");
-            print ("xFail::expectedFail::parseOutput @outArr[5] \n");
-            print ("xFail::expectedFail::parseOutput @outArr[6] \n");
-            print ("xFail::expectedFail::parseOutput @outArr[-1] \n");
-            print ("xFail::expectedFail::parseOutput $repPass \n");
-         }
-
-         my $size = @outArr-1;
-         if ($DEBUG) {
-            print ("size of line $size \n");
-         }
-         my $endOfDesc=$size-1;
-   
-         if ($repPass eq "PASS") {
-            $report=$pass;
-            $testId=@outArr[1];
-            @testName=@outArr[2..$endOfDesc];
-
-            my ($retVal,$xFailText)=$self->_searchExpectedFail($testId);
-
-            my $testReason=$self->_testNowPassing($testId,$retVal,$xFailText);
-
-            #_# print out the test results
-            print FOO_OUT ("$num/$totNum <$report> <Test Id: $testId> <Desc: @testName> $testReason \n"); 
-
-         } else {
-            $testId=@outArr[1];
-            my ($retVal,$xFailText)=$self->_searchExpectedFail($testId);
-            
-            if ($DEBUG) {
-               print ("xFail::expectedFail::parseOutput Id $retVal,$xFailText \n");
-            }
-         
-            @testName=@outArr[2..$endOfDesc];
-         
-            if ($retVal eq "TRUE"){
-               #_# found an expected FAIL (xFAIL)
-               $report=$xfail;
-               $testReason= "<Note: $xFailText>";
-            } else {
-               #_# print a regular FAIL
-               $report=$fail;
-               $testReason="";
-            }
-
-            #_# print out the test results
-            print FOO_OUT ("$num/$totNum <$report> <Test Id: $testId> <Desc: @testName> $testReason \n"); 
-
-         }
-
-      } else {
-         print FOO_OUT $line;
-      }
-   }
-   close(FOO);
-   close(FOO_OUT);
-}
-
-##############################################################################
-#
-##############################################################################
-
 =head1 _searchExpectedFail
 
 searches the list of expected fails for a match with testId.
@@ -608,8 +495,6 @@ sub _getTestType
 
    my %testTypes = (
       "build-namelist_test.pl"  => "namelistTest",
-      "test_driver.sh-i"   => "clmInteractive",
-      "test_driver.sh"   => "clmBatch",
       "clm-cesm.sh"   => "cesm"
    );
    

From 0c26697a620292a7dcd69f8eefa55a3ee759332f Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 11:22:42 -0600
Subject: [PATCH 0292/1248] Remove obsolete parts of expectedClmTestFails.xml:
 DID I rm ENOUGH?

---
 bld/unit_testers/xFail/expectedClmTestFails.xml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/bld/unit_testers/xFail/expectedClmTestFails.xml b/bld/unit_testers/xFail/expectedClmTestFails.xml
index c7cbfee488..380e614ea1 100644
--- a/bld/unit_testers/xFail/expectedClmTestFails.xml
+++ b/bld/unit_testers/xFail/expectedClmTestFails.xml
@@ -20,20 +20,6 @@
       </goldbach>
    </namelistTest>
 
-   <tools_test_driver>
-         <yellowstone>
-            <INTEL>
-            </INTEL>
-         </yellowstone>
-         <goldbach>
-            <INTEL>
-               <entry testId="sm684" failType="FAIL">goldbach not recognized</entry>
-               <entry testId="smf84" failType="FAIL">goldbach not recognized</entry>
-               <entry testId="smfc4" failType="FAIL">goldbach not recognized</entry>
-            </INTEL>
-         </goldbach>
-   </tools_test_driver>
-
    <unit_tests>
          <yellowstone>
             <INTEL>

From 882425a205ded67450455466ded69d034f5d39fa Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 11:26:11 -0600
Subject: [PATCH 0293/1248] Remove mention of test_driver_*.sh in .gitignore

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 1da8072fed..163bfeda2d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -75,7 +75,6 @@ buildnmlc
 td.*.status
 td.*.log
 td.*.status.xFail
-test_driver_*.sh
 
 # mksurfdata output
 surfdata_*.log

From 9407ce50522c2a624196fd4b892363cf8505b5ee Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 11:33:48 -0600
Subject: [PATCH 0294/1248] Remove reference to /test in /doc/.../testing.rst

---
 doc/source/users_guide/testing/testing.rst | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst
index bad1183fff..69ca1f7263 100644
--- a/doc/source/users_guide/testing/testing.rst
+++ b/doc/source/users_guide/testing/testing.rst
@@ -13,12 +13,6 @@ CIME Testing scripts
 
 We first introduce the test scripts that work for all CESM components. The CIME script **create_test** runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing <http://esmci.github.io/cime/users_guide/testing.html>`_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also see the `CTSM Wiki on Testing <https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide>`_.
 
-CTSM Tools Testing
-==================
-
-.. include:: ../../../../test/tools/README
-   :literal:
-
 CTSM Fortran Unit Tests
 =======================
 

From eedbadff362d140cd1f1a34803e525e25fb58236 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 21 May 2024 12:21:32 -0600
Subject: [PATCH 0295/1248] Check values for a basic run through with default
 input forcing

---
 src/biogeochem/DUSTMod.F90                    | 54 ++++++++++++++-
 .../test/DustEmis_test/test_DustEmis.pf       | 68 ++++++++++++++++++-
 2 files changed, 118 insertions(+), 4 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index e0e4e469a1..cd60bd859f 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -62,12 +62,14 @@ module DUSTMod
    contains
 
      procedure , public  :: Init
-     procedure , public  :: DustEmission   ! Dust mobilization 
-     procedure , public  :: DustDryDep     ! Turbulent dry deposition for dust
+     procedure , public  :: DustEmission    ! Dust mobilization
+     procedure , public  :: DustDryDep      ! Turbulent dry deposition for dust
+     procedure , public  :: WritePatchToLog ! Write information on the given patch to the log file
+     procedure , public  :: GetPatchVars    ! Get important variables on a given patch
      procedure , private :: InitAllocate 
      procedure , private :: InitHistory  
      procedure , private :: InitCold     
-     procedure , private :: InitDustVars   ! Initialize variables used in DustEmission method
+     procedure , private :: InitDustVars    ! Initialize variables used in DustEmission method
 
   end type dust_type
   !------------------------------------------------------------------------
@@ -209,6 +211,52 @@ subroutine InitCold(this, bounds)
 
   end subroutine InitCold
 
+    !-----------------------------------------------------------------------
+
+  subroutine WritePatchToLog(this, p)
+    !
+    ! !DESCRIPTION:
+    ! Write out information on dust emisisons for this patch to the log file
+    ! !ARGUMENTS:
+    class(dust_type), intent(in) :: this
+    integer         , intent(in) :: p      ! Patch to display
+
+    write(iulog,*) 'flx_mss_vrt_dst', this%flx_mss_vrt_dst_patch(p,:)
+    write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p)
+    write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p)
+    write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p)
+    write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p)
+    write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p)
+    write(iulog,*) 'mbl_bsn_fct', this%mbl_bsn_fct_col(p)
+ end subroutine WritePatchToLog
+
+    !-----------------------------------------------------------------------
+
+ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, &
+                         vlc_trb_2, vlc_trb_3, vlc_trb_4)
+   !
+   ! !DESCRIPTION:
+   ! Get important variables on the given patch
+   ! !ARGUMENTS:
+   class(dust_type)  , intent(in)  :: this
+   integer           , intent(in)  :: p      ! Patch to get
+   real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst)
+   real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot
+   real(r8), optional, intent(out) :: vlc_trb(ndst)
+   real(r8), optional, intent(out) :: vlc_trb_1
+   real(r8), optional, intent(out) :: vlc_trb_2
+   real(r8), optional, intent(out) :: vlc_trb_3
+   real(r8), optional, intent(out) :: vlc_trb_4
+
+   if ( present(flx_mss_vrt_dst    ) ) flx_mss_vrt_dst     = this%flx_mss_vrt_dst_patch(p,:)
+   if ( present(flx_mss_vrt_dst_tot) ) flx_mss_vrt_dst_tot = this%flx_mss_vrt_dst_tot_patch(p)
+   if ( present(vlc_trb  ) ) vlc_trb   = this%vlc_trb_patch(p,:)
+   if ( present(vlc_trb_1) ) vlc_trb_1 = this%vlc_trb_1_patch(p)
+   if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p)
+   if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p)
+   if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p)
+end subroutine GetPatchVars
+
   !------------------------------------------------------------------------
   subroutine DustEmission (this, bounds, &
        num_nolakep, filter_nolakep, &
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index 9be97453b0..08aa683964 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -5,7 +5,7 @@ module test_DustEmis
   use funit
   use unittestSubgridMod
   use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
-  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init
+  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
   use clm_varcon, only : clm_varcon_init, clm_varcon_clean
   use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting
@@ -19,9 +19,12 @@ module test_DustEmis
   use WaterType, only : water_type 
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
+  use abortutils, only : endrun
 
   implicit none
 
+  real(r8), parameter :: tol = 1.e-13_r8
+
   @TestCase
   type, extends(TestCase) :: TestDustEmis
      type(dust_type) :: dust_emis
@@ -40,6 +43,8 @@ module test_DustEmis
      procedure :: setupEnvironment
      procedure :: create_atm2lnd
      procedure :: create_fv
+     procedure :: print_patch
+     procedure :: validate_patch
   end type TestDustEmis
 
 contains
@@ -231,11 +236,61 @@ contains
 
   end subroutine create_fv
 
+  subroutine print_patch(this)
+    use LandunitType, only : lun
+    class(TestDustEmis), intent(inout) :: this
+    integer :: p, c, l
+
+    do l = bounds%begl, bounds%endl
+       print *, 'landunit type= ', lun%itype(l)
+    end do
+    do c = bounds%begc, bounds%endc
+       print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1)
+       print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1)
+       print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c)
+    end do
+    do p = bounds%begp, bounds%endp
+       print *, 'tlai = ', this%canopystate_inst%tlai_patch(p)
+       call this%dust_emis%WritePatchToLog( p )
+    end do
+    call endrun( "exit early")
+  end subroutine print_patch
+
+  !-----------------------------------------------------------------------
+  subroutine validate_patch(this, p)
+    class(TestDustEmis), intent(inout) :: this
+    integer, intent(in) :: p
+
+    real(r8) :: flx_mss_vrt_dst(ndst)
+    real(r8) :: flx_mss_vrt_dst_tot
+    real(r8) :: vlc_trb(ndst)
+    real(r8) :: vlc_trb_1
+    real(r8) :: vlc_trb_2
+    real(r8) :: vlc_trb_3
+    real(r8) :: vlc_trb_4
+
+    call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, &
+             flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, &
+             vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
+             vlc_trb_4=vlc_trb_4 )
+    @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot )
+    @assertEqual( vlc_trb(1), vlc_trb_1)
+    @assertEqual( vlc_trb(2), vlc_trb_2)
+    @assertEqual( vlc_trb(3), vlc_trb_3)
+    @assertEqual( vlc_trb(4), vlc_trb_4)
+  end subroutine validate_patch
+
   !-----------------------------------------------------------------------
 
   @Test
   subroutine check_dust_emis(this)
     class(TestDustEmis), intent(inout) :: this
+    integer :: p
+    real(r8) :: flx_mss_vrt_dst_tot
+    real(r8) :: vlc_trb_1
+    real(r8) :: vlc_trb_2
+    real(r8) :: vlc_trb_3
+    real(r8) :: vlc_trb_4
 
     call this%create_atm2lnd()
     call this%create_fv()
@@ -243,6 +298,17 @@ contains
                       this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
                       this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
     call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+    do p = bounds%begp, bounds%endp
+       call this%validate_patch(p)
+       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
+                               vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
+                               vlc_trb_4=vlc_trb_4)
+       @assertEqual( 0.0_r8, flx_mss_vrt_dst_tot )
+       @assertEqual( 3.319559266672431d-5, vlc_trb_1, tolerance=tol )
+       @assertEqual( 1.699714729099379d-5, vlc_trb_2, tolerance=tol )
+       @assertEqual( 9.163854318535118d-6, vlc_trb_3, tolerance=tol )
+       @assertEqual( 3.614237762488103d-5, vlc_trb_4, tolerance=tol )
+    end do
 
   end subroutine check_dust_emis
 

From 93c274d7570d8f33002ac0156fc4a977670feef2 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 12:30:38 -0600
Subject: [PATCH 0296/1248] Update README by removing mention of /test
 directory

---
 README | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README b/README
index 4699fec858..af45a14909 100644
--- a/README
+++ b/README
@@ -47,7 +47,6 @@ doc --------------- Documentation of CTSM.
 bld --------------- build-namelist scripts for CTSM.
 src --------------- CTSM Source code.
 lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)
-test -------------- CTSM Testing scripts for CTSM offline tools (deprecated)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
 manage_externals -- Script to manage the external source directories (deprecated)

From 802b989d5c408a36bccf07b24f2f8a2724e4ca59 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 21 May 2024 15:11:29 -0600
Subject: [PATCH 0297/1248] Second draft of ChangeLog/ChangeSum

---
 doc/ChangeLog | 37 ++++++++++++++++++++-----------------
 doc/ChangeSum |  2 +-
 2 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 5644ed295d..d68ef323ac 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,18 +1,18 @@
 ===============================================================
 Tag name: ctsm5.2.006
 Originator(s): slevis (Samuel Levis)
-Date: Fri May 17 16:17:54 MDT 2024
-One-line Summary: Update externals to cesm2_3_beta17
+Date: Tue 21 May 2024 02:59:05 PM MDT
+One-line Summary: Update externals to cesm2_3_beta17, remove mct, retire /test/tools
 
 Purpose and description of changes
 ----------------------------------
 
-#2493 update externals to beta17
-#2294 remove references to mct but do not remove /src/mct
+ #2493 update externals to beta17
+ #2294 remove mct but not in Externals.cfg
+ #2279 Retire the /test/tools framework for CESM test system custom tests that do the same thing
 
-Changes unrelated to the tag's title:
-#2546 fix error in cam4/cam5 test (ekluzek)
-Remove /test/tools/test_driver.sh
+ Changes unrelated to the tag's title:
+ #2546 fix error in cam4/cam5 test (ekluzek)
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
@@ -36,20 +36,23 @@ Does this tag change answers significantly for any of the following physics conf
 Bugs fixed
 ----------
 List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
-Fixes #2493 update externals to beta17
-Fixes #2546 fix error in cam4/cam5 test (unrelated)
+ Fixes #2493 update externals to beta17
+ Fixes #2279 Retire the /test/tools framework for CESM test system custom tests that do the same thing
+ Fixes #2546 fix error in cam4/cam5 test (unrelated)
 
 Notes of particular relevance for users
 ---------------------------------------
-Changes to documentation: Remove references to mct and cpl7
+Changes to documentation:
+ Remove references to mct and cpl7
 
-Substantial timing or memory changes: Not considered
+Substantial timing or memory changes:
+ Not considered
 
 Notes of particular relevance for developers:
 ---------------------------------------------
 Changes to tests or testing:
-I added a long list of izumi nag debug tests to ExpectedFailures as per
-https://github.com/ESCOMP/CMEPS/pull/460
+ I added a long list of izumi nag debug tests to ExpectedFailures as per
+ https://github.com/ESCOMP/CMEPS/pull/460
 
 Testing summary:
 ----------------
@@ -57,16 +60,16 @@ Testing summary:
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho -
+    derecho - PASS
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
-    (any machine) -
+    derecho - PASS
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
     derecho -----
-    izumi ------- IN PROGRESS
+    izumi ------- OK
 
   any other testing (give details below):
 
@@ -98,7 +101,7 @@ Changes answers relative to baseline:
 Other details
 -------------
 List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
-cism, ccs_config, cime, cmeps, cdeps
+ cism, ccs_config, cime, cmeps, cdeps
 
 Pull Requests that document the changes (include PR ids):
  https://github.com/ESCOMP/ctsm/pull/2539
diff --git a/doc/ChangeSum b/doc/ChangeSum
index c73cb19309..7f8cdaeead 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.006   slevis 05/17/2024 Update externals to cesm2_3_beta17
+       ctsm5.2.006   slevis 05/21/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems
        ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes
        ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev

From ae5dbeae61ef39be636a0293eac5f26defc2a5c5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 21 May 2024 20:04:17 -0600
Subject: [PATCH 0298/1248] Add more clean routines at the end so can do a
 different test that shows increasing wind has more dust emission

---
 src/biogeochem/DUSTMod.F90                    | 51 ++++++++--
 .../test/DustEmis_test/test_DustEmis.pf       | 94 +++++++++++++++----
 2 files changed, 121 insertions(+), 24 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index cd60bd859f..c34f3a6e06 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -66,6 +66,8 @@ module DUSTMod
      procedure , public  :: DustDryDep      ! Turbulent dry deposition for dust
      procedure , public  :: WritePatchToLog ! Write information on the given patch to the log file
      procedure , public  :: GetPatchVars    ! Get important variables on a given patch
+     procedure , public  :: GetConstVars    ! Get important constant variables
+     procedure , public  :: Clean           ! Deallocate data 
      procedure , private :: InitAllocate 
      procedure , private :: InitHistory  
      procedure , private :: InitCold     
@@ -94,6 +96,32 @@ subroutine Init(this, bounds, NLFilename)
 
   end subroutine Init
 
+
+
+  !------------------------------------------------------------------------
+  subroutine Clean(this)
+   !
+   ! !ARGUMENTS:
+   class (dust_type) :: this
+   !
+   ! !LOCAL VARIABLES:
+   !------------------------------------------------------------------------
+
+   deallocate(this%flx_mss_vrt_dst_patch)
+   deallocate(this%flx_mss_vrt_dst_tot_patch)
+   deallocate(this%vlc_trb_patch)
+   deallocate(this%vlc_trb_1_patch)
+   deallocate(this%vlc_trb_2_patch)
+   deallocate(this%vlc_trb_3_patch)
+   deallocate(this%vlc_trb_4_patch)
+   deallocate(this%mbl_bsn_fct_col)
+
+   deallocate (ovr_src_snk_mss)
+   deallocate (dmt_vwr)
+   deallocate (stk_crc)
+
+ end subroutine Clean
+
   !------------------------------------------------------------------------
   subroutine InitAllocate(this, bounds)
     !
@@ -221,19 +249,17 @@ subroutine WritePatchToLog(this, p)
     class(dust_type), intent(in) :: this
     integer         , intent(in) :: p      ! Patch to display
 
-    write(iulog,*) 'flx_mss_vrt_dst', this%flx_mss_vrt_dst_patch(p,:)
     write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p)
     write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p)
     write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p)
     write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p)
     write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p)
-    write(iulog,*) 'mbl_bsn_fct', this%mbl_bsn_fct_col(p)
- end subroutine WritePatchToLog
+  end subroutine WritePatchToLog
 
     !-----------------------------------------------------------------------
 
- subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, &
-                         vlc_trb_2, vlc_trb_3, vlc_trb_4)
+  subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, &
+                          vlc_trb_2, vlc_trb_3, vlc_trb_4)
    !
    ! !DESCRIPTION:
    ! Get important variables on the given patch
@@ -255,7 +281,20 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb,
    if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p)
    if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p)
    if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p)
-end subroutine GetPatchVars
+  end subroutine GetPatchVars
+
+    !-----------------------------------------------------------------------
+
+  subroutine GetConstVars(this, SaltationFactor )
+  !
+  ! !DESCRIPTION:
+  ! Get important constant variables
+  ! !ARGUMENTS:
+    class(dust_type)  , intent(in)  :: this
+    real(r8)          , intent(out) :: SaltationFactor
+
+    SaltationFactor = tmp1
+  end subroutine GetConstVars
 
   !------------------------------------------------------------------------
   subroutine DustEmission (this, bounds, &
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index 08aa683964..4f8f7093d7 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -8,7 +8,7 @@ module test_DustEmis
   use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
   use clm_varcon, only : clm_varcon_init, clm_varcon_clean
-  use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting
+  use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean
   use DUSTMod
   use shr_kind_mod , only : r8 => shr_kind_r8
   use unittestFilterBuilderMod, only : filter_from_range
@@ -16,7 +16,7 @@ module test_DustEmis
   use SoilStateType, only : soilstate_type
   use CanopyStateType, only : canopystate_type
   use TemperatureType, only : temperature_type
-  use WaterType, only : water_type 
+  use WaterType, only : water_type
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
   use abortutils, only : endrun
@@ -43,7 +43,7 @@ module test_DustEmis
      procedure :: setupEnvironment
      procedure :: create_atm2lnd
      procedure :: create_fv
-     procedure :: print_patch
+     procedure :: print_values
      procedure :: validate_patch
   end type TestDustEmis
 
@@ -116,7 +116,9 @@ contains
   subroutine tearDown(this)
     class(TestDustEmis), intent(inout) :: this
 
+    call this%dust_emis%Clean()
     call this%water_factory%teardown(this%water_inst)
+    call SnowHydrologyClean()
     call unittest_subgrid_teardown()
     call this%atm2lnd_inst%Clean()
     call clm_varcon_clean()
@@ -163,7 +165,7 @@ contains
     grc%londeg(:) = 0.0_r8
 
     grc%area(:) = 10.0_r8
-    
+
   end subroutine setupEnvironment
 
   !-----------------------------------------------------------------------
@@ -207,40 +209,43 @@ contains
     ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
     ! fields based on inputs. Excluded inputs are given a default value
     class(TestDustEmis), intent(inout) :: this
-    real(r8), intent(in), optional :: fv(:)
-    real(r8), intent(in), optional :: u10(:)
-    real(r8), intent(in), optional :: ram1(:)
+    real(r8), intent(in), optional :: fv
+    real(r8), intent(in), optional :: u10
+    real(r8), intent(in), optional :: ram1
 
-    real(r8), parameter :: fv_default = 0.2_r8
+    real(r8), parameter :: fv_default = 2.0_r8
     real(r8), parameter :: u10_default = 4._r8
     real(r8), parameter :: ram1_default = 200._r8
     ! ------------------------------------------------------------------------
 
     if (present(fv)) then
-       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv(:)
+       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv
     else
        this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default
     end if
 
     if (present(u10)) then
-       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10(:)
+       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10
     else
        this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default
     end if
 
     if (present(ram1)) then
-       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1(:)
+       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1
     else
        this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default
     end if
 
   end subroutine create_fv
 
-  subroutine print_patch(this)
+  subroutine print_values(this)
     use LandunitType, only : lun
+    use PatchType, only : patch
     class(TestDustEmis), intent(inout) :: this
+    real(r8) :: SaltationFactor
     integer :: p, c, l
 
+    call this%dust_emis%GetConstVars( SaltationFactor )
     do l = bounds%begl, bounds%endl
        print *, 'landunit type= ', lun%itype(l)
     end do
@@ -248,13 +253,22 @@ contains
        print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1)
        print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1)
        print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c)
+       print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c)
+       print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c))
     end do
     do p = bounds%begp, bounds%endp
+       print *, 'patch type= ', patch%itype(p)
+       print *, 'patch weight= ', patch%wtgcell(p)
+       print *, 'patch active= ', patch%active(p)
        print *, 'tlai = ', this%canopystate_inst%tlai_patch(p)
+       print *, 'tsai = ', this%canopystate_inst%tsai_patch(p)
+       c = patch%column(p)
+       print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) &
+                                     / this%frictionvel_inst%fv_patch(p)
        call this%dust_emis%WritePatchToLog( p )
     end do
     call endrun( "exit early")
-  end subroutine print_patch
+  end subroutine print_values
 
   !-----------------------------------------------------------------------
   subroutine validate_patch(this, p)
@@ -284,6 +298,7 @@ contains
 
   @Test
   subroutine check_dust_emis(this)
+    ! Check dust emissions for default values
     class(TestDustEmis), intent(inout) :: this
     integer :: p
     real(r8) :: flx_mss_vrt_dst_tot
@@ -303,15 +318,58 @@ contains
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
                                vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
                                vlc_trb_4=vlc_trb_4)
-       @assertEqual( 0.0_r8, flx_mss_vrt_dst_tot )
-       @assertEqual( 3.319559266672431d-5, vlc_trb_1, tolerance=tol )
-       @assertEqual( 1.699714729099379d-5, vlc_trb_2, tolerance=tol )
-       @assertEqual( 9.163854318535118d-6, vlc_trb_3, tolerance=tol )
-       @assertEqual( 3.614237762488103d-5, vlc_trb_4, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 2.239779135859605d-5, tolerance=tol )
+       @assertEqual( vlc_trb_1, 3.407721147709135d-003, tolerance=tol )
+       @assertEqual( vlc_trb_2, 4.961153753164878d-003, tolerance=tol )
+       @assertEqual( vlc_trb_3, 4.980100969983446d-003, tolerance=tol )
+       @assertEqual( vlc_trb_4, 4.977071672163210d-003, tolerance=tol )
     end do
 
   end subroutine check_dust_emis
 
+  @Test
+  subroutine check_dust_emis_increasing_wind(this)
+    ! Check dust emissions with increasing wind
+    class(TestDustEmis), intent(inout) :: this
+    integer :: p, c
+    real(r8) :: flx_mss_vrt_dst_tot
+    real(r8) :: vlc_trb_1
+    real(r8) :: vlc_trb_2
+    real(r8) :: vlc_trb_3
+    real(r8) :: vlc_trb_4
+    real(r8) :: fv = 4.0_r8
+    real(r8) :: u10 = 10._r8
+    real(r8) :: total_dust0, total_dust_higher
+
+    ! Run baseline u10
+    call this%create_atm2lnd()
+    call this%create_fv( u10=u10, fv=fv )
+    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+    do p = bounds%begp, bounds%endp
+       call this%validate_patch(p)
+       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+       total_dust0 = flx_mss_vrt_dst_tot
+       @assertEqual( flx_mss_vrt_dst_tot, 1.971366884000767d-4, tolerance=tol )
+    end do
+    ! Double u10 and show result is higher
+    call this%create_fv( u10=u10*2.0_r8, fv=fv)
+    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+    do p = bounds%begp, bounds%endp
+       call this%validate_patch(p)
+       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+       total_dust_higher = flx_mss_vrt_dst_tot
+       @assertEqual( flx_mss_vrt_dst_tot, 3.288208220877217d-4, tolerance=tol )
+    end do
+    @assertGreaterThan( total_dust_higher, total_dust0 )
+
+  end subroutine check_dust_emis_increasing_wind
+
   !-----------------------------------------------------------------------
 
 end module test_DustEmis
\ No newline at end of file

From f2500c7c6d05db9810b0c8610a7962a2da40064d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 21 May 2024 20:16:06 -0600
Subject: [PATCH 0299/1248] Tighten the tolerance for numbers on the order of
 e-3

---
 src/biogeochem/test/DustEmis_test/test_DustEmis.pf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index 4f8f7093d7..616fd776fc 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -23,7 +23,7 @@ module test_DustEmis
 
   implicit none
 
-  real(r8), parameter :: tol = 1.e-13_r8
+  real(r8), parameter :: tol = 1.e-18_r8
 
   @TestCase
   type, extends(TestCase) :: TestDustEmis

From 1ba3473c1999073f0ecba7e4cbcf8d0b7d56fae1 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 21 May 2024 21:14:01 -0600
Subject: [PATCH 0300/1248] Add a check that figures out the value of fv where
 the wind threshold won't be met and dust will be zero

---
 .../test/DustEmis_test/test_DustEmis.pf       | 37 ++++++++++++++++---
 1 file changed, 31 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index 616fd776fc..c7e7566778 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -19,7 +19,6 @@ module test_DustEmis
   use WaterType, only : water_type
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
-  use abortutils, only : endrun
 
   implicit none
 
@@ -267,7 +266,6 @@ contains
                                      / this%frictionvel_inst%fv_patch(p)
        call this%dust_emis%WritePatchToLog( p )
     end do
-    call endrun( "exit early")
   end subroutine print_values
 
   !-----------------------------------------------------------------------
@@ -327,16 +325,43 @@ contains
 
   end subroutine check_dust_emis
 
+    !-----------------------------------------------------------------------
+
+  @Test
+  subroutine dust_zero_for_fixed_ratio(this)
+    ! Check dust emissions are zero for a no wind
+    class(TestDustEmis), intent(inout) :: this
+    integer :: p
+    real(r8) :: flx_mss_vrt_dst_tot
+    real(r8) :: fv
+    real(r8) :: SaltationFactor
+
+    call this%create_atm2lnd()
+    call this%dust_emis%GetConstVars( SaltationFactor )
+    ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps))
+    fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15
+    call this%create_fv( fv=fv )
+    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+    call this%print_values()
+    do p = bounds%begp, bounds%endp
+       call this%validate_patch(p)
+       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+       @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
+    end do
+
+   end subroutine dust_zero_for_fixed_ratio
+
+  !-----------------------------------------------------------------------
+
   @Test
   subroutine check_dust_emis_increasing_wind(this)
     ! Check dust emissions with increasing wind
     class(TestDustEmis), intent(inout) :: this
     integer :: p, c
     real(r8) :: flx_mss_vrt_dst_tot
-    real(r8) :: vlc_trb_1
-    real(r8) :: vlc_trb_2
-    real(r8) :: vlc_trb_3
-    real(r8) :: vlc_trb_4
     real(r8) :: fv = 4.0_r8
     real(r8) :: u10 = 10._r8
     real(r8) :: total_dust0, total_dust_higher

From 3967d77a17e4e6a02362aec42aa3feb187ba6c72 Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Wed, 22 May 2024 10:28:47 -0600
Subject: [PATCH 0301/1248] new fates api 36 paramfile default

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 6ef91bb4a0..fdfeba7719 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -481,7 +481,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.35.0.0_12pft_c240326.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.0.0_12pft_c240517.nc</fates_paramfile>
 
 <!-- ================================================================== -->
 <!-- Default surface roughness parameterization                         -->

From 5b30740bd91e421639bb46239f4d921b8e767b54 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Wed, 22 May 2024 13:37:16 -0600
Subject: [PATCH 0302/1248] Pin FATES external to commit a997af5.

---
 Externals_CLM.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
index cfb7beb40f..a8d53e4fdb 100644
--- a/Externals_CLM.cfg
+++ b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/ckoven/fates
-branch = luh2_nocomp_merge
+hash = a997af58f38db8ffda259e11f3abcc65478a4903
 required = True
 
 [externals_description]

From 2a7ca01b2177b480e8897fd2921bf00a7ac9c48f Mon Sep 17 00:00:00 2001
From: loaner <loaner@eesaloaner-m53.local>
Date: Wed, 22 May 2024 17:43:48 -0700
Subject: [PATCH 0303/1248] add systemtest for potential vegetation spin up

---
 cime_config/SystemTests/pvt.py              | 120 ++++++++++++++++++++
 cime_config/SystemTests/systemtest_utils.py |  20 +++-
 2 files changed, 139 insertions(+), 1 deletion(-)
 create mode 100644 cime_config/SystemTests/pvt.py

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
new file mode 100644
index 0000000000..e18022220d
--- /dev/null
+++ b/cime_config/SystemTests/pvt.py
@@ -0,0 +1,120 @@
+"""
+FATES land use potential vegetation spin up + transient test
+
+This is a FATES specific test:
+
+1) conduct a spinup with use_fates_potentialveg on
+    - write restart file
+    - use CLM_ACCELERATED_SPINUP?
+2) run a transient landuse case with use_fates_lupft
+    - start from the restart file generated in (1)
+
+"""
+from CIME.XML.standard_module_setup import *
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+from systemtest_utils import read_user_nl_clm
+import shutil, glob, os
+
+logger = logging.getLogger(__name__)
+
+class PVT(SystemTestsCommon):
+    def __init_(self,case):
+        SystemTestsCommon.__init__(self,case)
+
+        # Do not allow PVT to be run with certain testmods
+        # Should this be targeted to a specific testmod for simplicity for now?
+        # Technically this could be run with the luh fates_harvest_modes
+        casebaseid = self._case.get_value("CASEBASEID")
+        casebasid = casebaseid.split("-")[-1]
+        if casebaseid[0:10] != "FatesLUPFT":
+            error_message = (
+                "Only call PVT with test FatesLUPFT"
+            )
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Only allow to run if resolution is 4x5 for now
+        # Eventually we could set this up to generate the necessary land use x pft mapping
+        # on the fly, although this would also require generating the land use timeseries
+        # regridding on the fly which is a more time consuming endevour currently
+        lnd_grid = self._case.get_value("LND_GRID")
+        if lnd_grid != "4x5":
+            error_message = (
+                "PVT can currently only be run with 4x5 resolution"
+            )
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+    def run_phase(self):
+        # -------------------------------------------------------------------
+        # (1) Run FATES spin-up case in potential vegetation mode
+        # -------------------------------------------------------------------
+        orig_case = self._case
+        orig_casevar = self._case.get_value("CASE")
+        caseroot = self._case.get_value("CASEROOT")
+
+        # clone the main case to create spinup case
+        logger.info("PVT log:  cloning setup")
+        clone_path = "{}.potveg".format(caseroot)
+        if os.path.exists(clone_path):
+            shutil.rmtree(clone_path)
+        logger.info("PVT log:  cloning")
+        clone = self._case.create_clone(clone_path, keepexe=True)
+        logger.info("PVT log: cloning complete")
+
+        # setup the clone case
+        os.chdir(clone_path)
+        self._set_active_case(clone)
+        self._setup_all()
+
+        # Modify the spin up case to use the potential vegetation mode.
+        # Checks for incompatible cases and necessary mapping files are
+        # handled in the build case.
+        # use_fates_lupft should be set to true in the testmod
+        # save off the harvest mode for reinstating later
+        found, hmode = self.read_user_nl_clm('fates_harvest_mode')
+        logger.info("PVT log:  modify user_nl_clm file for spin up run")
+        # TODO: remove fates_harvest_mode if found
+        self._append_to_user_nl_clm(
+            [
+                "use_fates_potentialveg = .true.",
+            ]
+        )
+
+        stop_n_pveg = 1
+        with clone:
+            # clone.set_value("CLM_ACCELERATED_SPINUP", "on")
+            clone.set_value("STOP_N", stop_n_pveg)
+
+        # Run the spin up case
+        # As per SSP test:
+        # "No history files expected, set suffix=None to avoid compare error"
+        logger.info("PVT log:  starting spin-up run")
+        dout_sr = clone.get_value("DOUT_S_ROOT")
+        self._skip_pnl = False
+        self.run_indv(suffix=None, st_archive=True)
+
+        # -------------------------------------------------------------------
+        # (2) Run FATES transient case using restart file from spin-up
+        # -------------------------------------------------------------------
+        os.chdir(caseroot)
+        self._set_active_case(orig_case)
+
+        # logger.info("PVT log:  modify user_nl_clm file for transient run")
+        # self._append_to_user_nl_clm(
+        #     [
+        #         "use_fates_potentialveg = .true.",
+        #     ]
+        # )
+
+
+        self._case.set_value("CLM_ACCELERATED_SPINUP", "off")
+        self._case.set_value("RUN_TYPE", "hybrid")
+        self._case.set_value("GET_REFCASE", False)
+        self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar))
+        self._case.set_value("RUN_REFDATE", "1700-01-01")
+        self._case.set_value("DOUT_S", False)
+        self._case.flush()
+
+        # do the restart run (short term archiving is off)
+        self.run_indv()
diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py
index c5ac986abd..8447934797 100644
--- a/cime_config/SystemTests/systemtest_utils.py
+++ b/cime_config/SystemTests/systemtest_utils.py
@@ -2,7 +2,7 @@
 Reduce code duplication by putting reused functions here.
 """
 
-import os, subprocess
+import os, subprocess, re
 
 
 def cmds_to_setup_conda(caseroot):
@@ -84,3 +84,21 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path):
     except:
         print(f"ERROR trying to run {tool_name}.")
         raise
+
+def read_user_nl_clm(self,namelist_option):
+    user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
+    with open(user_nl_clm_path) as f:
+        user_nl_clm_text = f.read()
+        reg = fr'{namelist_option}\s*=\s*([^\n]+)'
+        find_out = re.findall(reg, user_nl_clm_text)
+        # This could be more robust
+        if len(find_out) == 0:
+            return 0, False
+        elif len(find_out) > 1:
+            error_message = (
+                "ERROR: read_user_nl_clm: namelist option is set more than once"
+            )
+            # logger.error(error_message)
+            raise RuntimeError(error_message)
+        else:
+            return find_out[0], True

From fc1400f5154f86a6d3346aebce677fff506400e8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 22 May 2024 21:31:43 -0600
Subject: [PATCH 0304/1248] Add a check that when fsno is 1 dust emission is
 zeroed

---
 .../test/DustEmis_test/test_DustEmis.pf       | 76 ++++++++++++-------
 1 file changed, 50 insertions(+), 26 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index c7e7566778..b9b00ae4fa 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -325,34 +325,58 @@ contains
 
   end subroutine check_dust_emis
 
-    !-----------------------------------------------------------------------
+   !-----------------------------------------------------------------------
+
+ @Test
+ subroutine dust_zero_for_fixed_ratio(this)
+   ! Check dust emissions are zero for a no wind
+   class(TestDustEmis), intent(inout) :: this
+   integer :: p
+   real(r8) :: flx_mss_vrt_dst_tot
+   real(r8) :: fv
+   real(r8) :: SaltationFactor
+
+   call this%create_atm2lnd()
+   call this%dust_emis%GetConstVars( SaltationFactor )
+   ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps))
+   fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15
+   call this%create_fv( fv=fv )
+   call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                     this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                     this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+   call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+   call this%print_values()
+   do p = bounds%begp, bounds%endp
+      call this%validate_patch(p)
+      call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+      @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
+   end do
+
+  end subroutine dust_zero_for_fixed_ratio
 
-  @Test
-  subroutine dust_zero_for_fixed_ratio(this)
-    ! Check dust emissions are zero for a no wind
-    class(TestDustEmis), intent(inout) :: this
-    integer :: p
-    real(r8) :: flx_mss_vrt_dst_tot
-    real(r8) :: fv
-    real(r8) :: SaltationFactor
-
-    call this%create_atm2lnd()
-    call this%dust_emis%GetConstVars( SaltationFactor )
-    ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps))
-    fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15
-    call this%create_fv( fv=fv )
-    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
-    call this%print_values()
-    do p = bounds%begp, bounds%endp
-       call this%validate_patch(p)
-       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
-       @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
-    end do
+  !-----------------------------------------------------------------------
 
-   end subroutine dust_zero_for_fixed_ratio
+ @Test
+ subroutine dust_zero_when_fsno_one(this)
+   ! Check dust emissions are zero for a no wind
+   class(TestDustEmis), intent(inout) :: this
+   integer :: p
+   real(r8) :: flx_mss_vrt_dst_tot
+
+   call this%create_atm2lnd()
+   this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8
+   call this%create_fv( )
+   call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                     this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                     this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+   call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+   do p = bounds%begp, bounds%endp
+      call this%validate_patch(p)
+      call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+      @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
+   end do
+
+  end subroutine dust_zero_when_fsno_one
 
   !-----------------------------------------------------------------------
 

From ebdd3267f099fe995c379543a932dfc69b14b969 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 22 May 2024 21:54:28 -0600
Subject: [PATCH 0305/1248] Add a test that tlai set to 0.3 has zero dust
 emission

---
 .../test/DustEmis_test/test_DustEmis.pf       | 26 ++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index b9b00ae4fa..764947836d 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -358,7 +358,7 @@ contains
 
  @Test
  subroutine dust_zero_when_fsno_one(this)
-   ! Check dust emissions are zero for a no wind
+   ! Check dust emissions are zero when snow fraction is identically 1
    class(TestDustEmis), intent(inout) :: this
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
@@ -380,6 +380,30 @@ contains
 
   !-----------------------------------------------------------------------
 
+ @Test
+ subroutine dust_zero_when_tlai_high(this)
+   ! Check dust emissions are zero when LAI is high enough
+   class(TestDustEmis), intent(inout) :: this
+   integer :: p
+   real(r8) :: flx_mss_vrt_dst_tot
+
+   call this%create_atm2lnd()
+   call this%create_fv( )
+   this%canopystate_inst%tlai_patch(:) = 0.3_r8
+   call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                     this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                     this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+   call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+   do p = bounds%begp, bounds%endp
+      call this%validate_patch(p)
+      call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+      @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
+   end do
+
+  end subroutine dust_zero_when_tlai_high
+
+  !-----------------------------------------------------------------------
+
   @Test
   subroutine check_dust_emis_increasing_wind(this)
     ! Check dust emissions with increasing wind

From 171c981240b2b2c7f614813401f99795fb8c33dc Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 22 May 2024 22:58:36 -0600
Subject: [PATCH 0306/1248] Add test that dust emissions are zero for all
 non-veg landunits

---
 .../test/DustEmis_test/test_DustEmis.pf       | 29 ++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index 764947836d..a76c724480 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -371,7 +371,6 @@ contains
                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
    do p = bounds%begp, bounds%endp
-      call this%validate_patch(p)
       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
       @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
    end do
@@ -380,6 +379,34 @@ contains
 
   !-----------------------------------------------------------------------
 
+ @Test
+ subroutine dust_zero_non_veg_lu(this)
+   ! Check dust emissions are zero for non-veg landunits
+   use landunit_varcon, only: istcrop, max_lunit
+   use LandunitType, only : lun
+   class(TestDustEmis), intent(inout) :: this
+   integer :: p, l
+   real(r8) :: flx_mss_vrt_dst_tot
+
+   call this%create_atm2lnd()
+   call this%create_fv( )
+   ! Set the lanunit type for
+   do l = istcrop+1, max_lunit
+      lun%itype(bounds%begl:bounds%endl) = l
+      call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                        this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                        this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+      call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+      do p = bounds%begp, bounds%endp
+         call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+         @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
+      end do
+   end do
+
+  end subroutine dust_zero_non_veg_lu
+
+  !-----------------------------------------------------------------------
+
  @Test
  subroutine dust_zero_when_tlai_high(this)
    ! Check dust emissions are zero when LAI is high enough

From b7cf13f6dcfd6c975de294ef90122bb4e2fc0d3e Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 23 May 2024 13:47:07 -0700
Subject: [PATCH 0307/1248] add PVT system test to the config_test xml file

---
 cime_config/config_tests.xml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index c0b6afed9d..8a4388c664 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -123,6 +123,18 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="PVT">
+    <DESC>FATES potential vegetarion spin-up + land use transient run test</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <STOP_OPTION>ndays</STOP_OPTION>
+    <RUN_TYPE>startup</RUN_TYPE>
+    <STOP_N>4</STOP_N>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
   <test NAME="RXCROPMATURITY">
     <DESC>Generate prescribed maturity requirements, then test with them</DESC>
     <INFO_DBUG>1</INFO_DBUG>

From 8e35d80baf507185ef0dac47a4adee4bf975d47e Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 23 May 2024 14:29:02 -0600
Subject: [PATCH 0308/1248] add test mode for use_fates_lupft

---
 .../testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods      | 1 +
 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm    | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods
new file mode 100644
index 0000000000..4c7aa0f2b4
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods
@@ -0,0 +1 @@
+../Fates
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm
new file mode 100644
index 0000000000..10044848a0
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm
@@ -0,0 +1 @@
+use_fates_lupft = .true.

From a14ab0838951426162b7af5bb1a1a977cf6353cf Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 23 May 2024 14:53:35 -0600
Subject: [PATCH 0309/1248] Update cmeps to cmeps0.14.63 in Externals.cfg

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index 8ef524bf24..70d103a94b 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -48,7 +48,7 @@ tag = cime6.0.238_httpsbranch01
 required = True
 
 [cmeps]
-tag = cmeps0.14.60
+tag = cmeps0.14.63
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps

From af5451b7e37d53d1192fb87315d01fb16b527ba1 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 23 May 2024 14:39:45 -0700
Subject: [PATCH 0310/1248] remove tabs and correct whitespace

---
 bld/CLMBuildNamelist.pm | 58 ++++++++++++++++++++---------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index acdad5c5cc..b17a245715 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4520,22 +4520,22 @@ sub setup_logic_fates {
                        "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" );
 
         foreach my $var ( @list ) {
- 	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
-                      'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
+           add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
+                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
         }
 
- 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_potentialveg', 'use_fates'=>$nl_flags->{'use_fates'});
- 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
- 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
-                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), 
-                      'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'), 
-                      'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') );
- 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'},
-                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
-                      'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
- 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'},
-                      'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
-                      'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_potentialveg', 'use_fates'=>$nl_flags->{'use_fates'});
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
+                    'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
+                    'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'),
+                    'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') );
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'},
+                    'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
+                    'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'},
+                    'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
+                    'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
 
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');
@@ -4564,8 +4564,8 @@ sub setup_logic_fates {
 
               # fates landuse can't be on with FATES SP mode is active
               if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
-		  $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
-	      }
+                   $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
+              }
 
               # hydro isn't currently supported to work when FATES SP mode is active
               if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
@@ -4608,7 +4608,7 @@ sub setup_logic_fates {
                  if ( ! &value_is_true($nl->get_value($var)) ) {
                     $var = "fluh_timeseries";
                     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 
-           			'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
+                    'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
                     my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
                     if ( ! defined($nl->get_value($var))  ) {
                        $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" );
@@ -4616,21 +4616,21 @@ sub setup_logic_fates {
                        $log->fatal_error("$var does NOT point to a valid filename" );
                     }
                  }
-	      }
+              }
               $var = "use_fates_fixed_biogeog";
               if ( defined($nl->get_value($var))  ) {
                  if ( &value_is_true($nl->get_value($var)) ) {
-            	    $var = "flandusepftdat";
-            	    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-            	                'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
-            	    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
-            	    if ( ! defined($nl->get_value($var))  ) {
-            	      $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
-            	    } elsif ( ! -f "$fname" ) {
-            	      $log->fatal_error("$var does NOT point to a valid filename" );
-            	    }
-		 }
-	      }
+                    $var = "flandusepftdat";
+                    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
+                                'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
+                    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+                    if ( ! defined($nl->get_value($var))  ) {
+                      $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
+                    } elsif ( ! -f "$fname" ) {
+                      $log->fatal_error("$var does NOT point to a valid filename" );
+                    }
+                 }
+              }
            }
         }
         # check that fates landuse is on and harvest mode is off when potential veg switch is true

From 470b279dcc7c2563b719bbbbf67a696cad7f6481 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 23 May 2024 15:55:13 -0600
Subject: [PATCH 0311/1248] Add a fail test for bad dust mobilization

---
 src/biogeochem/DUSTMod.F90                    |  6 ++++--
 .../test/DustEmis_test/test_DustEmis.pf       | 21 +++++++++++++++++++
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index c34f3a6e06..8de7811aa1 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -445,8 +445,10 @@ subroutine DustEmission (this, bounds, &
       do fp = 1,num_nolakep
          p = filter_nolakep(fp)
          if (lnd_frc_mbl(p)>1.0_r8 .or. lnd_frc_mbl(p)<0.0_r8) then
-            write(iulog,*)'Error dstmbl: pft= ',p,' lnd_frc_mbl(p)= ',lnd_frc_mbl(p)
-            call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__))
+            write(iulog,*)'Error dstmbl: pft= ',p,' lnd_frc_mbl(p)= ',lnd_frc_mbl(p), &
+                           errMsg(sourcefile, __LINE__)
+            call endrun("Bad value for dust mobilization fraction")
+            return
          end if
       end do
 
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index a76c724480..a9b72a6e64 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -407,6 +407,27 @@ contains
 
   !-----------------------------------------------------------------------
 
+  @Test
+  subroutine aborts_on_bad_dust_mobility(this)
+    ! Check dust abort when dust mobility is bad
+    class(TestDustEmis), intent(inout) :: this
+    real(r8) :: flx_mss_vrt_dst_tot
+    character(100) :: expected_msg
+ 
+    call this%create_atm2lnd()
+    call this%create_fv( )
+    ! Dust should abort with an error on dust mobility when snow fraction greater than 1
+    this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + 1.e-15_r8
+    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
+                         this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
+                         this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+    expected_msg = "ABORTED: Bad value for dust mobilization fraction"
+    @assertExceptionRaised(expected_msg)
+
+  end subroutine aborts_on_bad_dust_mobility
+ 
+  !-----------------------------------------------------------------------
+
  @Test
  subroutine dust_zero_when_tlai_high(this)
    ! Check dust emissions are zero when LAI is high enough

From 07918b515c63183135ae85cb43919486b7153ded Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 23 May 2024 16:08:44 -0600
Subject: [PATCH 0312/1248] Replace DUSTMod with DustEmisZender2003 with VS
 code

---
 src/biogeochem/CMakeLists.txt                          | 2 +-
 src/biogeochem/CNVegStateType.F90                      | 2 +-
 src/biogeochem/{DUSTMod.F90 => DustEmisZender2003.F90} | 4 ++--
 src/biogeochem/test/DustEmis_test/test_DustEmis.pf     | 2 +-
 src/main/clm_driver.F90                                | 2 +-
 src/main/clm_instMod.F90                               | 2 +-
 src/main/lnd2atmMod.F90                                | 2 +-
 7 files changed, 8 insertions(+), 8 deletions(-)
 rename src/biogeochem/{DUSTMod.F90 => DustEmisZender2003.F90} (99%)

diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt
index 0f46dc665d..0dd06ac09e 100644
--- a/src/biogeochem/CMakeLists.txt
+++ b/src/biogeochem/CMakeLists.txt
@@ -6,7 +6,7 @@ list(APPEND clm_sources
   CNPhenologyMod.F90
   CNSpeciesMod.F90
   CNDVType.F90
-  DUSTMod.F90
+  DustEmisZender2003.F90
   CropReprPoolsMod.F90
   CropType.F90
   CNVegStateType.F90
diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90
index c286c0344f..98c1a6ce3a 100644
--- a/src/biogeochem/CNVegStateType.F90
+++ b/src/biogeochem/CNVegStateType.F90
@@ -519,7 +519,7 @@ subroutine InitCold(this, bounds)
 
     ! --------------------------------------------------------------------
     ! Initialize terms needed for dust model
-    ! TODO - move these terms to DUSTMod module variables
+    ! TODO - move these terms to DustEmisZender2003 module variables
     ! --------------------------------------------------------------------
 
     do c = bounds%begc, bounds%endc
diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DustEmisZender2003.F90
similarity index 99%
rename from src/biogeochem/DUSTMod.F90
rename to src/biogeochem/DustEmisZender2003.F90
index 8de7811aa1..22bbbe0742 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -1,4 +1,4 @@
-module DUSTMod
+module DustEmisZender2003
 
   !----------------------------------------------------------------------- 
   ! !DESCRIPTION: 
@@ -1033,4 +1033,4 @@ subroutine InitDustVars(this, bounds)
 
   end subroutine InitDustVars
 
-end module DUSTMod
+end module DustEmisZender2003
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index a9b72a6e64..ded09f7919 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -9,7 +9,7 @@ module test_DustEmis
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
   use clm_varcon, only : clm_varcon_init, clm_varcon_clean
   use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean
-  use DUSTMod
+  use DustEmisZender2003
   use shr_kind_mod , only : r8 => shr_kind_r8
   use unittestFilterBuilderMod, only : filter_from_range
   use atm2lndType, only : atm2lnd_type, atm2lnd_params_type
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index 00a98e61b4..f9db72e0ed 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -62,7 +62,7 @@ module clm_driver
   use ndepStreamMod          , only : ndep_interp
   use cropcalStreamMod       , only : cropcal_advance, cropcal_interp
   use ch4Mod                 , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check
-  use DUSTMod                , only : DustDryDep, DustEmission
+  use DustEmisZender2003                , only : DustDryDep, DustEmission
   use VOCEmissionMod         , only : VOCEmission
   !
   use filterMod              , only : setFilters
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index a24e05b27c..f11805a755 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -45,7 +45,7 @@ module clm_instMod
   use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
   use CropType                        , only : crop_type
   use DryDepVelocity                  , only : drydepvel_type
-  use DUSTMod                         , only : dust_type
+  use DustEmisZender2003                         , only : dust_type
   use EnergyFluxType                  , only : energyflux_type
   use FrictionVelocityMod             , only : frictionvel_type
   use GlacierSurfaceMassBalanceMod    , only : glacier_smb_type
diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90
index 1cda0cff91..b91feaabf9 100644
--- a/src/main/lnd2atmMod.F90
+++ b/src/main/lnd2atmMod.F90
@@ -20,7 +20,7 @@ module lnd2atmMod
   use lnd2atmType          , only : lnd2atm_type
   use atm2lndType          , only : atm2lnd_type
   use ch4Mod               , only : ch4_type
-  use DUSTMod              , only : dust_type
+  use DustEmisZender2003              , only : dust_type
   use DryDepVelocity       , only : drydepvel_type
   use VocEmissionMod       , only : vocemis_type
   use CNFireEmissionsMod   , only : fireemis_type

From 00d23e9adb4139847dc5f855ff4ce43bc845b41e Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 23 May 2024 16:48:55 -0600
Subject: [PATCH 0313/1248] correct add default for fluh and flandusepftdat

---
 bld/CLMBuildNamelist.pm | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b17a245715..d952e7fe89 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4607,8 +4607,8 @@ sub setup_logic_fates {
               if ( defined($nl->get_value($var))  ) {
                  if ( ! &value_is_true($nl->get_value($var)) ) {
                     $var = "fluh_timeseries";
-                    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 
-                    'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
+                    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
+           			'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
                     my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
                     if ( ! defined($nl->get_value($var))  ) {
                        $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" );
@@ -4620,17 +4620,17 @@ sub setup_logic_fates {
               $var = "use_fates_fixed_biogeog";
               if ( defined($nl->get_value($var))  ) {
                  if ( &value_is_true($nl->get_value($var)) ) {
-                    $var = "flandusepftdat";
-                    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                                'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
-                    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
-                    if ( ! defined($nl->get_value($var))  ) {
-                      $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
-                    } elsif ( ! -f "$fname" ) {
-                      $log->fatal_error("$var does NOT point to a valid filename" );
-                    }
-                 }
-              }
+            	    $var = "flandusepftdat";
+            	    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
+            	                'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
+            	    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+            	    if ( ! defined($nl->get_value($var))  ) {
+            	      $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
+            	    } elsif ( ! -f "$fname" ) {
+            	      $log->fatal_error("$var does NOT point to a valid filename" );
+            	    }
+		 }
+	      }
            }
         }
         # check that fates landuse is on and harvest mode is off when potential veg switch is true

From 2ac13bcb7aeec5a1772635edfe7c0f99be9c532d Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 23 May 2024 17:39:57 -0600
Subject: [PATCH 0314/1248] correct typos causing RunTimeError to be missed

---
 cime_config/SystemTests/pvt.py | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
index e18022220d..c45c514f39 100644
--- a/cime_config/SystemTests/pvt.py
+++ b/cime_config/SystemTests/pvt.py
@@ -18,20 +18,17 @@
 logger = logging.getLogger(__name__)
 
 class PVT(SystemTestsCommon):
-    def __init_(self,case):
+    def __init__(self,case):
         SystemTestsCommon.__init__(self,case)
 
         # Do not allow PVT to be run with certain testmods
         # Should this be targeted to a specific testmod for simplicity for now?
         # Technically this could be run with the luh fates_harvest_modes
+        error_message = None
         casebaseid = self._case.get_value("CASEBASEID")
-        casebasid = casebaseid.split("-")[-1]
+        casebaseid = casebaseid.split("-")[-1]
         if casebaseid[0:10] != "FatesLUPFT":
-            error_message = (
-                "Only call PVT with test FatesLUPFT"
-            )
-            logger.error(error_message)
-            raise RuntimeError(error_message)
+            error_message = (f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected.")
 
         # Only allow to run if resolution is 4x5 for now
         # Eventually we could set this up to generate the necessary land use x pft mapping
@@ -39,12 +36,11 @@ def __init_(self,case):
         # regridding on the fly which is a more time consuming endevour currently
         lnd_grid = self._case.get_value("LND_GRID")
         if lnd_grid != "4x5":
-            error_message = (
-                "PVT can currently only be run with 4x5 resolution"
-            )
+            error_message = (f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected.")
+
+        if error_message is not None:
             logger.error(error_message)
             raise RuntimeError(error_message)
-
     def run_phase(self):
         # -------------------------------------------------------------------
         # (1) Run FATES spin-up case in potential vegetation mode

From f4ff559c831533ab9c901d1f44e5744740a8f302 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 23 May 2024 16:45:42 -0700
Subject: [PATCH 0315/1248] remove tabs again

---
 bld/CLMBuildNamelist.pm | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index d952e7fe89..0fb7ba9692 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4608,7 +4608,7 @@ sub setup_logic_fates {
                  if ( ! &value_is_true($nl->get_value($var)) ) {
                     $var = "fluh_timeseries";
                     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
-           			'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+                                'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
                     my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
                     if ( ! defined($nl->get_value($var))  ) {
                        $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" );
@@ -4620,17 +4620,17 @@ sub setup_logic_fates {
               $var = "use_fates_fixed_biogeog";
               if ( defined($nl->get_value($var))  ) {
                  if ( &value_is_true($nl->get_value($var)) ) {
-            	    $var = "flandusepftdat";
-            	    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
-            	                'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
-            	    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
-            	    if ( ! defined($nl->get_value($var))  ) {
-            	      $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
-            	    } elsif ( ! -f "$fname" ) {
-            	      $log->fatal_error("$var does NOT point to a valid filename" );
-            	    }
-		 }
-	      }
+                    $var = "flandusepftdat";
+                    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
+                                'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
+                    my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+                    if ( ! defined($nl->get_value($var))  ) {
+                      $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
+                    } elsif ( ! -f "$fname" ) {
+                      $log->fatal_error("$var does NOT point to a valid filename" );
+                    }
+                 }
+              }
            }
         }
         # check that fates landuse is on and harvest mode is off when potential veg switch is true

From 03f89ea926cf5f4cfba56b079ce91e1536a5787f Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Thu, 23 May 2024 22:44:24 -0600
Subject: [PATCH 0316/1248] dmleung added a minor edit on subtimestep wind
 fluctuation (23 May 2024)

---
 src/biogeochem/DUSTMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 2986ed579b..e1348b8ebf 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -742,7 +742,7 @@ subroutine DustEmission (bounds, &
             if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
                u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
             else
-               u_sd_slt(p) = 0.001_r8   ! should have used 0 theoretically; used 0.001 here to avoid undefined values
+               u_sd_slt(p) = wnd_frc_slt * (0.001_r8)**0.333_r8   ! should have used 0 theoretically; used 0.001 here to avoid undefined values
             end if
 
             ! threshold velocities

From dd5671a824854ab270687cf669ee96656cad2fae Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Fri, 24 May 2024 09:56:34 -0600
Subject: [PATCH 0317/1248] Update streams file name and global attributes

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 7f9e3de6b4..4b8b7d3571 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1871,15 +1871,15 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldfilename_urbantv phys="clm6_0" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_0.9x1.25_simyr1849-2106_c200605.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm6_0"  hgrid="0.9x1.25" urban_explicit_ac=".true."
->/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_1" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_0.9x1.25_simyr1849-2106_c200605.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25" urban_explicit_ac=".true."
->/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".true."
->/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm4_5" hgrid="0.9x1.25"
 >lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 

From 8cc00387d6bb131f90ec08334c8e7b132d4388cf Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 11:22:27 -0600
Subject: [PATCH 0318/1248] Add a unit test shell for SoilStateInitTimeConsst

---
 src/biogeophys/CMakeLists.txt                 |  1 +
 src/biogeophys/test/CMakeLists.txt            |  1 +
 .../CMakeLists.txt                            |  6 ++++
 .../test_dust_soil_clay_functions.pf          | 29 +++++++++++++++++++
 4 files changed, 37 insertions(+)
 create mode 100644 src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt
 create mode 100644 src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf

diff --git a/src/biogeophys/CMakeLists.txt b/src/biogeophys/CMakeLists.txt
index 86edcca9f9..07b88b07bf 100644
--- a/src/biogeophys/CMakeLists.txt
+++ b/src/biogeophys/CMakeLists.txt
@@ -25,6 +25,7 @@ list(APPEND clm_sources
   SoilHydrologyType.F90
   SoilStateType.F90
   SoilWaterRetentionCurveMod.F90
+  SoilStateInitTimeConstMod.F90
   SolarAbsorbedType.F90
   PhotosynthesisMod.F90
   SurfaceAlbedoType.F90
diff --git a/src/biogeophys/test/CMakeLists.txt b/src/biogeophys/test/CMakeLists.txt
index 5c15858210..7a0a1e8fbb 100644
--- a/src/biogeophys/test/CMakeLists.txt
+++ b/src/biogeophys/test/CMakeLists.txt
@@ -5,6 +5,7 @@ add_subdirectory(HillslopeHydrology_test)
 add_subdirectory(SnowHydrology_test)
 add_subdirectory(Photosynthesis_test)
 add_subdirectory(Balance_test)
+add_subdirectory(SoilStateInitTimeConst_test)
 add_subdirectory(TotalWaterAndHeat_test)
 add_subdirectory(Wateratm2lnd_test)
 add_subdirectory(WaterTracerContainerType_test)
diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt b/src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt
new file mode 100644
index 0000000000..df58da9875
--- /dev/null
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt
@@ -0,0 +1,6 @@
+set (pfunit_sources
+  test_dust_soil_clay_functions.pf)
+
+add_pfunit_ctest(SoilStateInit
+  TEST_SOURCES "${pfunit_sources}"
+  LINK_LIBRARIES clm csm_share)
diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
new file mode 100644
index 0000000000..d3d9fc7e7f
--- /dev/null
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
@@ -0,0 +1,29 @@
+module test_dust_soil_clay_functions
+
+  ! Tests of SoilStateInitTimeConst functions for dust emission in regard to clay content
+
+  use funit
+  use SoilStateInitTimeConstMod
+  use shr_kind_mod , only : r8 => shr_kind_r8
+
+  implicit none
+
+  @TestCase
+  type, extends(TestCase) :: TestDustEmisSoilFunctions
+   contains
+     procedure :: setUp
+     procedure :: tearDown
+  end type TestDustEmisSoilFunctions
+
+contains
+
+  subroutine setUp(this)
+    class(TestDustEmisSoilFunctions), intent(inout) :: this
+  end subroutine setUp
+
+  subroutine tearDown(this)
+    class(TestDustEmisSoilFunctions), intent(inout) :: this
+
+  end subroutine tearDown
+
+end module test_dust_soil_clay_functions

From 679ececd1336838b9bcb6e51f900da94fbe91957 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 12:04:33 -0600
Subject: [PATCH 0319/1248] Add functions needed by dust emissions for soil
 characteristics

---
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 9122b56890..46759cb90b 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -715,4 +715,24 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
 
   end subroutine SoilStateInitTimeConst
 
+  !------------------------------------------------------------------------------
+
+  real(r8) function ThresholdSoilMoist( clay )
+  ! Calculate the threshold soil moisture needed for dust emission, based on clay content
+      real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%)
+
+      ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
+  end function ThresholdSoilMoist 
+
+  !------------------------------------------------------------------------------
+
+  real(r8) function MassFracClay( clay )
+  ! Calculate the mass fraction of clay needed for dust emission, based on clay content
+      real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%)
+
+      MassFracClay = min(clay * 0.01_r8, 0.20_r8)
+  end function MassFracClay 
+
+  !------------------------------------------------------------------------------
+
 end module SoilStateInitTimeConstMod

From 956ea907541cd514f44ea11c693e29bc72e4eca2 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Fri, 24 May 2024 13:18:42 -0600
Subject: [PATCH 0320/1248] dmleung added more comments on the impact of soil
 moisture threshold on dust emission calculation. 24 May 2024

---
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index bf2de65a29..3c8945e9d2 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -703,8 +703,12 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     do c = begc,endc
        g = col%gridcell(c)
 
-       !soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Jasper Kok et al. (2014) modified the equation of soil moisture effect for dust emissions using a tuning factor of a = 1. 0.01 is to convert the threshold gravimetric soil moisture from % to fraction. Danny M. Leung et al. (2023) followed K14 and used this equation for the paper's results. However, Danny Leung later (Dec 2023) decided to revert to Zender's choice and use a = 1 / (clay fraction), which overall encourages more dust emissions from seriamid and more marginal dust sources. dmleung added this detailed comment on 19 Feb 2024.
-       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with a = 1 / (clay fraction) being the tuning factor for soil moisture effect in Zender's dust emission scheme. Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) dust emission scheme in the CESM will use Zender's tuning of a = 1 / (clay fraction), which overall encourages more dust emissions from seriamid and more marginal dust sources. Another advantage of using this tuning factor instead of a = 1 is that the dust emission threshold is linearly dependent on the clay fraction instead of parabolically dependent on clay fraction as in the above line. This means that dust emission becomes a little less sensitive to clay content (soil texture). 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to convert surface clay fraction from percentage to fraction. dmleung added this detailed comment on 19 Feb 2024.
+       ! dmleung++ added 24 May 2024: The below calculates the threshold gravimetric water content for the dust emission calculation in DUSTMod.F90. The equation comes from Eq. 14 of Fecan et al. (1999; https://doi.org/10.1007/s00585-999-0149-7).
+       !gwc_thr_col = 0.17*clay3d + 0.0014*(clay3d**2), and we only concern the topmost soil layer. 
+       ! Charlie Zender later on added a tuning factor (a) such that the equation becomes gwc_thr_col = a*[0.17*clay3d + 0.0014*(clay3d**2)]. (Zender et al., 2003a; https://doi.org/10.1029/2002JD002775)
+       ! There are different options: E.g., a = 1 gives the first line below. E.g., Kok et al. (2014a, b) chose to use a = 1. A second choice is proposed by Charlie Zender (2003a):  a = 1/clay3d, which gives the second line below. 
+       !soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Jasper Kok et al. (2014) modified the equation of soil moisture effect for dust emissions using a tuning factor of a = 1. 0.01 is to convert the threshold gravimetric soil moisture from % to fraction. Danny M. Leung et al. (2023) followed K14 and used this equation for offline dust emission calculations using MERRA-2 met fields. Later, Leung et al. (2024) changed to a = 2 for CESM2 simulations. However, Danny Leung later (Dec 2023) decided to revert to Zender's choice and use a = 1 / (clay3d), which overall encourages more dust emissions from seriamid and more marginal dust sources. This note should probably be on the CLM tech note since dmleung has made a different decision for CESM than his own paper. dmleung added this detailed comment on 19 Feb 2024; edited 24 May 2024.
+       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with a = 1 / (%clay) being the tuning factor for soil moisture effect in Zender's dust emission scheme. Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) dust emission scheme in the CESM will use Zender's tuning of a = 1 / (%clay), which overall encourages more dust emissions from seriamid and more marginal dust sources. Another advantage of using this tuning factor instead of a = 1 is that the dust emission threshold is linearly dependent on the clay fraction instead of parabolically dependent on clay fraction as in the above line. This means that dust emission becomes a little less sensitive to clay content (soil texture). 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to convert surface clay fraction from percentage to fraction. dmleung added this detailed comment on 19 Feb 2024.
        soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
     end do
 

From 56048af762b22a98dab029a3d5b72f7499e7e058 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 13:26:42 -0600
Subject: [PATCH 0321/1248] Fill out functions and add unit testing for them,
 the failure test fails now

---
 src/biogeophys/SoilStateInitTimeConstMod.F90  | 20 ++++++-
 .../test_dust_soil_clay_functions.pf          | 55 ++++++++++++++++++-
 2 files changed, 71 insertions(+), 4 deletions(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 46759cb90b..a71a7285aa 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -17,6 +17,11 @@ module SoilStateInitTimeConstMod
   ! !PUBLIC MEMBER FUNCTIONS:
   public  :: SoilStateInitTimeConst
   public  :: readParams
+
+  ! PRIVATE FUNCTIONS MADE PUBLIC Just for unit-testing:
+  public :: ThresholdSoilMoist
+  public :: ThresholdSoilMoistKok2014
+  public :: MassFracClay
   !
   ! !PRIVATE MEMBER FUNCTIONS:
   private :: ReadNL
@@ -719,10 +724,19 @@ end subroutine SoilStateInitTimeConst
 
   real(r8) function ThresholdSoilMoist( clay )
   ! Calculate the threshold soil moisture needed for dust emission, based on clay content
-      real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%)
+      real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
       ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
-  end function ThresholdSoilMoist 
+  end function ThresholdSoilMoist
+
+  !------------------------------------------------------------------------------
+
+  real(r8) function ThresholdSoilMoistKok2014( clay )
+  ! Calculate the threshold soil moisture needed for dust emission, based on clay content
+      real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
+
+      ThresholdSoilMoistKok2014 = 0.01_r8*(0.17_r8*clay + 0.0014_r8*clay*clay)
+  end function ThresholdSoilMoistKok2014
 
   !------------------------------------------------------------------------------
 
@@ -731,7 +745,7 @@ real(r8) function MassFracClay( clay )
       real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%)
 
       MassFracClay = min(clay * 0.01_r8, 0.20_r8)
-  end function MassFracClay 
+  end function MassFracClay
 
   !------------------------------------------------------------------------------
 
diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
index d3d9fc7e7f..e612195aff 100644
--- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
@@ -15,6 +15,8 @@ module test_dust_soil_clay_functions
      procedure :: tearDown
   end type TestDustEmisSoilFunctions
 
+  real(r8), parameter :: tol = 1.e-15_r8
+
 contains
 
   subroutine setUp(this)
@@ -23,7 +25,58 @@ contains
 
   subroutine tearDown(this)
     class(TestDustEmisSoilFunctions), intent(inout) :: this
-
   end subroutine tearDown
 
+  @Test
+  subroutine TestClayOutOfRangeThreshold(this)
+    class(TestDustEmisSoilFunctions), intent(inout) :: this
+    real(r8) :: value
+    character(len=100) :: expected_msg
+
+    value = ThresholdSoilMoist( -1.e-15_r8 )
+    expected_msg = "ABORTED: Percent clay is less than zero"
+    @assertExceptionRaised(expected_msg)
+    value = ThresholdSoilMoist( 1._r8 + 1.-15_r8 )
+    expected_msg = "ABORTED: Percent clay is greater than 100"
+    @assertExceptionRaised(expected_msg)
+  end subroutine TestClayOutOfRangeThreshold
+
+  @Test
+  subroutine TestThresholdValues(this)
+    class(TestDustEmisSoilFunctions), intent(inout) :: this
+    real(r8) :: value
+
+    value = ThresholdSoilMoist( 0.0_r8 )
+    @assertEqual( value, 0.17_r8, tolerance=tol )
+    value = ThresholdSoilMoist( 100.0_r8 )
+    @assertEqual( value, 0.31_r8, tolerance=tol )
+  end subroutine TestThresholdValues
+
+  @Test
+  subroutine TestThresholdKok2014Values(this)
+    class(TestDustEmisSoilFunctions), intent(inout) :: this
+    real(r8) :: value
+
+    value = ThresholdSoilMoistKok2014( 0.0_r8 )
+    @assertEqual( value, 0.0_r8, tolerance=tol )
+    value = ThresholdSoilMoistKok2014( 100.0_r8 )
+    @assertEqual( value, 0.31_r8, tolerance=tol )
+    value = ThresholdSoilMoistKok2014( 1.0_r8 )
+    @assertEqual( value, 0.001714_r8, tolerance=tol )
+  end subroutine TestThresholdKok2014Values
+
+  @Test
+  subroutine TestClayMassFracValues(this)
+    class(TestDustEmisSoilFunctions), intent(inout) :: this
+    real(r8) :: value
+
+    value = MassFracClay( 0.0_r8 )
+    @assertEqual( value, 0.20_r8, tolerance=tol )
+    value = MassFracClay( 20.0_r8 )
+    @assertEqual( value, 0.20_r8, tolerance=tol )
+    value = MassFracClay( 100.0_r8 )
+    @assertEqual( value, 1.0_r8, tolerance=tol )
+
+  end subroutine TestClayMassFracValues
+
 end module test_dust_soil_clay_functions

From fc53412192c7fea8980b99fbc93324a10c17ba44 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 24 May 2024 13:49:32 -0600
Subject: [PATCH 0322/1248] Fix for the LILACSMOKE test to pass

---
 cime_config/SystemTests/lilacsmoke.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/SystemTests/lilacsmoke.py b/cime_config/SystemTests/lilacsmoke.py
index 66a94068da..366d5d1176 100644
--- a/cime_config/SystemTests/lilacsmoke.py
+++ b/cime_config/SystemTests/lilacsmoke.py
@@ -407,6 +407,7 @@ def run_phase(self):
         # case.get_mpirun_cmd creates a command that runs the executable given by
         # case.run_exe. So it's important that (elsewhere in this test script) we create a
         # link pointing from that to the atm_driver.exe executable.
+        self._case.load_env(reset=True)
         lid = new_lid()
         os.environ["OMP_NUM_THREADS"] = str(self._case.thread_count)
         cmd = self._case.get_mpirun_cmd(allow_unresolved_envvars=False)

From de8c0a33315693c9dc66b267bd255e703f9010c0 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 24 May 2024 13:53:13 -0600
Subject: [PATCH 0323/1248] update what new utility function returns as output

---
 cime_config/SystemTests/systemtest_utils.py | 41 ++++++++++++---------
 1 file changed, 23 insertions(+), 18 deletions(-)

diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py
index 8447934797..9470799a27 100644
--- a/cime_config/SystemTests/systemtest_utils.py
+++ b/cime_config/SystemTests/systemtest_utils.py
@@ -2,7 +2,7 @@
 Reduce code duplication by putting reused functions here.
 """
 
-import os, subprocess, re
+import os, subprocess, re, glob
 
 
 def cmds_to_setup_conda(caseroot):
@@ -84,21 +84,26 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path):
     except:
         print(f"ERROR trying to run {tool_name}.")
         raise
+"""
+Read a user_nl file and return the namelist option if found
+"""
+def find_user_nl_option(caseroot, component, namelist_option):
+    
+    # This is a copy of the CIME _get_list_of_user_nl_files
+    # which could be used if this moved into the CIME project
+    file_pattern = "user_nl_" + component + "*"
+    file_list = glob.glob(os.path.join(caseroot, file_pattern))
+    
+    # Check that there is at least one file
+    if len(file_list) == 0:
+        raise RuntimeError("No user_nl files found for component " + component)
 
-def read_user_nl_clm(self,namelist_option):
-    user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
-    with open(user_nl_clm_path) as f:
-        user_nl_clm_text = f.read()
-        reg = fr'{namelist_option}\s*=\s*([^\n]+)'
-        find_out = re.findall(reg, user_nl_clm_text)
-        # This could be more robust
-        if len(find_out) == 0:
-            return 0, False
-        elif len(find_out) > 1:
-            error_message = (
-                "ERROR: read_user_nl_clm: namelist option is set more than once"
-            )
-            # logger.error(error_message)
-            raise RuntimeError(error_message)
-        else:
-            return find_out[0], True
+    # Read through the file list and look for a match and return the whole entry
+    output = {}
+    for one_file in file_list:
+        with open(one_file, "r") as user_nl_file:
+            user_nl_text = user_nl_file.read()
+            reg = fr'{namelist_option}.*?(?=,|\n)'
+            find_out = re.findall(reg, user_nl_text)
+            output[one_file] = find_out
+    return output

From b7a0adfa71fa088718df13411e5c04aa83b8add7 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 24 May 2024 13:54:29 -0600
Subject: [PATCH 0324/1248] Rm expected fails associated w
 https://github.com/ESCOMP/CMEPS/pull/460

---
 cime_config/testdefs/ExpectedTestFails.xml | 85 ----------------------
 1 file changed, 85 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index a29e55cc9e..ef6a00993f 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -44,91 +44,6 @@
   </test>
 
   <!-- aux_clm test suite failures -->
-  <test name="ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-reduceOutput">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-reduceOutput">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-SNICARFRC">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm50Bgc.izumi_nag.clm-ciso">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-flexCN_FUN">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-luna">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-noFUN_flexCN">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-reduceOutput">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-o3lombardozzi2015">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_Ld9.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-clm60cam6LndTuningModeZDustSoilErod">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERP_D_P48x1.f10_f10_mg37.IHistClm60Bgc.izumi_nag.clm-decStart">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERS_D.f10_f10_mg37.I1850Clm60Sp.izumi_nag.clm-ExcessIceStreams">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-  <test name="ERS_D_Ld5.f10_f10_mg37.I2000Clm50Fates.izumi_nag.clm-FatesCold">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>https://github.com/ESCOMP/CMEPS/pull/460</issue>
-    </phase>
-  </test>
-
   <test name="SMS_D_Ld10.f10_f10_mg37.I2000Clm50BgcCrop.izumi_intel.clm-tracer_consistency">
     <phase name="RUN">
       <status>FAIL</status>

From 80bfb889db04d56d1b01e24c8102999ef3fe7cf7 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 13:58:25 -0600
Subject: [PATCH 0325/1248] Get the tests passing

---
 src/biogeophys/SoilStateInitTimeConstMod.F90             | 7 +++++++
 .../test_dust_soil_clay_functions.pf                     | 9 ++++-----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index a71a7285aa..3b71efe103 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -724,8 +724,15 @@ end subroutine SoilStateInitTimeConst
 
   real(r8) function ThresholdSoilMoist( clay )
   ! Calculate the threshold soil moisture needed for dust emission, based on clay content
+      use abortUtils    , only : endrun    
+      use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
+      if ( clay < 0.0_r8 .or. clay > 100.0_r8 )then
+         ThresholdSoilMoist = nan
+         call endrun( 'Clay fraction is out of bounds (0 to 100)')
+         return
+      end if
       ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
   end function ThresholdSoilMoist
 
diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
index e612195aff..f753bf1729 100644
--- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
@@ -34,10 +34,9 @@ contains
     character(len=100) :: expected_msg
 
     value = ThresholdSoilMoist( -1.e-15_r8 )
-    expected_msg = "ABORTED: Percent clay is less than zero"
+    expected_msg = "ABORTED: Clay fraction is out of bounds (0 to 100)"
     @assertExceptionRaised(expected_msg)
     value = ThresholdSoilMoist( 1._r8 + 1.-15_r8 )
-    expected_msg = "ABORTED: Percent clay is greater than 100"
     @assertExceptionRaised(expected_msg)
   end subroutine TestClayOutOfRangeThreshold
 
@@ -71,11 +70,11 @@ contains
     real(r8) :: value
 
     value = MassFracClay( 0.0_r8 )
-    @assertEqual( value, 0.20_r8, tolerance=tol )
+    @assertEqual( value, 0.0_r8, tolerance=tol )
     value = MassFracClay( 20.0_r8 )
     @assertEqual( value, 0.20_r8, tolerance=tol )
-    value = MassFracClay( 100.0_r8 )
-    @assertEqual( value, 1.0_r8, tolerance=tol )
+    value = MassFracClay( 25.0_r8 )
+    @assertEqual( value, 0.20_r8, tolerance=tol )
 
   end subroutine TestClayMassFracValues
 

From cd04c06c06e1399c262c970180f291d583eaf72b Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 24 May 2024 14:06:36 -0600
Subject: [PATCH 0326/1248] change dictionary to ordered dict

---
 cime_config/SystemTests/systemtest_utils.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py
index 9470799a27..2591ac4223 100644
--- a/cime_config/SystemTests/systemtest_utils.py
+++ b/cime_config/SystemTests/systemtest_utils.py
@@ -3,6 +3,7 @@
 """
 
 import os, subprocess, re, glob
+from collections import OrderedDict
 
 
 def cmds_to_setup_conda(caseroot):
@@ -99,7 +100,7 @@ def find_user_nl_option(caseroot, component, namelist_option):
         raise RuntimeError("No user_nl files found for component " + component)
 
     # Read through the file list and look for a match and return the whole entry
-    output = {}
+    output = OrderedDict()
     for one_file in file_list:
         with open(one_file, "r") as user_nl_file:
             user_nl_text = user_nl_file.read()

From 9fc13521793969bd15596a9194353c9dda168349 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 24 May 2024 14:28:48 -0600
Subject: [PATCH 0327/1248] Correct a testname in ExpectedTestFails.xml

---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index ef6a00993f..23e481222b 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -51,7 +51,7 @@
     </phase>
   </test>
 
-  <test name="PEM_D_Ld3.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam6LndTuningMode">
+  <test name="PEM_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam6LndTuningMode">
     <phase name="COMPARE_base_modpes">
       <status>FAIL</status>
       <issue>#2542</issue>

From bec3291f4bae382f3f89c2c178da7365bc0e4a4f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 14:31:45 -0600
Subject: [PATCH 0328/1248] Get unit tests passing again

---
 src/biogeochem/test/DustEmis_test/test_DustEmis.pf | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
index ded09f7919..ff154f3126 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf
@@ -19,6 +19,7 @@ module test_DustEmis
   use WaterType, only : water_type
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
+  use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay
 
   implicit none
 
@@ -155,8 +156,8 @@ contains
        ! considered bedrock
        col%nbedrock(c) = nlevsoi
 
-       this%soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
-       this%soilstate_inst%mss_frc_cly_vld_col(c) = 0.17_r8
+       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay )
+       this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
     end do
 
 
@@ -316,7 +317,7 @@ contains
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
                                vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
                                vlc_trb_4=vlc_trb_4)
-       @assertEqual( flx_mss_vrt_dst_tot, 2.239779135859605d-5, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 2.583480541056971d-6, tolerance=tol )
        @assertEqual( vlc_trb_1, 3.407721147709135d-003, tolerance=tol )
        @assertEqual( vlc_trb_2, 4.961153753164878d-003, tolerance=tol )
        @assertEqual( vlc_trb_3, 4.980100969983446d-003, tolerance=tol )
@@ -473,7 +474,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust0 = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 1.971366884000767d-4, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 2.273879554711299d-5, tolerance=tol )
     end do
     ! Double u10 and show result is higher
     call this%create_fv( u10=u10*2.0_r8, fv=fv)
@@ -485,7 +486,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust_higher = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 3.288208220877217d-4, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 3.792794484764924d-5, tolerance=tol )
     end do
     @assertGreaterThan( total_dust_higher, total_dust0 )
 

From 1e64bc3bfaeec854c09f24da6c9e9afac1135977 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 14:39:58 -0600
Subject: [PATCH 0329/1248] Increase tolerance a bit, as these numbers are
 small

---
 .../test_dust_soil_clay_functions.pf                            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
index f753bf1729..0e4ac8b3db 100644
--- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
@@ -15,7 +15,7 @@ module test_dust_soil_clay_functions
      procedure :: tearDown
   end type TestDustEmisSoilFunctions
 
-  real(r8), parameter :: tol = 1.e-15_r8
+  real(r8), parameter :: tol = 1.e-16_r8
 
 contains
 

From 150397c14052ebba30703e7e334078c13626a149 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 15:29:54 -0600
Subject: [PATCH 0330/1248] Start seperating Dust emis testing into the Base
 and Zender2003 versions

---
 .../test/DustEmis_test/CMakeLists.txt         |   3 +-
 .../test/DustEmis_test/test_DustEmisBase.pf   | 298 ++++++++++++++++++
 ...DustEmis.pf => test_DustEmisZender2003.pf} |   0
 3 files changed, 300 insertions(+), 1 deletion(-)
 create mode 100644 src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
 rename src/biogeochem/test/DustEmis_test/{test_DustEmis.pf => test_DustEmisZender2003.pf} (100%)

diff --git a/src/biogeochem/test/DustEmis_test/CMakeLists.txt b/src/biogeochem/test/DustEmis_test/CMakeLists.txt
index a618489386..49e3c16391 100644
--- a/src/biogeochem/test/DustEmis_test/CMakeLists.txt
+++ b/src/biogeochem/test/DustEmis_test/CMakeLists.txt
@@ -1,5 +1,6 @@
 set (pfunit_sources
-  test_DustEmis.pf)
+  test_DustEmisBase.pf
+  test_DustEmisZender2003.pf)
 
 add_pfunit_ctest(DustEmis
   TEST_SOURCES "${pfunit_sources}"
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
new file mode 100644
index 0000000000..b25ad5c44c
--- /dev/null
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
@@ -0,0 +1,298 @@
+module test_DustEmisBase
+
+  ! Tests of DustEmisBase
+
+  use funit
+  use unittestSubgridMod
+  use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
+  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
+  use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
+  use clm_varcon, only : clm_varcon_init, clm_varcon_clean
+  use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean
+  use DustEmisZender2003
+  use shr_kind_mod , only : r8 => shr_kind_r8
+  use unittestFilterBuilderMod, only : filter_from_range
+  use atm2lndType, only : atm2lnd_type, atm2lnd_params_type
+  use SoilStateType, only : soilstate_type
+  use CanopyStateType, only : canopystate_type
+  use TemperatureType, only : temperature_type
+  use WaterType, only : water_type
+  use FrictionVelocityMod, only : frictionvel_type
+  use unittestWaterTypeFactory, only : unittest_water_type_factory_type
+  use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay
+
+  implicit none
+
+  real(r8), parameter :: tol = 1.e-18_r8
+
+  @TestCase
+  type, extends(TestCase) :: TestDustEmisBase
+     type(dust_type) :: dust_emis
+     integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
+     integer :: num_nolakep              ! number of patches in non-lake filter
+     type(atm2lnd_type) :: atm2lnd_inst
+     type(soilstate_type) :: soilstate_inst
+     type(canopystate_type) :: canopystate_inst
+     type(temperature_type) :: temperature_inst
+     type(unittest_water_type_factory_type) :: water_factory
+     type(water_type) :: water_inst
+     type(frictionvel_type) :: frictionvel_inst
+   contains
+     procedure :: setUp
+     procedure :: tearDown
+     procedure :: setupEnvironment
+     procedure :: create_atm2lnd
+     procedure :: create_fv
+     procedure :: print_values
+     procedure :: validate_patch
+  end type TestDustEmisBase
+
+contains
+
+  !-----------------------------------------------------------------------
+
+  subroutine setUp(this)
+    use ColumnType, only : col
+    class(TestDustEmisBase), intent(inout) :: this
+
+    character(len=5) :: NLFilename = 'none'
+    real(r8), allocatable :: snow_depth_col(:)
+    real(r8), allocatable :: urb_em(:)
+    integer :: begl, endl, begc, endc
+    integer :: c
+    type(atm2lnd_params_type) :: atm2lnd_params
+
+    soil_layerstruct_predefined = '20SL_8.5m'
+    create_crop_landunit = .true.
+    use_crop = .false.
+    call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
+    call clm_varcon_init( is_simple_buildtemp=.true.)
+    call this%water_factory%init()
+    call this%water_factory%setup_before_subgrid( &
+        my_nlevsoi = nlevsoi, &
+        nlevgrnd_additional = nlevgrnd - nlevsoi, &
+        my_nlevsno = 3)
+    call setup_single_veg_patch( pft_type=0 )
+    begl = bounds%begl
+    endl = bounds%endl
+    begc = bounds%begc
+    endc = bounds%endc
+    allocate( urb_em(begl:endl) )
+
+    call this%dust_emis%Init( bounds, NLFilename )
+    call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
+    atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
+                                          glcmec_downscale_longwave = .false., &
+                                          lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
+    )
+    allocate (snow_depth_col(begc:endc))
+    snow_depth_col(begc:endc) = 0.0_r8
+    call SnowHydrologySetControlForTesting()
+    call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc))
+    call this%water_factory%setup_after_subgrid(snl = 3)
+    call this%soilstate_inst%Init(bounds)
+    do c = begc, endc
+       this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1)
+    end do
+    call this%setupEnvironment( )
+    call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
+    call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
+    call this%canopystate_inst%SetNMLForTesting()
+    call this%canopystate_inst%Init(bounds)
+    call this%frictionvel_inst%InitForTesting(bounds)
+    urb_em(begl:endl) = 0.99_r8
+    call this%temperature_inst%Init(bounds,           &
+                               em_roof_lun=urb_em(begl:endl), &
+                               em_wall_lun=urb_em(begl:endl), &
+                               em_improad_lun=urb_em(begl:endl), &
+                               em_perroad_lun=urb_em(begl:endl), &
+                               is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
+    deallocate (snow_depth_col )
+    deallocate( urb_em )
+  end subroutine setUp
+
+  !-----------------------------------------------------------------------
+
+  subroutine tearDown(this)
+    class(TestDustEmisBase), intent(inout) :: this
+
+    call this%dust_emis%Clean()
+    call this%water_factory%teardown(this%water_inst)
+    call SnowHydrologyClean()
+    call unittest_subgrid_teardown()
+    call this%atm2lnd_inst%Clean()
+    call clm_varcon_clean()
+    deallocate( this%filter_nolakep )
+  end subroutine tearDown
+
+  !-----------------------------------------------------------------------
+
+  subroutine setupEnvironment(this)
+    !
+    ! !DESCRIPTION:
+    ! Sets up the external environment used by Dust emissions - i.e., things accessed via
+    ! 'use' statements.
+    !
+    ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has
+    ! been completed.
+    !
+    use ColumnType, only : col
+    use GridcellType, only : grc
+    class(TestDustEmisBase), intent(in) :: this
+    !
+    integer :: c,j
+    real(r8), parameter :: clay = 10.0_r8
+
+    !-----------------------------------------------------------------------
+    col%dz(:,1:nlevgrnd) = 1.0_r8
+    do j = 1, nlevgrnd
+       do c = bounds%begc, bounds%endc
+          col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j)
+       end do
+    end do
+
+    do c = bounds%begc, bounds%endc
+       ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are
+       ! considered bedrock
+       col%nbedrock(c) = nlevsoi
+
+       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay )
+       this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
+    end do
+
+
+    ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager)
+    grc%londeg(:) = 0.0_r8
+
+    grc%area(:) = 10.0_r8
+
+  end subroutine setupEnvironment
+
+  !-----------------------------------------------------------------------
+
+  subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho )
+    ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets
+    ! forcing fields based on inputs. Excluded inputs are given a default value
+    class(TestDustEmisBase), intent(inout) :: this
+    real(r8), intent(in), optional :: forc_t(:)
+    real(r8), intent(in), optional :: forc_pbot(:)
+    real(r8), intent(in), optional :: forc_rho(:)
+
+    real(r8), parameter :: forc_t_default = 301._r8
+    real(r8), parameter :: forc_pbot_default = 100000._r8
+    real(r8), parameter :: forc_rho_default = 1.1_r8
+    ! ------------------------------------------------------------------------
+
+    if (present(forc_t)) then
+       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:)
+    else
+       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default
+    end if
+
+    if (present(forc_pbot)) then
+       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:)
+    else
+       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default
+    end if
+
+    if (present(forc_rho)) then
+       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:)
+    else
+       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default
+    end if
+
+  end subroutine create_atm2lnd
+
+  !-----------------------------------------------------------------------
+
+  subroutine create_fv(this, fv, u10, ram1)
+    ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
+    ! fields based on inputs. Excluded inputs are given a default value
+    class(TestDustEmisBase), intent(inout) :: this
+    real(r8), intent(in), optional :: fv
+    real(r8), intent(in), optional :: u10
+    real(r8), intent(in), optional :: ram1
+
+    real(r8), parameter :: fv_default = 2.0_r8
+    real(r8), parameter :: u10_default = 4._r8
+    real(r8), parameter :: ram1_default = 200._r8
+    ! ------------------------------------------------------------------------
+
+    if (present(fv)) then
+       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv
+    else
+       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default
+    end if
+
+    if (present(u10)) then
+       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10
+    else
+       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default
+    end if
+
+    if (present(ram1)) then
+       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1
+    else
+       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default
+    end if
+
+  end subroutine create_fv
+
+  subroutine print_values(this)
+    use LandunitType, only : lun
+    use PatchType, only : patch
+    class(TestDustEmisBase), intent(inout) :: this
+    real(r8) :: SaltationFactor
+    integer :: p, c, l
+
+    call this%dust_emis%GetConstVars( SaltationFactor )
+    do l = bounds%begl, bounds%endl
+       print *, 'landunit type= ', lun%itype(l)
+    end do
+    do c = bounds%begc, bounds%endc
+       print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1)
+       print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1)
+       print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c)
+       print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c)
+       print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c))
+    end do
+    do p = bounds%begp, bounds%endp
+       print *, 'patch type= ', patch%itype(p)
+       print *, 'patch weight= ', patch%wtgcell(p)
+       print *, 'patch active= ', patch%active(p)
+       print *, 'tlai = ', this%canopystate_inst%tlai_patch(p)
+       print *, 'tsai = ', this%canopystate_inst%tsai_patch(p)
+       c = patch%column(p)
+       print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) &
+                                     / this%frictionvel_inst%fv_patch(p)
+       call this%dust_emis%WritePatchToLog( p )
+    end do
+  end subroutine print_values
+
+  !-----------------------------------------------------------------------
+  subroutine validate_patch(this, p)
+    class(TestDustEmisBase), intent(inout) :: this
+    integer, intent(in) :: p
+
+    real(r8) :: flx_mss_vrt_dst(ndst)
+    real(r8) :: flx_mss_vrt_dst_tot
+    real(r8) :: vlc_trb(ndst)
+    real(r8) :: vlc_trb_1
+    real(r8) :: vlc_trb_2
+    real(r8) :: vlc_trb_3
+    real(r8) :: vlc_trb_4
+
+    call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, &
+             flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, &
+             vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
+             vlc_trb_4=vlc_trb_4 )
+    @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot )
+    @assertEqual( vlc_trb(1), vlc_trb_1)
+    @assertEqual( vlc_trb(2), vlc_trb_2)
+    @assertEqual( vlc_trb(3), vlc_trb_3)
+    @assertEqual( vlc_trb(4), vlc_trb_4)
+  end subroutine validate_patch
+
+  !-----------------------------------------------------------------------
+
+end module test_DustEmisBase
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
similarity index 100%
rename from src/biogeochem/test/DustEmis_test/test_DustEmis.pf
rename to src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf

From a189bb18d80be3ec911a26d7db81773fdfe8e9ca Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 24 May 2024 15:57:26 -0600
Subject: [PATCH 0331/1248] Get the unit tests to work again

---
 .../DustEmis_test/test_DustEmisZender2003.pf  | 38 +++++++++----------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index ff154f3126..c99f4bd97d 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -1,6 +1,6 @@
-module test_DustEmis
+module test_DustEmisZender2003
 
-  ! Tests of DustEmis
+  ! Tests of DustEmisZender2003
 
   use funit
   use unittestSubgridMod
@@ -26,7 +26,7 @@ module test_DustEmis
   real(r8), parameter :: tol = 1.e-18_r8
 
   @TestCase
-  type, extends(TestCase) :: TestDustEmis
+  type, extends(TestCase) :: TestDustEmisZender2003
      type(dust_type) :: dust_emis
      integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
      integer :: num_nolakep              ! number of patches in non-lake filter
@@ -45,7 +45,7 @@ module test_DustEmis
      procedure :: create_fv
      procedure :: print_values
      procedure :: validate_patch
-  end type TestDustEmis
+  end type TestDustEmisZender2003
 
 contains
 
@@ -53,7 +53,7 @@ contains
 
   subroutine setUp(this)
     use ColumnType, only : col
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
 
     character(len=5) :: NLFilename = 'none'
     real(r8), allocatable :: snow_depth_col(:)
@@ -114,7 +114,7 @@ contains
   !-----------------------------------------------------------------------
 
   subroutine tearDown(this)
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
 
     call this%dust_emis%Clean()
     call this%water_factory%teardown(this%water_inst)
@@ -138,7 +138,7 @@ contains
     !
     use ColumnType, only : col
     use GridcellType, only : grc
-    class(TestDustEmis), intent(in) :: this
+    class(TestDustEmisZender2003), intent(in) :: this
     !
     integer :: c,j
     real(r8), parameter :: clay = 10.0_r8
@@ -173,7 +173,7 @@ contains
   subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho )
     ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets
     ! forcing fields based on inputs. Excluded inputs are given a default value
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
     real(r8), intent(in), optional :: forc_t(:)
     real(r8), intent(in), optional :: forc_pbot(:)
     real(r8), intent(in), optional :: forc_rho(:)
@@ -208,7 +208,7 @@ contains
   subroutine create_fv(this, fv, u10, ram1)
     ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
     ! fields based on inputs. Excluded inputs are given a default value
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
     real(r8), intent(in), optional :: fv
     real(r8), intent(in), optional :: u10
     real(r8), intent(in), optional :: ram1
@@ -241,7 +241,7 @@ contains
   subroutine print_values(this)
     use LandunitType, only : lun
     use PatchType, only : patch
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
     real(r8) :: SaltationFactor
     integer :: p, c, l
 
@@ -271,7 +271,7 @@ contains
 
   !-----------------------------------------------------------------------
   subroutine validate_patch(this, p)
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
     integer, intent(in) :: p
 
     real(r8) :: flx_mss_vrt_dst(ndst)
@@ -298,7 +298,7 @@ contains
   @Test
   subroutine check_dust_emis(this)
     ! Check dust emissions for default values
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
     integer :: p
     real(r8) :: flx_mss_vrt_dst_tot
     real(r8) :: vlc_trb_1
@@ -331,7 +331,7 @@ contains
  @Test
  subroutine dust_zero_for_fixed_ratio(this)
    ! Check dust emissions are zero for a no wind
-   class(TestDustEmis), intent(inout) :: this
+   class(TestDustEmisZender2003), intent(inout) :: this
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
    real(r8) :: fv
@@ -360,7 +360,7 @@ contains
  @Test
  subroutine dust_zero_when_fsno_one(this)
    ! Check dust emissions are zero when snow fraction is identically 1
-   class(TestDustEmis), intent(inout) :: this
+   class(TestDustEmisZender2003), intent(inout) :: this
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
 
@@ -385,7 +385,7 @@ contains
    ! Check dust emissions are zero for non-veg landunits
    use landunit_varcon, only: istcrop, max_lunit
    use LandunitType, only : lun
-   class(TestDustEmis), intent(inout) :: this
+   class(TestDustEmisZender2003), intent(inout) :: this
    integer :: p, l
    real(r8) :: flx_mss_vrt_dst_tot
 
@@ -411,7 +411,7 @@ contains
   @Test
   subroutine aborts_on_bad_dust_mobility(this)
     ! Check dust abort when dust mobility is bad
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
     real(r8) :: flx_mss_vrt_dst_tot
     character(100) :: expected_msg
  
@@ -432,7 +432,7 @@ contains
  @Test
  subroutine dust_zero_when_tlai_high(this)
    ! Check dust emissions are zero when LAI is high enough
-   class(TestDustEmis), intent(inout) :: this
+   class(TestDustEmisZender2003), intent(inout) :: this
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
 
@@ -456,7 +456,7 @@ contains
   @Test
   subroutine check_dust_emis_increasing_wind(this)
     ! Check dust emissions with increasing wind
-    class(TestDustEmis), intent(inout) :: this
+    class(TestDustEmisZender2003), intent(inout) :: this
     integer :: p, c
     real(r8) :: flx_mss_vrt_dst_tot
     real(r8) :: fv = 4.0_r8
@@ -494,4 +494,4 @@ contains
 
   !-----------------------------------------------------------------------
 
-end module test_DustEmis
\ No newline at end of file
+end module test_DustEmisZender2003
\ No newline at end of file

From dab63611a6088551ff2959f1c04bcfbc4b61c2db Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 24 May 2024 16:13:59 -0600
Subject: [PATCH 0332/1248] pvt system init step update

---
 cime_config/SystemTests/pvt.py | 149 ++++++++++++++++++---------------
 1 file changed, 82 insertions(+), 67 deletions(-)

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
index c45c514f39..184c5de289 100644
--- a/cime_config/SystemTests/pvt.py
+++ b/cime_config/SystemTests/pvt.py
@@ -12,7 +12,8 @@
 """
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
-from systemtest_utils import read_user_nl_clm
+from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
+from systemtest_utils import find_user_nl_option
 import shutil, glob, os
 
 logger = logging.getLogger(__name__)
@@ -41,76 +42,90 @@ def __init__(self,case):
         if error_message is not None:
             logger.error(error_message)
             raise RuntimeError(error_message)
-    def run_phase(self):
-        # -------------------------------------------------------------------
-        # (1) Run FATES spin-up case in potential vegetation mode
-        # -------------------------------------------------------------------
-        orig_case = self._case
-        orig_casevar = self._case.get_value("CASE")
-        caseroot = self._case.get_value("CASEROOT")
-
-        # clone the main case to create spinup case
-        logger.info("PVT log:  cloning setup")
-        clone_path = "{}.potveg".format(caseroot)
-        if os.path.exists(clone_path):
-            shutil.rmtree(clone_path)
-        logger.info("PVT log:  cloning")
-        clone = self._case.create_clone(clone_path, keepexe=True)
-        logger.info("PVT log: cloning complete")
 
-        # setup the clone case
-        os.chdir(clone_path)
-        self._set_active_case(clone)
-        self._setup_all()
+        # Look to see if a harvest mode has been set in the namelist and save off for the transient run
+        # If there are more than one entries in the dict, i.e. multiple user_nl_clm's found, abort.
+        # If there are multiple enteries the user_nl_clm, use the last one as the dict is ordered
+        caseroot = self._case.get_value("CASEROOT")
+        harvest_mode_dict = find_user_nl_option(caseroot, 'clm', 'fates_harvest_mode')
+        harvest_mode = None
+        if len(harvest_mode_dict) == 1:
+            hmod = harvest_mode_dict[next(reversed(harvest_mode_dict))]
+            if len(hmod) != 0:
+                harvest_mode = hmod[-1]
+        elif (len(harvest_mode_dict)) > 1:
+            raise RuntimeError('Multiple user_nl_clm files found.  PVT assumes only a single user_nl_clm case')
 
         # Modify the spin up case to use the potential vegetation mode.
         # Checks for incompatible cases and necessary mapping files are
         # handled in the build case.
         # use_fates_lupft should be set to true in the testmod
-        # save off the harvest mode for reinstating later
-        found, hmode = self.read_user_nl_clm('fates_harvest_mode')
-        logger.info("PVT log:  modify user_nl_clm file for spin up run")
-        # TODO: remove fates_harvest_mode if found
-        self._append_to_user_nl_clm(
-            [
-                "use_fates_potentialveg = .true.",
-            ]
-        )
-
-        stop_n_pveg = 1
-        with clone:
-            # clone.set_value("CLM_ACCELERATED_SPINUP", "on")
-            clone.set_value("STOP_N", stop_n_pveg)
-
-        # Run the spin up case
-        # As per SSP test:
-        # "No history files expected, set suffix=None to avoid compare error"
-        logger.info("PVT log:  starting spin-up run")
-        dout_sr = clone.get_value("DOUT_S_ROOT")
-        self._skip_pnl = False
-        self.run_indv(suffix=None, st_archive=True)
+        # If the testmod has a fates harvest mode, make sure to append 'no_harvest'
+        # to the spin up case
 
-        # -------------------------------------------------------------------
-        # (2) Run FATES transient case using restart file from spin-up
-        # -------------------------------------------------------------------
-        os.chdir(caseroot)
-        self._set_active_case(orig_case)
-
-        # logger.info("PVT log:  modify user_nl_clm file for transient run")
-        # self._append_to_user_nl_clm(
-        #     [
-        #         "use_fates_potentialveg = .true.",
-        #     ]
-        # )
-
-
-        self._case.set_value("CLM_ACCELERATED_SPINUP", "off")
-        self._case.set_value("RUN_TYPE", "hybrid")
-        self._case.set_value("GET_REFCASE", False)
-        self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar))
-        self._case.set_value("RUN_REFDATE", "1700-01-01")
-        self._case.set_value("DOUT_S", False)
-        self._case.flush()
-
-        # do the restart run (short term archiving is off)
-        self.run_indv()
+        logger.info("PVT log:  modify user_nl_clm file for spin up run")
+        added_content = ["use_fates_potentialveg = .true."]
+        if harvest_mode is not None:
+            added_content.append("fates_harvest_mode = 'no_harvest'")
+        append_to_user_nl_files(caseroot, "clm", added_content)
+
+#    def run_phase(self):
+#        # -------------------------------------------------------------------
+#        # (1) Run FATES spin-up case in potential vegetation mode
+#        # -------------------------------------------------------------------
+#        orig_case = self._case
+#        orig_casevar = self._case.get_value("CASE")
+#        caseroot = self._case.get_value("CASEROOT")
+#
+#        # clone the main case to create spinup case
+#        logger.info("PVT log:  cloning setup")
+#        clone_path = "{}.potveg".format(caseroot)
+#        if os.path.exists(clone_path):
+#            shutil.rmtree(clone_path)
+#        logger.info("PVT log:  cloning")
+#        clone = self._case.create_clone(clone_path, keepexe=True)
+#        logger.info("PVT log: cloning complete")
+#
+#        # setup the clone case
+#        os.chdir(clone_path)
+#        self._set_active_case(clone)
+#        self._setup_all()
+#
+#
+#        stop_n_pveg = 1
+#        with clone:
+#            # clone.set_value("CLM_ACCELERATED_SPINUP", "on")
+#            clone.set_value("STOP_N", stop_n_pveg)
+#
+#        # Run the spin up case
+#        # As per SSP test:
+#        # "No history files expected, set suffix=None to avoid compare error"
+#        logger.info("PVT log:  starting spin-up run")
+#        dout_sr = clone.get_value("DOUT_S_ROOT")
+#        self._skip_pnl = False
+#        self.run_indv(suffix=None, st_archive=True)
+#
+#        # -------------------------------------------------------------------
+#        # (2) Run FATES transient case using restart file from spin-up
+#        # -------------------------------------------------------------------
+#        os.chdir(caseroot)
+#        self._set_active_case(orig_case)
+#
+#        # logger.info("PVT log:  modify user_nl_clm file for transient run")
+#        # self._append_to_user_nl_clm(
+#        #     [
+#        #         "use_fates_potentialveg = .true.",
+#        #     ]
+#        # )
+#
+#
+#        self._case.set_value("CLM_ACCELERATED_SPINUP", "off")
+#        self._case.set_value("RUN_TYPE", "hybrid")
+#        self._case.set_value("GET_REFCASE", False)
+#        self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar))
+#        self._case.set_value("RUN_REFDATE", "1700-01-01")
+#        self._case.set_value("DOUT_S", False)
+#        self._case.flush()
+#
+#        # do the restart run (short term archiving is off)
+#        self.run_indv()

From 175a3d01082437945f15660f75aca860c626d0a4 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 24 May 2024 18:14:18 -0600
Subject: [PATCH 0333/1248] pvt system test setup looks correct

---
 cime_config/SystemTests/pvt.py | 132 +++++++++++++--------------------
 1 file changed, 53 insertions(+), 79 deletions(-)

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
index 184c5de289..6b2a958eaa 100644
--- a/cime_config/SystemTests/pvt.py
+++ b/cime_config/SystemTests/pvt.py
@@ -43,89 +43,63 @@ def __init__(self,case):
             logger.error(error_message)
             raise RuntimeError(error_message)
 
-        # Look to see if a harvest mode has been set in the namelist and save off for the transient run
-        # If there are more than one entries in the dict, i.e. multiple user_nl_clm's found, abort.
-        # If there are multiple enteries the user_nl_clm, use the last one as the dict is ordered
+    def run_phase(self):
+        # -------------------------------------------------------------------
+        # (1) Run FATES spin-up case in potential vegetation mode
+        # -------------------------------------------------------------------
+        orig_case = self._case
+        orig_casevar = self._case.get_value("CASE")
         caseroot = self._case.get_value("CASEROOT")
-        harvest_mode_dict = find_user_nl_option(caseroot, 'clm', 'fates_harvest_mode')
-        harvest_mode = None
-        if len(harvest_mode_dict) == 1:
-            hmod = harvest_mode_dict[next(reversed(harvest_mode_dict))]
-            if len(hmod) != 0:
-                harvest_mode = hmod[-1]
-        elif (len(harvest_mode_dict)) > 1:
-            raise RuntimeError('Multiple user_nl_clm files found.  PVT assumes only a single user_nl_clm case')
+
+        # clone the main case to create spinup case
+        logger.info("PVT log:  cloning setup")
+        clone_path = "{}.potveg".format(caseroot)
+        if os.path.exists(clone_path):
+            shutil.rmtree(clone_path)
+        logger.info("PVT log:  cloning")
+        clone = self._case.create_clone(clone_path, keepexe=True)
+        logger.info("PVT log: cloning complete")
+
+        # setup the clone case
+        os.chdir(clone_path)
+        self._set_active_case(clone)
+
+        # set the clone case values
+        stop_n_pveg = 1
+        with clone:
+            # clone.set_value("CLM_ACCELERATED_SPINUP", "on")
+            clone.set_value("STOP_N", stop_n_pveg)
 
         # Modify the spin up case to use the potential vegetation mode.
         # Checks for incompatible cases and necessary mapping files are
         # handled in the build case.
-        # use_fates_lupft should be set to true in the testmod
-        # If the testmod has a fates harvest mode, make sure to append 'no_harvest'
-        # to the spin up case
+        # Turn off fates_harvest_mode for the spin up.
 
         logger.info("PVT log:  modify user_nl_clm file for spin up run")
-        added_content = ["use_fates_potentialveg = .true."]
-        if harvest_mode is not None:
-            added_content.append("fates_harvest_mode = 'no_harvest'")
-        append_to_user_nl_files(caseroot, "clm", added_content)
-
-#    def run_phase(self):
-#        # -------------------------------------------------------------------
-#        # (1) Run FATES spin-up case in potential vegetation mode
-#        # -------------------------------------------------------------------
-#        orig_case = self._case
-#        orig_casevar = self._case.get_value("CASE")
-#        caseroot = self._case.get_value("CASEROOT")
-#
-#        # clone the main case to create spinup case
-#        logger.info("PVT log:  cloning setup")
-#        clone_path = "{}.potveg".format(caseroot)
-#        if os.path.exists(clone_path):
-#            shutil.rmtree(clone_path)
-#        logger.info("PVT log:  cloning")
-#        clone = self._case.create_clone(clone_path, keepexe=True)
-#        logger.info("PVT log: cloning complete")
-#
-#        # setup the clone case
-#        os.chdir(clone_path)
-#        self._set_active_case(clone)
-#        self._setup_all()
-#
-#
-#        stop_n_pveg = 1
-#        with clone:
-#            # clone.set_value("CLM_ACCELERATED_SPINUP", "on")
-#            clone.set_value("STOP_N", stop_n_pveg)
-#
-#        # Run the spin up case
-#        # As per SSP test:
-#        # "No history files expected, set suffix=None to avoid compare error"
-#        logger.info("PVT log:  starting spin-up run")
-#        dout_sr = clone.get_value("DOUT_S_ROOT")
-#        self._skip_pnl = False
-#        self.run_indv(suffix=None, st_archive=True)
-#
-#        # -------------------------------------------------------------------
-#        # (2) Run FATES transient case using restart file from spin-up
-#        # -------------------------------------------------------------------
-#        os.chdir(caseroot)
-#        self._set_active_case(orig_case)
-#
-#        # logger.info("PVT log:  modify user_nl_clm file for transient run")
-#        # self._append_to_user_nl_clm(
-#        #     [
-#        #         "use_fates_potentialveg = .true.",
-#        #     ]
-#        # )
-#
-#
-#        self._case.set_value("CLM_ACCELERATED_SPINUP", "off")
-#        self._case.set_value("RUN_TYPE", "hybrid")
-#        self._case.set_value("GET_REFCASE", False)
-#        self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar))
-#        self._case.set_value("RUN_REFDATE", "1700-01-01")
-#        self._case.set_value("DOUT_S", False)
-#        self._case.flush()
-#
-#        # do the restart run (short term archiving is off)
-#        self.run_indv()
+        added_content = ["use_fates_potentialveg = .true.","fates_harvest_mode = 'no_harvest'"]
+        append_to_user_nl_files(clone_path, "clm", added_content)
+
+        # Run the spin up case
+        # As per SSP test:
+        # "No history files expected, set suffix=None to avoid compare error"
+        logger.info("PVT log:  starting spin-up run")
+        dout_sr = clone.get_value("DOUT_S_ROOT")
+        self._skip_pnl = False
+        self.run_indv(suffix=None, st_archive=True)
+
+        # -------------------------------------------------------------------
+        # (2) Run FATES transient case using restart file from spin-up
+        # -------------------------------------------------------------------
+        os.chdir(caseroot)
+        self._set_active_case(orig_case)
+
+        self._case.set_value("CLM_ACCELERATED_SPINUP", "off")
+        self._case.set_value("RUN_TYPE", "hybrid")
+        self._case.set_value("GET_REFCASE", False)
+        self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar))
+        self._case.set_value("RUN_REFDATE", "1700-01-01")
+        self._case.set_value("DOUT_S", False)
+        self._case.flush()
+
+        # do the restart run (short term archiving is off)
+        self.run_indv()

From 10728d91c8dcaeeb0719429ba11cf857fec50f68 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 24 May 2024 18:15:04 -0600
Subject: [PATCH 0334/1248] add non-Cold based testmod for spinup + transient

---
 .../testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods    | 1 +
 .../testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods
new file mode 100644
index 0000000000..1ceba4c200
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods
@@ -0,0 +1 @@
+../FatesLUPFT
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm
new file mode 100644
index 0000000000..426b41b49e
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm
@@ -0,0 +1 @@
+fates_harvest_mode = 'luhdata_area'

From a7b60fa5539991e0e75fff6c34c1b2f50f3b3e83 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 27 May 2024 17:34:56 -0600
Subject: [PATCH 0335/1248] first remove manage_externals and update docs

---
 .github/PULL_REQUEST_TEMPLATE.md              |    2 +-
 Externals.cfg                                 |   94 -
 Externals_CLM.cfg                             |    9 -
 README                                        |    6 +-
 manage_externals/.dir_locals.el               |   12 -
 manage_externals/.github/ISSUE_TEMPLATE.md    |    6 -
 .../.github/PULL_REQUEST_TEMPLATE.md          |   17 -
 .../.github/workflows/bumpversion.yml         |   19 -
 manage_externals/.github/workflows/tests.yml  |   30 -
 manage_externals/.gitignore                   |   17 -
 manage_externals/.travis.yml                  |   18 -
 manage_externals/LICENSE.txt                  |   34 -
 manage_externals/README.md                    |  231 --
 manage_externals/README_FIRST                 |   54 -
 manage_externals/checkout_externals           |   36 -
 manage_externals/manic/__init__.py            |    9 -
 manage_externals/manic/checkout.py            |  446 ----
 .../manic/externals_description.py            |  830 --------
 manage_externals/manic/externals_status.py    |  164 --
 manage_externals/manic/global_constants.py    |   18 -
 manage_externals/manic/repository.py          |   98 -
 manage_externals/manic/repository_factory.py  |   30 -
 manage_externals/manic/repository_git.py      |  859 --------
 manage_externals/manic/repository_svn.py      |  291 ---
 manage_externals/manic/sourcetree.py          |  425 ----
 manage_externals/manic/utils.py               |  330 ---
 manage_externals/test/.coveragerc             |    7 -
 manage_externals/test/.gitignore              |    7 -
 manage_externals/test/.pylint.rc              |  426 ----
 manage_externals/test/Makefile                |  124 --
 manage_externals/test/README.md               |   53 -
 manage_externals/test/doc/.gitignore          |    2 -
 manage_externals/test/doc/Makefile            |   20 -
 manage_externals/test/doc/conf.py             |  172 --
 manage_externals/test/doc/develop.rst         |  202 --
 manage_externals/test/doc/index.rst           |   22 -
 manage_externals/test/doc/testing.rst         |  123 --
 manage_externals/test/repos/README.md         |   33 -
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 7c9512c9c3..c4a381383b 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -16,7 +16,7 @@ Testing performed, if any:
 (List what testing you did to show your changes worked as expected)
 (This can be manual testing or running of the different test suites)
 (Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide)
-(aux_clm on cheyenne for intel/gnu and izumi for intel/gnu/nag/pgi is the standard for tags on master)
+(aux_clm on derecho for intel/gnu and izumi for intel/gnu/nag/nvhpc is the standard for tags on master)
 
 **NOTE: Be sure to check your coding style against the standard
 (https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines) and review
diff --git a/Externals.cfg b/Externals.cfg
deleted file mode 100644
index 70d103a94b..0000000000
--- a/Externals.cfg
+++ /dev/null
@@ -1,94 +0,0 @@
-[clm]
-local_path = .
-protocol = externals_only
-externals = Externals_CLM.cfg
-required = True
-
-[cism]
-local_path = components/cism
-protocol = git
-repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_100
-externals = Externals_CISM.cfg
-required = True
-
-[rtm]
-local_path = components/rtm
-protocol = git
-repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_79
-required = True
-
-[mosart]
-local_path = components/mosart
-protocol = git
-repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_49
-required = True
-
-[mizuRoute]
-tag = cesm-coupling.n02_v2.1.2
-protocol = git
-local_path = components/mizuroute
-repo_url = https://github.com/ESCOMP/mizuRoute
-required = True
-
-[ccs_config]
-tag = ccs_config_cesm0.0.106
-protocol = git
-repo_url = https://github.com/ESMCI/ccs_config_cesm.git
-local_path = ccs_config
-required = True
-
-[cime]
-local_path = cime
-protocol = git
-repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.238_httpsbranch01
-required = True
-
-[cmeps]
-tag = cmeps0.14.63
-protocol = git
-repo_url = https://github.com/ESCOMP/CMEPS.git
-local_path = components/cmeps
-required = True
-
-[cdeps]
-tag = cdeps1.0.33
-protocol = git
-repo_url = https://github.com/ESCOMP/CDEPS.git
-local_path = components/cdeps
-externals =  Externals_CDEPS.cfg
-required = True
-
-[share]
-tag = share1.0.18
-protocol = git
-repo_url = https://github.com/ESCOMP/CESM_share
-local_path = share
-required = True
-
-[mct]
-tag = MCT_2.11.0
-protocol = git
-repo_url = https://github.com/MCSclimate/MCT
-local_path = libraries/mct
-required = True
-
-[parallelio]
-tag = pio2_6_2
-protocol = git
-repo_url = https://github.com/NCAR/ParallelIO
-local_path = libraries/parallelio
-required = True
-
-[doc-builder]
-local_path = doc/doc-builder
-protocol = git
-repo_url = https://github.com/ESMCI/doc-builder
-tag = v1.0.8
-required = False
-
-[externals_description]
-schema_version = 1.0.0
diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
deleted file mode 100644
index 866b9ac5b2..0000000000
--- a/Externals_CLM.cfg
+++ /dev/null
@@ -1,9 +0,0 @@
-[fates]
-local_path = src/fates
-protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.73.0_api.35.0.0
-required = True
-
-[externals_description]
-schema_version = 1.0.0
diff --git a/README b/README
index af45a14909..0f1a38edf3 100644
--- a/README
+++ b/README
@@ -49,7 +49,7 @@ src --------------- CTSM Source code.
 lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
-manage_externals -- Script to manage the external source directories (deprecated)
+bin/git-fleximod -- Script to manage the external source directories
 py_env_create ----- Script to setup the python environment for CTSM python tools using conda
 python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts
 
@@ -73,7 +73,6 @@ Top level documentation ($CTSMROOT):
 README ------------------- This file
 README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git
 README.rst --------------- File that displays under the project in github
-README_EXTERNALS.rst ----- Information on how to work with manage_externals for CTSM (deprecated)
 CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project
 Copyright ---------------- CESM Copyright file
 doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the
@@ -97,9 +96,6 @@ bld/namelist_files/namelist_defaults_ctsm.xml ----- Default values
 Important files in main directories (under $CTSMROOT):
 =============================================================================================
 
-Externals.cfg --------------- File for management of the main high level external (deprecated)
-Externals_CLM.cfg ----------- File for management of the CTSM specific externals (i.e. FATES)
-
 run_sys_tests --------------- Python script to send the standard CTSM testing off (submits
                               the create_test test suite for several different compilers on the
                               machines we do standard CTSM testing on).
diff --git a/manage_externals/.dir_locals.el b/manage_externals/.dir_locals.el
deleted file mode 100644
index a370490e92..0000000000
--- a/manage_externals/.dir_locals.el
+++ /dev/null
@@ -1,12 +0,0 @@
-; -*- mode: Lisp -*-
-
-((python-mode
-  . (
-     ;; fill the paragraph to 80 columns when using M-q
-     (fill-column . 80)
-
-     ;; Use 4 spaces to indent in Python
-     (python-indent-offset . 4)
-     (indent-tabs-mode . nil)
-     )))
-
diff --git a/manage_externals/.github/ISSUE_TEMPLATE.md b/manage_externals/.github/ISSUE_TEMPLATE.md
deleted file mode 100644
index 8ecb2ae64b..0000000000
--- a/manage_externals/.github/ISSUE_TEMPLATE.md
+++ /dev/null
@@ -1,6 +0,0 @@
-### Summary of Issue:
-### Expected behavior and actual behavior:
-### Steps to reproduce the problem (should include model description file(s) or link to publi c repository):
-### What is the changeset ID of the code, and the machine you are using:
-### have you modified the code? If so, it must be committed and available for testing:
-### Screen output or log file showing the error message and context:
diff --git a/manage_externals/.github/PULL_REQUEST_TEMPLATE.md b/manage_externals/.github/PULL_REQUEST_TEMPLATE.md
deleted file mode 100644
index b68b1fb5e2..0000000000
--- a/manage_externals/.github/PULL_REQUEST_TEMPLATE.md
+++ /dev/null
@@ -1,17 +0,0 @@
-[ 50 character, one line summary ]
-
-[ Description of the changes in this commit. It should be enough
-  information for someone not following this development to understand. 
-  Lines should be wrapped at about 72 characters. ]
-
-User interface changes?: [ No/Yes ]
-[ If yes, describe what changed, and steps taken to ensure backward compatibilty ]
-
-Fixes: [Github issue #s] And brief description of each issue.
-
-Testing:
-  test removed:
-  unit tests:
-  system tests:
-  manual testing:
-
diff --git a/manage_externals/.github/workflows/bumpversion.yml b/manage_externals/.github/workflows/bumpversion.yml
deleted file mode 100644
index f4dc9b7ca5..0000000000
--- a/manage_externals/.github/workflows/bumpversion.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-name: Bump version
-on:
-  push:
-    branches:
-      - main
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Bump version and push tag
-        id: tag_version
-        uses: mathieudutour/github-tag-action@v5.5
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          create_annotated_tag: true
-          default_bump: patch
-          dry_run: false
-          tag_prefix: manic-
diff --git a/manage_externals/.github/workflows/tests.yml b/manage_externals/.github/workflows/tests.yml
deleted file mode 100644
index dd75b91b49..0000000000
--- a/manage_externals/.github/workflows/tests.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-# This is a workflow to compile the cmeps source without cime
-name: Test Manic
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  test-manic:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Test Manic
-        run: |
-          pushd test
-          git config --global user.email "devnull@example.com"
-          git config --global user.name "GITHUB tester"
-          git config --global protocol.file.allow always
-          make utest
-          make stest
-          popd
-
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
diff --git a/manage_externals/.gitignore b/manage_externals/.gitignore
deleted file mode 100644
index a71ac0cd75..0000000000
--- a/manage_externals/.gitignore
+++ /dev/null
@@ -1,17 +0,0 @@
-# directories that are checked out by the tool
-cime/
-cime_config/
-components/
-
-# generated local files
-*.log
-
-# editor files
-*~
-*.bak
-
-# generated python files
-*.pyc
-
-# test tmp file
-test/tmp
diff --git a/manage_externals/.travis.yml b/manage_externals/.travis.yml
deleted file mode 100644
index d9b24c584d..0000000000
--- a/manage_externals/.travis.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-language: python
-os: linux
-python:
-  - "3.4"
-  - "3.5"
-  - "3.6"
-  - "3.7"
-  - "3.8"
-install:
-  - pip install -r test/requirements.txt
-before_script:
-  - git --version
-script:
-  - cd test; make test
-  - cd test; make lint
-after_success:
-  - cd test; make coverage
-  - cd test; coveralls
diff --git a/manage_externals/LICENSE.txt b/manage_externals/LICENSE.txt
deleted file mode 100644
index 665ee03fbc..0000000000
--- a/manage_externals/LICENSE.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-Copyright (c) 2017-2018, University Corporation for Atmospheric Research (UCAR)
-All rights reserved.
-
-Developed by: 
-              University Corporation for Atmospheric Research - National Center for Atmospheric Research
-              https://www2.cesm.ucar.edu/working-groups/sewg
-
-Permission is hereby granted, free of charge, to any person obtaining 
-a copy of this software and associated documentation files (the "Software"), 
-to deal with the Software without restriction, including without limitation 
-the rights to use, copy, modify, merge, publish, distribute, sublicense, 
-and/or sell copies of the Software, and to permit persons to whom 
-the Software is furnished to do so, subject to the following conditions:
-
-    - Redistributions of source code must retain the above copyright notice, 
-      this list of conditions and the following disclaimers.
-    - Redistributions in binary form must reproduce the above copyright notice, 
-      this list of conditions and the following disclaimers in the documentation 
-      and/or other materials provided with the distribution.
-    - Neither the names of [Name of Development Group, UCAR], 
-      nor the names of its contributors may be used to endorse or promote 
-      products derived from this Software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-POSSIBILITY OF SUCH DAMAGE.		
diff --git a/manage_externals/README.md b/manage_externals/README.md
deleted file mode 100644
index 9475301b5d..0000000000
--- a/manage_externals/README.md
+++ /dev/null
@@ -1,231 +0,0 @@
--- AUTOMATICALLY GENERATED FILE. DO NOT EDIT --
-
-[![Build Status](https://travis-ci.org/ESMCI/manage_externals.svg?branch=master)](https://travis-ci.org/ESMCI/manage_externals)[![Coverage Status](https://coveralls.io/repos/github/ESMCI/manage_externals/badge.svg?branch=master)](https://coveralls.io/github/ESMCI/manage_externals?branch=master)
-```
-usage: checkout_externals [-h] [-e [EXTERNALS]] [-o] [-S] [-v] [--backtrace]
-                          [-d] [--no-logging]
-
-checkout_externals manages checking out groups of externals from revision
-control based on a externals description file. By default only the
-required externals are checkout out.
-
-Operations performed by manage_externals utilities are explicit and
-data driven. checkout_externals will always make the working copy *exactly*
-match what is in the externals file when modifying the working copy of
-a repository.
-
-If checkout_externals isn't doing what you expected, double check the contents
-of the externals description file.
-
-Running checkout_externals without the '--status' option will always attempt to
-synchronize the working copy to exactly match the externals description.
-
-optional arguments:
-  -h, --help            show this help message and exit
-  -e [EXTERNALS], --externals [EXTERNALS]
-                        The externals description filename. Default:
-                        Externals.cfg.
-  -o, --optional        By default only the required externals are checked
-                        out. This flag will also checkout the optional
-                        externals.
-  -S, --status          Output status of the repositories managed by
-                        checkout_externals. By default only summary
-                        information is provided. Use verbose output to see
-                        details.
-  -v, --verbose         Output additional information to the screen and log
-                        file. This flag can be used up to two times,
-                        increasing the verbosity level each time.
-  --backtrace           DEVELOPER: show exception backtraces as extra
-                        debugging output
-  -d, --debug           DEVELOPER: output additional debugging information to
-                        the screen and log file.
-  --no-logging          DEVELOPER: disable logging.
-
-```
-NOTE: checkout_externals *MUST* be run from the root of the source tree it
-is managing. For example, if you cloned a repository with:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-Then the root of the source tree is /path/to/some-project-dev. If you
-obtained a sub-project via a checkout of another project:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-and you need to checkout the sub-project externals, then the root of the
-source tree is /path/to/some-project-dev. Do *NOT* run checkout_externals
-from within /path/to/some-project-dev/sub-project
-
-The root of the source tree will be referred to as `${SRC_ROOT}` below.
-
-# Supported workflows
-
-  * Checkout all required components from the default externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals
-
-  * To update all required components to the current values in the
-    externals description file, re-run checkout_externals:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals
-
-    If there are *any* modifications to *any* working copy according
-    to the git or svn 'status' command, checkout_externals
-    will not update any external repositories. Modifications
-    include: modified files, added files, removed files, or missing
-    files.
-
-    To avoid this safety check, edit the externals description file
-    and comment out the modified external block.
-
-  * Checkout all required components from a user specified externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals --externals my-externals.cfg
-
-  * Status summary of the repositories managed by checkout_externals:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals --status
-
-              ./cime
-          s   ./components/cism
-              ./components/mosart
-          e-o ./components/rtm
-           M  ./src/fates
-          e-o ./tools/PTCLM
-
-    where:
-      * column one indicates the status of the repository in relation
-        to the externals description file.
-      * column two indicates whether the working copy has modified files.
-      * column three shows how the repository is managed, optional or required
-
-    Column one will be one of these values:
-      * s : out-of-sync : repository is checked out at a different commit
-            compared with the externals description
-      * e : empty : directory does not exist - checkout_externals has not been run
-      * ? : unknown : directory exists but .git or .svn directories are missing
-
-    Column two will be one of these values:
-      * M : Modified : modified, added, deleted or missing files
-      *   : blank / space : clean
-      * - : dash : no meaningful state, for empty repositories
-
-    Column three will be one of these values:
-      * o : optional : optionally repository
-      *   : blank / space : required repository
-
-  * Detailed git or svn status of the repositories managed by checkout_externals:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/checkout_externals --status --verbose
-
-# Externals description file
-
-  The externals description contains a list of the external
-  repositories that are used and their version control locations. The
-  file format is the standard ini/cfg configuration file format. Each
-  external is defined by a section containing the component name in
-  square brackets:
-
-  * name (string) : component name, e.g. [cime], [cism], etc.
-
-  Each section has the following keyword-value pairs:
-
-  * required (boolean) : whether the component is a required checkout,
-    'true' or 'false'.
-
-  * local_path (string) : component path *relative* to where
-    checkout_externals is called.
-
-  * protoctol (string) : version control protocol that is used to
-    manage the component.  Valid values are 'git', 'svn',
-    'externals_only'.
-
-    Switching an external between different protocols is not
-    supported, e.g. from svn to git. To switch protocols, you need to
-    manually move the old working copy to a new location.
-
-    Note: 'externals_only' will only process the external's own
-    external description file without trying to manage a repository
-    for the component. This is used for retreiving externals for
-    standalone components like cam and clm. If the source root of the
-    externals_only component is the same as the main source root, then
-    the local path must be set to '.', the unix current working
-    directory, e. g. 'local_path = .'
-
-  * repo_url (string) : URL for the repository location, examples:
-    * https://svn-ccsm-models.cgd.ucar.edu/glc
-    * git@github.com:esmci/cime.git
-    * /path/to/local/repository
-    * .
-
-    NOTE: To operate on only the local clone and and ignore remote
-    repositories, set the url to '.' (the unix current path),
-    i.e. 'repo_url = .' . This can be used to checkout a local branch
-    instead of the upstream branch.
-
-    If a repo url is determined to be a local path (not a network url)
-    then user expansion, e.g. ~/, and environment variable expansion,
-    e.g. $HOME or $REPO_ROOT, will be performed.
-
-    Relative paths are difficult to get correct, especially for mixed
-    use repos. It is advised that local paths expand to absolute paths.
-    If relative paths are used, they should be relative to one level
-    above local_path. If local path is 'src/foo', the the relative url
-    should be relative to 'src'.
-
-  * tag (string) : tag to checkout
-
-  * hash (string) : the git hash to checkout. Only applies to git
-    repositories.
-
-  * branch (string) : branch to checkout from the specified
-    repository. Specifying a branch on a remote repository means that
-    checkout_externals will checkout the version of the branch in the remote,
-    not the the version in the local repository (if it exists).
-
-    Note: one and only one of tag, branch hash must be supplied.
-
-  * externals (string) : used to make manage_externals aware of
-    sub-externals required by an external. This is a relative path to
-    the external's root directory. For example, the main externals
-    description has an external checkout out at 'src/useful_library'.
-    useful_library requires additional externals to be complete.
-    Those additional externals are managed from the source root by the
-    externals description file pointed 'useful_library/sub-xternals.cfg',
-    Then the main 'externals' field in the top level repo should point to
-    'sub-externals.cfg'.
-    Note that by default, `checkout_externals` will clone an external's
-    submodules. As a special case, the entry, `externals = None`, will
-    prevent this behavior. For more control over which externals are
-    checked out, create an externals file (and see the `from_submodule`
-    configuration entry below).
-
-  * from_submodule (True / False) : used to pull the repo_url, local_path,
-    and hash properties for this external from the .gitmodules file in
-    this repository. Note that the section name (the entry in square
-    brackets) must match the name in the .gitmodules file.
-    If from_submodule is True, the protocol must be git and no repo_url,
-    local_path, hash, branch, or tag entries are allowed.
-    Default: False
-
-  * sparse (string) : used to control a sparse checkout. This optional
-    entry should point to a filename (path relative to local_path) that
-    contains instructions on which repository paths to include (or
-    exclude) from the working tree.
-    See the "SPARSE CHECKOUT" section of https://git-scm.com/docs/git-read-tree
-    Default: sparse checkout is disabled
-
-  * Lines begining with '#' or ';' are comments and will be ignored.
-
-# Obtaining this tool, reporting issues, etc.
-
-  The master repository for manage_externals is
-  https://github.com/ESMCI/manage_externals. Any issues with this tool
-  should be reported there.
diff --git a/manage_externals/README_FIRST b/manage_externals/README_FIRST
deleted file mode 100644
index c8a47d7806..0000000000
--- a/manage_externals/README_FIRST
+++ /dev/null
@@ -1,54 +0,0 @@
-CESM is comprised of a number of different components that are
-developed and managed independently. Each component may have
-additional 'external' dependancies and optional parts that are also
-developed and managed independently.
-
-The checkout_externals.py tool manages retreiving and updating the
-components and their externals so you have a complete set of source
-files for the model.
-
-checkout_externals.py relies on a model description file that
-describes what components are needed, where to find them and where to
-put them in the source tree. The default file is called "CESM.xml"
-regardless of whether you are checking out CESM or a standalone
-component.
-
-checkout_externals requires access to git and svn repositories that
-require authentication. checkout_externals may pass through
-authentication requests, but it will not cache them for you. For the
-best and most robust user experience, you should have svn and git
-working without password authentication. See:
-
-    https://help.github.com/articles/connecting-to-github-with-ssh/
-
-    ?svn ref?
-
-NOTE: checkout_externals.py *MUST* be run from the root of the source
-tree it is managing. For example, if you cloned CLM with:
-
-    $ git clone git@github.com/ncar/clm clm-dev
-
-Then the root of the source tree is /path/to/cesm-dev. If you obtained
-CLM via an svn checkout of CESM and you need to checkout the CLM
-externals, then the root of the source tree for CLM is:
-
-    /path/to/cesm-dev/components/clm
-
-The root of the source tree will be referred to as ${SRC_ROOT} below.
-
-To get started quickly, checkout all required components from the
-default model description file:
-
-    $ cd ${SRC_ROOT}
-    $ ./checkout_cesm/checkout_externals.py
-
-For additional information about using checkout model, please see:
-
-    ${SRC_ROOT}/checkout_cesm/README
-
-or run:
-
-    $ cd ${SRC_ROOT}
-    $ ./checkout_cesm/checkout_externals.py --help
-
-
diff --git a/manage_externals/checkout_externals b/manage_externals/checkout_externals
deleted file mode 100755
index 48bce24010..0000000000
--- a/manage_externals/checkout_externals
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env python3
-
-"""Main driver wrapper around the manic/checkout utility.
-
-Tool to assemble external respositories represented in an externals
-description file.
-
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import sys
-import traceback
-
-import manic
-
-if sys.hexversion < 0x02070000:
-    print(70 * '*')
-    print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0]))
-    print('It appears that you are running python {0}'.format(
-        '.'.join(str(x) for x in sys.version_info[0:3])))
-    print(70 * '*')
-    sys.exit(1)
-
-
-if __name__ == '__main__':
-    ARGS = manic.checkout.commandline_arguments()
-    try:
-        RET_STATUS, _ = manic.checkout.main(ARGS)
-        sys.exit(RET_STATUS)
-    except Exception as error:  # pylint: disable=broad-except
-        manic.printlog(str(error))
-        if ARGS.backtrace:
-            traceback.print_exc()
-        sys.exit(1)
diff --git a/manage_externals/manic/__init__.py b/manage_externals/manic/__init__.py
deleted file mode 100644
index 11badedd3b..0000000000
--- a/manage_externals/manic/__init__.py
+++ /dev/null
@@ -1,9 +0,0 @@
-"""Public API for the manage_externals library
-"""
-
-from manic import checkout
-from manic.utils import printlog
-
-__all__ = [
-    'checkout', 'printlog',
-]
diff --git a/manage_externals/manic/checkout.py b/manage_externals/manic/checkout.py
deleted file mode 100755
index 3f5537adce..0000000000
--- a/manage_externals/manic/checkout.py
+++ /dev/null
@@ -1,446 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-Tool to assemble repositories represented in a model-description file.
-
-If loaded as a module (e.g., in a component's buildcpp), it can be used
-to check the validity of existing subdirectories and load missing sources.
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import argparse
-import logging
-import os
-import os.path
-import sys
-
-from manic.externals_description import create_externals_description
-from manic.externals_description import read_externals_description_file
-from manic.externals_status import check_safe_to_update_repos
-from manic.sourcetree import SourceTree
-from manic.utils import printlog, fatal_error
-from manic.global_constants import VERSION_SEPERATOR, LOG_FILE_NAME
-
-if sys.hexversion < 0x02070000:
-    print(70 * '*')
-    print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0]))
-    print('It appears that you are running python {0}'.format(
-        VERSION_SEPERATOR.join(str(x) for x in sys.version_info[0:3])))
-    print(70 * '*')
-    sys.exit(1)
-
-
-# ---------------------------------------------------------------------
-#
-# User input
-#
-# ---------------------------------------------------------------------
-def commandline_arguments(args=None):
-    """Process the command line arguments
-
-    Params: args - optional args. Should only be used during systems
-    testing.
-
-    Returns: processed command line arguments
-    """
-    description = '''
-
-%(prog)s manages checking out groups of externals from revision
-control based on an externals description file. By default only the
-required externals are checkout out.
-
-Running %(prog)s without the '--status' option will always attempt to
-synchronize the working copy to exactly match the externals description.
-'''
-
-    epilog = '''
-```
-NOTE: %(prog)s *MUST* be run from the root of the source tree it
-is managing. For example, if you cloned a repository with:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-Then the root of the source tree is /path/to/some-project-dev. If you
-obtained a sub-project via a checkout of another project:
-
-    $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev
-
-and you need to checkout the sub-project externals, then the root of the
-source tree remains /path/to/some-project-dev. Do *NOT* run %(prog)s
-from within /path/to/some-project-dev/sub-project
-
-The root of the source tree will be referred to as `${SRC_ROOT}` below.
-
-
-# Supported workflows
-
-  * Checkout all required components from the default externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s
-
-  * To update all required components to the current values in the
-    externals description file, re-run %(prog)s:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s
-
-    If there are *any* modifications to *any* working copy according
-    to the git or svn 'status' command, %(prog)s
-    will not update any external repositories. Modifications
-    include: modified files, added files, removed files, or missing
-    files.
-
-    To avoid this safety check, edit the externals description file
-    and comment out the modified external block.
-
-  * Checkout all required components from a user specified externals
-    description file:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s --externals my-externals.cfg
-
-  * Status summary of the repositories managed by %(prog)s:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s --status
-
-              ./cime
-          s   ./components/cism
-              ./components/mosart
-          e-o ./components/rtm
-           M  ./src/fates
-          e-o ./tools/PTCLM
-
-
-    where:
-      * column one indicates the status of the repository in relation
-        to the externals description file.
-      * column two indicates whether the working copy has modified files.
-      * column three shows how the repository is managed, optional or required
-
-    Column one will be one of these values:
-      * s : out-of-sync : repository is checked out at a different commit
-            compared with the externals description
-      * e : empty : directory does not exist - %(prog)s has not been run
-      * ? : unknown : directory exists but .git or .svn directories are missing
-
-    Column two will be one of these values:
-      * M : Modified : modified, added, deleted or missing files
-      *   : blank / space : clean
-      * - : dash : no meaningful state, for empty repositories
-
-    Column three will be one of these values:
-      * o : optional : optionally repository
-      *   : blank / space : required repository
-
-  * Detailed git or svn status of the repositories managed by %(prog)s:
-
-        $ cd ${SRC_ROOT}
-        $ ./manage_externals/%(prog)s --status --verbose
-
-# Externals description file
-
-  The externals description contains a list of the external
-  repositories that are used and their version control locations. The
-  file format is the standard ini/cfg configuration file format. Each
-  external is defined by a section containing the component name in
-  square brackets:
-
-  * name (string) : component name, e.g. [cime], [cism], etc.
-
-  Each section has the following keyword-value pairs:
-
-  * required (boolean) : whether the component is a required checkout,
-    'true' or 'false'.
-
-  * local_path (string) : component path *relative* to where
-    %(prog)s is called.
-
-  * protoctol (string) : version control protocol that is used to
-    manage the component.  Valid values are 'git', 'svn',
-    'externals_only'.
-
-    Switching an external between different protocols is not
-    supported, e.g. from svn to git. To switch protocols, you need to
-    manually move the old working copy to a new location.
-
-    Note: 'externals_only' will only process the external's own
-    external description file without trying to manage a repository
-    for the component. This is used for retrieving externals for
-    standalone components like cam and ctsm which also serve as
-    sub-components within a larger project. If the source root of the
-    externals_only component is the same as the main source root, then
-    the local path must be set to '.', the unix current working
-    directory, e. g. 'local_path = .'
-
-  * repo_url (string) : URL for the repository location, examples:
-    * https://svn-ccsm-models.cgd.ucar.edu/glc
-    * git@github.com:esmci/cime.git
-    * /path/to/local/repository
-    * .
-
-    NOTE: To operate on only the local clone and and ignore remote
-    repositories, set the url to '.' (the unix current path),
-    i.e. 'repo_url = .' . This can be used to checkout a local branch
-    instead of the upstream branch.
-
-    If a repo url is determined to be a local path (not a network url)
-    then user expansion, e.g. ~/, and environment variable expansion,
-    e.g. $HOME or $REPO_ROOT, will be performed.
-
-    Relative paths are difficult to get correct, especially for mixed
-    use repos. It is advised that local paths expand to absolute paths.
-    If relative paths are used, they should be relative to one level
-    above local_path. If local path is 'src/foo', the the relative url
-    should be relative to 'src'.
-
-  * tag (string) : tag to checkout
-
-  * hash (string) : the git hash to checkout. Only applies to git
-    repositories.
-
-  * branch (string) : branch to checkout from the specified
-    repository. Specifying a branch on a remote repository means that
-    %(prog)s will checkout the version of the branch in the remote,
-    not the the version in the local repository (if it exists).
-
-    Note: one and only one of tag, branch hash must be supplied.
-
-  * externals (string) : used to make manage_externals aware of
-    sub-externals required by an external. This is a relative path to
-    the external's root directory. For example, if LIBX is often used
-    as a sub-external, it might have an externals file (for its
-    externals) called Externals_LIBX.cfg. To use libx as a standalone
-    checkout, it would have another file, Externals.cfg with the
-    following entry:
-
-    [ libx ]
-    local_path = .
-    protocol = externals_only
-    externals = Externals_LIBX.cfg
-    required = True
-
-    Now, %(prog)s will process Externals.cfg and also process
-    Externals_LIBX.cfg as if it was a sub-external.
-
-    Note that by default, checkout_externals will clone an external's
-    submodules. As a special case, the entry, "externals = None", will
-    prevent this behavior. For more control over which externals are
-    checked out, create an externals file (and see the from_submodule
-    configuration entry below).
-
-  * from_submodule (True / False) : used to pull the repo_url, local_path,
-    and hash properties for this external from the .gitmodules file in
-    this repository. Note that the section name (the entry in square
-    brackets) must match the name in the .gitmodules file.
-    If from_submodule is True, the protocol must be git and no repo_url,
-    local_path, hash, branch, or tag entries are allowed.
-    Default: False
-
-  * sparse (string) : used to control a sparse checkout. This optional
-    entry should point to a filename (path relative to local_path) that
-    contains instructions on which repository paths to include (or
-    exclude) from the working tree.
-    See the "SPARSE CHECKOUT" section of https://git-scm.com/docs/git-read-tree
-    Default: sparse checkout is disabled
-
-  * Lines beginning with '#' or ';' are comments and will be ignored.
-
-# Obtaining this tool, reporting issues, etc.
-
-  The master repository for manage_externals is
-  https://github.com/ESMCI/manage_externals. Any issues with this tool
-  should be reported there.
-
-# Troubleshooting
-
-Operations performed by manage_externals utilities are explicit and
-data driven. %(prog)s will always attempt to make the working copy
-*exactly* match what is in the externals file when modifying the
-working copy of a repository.
-
-If %(prog)s is not doing what you expected, double check the contents
-of the externals description file or examine the output of
-./manage_externals/%(prog)s --status
-
-'''
-
-    parser = argparse.ArgumentParser(
-        description=description, epilog=epilog,
-        formatter_class=argparse.RawDescriptionHelpFormatter)
-
-    #
-    # user options
-    #
-    parser.add_argument("components", nargs="*",
-                        help="Specific component(s) to checkout. By default, "
-                        "all required externals are checked out.")
-
-    parser.add_argument('-e', '--externals', nargs='?',
-                        default='Externals.cfg',
-                        help='The externals description filename. '
-                        'Default: %(default)s.')
-
-    parser.add_argument('-x', '--exclude', nargs='*',
-                        help='Component(s) listed in the externals file which should be ignored.')
-
-    parser.add_argument('-o', '--optional', action='store_true', default=False,
-                        help='By default only the required externals '
-                        'are checked out. This flag will also checkout the '
-                        'optional externals.')
-
-    parser.add_argument('-S', '--status', action='store_true', default=False,
-                        help='Output the status of the repositories managed by '
-                        '%(prog)s. By default only summary information '
-                        'is provided. Use the verbose option to see details.')
-
-    parser.add_argument('-v', '--verbose', action='count', default=0,
-                        help='Output additional information to '
-                        'the screen and log file. This flag can be '
-                        'used up to two times, increasing the '
-                        'verbosity level each time.')
-
-    parser.add_argument('--svn-ignore-ancestry', action='store_true', default=False,
-                        help='By default, subversion will abort if a component is '
-                        'already checked out and there is no common ancestry with '
-                        'the new URL. This flag passes the "--ignore-ancestry" flag '
-                        'to the svn switch call. (This is not recommended unless '
-                        'you are sure about what you are doing.)')
-
-    #
-    # developer options
-    #
-    parser.add_argument('--backtrace', action='store_true',
-                        help='DEVELOPER: show exception backtraces as extra '
-                        'debugging output')
-
-    parser.add_argument('-d', '--debug', action='store_true', default=False,
-                        help='DEVELOPER: output additional debugging '
-                        'information to the screen and log file.')
-
-    logging_group = parser.add_mutually_exclusive_group()
-
-    logging_group.add_argument('--logging', dest='do_logging',
-                               action='store_true',
-                               help='DEVELOPER: enable logging.')
-    logging_group.add_argument('--no-logging', dest='do_logging',
-                               action='store_false', default=False,
-                               help='DEVELOPER: disable logging '
-                               '(this is the default)')
-
-    if args:
-        options = parser.parse_args(args)
-    else:
-        options = parser.parse_args()
-    return options
-
-def _dirty_local_repo_msg(program_name, config_file):
-    return """The external repositories labeled with 'M' above are not in a clean state.
-The following are four options for how to proceed:
-(1) Go into each external that is not in a clean state and issue either a 'git status' or
-    an 'svn status' command (depending on whether the external is managed by git or
-    svn). Either revert or commit your changes so that all externals are in a clean
-    state. (To revert changes in git, follow the instructions given when you run 'git
-    status'.) (Note, though, that it is okay to have untracked files in your working
-    directory.) Then rerun {program_name}.
-(2) Alternatively, you do not have to rely on {program_name}. Instead, you can manually
-    update out-of-sync externals (labeled with 's' above) as described in the
-    configuration file {config_file}. (For example, run 'git fetch' and 'git checkout'
-    commands to checkout the appropriate tags for each external, as given in
-    {config_file}.)
-(3) You can also use {program_name} to manage most, but not all externals: You can specify
-    one or more externals to ignore using the '-x' or '--exclude' argument to
-    {program_name}. Excluding externals labeled with 'M' will allow {program_name} to
-    update the other, non-excluded externals.
-(4) As a last resort, if you are confident that there is no work that needs to be saved
-    from a given external, you can remove that external (via "rm -rf [directory]") and
-    then rerun the {program_name} tool. This option is mainly useful as a workaround for
-    issues with this tool (such as https://github.com/ESMCI/manage_externals/issues/157).
-The external repositories labeled with '?' above are not under version
-control using the expected protocol. If you are sure you want to switch
-protocols, and you don't have any work you need to save from this
-directory, then run "rm -rf [directory]" before rerunning the
-{program_name} tool.
-""".format(program_name=program_name, config_file=config_file)
-# ---------------------------------------------------------------------
-#
-# main
-#
-# ---------------------------------------------------------------------
-def main(args):
-    """
-    Function to call when module is called from the command line.
-    Parse externals file and load required repositories or all repositories if
-    the --all option is passed.
-
-    Returns a tuple (overall_status, tree_status). overall_status is 0
-    on success, non-zero on failure. tree_status is a dict mapping local path
-    to ExternalStatus -- if no checkout is happening. If checkout is happening, tree_status
-    is None.
-    """
-    if args.do_logging:
-        logging.basicConfig(filename=LOG_FILE_NAME,
-                            format='%(levelname)s : %(asctime)s : %(message)s',
-                            datefmt='%Y-%m-%d %H:%M:%S',
-                            level=logging.DEBUG)
-
-    program_name = os.path.basename(sys.argv[0])
-    logging.info('Beginning of %s', program_name)
-
-    load_all = False
-    if args.optional:
-        load_all = True
-
-    root_dir = os.path.abspath(os.getcwd())
-    model_data = read_externals_description_file(root_dir, args.externals)
-    ext_description = create_externals_description(
-        model_data, components=args.components, exclude=args.exclude)
-
-    for comp in args.components:
-        if comp not in ext_description.keys():
-            # Note we can't print out the list of found externals because
-            # they were filtered in create_externals_description above.
-            fatal_error(
-                "No component {} found in {}".format(
-                    comp, args.externals))
-
-    source_tree = SourceTree(root_dir, ext_description, svn_ignore_ancestry=args.svn_ignore_ancestry)
-    if args.components:
-        components_str = 'specified components'
-    else:
-        components_str = 'required & optional components'
-    printlog('Checking local status of ' + components_str + ': ', end='')
-    tree_status = source_tree.status(print_progress=True)
-    printlog('')
-
-    if args.status:
-        # user requested status-only
-        for comp in sorted(tree_status):
-            tree_status[comp].log_status_message(args.verbose)
-    else:
-        # checkout / update the external repositories.
-        safe_to_update = check_safe_to_update_repos(tree_status)
-        if not safe_to_update:
-            # print status
-            for comp in sorted(tree_status):
-                tree_status[comp].log_status_message(args.verbose)
-            # exit gracefully
-            printlog('-' * 70)
-            printlog(_dirty_local_repo_msg(program_name, args.externals))
-            printlog('-' * 70)
-        else:
-            if not args.components:
-                source_tree.checkout(args.verbose, load_all)
-            for comp in args.components:
-                source_tree.checkout(args.verbose, load_all, load_comp=comp)
-            printlog('')
-            # New tree status is unknown, don't return anything.
-            tree_status = None
-
-    logging.info('%s completed without exceptions.', program_name)
-    # NOTE(bja, 2017-11) tree status is used by the systems tests
-    return 0, tree_status
diff --git a/manage_externals/manic/externals_description.py b/manage_externals/manic/externals_description.py
deleted file mode 100644
index 546e7fdcb4..0000000000
--- a/manage_externals/manic/externals_description.py
+++ /dev/null
@@ -1,830 +0,0 @@
-#!/usr/bin/env python3
-
-"""Model description
-
-Model description is the representation of the various externals
-included in the model. It processes in input data structure, and
-converts it into a standard interface that is used by the rest of the
-system.
-
-To maintain backward compatibility, externals description files should
-follow semantic versioning rules, http://semver.org/
-
-
-
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import logging
-import os
-import os.path
-import re
-
-# ConfigParser in python2 was renamed to configparser in python3.
-# In python2, ConfigParser returns byte strings, str, instead of unicode.
-# We need unicode to be compatible with xml and json parser and python3.
-try:
-    # python2
-    from ConfigParser import SafeConfigParser as config_parser
-    from ConfigParser import MissingSectionHeaderError
-    from ConfigParser import NoSectionError, NoOptionError
-
-    USE_PYTHON2 = True
-
-    def config_string_cleaner(text):
-        """convert strings into unicode
-        """
-        return text.decode('utf-8')
-except ImportError:
-    # python3
-    from configparser import ConfigParser as config_parser
-    from configparser import MissingSectionHeaderError
-    from configparser import NoSectionError, NoOptionError
-
-    USE_PYTHON2 = False
-
-    def config_string_cleaner(text):
-        """Python3 already uses unicode strings, so just return the string
-        without modification.
-
-        """
-        return text
-
-from .utils import printlog, fatal_error, str_to_bool, expand_local_url
-from .utils import execute_subprocess
-from .global_constants import EMPTY_STR, PPRINTER, VERSION_SEPERATOR
-
-#
-# Globals
-#
-DESCRIPTION_SECTION = 'externals_description'
-VERSION_ITEM = 'schema_version'
-
-
-def read_externals_description_file(root_dir, file_name):
-    """Read a file containing an externals description and
-    create its internal representation.
-
-    """
-    root_dir = os.path.abspath(root_dir)
-    msg = 'In directory : {0}'.format(root_dir)
-    logging.info(msg)
-    printlog('Processing externals description file : {0} ({1})'.format(file_name,
-                                                                        root_dir))
-
-    file_path = os.path.join(root_dir, file_name)
-    if not os.path.exists(file_name):
-        if file_name.lower() == "none":
-            msg = ('INTERNAL ERROR: Attempt to read externals file '
-                   'from {0} when not configured'.format(file_path))
-        else:
-            msg = ('ERROR: Model description file, "{0}", does not '
-                   'exist at path:\n    {1}\nDid you run from the root of '
-                   'the source tree?'.format(file_name, file_path))
-
-        fatal_error(msg)
-
-    externals_description = None
-    if file_name == ExternalsDescription.GIT_SUBMODULES_FILENAME:
-        externals_description = _read_gitmodules_file(root_dir, file_name)
-    else:
-        try:
-            config = config_parser()
-            config.read(file_path)
-            externals_description = config
-        except MissingSectionHeaderError:
-            # not a cfg file
-            pass
-
-    if externals_description is None:
-        msg = 'Unknown file format!'
-        fatal_error(msg)
-
-    return externals_description
-
-class LstripReader(object):
-    "LstripReader formats .gitmodules files to be acceptable for configparser"
-    def __init__(self, filename):
-        with open(filename, 'r') as infile:
-            lines = infile.readlines()
-        self._lines = list()
-        self._num_lines = len(lines)
-        self._index = 0
-        for line in lines:
-            self._lines.append(line.lstrip())
-
-    def readlines(self):
-        """Return all the lines from this object's file"""
-        return self._lines
-
-    def readline(self, size=-1):
-        """Format and return the next line or raise StopIteration"""
-        try:
-            line = self.next()
-        except StopIteration:
-            line = ''
-
-        if (size > 0) and (len(line) < size):
-            return line[0:size]
-
-        return line
-
-    def __iter__(self):
-        """Begin an iteration"""
-        self._index = 0
-        return self
-
-    def next(self):
-        """Return the next line or raise StopIteration"""
-        if self._index >= self._num_lines:
-            raise StopIteration
-
-        self._index = self._index + 1
-        return self._lines[self._index - 1]
-
-    def __next__(self):
-        return self.next()
-
-def git_submodule_status(repo_dir):
-    """Run the git submodule status command to obtain submodule hashes.
-        """
-    # This function is here instead of GitRepository to avoid a dependency loop
-    cmd = 'git -C {repo_dir} submodule status'.format(
-        repo_dir=repo_dir).split()
-    git_output = execute_subprocess(cmd, output_to_caller=True)
-    submodules = {}
-    submods = git_output.split('\n')
-    for submod in submods:
-        if submod:
-            status = submod[0]
-            items = submod[1:].split(' ')
-            if len(items) > 2:
-                tag = items[2]
-            else:
-                tag = None
-
-            submodules[items[1]] = {'hash':items[0], 'status':status, 'tag':tag}
-
-    return submodules
-
-def parse_submodules_desc_section(section_items, file_path):
-    """Find the path and url for this submodule description"""
-    path = None
-    url = None
-    for item in section_items:
-        name = item[0].strip().lower()
-        if name == 'path':
-            path = item[1].strip()
-        elif name == 'url':
-            url = item[1].strip()
-        elif name == 'branch':
-            # We do not care about branch since we have a hash - silently ignore
-            pass
-        else:
-            msg = 'WARNING: Ignoring unknown {} property, in {}'
-            msg = msg.format(item[0], file_path) # fool pylint
-            logging.warning(msg)
-
-    return path, url
-
-def _read_gitmodules_file(root_dir, file_name):
-    # pylint: disable=deprecated-method
-    # Disabling this check because the method is only used for python2
-    # pylint: disable=too-many-locals
-    # pylint: disable=too-many-branches
-    # pylint: disable=too-many-statements
-    """Read a .gitmodules file and convert it to be compatible with an
-    externals description.
-    """
-    root_dir = os.path.abspath(root_dir)
-    msg = 'In directory : {0}'.format(root_dir)
-    logging.info(msg)
-
-    file_path = os.path.join(root_dir, file_name)
-    if not os.path.exists(file_name):
-        msg = ('ERROR: submodules description file, "{0}", does not '
-               'exist in dir:\n    {1}'.format(file_name, root_dir))
-        fatal_error(msg)
-
-    submodules_description = None
-    externals_description = None
-    try:
-        config = config_parser()
-        if USE_PYTHON2:
-            config.readfp(LstripReader(file_path), filename=file_name)
-        else:
-            config.read_file(LstripReader(file_path), source=file_name)
-
-        submodules_description = config
-    except MissingSectionHeaderError:
-        # not a cfg file
-        pass
-
-    if submodules_description is None:
-        msg = 'Unknown file format!'
-        fatal_error(msg)
-    else:
-        # Convert the submodules description to an externals description
-        externals_description = config_parser()
-        # We need to grab all the commit hashes for this repo
-        submods = git_submodule_status(root_dir)
-        for section in submodules_description.sections():
-            if section[0:9] == 'submodule':
-                sec_name = section[9:].strip(' "')
-                externals_description.add_section(sec_name)
-                section_items = submodules_description.items(section)
-                path, url = parse_submodules_desc_section(section_items,
-                                                          file_path)
-
-                if path is None:
-                    msg = 'Submodule {} missing path'.format(sec_name)
-                    fatal_error(msg)
-
-                if url is None:
-                    msg = 'Submodule {} missing url'.format(sec_name)
-                    fatal_error(msg)
-
-                externals_description.set(sec_name,
-                                          ExternalsDescription.PATH, path)
-                externals_description.set(sec_name,
-                                          ExternalsDescription.PROTOCOL, 'git')
-                externals_description.set(sec_name,
-                                          ExternalsDescription.REPO_URL, url)
-                externals_description.set(sec_name,
-                                          ExternalsDescription.REQUIRED, 'True')
-                if sec_name in submods:
-                    submod_name = sec_name
-                else:
-                    # The section name does not have to match the path
-                    submod_name = path
-
-                if submod_name in submods:
-                    git_hash = submods[submod_name]['hash']
-                    externals_description.set(sec_name,
-                                              ExternalsDescription.HASH,
-                                              git_hash)
-                else:
-                    emsg = "submodule status has no section, '{}'"
-                    emsg += "\nCheck section names in externals config file"
-                    fatal_error(emsg.format(submod_name))
-
-        # Required items
-        externals_description.add_section(DESCRIPTION_SECTION)
-        externals_description.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.0')
-
-    return externals_description
-
-def create_externals_description(
-        model_data, model_format='cfg', components=None, exclude=None, parent_repo=None):
-    """Create the a externals description object from the provided data
-        
-    components: list of component names to include, None to include all. If a
-                name isn't found, it is silently omitted from the return value.
-    exclude: list of component names to skip.
-    """
-    externals_description = None
-    if model_format == 'dict':
-        externals_description = ExternalsDescriptionDict(
-            model_data, components=components, exclude=exclude)
-    elif model_format == 'cfg':
-        major, _, _ = get_cfg_schema_version(model_data)
-        if major == 1:
-            externals_description = ExternalsDescriptionConfigV1(
-                model_data, components=components, exclude=exclude, parent_repo=parent_repo)
-        else:
-            msg = ('Externals description file has unsupported schema '
-                   'version "{0}".'.format(major))
-            fatal_error(msg)
-    else:
-        msg = 'Unknown model data format "{0}"'.format(model_format)
-        fatal_error(msg)
-    return externals_description
-
-
-def get_cfg_schema_version(model_cfg):
-    """Extract the major, minor, patch version of the config file schema
-
-    Params:
-    model_cfg - config parser object containing the externas description data
-
-    Returns:
-    major = integer major version
-    minor = integer minor version
-    patch = integer patch version
-    """
-    semver_str = ''
-    try:
-        semver_str = model_cfg.get(DESCRIPTION_SECTION, VERSION_ITEM)
-    except (NoSectionError, NoOptionError):
-        msg = ('externals description file must have the required '
-               'section: "{0}" and item "{1}"'.format(DESCRIPTION_SECTION,
-                                                      VERSION_ITEM))
-        fatal_error(msg)
-
-    # NOTE(bja, 2017-11) Assume we don't care about the
-    # build/pre-release metadata for now!
-    version_list = re.split(r'[-+]', semver_str)
-    version_str = version_list[0]
-    version = version_str.split(VERSION_SEPERATOR)
-    try:
-        major = int(version[0].strip())
-        minor = int(version[1].strip())
-        patch = int(version[2].strip())
-    except ValueError:
-        msg = ('Config file schema version must have integer digits for '
-               'major, minor and patch versions. '
-               'Received "{0}"'.format(version_str))
-        fatal_error(msg)
-    return major, minor, patch
-
-
-class ExternalsDescription(dict):
-    """Base externals description class that is independent of the user input
-    format. Different input formats can all be converted to this
-    representation to provide a consistent represtentation for the
-    rest of the objects in the system.
-
-    NOTE(bja, 2018-03): do NOT define _schema_major etc at the class
-    level in the base class. The nested/recursive nature of externals
-    means different schema versions may be present in a single run!
-
-    All inheriting classes must overwrite:
-        self._schema_major and self._input_major
-        self._schema_minor and self._input_minor
-        self._schema_patch and self._input_patch
-
-    where _schema_x is the supported schema, _input_x is the user
-    input value.
-
-    """
-    # keywords defining the interface into the externals description data; these
-    # are brought together by the schema below.
-    EXTERNALS = 'externals'  # path to externals file.
-    BRANCH = 'branch'
-    SUBMODULE = 'from_submodule'
-    HASH = 'hash'
-    NAME = 'name'
-    PATH = 'local_path'
-    PROTOCOL = 'protocol'
-    REPO = 'repo'
-    REPO_URL = 'repo_url'
-    REQUIRED = 'required'
-    TAG = 'tag'
-    SPARSE = 'sparse'
-
-    PROTOCOL_EXTERNALS_ONLY = 'externals_only'
-    PROTOCOL_GIT = 'git'
-    PROTOCOL_SVN = 'svn'
-    GIT_SUBMODULES_FILENAME = '.gitmodules'
-    KNOWN_PRROTOCOLS = [PROTOCOL_GIT, PROTOCOL_SVN, PROTOCOL_EXTERNALS_ONLY]
-
-    # v1 xml keywords
-    _V1_TREE_PATH = 'TREE_PATH'
-    _V1_ROOT = 'ROOT'
-    _V1_TAG = 'TAG'
-    _V1_BRANCH = 'BRANCH'
-    _V1_REQ_SOURCE = 'REQ_SOURCE'
-
-    # Dictionary keys are component names. The corresponding values are laid out
-    # according to this schema.
-    _source_schema = {REQUIRED: True,
-                      PATH: 'string',
-                      EXTERNALS: 'string',
-                      SUBMODULE : True,
-                      REPO: {PROTOCOL: 'string',
-                             REPO_URL: 'string',
-                             TAG: 'string',
-                             BRANCH: 'string',
-                             HASH: 'string',
-                             SPARSE: 'string',
-                            }
-                     }
-
-    def __init__(self, parent_repo=None):
-        """Convert the xml into a standardized dict that can be used to
-        construct the source objects
-
-        """
-        dict.__init__(self)
-
-        self._schema_major = None
-        self._schema_minor = None
-        self._schema_patch = None
-        self._input_major = None
-        self._input_minor = None
-        self._input_patch = None
-        self._parent_repo = parent_repo
-
-    def _verify_schema_version(self):
-        """Use semantic versioning rules to verify we can process this schema.
-
-        """
-        known = '{0}.{1}.{2}'.format(self._schema_major,
-                                     self._schema_minor,
-                                     self._schema_patch)
-        received = '{0}.{1}.{2}'.format(self._input_major,
-                                        self._input_minor,
-                                        self._input_patch)
-
-        if self._input_major != self._schema_major:
-            # should never get here, the factory should handle this correctly!
-            msg = ('DEV_ERROR: version "{0}" parser received '
-                   'version "{1}" input.'.format(known, received))
-            fatal_error(msg)
-
-        if self._input_minor > self._schema_minor:
-            msg = ('Incompatible schema version:\n'
-                   '  User supplied schema version "{0}" is too new."\n'
-                   '  Can only process version "{1}" files and '
-                   'older.'.format(received, known))
-            fatal_error(msg)
-
-        if self._input_patch > self._schema_patch:
-            # NOTE(bja, 2018-03) ignoring for now... Not clear what
-            # conditions the test is needed.
-            pass
-
-    def _check_user_input(self):
-        """Run a series of checks to attempt to validate the user input and
-        detect errors as soon as possible.
-
-        NOTE(bja, 2018-03) These checks are called *after* the file is
-        read. That means the schema check can not occur here.
-
-        Note: the order is important. check_optional will create
-        optional with null data. run check_data first to ensure
-        required data was provided correctly by the user.
-
-        """
-        self._check_data()
-        self._check_optional()
-        self._validate()
-
-    def _check_data(self):
-        # pylint: disable=too-many-branches,too-many-statements
-        """Check user supplied data is valid where possible.
-        """
-        for ext_name in self.keys():
-            if (self[ext_name][self.REPO][self.PROTOCOL]
-                    not in self.KNOWN_PRROTOCOLS):
-                msg = 'Unknown repository protocol "{0}" in "{1}".'.format(
-                    self[ext_name][self.REPO][self.PROTOCOL], ext_name)
-                fatal_error(msg)
-
-            if (self[ext_name][self.REPO][self.PROTOCOL] ==
-                    self.PROTOCOL_SVN):
-                if self.HASH in self[ext_name][self.REPO]:
-                    msg = ('In repo description for "{0}". svn repositories '
-                           'may not include the "hash" keyword.'.format(
-                               ext_name))
-                    fatal_error(msg)
-
-            if ((self[ext_name][self.REPO][self.PROTOCOL] != self.PROTOCOL_GIT)
-                    and (self.SUBMODULE in self[ext_name])):
-                msg = ('self.SUBMODULE is only supported with {0} protocol, '
-                       '"{1}" is defined as an {2} repository')
-                fatal_error(msg.format(self.PROTOCOL_GIT, ext_name,
-                                       self[ext_name][self.REPO][self.PROTOCOL]))
-
-            if (self[ext_name][self.REPO][self.PROTOCOL] !=
-                    self.PROTOCOL_EXTERNALS_ONLY):
-                ref_count = 0
-                found_refs = ''
-                if self.TAG in self[ext_name][self.REPO]:
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.TAG, self[ext_name][self.REPO][self.TAG],
-                        found_refs)
-                if self.BRANCH in self[ext_name][self.REPO]:
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.BRANCH, self[ext_name][self.REPO][self.BRANCH],
-                        found_refs)
-                if self.HASH in self[ext_name][self.REPO]:
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.HASH, self[ext_name][self.REPO][self.HASH],
-                        found_refs)
-                if (self.SUBMODULE in self[ext_name] and
-                        self[ext_name][self.SUBMODULE]):
-                    ref_count += 1
-                    found_refs = '"{0} = {1}", {2}'.format(
-                        self.SUBMODULE,
-                        self[ext_name][self.SUBMODULE], found_refs)
-
-                if ref_count > 1:
-                    msg = 'Model description is over specified! '
-                    if self.SUBMODULE in self[ext_name]:
-                        msg += ('from_submodule is not compatible with '
-                                '"tag", "branch", or "hash" ')
-                    else:
-                        msg += (' Only one of "tag", "branch", or "hash" '
-                                'may be specified ')
-
-                    msg += 'for repo description of "{0}".'.format(ext_name)
-                    msg = '{0}\nFound: {1}'.format(msg, found_refs)
-                    fatal_error(msg)
-                elif ref_count < 1:
-                    msg = ('Model description is under specified! One of '
-                           '"tag", "branch", or "hash" must be specified for '
-                           'repo description of "{0}"'.format(ext_name))
-                    fatal_error(msg)
-
-                if (self.REPO_URL not in self[ext_name][self.REPO] and
-                        (self.SUBMODULE not in self[ext_name] or
-                         not self[ext_name][self.SUBMODULE])):
-                    msg = ('Model description is under specified! Must have '
-                           '"repo_url" in repo '
-                           'description for "{0}"'.format(ext_name))
-                    fatal_error(msg)
-
-                if (self.SUBMODULE in self[ext_name] and
-                        self[ext_name][self.SUBMODULE]):
-                    if self.REPO_URL in self[ext_name][self.REPO]:
-                        msg = ('Model description is over specified! '
-                               'from_submodule keyword is not compatible '
-                               'with {0} keyword for'.format(self.REPO_URL))
-                        msg = '{0} repo description of "{1}"'.format(msg,
-                                                                     ext_name)
-                        fatal_error(msg)
-
-                    if self.PATH in self[ext_name]:
-                        msg = ('Model description is over specified! '
-                               'from_submodule keyword is not compatible with '
-                               '{0} keyword for'.format(self.PATH))
-                        msg = '{0} repo description of "{1}"'.format(msg,
-                                                                     ext_name)
-                        fatal_error(msg)
-
-                if self.REPO_URL in self[ext_name][self.REPO]:
-                    url = expand_local_url(
-                        self[ext_name][self.REPO][self.REPO_URL], ext_name)
-                    self[ext_name][self.REPO][self.REPO_URL] = url
-
-    def _check_optional(self):
-        # pylint: disable=too-many-branches
-        """Some fields like externals, repo:tag repo:branch are
-        (conditionally) optional. We don't want the user to be
-        required to enter them in every externals description file, but
-        still want to validate the input. Check conditions and add
-        default values if appropriate.
-
-        """
-        submod_desc = None      # Only load submodules info once
-        for field in self:
-            # truely optional
-            if self.EXTERNALS not in self[field]:
-                self[field][self.EXTERNALS] = EMPTY_STR
-
-            # git and svn repos must tags and branches for validation purposes.
-            if self.TAG not in self[field][self.REPO]:
-                self[field][self.REPO][self.TAG] = EMPTY_STR
-            if self.BRANCH not in self[field][self.REPO]:
-                self[field][self.REPO][self.BRANCH] = EMPTY_STR
-            if self.HASH not in self[field][self.REPO]:
-                self[field][self.REPO][self.HASH] = EMPTY_STR
-            if self.REPO_URL not in self[field][self.REPO]:
-                self[field][self.REPO][self.REPO_URL] = EMPTY_STR
-            if self.SPARSE not in self[field][self.REPO]:
-                self[field][self.REPO][self.SPARSE] = EMPTY_STR
-
-            # from_submodule has a complex relationship with other fields
-            if self.SUBMODULE in self[field]:
-                # User wants to use submodule information, is it available?
-                if self._parent_repo is None:
-                    # No parent == no submodule information
-                    PPRINTER.pprint(self[field])
-                    msg = 'No parent submodule for "{0}"'.format(field)
-                    fatal_error(msg)
-                elif self._parent_repo.protocol() != self.PROTOCOL_GIT:
-                    PPRINTER.pprint(self[field])
-                    msg = 'Parent protocol, "{0}", does not support submodules'
-                    fatal_error(msg.format(self._parent_repo.protocol()))
-                else:
-                    args = self._repo_config_from_submodule(field, submod_desc)
-                    repo_url, repo_path, ref_hash, submod_desc = args
-
-                    if repo_url is None:
-                        msg = ('Cannot checkout "{0}" as a submodule, '
-                               'repo not found in {1} file')
-                        fatal_error(msg.format(field,
-                                               self.GIT_SUBMODULES_FILENAME))
-                    # Fill in submodule fields
-                    self[field][self.REPO][self.REPO_URL] = repo_url
-                    self[field][self.REPO][self.HASH] = ref_hash
-                    self[field][self.PATH] = repo_path
-
-                if self[field][self.SUBMODULE]:
-                    # We should get everything from the parent submodule
-                    # configuration.
-                    pass
-                # No else (from _submodule = False is the default)
-            else:
-                # Add the default value (not using submodule information)
-                self[field][self.SUBMODULE] = False
-
-    def _repo_config_from_submodule(self, field, submod_desc):
-        """Find the external config information for a repository from
-        its submodule configuration information.
-        """
-        if submod_desc is None:
-            repo_path = os.getcwd() # Is this always correct?
-            submod_file = self._parent_repo.submodules_file(repo_path=repo_path)
-            if submod_file is None:
-                msg = ('Cannot checkout "{0}" from submodule information\n'
-                       '       Parent repo, "{1}" does not have submodules')
-                fatal_error(msg.format(field, self._parent_repo.name()))
-
-            printlog(
-                'Processing submodules description file : {0} ({1})'.format(
-                    submod_file, repo_path))
-            submod_model_data= _read_gitmodules_file(repo_path, submod_file)
-            submod_desc = create_externals_description(submod_model_data)
-
-        # Can we find our external?
-        repo_url = None
-        repo_path = None
-        ref_hash = None
-        for ext_field in submod_desc:
-            if field == ext_field:
-                ext = submod_desc[ext_field]
-                repo_url = ext[self.REPO][self.REPO_URL]
-                repo_path = ext[self.PATH]
-                ref_hash = ext[self.REPO][self.HASH]
-                break
-
-        return repo_url, repo_path, ref_hash, submod_desc
-
-    def _validate(self):
-        """Validate that the parsed externals description contains all necessary
-        fields.
-
-        """
-        def print_compare_difference(data_a, data_b, loc_a, loc_b):
-            """Look through the data structures and print the differences.
-
-            """
-            for item in data_a:
-                if item in data_b:
-                    if not isinstance(data_b[item], type(data_a[item])):
-                        printlog("    {item}: {loc} = {val} ({val_type})".format(
-                            item=item, loc=loc_a, val=data_a[item],
-                            val_type=type(data_a[item])))
-                        printlog("    {item}  {loc} = {val} ({val_type})".format(
-                            item=' ' * len(item), loc=loc_b, val=data_b[item],
-                            val_type=type(data_b[item])))
-                else:
-                    printlog("    {item}: {loc} = {val} ({val_type})".format(
-                        item=item, loc=loc_a, val=data_a[item],
-                        val_type=type(data_a[item])))
-                    printlog("    {item}  {loc} missing".format(
-                        item=' ' * len(item), loc=loc_b))
-
-        def validate_data_struct(schema, data):
-            """Compare a data structure against a schema and validate all required
-            fields are present.
-
-            """
-            is_valid = False
-            in_ref = True
-            valid = True
-            if isinstance(schema, dict) and isinstance(data, dict):
-                # Both are dicts, recursively verify that all fields
-                # in schema are present in the data.
-                for key in schema:
-                    in_ref = in_ref and (key in data)
-                    if in_ref:
-                        valid = valid and (
-                            validate_data_struct(schema[key], data[key]))
-
-                is_valid = in_ref and valid
-            else:
-                # non-recursive structure. verify data and schema have
-                # the same type.
-                is_valid = isinstance(data, type(schema))
-
-            if not is_valid:
-                printlog("  Unmatched schema and input:")
-                if isinstance(schema, dict):
-                    print_compare_difference(schema, data, 'schema', 'input')
-                    print_compare_difference(data, schema, 'input', 'schema')
-                else:
-                    printlog("    schema = {0} ({1})".format(
-                        schema, type(schema)))
-                    printlog("    input = {0} ({1})".format(data, type(data)))
-
-            return is_valid
-
-        for field in self:
-            valid = validate_data_struct(self._source_schema, self[field])
-            if not valid:
-                PPRINTER.pprint(self._source_schema)
-                PPRINTER.pprint(self[field])
-                msg = 'ERROR: source for "{0}" did not validate'.format(field)
-                fatal_error(msg)
-
-
-class ExternalsDescriptionDict(ExternalsDescription):
-    """Create a externals description object from a dictionary using the API
-    representations. Primarily used to simplify creating model
-    description files for unit testing.
-
-    """
-
-    def __init__(self, model_data, components=None, exclude=None):
-        """Parse a native dictionary into a externals description.
-        """
-        ExternalsDescription.__init__(self)
-        self._schema_major = 1
-        self._schema_minor = 0
-        self._schema_patch = 0
-        self._input_major = 1
-        self._input_minor = 0
-        self._input_patch = 0
-        self._verify_schema_version()
-        if components:
-            for key in list(model_data.keys()):
-                if key not in components:
-                    del model_data[key]
-
-        if exclude:
-            for key in list(model_data.keys()):
-                if key in exclude:
-                    del model_data[key]
-
-        self.update(model_data)
-        self._check_user_input()
-
-
-class ExternalsDescriptionConfigV1(ExternalsDescription):
-    """Create a externals description object from a config_parser object,
-    schema version 1.
-
-    """
-
-    def __init__(self, model_data, components=None, exclude=None, parent_repo=None):
-        """Convert the config data into a standardized dict that can be used to
-        construct the source objects
-
-        components: list of component names to include, None to include all.
-        exclude: list of component names to skip.
-        """
-        ExternalsDescription.__init__(self, parent_repo=parent_repo)
-        self._schema_major = 1
-        self._schema_minor = 1
-        self._schema_patch = 0
-        self._input_major, self._input_minor, self._input_patch = \
-            get_cfg_schema_version(model_data)
-        self._verify_schema_version()
-        self._remove_metadata(model_data)
-        self._parse_cfg(model_data, components=components, exclude=exclude)
-        self._check_user_input()
-
-    @staticmethod
-    def _remove_metadata(model_data):
-        """Remove the metadata section from the model configuration file so
-        that it is simpler to look through the file and construct the
-        externals description.
-
-        """
-        model_data.remove_section(DESCRIPTION_SECTION)
-
-    def _parse_cfg(self, cfg_data, components=None, exclude=None):
-        """Parse a config_parser object into a externals description.
-
-        components: list of component names to include, None to include all.
-        exclude: list of component names to skip.
-        """
-        def list_to_dict(input_list, convert_to_lower_case=True):
-            """Convert a list of key-value pairs into a dictionary.
-            """
-            output_dict = {}
-            for item in input_list:
-                key = config_string_cleaner(item[0].strip())
-                value = config_string_cleaner(item[1].strip())
-                if convert_to_lower_case:
-                    key = key.lower()
-                output_dict[key] = value
-            return output_dict
-
-        for section in cfg_data.sections():
-            name = config_string_cleaner(section.lower().strip())
-            if (components and name not in components) or (exclude and name in exclude):
-                continue
-            self[name] = {}
-            self[name].update(list_to_dict(cfg_data.items(section)))
-            self[name][self.REPO] = {}
-            loop_keys = self[name].copy().keys()
-            for item in loop_keys:
-                if item in self._source_schema:
-                    if isinstance(self._source_schema[item], bool):
-                        self[name][item] = str_to_bool(self[name][item])
-                elif item in self._source_schema[self.REPO]:
-                    self[name][self.REPO][item] = self[name][item]
-                    del self[name][item]
-                else:
-                    msg = ('Invalid input: "{sect}" contains unknown '
-                           'item "{item}".'.format(sect=name, item=item))
-                    fatal_error(msg)
diff --git a/manage_externals/manic/externals_status.py b/manage_externals/manic/externals_status.py
deleted file mode 100644
index 6bc29e9732..0000000000
--- a/manage_externals/manic/externals_status.py
+++ /dev/null
@@ -1,164 +0,0 @@
-"""ExternalStatus
-
-Class to store status and state information about repositories and
-create a string representation.
-
-"""
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-from .global_constants import EMPTY_STR
-from .utils import printlog, indent_string
-from .global_constants import VERBOSITY_VERBOSE, VERBOSITY_DUMP
-
-
-class ExternalStatus(object):
-    """Class to represent the status of a given source repository or tree.
-
-    Individual repositories determine their own status in the
-    Repository objects. This object is just resposible for storing the
-    information and passing it up to a higher level for reporting or
-    global decisions.
-
-    There are two states of concern:
-
-    * If the repository is in-sync with the externals description file.
-
-    * If the repostiory working copy is clean and there are no pending
-    transactions (e.g. add, remove, rename, untracked files).
-
-    """
-    # sync_state and clean_state can be one of the following:
-    DEFAULT = '-'  # not set yet (sync_state).  clean_state can be this if sync_state is EMPTY.
-    UNKNOWN = '?'
-    EMPTY = 'e'
-    MODEL_MODIFIED = 's'  # repo version != externals (sync_state only)
-    DIRTY = 'M'       # repo is dirty (clean_state only)
-    STATUS_OK = ' '   # repo is clean (clean_state) or matches externals version (sync_state)
-    STATUS_ERROR = '!'
-
-    # source_type can be one of the following:
-    OPTIONAL = 'o'
-    STANDALONE = 's'
-    MANAGED = ' '
-
-    def __init__(self):
-        self.sync_state = self.DEFAULT
-        self.clean_state = self.DEFAULT
-        self.source_type = self.DEFAULT
-        self.path = EMPTY_STR
-        self.current_version = EMPTY_STR
-        self.expected_version = EMPTY_STR
-        self.status_output = EMPTY_STR
-
-    def log_status_message(self, verbosity):
-        """Write status message to the screen and log file
-        """
-        printlog(self._default_status_message())
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog(self._verbose_status_message())
-        if verbosity >= VERBOSITY_DUMP:
-            printlog(self._dump_status_message())
-
-    def __repr__(self):
-        return self._default_status_message()
-
-    def _default_status_message(self):
-        """Return the default terse status message string
-        """
-        return '{sync}{clean}{src_type} {path}'.format(
-            sync=self.sync_state, clean=self.clean_state,
-            src_type=self.source_type, path=self.path)
-
-    def _verbose_status_message(self):
-        """Return the verbose status message string
-        """
-        clean_str = self.DEFAULT
-        if self.clean_state == self.STATUS_OK:
-            clean_str = 'clean sandbox'
-        elif self.clean_state == self.DIRTY:
-            clean_str = 'modified sandbox'
-
-        sync_str = 'on {0}'.format(self.current_version)
-        if self.sync_state != self.STATUS_OK:
-            sync_str = '{current} --> {expected}'.format(
-                current=self.current_version, expected=self.expected_version)
-        return '        {clean}, {sync}'.format(clean=clean_str, sync=sync_str)
-
-    def _dump_status_message(self):
-        """Return the dump status message string
-        """
-        return indent_string(self.status_output, 12)
-
-    def safe_to_update(self):
-        """Report if it is safe to update a repository. Safe is defined as:
-
-        * If a repository is empty, it is safe to update.
-
-        * If a repository exists and has a clean working copy state
-        with no pending transactions.
-
-        """
-        safe_to_update = False
-        repo_exists = self.exists()
-        if not repo_exists:
-            safe_to_update = True
-        else:
-            # If the repo exists, it must be in ok or modified
-            # sync_state. Any other sync_state at this point
-            # represents a logic error that should have been handled
-            # before now!
-            sync_safe = ((self.sync_state == ExternalStatus.STATUS_OK) or
-                         (self.sync_state == ExternalStatus.MODEL_MODIFIED))
-            if sync_safe:
-                # The clean_state must be STATUS_OK to update. Otherwise we
-                # are dirty or there was a missed error previously.
-                if self.clean_state == ExternalStatus.STATUS_OK:
-                    safe_to_update = True
-        return safe_to_update
-
-    def exists(self):
-        """Determine if the repo exists. This is indicated by:
-
-        * sync_state is not EMPTY
-
-            * if the sync_state is empty, then the valid states for
-              clean_state are default, empty or unknown. Anything else
-              and there was probably an internal logic error.
-
-        NOTE(bja, 2017-10) For the moment we are considering a
-        sync_state of default or unknown to require user intervention,
-        but we may want to relax this convention. This is probably a
-        result of a network error or internal logic error but more
-        testing is needed.
-
-        """
-        is_empty = (self.sync_state == ExternalStatus.EMPTY)
-        clean_valid = ((self.clean_state == ExternalStatus.DEFAULT) or
-                       (self.clean_state == ExternalStatus.EMPTY) or
-                       (self.clean_state == ExternalStatus.UNKNOWN))
-
-        if is_empty and clean_valid:
-            exists = False
-        else:
-            exists = True
-        return exists
-
-
-def check_safe_to_update_repos(tree_status):
-    """Check if *ALL* repositories are in a safe state to update. We don't
-    want to do a partial update of the repositories then die, leaving
-    the model in an inconsistent state.
-
-    Note: if there is an update to do, the repositories will by
-    definiation be out of synce with the externals description, so we
-    can't use that as criteria for updating.
-
-    """
-    safe_to_update = True
-    for comp in tree_status:
-        stat = tree_status[comp]
-        safe_to_update &= stat.safe_to_update()
-
-    return safe_to_update
diff --git a/manage_externals/manic/global_constants.py b/manage_externals/manic/global_constants.py
deleted file mode 100644
index 0e91cffc90..0000000000
--- a/manage_externals/manic/global_constants.py
+++ /dev/null
@@ -1,18 +0,0 @@
-"""Globals shared across modules
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import pprint
-
-EMPTY_STR = ''
-LOCAL_PATH_INDICATOR = '.'
-VERSION_SEPERATOR = '.'
-LOG_FILE_NAME = 'manage_externals.log'
-PPRINTER = pprint.PrettyPrinter(indent=4)
-
-VERBOSITY_DEFAULT = 0
-VERBOSITY_VERBOSE = 1
-VERBOSITY_DUMP = 2
diff --git a/manage_externals/manic/repository.py b/manage_externals/manic/repository.py
deleted file mode 100644
index ea4230fb7b..0000000000
--- a/manage_externals/manic/repository.py
+++ /dev/null
@@ -1,98 +0,0 @@
-"""Base class representation of a repository
-"""
-
-from .externals_description import ExternalsDescription
-from .utils import fatal_error
-from .global_constants import EMPTY_STR
-
-
-class Repository(object):
-    """
-    Class to represent and operate on a repository description.
-    """
-
-    def __init__(self, component_name, repo):
-        """
-        Parse repo externals description
-        """
-        self._name = component_name
-        self._protocol = repo[ExternalsDescription.PROTOCOL]
-        self._tag = repo[ExternalsDescription.TAG]
-        self._branch = repo[ExternalsDescription.BRANCH]
-        self._hash = repo[ExternalsDescription.HASH]
-        self._url = repo[ExternalsDescription.REPO_URL]
-        self._sparse = repo[ExternalsDescription.SPARSE]
-
-        if self._url is EMPTY_STR:
-            fatal_error('repo must have a URL')
-
-        if ((self._tag is EMPTY_STR) and (self._branch is EMPTY_STR) and
-                (self._hash is EMPTY_STR)):
-            fatal_error('{0} repo must have a branch, tag or hash element')
-
-        ref_count = 0
-        if self._tag is not EMPTY_STR:
-            ref_count += 1
-        if self._branch is not EMPTY_STR:
-            ref_count += 1
-        if self._hash is not EMPTY_STR:
-            ref_count += 1
-        if ref_count != 1:
-            fatal_error('repo {0} must have exactly one of '
-                        'tag, branch or hash.'.format(self._name))
-
-    def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive):  # pylint: disable=unused-argument
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly update the source.
-        If the repo destination directory does not exist, checkout the correce
-        branch or tag.
-        NB: <recursive> is include as an argument for compatibility with
-            git functionality (repository_git.py)
-        """
-        msg = ('DEV_ERROR: checkout method must be implemented in all '
-               'repository classes! {0}'.format(self.__class__.__name__))
-        fatal_error(msg)
-
-    def status(self, stat, repo_dir_path):  # pylint: disable=unused-argument
-        """Report the status of the repo
-
-        """
-        msg = ('DEV_ERROR: status method must be implemented in all '
-               'repository classes! {0}'.format(self.__class__.__name__))
-        fatal_error(msg)
-
-    def submodules_file(self, repo_path=None):
-        # pylint: disable=no-self-use,unused-argument
-        """Stub for use by non-git VC systems"""
-        return None
-
-    def url(self):
-        """Public access of repo url.
-        """
-        return self._url
-
-    def tag(self):
-        """Public access of repo tag
-        """
-        return self._tag
-
-    def branch(self):
-        """Public access of repo branch.
-        """
-        return self._branch
-
-    def hash(self):
-        """Public access of repo hash.
-        """
-        return self._hash
-
-    def name(self):
-        """Public access of repo name.
-        """
-        return self._name
-
-    def protocol(self):
-        """Public access of repo protocol.
-        """
-        return self._protocol
diff --git a/manage_externals/manic/repository_factory.py b/manage_externals/manic/repository_factory.py
deleted file mode 100644
index 18c73ffc4b..0000000000
--- a/manage_externals/manic/repository_factory.py
+++ /dev/null
@@ -1,30 +0,0 @@
-"""Factory for creating and initializing the appropriate repository class
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-from .repository_git import GitRepository
-from .repository_svn import SvnRepository
-from .externals_description import ExternalsDescription
-from .utils import fatal_error
-
-
-def create_repository(component_name, repo_info, svn_ignore_ancestry=False):
-    """Determine what type of repository we have, i.e. git or svn, and
-    create the appropriate object.
-
-    Can return None (e.g. if protocol is 'externals_only').
-    """
-    protocol = repo_info[ExternalsDescription.PROTOCOL].lower()
-    if protocol == 'git':
-        repo = GitRepository(component_name, repo_info)
-    elif protocol == 'svn':
-        repo = SvnRepository(component_name, repo_info, ignore_ancestry=svn_ignore_ancestry)
-    elif protocol == 'externals_only':
-        repo = None
-    else:
-        msg = 'Unknown repo protocol "{0}"'.format(protocol)
-        fatal_error(msg)
-    return repo
diff --git a/manage_externals/manic/repository_git.py b/manage_externals/manic/repository_git.py
deleted file mode 100644
index aab1a468a8..0000000000
--- a/manage_externals/manic/repository_git.py
+++ /dev/null
@@ -1,859 +0,0 @@
-"""Class for interacting with git repositories
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import copy
-import os
-import sys
-
-from .global_constants import EMPTY_STR, LOCAL_PATH_INDICATOR
-from .global_constants import VERBOSITY_VERBOSE
-from .repository import Repository
-from .externals_status import ExternalStatus
-from .externals_description import ExternalsDescription, git_submodule_status
-from .utils import expand_local_url, split_remote_url, is_remote_url
-from .utils import fatal_error, printlog
-from .utils import execute_subprocess
-
-
-class GitRepository(Repository):
-    """Class to represent and operate on a repository description.
-
-    For testing purpose, all system calls to git should:
-
-    * be isolated in separate functions with no application logic
-      * of the form:
-         - cmd = 'git -C {dirname} ...'.format(dirname=dirname).split()
-         - value = execute_subprocess(cmd, output_to_caller={T|F},
-                                      status_to_caller={T|F})
-         - return value
-      * be static methods (not rely on self)
-      * name as _git_subcommand_args(user_args)
-
-    This convention allows easy unit testing of the repository logic
-    by mocking the specific calls to return predefined results.
-
-    """
-
-    def __init__(self, component_name, repo):
-        """
-        repo: ExternalsDescription.
-        """
-        Repository.__init__(self, component_name, repo)
-        self._gitmodules = None
-        self._submods = None
-
-    # ----------------------------------------------------------------
-    #
-    # Public API, defined by Repository
-    #
-    # ----------------------------------------------------------------
-    def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive):
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly update the source.
-        If the repo destination directory does not exist, checkout the correct
-        branch or tag.
-        """
-        repo_dir_path = os.path.join(base_dir_path, repo_dir_name)
-        repo_dir_exists = os.path.exists(repo_dir_path)
-        if (repo_dir_exists and not os.listdir(
-                repo_dir_path)) or not repo_dir_exists:
-            self._clone_repo(base_dir_path, repo_dir_name, verbosity)
-        self._checkout_ref(repo_dir_path, verbosity, recursive)
-        gmpath = os.path.join(repo_dir_path,
-                              ExternalsDescription.GIT_SUBMODULES_FILENAME)
-        if os.path.exists(gmpath):
-            self._gitmodules = gmpath
-            self._submods = git_submodule_status(repo_dir_path)
-        else:
-            self._gitmodules = None
-            self._submods = None
-
-    def status(self, stat, repo_dir_path):
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly update the source.
-        If the repo destination directory does not exist, checkout the correct
-        branch or tag.
-        """
-        self._check_sync(stat, repo_dir_path)
-        if os.path.exists(repo_dir_path):
-            self._status_summary(stat, repo_dir_path)
-
-    def submodules_file(self, repo_path=None):
-        if repo_path is not None:
-            gmpath = os.path.join(repo_path,
-                                  ExternalsDescription.GIT_SUBMODULES_FILENAME)
-            if os.path.exists(gmpath):
-                self._gitmodules = gmpath
-                self._submods = git_submodule_status(repo_path)
-
-        return self._gitmodules
-
-    # ----------------------------------------------------------------
-    #
-    # Internal work functions
-    #
-    # ----------------------------------------------------------------
-    def _clone_repo(self, base_dir_path, repo_dir_name, verbosity):
-        """Clones repo_dir_name into base_dir_path.
-        """
-        self._git_clone(self._url, os.path.join(base_dir_path, repo_dir_name),
-                        verbosity=verbosity)
-
-    def _current_ref(self, dirname):
-        """Determine the *name* associated with HEAD at dirname.
-
-        If we're on a tag, then returns the tag name; otherwise, returns
-        the current hash. Returns an empty string if no reference can be
-        determined (e.g., if we're not actually in a git repository).
-
-        If we're on a branch, then the branch name is also included in
-        the returned string (in addition to the tag / hash).
-        """
-        ref_found = False
-
-        # If we're exactly at a tag, use that as the current ref
-        tag_found, tag_name = self._git_current_tag(dirname)
-        if tag_found:
-            current_ref = tag_name
-            ref_found = True
-
-        if not ref_found:
-            # Otherwise, use current hash as the current ref
-            hash_found, hash_name = self._git_current_hash(dirname)
-            if hash_found:
-                current_ref = hash_name
-                ref_found = True
-
-        if ref_found:
-            # If we're on a branch, include branch name in current ref
-            branch_found, branch_name = self._git_current_branch(dirname)
-            if branch_found:
-                current_ref = "{} (branch {})".format(current_ref, branch_name)
-        else:
-            # If we still can't find a ref, return empty string. This
-            # can happen if we're not actually in a git repo
-            current_ref = ''
-
-        return current_ref
-
-    def _check_sync(self, stat, repo_dir_path):
-        """Determine whether a git repository is in-sync with the model
-        description.
-
-        Because repos can have multiple remotes, the only criteria is
-        whether the branch or tag is the same.
-
-        """
-        if not os.path.exists(repo_dir_path):
-            # NOTE(bja, 2017-10) condition should have been determined
-            # by _Source() object and should never be here!
-            stat.sync_state = ExternalStatus.STATUS_ERROR
-        else:
-            git_dir = os.path.join(repo_dir_path, '.git')
-            if not os.path.exists(git_dir):
-                # NOTE(bja, 2017-10) directory exists, but no git repo
-                # info.... Can't test with subprocess git command
-                # because git will move up directory tree until it
-                # finds the parent repo git dir!
-                stat.sync_state = ExternalStatus.UNKNOWN
-            else:
-                self._check_sync_logic(stat, repo_dir_path)
-
-    def _check_sync_logic(self, stat, repo_dir_path):
-        """Compare the underlying hashes of the currently checkout ref and the
-        expected ref.
-
-        Output: sets the sync_state as well as the current and
-        expected ref in the input status object.
-
-        """
-        def compare_refs(current_ref, expected_ref):
-            """Compare the current and expected ref.
-
-            """
-            if current_ref == expected_ref:
-                status = ExternalStatus.STATUS_OK
-            else:
-                status = ExternalStatus.MODEL_MODIFIED
-            return status
-
-        # get the full hash of the current commit
-        _, current_ref = self._git_current_hash(repo_dir_path)
-
-        if self._branch:
-            if self._url == LOCAL_PATH_INDICATOR:
-                expected_ref = self._branch
-            else:
-                remote_name = self._remote_name_for_url(self._url,
-                                                        repo_dir_path)
-                if not remote_name:
-                    # git doesn't know about this remote. by definition
-                    # this is a modified state.
-                    expected_ref = "unknown_remote/{0}".format(self._branch)
-                else:
-                    expected_ref = "{0}/{1}".format(remote_name, self._branch)
-        elif self._hash:
-            expected_ref = self._hash
-        elif self._tag:
-            expected_ref = self._tag
-        else:
-            msg = 'In repo "{0}": none of branch, hash or tag are set'.format(
-                self._name)
-            fatal_error(msg)
-
-        # record the *names* of the current and expected branches
-        stat.current_version = self._current_ref(repo_dir_path)
-        stat.expected_version = copy.deepcopy(expected_ref)
-
-        if current_ref == EMPTY_STR:
-            stat.sync_state = ExternalStatus.UNKNOWN
-        else:
-            # get the underlying hash of the expected ref
-            revparse_status, expected_ref_hash = self._git_revparse_commit(
-                expected_ref, repo_dir_path)
-            if revparse_status:
-                # We failed to get the hash associated with
-                # expected_ref. Maybe we should assign this to some special
-                # status, but for now we're just calling this out-of-sync to
-                # remain consistent with how this worked before.
-                stat.sync_state = ExternalStatus.MODEL_MODIFIED
-            else:
-                # compare the underlying hashes
-                stat.sync_state = compare_refs(current_ref, expected_ref_hash)
-
-    @classmethod
-    def _remote_name_for_url(cls, remote_url, dirname):
-        """Return the remote name matching remote_url (or None)
-
-        """
-        git_output = cls._git_remote_verbose(dirname)
-        git_output = git_output.splitlines()
-        for line in git_output:
-            data = line.strip()
-            if not data:
-                continue
-            data = data.split()
-            name = data[0].strip()
-            url = data[1].strip()
-            if remote_url == url:
-                return name
-        return None
-
-    def _create_remote_name(self):
-        """The url specified in the externals description file was not known
-        to git. We need to add it, which means adding a unique and
-        safe name....
-
-        The assigned name needs to be safe for git to use, e.g. can't
-        look like a path 'foo/bar' and work with both remote and local paths.
-
-        Remote paths include but are not limited to: git, ssh, https,
-        github, gitlab, bitbucket, custom server, etc.
-
-        Local paths can be relative or absolute. They may contain
-        shell variables, e.g. ${REPO_ROOT}/repo_name, or username
-        expansion, i.e. ~/ or ~someuser/.
-
-        Relative paths must be at least one layer of redirection, i.e.
-        container/../ext_repo, but may be many layers deep, e.g.
-        container/../../../../../ext_repo
-
-        NOTE(bja, 2017-11)
-
-            The base name below may not be unique, for example if the
-            user has local paths like:
-
-            /path/to/my/repos/nice_repo
-            /path/to/other/repos/nice_repo
-
-            But the current implementation should cover most common
-            use cases for remotes and still provide usable names.
-
-        """
-        url = copy.deepcopy(self._url)
-        if is_remote_url(url):
-            url = split_remote_url(url)
-        else:
-            url = expand_local_url(url, self._name)
-        url = url.split('/')
-        repo_name = url[-1]
-        base_name = url[-2]
-        # repo name should nominally already be something that git can
-        # deal with. We need to remove other possibly troublesome
-        # punctuation, e.g. /, $, from the base name.
-        unsafe_characters = '!@#$%^&*()[]{}\\/,;~'
-        for unsafe in unsafe_characters:
-            base_name = base_name.replace(unsafe, '')
-        remote_name = "{0}_{1}".format(base_name, repo_name)
-        return remote_name
-
-    def _checkout_ref(self, repo_dir, verbosity, submodules):
-        """Checkout the user supplied reference
-        if <submodules> is True, recursively initialize and update
-        the repo's submodules
-        """
-        # import pdb; pdb.set_trace()
-        if self._url.strip() == LOCAL_PATH_INDICATOR:
-            self._checkout_local_ref(verbosity, submodules, repo_dir)
-        else:
-            self._checkout_external_ref(verbosity, submodules, repo_dir)
-
-        if self._sparse:
-            self._sparse_checkout(repo_dir, verbosity)
-
-
-    def _checkout_local_ref(self, verbosity, submodules, dirname):
-        """Checkout the reference considering the local repo only. Do not
-        fetch any additional remotes or specify the remote when
-        checkout out the ref.
-        if <submodules> is True, recursively initialize and update
-        the repo's submodules
-        """
-        if self._tag:
-            ref = self._tag
-        elif self._branch:
-            ref = self._branch
-        else:
-            ref = self._hash
-
-        self._check_for_valid_ref(ref, remote_name=None,
-                                  dirname=dirname)
-        self._git_checkout_ref(ref, verbosity, submodules, dirname)
-
-    def _checkout_external_ref(self, verbosity, submodules, dirname):
-        """Checkout the reference from a remote repository into dirname.
-        if <submodules> is True, recursively initialize and update
-        the repo's submodules. 
-        Note that this results in a 'detached HEAD' state if checking out
-        a branch, because we check out the remote branch rather than the
-        local. See https://github.com/ESMCI/manage_externals/issues/34 for 
-        more discussion.
-        """
-        if self._tag:
-            ref = self._tag
-        elif self._branch:
-            ref = self._branch
-        else:
-            ref = self._hash
-
-        remote_name = self._remote_name_for_url(self._url, dirname)
-        if not remote_name:
-            remote_name = self._create_remote_name()
-            self._git_remote_add(remote_name, self._url, dirname)
-        self._git_fetch(remote_name, dirname)
-
-        # NOTE(bja, 2018-03) we need to send separate ref and remote
-        # name to check_for_vaild_ref, but the combined name to
-        # checkout_ref!
-        self._check_for_valid_ref(ref, remote_name, dirname)
-
-        if self._branch:
-            # Prepend remote name to branch. This means we avoid various
-            # special cases if the local branch is not tracking the remote or
-            # cannot be trivially fast-forwarded to match; but, it also
-            # means we end up in a 'detached HEAD' state.
-            ref = '{0}/{1}'.format(remote_name, ref)
-        self._git_checkout_ref(ref, verbosity, submodules, dirname)
-
-    def _sparse_checkout(self, repo_dir, verbosity):
-        """Use git read-tree to thin the working tree."""
-        cmd = ['cp', os.path.join(repo_dir, self._sparse),
-               os.path.join(repo_dir,
-                            '.git/info/sparse-checkout')]
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-        self._git_sparse_checkout(verbosity, repo_dir)
-
-    def _check_for_valid_ref(self, ref, remote_name, dirname):
-        """Try some basic sanity checks on the user supplied reference so we
-        can provide a more useful error message than calledprocess
-        error...
-
-        remote_name can be NOne
-        """
-        is_tag = self._ref_is_tag(ref, dirname)
-        is_branch = self._ref_is_branch(ref, remote_name, dirname)
-        is_hash = self._ref_is_hash(ref, dirname)
-        is_valid = is_tag or is_branch or is_hash
-        if not is_valid:
-            msg = ('In repo "{0}": reference "{1}" does not appear to be a '
-                   'valid tag, branch or hash! Please verify the reference '
-                   'name (e.g. spelling), is available from: {2} '.format(
-                       self._name, ref, self._url))
-            fatal_error(msg)
-
-        if is_tag:
-            is_unique_tag, msg = self._is_unique_tag(ref, remote_name,
-                                                     dirname)
-            if not is_unique_tag:
-                msg = ('In repo "{0}": tag "{1}" {2}'.format(
-                    self._name, self._tag, msg))
-                fatal_error(msg)
-
-        return is_valid
-
-    def _is_unique_tag(self, ref, remote_name, dirname):
-        """Verify that a reference is a valid tag and is unique (not a branch)
-
-        Tags may be tag names, or SHA id's. It is also possible that a
-        branch and tag have the some name.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_tag = self._ref_is_tag(ref, dirname)
-        is_branch = self._ref_is_branch(ref, remote_name, dirname)
-        is_hash = self._ref_is_hash(ref, dirname)
-
-        msg = ''
-        is_unique_tag = False
-        if is_tag and not is_branch:
-            # unique tag
-            msg = 'is ok'
-            is_unique_tag = True
-        elif is_tag and is_branch:
-            msg = ('is both a branch and a tag. git may checkout the branch '
-                   'instead of the tag depending on your version of git.')
-            is_unique_tag = False
-        elif not is_tag and is_branch:
-            msg = ('is a branch, and not a tag. If you intended to checkout '
-                   'a branch, please change the externals description to be '
-                   'a branch. If you intended to checkout a tag, it does not '
-                   'exist. Please check the name.')
-            is_unique_tag = False
-        else:  # not is_tag and not is_branch:
-            if is_hash:
-                # probably a sha1 or HEAD, etc, we call it a tag
-                msg = 'is ok'
-                is_unique_tag = True
-            else:
-                # undetermined state.
-                msg = ('does not appear to be a valid tag, branch or hash! '
-                       'Please check the name and repository.')
-                is_unique_tag = False
-
-        return is_unique_tag, msg
-
-    def _ref_is_tag(self, ref, dirname):
-        """Verify that a reference is a valid tag according to git.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-        """
-        is_tag = False
-        value = self._git_showref_tag(ref, dirname)
-        if value == 0:
-            is_tag = True
-        return is_tag
-
-    def _ref_is_branch(self, ref, remote_name, dirname):
-        """Verify if a ref is any kind of branch (local, tracked remote,
-        untracked remote).
-
-        remote_name can be None.
-        """
-        local_branch = False
-        remote_branch = False
-        if remote_name:
-            remote_branch = self._ref_is_remote_branch(ref, remote_name,
-                                                       dirname)
-        local_branch = self._ref_is_local_branch(ref, dirname)
-
-        is_branch = False
-        if local_branch or remote_branch:
-            is_branch = True
-        return is_branch
-
-    def _ref_is_local_branch(self, ref, dirname):
-        """Verify that a reference is a valid branch according to git.
-
-        show-ref branch returns local branches that have been
-        previously checked out. It will not necessarily pick up
-        untracked remote branches.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_branch = False
-        value = self._git_showref_branch(ref, dirname)
-        if value == 0:
-            is_branch = True
-        return is_branch
-
-    def _ref_is_remote_branch(self, ref, remote_name, dirname):
-        """Verify that a reference is a valid branch according to git.
-
-        show-ref branch returns local branches that have been
-        previously checked out. It will not necessarily pick up
-        untracked remote branches.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_branch = False
-        value = self._git_lsremote_branch(ref, remote_name, dirname)
-        if value == 0:
-            is_branch = True
-        return is_branch
-
-    def _ref_is_commit(self, ref, dirname):
-        """Verify that a reference is a valid commit according to git.
-
-        This could be a tag, branch, sha1 id, HEAD and potentially others...
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-        """
-        is_commit = False
-        value, _ = self._git_revparse_commit(ref, dirname)
-        if value == 0:
-            is_commit = True
-        return is_commit
-
-    def _ref_is_hash(self, ref, dirname):
-        """Verify that a reference is a valid hash according to git.
-
-        Git doesn't seem to provide an exact way to determine if user
-        supplied reference is an actual hash. So we verify that the
-        ref is a valid commit and return the underlying commit
-        hash. Then check that the commit hash begins with the user
-        supplied string.
-
-        Note: values returned by git_showref_* and git_revparse are
-        shell return codes, which are zero for success, non-zero for
-        error!
-
-        """
-        is_hash = False
-        status, git_output = self._git_revparse_commit(ref, dirname)
-        if status == 0:
-            if git_output.strip().startswith(ref):
-                is_hash = True
-        return is_hash
-
-    def _status_summary(self, stat, repo_dir_path):
-        """Determine the clean/dirty status of a git repository
-
-        """
-        git_output = self._git_status_porcelain_v1z(repo_dir_path)
-        is_dirty = self._status_v1z_is_dirty(git_output)
-        if is_dirty:
-            stat.clean_state = ExternalStatus.DIRTY
-        else:
-            stat.clean_state = ExternalStatus.STATUS_OK
-
-        # Now save the verbose status output incase the user wants to
-        # see it.
-        stat.status_output = self._git_status_verbose(repo_dir_path)
-
-    @staticmethod
-    def _status_v1z_is_dirty(git_output):
-        """Parse the git status output from --porcelain=v1 -z and determine if
-        the repo status is clean or dirty. Dirty means:
-
-        * modified files
-        * missing files
-        * added files
-        * removed
-        * renamed
-        * unmerged
-
-        Whether untracked files are considered depends on how the status
-        command was run (i.e., whether it was run with the '-u' option).
-
-        NOTE: Based on the above definition, the porcelain status
-        should be an empty string to be considered 'clean'. Of course
-        this assumes we only get an empty string from an status
-        command on a clean checkout, and not some error
-        condition... Could alse use 'git diff --quiet'.
-
-        """
-        is_dirty = False
-        if git_output:
-            is_dirty = True
-        return is_dirty
-
-    # ----------------------------------------------------------------
-    #
-    # system call to git for information gathering
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _git_current_hash(dirname):
-        """Return the full hash of the currently checked-out version.
-
-        Returns a tuple, (hash_found, hash), where hash_found is a
-        logical specifying whether a hash was found for HEAD (False
-        could mean we're not in a git repository at all). (If hash_found
-        is False, then hash is ''.)
-        """
-        status, git_output = GitRepository._git_revparse_commit("HEAD",
-                                                                dirname)
-        hash_found = not status
-        if not hash_found:
-            git_output = ''
-        return hash_found, git_output
-
-    @staticmethod
-    def _git_current_remote_branch(dirname):
-        """Determines the name of the current remote branch, if any.
-
-        if dir is None, uses the cwd.
-
-        Returns a tuple, (branch_found, branch_name), where branch_found
-        is a bool specifying whether a branch name was found for
-        HEAD. (If branch_found is False, then branch_name is '').
-        branch_name is in the format '$remote/$branch', e.g. 'origin/foo'.
-        """
-        branch_found = False
-        branch_name = ''
-        
-        cmd = 'git -C {dirname} log -n 1 --pretty=%d HEAD'.format(
-            dirname=dirname).split()
-        status, git_output = execute_subprocess(cmd,
-                                                output_to_caller=True,
-                                                status_to_caller=True)
-        branch_found = 'HEAD,' in git_output
-        if branch_found:
-            # git_output is of the form " (HEAD, origin/blah)"
-            branch_name = git_output.split(',')[1].strip()[:-1]
-        return branch_found, branch_name
-    
-    @staticmethod
-    def _git_current_branch(dirname):
-        """Determines the name of the current local branch.
-
-        Returns a tuple, (branch_found, branch_name), where branch_found
-        is a bool specifying whether a branch name was found for
-        HEAD. (If branch_found is False, then branch_name is ''.)
-        Note that currently we check out the remote branch rather than
-        the local, so this command does not return the just-checked-out
-        branch. See _git_current_remote_branch.
-        """
-        cmd = 'git -C {dirname} symbolic-ref --short -q HEAD'.format(
-            dirname=dirname).split()
-        status, git_output = execute_subprocess(cmd,
-                                                output_to_caller=True,
-                                                status_to_caller=True)
-        branch_found = not status
-        if branch_found:
-            git_output = git_output.strip()
-        else:
-            git_output = ''
-        return branch_found, git_output
-
-    @staticmethod
-    def _git_current_tag(dirname):
-        """Determines the name tag corresponding to HEAD (if any).
-
-        if dirname is None, uses the cwd.
-
-        Returns a tuple, (tag_found, tag_name), where tag_found is a
-        bool specifying whether we found a tag name corresponding to
-        HEAD. (If tag_found is False, then tag_name is ''.)
-        """
-        cmd = 'git -C {dirname} describe --exact-match --tags HEAD'.format(
-            dirname=dirname).split()
-        status, git_output = execute_subprocess(cmd,
-                                                output_to_caller=True,
-                                                status_to_caller=True)
-        tag_found = not status
-        if tag_found:
-            git_output = git_output.strip()
-        else:
-            git_output = ''
-        return tag_found, git_output
-
-    @staticmethod
-    def _git_showref_tag(ref, dirname):
-        """Run git show-ref check if the user supplied ref is a tag.
-
-        could also use git rev-parse --quiet --verify tagname^{tag}
-        """
-        cmd = ('git -C {dirname} show-ref --quiet --verify refs/tags/{ref}'
-               .format(dirname=dirname, ref=ref).split())
-        status = execute_subprocess(cmd, status_to_caller=True)
-        return status
-
-    @staticmethod
-    def _git_showref_branch(ref, dirname):
-        """Run git show-ref check if the user supplied ref is a local or
-        tracked remote branch.
-
-        """
-        cmd = ('git -C {dirname} show-ref --quiet --verify refs/heads/{ref}'
-               .format(dirname=dirname, ref=ref).split())
-        status = execute_subprocess(cmd, status_to_caller=True)
-        return status
-
-    @staticmethod
-    def _git_lsremote_branch(ref, remote_name, dirname):
-        """Run git ls-remote to check if the user supplied ref is a remote
-        branch that is not being tracked
-
-        """
-        cmd = ('git -C {dirname} ls-remote --exit-code --heads '
-               '{remote_name} {ref}').format(
-                   dirname=dirname, remote_name=remote_name, ref=ref).split()
-        status, output = execute_subprocess(cmd, status_to_caller=True, output_to_caller=True)
-        if not status and not f"refs/heads/{ref}" in output:
-            # In this case the ref is contained in the branch name but is not the complete branch name
-            return -1
-        return status
-
-    @staticmethod
-    def _git_revparse_commit(ref, dirname):
-        """Run git rev-parse to detect if a reference is a SHA, HEAD or other
-        valid commit.
-
-        """
-        cmd = ('git -C {dirname} rev-parse --quiet --verify {ref}^{commit}'
-               .format(dirname=dirname, ref=ref, commit='{commit}').split())
-        status, git_output = execute_subprocess(cmd, status_to_caller=True,
-                                                output_to_caller=True)
-        git_output = git_output.strip()
-        return status, git_output
-
-    @staticmethod
-    def _git_status_porcelain_v1z(dirname):
-        """Run git status to obtain repository information.
-
-        This is run with '--untracked=no' to ignore untracked files.
-
-        The machine-portable format that is guaranteed not to change
-        between git versions or *user configuration*.
-
-        """
-        cmd = ('git -C {dirname} status --untracked-files=no --porcelain -z'
-               .format(dirname=dirname)).split()
-        git_output = execute_subprocess(cmd, output_to_caller=True)
-        return git_output
-
-    @staticmethod
-    def _git_status_verbose(dirname):
-        """Run the git status command to obtain repository information.
-        """
-        cmd = 'git -C {dirname} status'.format(dirname=dirname).split()
-        git_output = execute_subprocess(cmd, output_to_caller=True)
-        return git_output
-
-    @staticmethod
-    def _git_remote_verbose(dirname):
-        """Run the git remote command to obtain repository information.
-
-        Returned string is of the form:
-        myfork  git@github.com:johnpaulalex/manage_externals_jp.git (fetch)
-        myfork  git@github.com:johnpaulalex/manage_externals_jp.git (push)
-        """
-        cmd = 'git -C {dirname} remote --verbose'.format(
-            dirname=dirname).split()
-        return execute_subprocess(cmd, output_to_caller=True)
-
-    @staticmethod
-    def has_submodules(repo_dir_path):
-        """Return True iff the repository at <repo_dir_path> has a 
-        '.gitmodules' file
-        """
-        fname = os.path.join(repo_dir_path,
-                             ExternalsDescription.GIT_SUBMODULES_FILENAME)
-
-        return os.path.exists(fname)
-
-    # ----------------------------------------------------------------
-    #
-    # system call to git for sideffects modifying the working tree
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _git_clone(url, repo_dir_name, verbosity):
-        """Clones url into repo_dir_name.
-        """
-        cmd = 'git clone --quiet {url} {repo_dir_name}'.format(
-            url=url, repo_dir_name=repo_dir_name).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_remote_add(name, url, dirname):
-        """Run the git remote command for the side effect of adding a remote
-        """
-        cmd = 'git -C {dirname} remote add {name} {url}'.format(
-            dirname=dirname, name=name, url=url).split()
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_fetch(remote_name, dirname):
-        """Run the git fetch command for the side effect of updating the repo
-        """
-        cmd = 'git -C {dirname} fetch --quiet --tags {remote_name}'.format(
-            dirname=dirname, remote_name=remote_name).split()
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_checkout_ref(ref, verbosity, submodules, dirname):
-        """Run the git checkout command for the side effect of updating the repo
-
-        Param: ref is a reference to a local or remote object in the
-        form 'origin/my_feature', or 'tag1'.
-
-        """
-        cmd = 'git -C {dirname} checkout --quiet {ref}'.format(
-            dirname=dirname, ref=ref).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-        if submodules:
-            GitRepository._git_update_submodules(verbosity, dirname)
-
-    @staticmethod
-    def _git_sparse_checkout(verbosity, dirname):
-        """Configure repo via read-tree."""
-        cmd = 'git -C {dirname} config core.sparsecheckout true'.format(
-            dirname=dirname).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-        cmd = 'git -C {dirname} read-tree -mu HEAD'.format(
-            dirname=dirname).split()
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _git_update_submodules(verbosity, dirname):
-        """Run git submodule update for the side effect of updating this
-        repo's submodules.
-        """
-        # due to https://vielmetti.typepad.com/logbook/2022/10/git-security-fixes-lead-to-fatal-transport-file-not-allowed-error-in-ci-systems-cve-2022-39253.html
-        # submodules from file doesn't work without overriding the protocol, this is done
-        # for testing submodule support but should not be done in practice
-        file_protocol = ""
-        if 'unittest' in sys.modules.keys():
-            file_protocol = "-c protocol.file.allow=always"
-
-        # First, verify that we have a .gitmodules file
-        if os.path.exists(
-                os.path.join(dirname,
-                             ExternalsDescription.GIT_SUBMODULES_FILENAME)):
-            cmd = ('git {file_protocol} -C {dirname} submodule update --init --recursive'
-                   .format(file_protocol=file_protocol, dirname=dirname)).split()
-            if verbosity >= VERBOSITY_VERBOSE:
-                printlog('    {0}'.format(' '.join(cmd)))
-
-            execute_subprocess(cmd)
diff --git a/manage_externals/manic/repository_svn.py b/manage_externals/manic/repository_svn.py
deleted file mode 100644
index 32a71184b4..0000000000
--- a/manage_externals/manic/repository_svn.py
+++ /dev/null
@@ -1,291 +0,0 @@
-"""Class for interacting with svn repositories
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import re
-import xml.etree.ElementTree as ET
-
-from .global_constants import EMPTY_STR, VERBOSITY_VERBOSE
-from .repository import Repository
-from .externals_status import ExternalStatus
-from .utils import fatal_error, indent_string, printlog
-from .utils import execute_subprocess
-
-
-class SvnRepository(Repository):
-    """
-    Class to represent and operate on a repository description.
-
-    For testing purpose, all system calls to svn should:
-
-    * be isolated in separate functions with no application logic
-      * of the form:
-         - cmd = ['svn', ...]
-         - value = execute_subprocess(cmd, output_to_caller={T|F},
-                                      status_to_caller={T|F})
-         - return value
-      * be static methods (not rely on self)
-      * name as _svn_subcommand_args(user_args)
-
-    This convention allows easy unit testing of the repository logic
-    by mocking the specific calls to return predefined results.
-
-    """
-    RE_URLLINE = re.compile(r'^URL:')
-
-    def __init__(self, component_name, repo, ignore_ancestry=False):
-        """
-        Parse repo (a <repo> XML element).
-        """
-        Repository.__init__(self, component_name, repo)
-        if 'github.com' in self._url:
-            msg = "SVN access to github.com is no longer supported"
-            fatal_error(msg)
-        self._ignore_ancestry = ignore_ancestry
-        if self._url.endswith('/'):
-            # there is already a '/' separator in the URL; no need to add another
-            url_sep = ''
-        else:
-            url_sep = '/'
-        if self._branch:
-            self._url = self._url + url_sep + self._branch
-        elif self._tag:
-            self._url = self._url + url_sep + self._tag
-        else:
-            msg = "DEV_ERROR in svn repository. Shouldn't be here!"
-            fatal_error(msg)
-
-    # ----------------------------------------------------------------
-    #
-    # Public API, defined by Repository
-    #
-    # ----------------------------------------------------------------
-    def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive):  # pylint: disable=unused-argument
-        """Checkout or update the working copy
-
-        If the repo destination directory exists, switch the sandbox to
-        match the externals description.
-
-        If the repo destination directory does not exist, checkout the
-        correct branch or tag.
-        NB: <recursive> is include as an argument for compatibility with
-            git functionality (repository_git.py)
-
-        """
-        repo_dir_path = os.path.join(base_dir_path, repo_dir_name)
-        if os.path.exists(repo_dir_path):
-            cwd = os.getcwd()
-            os.chdir(repo_dir_path)
-            self._svn_switch(self._url, self._ignore_ancestry, verbosity)
-            # svn switch can lead to a conflict state, but it gives a
-            # return code of 0. So now we need to make sure that we're
-            # in a clean (non-conflict) state.
-            self._abort_if_dirty(repo_dir_path,
-                                 "Expected clean state following switch")
-            os.chdir(cwd)
-        else:
-            self._svn_checkout(self._url, repo_dir_path, verbosity)
-
-    def status(self, stat, repo_dir_path):
-        """
-        Check and report the status of the repository
-        """
-        self._check_sync(stat, repo_dir_path)
-        if os.path.exists(repo_dir_path):
-            self._status_summary(stat, repo_dir_path)
-
-    # ----------------------------------------------------------------
-    #
-    # Internal work functions
-    #
-    # ----------------------------------------------------------------
-    def _check_sync(self, stat, repo_dir_path):
-        """Check to see if repository directory exists and is at the expected
-        url.  Return: status object
-
-        """
-        if not os.path.exists(repo_dir_path):
-            # NOTE(bja, 2017-10) this state should have been handled by
-            # the source object and we never get here!
-            stat.sync_state = ExternalStatus.STATUS_ERROR
-        else:
-            svn_output = self._svn_info(repo_dir_path)
-            if not svn_output:
-                # directory exists, but info returned nothing. .svn
-                # directory removed or incomplete checkout?
-                stat.sync_state = ExternalStatus.UNKNOWN
-            else:
-                stat.sync_state, stat.current_version = \
-                    self._check_url(svn_output, self._url)
-            stat.expected_version = '/'.join(self._url.split('/')[3:])
-
-    def _abort_if_dirty(self, repo_dir_path, message):
-        """Check if the repo is in a dirty state; if so, abort with a
-        helpful message.
-
-        """
-
-        stat = ExternalStatus()
-        self._status_summary(stat, repo_dir_path)
-        if stat.clean_state != ExternalStatus.STATUS_OK:
-            status = self._svn_status_verbose(repo_dir_path)
-            status = indent_string(status, 4)
-            errmsg = """In directory
-    {cwd}
-
-svn status now shows:
-{status}
-
-ERROR: {message}
-
-One possible cause of this problem is that there may have been untracked
-files in your working directory that had the same name as tracked files
-in the new revision.
-
-To recover: Clean up the above directory (resolving conflicts, etc.),
-then rerun checkout_externals.
-""".format(cwd=repo_dir_path, message=message, status=status)
-
-            fatal_error(errmsg)
-
-    @staticmethod
-    def _check_url(svn_output, expected_url):
-        """Determine the svn url from svn info output and return whether it
-        matches the expected value.
-
-        """
-        url = None
-        for line in svn_output.splitlines():
-            if SvnRepository.RE_URLLINE.match(line):
-                url = line.split(': ')[1].strip()
-                break
-        if not url:
-            status = ExternalStatus.UNKNOWN
-        elif url == expected_url:
-            status = ExternalStatus.STATUS_OK
-        else:
-            status = ExternalStatus.MODEL_MODIFIED
-
-        if url:
-            current_version = '/'.join(url.split('/')[3:])
-        else:
-            current_version = EMPTY_STR
-
-        return status, current_version
-
-    def _status_summary(self, stat, repo_dir_path):
-        """Report whether the svn repository is in-sync with the model
-        description and whether the sandbox is clean or dirty.
-
-        """
-        svn_output = self._svn_status_xml(repo_dir_path)
-        is_dirty = self.xml_status_is_dirty(svn_output)
-        if is_dirty:
-            stat.clean_state = ExternalStatus.DIRTY
-        else:
-            stat.clean_state = ExternalStatus.STATUS_OK
-
-        # Now save the verbose status output incase the user wants to
-        # see it.
-        stat.status_output = self._svn_status_verbose(repo_dir_path)
-
-    @staticmethod
-    def xml_status_is_dirty(svn_output):
-        """Parse svn status xml output and determine if the working copy is
-        clean or dirty. Dirty is defined as:
-
-        * modified files
-        * added files
-        * deleted files
-        * missing files
-
-        Unversioned files do not affect the clean/dirty status.
-
-        'external' is also an acceptable state
-
-        """
-        # pylint: disable=invalid-name
-        SVN_EXTERNAL = 'external'
-        SVN_UNVERSIONED = 'unversioned'
-        # pylint: enable=invalid-name
-
-        is_dirty = False
-        try:
-            xml_status = ET.fromstring(svn_output)
-        except BaseException:
-            fatal_error(
-                "SVN returned invalid XML message {}".format(svn_output))
-        xml_target = xml_status.find('./target')
-        entries = xml_target.findall('./entry')
-        for entry in entries:
-            status = entry.find('./wc-status')
-            item = status.get('item')
-            if item == SVN_EXTERNAL:
-                continue
-            if item == SVN_UNVERSIONED:
-                continue
-            is_dirty = True
-            break
-        return is_dirty
-
-    # ----------------------------------------------------------------
-    #
-    # system call to svn for information gathering
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _svn_info(repo_dir_path):
-        """Return results of svn info command
-        """
-        cmd = ['svn', 'info', repo_dir_path]
-        output = execute_subprocess(cmd, output_to_caller=True)
-        return output
-
-    @staticmethod
-    def _svn_status_verbose(repo_dir_path):
-        """capture the full svn status output
-        """
-        cmd = ['svn', 'status', repo_dir_path]
-        svn_output = execute_subprocess(cmd, output_to_caller=True)
-        return svn_output
-
-    @staticmethod
-    def _svn_status_xml(repo_dir_path):
-        """
-        Get status of the subversion sandbox in repo_dir
-        """
-        cmd = ['svn', 'status', '--xml', repo_dir_path]
-        svn_output = execute_subprocess(cmd, output_to_caller=True)
-        return svn_output
-
-    # ----------------------------------------------------------------
-    #
-    # system call to svn for sideffects modifying the working tree
-    #
-    # ----------------------------------------------------------------
-    @staticmethod
-    def _svn_checkout(url, repo_dir_path, verbosity):
-        """
-        Checkout a subversion repository (repo_url) to checkout_dir.
-        """
-        cmd = ['svn', 'checkout', '--quiet', url, repo_dir_path]
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
-
-    @staticmethod
-    def _svn_switch(url, ignore_ancestry, verbosity):
-        """
-        Switch branches for in an svn sandbox
-        """
-        cmd = ['svn', 'switch', '--quiet']
-        if ignore_ancestry:
-            cmd.append('--ignore-ancestry')
-        cmd.append(url)
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('    {0}'.format(' '.join(cmd)))
-        execute_subprocess(cmd)
diff --git a/manage_externals/manic/sourcetree.py b/manage_externals/manic/sourcetree.py
deleted file mode 100644
index cf2a5b7569..0000000000
--- a/manage_externals/manic/sourcetree.py
+++ /dev/null
@@ -1,425 +0,0 @@
-"""
-Classes to represent an externals config file (SourceTree) and the components
-within it (_External).
-"""
-
-import errno
-import logging
-import os
-
-from .externals_description import ExternalsDescription
-from .externals_description import read_externals_description_file
-from .externals_description import create_externals_description
-from .repository_factory import create_repository
-from .repository_git import GitRepository
-from .externals_status import ExternalStatus
-from .utils import fatal_error, printlog
-from .global_constants import EMPTY_STR, LOCAL_PATH_INDICATOR
-from .global_constants import VERBOSITY_VERBOSE
-
-class _External(object):
-    """
-    A single component hosted in an external repository (and any children).
-
-    The component may or may not be checked-out upon construction.
-    """
-    # pylint: disable=R0902
-
-    def __init__(self, root_dir, name, local_path, required, subexternals_path,
-                 repo, svn_ignore_ancestry, subexternal_sourcetree):
-        """Create a single external component (checked out or not).
-
-        Input:
-            root_dir : string - the (checked-out) parent repo's root dir.
-            local_path : string - this external's (checked-out) subdir relative
-            to root_dir, e.g. "components/mom"
-            repo: Repository - the repo object for this external. Can be None (e.g. if this external just refers to another external file).
-
-            name : string - name of this external (as named by the parent 
-            reference).  May or may not correspond to something in the path.
-
-            ext_description : dict - source ExternalsDescription object
-
-            svn_ignore_ancestry : bool - use --ignore-externals with svn switch
-
-            subexternals_path: string - path to sub-externals config file, if any. Relative to local_path, or special value 'none'.
-            subexternal_sourcetree: SourceTree - corresponding to subexternals_path, if subexternals_path exists (it might not, if it is not checked out yet).
-        """
-        self._name = name
-        self._required = required
-        
-        self._stat = None  # Populated in status()
-
-        self._local_path = local_path
-        # _repo_dir_path : full repository directory, e.g.
-        # "<root_dir>/components/mom"
-        repo_dir = os.path.join(root_dir, local_path)
-        self._repo_dir_path = os.path.abspath(repo_dir)
-        # _base_dir_path : base directory *containing* the repository, e.g.
-        # "<root_dir>/components"
-        self._base_dir_path = os.path.dirname(self._repo_dir_path)
-        # _repo_dir_name : base_dir_path + repo_dir_name = repo_dir_path
-        # e.g., "mom"
-        self._repo_dir_name = os.path.basename(self._repo_dir_path)
-        self._repo = repo
-
-        # Does this component have subcomponents aka an externals config?
-        self._subexternals_path = subexternals_path
-        self._subexternal_sourcetree = subexternal_sourcetree
-        
-
-    def get_name(self):
-        """
-        Return the external object's name
-        """
-        return self._name
-
-    def get_local_path(self):
-        """
-        Return the external object's path
-        """
-        return self._local_path
-
-    def get_repo_dir_path(self):
-        return self._repo_dir_path
-
-    def get_subexternals_path(self):
-        return self._subexternals_path
-
-    def get_repo(self):
-        return self._repo
-    
-    def status(self, force=False, print_progress=False):
-        """
-        Returns status of this component and all subcomponents.
-
-        Returns a dict mapping our local path (not component name!) to an
-        ExternalStatus dict. Any subcomponents will have their own top-level
-        path keys.  Note the return value includes entries for this and all 
-        subcomponents regardless of whether they are locally installed or not.
-
-        Side-effect: If self._stat is empty or force is True, calculates _stat.
-        """
-        calc_stat = force or not self._stat
-
-        if calc_stat:
-            self._stat = ExternalStatus()
-            self._stat.path = self.get_local_path()
-            if not self._required:
-                self._stat.source_type = ExternalStatus.OPTIONAL
-            elif self._local_path == LOCAL_PATH_INDICATOR:
-                # LOCAL_PATH_INDICATOR, '.' paths, are standalone
-                # component directories that are not managed by
-                # checkout_subexternals.
-                self._stat.source_type = ExternalStatus.STANDALONE
-            else:
-                # managed by checkout_subexternals
-                self._stat.source_type = ExternalStatus.MANAGED
-
-        subcomponent_stats = {}
-        if not os.path.exists(self._repo_dir_path):
-            if calc_stat:
-                # No local repository.
-                self._stat.sync_state = ExternalStatus.EMPTY
-                msg = ('status check: repository directory for "{0}" does not '
-                       'exist.'.format(self._name))
-                logging.info(msg)
-                self._stat.current_version = 'not checked out'
-                # NOTE(bja, 2018-01) directory doesn't exist, so we cannot
-                # use repo to determine the expected version. We just take
-                # a best-guess based on the assumption that only tag or
-                # branch should be set, but not both.
-                if not self._repo:
-                    self._stat.expected_version = 'unknown'
-                else:
-                    self._stat.expected_version = self._repo.tag() + self._repo.branch()
-        else:
-            # Merge local repository state (e.g. clean/dirty) into self._stat.
-            if calc_stat and self._repo:
-                self._repo.status(self._stat, self._repo_dir_path)
-
-            # Status of subcomponents, if any.
-            if self._subexternals_path and self._subexternal_sourcetree:
-                cwd = os.getcwd()
-                # SourceTree.status() expects to be called from the correct
-                # root directory.
-                os.chdir(self._repo_dir_path)
-                subcomponent_stats = self._subexternal_sourcetree.status(self._local_path, force=force, print_progress=print_progress)
-                os.chdir(cwd)
-
-        # Merge our status + subcomponent statuses into one return dict keyed
-        # by component path.
-        all_stats = {}
-        # don't add the root component because we don't manage it
-        # and can't provide useful info about it.
-        if self._local_path != LOCAL_PATH_INDICATOR:
-            # store the stats under the local_path, not comp name so
-            # it will be sorted correctly
-            all_stats[self._stat.path] = self._stat
-
-        if subcomponent_stats:
-            all_stats.update(subcomponent_stats)
-
-        return all_stats
-
-    def checkout(self, verbosity):
-        """
-        If the repo destination directory exists, ensure it is correct (from
-        correct URL, correct branch or tag), and possibly updateit.
-        If the repo destination directory does not exist, checkout the correct
-        branch or tag.
-        Does not check out sub-externals, see SourceTree.checkout().
-        """
-        # Make sure we are in correct location
-        if not os.path.exists(self._repo_dir_path):
-            # repository directory doesn't exist. Need to check it
-            # out, and for that we need the base_dir_path to exist
-            try:
-                os.makedirs(self._base_dir_path)
-            except OSError as error:
-                if error.errno != errno.EEXIST:
-                    msg = 'Could not create directory "{0}"'.format(
-                        self._base_dir_path)
-                    fatal_error(msg)
-
-        if not self._stat:
-            self.status()
-            assert self._stat
-            
-        if self._stat.source_type != ExternalStatus.STANDALONE:
-            if verbosity >= VERBOSITY_VERBOSE:
-                # NOTE(bja, 2018-01) probably do not want to pass
-                # verbosity in this case, because if (verbosity ==
-                # VERBOSITY_DUMP), then the previous status output would
-                # also be dumped, adding noise to the output.
-                self._stat.log_status_message(VERBOSITY_VERBOSE)
-
-        if self._repo:
-            if self._stat.sync_state == ExternalStatus.STATUS_OK:
-                # If we're already in sync, avoid showing verbose output
-                # from the checkout command, unless the verbosity level
-                # is 2 or more.
-                checkout_verbosity = verbosity - 1
-            else:
-                checkout_verbosity = verbosity
-
-            self._repo.checkout(self._base_dir_path, self._repo_dir_name,
-                                checkout_verbosity, self.clone_recursive())
-
-    def replace_subexternal_sourcetree(self, sourcetree):
-        self._subexternal_sourcetree = sourcetree
-
-    def clone_recursive(self):
-        'Return True iff any .gitmodules files should be processed'
-        # Try recursive .gitmodules unless there is an externals entry
-        recursive = not self._subexternals_path
-
-        return recursive
-
-
-class SourceTree(object):
-    """
-    SourceTree represents a group of managed externals.
-
-    Those externals may not be checked out locally yet, they might only
-    have Repository objects pointing to their respective repositories.
-    """
-
-    @classmethod
-    def from_externals_file(cls, parent_repo_dir_path, parent_repo,
-                            externals_path):
-        """Creates a SourceTree representing the given externals file.
-        
-        Looks up a git submodules file as an optional backup if there is no
-        externals file specified.
-
-        Returns None if there is no externals file (i.e. it's None or 'none'),
-        or if the externals file hasn't been checked out yet.
-
-        parent_repo_dir_path: parent repo root dir
-        parent_repo: parent repo.
-        externals_path: path to externals file, relative to parent_repo_dir_path.
-        """
-        if not os.path.exists(parent_repo_dir_path):
-            # NOTE(bja, 2017-10) repository has not been checked out
-            # yet, can't process the externals file. Assume we are
-            # checking status before code is checkoud out and this
-            # will be handled correctly later.
-            return None
-
-        if externals_path.lower() == 'none':
-            # With explicit 'none', do not look for git submodules file.
-            return None
-
-        cwd = os.getcwd()
-        os.chdir(parent_repo_dir_path)
-        
-        if not externals_path:
-            if GitRepository.has_submodules(parent_repo_dir_path):
-                externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME
-            else:
-                return None
-
-        if not os.path.exists(externals_path):
-            # NOTE(bja, 2017-10) this check is redundant with the one
-            # in read_externals_description_file!
-            msg = ('Externals description file "{0}" '
-                   'does not exist! In directory: {1}'.format(
-                       externals_path, parent_repo_dir_path))
-            fatal_error(msg)
-
-        externals_root = parent_repo_dir_path
-        # model_data is a dict-like object which mirrors the file format.
-        model_data = read_externals_description_file(externals_root,
-                                                     externals_path)
-        # ext_description is another dict-like object (see ExternalsDescription)
-        ext_description = create_externals_description(model_data,
-                                                       parent_repo=parent_repo)
-        externals_sourcetree = SourceTree(externals_root, ext_description)
-        os.chdir(cwd)
-        return externals_sourcetree
-    
-    def __init__(self, root_dir, ext_description, svn_ignore_ancestry=False):
-        """
-        Build a SourceTree object from an ExternalDescription.
-
-        root_dir: the (checked-out) parent repo root dir.
-        """
-        self._root_dir = os.path.abspath(root_dir)
-        self._all_components = {}  # component_name -> _External
-        self._required_compnames = []
-        for comp, desc in ext_description.items():
-            local_path = desc[ExternalsDescription.PATH]
-            required = desc[ExternalsDescription.REQUIRED]
-            repo_info = desc[ExternalsDescription.REPO]
-            subexternals_path = desc[ExternalsDescription.EXTERNALS]
-
-            repo = create_repository(comp,
-                                     repo_info,
-                                     svn_ignore_ancestry=svn_ignore_ancestry)
-
-            sourcetree = None
-            # Treat a .gitmodules file as a backup externals config
-            if not subexternals_path:
-                parent_repo_dir_path = os.path.abspath(os.path.join(root_dir,
-                                                             local_path))
-                if GitRepository.has_submodules(parent_repo_dir_path):
-                    subexternals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME
-            
-            # Might return None (if the subexternal isn't checked out yet, or subexternal is None or 'none')
-            subexternal_sourcetree = SourceTree.from_externals_file(
-                os.path.join(self._root_dir, local_path),
-                repo,
-                subexternals_path)
-            src = _External(self._root_dir, comp, local_path, required,
-                            subexternals_path, repo, svn_ignore_ancestry,
-                            subexternal_sourcetree)
-            
-            self._all_components[comp] = src
-            if required:
-                self._required_compnames.append(comp)
-
-    def status(self, relative_path_base=LOCAL_PATH_INDICATOR,
-               force=False, print_progress=False):
-        """Return a dictionary of local path->ExternalStatus.
-
-        Notes about the returned dictionary:
-          * It is keyed by local path (e.g. 'components/mom'), not by
-            component name (e.g. 'mom').
-          * It contains top-level keys for all traversed components, whether
-            discovered by recursion or top-level.
-          * It contains entries for all components regardless of whether they
-            are locally installed or not, or required or optional.
-x        """
-        load_comps = self._all_components.keys()
-
-        summary = {}  # Holds merged statuses from all components.
-        for comp in load_comps:
-            if print_progress:
-                printlog('{0}, '.format(comp), end='')
-            stat = self._all_components[comp].status(force=force,
-                                                     print_progress=print_progress)
-
-            # Returned status dictionary is keyed by local path; prepend
-            # relative_path_base if not already there.
-            stat_final = {}
-            for name in stat.keys():
-                if stat[name].path.startswith(relative_path_base):
-                    stat_final[name] = stat[name]
-                else:
-                    modified_path = os.path.join(relative_path_base,
-                                                 stat[name].path)
-                    stat_final[modified_path] = stat[name]
-                    stat_final[modified_path].path = modified_path
-            summary.update(stat_final)
-
-        return summary
-
-    def _find_installed_optional_components(self):
-        """Returns a list of installed optional component names, if any."""
-        installed_comps = []
-        for comp_name, ext in self._all_components.items():
-            if comp_name in self._required_compnames:
-                continue
-            # Note that in practice we expect this status to be cached.
-            path_to_stat = ext.status()
-
-            # If any part of this component exists locally, consider it
-            # installed and therefore eligible for updating.
-            if any(s.sync_state != ExternalStatus.EMPTY
-                   for s in path_to_stat.values()):
-                installed_comps.append(comp_name)
-        return installed_comps
-
-    def checkout(self, verbosity, load_all, load_comp=None):
-        """
-        Checkout or update indicated components into the configured subdirs.
-
-        If load_all is True, checkout all externals (required + optional), recursively.
-        If load_all is False and load_comp is set, checkout load_comp (and any required subexternals, plus any optional subexternals that are already checked out, recursively)
-        If load_all is False and load_comp is None, checkout all required externals, plus any optionals that are already checked out, recursively.
-        """
-        if load_all:
-            tmp_comps = self._all_components.keys()
-        elif load_comp is not None:
-            tmp_comps = [load_comp]
-        else:
-            local_optional_compnames = self._find_installed_optional_components()
-            tmp_comps = self._required_compnames + local_optional_compnames
-            if local_optional_compnames:
-                printlog('Found locally installed optional components: ' +
-                         ', '.join(local_optional_compnames))
-                bad_compnames = set(local_optional_compnames) - set(self._all_components.keys())
-                if bad_compnames:
-                    printlog('Internal error: found locally installed components that are not in the global list of all components: ' + ','.join(bad_compnames))
-
-        if verbosity >= VERBOSITY_VERBOSE:
-            printlog('Checking out externals: ')
-        else:
-            printlog('Checking out externals: ', end='')
-
-        # Sort by path so that if paths are nested the
-        # parent repo is checked out first.
-        load_comps = sorted(tmp_comps, key=lambda comp: self._all_components[comp].get_local_path())
-
-        # checkout.
-        for comp_name in load_comps:
-            if verbosity < VERBOSITY_VERBOSE:
-                printlog('{0}, '.format(comp_name), end='')
-            else:
-                # verbose output handled by the _External object, just
-                # output a newline
-                printlog(EMPTY_STR)
-            c = self._all_components[comp_name]
-            # Does not recurse.
-            c.checkout(verbosity)
-            # Recursively check out subexternals, if any. Returns None
-            # if there's no subexternals path.
-            component_subexternal_sourcetree = SourceTree.from_externals_file(
-                    c.get_repo_dir_path(),
-                    c.get_repo(),
-                    c.get_subexternals_path())
-            c.replace_subexternal_sourcetree(component_subexternal_sourcetree)
-            if component_subexternal_sourcetree:
-                component_subexternal_sourcetree.checkout(verbosity, load_all)
-        printlog('')
diff --git a/manage_externals/manic/utils.py b/manage_externals/manic/utils.py
deleted file mode 100644
index 9c63ffe65e..0000000000
--- a/manage_externals/manic/utils.py
+++ /dev/null
@@ -1,330 +0,0 @@
-#!/usr/bin/env python3
-"""
-Common public utilities for manic package
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import logging
-import os
-import subprocess
-import sys
-from threading import Timer
-
-from .global_constants import LOCAL_PATH_INDICATOR
-
-# ---------------------------------------------------------------------
-#
-# screen and logging output and functions to massage text for output
-#
-# ---------------------------------------------------------------------
-
-
-def log_process_output(output):
-    """Log each line of process output at debug level so it can be
-    filtered if necessary. By default, output is a single string, and
-    logging.debug(output) will only put log info heading on the first
-    line. This makes it hard to filter with grep.
-
-    """
-    output = output.split('\n')
-    for line in output:
-        logging.debug(line)
-
-
-def printlog(msg, **kwargs):
-    """Wrapper script around print to ensure that everything printed to
-    the screen also gets logged.
-
-    """
-    logging.info(msg)
-    if kwargs:
-        print(msg, **kwargs)
-    else:
-        print(msg)
-    sys.stdout.flush()
-
-
-def last_n_lines(the_string, n_lines, truncation_message=None):
-    """Returns the last n lines of the given string
-
-    Args:
-        the_string: str
-        n_lines: int
-        truncation_message: str, optional
-
-    Returns a string containing the last n lines of the_string
-
-    If truncation_message is provided, the returned string begins with
-    the given message if and only if the string is greater than n lines
-    to begin with.
-    """
-
-    lines = the_string.splitlines(True)
-    if len(lines) <= n_lines:
-        return_val = the_string
-    else:
-        lines_subset = lines[-n_lines:]
-        str_truncated = ''.join(lines_subset)
-        if truncation_message:
-            str_truncated = truncation_message + '\n' + str_truncated
-        return_val = str_truncated
-
-    return return_val
-
-
-def indent_string(the_string, indent_level):
-    """Indents the given string by a given number of spaces
-
-    Args:
-       the_string: str
-       indent_level: int
-
-    Returns a new string that is the same as the_string, except that
-    each line is indented by 'indent_level' spaces.
-
-    In python3, this can be done with textwrap.indent.
-    """
-
-    lines = the_string.splitlines(True)
-    padding = ' ' * indent_level
-    lines_indented = [padding + line for line in lines]
-    return ''.join(lines_indented)
-
-# ---------------------------------------------------------------------
-#
-# error handling
-#
-# ---------------------------------------------------------------------
-
-
-def fatal_error(message):
-    """
-    Error output function
-    """
-    logging.error(message)
-    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
-
-
-# ---------------------------------------------------------------------
-#
-# Data conversion / manipulation
-#
-# ---------------------------------------------------------------------
-def str_to_bool(bool_str):
-    """Convert a sting representation of as boolean into a true boolean.
-
-    Conversion should be case insensitive.
-    """
-    value = None
-    str_lower = bool_str.lower()
-    if str_lower in ('true', 't'):
-        value = True
-    elif str_lower in ('false', 'f'):
-        value = False
-    if value is None:
-        msg = ('ERROR: invalid boolean string value "{0}". '
-               'Must be "true" or "false"'.format(bool_str))
-        fatal_error(msg)
-    return value
-
-
-REMOTE_PREFIXES = ['http://', 'https://', 'ssh://', 'git@']
-
-
-def is_remote_url(url):
-    """check if the user provided a local file path instead of a
-       remote. If so, it must be expanded to an absolute
-       path.
-
-    """
-    remote_url = False
-    for prefix in REMOTE_PREFIXES:
-        if url.startswith(prefix):
-            remote_url = True
-    return remote_url
-
-
-def split_remote_url(url):
-    """check if the user provided a local file path or a
-       remote. If remote, try to strip off protocol info.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        return url
-
-    for prefix in REMOTE_PREFIXES:
-        url = url.replace(prefix, '')
-
-    if '@' in url:
-        url = url.split('@')[1]
-
-    if ':' in url:
-        url = url.split(':')[1]
-
-    return url
-
-
-def expand_local_url(url, field):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
-    represent local copy only, don't work with the remotes.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        if url.strip() == LOCAL_PATH_INDICATOR:
-            pass
-        else:
-            url = os.path.expandvars(url)
-            url = os.path.expanduser(url)
-            if not os.path.isabs(url):
-                msg = ('WARNING: Externals description for "{0}" contains a '
-                       'url that is not remote and does not expand to an '
-                       'absolute path. Version control operations may '
-                       'fail.\n\nurl={1}'.format(field, url))
-                printlog(msg)
-            else:
-                url = os.path.normpath(url)
-    return url
-
-
-# ---------------------------------------------------------------------
-#
-# subprocess
-#
-# ---------------------------------------------------------------------
-
-# Give the user a helpful message if we detect that a command seems to
-# be hanging.
-_HANGING_SEC = 300
-
-
-def _hanging_msg(working_directory, command):
-    print("""
-
-Command '{command}'
-from directory {working_directory}
-has taken {hanging_sec} seconds. It may be hanging.
-
-The command will continue to run, but you may want to abort
-manage_externals with ^C and investigate. A possible cause of hangs is
-when svn or git require authentication to access a private
-repository. On some systems, svn and git requests for authentication
-information will not be displayed to the user. In this case, the program
-will appear to hang. Ensure you can run svn and git manually and access
-all repositories without entering your authentication information.
-
-""".format(command=command,
-           working_directory=working_directory,
-           hanging_sec=_HANGING_SEC))
-
-
-def execute_subprocess(commands, status_to_caller=False,
-                       output_to_caller=False):
-    """Wrapper around subprocess.check_output to handle common
-    exceptions.
-
-    check_output runs a command with arguments and waits
-    for it to complete.
-
-    check_output raises an exception on a nonzero return code.  if
-    status_to_caller is true, execute_subprocess returns the subprocess
-    return code, otherwise execute_subprocess treats non-zero return
-    status as an error and raises an exception.
-
-    """
-    cwd = os.getcwd()
-    msg = 'In directory: {0}\nexecute_subprocess running command:'.format(cwd)
-    logging.info(msg)
-    commands_str = ' '.join(commands)
-    logging.info(commands_str)
-    return_to_caller = status_to_caller or output_to_caller
-    status = -1
-    output = ''
-    hanging_timer = Timer(_HANGING_SEC, _hanging_msg,
-                          kwargs={"working_directory": cwd,
-                                  "command": commands_str})
-    hanging_timer.start()
-    try:
-        output = subprocess.check_output(commands, stderr=subprocess.STDOUT,
-                                         universal_newlines=True)
-        log_process_output(output)
-        status = 0
-    except OSError as error:
-        msg = failed_command_msg(
-            'Command execution failed. Does the executable exist?',
-            commands)
-        logging.error(error)
-        fatal_error(msg)
-    except ValueError as error:
-        msg = failed_command_msg(
-            'DEV_ERROR: Invalid arguments trying to run subprocess',
-            commands)
-        logging.error(error)
-        fatal_error(msg)
-    except subprocess.CalledProcessError as error:
-        # Only report the error if we are NOT returning to the
-        # caller. If we are returning to the caller, then it may be a
-        # simple status check. If returning, it is the callers
-        # responsibility determine if an error occurred and handle it
-        # appropriately.
-        if not return_to_caller:
-            msg_context = ('Process did not run successfully; '
-                           'returned status {0}'.format(error.returncode))
-            msg = failed_command_msg(msg_context, commands,
-                                     output=error.output)
-            logging.error(error)
-            logging.error(msg)
-            log_process_output(error.output)
-            fatal_error(msg)
-        status = error.returncode
-    finally:
-        hanging_timer.cancel()
-
-    if status_to_caller and output_to_caller:
-        ret_value = (status, output)
-    elif status_to_caller:
-        ret_value = status
-    elif output_to_caller:
-        ret_value = output
-    else:
-        ret_value = None
-
-    return ret_value
-
-
-def failed_command_msg(msg_context, command, output=None):
-    """Template for consistent error messages from subprocess calls.
-
-    If 'output' is given, it should provide the output from the failed
-    command
-    """
-
-    if output:
-        output_truncated = last_n_lines(output, 20,
-                                        truncation_message='[... Output truncated for brevity ...]')
-        errmsg = ('Failed with output:\n' +
-                  indent_string(output_truncated, 4) +
-                  '\nERROR: ')
-    else:
-        errmsg = ''
-
-    command_str = ' '.join(command)
-    errmsg += """In directory
-    {cwd}
-{context}:
-    {command}
-""".format(cwd=os.getcwd(), context=msg_context, command=command_str)
-
-    if output:
-        errmsg += 'See above for output from failed command.\n'
-
-    return errmsg
diff --git a/manage_externals/test/.coveragerc b/manage_externals/test/.coveragerc
deleted file mode 100644
index 8b681888b8..0000000000
--- a/manage_externals/test/.coveragerc
+++ /dev/null
@@ -1,7 +0,0 @@
-[run]
-branch = True
-omit = test_unit_*.py
-       test_sys_*.py
-       /usr/*
-       .local/*
-       */site-packages/*
\ No newline at end of file
diff --git a/manage_externals/test/.gitignore b/manage_externals/test/.gitignore
deleted file mode 100644
index dd5795998f..0000000000
--- a/manage_externals/test/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-# virtual environments
-env_python*
-
-# python code coverage tool output
-.coverage
-htmlcov
-
diff --git a/manage_externals/test/.pylint.rc b/manage_externals/test/.pylint.rc
deleted file mode 100644
index 64abd03e42..0000000000
--- a/manage_externals/test/.pylint.rc
+++ /dev/null
@@ -1,426 +0,0 @@
-[MASTER]
-
-# A comma-separated list of package or module names from where C extensions may
-# be loaded. Extensions are loading into the active Python interpreter and may
-# run arbitrary code
-extension-pkg-whitelist=
-
-# Add files or directories to the blacklist. They should be base names, not
-# paths.
-ignore=.git,.svn,env2
-
-# Add files or directories matching the regex patterns to the blacklist. The
-# regex matches against base names, not paths.
-ignore-patterns=
-
-# Python code to execute, usually for sys.path manipulation such as
-# pygtk.require().
-#init-hook=
-
-# Use multiple processes to speed up Pylint.
-jobs=1
-
-# List of plugins (as comma separated values of python modules names) to load,
-# usually to register additional checkers.
-load-plugins=
-
-# Pickle collected data for later comparisons.
-persistent=yes
-
-# Specify a configuration file.
-#rcfile=
-
-# Allow loading of arbitrary C extensions. Extensions are imported into the
-# active Python interpreter and may run arbitrary code.
-unsafe-load-any-extension=no
-
-
-[MESSAGES CONTROL]
-
-# Only show warnings with the listed confidence levels. Leave empty to show
-# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED
-confidence=
-
-# Disable the message, report, category or checker with the given id(s). You
-# can either give multiple identifiers separated by comma (,) or put this
-# option multiple times (only on the command line, not in the configuration
-# file where it should appear only once).You can also use "--disable=all" to
-# disable everything first and then reenable specific checks. For example, if
-# you want to run only the similarities checker, you can use "--disable=all
-# --enable=similarities". If you want to run only the classes checker, but have
-# no Warning level messages displayed, use"--disable=all --enable=classes
-# --disable=W"
-disable=bad-continuation,useless-object-inheritance
-
-
-# Enable the message, report, category or checker with the given id(s). You can
-# either give multiple identifier separated by comma (,) or put this option
-# multiple time (only on the command line, not in the configuration file where
-# it should appear only once). See also the "--disable" option for examples.
-enable=
-
-
-[REPORTS]
-
-# Python expression which should return a note less than 10 (10 is the highest
-# note). You have access to the variables errors warning, statement which
-# respectively contain the number of errors / warnings messages and the total
-# number of statements analyzed. This is used by the global evaluation report
-# (RP0004).
-evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
-
-# Template used to display messages. This is a python new-style format string
-# used to format the message information. See doc for all details
-msg-template={msg_id}:{line:3d},{column:2d}: {msg} ({symbol})
-
-# Set the output format. Available formats are text, parseable, colorized, json
-# and msvs (visual studio).You can also give a reporter class, eg
-# mypackage.mymodule.MyReporterClass.
-output-format=text
-
-# Tells whether to display a full report or only the messages
-#reports=yes
-
-# Activate the evaluation score.
-score=yes
-
-
-[REFACTORING]
-
-# Maximum number of nested blocks for function / method body
-max-nested-blocks=5
-
-
-[BASIC]
-
-# Naming hint for argument names
-argument-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct argument names
-argument-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Naming hint for attribute names
-attr-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct attribute names
-attr-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Bad variable names which should always be refused, separated by a comma
-bad-names=foo,bar,baz,toto,tutu,tata
-
-# Naming hint for class attribute names
-class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
-
-# Regular expression matching correct class attribute names
-class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
-
-# Naming hint for class names
-class-name-hint=[A-Z_][a-zA-Z0-9]+$
-
-# Regular expression matching correct class names
-class-rgx=[A-Z_][a-zA-Z0-9]+$
-
-# Naming hint for constant names
-const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
-# Regular expression matching correct constant names
-const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
-# Minimum line length for functions/classes that require docstrings, shorter
-# ones are exempt.
-docstring-min-length=-1
-
-# Naming hint for function names
-function-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct function names
-function-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Good variable names which should always be accepted, separated by a comma
-good-names=i,j,k,ex,Run,_
-
-# Include a hint for the correct naming format with invalid-name
-include-naming-hint=no
-
-# Naming hint for inline iteration names
-inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
-
-# Regular expression matching correct inline iteration names
-inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
-
-# Naming hint for method names
-method-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct method names
-method-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Naming hint for module names
-module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
-# Regular expression matching correct module names
-module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
-# Colon-delimited sets of names that determine each other's naming style when
-# the name regexes allow several styles.
-name-group=
-
-# Regular expression which should only match function or class names that do
-# not require a docstring.
-no-docstring-rgx=^_
-
-# List of decorators that produce properties, such as abc.abstractproperty. Add
-# to this list to register other decorators that produce valid properties.
-property-classes=abc.abstractproperty
-
-# Naming hint for variable names
-variable-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-# Regular expression matching correct variable names
-variable-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
-
-[FORMAT]
-
-# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
-expected-line-ending-format=
-
-# Regexp for a line that is allowed to be longer than the limit.
-ignore-long-lines=^\s*(# )?<?https?://\S+>?$
-
-# Number of spaces of indent required inside a hanging  or continued line.
-indent-after-paren=4
-
-# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
-# tab).
-indent-string='    '
-
-# Maximum number of characters on a single line.
-max-line-length=100
-
-# Maximum number of lines in a module
-max-module-lines=1000
-
-# List of optional constructs for which whitespace checking is disabled. `dict-
-# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
-# `trailing-comma` allows a space between comma and closing bracket: (a, ).
-# `empty-line` allows space-only lines.
-no-space-check=trailing-comma,dict-separator
-
-# Allow the body of a class to be on the same line as the declaration if body
-# contains single statement.
-single-line-class-stmt=no
-
-# Allow the body of an if to be on the same line as the test if there is no
-# else.
-single-line-if-stmt=no
-
-
-[LOGGING]
-
-# Logging modules to check that the string format arguments are in logging
-# function parameter format
-logging-modules=logging
-
-
-[MISCELLANEOUS]
-
-# List of note tags to take in consideration, separated by a comma.
-notes=FIXME,XXX,TODO
-
-
-[SIMILARITIES]
-
-# Ignore comments when computing similarities.
-ignore-comments=yes
-
-# Ignore docstrings when computing similarities.
-ignore-docstrings=yes
-
-# Ignore imports when computing similarities.
-ignore-imports=no
-
-# Minimum lines number of a similarity.
-min-similarity-lines=4
-
-
-[SPELLING]
-
-# Spelling dictionary name. Available dictionaries: none. To make it working
-# install python-enchant package.
-spelling-dict=
-
-# List of comma separated words that should not be checked.
-spelling-ignore-words=
-
-# A path to a file that contains private dictionary; one word per line.
-spelling-private-dict-file=
-
-# Tells whether to store unknown words to indicated private dictionary in
-# --spelling-private-dict-file option instead of raising a message.
-spelling-store-unknown-words=no
-
-
-[TYPECHECK]
-
-# List of decorators that produce context managers, such as
-# contextlib.contextmanager. Add to this list to register other decorators that
-# produce valid context managers.
-contextmanager-decorators=contextlib.contextmanager
-
-# List of members which are set dynamically and missed by pylint inference
-# system, and so shouldn't trigger E1101 when accessed. Python regular
-# expressions are accepted.
-generated-members=
-
-# Tells whether missing members accessed in mixin class should be ignored. A
-# mixin class is detected if its name ends with "mixin" (case insensitive).
-ignore-mixin-members=yes
-
-# This flag controls whether pylint should warn about no-member and similar
-# checks whenever an opaque object is returned when inferring. The inference
-# can return multiple potential results while evaluating a Python object, but
-# some branches might not be evaluated, which results in partial inference. In
-# that case, it might be useful to still emit no-member and other checks for
-# the rest of the inferred objects.
-ignore-on-opaque-inference=yes
-
-# List of class names for which member attributes should not be checked (useful
-# for classes with dynamically set attributes). This supports the use of
-# qualified names.
-ignored-classes=optparse.Values,thread._local,_thread._local
-
-# List of module names for which member attributes should not be checked
-# (useful for modules/projects where namespaces are manipulated during runtime
-# and thus existing member attributes cannot be deduced by static analysis. It
-# supports qualified module names, as well as Unix pattern matching.
-ignored-modules=
-
-# Show a hint with possible names when a member name was not found. The aspect
-# of finding the hint is based on edit distance.
-missing-member-hint=yes
-
-# The minimum edit distance a name should have in order to be considered a
-# similar match for a missing member name.
-missing-member-hint-distance=1
-
-# The total number of similar names that should be taken in consideration when
-# showing a hint for a missing member.
-missing-member-max-choices=1
-
-
-[VARIABLES]
-
-# List of additional names supposed to be defined in builtins. Remember that
-# you should avoid to define new builtins when possible.
-additional-builtins=
-
-# Tells whether unused global variables should be treated as a violation.
-allow-global-unused-variables=yes
-
-# List of strings which can identify a callback function by name. A callback
-# name must start or end with one of those strings.
-callbacks=cb_,_cb
-
-# A regular expression matching the name of dummy variables (i.e. expectedly
-# not used).
-dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_
-
-# Argument names that match this expression will be ignored. Default to name
-# with leading underscore
-ignored-argument-names=_.*|^ignored_|^unused_
-
-# Tells whether we should check for unused import in __init__ files.
-init-import=no
-
-# List of qualified module names which can have objects that can redefine
-# builtins.
-redefining-builtins-modules=six.moves,future.builtins
-
-
-[CLASSES]
-
-# List of method names used to declare (i.e. assign) instance attributes.
-defining-attr-methods=__init__,__new__,setUp
-
-# List of member names, which should be excluded from the protected access
-# warning.
-exclude-protected=_asdict,_fields,_replace,_source,_make
-
-# List of valid names for the first argument in a class method.
-valid-classmethod-first-arg=cls
-
-# List of valid names for the first argument in a metaclass class method.
-valid-metaclass-classmethod-first-arg=mcs
-
-
-[DESIGN]
-
-# Maximum number of arguments for function / method
-max-args=5
-
-# Maximum number of attributes for a class (see R0902).
-max-attributes=7
-
-# Maximum number of boolean expressions in a if statement
-max-bool-expr=5
-
-# Maximum number of branch for function / method body
-max-branches=12
-
-# Maximum number of locals for function / method body
-max-locals=15
-
-# Maximum number of parents for a class (see R0901).
-max-parents=7
-
-# Maximum number of public methods for a class (see R0904).
-max-public-methods=20
-
-# Maximum number of return / yield for function / method body
-max-returns=6
-
-# Maximum number of statements in function / method body
-max-statements=50
-
-# Minimum number of public methods for a class (see R0903).
-min-public-methods=2
-
-
-[IMPORTS]
-
-# Allow wildcard imports from modules that define __all__.
-allow-wildcard-with-all=no
-
-# Analyse import fallback blocks. This can be used to support both Python 2 and
-# 3 compatible code, which means that the block might have code that exists
-# only in one or another interpreter, leading to false positives when analysed.
-analyse-fallback-blocks=no
-
-# Deprecated modules which should not be used, separated by a comma
-deprecated-modules=regsub,TERMIOS,Bastion,rexec
-
-# Create a graph of external dependencies in the given file (report RP0402 must
-# not be disabled)
-ext-import-graph=
-
-# Create a graph of every (i.e. internal and external) dependencies in the
-# given file (report RP0402 must not be disabled)
-import-graph=
-
-# Create a graph of internal dependencies in the given file (report RP0402 must
-# not be disabled)
-int-import-graph=
-
-# Force import order to recognize a module as part of the standard
-# compatibility libraries.
-known-standard-library=
-
-# Force import order to recognize a module as part of a third party library.
-known-third-party=enchant
-
-
-[EXCEPTIONS]
-
-# Exceptions that will emit a warning when being caught. Defaults to
-# "Exception"
-overgeneral-exceptions=Exception
diff --git a/manage_externals/test/Makefile b/manage_externals/test/Makefile
deleted file mode 100644
index 293e360757..0000000000
--- a/manage_externals/test/Makefile
+++ /dev/null
@@ -1,124 +0,0 @@
-python = not-set
-verbose = not-set
-debug = not-set
-
-ifneq ($(python), not-set)
-PYTHON=$(python)
-else
-PYTHON=python
-endif
-
-# we need the python path to point one level up to access the package
-# and executables
-PYPATH=PYTHONPATH=..:
-
-# common args for running tests
-TEST_ARGS=-m unittest discover
-
-ifeq ($(debug), not-set)
-    ifeq ($(verbose), not-set)
-        # summary only output
-        TEST_ARGS+=--buffer
-    else
-        # show individual test summary
-        TEST_ARGS+=--buffer --verbose
-    endif
-else
-    # show detailed test output
-    TEST_ARGS+=--verbose
-endif
-
-
-# auto reformat the code
-AUTOPEP8=autopep8
-AUTOPEP8_ARGS=--aggressive --in-place 
-
-# run lint
-PYLINT=pylint
-PYLINT_ARGS=-j 2 --rcfile=.pylint.rc
-
-# code coverage
-COVERAGE=coverage
-COVERAGE_ARGS=--rcfile=.coveragerc
-
-# source files
-SRC = \
-	../checkout_externals \
-	../manic/*.py
-
-CHECKOUT_EXE = ../checkout_externals
-
-TEST_DIR = .
-
-README = ../README.md
-
-#
-# testing
-#
-.PHONY : utest
-utest : FORCE
-	$(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_unit_*.py'
-
-.PHONY : stest
-stest : FORCE
-	$(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_sys_*.py'
-
-.PHONY : test
-test : utest stest
-
-#
-# documentation
-#
-.PHONY : readme
-readme : $(CHECKOUT_EXE)
-	printf "%s\n\n" "-- AUTOMATICALLY GENERATED FILE. DO NOT EDIT --" > $(README)
-	printf "%s" '[![Build Status](https://travis-ci.org/ESMCI/manage_externals.svg?branch=master)](https://travis-ci.org/ESMCI/manage_externals)' >> $(README)
-	printf "%s" '[![Coverage Status](https://coveralls.io/repos/github/ESMCI/manage_externals/badge.svg?branch=master)](https://coveralls.io/github/ESMCI/manage_externals?branch=master)' >> $(README)
-	printf "\n%s\n" '```' >> $(README)
-	$(CHECKOUT_EXE) --help >> $(README)
-
-#
-# coding standards
-#
-.PHONY : style
-style : FORCE
-	$(AUTOPEP8) $(AUTOPEP8_ARGS) --recursive $(SRC) $(TEST_DIR)/test_*.py
-
-.PHONY : lint
-lint : FORCE
-	$(PYLINT) $(PYLINT_ARGS) $(SRC) $(TEST_DIR)/test_*.py
-
-.PHONY : stylint
-stylint : style lint
-
-.PHONY : coverage
-# Need to use a single coverage run with a single pattern rather than
-# using two separate commands with separate patterns for test_unit_*.py
-# and test_sys_*.py: The latter clobbers some results from the first
-# run, even if we use the --append flag to 'coverage run'.
-coverage : FORCE
-	$(PYPATH) $(COVERAGE) erase
-	$(PYPATH) $(COVERAGE) run $(COVERAGE_ARGS) $(TEST_ARGS) --pattern 'test_*.py'
-	$(PYPATH) $(COVERAGE) html
-
-#
-# virtual environment creation
-#
-.PHONY : env
-env : FORCE
-	$(PYPATH) virtualenv --python $(PYTHON) $@_$(PYTHON)
-	. $@_$(PYTHON)/bin/activate; pip install -r requirements.txt
-
-#
-# utilites
-#
-.PHONY : clean
-clean : FORCE
-	-rm -rf *~ *.pyc tmp fake htmlcov
-
-.PHONY : clobber
-clobber : clean
-	-rm -rf env_*
-
-FORCE : 
-
diff --git a/manage_externals/test/README.md b/manage_externals/test/README.md
deleted file mode 100644
index 1e8f2eaa77..0000000000
--- a/manage_externals/test/README.md
+++ /dev/null
@@ -1,53 +0,0 @@
-# Testing for checkout_externals
-
-## Unit tests
-
-```SH
-    cd checkout_externals/test
-    make utest
-```
-
-## System tests
-
-```SH
-    cd checkout_externals/test
-    make stest
-```
-
-Example to run a single test:
-```SH
-    cd checkout_externals
-    python -m unittest test.test_sys_checkout.TestSysCheckout.test_container_simple_required
-```
-
-## Static analysis
-
-checkout_externals is difficult to test thoroughly because it relies
-on git and svn, and svn requires a live network connection and
-repository. Static analysis will help catch bugs in code paths that
-are not being executed, but it requires conforming to community
-standards and best practices. autopep8 and pylint should be run
-regularly for automatic code formatting and linting.
-
-```SH
-    cd checkout_externals/test
-    make lint
-```
-
-The canonical formatting for the code is whatever autopep8
-generates. All issues identified by pylint should be addressed.
-
-
-## Code coverage
-
-All changes to the code should include maintaining existing tests and
-writing new tests for new or changed functionality. To ensure test
-coverage, run the code coverage tool:
-
-```SH
-    cd checkout_externals/test
-    make coverage
-    open -a Firefox.app htmlcov/index.html
-```
-
-
diff --git a/manage_externals/test/doc/.gitignore b/manage_externals/test/doc/.gitignore
deleted file mode 100644
index d4e11e5ea0..0000000000
--- a/manage_externals/test/doc/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-_build
-
diff --git a/manage_externals/test/doc/Makefile b/manage_externals/test/doc/Makefile
deleted file mode 100644
index 18f4d5bf99..0000000000
--- a/manage_externals/test/doc/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = ManageExternals
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/manage_externals/test/doc/conf.py b/manage_externals/test/doc/conf.py
deleted file mode 100644
index 469c0b0dc5..0000000000
--- a/manage_externals/test/doc/conf.py
+++ /dev/null
@@ -1,172 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# Manage Externals documentation build configuration file, created by
-# sphinx-quickstart on Wed Nov 29 10:53:25 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'Manage Externals'
-copyright = u'2017, CSEG at NCAR'
-author = u'CSEG at NCAR'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = u'1.0.0'
-# The full version, including alpha/beta/rc tags.
-release = u'1.0.0'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'alabaster'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Custom sidebar templates, must be a dictionary that maps document names
-# to template names.
-#
-# This is required for the alabaster theme
-# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
-html_sidebars = {
-    '**': [
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-    ]
-}
-
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'ManageExternalsdoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, 'ManageExternals.tex', u'Manage Externals Documentation',
-     u'CSEG at NCAR', 'manual'),
-]
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'manageexternals', u'Manage Externals Documentation',
-     [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'ManageExternals', u'Manage Externals Documentation',
-     author, 'ManageExternals', 'One line description of project.',
-     'Miscellaneous'),
-]
-
-
-
diff --git a/manage_externals/test/doc/develop.rst b/manage_externals/test/doc/develop.rst
deleted file mode 100644
index b817b7b093..0000000000
--- a/manage_externals/test/doc/develop.rst
+++ /dev/null
@@ -1,202 +0,0 @@
-Developer Guidelines
-====================
-
-The manage externals utilities are a light weight replacement for svn
-externals that will work with git repositories pulling in a mixture of
-git and svn dependencies.
-
-Given an externals description and a working copy:
-
-* *checkout_externals* attempts to make the working copy agree with the
-  externals description
-
-* *generate_externals* attempts to make the externals description agree
-  with the working copy.
-
-For these operations utilities should:
-
-* operate consistently across git and svn
-
-* operate simply with minimal user complexity
-
-* robustly across a wide range of repository states
-
-* provide explicit error messages when a problem occurs
-
-* leave the working copy in a valid state
-  
-The utilities in manage externals are **NOT** generic wrappers around
-revision control operations or a replacement for common tasks. Users
-are expected to:
-
-* create branches prior to starting development
-  
-* add remotes and push changes
-
-* create tags
-  
-* delete branches
-
-These types of tasks are often highly workflow dependent, e.g. branch
-naming conventions may vary between repositories, have the potential
-to destroy user data, introduce significant code complexit and 'edge
-cases' that are extremely difficult to detect and test, and often
-require subtle decision making, especially if a problem occurs.
-
-Users who want to automate these types are encouraged to create their
-own tools. The externals description files are explicitly versioned
-and the internal APIs are intended to be stable for these purposes.
-
-Core Design Principles
------------------------
-
-1. Users can, and are actively encouraged to, modify the externals
-   directories using revision control outside of manage_externals
-   tools. You can't make any assumptions about the state of the
-   working copy. Examples: adding a remote, creating a branch,
-   switching to a branch, deleting the directory entirely.
-      
-2. Give that the user can do anything, the manage externals library
-   can not preserve state between calls. The only information it can
-   rely on is what it expectes based on the content of the externals
-   description file, and what the actual state of the directory tree
-   is.
-
-3. Do *not* do anything that will possibly destroy user data!
-
-   a. Do not remove files from the file system. We are operating on
-      user supplied input. If you don't call 'rm', you can't
-      accidentally remove the user's data. Thinking of calling
-      ``shutil.rmtree(user_input)``? What if the user accidentally
-      specified user_input such that it resolves to their home
-      directory.... Yeah. Don't go there.
-
-   b. Rely on git and svn to do their job as much as possible. Don't
-      duplicate functionality. Examples:
-
-      i. We require the working copies to be 'clean' as reported by
-         ``git status`` and ``svn status``. What if there are misc
-         editor files floating around that prevent an update? Use the
-         git and svn ignore functionality so they are not
-         reported. Don't try to remove them from manage_externals or
-         determine if they are 'safe' to ignore.
-
-      ii. Do not use '--force'. Ever. This is a sign you are doing
-          something dangerous, it may not be what the user
-          wants. Remember, they are encouraged to modify their repo.
-
-4. There are often multiple ways to obtain a particular piece of
-   information from git. Scraping screen output is brittle and
-   generally not considered a stable API across different versions of
-   git. Given a choice between:
-          
-    a. a lower level git 'plumbing' command that processes a
-       specific request and returns a sucess/failure status.
-
-    b. high level git command that produces a bunch of output
-       that must be processed.
-
-   We always prefer the former. It almost always involves
-   writing and maintaining less code and is more likely to be
-   stable.
-
-5. Backward compatibility is critical. We have *nested*
-   repositories. They are trivially easy to change versions. They may
-   have very different versions of the top level manage_externals. The
-   ability to read and work with old model description files is
-   critical to avoid problems for users. We also have automated tools
-   (testdb) that must generate and read external description
-   files. Backward compatibility will make staging changes vastly
-   simpler.
-   
-Model Users
------------
-
-Consider the needs of the following model userswhen developing manage_externals:
-
-* Users who will checkout the code once, and never change versions.
-
-* Users who will checkout the code once, then work for several years,
-  never updating. before trying to update or request integration.
-
-* Users develope code but do not use revision control beyond the
-  initial checkout. If they have modified or untracked files in the
-  repo, they may be irreplacable. Don't destroy user data.
-
-* Intermediate users who are working with multiple repos or branches
-  on a regular basis. They may only use manage_externals weekly or
-  monthly. Keep the user interface and documentation simple and
-  explicit. The more command line options they have to remember or
-  look up, the more frustrated they git.
-  
-* Software engineers who use the tools multiple times a day. It should
-  get out of their way.
-
-User Interface
---------------
-
-Basic operation for the most standard use cases should be kept as
-simple as possible. Many users will only rarely run the manage
-utilities. Even advanced users don't like reading a lot of help
-documentation or struggling to remember commands and piece together
-what they need to run. Having many command line options, even if not
-needed, is exteremly frustrating and overwhelming for most users. A few
-simple, explicitly named commands are better than a single command
-with many options.
-
-How will users get help if something goes wrong? This is a custom,
-one-off solution. Searching the internet for manage_externals, will
-only return the user doc for this project at best. There isn't likely
-to be a stackoverflow question or blog post where someone else already
-answered a user's question. And very few people outside this community
-will be able to provide help if something goes wrong. The sooner we
-kick users out of these utilities and into standard version control
-tools, the better off they are going to be if they run into a problem.
-  
-Repositories
-------------
-
-There are three basic types of repositories that must be considered:
-
-* container repositories - repositories that are always top level
-  repositories, and have a group of externals that must be managed.
-
-* simple repositories - repositories that are externals to another
-  repository, and do not have any of their own externals that will be
-  managed.
-
-* mixed use repositories - repositories that can act as a top level
-  container repository or as an external to a top level
-  container. They may also have their own sub-externals that are
-  required. They may have different externals needs depening on
-  whether they are top level or not.
-
-Repositories must be able to checkout and switch to both branches and
-tags.
-
-Development
-===========
-
-The functionality to manage externals is broken into a library of core
-functionality and applications built with the library.
-
-The core library is called 'manic', pseduo-homophone of (man)age
-(ex)ternals that is: short, pronounceable and spell-checkable. It is
-also no more or less meaningful to an unfamiliar user than a random
-jumble of letters forming an acronym.
-
-The core architecture of manic is:
-
-* externals description - an abstract description on an external,
-  including of how to obtain it, where to obtain it, where it goes in
-  the working tree.
-
-* externals - the software object representing an external.
-  
-* source trees - collection of externals
-  
-* repository wrappers - object oriented wrappers around repository
-  operations. So the higher level management of the soure tree and
-  external does not have to be concerned with how a particular
-  external is obtained and managed.
-  
diff --git a/manage_externals/test/doc/index.rst b/manage_externals/test/doc/index.rst
deleted file mode 100644
index 9ab287ad8c..0000000000
--- a/manage_externals/test/doc/index.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-.. Manage Externals documentation master file, created by
-   sphinx-quickstart on Wed Nov 29 10:53:25 2017.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to Manage Externals's documentation!
-============================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-
-   develop.rst
-   testing.rst
-   
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/manage_externals/test/doc/testing.rst b/manage_externals/test/doc/testing.rst
deleted file mode 100644
index 623f0e431c..0000000000
--- a/manage_externals/test/doc/testing.rst
+++ /dev/null
@@ -1,123 +0,0 @@
-Testing
-=======
-
-The manage_externals package has an automated test suite. All pull
-requests are expected to pass 100% of the automated tests, as well as
-be pep8 and lint 'clean' and maintain approximately constant (at a
-minimum) level of code coverage.
-
-Quick Start
------------
-
-Do nothing approach
-~~~~~~~~~~~~~~~~~~~
-
-When you create a pull request on GitHub, Travis-CI continuous
-integration testing will run the test suite in both python2 and
-python3. Test results, lint results, and code coverage results are
-available online.
-
-Do something approach
-~~~~~~~~~~~~~~~~~~~~~
-
-In the test directory, run:
-
-.. code-block:: shell
-
-    make env
-    make lint
-    make test
-    make coverage
-
- 
-Automated Testing
------------------
-
-The manage_externals manic library and executables are developed to be
-python2 and python3 compatible using only the standard library. The
-test suites meet the same requirements. But additional tools are
-required to provide lint and code coverage metrics and generate
-documentation. The requirements are maintained in the requirements.txt
-file, and can be automatically installed into an isolated environment
-via Makefile.
-
-Bootstrap requirements:
-
-* python2 - version 2.7.x or later
-
-* python3 - version 3.6 tested other versions may work
-
-* pip and virtualenv for python2 and python3
-
-Note: all make rules can be of the form ``make python=pythonX rule``
-or ``make rule`` depending if you want to use the default system
-python or specify a specific version.
-
-The Makefile in the test directory has the following rules:
-
-* ``make python=pythonX env`` - create a python virtual environment
-  for python2 or python3 and install all required packages. These
-  packages are required to run lint or coverage.
-
-* ``make style`` - runs autopep8
-
-* ``make lint`` - runs autopep8 and pylint
-
-* ``make test`` - run the full test suite
-
-* ``make utest`` - run jus the unit tests
-
-* ``make stest`` - run jus the system integration tests
-
-* ``make coverage`` - run the full test suite through the code
-  coverage tool and generate an html report.
-
-* ``make readme`` - automatically generate the README files.
-
-* ``make clean`` - remove editor and pyc files
-
-* ``make clobber`` - remove all generated test files, including
-  virtual environments, coverage reports, and temporary test
-  repository directories.
-
-Unit Tests
-----------
-
-Unit tests are probably not 'true unit tests' for the pedantic, but
-are pragmatic unit tests. They cover small practicle code blocks:
-functions, class methods, and groups of functions and class methods.
-
-System Integration Tests
-------------------------
-
-NOTE(bja, 2017-11) The systems integration tests currently do not include svn repositories.
-
-The manage_externals package is extremely tedious and error prone to test manually.
-
-Combinations that must be tested to ensure basic functionality are:
-
-* container repository pulling in simple externals
-
-* container repository pulling in mixed externals with sub-externals.
-
-* mixed repository acting as a container, pulling in simple externals and sub-externals
-
-Automatic system tests are handled the same way manual testing is done:
-
-* clone a test repository
-
-* create an externals description file for the test
-
-* run the executable with the desired args
-
-* check the results
-
-* potentially modify the repo (checkout a different branch)
-
-* rerun and test
-
-* etc
-
-The automated system stores small test repositories in the main repo
-by adding them as bare repositories. These repos are cloned via a
-subprocess call to git and manipulated during the tests. 
diff --git a/manage_externals/test/repos/README.md b/manage_externals/test/repos/README.md
deleted file mode 100644
index 026b684ea3..0000000000
--- a/manage_externals/test/repos/README.md
+++ /dev/null
@@ -1,33 +0,0 @@
-Git and svn repositories for testing git and svn-related behavior.  For usage and terminology notes, see test/test_sys_checkout.py.
-
-For git repos: To list files and view file contents at HEAD:
-```
-cd <repo_dir>
-git ls-tree --full-tree -r --name-only HEAD
-git cat-file -p HEAD:<filename>
-```
-
-File contents at a glance:
-```
-container.git/
-  readme.txt
-
-simple-ext.git/
-  (has branches: feature2, feature3)
-  (has tags: tag1, tag2)
-  readme.txt
-  simple_subdir/subdir_file.txt
-
-simple-ext-fork.git/
-  (has tags: abandoned-feature, forked-feature-v1, tag1)
-  (has branch: feature2)
-  readme.txt
-
-mixed-cont-ext.git/
-  (has branch: new-feature)
-  readme.txt
-  sub-externals.cfg ('simp_branch' section refers to 'feature2' branch in simple-ext.git/ repo)
-
-error/
-   (no git repo here, just a readme.txt in the clear)
-```
diff --git a/manage_externals/test/repos/container.git/HEAD b/manage_externals/test/repos/container.git/HEAD
deleted file mode 100644
index cb089cd89a..0000000000
--- a/manage_externals/test/repos/container.git/HEAD
+++ /dev/null
@@ -1 +0,0 @@
-ref: refs/heads/master
diff --git a/manage_externals/test/repos/container.git/config b/manage_externals/test/repos/container.git/config
deleted file mode 100644
index e6da231579..0000000000
--- a/manage_externals/test/repos/container.git/config
+++ /dev/null
@@ -1,6 +0,0 @@
-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = true
-	ignorecase = true
-	precomposeunicode = true
diff --git a/manage_externals/test/repos/container.git/description b/manage_externals/test/repos/container.git/description
deleted file mode 100644
index 498b267a8c..0000000000
--- a/manage_externals/test/repos/container.git/description
+++ /dev/null
@@ -1 +0,0 @@
-Unnamed repository; edit this file 'description' to name the repository.
diff --git a/manage_externals/test/repos/container.git/info/exclude b/manage_externals/test/repos/container.git/info/exclude
deleted file mode 100644
index a5196d1be8..0000000000
--- a/manage_externals/test/repos/container.git/info/exclude
+++ /dev/null
@@ -1,6 +0,0 @@
-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
-# *.[oa]
-# *~
diff --git a/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801 b/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801
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index f65234e17f32800b1be0aa9908cc706458b14605..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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GIT binary patch
literal 0
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diff --git a/manage_externals/test/repos/container.git/objects/f9/e08370a737e941de6f6492e3f427c2ef4c1a03 b/manage_externals/test/repos/container.git/objects/f9/e08370a737e941de6f6492e3f427c2ef4c1a03
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GIT binary patch
literal 0
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diff --git a/manage_externals/test/repos/container.git/refs/heads/master b/manage_externals/test/repos/container.git/refs/heads/master
deleted file mode 100644
index 3ae00f3af0..0000000000
--- a/manage_externals/test/repos/container.git/refs/heads/master
+++ /dev/null
@@ -1 +0,0 @@
-715b8f3e4afe1802a178e1d603af404ba45d59de
diff --git a/manage_externals/test/repos/error/readme.txt b/manage_externals/test/repos/error/readme.txt
deleted file mode 100644
index 6b5753377e..0000000000
--- a/manage_externals/test/repos/error/readme.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-Invalid or corrupted git repository (.git dir exists, but is empty) for error
-testing.
- 
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/HEAD b/manage_externals/test/repos/mixed-cont-ext.git/HEAD
deleted file mode 100644
index cb089cd89a..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/HEAD
+++ /dev/null
@@ -1 +0,0 @@
-ref: refs/heads/master
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/config b/manage_externals/test/repos/mixed-cont-ext.git/config
deleted file mode 100644
index e6da231579..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/config
+++ /dev/null
@@ -1,6 +0,0 @@
-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = true
-	ignorecase = true
-	precomposeunicode = true
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/description b/manage_externals/test/repos/mixed-cont-ext.git/description
deleted file mode 100644
index 498b267a8c..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/description
+++ /dev/null
@@ -1 +0,0 @@
-Unnamed repository; edit this file 'description' to name the repository.
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/info/exclude b/manage_externals/test/repos/mixed-cont-ext.git/info/exclude
deleted file mode 100644
index a5196d1be8..0000000000
--- a/manage_externals/test/repos/mixed-cont-ext.git/info/exclude
+++ /dev/null
@@ -1,6 +0,0 @@
-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
-# *.[oa]
-# *~
diff --git a/manage_externals/test/repos/mixed-cont-ext.git/objects/00/437ac2000d5f06fb8a572a01a5bbdae98b17cb b/manage_externals/test/repos/mixed-cont-ext.git/objects/00/437ac2000d5f06fb8a572a01a5bbdae98b17cb
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GIT binary patch
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diff --git a/manage_externals/test/repos/mixed-cont-ext.git/objects/14/368b701616a8c53820b610414a4b9a07540cf6 b/manage_externals/test/repos/mixed-cont-ext.git/objects/14/368b701616a8c53820b610414a4b9a07540cf6
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diff --git a/manage_externals/test/repos/mixed-cont-ext.git/objects/6f/c379457ecb4e576a13c7610ae1fa73f845ee6a b/manage_externals/test/repos/mixed-cont-ext.git/objects/6f/c379457ecb4e576a13c7610ae1fa73f845ee6a
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diff --git a/manage_externals/test/repos/mixed-cont-ext.git/objects/95/80ecc12f16334ce44e42287d5d46f927bb7b75 b/manage_externals/test/repos/mixed-cont-ext.git/objects/95/80ecc12f16334ce44e42287d5d46f927bb7b75
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diff --git a/manage_externals/test/repos/mixed-cont-ext.git/objects/a9/288dcd8a719a1f4ed3cba43a2a387ae7cd60fd b/manage_externals/test/repos/mixed-cont-ext.git/objects/a9/288dcd8a719a1f4ed3cba43a2a387ae7cd60fd
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diff --git a/manage_externals/test/repos/mixed-cont-ext.git/objects/fd/15a5ad5204356229c60a831d2a8120a43ac901 b/manage_externals/test/repos/mixed-cont-ext.git/objects/fd/15a5ad5204356229c60a831d2a8120a43ac901
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diff --git a/manage_externals/test/repos/mixed-cont-ext.git/refs/heads/master b/manage_externals/test/repos/mixed-cont-ext.git/refs/heads/master
deleted file mode 100644
index 1e0eef1ea3..0000000000
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deleted file mode 100644
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+++ /dev/null
@@ -1 +0,0 @@
-ref: refs/heads/master
diff --git a/manage_externals/test/repos/simple-ext-fork.git/config b/manage_externals/test/repos/simple-ext-fork.git/config
deleted file mode 100644
index 04eba17870..0000000000
--- a/manage_externals/test/repos/simple-ext-fork.git/config
+++ /dev/null
@@ -1,8 +0,0 @@
-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = true
-	ignorecase = true
-	precomposeunicode = true
-[remote "origin"]
-	url = /Users/andreb/projects/ncar/git-conversion/checkout-model-dev/cesm-demo-externals/manage_externals/test/repos/simple-ext.git
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deleted file mode 100644
index 498b267a8c..0000000000
--- a/manage_externals/test/repos/simple-ext-fork.git/description
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@@ -1 +0,0 @@
-Unnamed repository; edit this file 'description' to name the repository.
diff --git a/manage_externals/test/repos/simple-ext-fork.git/info/exclude b/manage_externals/test/repos/simple-ext-fork.git/info/exclude
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index a5196d1be8..0000000000
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@@ -1,6 +0,0 @@
-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
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-# pack-refs with: peeled fully-peeled sorted 
-36418b4e5665956a90725c9a1b5a8e551c5f3d48 refs/heads/feature2
-9b75494003deca69527bb64bcaa352e801611dd2 refs/heads/master
-11a76e3d9a67313dec7ce1230852ab5c86352c5c refs/tags/tag1
-^9b75494003deca69527bb64bcaa352e801611dd2
diff --git a/manage_externals/test/repos/simple-ext-fork.git/refs/heads/feature2 b/manage_externals/test/repos/simple-ext-fork.git/refs/heads/feature2
deleted file mode 100644
index d223b0362d..0000000000
--- a/manage_externals/test/repos/simple-ext-fork.git/refs/heads/feature2
+++ /dev/null
@@ -1 +0,0 @@
-f268d4e56d067da9bd1d85e55bdc40a8bd2b0bca
diff --git a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/abandoned-feature b/manage_externals/test/repos/simple-ext-fork.git/refs/tags/abandoned-feature
deleted file mode 100644
index 8a18bf08e9..0000000000
--- a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/abandoned-feature
+++ /dev/null
@@ -1 +0,0 @@
-a42fe9144f5707bc1e9515ce1b44681f7aba6f95
diff --git a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1 b/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1
deleted file mode 100644
index 2764b552d5..0000000000
--- a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1
+++ /dev/null
@@ -1 +0,0 @@
-8d2b3b35126224c975d23f109aa1e3cbac452989
diff --git a/manage_externals/test/repos/simple-ext.git/HEAD b/manage_externals/test/repos/simple-ext.git/HEAD
deleted file mode 100644
index cb089cd89a..0000000000
--- a/manage_externals/test/repos/simple-ext.git/HEAD
+++ /dev/null
@@ -1 +0,0 @@
-ref: refs/heads/master
diff --git a/manage_externals/test/repos/simple-ext.git/config b/manage_externals/test/repos/simple-ext.git/config
deleted file mode 100644
index e6da231579..0000000000
--- a/manage_externals/test/repos/simple-ext.git/config
+++ /dev/null
@@ -1,6 +0,0 @@
-[core]
-	repositoryformatversion = 0
-	filemode = true
-	bare = true
-	ignorecase = true
-	precomposeunicode = true
diff --git a/manage_externals/test/repos/simple-ext.git/description b/manage_externals/test/repos/simple-ext.git/description
deleted file mode 100644
index 498b267a8c..0000000000
--- a/manage_externals/test/repos/simple-ext.git/description
+++ /dev/null
@@ -1 +0,0 @@
-Unnamed repository; edit this file 'description' to name the repository.
diff --git a/manage_externals/test/repos/simple-ext.git/info/exclude b/manage_externals/test/repos/simple-ext.git/info/exclude
deleted file mode 100644
index a5196d1be8..0000000000
--- a/manage_externals/test/repos/simple-ext.git/info/exclude
+++ /dev/null
@@ -1,6 +0,0 @@
-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
-# *.[oa]
-# *~
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GIT binary patch
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GIT binary patch
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/heads/feature2 b/manage_externals/test/repos/simple-ext.git/refs/heads/feature2
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index dd24079fce..0000000000
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index adf1ccb002..0000000000
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/tags/tag1 b/manage_externals/test/repos/simple-ext.git/refs/tags/tag1
deleted file mode 100644
index ee595be8bd..0000000000
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diff --git a/manage_externals/test/repos/simple-ext.git/refs/tags/tag2 b/manage_externals/test/repos/simple-ext.git/refs/tags/tag2
deleted file mode 100644
index 4160b6c494..0000000000
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diff --git a/manage_externals/test/repos/simple-ext.svn/README.txt b/manage_externals/test/repos/simple-ext.svn/README.txt
deleted file mode 100644
index 9935818a1b..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/README.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a Subversion repository; use the 'svnadmin' and 'svnlook' 
-tools to examine it.  Do not add, delete, or modify files here 
-unless you know how to avoid corrupting the repository.
-
-Visit http://subversion.apache.org/ for more information.
diff --git a/manage_externals/test/repos/simple-ext.svn/conf/authz b/manage_externals/test/repos/simple-ext.svn/conf/authz
deleted file mode 100644
index 0b9a41074e..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/conf/authz
+++ /dev/null
@@ -1,32 +0,0 @@
-### This file is an example authorization file for svnserve.
-### Its format is identical to that of mod_authz_svn authorization
-### files.
-### As shown below each section defines authorizations for the path and
-### (optional) repository specified by the section name.
-### The authorizations follow. An authorization line can refer to:
-###  - a single user,
-###  - a group of users defined in a special [groups] section,
-###  - an alias defined in a special [aliases] section,
-###  - all authenticated users, using the '$authenticated' token,
-###  - only anonymous users, using the '$anonymous' token,
-###  - anyone, using the '*' wildcard.
-###
-### A match can be inverted by prefixing the rule with '~'. Rules can
-### grant read ('r') access, read-write ('rw') access, or no access
-### ('').
-
-[aliases]
-# joe = /C=XZ/ST=Dessert/L=Snake City/O=Snake Oil, Ltd./OU=Research Institute/CN=Joe Average
-
-[groups]
-# harry_and_sally = harry,sally
-# harry_sally_and_joe = harry,sally,&joe
-
-# [/foo/bar]
-# harry = rw
-# &joe = r
-# * =
-
-# [repository:/baz/fuz]
-# @harry_and_sally = rw
-# * = r
diff --git a/manage_externals/test/repos/simple-ext.svn/conf/hooks-env.tmpl b/manage_externals/test/repos/simple-ext.svn/conf/hooks-env.tmpl
deleted file mode 100644
index ee965c316c..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/conf/hooks-env.tmpl
+++ /dev/null
@@ -1,19 +0,0 @@
-### This file is an example hook script environment configuration file.
-### Hook scripts run in an empty environment by default.
-### As shown below each section defines environment variables for a
-### particular hook script. The [default] section defines environment
-### variables for all hook scripts, unless overridden by a hook-specific
-### section.
-
-### This example configures a UTF-8 locale for all hook scripts, so that 
-### special characters, such as umlauts, may be printed to stderr.
-### If UTF-8 is used with a mod_dav_svn server, the SVNUseUTF8 option must
-### also be set to 'yes' in httpd.conf.
-### With svnserve, the LANG environment variable of the svnserve process
-### must be set to the same value as given here.
-[default]
-LANG = en_US.UTF-8
-
-### This sets the PATH environment variable for the pre-commit hook.
-[pre-commit]
-PATH = /usr/local/bin:/usr/bin:/usr/sbin
diff --git a/manage_externals/test/repos/simple-ext.svn/conf/passwd b/manage_externals/test/repos/simple-ext.svn/conf/passwd
deleted file mode 100644
index ecaa08dcec..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/conf/passwd
+++ /dev/null
@@ -1,8 +0,0 @@
-### This file is an example password file for svnserve.
-### Its format is similar to that of svnserve.conf. As shown in the
-### example below it contains one section labelled [users].
-### The name and password for each user follow, one account per line.
-
-[users]
-# harry = harryssecret
-# sally = sallyssecret
diff --git a/manage_externals/test/repos/simple-ext.svn/conf/svnserve.conf b/manage_externals/test/repos/simple-ext.svn/conf/svnserve.conf
deleted file mode 100644
index 6cefc17b3e..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/conf/svnserve.conf
+++ /dev/null
@@ -1,81 +0,0 @@
-### This file controls the configuration of the svnserve daemon, if you
-### use it to allow access to this repository.  (If you only allow
-### access through http: and/or file: URLs, then this file is
-### irrelevant.)
-
-### Visit http://subversion.apache.org/ for more information.
-
-[general]
-### The anon-access and auth-access options control access to the
-### repository for unauthenticated (a.k.a. anonymous) users and
-### authenticated users, respectively.
-### Valid values are "write", "read", and "none".
-### Setting the value to "none" prohibits both reading and writing;
-### "read" allows read-only access, and "write" allows complete 
-### read/write access to the repository.
-### The sample settings below are the defaults and specify that anonymous
-### users have read-only access to the repository, while authenticated
-### users have read and write access to the repository.
-# anon-access = read
-# auth-access = write
-### The password-db option controls the location of the password
-### database file.  Unless you specify a path starting with a /,
-### the file's location is relative to the directory containing
-### this configuration file.
-### If SASL is enabled (see below), this file will NOT be used.
-### Uncomment the line below to use the default password file.
-# password-db = passwd
-### The authz-db option controls the location of the authorization
-### rules for path-based access control.  Unless you specify a path
-### starting with a /, the file's location is relative to the
-### directory containing this file.  The specified path may be a
-### repository relative URL (^/) or an absolute file:// URL to a text
-### file in a Subversion repository.  If you don't specify an authz-db,
-### no path-based access control is done.
-### Uncomment the line below to use the default authorization file.
-# authz-db = authz
-### The groups-db option controls the location of the file with the
-### group definitions and allows maintaining groups separately from the
-### authorization rules.  The groups-db file is of the same format as the
-### authz-db file and should contain a single [groups] section with the
-### group definitions.  If the option is enabled, the authz-db file cannot
-### contain a [groups] section.  Unless you specify a path starting with
-### a /, the file's location is relative to the directory containing this
-### file.  The specified path may be a repository relative URL (^/) or an
-### absolute file:// URL to a text file in a Subversion repository.
-### This option is not being used by default.
-# groups-db = groups
-### This option specifies the authentication realm of the repository.
-### If two repositories have the same authentication realm, they should
-### have the same password database, and vice versa.  The default realm
-### is repository's uuid.
-# realm = My First Repository
-### The force-username-case option causes svnserve to case-normalize
-### usernames before comparing them against the authorization rules in the
-### authz-db file configured above.  Valid values are "upper" (to upper-
-### case the usernames), "lower" (to lowercase the usernames), and
-### "none" (to compare usernames as-is without case conversion, which
-### is the default behavior).
-# force-username-case = none
-### The hooks-env options specifies a path to the hook script environment 
-### configuration file. This option overrides the per-repository default
-### and can be used to configure the hook script environment for multiple 
-### repositories in a single file, if an absolute path is specified.
-### Unless you specify an absolute path, the file's location is relative
-### to the directory containing this file.
-# hooks-env = hooks-env
-
-[sasl]
-### This option specifies whether you want to use the Cyrus SASL
-### library for authentication. Default is false.
-### Enabling this option requires svnserve to have been built with Cyrus
-### SASL support; to check, run 'svnserve --version' and look for a line
-### reading 'Cyrus SASL authentication is available.'
-# use-sasl = true
-### These options specify the desired strength of the security layer
-### that you want SASL to provide. 0 means no encryption, 1 means
-### integrity-checking only, values larger than 1 are correlated
-### to the effective key length for encryption (e.g. 128 means 128-bit
-### encryption). The values below are the defaults.
-# min-encryption = 0
-# max-encryption = 256
diff --git a/manage_externals/test/repos/simple-ext.svn/db/current b/manage_externals/test/repos/simple-ext.svn/db/current
deleted file mode 100644
index 00750edc07..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/current
+++ /dev/null
@@ -1 +0,0 @@
-3
diff --git a/manage_externals/test/repos/simple-ext.svn/db/format b/manage_externals/test/repos/simple-ext.svn/db/format
deleted file mode 100644
index 5dd0c22198..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/format
+++ /dev/null
@@ -1,3 +0,0 @@
-8
-layout sharded 1000
-addressing logical
diff --git a/manage_externals/test/repos/simple-ext.svn/db/fs-type b/manage_externals/test/repos/simple-ext.svn/db/fs-type
deleted file mode 100644
index 4fdd95313f..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/fs-type
+++ /dev/null
@@ -1 +0,0 @@
-fsfs
diff --git a/manage_externals/test/repos/simple-ext.svn/db/fsfs.conf b/manage_externals/test/repos/simple-ext.svn/db/fsfs.conf
deleted file mode 100644
index ac6877a727..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/fsfs.conf
+++ /dev/null
@@ -1,200 +0,0 @@
-### This file controls the configuration of the FSFS filesystem.
-
-[memcached-servers]
-### These options name memcached servers used to cache internal FSFS
-### data.  See http://www.danga.com/memcached/ for more information on
-### memcached.  To use memcached with FSFS, run one or more memcached
-### servers, and specify each of them as an option like so:
-# first-server = 127.0.0.1:11211
-# remote-memcached = mymemcached.corp.example.com:11212
-### The option name is ignored; the value is of the form HOST:PORT.
-### memcached servers can be shared between multiple repositories;
-### however, if you do this, you *must* ensure that repositories have
-### distinct UUIDs and paths, or else cached data from one repository
-### might be used by another accidentally.  Note also that memcached has
-### no authentication for reads or writes, so you must ensure that your
-### memcached servers are only accessible by trusted users.
-
-[caches]
-### When a cache-related error occurs, normally Subversion ignores it
-### and continues, logging an error if the server is appropriately
-### configured (and ignoring it with file:// access).  To make
-### Subversion never ignore cache errors, uncomment this line.
-# fail-stop = true
-
-[rep-sharing]
-### To conserve space, the filesystem can optionally avoid storing
-### duplicate representations.  This comes at a slight cost in
-### performance, as maintaining a database of shared representations can
-### increase commit times.  The space savings are dependent upon the size
-### of the repository, the number of objects it contains and the amount of
-### duplication between them, usually a function of the branching and
-### merging process.
-###
-### The following parameter enables rep-sharing in the repository.  It can
-### be switched on and off at will, but for best space-saving results
-### should be enabled consistently over the life of the repository.
-### 'svnadmin verify' will check the rep-cache regardless of this setting.
-### rep-sharing is enabled by default.
-# enable-rep-sharing = true
-
-[deltification]
-### To conserve space, the filesystem stores data as differences against
-### existing representations.  This comes at a slight cost in performance,
-### as calculating differences can increase commit times.  Reading data
-### will also create higher CPU load and the data will be fragmented.
-### Since deltification tends to save significant amounts of disk space,
-### the overall I/O load can actually be lower.
-###
-### The options in this section allow for tuning the deltification
-### strategy.  Their effects on data size and server performance may vary
-### from one repository to another.  Versions prior to 1.8 will ignore
-### this section.
-###
-### The following parameter enables deltification for directories. It can
-### be switched on and off at will, but for best space-saving results
-### should be enabled consistently over the lifetime of the repository.
-### Repositories containing large directories will benefit greatly.
-### In rarely accessed repositories, the I/O overhead may be significant
-### as caches will most likely be low.
-### directory deltification is enabled by default.
-# enable-dir-deltification = true
-###
-### The following parameter enables deltification for properties on files
-### and directories.  Overall, this is a minor tuning option but can save
-### some disk space if you merge frequently or frequently change node
-### properties.  You should not activate this if rep-sharing has been
-### disabled because this may result in a net increase in repository size.
-### property deltification is enabled by default.
-# enable-props-deltification = true
-###
-### During commit, the server may need to walk the whole change history of
-### of a given node to find a suitable deltification base.  This linear
-### process can impact commit times, svnadmin load and similar operations.
-### This setting limits the depth of the deltification history.  If the
-### threshold has been reached, the node will be stored as fulltext and a
-### new deltification history begins.
-### Note, this is unrelated to svn log.
-### Very large values rarely provide significant additional savings but
-### can impact performance greatly - in particular if directory
-### deltification has been activated.  Very small values may be useful in
-### repositories that are dominated by large, changing binaries.
-### Should be a power of two minus 1.  A value of 0 will effectively
-### disable deltification.
-### For 1.8, the default value is 1023; earlier versions have no limit.
-# max-deltification-walk = 1023
-###
-### The skip-delta scheme used by FSFS tends to repeatably store redundant
-### delta information where a simple delta against the latest version is
-### often smaller.  By default, 1.8+ will therefore use skip deltas only
-### after the linear chain of deltas has grown beyond the threshold
-### specified by this setting.
-### Values up to 64 can result in some reduction in repository size for
-### the cost of quickly increasing I/O and CPU costs. Similarly, smaller
-### numbers can reduce those costs at the cost of more disk space.  For
-### rarely read repositories or those containing larger binaries, this may
-### present a better trade-off.
-### Should be a power of two.  A value of 1 or smaller will cause the
-### exclusive use of skip-deltas (as in pre-1.8).
-### For 1.8, the default value is 16; earlier versions use 1.
-# max-linear-deltification = 16
-###
-### After deltification, we compress the data to minimize on-disk size.
-### This setting controls the compression algorithm, which will be used in
-### future revisions.  It can be used to either disable compression or to
-### select between available algorithms (zlib, lz4).  zlib is a general-
-### purpose compression algorithm.  lz4 is a fast compression algorithm
-### which should be preferred for repositories with large and, possibly,
-### incompressible files.  Note that the compression ratio of lz4 is
-### usually lower than the one provided by zlib, but using it can
-### significantly speed up commits as well as reading the data.
-### lz4 compression algorithm is supported, starting from format 8
-### repositories, available in Subversion 1.10 and higher.
-### The syntax of this option is:
-###   compression = none | lz4 | zlib | zlib-1 ... zlib-9
-### Versions prior to Subversion 1.10 will ignore this option.
-### The default value is 'lz4' if supported by the repository format and
-### 'zlib' otherwise.  'zlib' is currently equivalent to 'zlib-5'.
-# compression = lz4
-###
-### DEPRECATED: The new 'compression' option deprecates previously used
-### 'compression-level' option, which was used to configure zlib compression.
-### For compatibility with previous versions of Subversion, this option can
-### still be used (and it will result in zlib compression with the
-### corresponding compression level).
-###   compression-level = 0 ... 9 (default is 5)
-
-[packed-revprops]
-### This parameter controls the size (in kBytes) of packed revprop files.
-### Revprops of consecutive revisions will be concatenated into a single
-### file up to but not exceeding the threshold given here.  However, each
-### pack file may be much smaller and revprops of a single revision may be
-### much larger than the limit set here.  The threshold will be applied
-### before optional compression takes place.
-### Large values will reduce disk space usage at the expense of increased
-### latency and CPU usage reading and changing individual revprops.
-### Values smaller than 4 kByte will not improve latency any further and 
-### quickly render revprop packing ineffective.
-### revprop-pack-size is 16 kBytes by default for non-compressed revprop
-### pack files and 64 kBytes when compression has been enabled.
-# revprop-pack-size = 16
-###
-### To save disk space, packed revprop files may be compressed.  Standard
-### revprops tend to allow for very effective compression.  Reading and
-### even more so writing, become significantly more CPU intensive.
-### Compressing packed revprops is disabled by default.
-# compress-packed-revprops = false
-
-[io]
-### Parameters in this section control the data access granularity in
-### format 7 repositories and later.  The defaults should translate into
-### decent performance over a wide range of setups.
-###
-### When a specific piece of information needs to be read from disk,  a
-### data block is being read at once and its contents are being cached.
-### If the repository is being stored on a RAID, the block size should be
-### either 50% or 100% of RAID block size / granularity.  Also, your file
-### system blocks/clusters should be properly aligned and sized.  In that
-### setup, each access will hit only one disk (minimizes I/O load) but
-### uses all the data provided by the disk in a single access.
-### For SSD-based storage systems, slightly lower values around 16 kB
-### may improve latency while still maximizing throughput.  If block-read
-### has not been enabled, this will be capped to 4 kBytes.
-### Can be changed at any time but must be a power of 2.
-### block-size is given in kBytes and with a default of 64 kBytes.
-# block-size = 64
-###
-### The log-to-phys index maps data item numbers to offsets within the
-### rev or pack file.  This index is organized in pages of a fixed maximum
-### capacity.  To access an item, the page table and the respective page
-### must be read.
-### This parameter only affects revisions with thousands of changed paths.
-### If you have several extremely large revisions (~1 mio changes), think
-### about increasing this setting.  Reducing the value will rarely result
-### in a net speedup.
-### This is an expert setting.  Must be a power of 2.
-### l2p-page-size is 8192 entries by default.
-# l2p-page-size = 8192
-###
-### The phys-to-log index maps positions within the rev or pack file to
-### to data items,  i.e. describes what piece of information is being
-### stored at any particular offset.  The index describes the rev file
-### in chunks (pages) and keeps a global list of all those pages.  Large
-### pages mean a shorter page table but a larger per-page description of
-### data items in it.  The latency sweetspot depends on the change size
-### distribution but covers a relatively wide range.
-### If the repository contains very large files,  i.e. individual changes
-### of tens of MB each,  increasing the page size will shorten the index
-### file at the expense of a slightly increased latency in sections with
-### smaller changes.
-### For source code repositories, this should be about 16x the block-size.
-### Must be a power of 2.
-### p2l-page-size is given in kBytes and with a default of 1024 kBytes.
-# p2l-page-size = 1024
-
-[debug]
-###
-### Whether to verify each new revision immediately before finalizing
-### the commit.  This is disabled by default except in maintainer-mode
-### builds.
-# verify-before-commit = false
diff --git a/manage_externals/test/repos/simple-ext.svn/db/min-unpacked-rev b/manage_externals/test/repos/simple-ext.svn/db/min-unpacked-rev
deleted file mode 100644
index 573541ac97..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/min-unpacked-rev
+++ /dev/null
@@ -1 +0,0 @@
-0
diff --git a/manage_externals/test/repos/simple-ext.svn/db/rep-cache.db b/manage_externals/test/repos/simple-ext.svn/db/rep-cache.db
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diff --git a/manage_externals/test/repos/simple-ext.svn/db/rep-cache.db-journal b/manage_externals/test/repos/simple-ext.svn/db/rep-cache.db-journal
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diff --git a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/0 b/manage_externals/test/repos/simple-ext.svn/db/revprops/0/0
deleted file mode 100644
index 92768005d3..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/0
+++ /dev/null
@@ -1,5 +0,0 @@
-K 8
-svn:date
-V 27
-2023-11-16T20:11:46.318861Z
-END
diff --git a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/1 b/manage_externals/test/repos/simple-ext.svn/db/revprops/0/1
deleted file mode 100644
index aa95a9de9f..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/1
+++ /dev/null
@@ -1,13 +0,0 @@
-K 10
-svn:author
-V 5
-sacks
-K 8
-svn:date
-V 27
-2023-11-16T20:15:56.917904Z
-K 7
-svn:log
-V 30
-Setting up directory structure
-END
diff --git a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/2 b/manage_externals/test/repos/simple-ext.svn/db/revprops/0/2
deleted file mode 100644
index 3d04d8909a..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/2
+++ /dev/null
@@ -1,13 +0,0 @@
-K 10
-svn:author
-V 5
-sacks
-K 8
-svn:date
-V 27
-2023-11-16T20:27:31.407916Z
-K 7
-svn:log
-V 10
-Add README
-END
diff --git a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/3 b/manage_externals/test/repos/simple-ext.svn/db/revprops/0/3
deleted file mode 100644
index de20268415..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/revprops/0/3
+++ /dev/null
@@ -1,13 +0,0 @@
-K 10
-svn:author
-V 5
-sacks
-K 8
-svn:date
-V 27
-2023-11-16T21:14:43.366717Z
-K 7
-svn:log
-V 27
-Creating cesm2.0.beta07 tag
-END
diff --git a/manage_externals/test/repos/simple-ext.svn/db/revs/0/0 b/manage_externals/test/repos/simple-ext.svn/db/revs/0/0
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diff --git a/manage_externals/test/repos/simple-ext.svn/db/revs/0/3 b/manage_externals/test/repos/simple-ext.svn/db/revs/0/3
deleted file mode 100644
index f437a6d530890a7f7e200288d222e3c01e398c87..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/manage_externals/test/repos/simple-ext.svn/db/txn-current b/manage_externals/test/repos/simple-ext.svn/db/txn-current
deleted file mode 100644
index 00750edc07..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/txn-current
+++ /dev/null
@@ -1 +0,0 @@
-3
diff --git a/manage_externals/test/repos/simple-ext.svn/db/txn-current-lock b/manage_externals/test/repos/simple-ext.svn/db/txn-current-lock
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/manage_externals/test/repos/simple-ext.svn/db/uuid b/manage_externals/test/repos/simple-ext.svn/db/uuid
deleted file mode 100644
index 0b16502652..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/db/uuid
+++ /dev/null
@@ -1,2 +0,0 @@
-1c80dd47-0c07-4207-8ee0-e60dd9d98853
-31d57ab1-759c-4129-a63d-898c774d96c9
diff --git a/manage_externals/test/repos/simple-ext.svn/db/write-lock b/manage_externals/test/repos/simple-ext.svn/db/write-lock
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/manage_externals/test/repos/simple-ext.svn/format b/manage_externals/test/repos/simple-ext.svn/format
deleted file mode 100644
index 7ed6ff82de..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/format
+++ /dev/null
@@ -1 +0,0 @@
-5
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/post-commit.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/post-commit.tmpl
deleted file mode 100755
index 988f041fa5..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/post-commit.tmpl
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/bin/sh
-
-# POST-COMMIT HOOK
-#
-# The post-commit hook is invoked after a commit.  Subversion runs
-# this hook by invoking a program (script, executable, binary, etc.)
-# named 'post-commit' (for which this file is a template) with the 
-# following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] REV          (the number of the revision just committed)
-#   [3] TXN-NAME     (the name of the transaction that has become REV)
-#
-# Because the commit has already completed and cannot be undone,
-# the exit code of the hook program is ignored.  The hook program
-# can use the 'svnlook' utility to help it examine the
-# newly-committed tree.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'post-commit'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'post-commit' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'post-commit.bat' or 'post-commit.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-REV="$2"
-TXN_NAME="$3"
-
-mailer.py commit "$REPOS" "$REV" /path/to/mailer.conf
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/post-lock.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/post-lock.tmpl
deleted file mode 100755
index 96f2165209..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/post-lock.tmpl
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/bin/sh
-
-# POST-LOCK HOOK
-#
-# The post-lock hook is run after a path is locked.  Subversion runs
-# this hook by invoking a program (script, executable, binary, etc.)
-# named 'post-lock' (for which this file is a template) with the 
-# following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] USER         (the user who created the lock)
-#
-# The paths that were just locked are passed to the hook via STDIN.
-#
-# Because the locks have already been created and cannot be undone,
-# the exit code of the hook program is ignored.  The hook program
-# can use the 'svnlook' utility to examine the paths in the repository
-# but since the hook is invoked asynchronously the newly-created locks
-# may no longer be present.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'post-lock'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'post-lock' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'post-lock.bat' or 'post-lock.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-USER="$2"
-
-# Send email to interested parties, let them know a lock was created:
-mailer.py lock "$REPOS" "$USER" /path/to/mailer.conf
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/post-revprop-change.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/post-revprop-change.tmpl
deleted file mode 100755
index de1b914648..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/post-revprop-change.tmpl
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/bin/sh
-
-# POST-REVPROP-CHANGE HOOK
-#
-# The post-revprop-change hook is invoked after a revision property
-# has been added, modified or deleted.  Subversion runs this hook by
-# invoking a program (script, executable, binary, etc.) named
-# 'post-revprop-change' (for which this file is a template), with the
-# following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] REV          (the revision that was tweaked)
-#   [3] USER         (the username of the person tweaking the property)
-#   [4] PROPNAME     (the property that was changed)
-#   [5] ACTION       (the property was 'A'dded, 'M'odified, or 'D'eleted)
-#
-#   [STDIN] PROPVAL  ** the old property value is passed via STDIN.
-#
-# Because the propchange has already completed and cannot be undone,
-# the exit code of the hook program is ignored.  The hook program
-# can use the 'svnlook' utility to help it examine the
-# new property value.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'post-revprop-change'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'post-revprop-change' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'post-revprop-change.bat' or 'post-revprop-change.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-REV="$2"
-USER="$3"
-PROPNAME="$4"
-ACTION="$5"
-
-mailer.py propchange2 "$REPOS" "$REV" "$USER" "$PROPNAME" "$ACTION" /path/to/mailer.conf
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/post-unlock.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/post-unlock.tmpl
deleted file mode 100755
index e33f793c25..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/post-unlock.tmpl
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/bin/sh
-
-# POST-UNLOCK HOOK
-#
-# The post-unlock hook runs after a path is unlocked.  Subversion runs
-# this hook by invoking a program (script, executable, binary, etc.)
-# named 'post-unlock' (for which this file is a template) with the 
-# following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] USER         (the user who destroyed the lock)
-#
-# The paths that were just unlocked are passed to the hook via STDIN.
-#
-# Because the lock has already been destroyed and cannot be undone,
-# the exit code of the hook program is ignored.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'post-unlock'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'post-unlock' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'post-unlock.bat' or 'post-unlock.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-USER="$2"
-
-# Send email to interested parties, let them know a lock was removed:
-mailer.py unlock "$REPOS" "$USER" /path/to/mailer.conf
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/pre-commit.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/pre-commit.tmpl
deleted file mode 100755
index 626e72300c..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/pre-commit.tmpl
+++ /dev/null
@@ -1,91 +0,0 @@
-#!/bin/sh
-
-# PRE-COMMIT HOOK
-#
-# The pre-commit hook is invoked before a Subversion txn is
-# committed.  Subversion runs this hook by invoking a program
-# (script, executable, binary, etc.) named 'pre-commit' (for which
-# this file is a template), with the following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] TXN-NAME     (the name of the txn about to be committed)
-#
-#   [STDIN] LOCK-TOKENS ** the lock tokens are passed via STDIN.
-#
-#   If STDIN contains the line "LOCK-TOKENS:\n" (the "\n" denotes a
-#   single newline), the lines following it are the lock tokens for
-#   this commit.  The end of the list is marked by a line containing
-#   only a newline character.
-#
-#   Each lock token line consists of a URI-escaped path, followed
-#   by the separator character '|', followed by the lock token string,
-#   followed by a newline.
-#
-# If the hook program exits with success, the txn is committed; but
-# if it exits with failure (non-zero), the txn is aborted, no commit
-# takes place, and STDERR is returned to the client.   The hook
-# program can use the 'svnlook' utility to help it examine the txn.
-#
-#   ***  NOTE: THE HOOK PROGRAM MUST NOT MODIFY THE TXN, EXCEPT  ***
-#   ***  FOR REVISION PROPERTIES (like svn:log or svn:author).   ***
-#
-#   This is why we recommend using the read-only 'svnlook' utility.
-#   In the future, Subversion may enforce the rule that pre-commit
-#   hooks should not modify the versioned data in txns, or else come
-#   up with a mechanism to make it safe to do so (by informing the
-#   committing client of the changes).  However, right now neither
-#   mechanism is implemented, so hook writers just have to be careful.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'pre-commit'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'pre-commit' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'pre-commit.bat' or 'pre-commit.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-TXN="$2"
-
-# Make sure that the log message contains some text.
-SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook
-$SVNLOOK log -t "$TXN" "$REPOS" | \
-   grep "[a-zA-Z0-9]" > /dev/null || exit 1
-
-# Check that the author of this commit has the rights to perform
-# the commit on the files and directories being modified.
-commit-access-control.pl "$REPOS" "$TXN" commit-access-control.cfg || exit 1
-
-# All checks passed, so allow the commit.
-exit 0
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/pre-lock.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/pre-lock.tmpl
deleted file mode 100755
index 148582a689..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/pre-lock.tmpl
+++ /dev/null
@@ -1,95 +0,0 @@
-#!/bin/sh
-
-# PRE-LOCK HOOK
-#
-# The pre-lock hook is invoked before an exclusive lock is
-# created.  Subversion runs this hook by invoking a program 
-# (script, executable, binary, etc.) named 'pre-lock' (for which
-# this file is a template), with the following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] PATH         (the path in the repository about to be locked)
-#   [3] USER         (the user creating the lock)
-#   [4] COMMENT      (the comment of the lock)
-#   [5] STEAL-LOCK   (1 if the user is trying to steal the lock, else 0)
-#
-# If the hook program outputs anything on stdout, the output string will
-# be used as the lock token for this lock operation.  If you choose to use
-# this feature, you must guarantee the tokens generated are unique across
-# the repository each time.
-#
-# If the hook program exits with success, the lock is created; but
-# if it exits with failure (non-zero), the lock action is aborted
-# and STDERR is returned to the client.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'pre-lock'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'pre-lock' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'pre-lock.bat' or 'pre-lock.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-PATH="$2"
-USER="$3"
-COMMENT="$4"
-STEAL="$5"
-
-# If a lock exists and is owned by a different person, don't allow it
-# to be stolen (e.g., with 'svn lock --force ...').
-
-# (Maybe this script could send email to the lock owner?)
-SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook
-GREP=/bin/grep
-SED=/bin/sed
-
-LOCK_OWNER=`$SVNLOOK lock "$REPOS" "$PATH" | \
-            $GREP '^Owner: ' | $SED 's/Owner: //'`
-
-# If we get no result from svnlook, there's no lock, allow the lock to
-# happen:
-if [ "$LOCK_OWNER" = "" ]; then
-  exit 0
-fi
-
-# If the person locking matches the lock's owner, allow the lock to
-# happen:
-if [ "$LOCK_OWNER" = "$USER" ]; then
-  exit 0
-fi
-
-# Otherwise, we've got an owner mismatch, so return failure:
-echo "Error: $PATH already locked by ${LOCK_OWNER}." 1>&2
-exit 1
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl
deleted file mode 100755
index 8b065d7c79..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/bin/sh
-
-# PRE-REVPROP-CHANGE HOOK
-#
-# The pre-revprop-change hook is invoked before a revision property
-# is added, modified or deleted.  Subversion runs this hook by invoking
-# a program (script, executable, binary, etc.) named 'pre-revprop-change'
-# (for which this file is a template), with the following ordered
-# arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] REV          (the revision being tweaked)
-#   [3] USER         (the username of the person tweaking the property)
-#   [4] PROPNAME     (the property being set on the revision)
-#   [5] ACTION       (the property is being 'A'dded, 'M'odified, or 'D'eleted)
-#
-#   [STDIN] PROPVAL  ** the new property value is passed via STDIN.
-#
-# If the hook program exits with success, the propchange happens; but
-# if it exits with failure (non-zero), the propchange doesn't happen.
-# The hook program can use the 'svnlook' utility to examine the 
-# existing value of the revision property.
-#
-# WARNING: unlike other hooks, this hook MUST exist for revision
-# properties to be changed.  If the hook does not exist, Subversion 
-# will behave as if the hook were present, but failed.  The reason
-# for this is that revision properties are UNVERSIONED, meaning that
-# a successful propchange is destructive;  the old value is gone
-# forever.  We recommend the hook back up the old value somewhere.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'pre-revprop-change'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'pre-revprop-change' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'pre-revprop-change.bat' or 'pre-revprop-change.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-REV="$2"
-USER="$3"
-PROPNAME="$4"
-ACTION="$5"
-
-if [ "$ACTION" = "M" -a "$PROPNAME" = "svn:log" ]; then exit 0; fi
-
-echo "Changing revision properties other than svn:log is prohibited" >&2
-exit 1
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl
deleted file mode 100755
index 9ba99d071b..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/bin/sh
-
-# PRE-UNLOCK HOOK
-#
-# The pre-unlock hook is invoked before an exclusive lock is
-# destroyed.  Subversion runs this hook by invoking a program 
-# (script, executable, binary, etc.) named 'pre-unlock' (for which
-# this file is a template), with the following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] PATH         (the path in the repository about to be unlocked)
-#   [3] USER         (the user destroying the lock)
-#   [4] TOKEN        (the lock token to be destroyed)
-#   [5] BREAK-UNLOCK (1 if the user is breaking the lock, else 0)
-#
-# If the hook program exits with success, the lock is destroyed; but
-# if it exits with failure (non-zero), the unlock action is aborted
-# and STDERR is returned to the client.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'pre-unlock'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'pre-unlock' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'pre-unlock.bat' or 'pre-unlock.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-PATH="$2"
-USER="$3"
-TOKEN="$4"
-BREAK="$5"
-
-# If a lock is owned by a different person, don't allow it be broken.
-# (Maybe this script could send email to the lock owner?)
-
-SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook
-GREP=/bin/grep
-SED=/bin/sed
-
-LOCK_OWNER=`$SVNLOOK lock "$REPOS" "$PATH" | \
-            $GREP '^Owner: ' | $SED 's/Owner: //'`
-
-# If we get no result from svnlook, there's no lock, return success:
-if [ "$LOCK_OWNER" = "" ]; then
-  exit 0
-fi
-
-# If the person unlocking matches the lock's owner, return success:
-if [ "$LOCK_OWNER" = "$USER" ]; then
-  exit 0
-fi
-
-# Otherwise, we've got an owner mismatch, so return failure:
-echo "Error: $PATH locked by ${LOCK_OWNER}." 1>&2
-exit 1
diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/start-commit.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/start-commit.tmpl
deleted file mode 100755
index 1395e8315a..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/hooks/start-commit.tmpl
+++ /dev/null
@@ -1,81 +0,0 @@
-#!/bin/sh
-
-# START-COMMIT HOOK
-#
-# The start-commit hook is invoked immediately after a Subversion txn is
-# created and populated with initial revprops in the process of doing a
-# commit. Subversion runs this hook by invoking a program (script, 
-# executable, binary, etc.) named 'start-commit' (for which this file
-# is a template) with the following ordered arguments:
-#
-#   [1] REPOS-PATH   (the path to this repository)
-#   [2] USER         (the authenticated user attempting to commit)
-#   [3] CAPABILITIES (a colon-separated list of capabilities reported
-#                     by the client; see note below)
-#   [4] TXN-NAME     (the name of the commit txn just created)
-#
-# Note: The CAPABILITIES parameter is new in Subversion 1.5, and 1.5
-# clients will typically report at least the "mergeinfo" capability.
-# If there are other capabilities, then the list is colon-separated,
-# e.g.: "mergeinfo:some-other-capability" (the order is undefined).
-#
-# The list is self-reported by the client.  Therefore, you should not
-# make security assumptions based on the capabilities list, nor should
-# you assume that clients reliably report every capability they have.
-#
-# Note: The TXN-NAME parameter is new in Subversion 1.8.  Prior to version
-# 1.8, the start-commit hook was invoked before the commit txn was even
-# created, so the ability to inspect the commit txn and its metadata from
-# within the start-commit hook was not possible.
-# 
-# If the hook program exits with success, the commit continues; but
-# if it exits with failure (non-zero), the commit is stopped before
-# a Subversion txn is created, and STDERR is returned to the client.
-#
-# The default working directory for the invocation is undefined, so
-# the program should set one explicitly if it cares.
-#
-# On a Unix system, the normal procedure is to have 'start-commit'
-# invoke other programs to do the real work, though it may do the
-# work itself too.
-#
-# Note that 'start-commit' must be executable by the user(s) who will
-# invoke it (typically the user httpd runs as), and that user must
-# have filesystem-level permission to access the repository.
-#
-# On a Windows system, you should name the hook program
-# 'start-commit.bat' or 'start-commit.exe',
-# but the basic idea is the same.
-#
-# The hook program runs in an empty environment, unless the server is
-# explicitly configured otherwise.  For example, a common problem is for
-# the PATH environment variable to not be set to its usual value, so
-# that subprograms fail to launch unless invoked via absolute path.
-# If you're having unexpected problems with a hook program, the
-# culprit may be unusual (or missing) environment variables.
-#
-# CAUTION:
-# For security reasons, you MUST always properly quote arguments when
-# you use them, as those arguments could contain whitespace or other
-# problematic characters. Additionally, you should delimit the list
-# of options with "--" before passing the arguments, so malicious
-# clients cannot bootleg unexpected options to the commands your
-# script aims to execute.
-# For similar reasons, you should also add a trailing @ to URLs which
-# are passed to SVN commands accepting URLs with peg revisions.
-#
-# Here is an example hook script, for a Unix /bin/sh interpreter.
-# For more examples and pre-written hooks, see those in
-# the Subversion repository at
-# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and
-# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/
-
-
-REPOS="$1"
-USER="$2"
-
-commit-allower.pl --repository "$REPOS" --user "$USER" || exit 1
-special-auth-check.py --user "$USER" --auth-level 3 || exit 1
-
-# All checks passed, so allow the commit.
-exit 0
diff --git a/manage_externals/test/repos/simple-ext.svn/locks/db-logs.lock b/manage_externals/test/repos/simple-ext.svn/locks/db-logs.lock
deleted file mode 100644
index 20dd6369be..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/locks/db-logs.lock
+++ /dev/null
@@ -1,3 +0,0 @@
-This file is not used by Subversion 1.3.x or later.
-However, its existence is required for compatibility with
-Subversion 1.2.x or earlier.
diff --git a/manage_externals/test/repos/simple-ext.svn/locks/db.lock b/manage_externals/test/repos/simple-ext.svn/locks/db.lock
deleted file mode 100644
index 20dd6369be..0000000000
--- a/manage_externals/test/repos/simple-ext.svn/locks/db.lock
+++ /dev/null
@@ -1,3 +0,0 @@
-This file is not used by Subversion 1.3.x or later.
-However, its existence is required for compatibility with
-Subversion 1.2.x or earlier.
diff --git a/manage_externals/test/requirements.txt b/manage_externals/test/requirements.txt
deleted file mode 100644
index d66f6f1e67..0000000000
--- a/manage_externals/test/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-pylint>=1.7.0
-autopep8>=1.3.0
-coverage>=4.4.0
-coveralls>=1.2.0
-sphinx>=1.6.0
diff --git a/manage_externals/test/test_sys_checkout.py b/manage_externals/test/test_sys_checkout.py
deleted file mode 100755
index 664160dc99..0000000000
--- a/manage_externals/test/test_sys_checkout.py
+++ /dev/null
@@ -1,1871 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Terminology: 
-  * 'container': a repo that has externals
-  * 'simple': a repo that has no externals, but is referenced as an external by another repo.
-  * 'mixed': a repo that both has externals and is referenced as an external by another repo.
-
-  * 'clean': the local repo matches the version in the externals and has no local modifications.
-  * 'empty': the external isn't checked out at all.
-
-Note: this script assume the path to the manic and
-checkout_externals module is already in the python path. This is
-usually handled by the makefile. If you call it directly, you may need
-to adjust your path.
-
-NOTE(bja, 2017-11) If a test fails, we want to keep the repo for that
-test. But the tests will keep running, so we need a unique name. Also,
-tearDown is always called after each test. I haven't figured out how
-to determine if an assertion failed and whether it is safe to clean up
-the test repos.
-
-So the solution is:
-
-* assign a unique id to each test repo.
-
-* never cleanup during the run.
-
-* Erase any existing repos at the begining of the module in
-setUpModule.
-"""
-
-# NOTE(bja, 2017-11) pylint complains that the module is too big, but
-# I'm still working on how to break up the tests and still have the
-# temporary directory be preserved....
-# pylint: disable=too-many-lines
-
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import logging
-import os
-import os.path
-import shutil
-import unittest
-
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import DESCRIPTION_SECTION, VERSION_ITEM
-from manic.externals_description import git_submodule_status
-from manic.externals_status import ExternalStatus
-from manic.repository_git import GitRepository
-from manic.utils import printlog, execute_subprocess
-from manic.global_constants import LOCAL_PATH_INDICATOR, VERBOSITY_DEFAULT
-from manic.global_constants import LOG_FILE_NAME
-from manic import checkout
-
-# ConfigParser was renamed in python2 to configparser. In python2,
-# ConfigParser returns byte strings, str, instead of unicode. We need
-# unicode to be compatible with xml and json parser and python3.
-try:
-    # python2
-    from ConfigParser import SafeConfigParser as config_parser
-except ImportError:
-    # python3
-    from configparser import ConfigParser as config_parser
-
-# ---------------------------------------------------------------------
-#
-# Global constants
-#
-# ---------------------------------------------------------------------
-
-
-# Module-wide root directory for all the per-test subdirs we'll create on
-# the fly (which are placed under wherever $CWD is when the test runs).
-# Set by setupModule().
-module_tmp_root_dir = None
-TMP_REPO_DIR_NAME = 'tmp'  # subdir under $CWD
-
-# subdir under test/ that holds all of our checked-in repositories (which we
-# will clone for these tests).
-BARE_REPO_ROOT_NAME = 'repos'
-
-# Environment var referenced by checked-in externals file in mixed-cont-ext.git,
-# which should be pointed to the fully-resolved BARE_REPO_ROOT_NAME directory.
-# We explicitly clear this after every test, via tearDown().
-MIXED_CONT_EXT_ROOT_ENV_VAR = 'MANIC_TEST_BARE_REPO_ROOT'
-
-# Subdirs under bare repo root, each holding a repository. For more info
-# on the contents of these repositories, see test/repos/README.md. In these
-# tests the 'parent' repos are cloned as a starting point, whereas the 'child'
-# repos are checked out when the tests run checkout_externals.
-CONTAINER_REPO = 'container.git'     # Parent repo
-SIMPLE_REPO = 'simple-ext.git'       # Child repo
-SIMPLE_FORK_REPO = 'simple-ext-fork.git'  # Child repo
-MIXED_REPO = 'mixed-cont-ext.git'    # Both parent and child
-SVN_TEST_REPO = 'simple-ext.svn'     # Subversion repository
-
-# Standard (arbitrary) external names for test configs
-TAG_SECTION = 'simp_tag'
-BRANCH_SECTION = 'simp_branch'
-HASH_SECTION = 'simp_hash'
-
-# All the configs we construct check out their externals into these local paths.
-EXTERNALS_PATH = 'externals'
-SUB_EXTERNALS_PATH = 'src'  # For mixed test repos, 
-
-# For testing behavior with '.' instead of an explicit paths.
-SIMPLE_LOCAL_ONLY_NAME = '.'
-
-# Externals files.
-CFG_NAME = 'externals.cfg'  # We construct this on a per-test basis.
-CFG_SUB_NAME = 'sub-externals.cfg' # Already exists in mixed-cont-ext repo.
-
-# Arbitrary text file in all the test repos.
-README_NAME = 'readme.txt'  
-
-# Branch that exists in both the simple and simple-fork repos.
-REMOTE_BRANCH_FEATURE2 = 'feature2'
-
-# Disable too-many-public-methods error
-# pylint: disable=R0904
-
-def setUpModule():  # pylint: disable=C0103
-    """Setup for all tests in this module. It is called once per module!
-    """
-    logging.basicConfig(filename=LOG_FILE_NAME,
-                        format='%(levelname)s : %(asctime)s : %(message)s',
-                        datefmt='%Y-%m-%d %H:%M:%S',
-                        level=logging.DEBUG)
-    repo_root = os.path.join(os.getcwd(), TMP_REPO_DIR_NAME)
-    repo_root = os.path.abspath(repo_root)
-    # delete if it exists from previous runs
-    try:
-        shutil.rmtree(repo_root)
-    except BaseException:
-        pass
-    # create clean dir for this run
-    os.mkdir(repo_root)
-
-    # Make available to all tests in this file.
-    global module_tmp_root_dir
-    assert module_tmp_root_dir == None, module_tmp_root_dir
-    module_tmp_root_dir = repo_root
-
-
-class RepoUtils(object):
-    """Convenience methods for interacting with git repos."""
-    @staticmethod
-    def create_branch(repo_base_dir, external_name, branch, with_commit=False):
-        """Create branch and optionally (with_commit) add a single commit.
-        """
-        # pylint: disable=R0913
-        cwd = os.getcwd()
-        repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name)
-        os.chdir(repo_root)
-        cmd = ['git', 'checkout', '-b', branch, ]
-        execute_subprocess(cmd)
-        if with_commit:
-            msg = 'start work on {0}'.format(branch)
-            with open(README_NAME, 'a') as handle:
-                handle.write(msg)
-            cmd = ['git', 'add', README_NAME, ]
-            execute_subprocess(cmd)
-            cmd = ['git', 'commit', '-m', msg, ]
-            execute_subprocess(cmd)
-        os.chdir(cwd)
-
-    @staticmethod
-    def create_commit(repo_base_dir, external_name):
-        """Make a commit to the given external.
-        
-        This is used to test sync state changes from local commits on
-        detached heads and tracking branches.
-        """
-        cwd = os.getcwd()
-        repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name)
-        os.chdir(repo_root)
-
-        msg = 'work on great new feature!'
-        with open(README_NAME, 'a') as handle:
-            handle.write(msg)
-        cmd = ['git', 'add', README_NAME, ]
-        execute_subprocess(cmd)
-        cmd = ['git', 'commit', '-m', msg, ]
-        execute_subprocess(cmd)
-        os.chdir(cwd)
-
-    @staticmethod
-    def clone_test_repo(bare_root, test_id, parent_repo_name, dest_dir_in):
-        """Clone repo at <bare_root>/<parent_repo_name> into dest_dir_in or local per-test-subdir.
-
-        Returns output dir.
-        """
-        parent_repo_dir = os.path.join(bare_root, parent_repo_name)
-        if dest_dir_in is None:
-            # create unique subdir for this test
-            test_dir_name = test_id
-            print("Test repository name: {0}".format(test_dir_name))
-            dest_dir = os.path.join(module_tmp_root_dir, test_dir_name)
-        else:
-            dest_dir = dest_dir_in
-
-        # pylint: disable=W0212
-        GitRepository._git_clone(parent_repo_dir, dest_dir, VERBOSITY_DEFAULT)
-        return dest_dir
-
-    @staticmethod
-    def add_file_to_repo(under_test_dir, filename, tracked):
-        """Add a file to the repository so we can put it into a dirty state
-
-        """
-        cwd = os.getcwd()
-        os.chdir(under_test_dir)
-        with open(filename, 'w') as tmp:
-            tmp.write('Hello, world!')
-
-        if tracked:
-            # NOTE(bja, 2018-01) brittle hack to obtain repo dir and
-            # file name
-            path_data = filename.split('/')
-            repo_dir = os.path.join(path_data[0], path_data[1])
-            os.chdir(repo_dir)
-            tracked_file = path_data[2]
-            cmd = ['git', 'add', tracked_file]
-            execute_subprocess(cmd)
-
-        os.chdir(cwd)
-
-class GenerateExternalsDescriptionCfgV1(object):
-    """Building blocks to create ExternalsDescriptionCfgV1 files.
-
-    Basic usage: create_config() multiple create_*(), then write_config().
-    Optionally after that: write_with_*().
-    """
-
-    def __init__(self, bare_root):
-        self._schema_version = '1.1.0'
-        self._config = None
-
-        # directory where we have test repositories (which we will clone for
-        # tests)
-        self._bare_root = bare_root
-
-    def write_config(self, dest_dir, filename=CFG_NAME):
-        """Write self._config to disk
-
-        """
-        dest_path = os.path.join(dest_dir, filename)
-        with open(dest_path, 'w') as configfile:
-            self._config.write(configfile)
-
-    def create_config(self):
-        """Create an config object and add the required metadata section
-
-        """
-        self._config = config_parser()
-        self.create_metadata()
-
-    def create_metadata(self):
-        """Create the metadata section of the config file
-        """
-        self._config.add_section(DESCRIPTION_SECTION)
-
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM,
-                         self._schema_version)
-
-    def url_for_repo_path(self, repo_path, repo_path_abs=None):
-        if repo_path_abs is not None:
-            return repo_path_abs
-        else:
-            return os.path.join(self._bare_root, repo_path)
-        
-    def create_section(self, repo_path, name, tag='', branch='',
-                       ref_hash='', required=True, path=EXTERNALS_PATH,
-                       sub_externals='', repo_path_abs=None, from_submodule=False,
-                       sparse='', nested=False):
-        # pylint: disable=too-many-branches
-        """Create a config ExternalsDescription section with the given name.
-
-        Autofills some items and handles some optional items.
-
-        repo_path_abs overrides repo_path (which is relative to the bare repo)
-        path is a subdir under repo_path to check out to.
-        """
-        # pylint: disable=R0913
-        self._config.add_section(name)
-        if not from_submodule:
-            if nested:
-                self._config.set(name, ExternalsDescription.PATH, path)
-            else:
-                self._config.set(name, ExternalsDescription.PATH,
-                                 os.path.join(path, name))
-
-        self._config.set(name, ExternalsDescription.PROTOCOL,
-                         ExternalsDescription.PROTOCOL_GIT)
-
-        # from_submodules is incompatible with some other options, turn them off
-        if (from_submodule and
-                ((repo_path_abs is not None) or tag or ref_hash or branch)):
-            printlog('create_section: "from_submodule" is incompatible with '
-                     '"repo_url", "tag", "hash", and "branch" options;\n'
-                     'Ignoring those options for {}'.format(name))
-            repo_url = None
-            tag = ''
-            ref_hash = ''
-            branch = ''
-
-        repo_url = self.url_for_repo_path(repo_path, repo_path_abs)
-
-        if not from_submodule:
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        self._config.set(name, ExternalsDescription.REQUIRED, str(required))
-
-        if tag:
-            self._config.set(name, ExternalsDescription.TAG, tag)
-
-        if branch:
-            self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-        if ref_hash:
-            self._config.set(name, ExternalsDescription.HASH, ref_hash)
-
-        if sub_externals:
-            self._config.set(name, ExternalsDescription.EXTERNALS,
-                             sub_externals)
-
-        if sparse:
-            self._config.set(name, ExternalsDescription.SPARSE, sparse)
-
-        if from_submodule:
-            self._config.set(name, ExternalsDescription.SUBMODULE, "True")
-
-    def create_section_reference_to_subexternal(self, name):
-        """Just a reference to another externals file.
-
-        """
-        # pylint: disable=R0913
-        self._config.add_section(name)
-        self._config.set(name, ExternalsDescription.PATH, LOCAL_PATH_INDICATOR)
-
-        self._config.set(name, ExternalsDescription.PROTOCOL,
-                         ExternalsDescription.PROTOCOL_EXTERNALS_ONLY)
-
-        self._config.set(name, ExternalsDescription.REPO_URL,
-                         LOCAL_PATH_INDICATOR)
-
-        self._config.set(name, ExternalsDescription.REQUIRED, str(True))
-
-        self._config.set(name, ExternalsDescription.EXTERNALS, CFG_SUB_NAME)
-
-    def create_svn_external(self, name, url, tag='', branch=''):
-        """Create a config section for an svn repository.
-
-        """
-        self._config.add_section(name)
-        self._config.set(name, ExternalsDescription.PATH,
-                         os.path.join(EXTERNALS_PATH, name))
-
-        self._config.set(name, ExternalsDescription.PROTOCOL,
-                         ExternalsDescription.PROTOCOL_SVN)
-
-        self._config.set(name, ExternalsDescription.REPO_URL, url)
-
-        self._config.set(name, ExternalsDescription.REQUIRED, str(True))
-
-        if tag:
-            self._config.set(name, ExternalsDescription.TAG, tag)
-
-        if branch:
-            self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-    def write_with_git_branch(self, dest_dir, name, branch, new_remote_repo_path=None):
-        """Update fields in our config and write it to disk.
-
-        name is the key of the ExternalsDescription in self._config to update.
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-        if new_remote_repo_path:
-            if new_remote_repo_path == SIMPLE_LOCAL_ONLY_NAME:
-                repo_url = SIMPLE_LOCAL_ONLY_NAME
-            else:
-                repo_url = os.path.join(self._bare_root, new_remote_repo_path)
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        try:
-            # remove the tag if it existed
-            self._config.remove_option(name, ExternalsDescription.TAG)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_with_svn_branch(self, dest_dir, name, branch):
-        """Update a repository branch, and potentially the remote.
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.BRANCH, branch)
-
-        try:
-            # remove the tag if it existed
-            self._config.remove_option(name, ExternalsDescription.TAG)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_with_tag_and_remote_repo(self, dest_dir, name, tag, new_remote_repo_path,
-                                       remove_branch=True):
-        """Update a repository tag and the remote.
-
-        NOTE(bja, 2017-11) remove_branch=False should result in an
-        overspecified external with both a branch and tag. This is
-        used for error condition testing.
-
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.TAG, tag)
-
-        if new_remote_repo_path:
-            repo_url = os.path.join(self._bare_root, new_remote_repo_path)
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        try:
-            # remove the branch if it existed
-            if remove_branch:
-                self._config.remove_option(name, ExternalsDescription.BRANCH)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_without_branch_tag(self, dest_dir, name):
-        """Update a repository protocol, and potentially the remote
-        """
-        # pylint: disable=R0913
-        try:
-            # remove the branch if it existed
-            self._config.remove_option(name, ExternalsDescription.BRANCH)
-        except BaseException:
-            pass
-
-        try:
-            # remove the tag if it existed
-            self._config.remove_option(name, ExternalsDescription.TAG)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_without_repo_url(self, dest_dir, name):
-        """Update a repository protocol, and potentially the remote
-        """
-        # pylint: disable=R0913
-        try:
-            # remove the repo url if it existed
-            self._config.remove_option(name, ExternalsDescription.REPO_URL)
-        except BaseException:
-            pass
-
-        self.write_config(dest_dir)
-
-    def write_with_protocol(self, dest_dir, name, protocol, repo_path=None):
-        """Update a repository protocol, and potentially the remote
-        """
-        # pylint: disable=R0913
-        self._config.set(name, ExternalsDescription.PROTOCOL, protocol)
-
-        if repo_path:
-            repo_url = os.path.join(self._bare_root, repo_path)
-            self._config.set(name, ExternalsDescription.REPO_URL, repo_url)
-
-        self.write_config(dest_dir)
-
-
-def _execute_checkout_in_dir(dirname, args, debug_env=''):
-    """Execute the checkout command in the appropriate repo dir with the
-    specified additional args. 
-
-    args should be a list of strings.
-    debug_env shuld be a string of the form 'FOO=bar' or the empty string. 
-
-    Note that we are calling the command line processing and main
-    routines and not using a subprocess call so that we get code
-    coverage results! Note this means that environment variables are passed
-    to checkout_externals via os.environ; debug_env is just used to aid
-    manual reproducibility of a given call.
-
-    Returns (overall_status, tree_status)
-    where overall_status is 0 for success, nonzero otherwise.
-    and tree_status is set if --status was passed in, None otherwise.
-
-    Note this command executes the checkout command, it doesn't
-    necessarily do any checking out (e.g. if --status is passed in).
-    """
-    cwd = os.getcwd()
-
-    # Construct a command line for reproducibility; this command is not
-    # actually executed in the test.
-    os.chdir(dirname)
-    cmdline = ['--externals', CFG_NAME, ]
-    cmdline += args
-    manual_cmd = ('Running equivalent of:\n'
-                  'pushd {dirname}; '
-                  '{debug_env} /path/to/checkout_externals {args}'.format(
-                      dirname=dirname, debug_env=debug_env,
-                      args=' '.join(cmdline)))
-    printlog(manual_cmd)
-    options = checkout.commandline_arguments(cmdline)
-    overall_status, tree_status = checkout.main(options)
-    os.chdir(cwd)
-    return overall_status, tree_status
-        
-class BaseTestSysCheckout(unittest.TestCase):
-    """Base class of reusable systems level test setup for
-    checkout_externals
-
-    """
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic.
-    # pylint: disable=invalid-name
-
-    # Command-line args for checkout_externals, used in execute_checkout_in_dir()
-    status_args = ['--status']
-    checkout_args = []
-    optional_args = ['--optional']
-    verbose_args = ['--status', '--verbose']
-
-    def setUp(self):
-        """Setup for all individual checkout_externals tests
-        """
-        # directory we want to return to after the test system and
-        # checkout_externals are done cd'ing all over the place.
-        self._return_dir = os.getcwd()
-
-        self._test_id = self.id().split('.')[-1]
-
-        # find root
-        if os.path.exists(os.path.join(os.getcwd(), 'checkout_externals')):
-            root_dir = os.path.abspath(os.getcwd())
-        else:
-            # maybe we are in a subdir, search up
-            root_dir = os.path.abspath(os.path.join(os.getcwd(), os.pardir))
-            while os.path.basename(root_dir):
-                if os.path.exists(os.path.join(root_dir, 'checkout_externals')):
-                    break
-                root_dir = os.path.dirname(root_dir)
-
-        if not os.path.exists(os.path.join(root_dir, 'checkout_externals')):
-            raise RuntimeError('Cannot find checkout_externals')
-
-        # path to the executable
-        self._checkout = os.path.join(root_dir, 'checkout_externals')
-
-        # directory where we have test repositories (which we will clone for
-        # tests)
-        self._bare_root = os.path.abspath(
-            os.path.join(root_dir, 'test', BARE_REPO_ROOT_NAME))
-
-        # set the input file generator
-        self._generator = GenerateExternalsDescriptionCfgV1(self._bare_root)
-        # set the input file generator for secondary externals
-        self._sub_generator = GenerateExternalsDescriptionCfgV1(self._bare_root)
-
-    def tearDown(self):
-        """Tear down for individual tests
-        """
-        # return to our common starting point
-        os.chdir(self._return_dir)
-        
-        # (in case this was set) Don't pollute environment of other tests.
-        os.environ.pop(MIXED_CONT_EXT_ROOT_ENV_VAR,
-                       None)  # Don't care if key wasn't set.
-
-    def clone_test_repo(self, parent_repo_name, dest_dir_in=None):
-        """Clones repo under self._bare_root"""
-        return RepoUtils.clone_test_repo(self._bare_root, self._test_id,
-                                         parent_repo_name, dest_dir_in)
-
-    def execute_checkout_in_dir(self, dirname, args, debug_env=''):
-        overall_status, tree_status = _execute_checkout_in_dir(dirname, args,
-                                                               debug_env=debug_env)
-        self.assertEqual(overall_status, 0)
-        return tree_status
-
-    def execute_checkout_with_status(self, dirname, args, debug_env=''):
-        """Calls checkout a second time to get status if needed."""
-        tree_status = self.execute_checkout_in_dir(
-            dirname, args, debug_env=debug_env)
-        if tree_status is None:
-            tree_status = self.execute_checkout_in_dir(dirname,
-                                                       self.status_args,
-                                                       debug_env=debug_env)
-            self.assertNotEqual(tree_status, None)
-        return tree_status
-    
-    def _check_sync_clean(self, ext_status, expected_sync_state,
-                          expected_clean_state):
-        self.assertEqual(ext_status.sync_state, expected_sync_state)
-        self.assertEqual(ext_status.clean_state, expected_clean_state)
-
-    @staticmethod
-    def _external_path(section_name, base_path=EXTERNALS_PATH):
-        return './{0}/{1}'.format(base_path, section_name)
-        
-    def _check_file_exists(self, repo_dir, pathname):
-        "Check that <pathname> exists in <repo_dir>"
-        self.assertTrue(os.path.exists(os.path.join(repo_dir, pathname)))
-
-    def _check_file_absent(self, repo_dir, pathname):
-        "Check that <pathname> does not exist in <repo_dir>"
-        self.assertFalse(os.path.exists(os.path.join(repo_dir, pathname)))
-
-
-class TestSysCheckout(BaseTestSysCheckout):
-    """Run systems level tests of checkout_externals
-    """
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic.
-    # pylint: disable=invalid-name
-
-    # ----------------------------------------------------------------
-    #
-    # Run systems tests
-    #
-    # ----------------------------------------------------------------
-    def test_required_bytag(self):
-        """Check out a required external pointing to a git tag."""
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                       tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        local_path_rel = self._external_path(TAG_SECTION)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        local_path_abs = os.path.join(cloned_repo_dir, local_path_rel)
-        self.assertFalse(os.path.exists(local_path_abs))
-
-        # after checkout, the external is 'clean' aka at the correct version.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # Actually checked out the desired repo.
-        self.assertEqual('origin', GitRepository._remote_name_for_url(
-            # Which url to look up
-            self._generator.url_for_repo_path(SIMPLE_REPO),
-            # Which directory has the local checked-out repo.
-            dirname=local_path_abs))
-        
-        # Actually checked out the desired tag.
-        (tag_found, tag_name) = GitRepository._git_current_tag(local_path_abs)
-        self.assertEqual(tag_name, 'tag1')
-
-        # Check existence of some simp_tag files
-        tag_path = os.path.join('externals', TAG_SECTION)
-        self._check_file_exists(cloned_repo_dir,
-                                os.path.join(tag_path, README_NAME))
-        # Subrepo should not exist (not referenced by configs).
-        self._check_file_absent(cloned_repo_dir, os.path.join(tag_path,
-                                                             'simple_subdir',
-                                                             'subdir_file.txt'))
-        
-    def test_required_bybranch(self):
-        """Check out a required external pointing to a git branch."""
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        local_path_rel = self._external_path(BRANCH_SECTION)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        local_path_abs = os.path.join(cloned_repo_dir, local_path_rel)
-        self.assertFalse(os.path.exists(local_path_abs))
-
-        # after checkout, the external is 'clean' aka at the correct version.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertTrue(os.path.exists(local_path_abs))
-
-        # Actually checked out the desired repo.
-        self.assertEqual('origin', GitRepository._remote_name_for_url(
-            # Which url to look up
-            self._generator.url_for_repo_path(SIMPLE_REPO),
-            # Which directory has the local checked-out repo.
-            dirname=local_path_abs))
-
-        # Actually checked out the desired branch. 
-        (branch_found, branch_name) = GitRepository._git_current_remote_branch(
-            local_path_abs)
-        self.assertEquals(branch_name, 'origin/' + REMOTE_BRANCH_FEATURE2)
-        
-    def test_required_byhash(self):
-        """Check out a required external pointing to a git hash."""
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, HASH_SECTION,
-                                       ref_hash='60b1cc1a38d63')
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        local_path_rel = self._external_path(HASH_SECTION)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        local_path_abs = os.path.join(cloned_repo_dir, local_path_rel)
-        self.assertFalse(os.path.exists(local_path_abs))
-
-        # after checkout, the externals are 'clean' aka at their correct version.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[local_path_rel],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # Actually checked out the desired repo.
-        self.assertEqual('origin', GitRepository._remote_name_for_url(
-            # Which url to look up
-            self._generator.url_for_repo_path(SIMPLE_REPO),
-            # Which directory has the local checked-out repo.
-            dirname=local_path_abs))
-
-        # Actually checked out the desired hash.
-        (hash_found, hash_name) = GitRepository._git_current_hash(
-            local_path_abs)
-        self.assertTrue(hash_name.startswith('60b1cc1a38d63'),
-                        msg=hash_name)
-        
-    def test_container_nested_required(self):
-        """Verify that a container with nested subrepos generates the correct initial status.
-        Tests over all possible permutations
-        """
-        # Output subdirs for each of the externals, to test that one external can be
-        # checked out in a subdir of another.
-        NESTED_SUBDIR = ['./fred', './fred/wilma', './fred/wilma/barney']
-
-        # Assert that each type of external (e.g. tag vs branch) can be at any parent level
-        # (e.g. child/parent/grandparent).
-        orders = [[0, 1, 2], [1, 2, 0], [2, 0, 1],
-                  [0, 2, 1], [2, 1, 0], [1, 0, 2]]
-        for n, order in enumerate(orders):
-            dest_dir = os.path.join(module_tmp_root_dir, self._test_id,
-                                    "test"+str(n))
-            cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO,
-                                                   dest_dir_in=dest_dir)
-            self._generator.create_config()
-            # We happen to check out each section via a different reference (tag/branch/hash) but
-            # those don't really matter, we just need to check out three repos into a nested set of
-            # directories.
-            self._generator.create_section(
-                SIMPLE_REPO, TAG_SECTION, nested=True,
-                tag='tag1', path=NESTED_SUBDIR[order[0]])
-            self._generator.create_section(
-                SIMPLE_REPO, BRANCH_SECTION, nested=True,
-                branch=REMOTE_BRANCH_FEATURE2, path=NESTED_SUBDIR[order[1]])
-            self._generator.create_section(
-                SIMPLE_REPO, HASH_SECTION, nested=True,
-                ref_hash='60b1cc1a38d63', path=NESTED_SUBDIR[order[2]])
-            self._generator.write_config(cloned_repo_dir)
-
-            # all externals start out 'empty' aka not checked out.
-            tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                                self.status_args)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]],
-                                   ExternalStatus.EMPTY,
-                                   ExternalStatus.DEFAULT)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]],
-                                   ExternalStatus.EMPTY,
-                                   ExternalStatus.DEFAULT)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]],
-                                   ExternalStatus.EMPTY,
-                                   ExternalStatus.DEFAULT)
-
-            # after checkout, all the repos are 'clean'.
-            tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                     self.checkout_args)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]],
-                                   ExternalStatus.STATUS_OK,
-                                   ExternalStatus.STATUS_OK)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]],
-                                   ExternalStatus.STATUS_OK,
-                                   ExternalStatus.STATUS_OK)
-            self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]],
-                                   ExternalStatus.STATUS_OK,
-                                   ExternalStatus.STATUS_OK)
-            
-    def test_container_simple_optional(self):
-        """Verify that container with an optional simple subrepos generates
-        the correct initial status.
-
-        """
-        # create repo and externals config.
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, 'simp_req',
-                            tag='tag1')
-
-        self._generator.create_section(SIMPLE_REPO, 'simp_opt',
-                            tag='tag1', required=False)
-
-        self._generator.write_config(cloned_repo_dir)
-
-        # all externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        req_status = tree[self._external_path('simp_req')]
-        self._check_sync_clean(req_status,
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self.assertEqual(req_status.source_type, ExternalStatus.MANAGED)
-
-        opt_status = tree[self._external_path('simp_opt')]
-        self._check_sync_clean(opt_status,
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL)
-
-        # after checkout, required external is clean, optional is still empty.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        req_status = tree[self._external_path('simp_req')]
-        self._check_sync_clean(req_status,
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertEqual(req_status.source_type, ExternalStatus.MANAGED)
-        
-        opt_status = tree[self._external_path('simp_opt')]
-        self._check_sync_clean(opt_status,
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL)
-
-        # after checking out optionals, the optional external is also clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.optional_args)
-        req_status = tree[self._external_path('simp_req')]        
-        self._check_sync_clean(req_status,
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertEqual(req_status.source_type, ExternalStatus.MANAGED)
-
-        opt_status = tree[self._external_path('simp_opt')]
-        self._check_sync_clean(opt_status,
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL)
-
-    def test_container_simple_verbose(self):
-        """Verify that verbose status matches non-verbose.
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # after checkout, all externals should be 'clean'.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # 'Verbose' status should tell the same story.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.verbose_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_simple_dirty(self):
-        """Verify that a container with a new tracked file is marked dirty.
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # checkout, should start out clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # add a tracked file to the simp_tag external, should be dirty.
-        RepoUtils.add_file_to_repo(cloned_repo_dir,
-                                   'externals/{0}/tmp.txt'.format(TAG_SECTION),
-                                   tracked=True)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.DIRTY)
-
-        # Re-checkout; simp_tag should still be dirty.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.DIRTY)
-
-    def test_container_simple_untracked(self):
-        """Verify that a container with simple subrepos and a untracked files
-        is not considered 'dirty' and will attempt an update.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                       tag='tag1')
-        self._generator.write_config(cloned_repo_dir)
-
-        # checkout, should start out clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # add an untracked file to the simp_tag external, should stay clean.
-        RepoUtils.add_file_to_repo(cloned_repo_dir,
-                                   'externals/{0}/tmp.txt'.format(TAG_SECTION),
-                                   tracked=False)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        
-        # After checkout, the external should still be 'clean'.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_simple_detached_sync(self):
-        """Verify that a container with simple subrepos generates the correct
-        out of sync status when making commits from a detached head
-        state. 
-
-        For more info about 'detached head' state: https://www.cloudbees.com/blog/git-detached-head
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        
-        self._generator.create_section(SIMPLE_REPO, 'simp_hash',
-                                 ref_hash='60b1cc1a38d63')
-        
-        self._generator.write_config(cloned_repo_dir)
-
-        # externals start out 'empty' aka not checked out.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-
-        # checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # Commit on top of the tag and hash (creating the detached head state in those two
-        # externals' repos)
-        # The branch commit does not create the detached head state, but here for completeness.
-        RepoUtils.create_commit(cloned_repo_dir, TAG_SECTION)
-        RepoUtils.create_commit(cloned_repo_dir, HASH_SECTION)
-        RepoUtils.create_commit(cloned_repo_dir, BRANCH_SECTION)
-
-        # sync status of all three should be 'modified' (uncommitted changes)
-        # clean status is 'ok' (matches externals version)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # after checkout, all externals should be totally clean (no uncommitted changes,
-        # and matches externals version).
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_remote_branch(self):
-        """Verify that a container with remote branch change works
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the branch external to point to a different remote with the same branch,
-        # then simp_branch should be out of sync
-        self._generator.write_with_git_branch(cloned_repo_dir,
-                                              name=BRANCH_SECTION,
-                                              branch=REMOTE_BRANCH_FEATURE2,
-                                              new_remote_repo_path=SIMPLE_FORK_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # checkout new externals, now simp_branch should be clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_remote_tag_same_branch(self):
-        """Verify that a container with remote tag change works. The new tag
-        should not be in the original repo, only the new remote
-        fork. The new tag is automatically fetched because it is on
-        the branch.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the config file to point to a different remote with
-        # the new tag replacing the old branch. Tag MUST NOT be in the original
-        # repo! status of simp_branch should then be out of sync
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='forked-feature-v1',
-                                                       new_remote_repo_path=SIMPLE_FORK_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.status_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # checkout new externals, then should be synced.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_remote_tag_fetch_all(self):
-        """Verify that a container with remote tag change works. The new tag
-        should not be in the original repo, only the new remote
-        fork. It should also not be on a branch that will be fetched,
-        and therefore not fetched by default with 'git fetch'. It will
-        only be retrieved by 'git fetch --tags'
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the config file to point to a different remote with
-        # the new tag instead of the old branch. Tag MUST NOT be in the original
-        # repo! status of simp_branch should then be out of sync.
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='abandoned-feature',
-                                                       new_remote_repo_path=SIMPLE_FORK_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-
-        # checkout new externals, should be clean again.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_preserve_dot(self):
-        """Verify that after inital checkout, modifying an external git repo
-        url to '.' and the current branch will leave it unchanged.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # initial checkout
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update the config file to point to a different remote with
-        # the same branch.
-        self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION,
-                                              branch=REMOTE_BRANCH_FEATURE2,
-                                              new_remote_repo_path=SIMPLE_FORK_REPO)
-        # after checkout, should be clean again.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # update branch to point to a new branch that only exists in
-        # the local fork
-        RepoUtils.create_branch(cloned_repo_dir, external_name=BRANCH_SECTION,
-                                branch='private-feature', with_commit=True)
-        self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION,
-                                              branch='private-feature',
-                                              new_remote_repo_path=SIMPLE_LOCAL_ONLY_NAME)
-        # after checkout, should be clean again.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_container_mixed_subrepo(self):
-        """Verify container with mixed subrepo.
-
-        The mixed subrepo has a sub-externals file with different
-        sub-externals on different branches.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        self._generator.create_config()
-        self._generator.create_section(MIXED_REPO, 'mixed_req',
-                                       branch='master', sub_externals=CFG_SUB_NAME)
-        self._generator.write_config(cloned_repo_dir)
-
-        # The subrepo has a repo_url that uses this environment variable.
-        # It'll be cleared in tearDown().
-        os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root
-        debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root 
-        
-        # inital checkout: all requireds are clean, and optional is empty.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args,
-                                                 debug_env=debug_env)
-        mixed_req_path = self._external_path('mixed_req')
-        self._check_sync_clean(tree[mixed_req_path],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        sub_ext_base_path = "{0}/{1}/{2}".format(EXTERNALS_PATH, 'mixed_req', SUB_EXTERNALS_PATH)
-        # The already-checked-in subexternals file has a 'simp_branch' section
-        self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # update the mixed-use external to point to different branch
-        # status should become out of sync for mixed_req, but sub-externals
-        # are still in sync
-        self._generator.write_with_git_branch(cloned_repo_dir, name='mixed_req',
-                                              branch='new-feature',
-                                              new_remote_repo_path=MIXED_REPO)
-        tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args,
-                                            debug_env=debug_env)
-        self._check_sync_clean(tree[mixed_req_path],
-                               ExternalStatus.MODEL_MODIFIED,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # run the checkout. Now the mixed use external and its sub-externals should be clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args,
-                                                 debug_env=debug_env)
-        self._check_sync_clean(tree[mixed_req_path],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        
-    def test_container_component(self):
-        """Verify that optional component checkout works
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        # create the top level externals file
-        self._generator.create_config()
-        # Optional external, by tag.
-        self._generator.create_section(SIMPLE_REPO, 'simp_opt',
-                                       tag='tag1', required=False)
-
-        # Required external, by branch.
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-
-        # Required external, by hash.
-        self._generator.create_section(SIMPLE_REPO, HASH_SECTION,
-                                       ref_hash='60b1cc1a38d63')
-        self._generator.write_config(cloned_repo_dir)
-        
-        # inital checkout, first try a nonexistent component argument noref
-        checkout_args = ['simp_opt', 'noref']
-        checkout_args.extend(self.checkout_args)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, checkout_args)
-
-        # Now explicitly check out one optional component..
-        # Explicitly listed component (opt) should be present, the other two not.
-        checkout_args = ['simp_opt']
-        checkout_args.extend(self.checkout_args)
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 checkout_args)
-        self._check_sync_clean(tree[self._external_path('simp_opt')],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-
-        # Check out a second component, this one required.
-        # Explicitly listed component (branch) should be present, the still-unlisted one (tag) not.
-        checkout_args.append(BRANCH_SECTION)
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 checkout_args)
-        self._check_sync_clean(tree[self._external_path('simp_opt')],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-
-
-    def test_container_exclude_component(self):
-        """Verify that exclude component checkout works
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                 tag='tag1')
-        
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                 branch=REMOTE_BRANCH_FEATURE2)
-        
-        self._generator.create_section(SIMPLE_REPO, 'simp_hash',
-                                 ref_hash='60b1cc1a38d63')
-        
-        self._generator.write_config(cloned_repo_dir)
-
-        # inital checkout should result in all externals being clean except excluded TAG_SECTION.
-        checkout_args = ['--exclude', TAG_SECTION]
-        checkout_args.extend(self.checkout_args)
-        tree = self.execute_checkout_with_status(cloned_repo_dir, checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.EMPTY,
-                               ExternalStatus.DEFAULT)
-        self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path(HASH_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def test_subexternal(self):
-        """Verify that an externals file can be brought in as a reference.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(MIXED_REPO)
-
-        self._generator.create_config()
-        self._generator.create_section_reference_to_subexternal('mixed_base')
-        self._generator.write_config(cloned_repo_dir)
-
-        # The subrepo has a repo_url that uses this environment variable.
-        # It'll be cleared in tearDown().
-        os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root
-        debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root 
-
-        # After checkout, confirm required's are clean and the referenced
-        # subexternal's contents are also clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args,
-                                                 debug_env=debug_env)
-        
-        self._check_sync_clean(
-            tree[self._external_path(BRANCH_SECTION, base_path=SUB_EXTERNALS_PATH)],
-            ExternalStatus.STATUS_OK,
-            ExternalStatus.STATUS_OK)
-
-    def test_container_sparse(self):
-        """Verify that 'full' container with simple subrepo
-        can run a sparse checkout and generate the correct initial status.
-
-        """
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        # Create a file to list filenames to checkout.
-        sparse_filename = 'sparse_checkout'
-        with open(os.path.join(cloned_repo_dir, sparse_filename), 'w') as sfile:
-            sfile.write(README_NAME)
-
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION,
-                                       tag='tag2')
-
-        # Same tag as above, but with a sparse file too.
-        sparse_relpath = '../../' + sparse_filename
-        self._generator.create_section(SIMPLE_REPO, 'simp_sparse',
-                                       tag='tag2', sparse=sparse_relpath)
-
-        self._generator.write_config(cloned_repo_dir)
-
-        # inital checkout, confirm required's are clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._external_path('simp_sparse')],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-        # Check existence of some files - full set in TAG_SECTION, and sparse set
-        # in 'simp_sparse'.
-        subrepo_path = os.path.join('externals', TAG_SECTION)
-        self._check_file_exists(cloned_repo_dir,
-                                os.path.join(subrepo_path, README_NAME))
-        self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path,
-                                                             'simple_subdir',
-                                                             'subdir_file.txt'))
-        subrepo_path = os.path.join('externals', 'simp_sparse')
-        self._check_file_exists(cloned_repo_dir,
-                                os.path.join(subrepo_path, README_NAME))
-        self._check_file_absent(cloned_repo_dir, os.path.join(subrepo_path,
-                                                             'simple_subdir',
-                                                             'subdir_file.txt'))
-
-class TestSysCheckoutSVN(BaseTestSysCheckout):
-    """Run systems level tests of checkout_externals accessing svn repositories
-
-    SVN tests - these tests use the svn repository interface.
-    """
-
-    @staticmethod
-    def _svn_branch_name():
-        return './{0}/svn_branch'.format(EXTERNALS_PATH)
-
-    @staticmethod
-    def _svn_tag_name():
-        return './{0}/svn_tag'.format(EXTERNALS_PATH)
-    
-    def _svn_test_repo_url(self):
-        return 'file://' + os.path.join(self._bare_root, SVN_TEST_REPO)
-
-    def _check_tag_branch_svn_tag_clean(self, tree):
-        self._check_sync_clean(tree[self._external_path(TAG_SECTION)],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._svn_branch_name()],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-        self._check_sync_clean(tree[self._svn_tag_name()],
-                               ExternalStatus.STATUS_OK,
-                               ExternalStatus.STATUS_OK)
-
-    def _have_svn_access(self):
-        """Check if we have svn access so we can enable tests that use svn.
-
-        """
-        have_svn = False
-        cmd = ['svn', 'ls', self._svn_test_repo_url(), ]
-        try:
-            execute_subprocess(cmd)
-            have_svn = True
-        except BaseException:
-            pass
-        return have_svn
-
-    def _skip_if_no_svn_access(self):
-        """Function decorator to disable svn tests when svn isn't available
-        """
-        have_svn = self._have_svn_access()
-        if not have_svn:
-            raise unittest.SkipTest("No svn access")
-
-    def test_container_simple_svn(self):
-        """Verify that a container repo can pull in an svn branch and svn tag.
-
-        """
-        self._skip_if_no_svn_access()
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-
-        self._generator.create_config()
-        # Git repo.
-        self._generator.create_section(SIMPLE_REPO, TAG_SECTION, tag='tag1')
-
-        # Svn repos.
-        self._generator.create_svn_external('svn_branch', self._svn_test_repo_url(), branch='trunk')
-        self._generator.create_svn_external('svn_tag', self._svn_test_repo_url(), tag='tags/cesm2.0.beta07')
-
-        self._generator.write_config(cloned_repo_dir)
-
-        # checkout, make sure all sections are clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_tag_branch_svn_tag_clean(tree)
-
-        # update description file to make the tag into a branch and
-        # trigger a switch
-        self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag',
-                                              'trunk')
-
-        # checkout, again the results should be clean.
-        tree = self.execute_checkout_with_status(cloned_repo_dir,
-                                                 self.checkout_args)
-        self._check_tag_branch_svn_tag_clean(tree)
-
-        # add an untracked file to the repo
-        tracked = False
-        RepoUtils.add_file_to_repo(cloned_repo_dir,
-                                   'externals/svn_branch/tmp.txt', tracked)
-
-        # run a no-op checkout.
-        self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-        # update description file to make the branch into a tag and
-        # trigger a modified sync status
-        self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag',
-                                              'tags/cesm2.0.beta07')
-
-        self.execute_checkout_in_dir(cloned_repo_dir,self.checkout_args)
-
-        # verify status is still clean and unmodified, last
-        # checkout modified the working dir state.
-        tree = self.execute_checkout_in_dir(cloned_repo_dir,
-                                            self.verbose_args)
-        self._check_tag_branch_svn_tag_clean(tree)
-
-class TestSubrepoCheckout(BaseTestSysCheckout):
-    # Need to store information at setUp time for checking
-    # pylint: disable=too-many-instance-attributes
-    """Run tests to ensure proper handling of repos with submodules.
-
-    By default, submodules in git repositories are checked out. A git
-    repository checked out as a submodule is treated as if it was
-    listed in an external with the same properties as in the source
-    .gitmodules file.
-    """
-
-    def setUp(self):
-        """Setup for all submodule checkout tests
-        Create a repo with two submodule repositories.
-        """
-
-        # Run the basic setup
-        super().setUp()
-        # create test repo
-        # We need to do this here (rather than have a static repo) because
-        # git submodules do not allow for variables in .gitmodules files
-        self._test_repo_name = 'test_repo_with_submodules'
-        self._bare_branch_name = 'subrepo_branch'
-        self._config_branch_name = 'subrepo_config_branch'
-        self._container_extern_name = 'externals_container.cfg'
-        self._my_test_dir = os.path.join(module_tmp_root_dir, self._test_id)
-        self._repo_dir = os.path.join(self._my_test_dir, self._test_repo_name)
-        self._checkout_dir = 'repo_with_submodules'
-        check_dir = self.clone_test_repo(CONTAINER_REPO,
-                                         dest_dir_in=self._repo_dir)
-        self.assertTrue(self._repo_dir == check_dir)
-        # Add the submodules
-        cwd = os.getcwd()
-        fork_repo_dir = os.path.join(self._bare_root, SIMPLE_FORK_REPO)
-        simple_repo_dir = os.path.join(self._bare_root, SIMPLE_REPO)
-        self._simple_ext_fork_name = os.path.splitext(SIMPLE_FORK_REPO)[0]
-        self._simple_ext_name = os.path.join('sourc',
-                                             os.path.splitext(SIMPLE_REPO)[0])
-        os.chdir(self._repo_dir)
-        # Add a branch with a subrepo
-        cmd = ['git', 'branch', self._bare_branch_name, 'master']
-        execute_subprocess(cmd)
-        cmd = ['git', 'checkout', self._bare_branch_name]
-        execute_subprocess(cmd)
-        cmd = ['git', '-c', 'protocol.file.allow=always','submodule', 'add', fork_repo_dir]
-        execute_subprocess(cmd)
-        cmd = ['git', 'commit', '-am', "'Added simple-ext-fork as a submodule'"]
-        execute_subprocess(cmd)
-        # Save the fork repo hash for comparison
-        os.chdir(self._simple_ext_fork_name)
-        self._fork_hash_check = self.get_git_hash()
-        os.chdir(self._repo_dir)
-        # Now, create a branch to test from_sbmodule
-        cmd = ['git', 'branch',
-               self._config_branch_name, self._bare_branch_name]
-        execute_subprocess(cmd)
-        cmd = ['git', 'checkout', self._config_branch_name]
-        execute_subprocess(cmd)
-        cmd = ['git', '-c', 'protocol.file.allow=always', 'submodule', 'add', '--name', SIMPLE_REPO,
-               simple_repo_dir, self._simple_ext_name]
-        execute_subprocess(cmd)
-        # Checkout feature2
-        os.chdir(self._simple_ext_name)
-        cmd = ['git', 'branch', 'feature2', 'origin/feature2']
-        execute_subprocess(cmd)
-        cmd = ['git', 'checkout', 'feature2']
-        execute_subprocess(cmd)
-        # Save the fork repo hash for comparison
-        self._simple_hash_check = self.get_git_hash()
-        os.chdir(self._repo_dir)
-        self.write_externals_config(filename=self._container_extern_name,
-                                    dest_dir=self._repo_dir, from_submodule=True)
-        cmd = ['git', 'add', self._container_extern_name]
-        execute_subprocess(cmd)
-        cmd = ['git', 'commit', '-am', "'Added simple-ext as a submodule'"]
-        execute_subprocess(cmd)
-        # Reset to master
-        cmd = ['git', 'checkout', 'master']
-        execute_subprocess(cmd)
-        os.chdir(cwd)
-
-    @staticmethod
-    def get_git_hash(revision="HEAD"):
-        """Return the hash for <revision>"""
-        cmd = ['git', 'rev-parse', revision]
-        git_out = execute_subprocess(cmd, output_to_caller=True)
-        return git_out.strip()
-
-    def write_externals_config(self, name='', dest_dir=None,
-                               filename=CFG_NAME,
-                               branch_name=None, sub_externals=None,
-                               from_submodule=False):
-        # pylint: disable=too-many-arguments
-        """Create a container externals file with only simple externals.
-
-        """
-        self._generator.create_config()
-
-        if dest_dir is None:
-            dest_dir = self._my_test_dir
-
-        if from_submodule:
-            self._generator.create_section(SIMPLE_FORK_REPO,
-                                           self._simple_ext_fork_name,
-                                           from_submodule=True)
-            self._generator.create_section(SIMPLE_REPO,
-                                           self._simple_ext_name,
-                                           branch='feature3', path='',
-                                           from_submodule=False)
-        else:
-            if branch_name is None:
-                branch_name = 'master'
-
-            self._generator.create_section(self._test_repo_name,
-                                           self._checkout_dir,
-                                           branch=branch_name,
-                                           path=name, sub_externals=sub_externals,
-                                           repo_path_abs=self._repo_dir)
-
-        self._generator.write_config(dest_dir, filename=filename)
-
-    def idempotence_check(self, checkout_dir):
-        """Verify that calling checkout_externals and
-        checkout_externals --status does not cause errors"""
-        cwd = os.getcwd()
-        os.chdir(checkout_dir)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.status_args)
-        os.chdir(cwd)
-
-    def test_submodule_checkout_bare(self):
-        """Verify that a git repo with submodule is properly checked out
-        This test if for where there is no 'externals' keyword in the
-        parent repo.
-        Correct behavior is that the submodule is checked out using
-        normal git submodule behavior.
-        """
-        simple_ext_fork_tag = "(tag1)"
-        simple_ext_fork_status = " "
-        self.write_externals_config(branch_name=self._bare_branch_name)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        cwd = os.getcwd()
-        checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir)
-        fork_file = os.path.join(checkout_dir,
-                                 self._simple_ext_fork_name, "readme.txt")
-        self.assertTrue(os.path.exists(fork_file))
-
-        submods = git_submodule_status(checkout_dir)
-        print('checking status of', checkout_dir, ':', submods)
-        self.assertEqual(len(submods.keys()), 1)
-        self.assertTrue(self._simple_ext_fork_name in submods)
-        submod = submods[self._simple_ext_fork_name]
-        self.assertTrue('hash' in submod)
-        self.assertEqual(submod['hash'], self._fork_hash_check)
-        self.assertTrue('status' in submod)
-        self.assertEqual(submod['status'], simple_ext_fork_status)
-        self.assertTrue('tag' in submod)
-        self.assertEqual(submod['tag'], simple_ext_fork_tag)
-        self.idempotence_check(checkout_dir)
-
-    def test_submodule_checkout_none(self):
-        """Verify that a git repo with submodule is properly checked out
-        This test is for when 'externals=None' is in parent repo's
-        externals cfg file.
-        Correct behavior is the submodle is not checked out.
-        """
-        self.write_externals_config(branch_name=self._bare_branch_name,
-                                    sub_externals="none")
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        cwd = os.getcwd()
-        checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir)
-        fork_file = os.path.join(checkout_dir,
-                                 self._simple_ext_fork_name, "readme.txt")
-        self.assertFalse(os.path.exists(fork_file))
-        os.chdir(cwd)
-        self.idempotence_check(checkout_dir)
-
-    def test_submodule_checkout_config(self): # pylint: disable=too-many-locals
-        """Verify that a git repo with submodule is properly checked out
-        This test if for when the 'from_submodule' keyword is used in the
-        parent repo.
-        Correct behavior is that the submodule is checked out using
-        normal git submodule behavior.
-        """
-        tag_check = None # Not checked out as submodule
-        status_check = "-" # Not checked out as submodule
-        self.write_externals_config(branch_name=self._config_branch_name,
-                                    sub_externals=self._container_extern_name)
-        self.execute_checkout_in_dir(self._my_test_dir,
-                                     self.checkout_args)
-        cwd = os.getcwd()
-        checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir)
-        fork_file = os.path.join(checkout_dir,
-                                 self._simple_ext_fork_name, "readme.txt")
-        self.assertTrue(os.path.exists(fork_file))
-        os.chdir(checkout_dir)
-        # Check submodule status
-        submods = git_submodule_status(checkout_dir)
-        self.assertEqual(len(submods.keys()), 2)
-        self.assertTrue(self._simple_ext_fork_name in submods)
-        submod = submods[self._simple_ext_fork_name]
-        self.assertTrue('hash' in submod)
-        self.assertEqual(submod['hash'], self._fork_hash_check)
-        self.assertTrue('status' in submod)
-        self.assertEqual(submod['status'], status_check)
-        self.assertTrue('tag' in submod)
-        self.assertEqual(submod['tag'], tag_check)
-        self.assertTrue(self._simple_ext_name in submods)
-        submod = submods[self._simple_ext_name]
-        self.assertTrue('hash' in submod)
-        self.assertEqual(submod['hash'], self._simple_hash_check)
-        self.assertTrue('status' in submod)
-        self.assertEqual(submod['status'], status_check)
-        self.assertTrue('tag' in submod)
-        self.assertEqual(submod['tag'], tag_check)
-        # Check fork repo status
-        os.chdir(self._simple_ext_fork_name)
-        self.assertEqual(self.get_git_hash(), self._fork_hash_check)
-        os.chdir(checkout_dir)
-        os.chdir(self._simple_ext_name)
-        hash_check = self.get_git_hash('origin/feature3')
-        self.assertEqual(self.get_git_hash(), hash_check)
-        os.chdir(cwd)
-        self.idempotence_check(checkout_dir)
-
-class TestSysCheckoutErrors(BaseTestSysCheckout):
-    """Run systems level tests of error conditions in checkout_externals
-
-    Error conditions - these tests are designed to trigger specific
-    error conditions and ensure that they are being handled as
-    runtime errors (and hopefully usefull error messages) instead of
-    the default internal message that won't mean anything to the
-    user, e.g. key error, called process error, etc.
-
-    These are not 'expected failures'. They are pass when a
-    RuntimeError is raised, fail if any other error is raised (or no
-    error is raised).
-
-    """
-
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic.
-    # pylint: disable=invalid-name
-
-    def test_error_unknown_protocol(self):
-        """Verify that a runtime error is raised when the user specified repo
-        protocol is not known.
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION,
-                                            'this-protocol-does-not-exist')
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_switch_protocol(self):
-        """Verify that a runtime error is raised when the user switches
-        protocols, git to svn.
-
-        TODO(bja, 2017-11) This correctly results in an error, but it
-        isn't a helpful error message.
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION, 'svn')
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_unknown_tag(self):
-        """Verify that a runtime error is raised when the user specified tag
-        does not exist.
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='this-tag-does-not-exist',
-                                                       new_remote_repo_path=SIMPLE_REPO)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_overspecify_tag_branch(self):
-        """Verify that a runtime error is raised when the user specified both
-        tag and a branch
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION,
-                                                       tag='this-tag-does-not-exist',
-                                                       new_remote_repo_path=SIMPLE_REPO,
-                                                       remove_branch=False)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_underspecify_tag_branch(self):
-        """Verify that a runtime error is raised when the user specified
-        neither a tag or a branch
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_without_branch_tag(cloned_repo_dir, BRANCH_SECTION)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-    def test_error_missing_url(self):
-        """Verify that a runtime error is raised when the user specified
-        neither a tag or a branch
-
-        """
-        # create repo
-        cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO)
-        self._generator.create_config()
-        self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION,
-                                       branch=REMOTE_BRANCH_FEATURE2)
-        self._generator.write_config(cloned_repo_dir)
-
-        # update the config file to point to a different remote with
-        # the tag instead of branch. Tag MUST NOT be in the original
-        # repo!
-        self._generator.write_without_repo_url(cloned_repo_dir,
-                                               BRANCH_SECTION)
-
-        with self.assertRaises(RuntimeError):
-            self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_sys_repository_git.py b/manage_externals/test/test_sys_repository_git.py
deleted file mode 100644
index 7e5fb5020d..0000000000
--- a/manage_externals/test/test_sys_repository_git.py
+++ /dev/null
@@ -1,238 +0,0 @@
-#!/usr/bin/env python3
-
-"""Tests of some of the functionality in repository_git.py that actually
-interacts with git repositories.
-
-We're calling these "system" tests because we expect them to be a lot
-slower than most of the unit tests.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import shutil
-import tempfile
-import unittest
-
-from manic.repository_git import GitRepository
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.utils import execute_subprocess
-
-# NOTE(wjs, 2018-04-09) I find a mix of camel case and underscores to be
-# more readable for unit test names, so I'm disabling pylint's naming
-# convention check
-# pylint: disable=C0103
-
-# Allow access to protected members
-# pylint: disable=W0212
-
-
-class GitTestCase(unittest.TestCase):
-    """Adds some git-specific unit test functionality on top of TestCase"""
-
-    def assertIsHash(self, maybe_hash):
-        """Assert that the string given by maybe_hash really does look
-        like a git hash.
-        """
-
-        # Ensure it is non-empty
-        self.assertTrue(maybe_hash, msg="maybe_hash is empty")
-
-        # Ensure it has a single string
-        self.assertEqual(1, len(maybe_hash.split()),
-                         msg="maybe_hash has multiple strings: {}".format(maybe_hash))
-
-        # Ensure that the only characters in the string are ones allowed
-        # in hashes
-        allowed_chars_set = set('0123456789abcdef')
-        self.assertTrue(set(maybe_hash) <= allowed_chars_set,
-                        msg="maybe_hash has non-hash characters: {}".format(maybe_hash))
-
-
-class TestGitTestCase(GitTestCase):
-    """Tests GitTestCase"""
-
-    def test_assertIsHash_true(self):
-        """Ensure that assertIsHash passes for something that looks
-        like a hash"""
-        self.assertIsHash('abc123')
-
-    def test_assertIsHash_empty(self):
-        """Ensure that assertIsHash raises an AssertionError for an
-        empty string"""
-        with self.assertRaises(AssertionError):
-            self.assertIsHash('')
-
-    def test_assertIsHash_multipleStrings(self):
-        """Ensure that assertIsHash raises an AssertionError when
-        given multiple strings"""
-        with self.assertRaises(AssertionError):
-            self.assertIsHash('abc123 def456')
-
-    def test_assertIsHash_badChar(self):
-        """Ensure that assertIsHash raises an AssertionError when given a
-        string that has a character that doesn't belong in a hash
-        """
-        with self.assertRaises(AssertionError):
-            self.assertIsHash('abc123g')
-
-
-class TestGitRepositoryGitCommands(GitTestCase):
-    """Test some git commands in RepositoryGit
-
-    It's silly that we need to create a repository in order to test
-    these git commands. Much or all of the git functionality that is
-    currently in repository_git.py should eventually be moved to a
-    separate module that is solely responsible for wrapping git
-    commands; that would allow us to test it independently of this
-    repository class.
-    """
-
-    # ========================================================================
-    # Test helper functions
-    # ========================================================================
-
-    def setUp(self):
-        # directory we want to return to after the test system and
-        # checkout_externals are done cd'ing all over the place.
-        self._return_dir = os.getcwd()
-
-        self._tmpdir = tempfile.mkdtemp()
-        os.chdir(self._tmpdir)
-
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG:
-                 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: '',
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    def tearDown(self):
-        # return to our common starting point
-        os.chdir(self._return_dir)
-
-        shutil.rmtree(self._tmpdir, ignore_errors=True)
-
-    @staticmethod
-    def make_cwd_git_repo():
-        """Turn the current directory into an empty git repository"""
-        execute_subprocess(['git', 'init'])
-
-    @staticmethod
-    def add_cwd_git_commit():
-        """Add a git commit in the current directory"""
-        with open('README', 'a') as myfile:
-            myfile.write('more info')
-        execute_subprocess(['git', 'add', 'README'])
-        execute_subprocess(['git', 'commit', '-m', 'my commit message'])
-
-    @staticmethod
-    def checkout_cwd_git_branch(branchname):
-        """Checkout a new branch in the current directory"""
-        execute_subprocess(['git', 'checkout', '-b', branchname])
-
-    @staticmethod
-    def make_cwd_git_tag(tagname):
-        """Make a lightweight tag at the current commit"""
-        execute_subprocess(['git', 'tag', '-m', 'making a tag', tagname])
-
-    @staticmethod
-    def checkout_cwd_ref(refname):
-        """Checkout the given refname in the current directory"""
-        execute_subprocess(['git', 'checkout', refname])
-
-    # ========================================================================
-    # Begin actual tests
-    # ========================================================================
-
-    def test_currentHash_returnsHash(self):
-        """Ensure that the _git_current_hash function returns a hash"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        hash_found, myhash = self._repo._git_current_hash(os.getcwd())
-        self.assertTrue(hash_found)
-        self.assertIsHash(myhash)
-
-    def test_currentHash_outsideGitRepo(self):
-        """Ensure that the _git_current_hash function returns False when
-        outside a git repository"""
-        hash_found, myhash = self._repo._git_current_hash(os.getcwd())
-        self.assertFalse(hash_found)
-        self.assertEqual('', myhash)
-
-    def test_currentBranch_onBranch(self):
-        """Ensure that the _git_current_branch function returns the name
-        of the branch"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.checkout_cwd_git_branch('foo')
-        branch_found, mybranch = self._repo._git_current_branch(os.getcwd())
-        self.assertTrue(branch_found)
-        self.assertEqual('foo', mybranch)
-
-    def test_currentBranch_notOnBranch(self):
-        """Ensure that the _git_current_branch function returns False
-        when not on a branch"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.make_cwd_git_tag('mytag')
-        self.checkout_cwd_ref('mytag')
-        branch_found, mybranch = self._repo._git_current_branch(os.getcwd())
-        self.assertFalse(branch_found)
-        self.assertEqual('', mybranch)
-
-    def test_currentBranch_outsideGitRepo(self):
-        """Ensure that the _git_current_branch function returns False
-        when outside a git repository"""
-        branch_found, mybranch = self._repo._git_current_branch(os.getcwd())
-        self.assertFalse(branch_found)
-        self.assertEqual('', mybranch)
-
-    def test_currentTag_onTag(self):
-        """Ensure that the _git_current_tag function returns the name of
-        the tag"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.make_cwd_git_tag('some_tag')
-        tag_found, mytag = self._repo._git_current_tag(os.getcwd())            
-        self.assertTrue(tag_found)
-        self.assertEqual('some_tag', mytag)
-
-    def test_currentTag_notOnTag(self):
-        """Ensure tha the _git_current_tag function returns False when
-        not on a tag"""
-        self.make_cwd_git_repo()
-        self.add_cwd_git_commit()
-        self.make_cwd_git_tag('some_tag')
-        self.add_cwd_git_commit()
-        tag_found, mytag = self._repo._git_current_tag(os.getcwd())
-        self.assertFalse(tag_found)
-        self.assertEqual('', mytag)
-
-    def test_currentTag_outsideGitRepo(self):
-        """Ensure that the _git_current_tag function returns False when
-        outside a git repository"""
-        tag_found, mytag = self._repo._git_current_tag(os.getcwd())
-        self.assertFalse(tag_found)
-        self.assertEqual('', mytag)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_externals_description.py b/manage_externals/test/test_unit_externals_description.py
deleted file mode 100644
index 30e5288499..0000000000
--- a/manage_externals/test/test_unit_externals_description.py
+++ /dev/null
@@ -1,478 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import os.path
-import shutil
-import unittest
-
-try:
-    # python2
-    from ConfigParser import SafeConfigParser as config_parser
-
-    def config_string_cleaner(text):
-        """convert strings into unicode
-        """
-        return text.decode('utf-8')
-except ImportError:
-    # python3
-    from configparser import ConfigParser as config_parser
-
-    def config_string_cleaner(text):
-        """Python3 already uses unicode strings, so just return the string
-        without modification.
-
-        """
-        return text
-
-from manic.externals_description import DESCRIPTION_SECTION, VERSION_ITEM
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.externals_description import ExternalsDescriptionConfigV1
-from manic.externals_description import get_cfg_schema_version
-from manic.externals_description import read_externals_description_file
-from manic.externals_description import create_externals_description
-
-from manic.global_constants import EMPTY_STR
-
-
-class TestCfgSchemaVersion(unittest.TestCase):
-    """Test that schema identification for the externals description
-    returns the correct results.
-
-    """
-
-    def setUp(self):
-        """Reusable config object
-        """
-        self._config = config_parser()
-        self._config.add_section('section1')
-        self._config.set('section1', 'keword', 'value')
-
-        self._config.add_section(DESCRIPTION_SECTION)
-
-    def test_schema_version_valid(self):
-        """Test that schema identification returns the correct version for a
-        valid tag.
-
-        """
-        version_str = '2.1.3'
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, version_str)
-        major, minor, patch = get_cfg_schema_version(self._config)
-        expected_major = 2
-        expected_minor = 1
-        expected_patch = 3
-        self.assertEqual(expected_major, major)
-        self.assertEqual(expected_minor, minor)
-        self.assertEqual(expected_patch, patch)
-
-    def test_schema_section_missing(self):
-        """Test that an error is returned if the schema section is missing
-        from the input file.
-
-        """
-        self._config.remove_section(DESCRIPTION_SECTION)
-        with self.assertRaises(RuntimeError):
-            get_cfg_schema_version(self._config)
-
-    def test_schema_version_missing(self):
-        """Test that a externals description file without a version raises a
-        runtime error.
-
-        """
-        # Note: the default setup method shouldn't include a version
-        # keyword, but remove it just to be future proof....
-        self._config.remove_option(DESCRIPTION_SECTION, VERSION_ITEM)
-        with self.assertRaises(RuntimeError):
-            get_cfg_schema_version(self._config)
-
-    def test_schema_version_not_int(self):
-        """Test that a externals description file a version that doesn't
-        decompose to integer major, minor and patch versions raises
-        runtime error.
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, 'unknown')
-        with self.assertRaises(RuntimeError):
-            get_cfg_schema_version(self._config)
-
-
-class TestModelDescritionConfigV1(unittest.TestCase):
-    """Test that parsing config/ini fileproduces a correct dictionary
-    for the externals description.
-
-    """
-    # pylint: disable=R0902
-
-    def setUp(self):
-        """Boiler plate construction of string containing xml for multiple components.
-        """
-        self._comp1_name = 'comp1'
-        self._comp1_path = 'path/to/comp1'
-        self._comp1_protocol = 'svn'
-        self._comp1_url = 'https://svn.somewhere.com/path/of/comp1'
-        self._comp1_tag = 'a_nice_tag_v1'
-        self._comp1_is_required = 'True'
-        self._comp1_externals = ''
-
-        self._comp2_name = 'comp2'
-        self._comp2_path = 'path/to/comp2'
-        self._comp2_protocol = 'git'
-        self._comp2_url = '/local/clone/of/comp2'
-        self._comp2_branch = 'a_very_nice_branch'
-        self._comp2_is_required = 'False'
-        self._comp2_externals = 'path/to/comp2.cfg'
-
-    def _setup_comp1(self, config):
-        """Boiler plate construction of xml string for componet 1
-        """
-        config.add_section(self._comp1_name)
-        config.set(self._comp1_name, 'local_path', self._comp1_path)
-        config.set(self._comp1_name, 'protocol', self._comp1_protocol)
-        config.set(self._comp1_name, 'repo_url', self._comp1_url)
-        config.set(self._comp1_name, 'tag', self._comp1_tag)
-        config.set(self._comp1_name, 'required', self._comp1_is_required)
-
-    def _setup_comp2(self, config):
-        """Boiler plate construction of xml string for componet 2
-        """
-        config.add_section(self._comp2_name)
-        config.set(self._comp2_name, 'local_path', self._comp2_path)
-        config.set(self._comp2_name, 'protocol', self._comp2_protocol)
-        config.set(self._comp2_name, 'repo_url', self._comp2_url)
-        config.set(self._comp2_name, 'branch', self._comp2_branch)
-        config.set(self._comp2_name, 'required', self._comp2_is_required)
-        config.set(self._comp2_name, 'externals', self._comp2_externals)
-
-    @staticmethod
-    def _setup_externals_description(config):
-        """Add the required exernals description section
-        """
-
-        config.add_section(DESCRIPTION_SECTION)
-        config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.1')
-
-    def _check_comp1(self, model):
-        """Test that component one was constructed correctly.
-        """
-        self.assertTrue(self._comp1_name in model)
-        comp1 = model[self._comp1_name]
-        self.assertEqual(comp1[ExternalsDescription.PATH], self._comp1_path)
-        self.assertTrue(comp1[ExternalsDescription.REQUIRED])
-        repo = comp1[ExternalsDescription.REPO]
-        self.assertEqual(repo[ExternalsDescription.PROTOCOL],
-                         self._comp1_protocol)
-        self.assertEqual(repo[ExternalsDescription.REPO_URL], self._comp1_url)
-        self.assertEqual(repo[ExternalsDescription.TAG], self._comp1_tag)
-        self.assertEqual(EMPTY_STR, comp1[ExternalsDescription.EXTERNALS])
-
-    def _check_comp2(self, model):
-        """Test that component two was constucted correctly.
-        """
-        self.assertTrue(self._comp2_name in model)
-        comp2 = model[self._comp2_name]
-        self.assertEqual(comp2[ExternalsDescription.PATH], self._comp2_path)
-        self.assertFalse(comp2[ExternalsDescription.REQUIRED])
-        repo = comp2[ExternalsDescription.REPO]
-        self.assertEqual(repo[ExternalsDescription.PROTOCOL],
-                         self._comp2_protocol)
-        self.assertEqual(repo[ExternalsDescription.REPO_URL], self._comp2_url)
-        self.assertEqual(repo[ExternalsDescription.BRANCH], self._comp2_branch)
-        self.assertEqual(self._comp2_externals,
-                         comp2[ExternalsDescription.EXTERNALS])
-
-    def test_one_tag_required(self):
-        """Test that a component source with a tag is correctly parsed.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        model = ExternalsDescriptionConfigV1(config)
-        print(model)
-        self._check_comp1(model)
-
-    def test_one_branch_externals(self):
-        """Test that a component source with a branch is correctly parsed.
-        """
-        config = config_parser()
-        self._setup_comp2(config)
-        self._setup_externals_description(config)
-        model = ExternalsDescriptionConfigV1(config)
-        print(model)
-        self._check_comp2(model)
-
-    def test_two_sources(self):
-        """Test that multiple component sources are correctly parsed.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_comp2(config)
-        self._setup_externals_description(config)
-        model = ExternalsDescriptionConfigV1(config)
-        print(model)
-        self._check_comp1(model)
-        self._check_comp2(model)
-
-    def test_cfg_v1_reject_unknown_item(self):
-        """Test that a v1 description object will reject unknown items
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        config.set(self._comp1_name, 'junk', 'foobar')
-        with self.assertRaises(RuntimeError):
-            ExternalsDescriptionConfigV1(config)
-
-    def test_cfg_v1_reject_v2(self):
-        """Test that a v1 description object won't try to parse a v2 file.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        config.set(DESCRIPTION_SECTION, VERSION_ITEM, '2.0.1')
-        with self.assertRaises(RuntimeError):
-            ExternalsDescriptionConfigV1(config)
-
-    def test_cfg_v1_reject_v1_too_new(self):
-        """Test that a v1 description object won't try to parse a v2 file.
-        """
-        config = config_parser()
-        self._setup_comp1(config)
-        self._setup_externals_description(config)
-        config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.100.0')
-        with self.assertRaises(RuntimeError):
-            ExternalsDescriptionConfigV1(config)
-
-
-class TestReadExternalsDescription(unittest.TestCase):
-    """Test the application logic of read_externals_description_file
-    """
-    TMP_FAKE_DIR = 'fake'
-
-    def setUp(self):
-        """Setup directory for tests
-        """
-        if not os.path.exists(self.TMP_FAKE_DIR):
-            os.makedirs(self.TMP_FAKE_DIR)
-
-    def tearDown(self):
-        """Cleanup tmp stuff on the file system
-        """
-        if os.path.exists(self.TMP_FAKE_DIR):
-            shutil.rmtree(self.TMP_FAKE_DIR)
-
-    def test_no_file_error(self):
-        """Test that a runtime error is raised when the file does not exist
-
-        """
-        root_dir = os.getcwd()
-        filename = 'this-file-should-not-exist'
-        with self.assertRaises(RuntimeError):
-            read_externals_description_file(root_dir, filename)
-
-    def test_no_dir_error(self):
-        """Test that a runtime error is raised when the file does not exist
-
-        """
-        root_dir = '/path/to/some/repo'
-        filename = 'externals.cfg'
-        with self.assertRaises(RuntimeError):
-            read_externals_description_file(root_dir, filename)
-
-    def test_no_invalid_error(self):
-        """Test that a runtime error is raised when the file format is invalid
-
-        """
-        root_dir = os.getcwd()
-        filename = 'externals.cfg'
-        file_path = os.path.join(root_dir, filename)
-        file_path = os.path.abspath(file_path)
-        contents = """
-<source_tree version='1.0.0'>
-invalid file format
-</sourc_tree>"""
-        with open(file_path, 'w') as fhandle:
-            fhandle.write(contents)
-        with self.assertRaises(RuntimeError):
-            read_externals_description_file(root_dir, filename)
-        os.remove(file_path)
-
-
-class TestCreateExternalsDescription(unittest.TestCase):
-    """Test the application logic of creat_externals_description
-    """
-
-    def setUp(self):
-        """Create config object used as basis for all tests
-        """
-        self._config = config_parser()
-        self._gmconfig = config_parser()
-        self.setup_config()
-
-    def setup_config(self):
-        """Boiler plate construction of xml string for componet 1
-        """
-        # Create a standard externals config with a single external
-        name = 'test'
-        self._config.add_section(name)
-        self._config.set(name, ExternalsDescription.PATH, 'externals')
-        self._config.set(name, ExternalsDescription.PROTOCOL, 'git')
-        self._config.set(name, ExternalsDescription.REPO_URL, '/path/to/repo')
-        self._config.set(name, ExternalsDescription.TAG, 'test_tag')
-        self._config.set(name, ExternalsDescription.REQUIRED, 'True')
-
-        self._config.add_section(DESCRIPTION_SECTION)
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.0')
-
-        # Create a .gitmodules test
-        name = 'submodule "gitmodules_test"'
-        self._gmconfig.add_section(name)
-        self._gmconfig.set(name, "path", 'externals/test')
-        self._gmconfig.set(name, "url", '/path/to/repo')
-        # NOTE(goldy, 2019-03) Should test other possible keywords such as
-        # fetchRecurseSubmodules, ignore, and shallow
-
-    @staticmethod
-    def setup_dict_config():
-        """Create the full container dictionary with simple and mixed use
-        externals
-
-        """
-        rdatat = {ExternalsDescription.PROTOCOL: 'git',
-                  ExternalsDescription.REPO_URL: 'simple-ext.git',
-                  ExternalsDescription.TAG: 'tag1'}
-        rdatab = {ExternalsDescription.PROTOCOL: 'git',
-                  ExternalsDescription.REPO_URL: 'simple-ext.git',
-                  ExternalsDescription.BRANCH: 'feature2'}
-        rdatam = {ExternalsDescription.PROTOCOL: 'git',
-                  ExternalsDescription.REPO_URL: 'mixed-cont-ext.git',
-                  ExternalsDescription.BRANCH: 'master'}
-        desc = {'simp_tag': {ExternalsDescription.REQUIRED: True,
-                             ExternalsDescription.PATH: 'simp_tag',
-                             ExternalsDescription.EXTERNALS: EMPTY_STR,
-                             ExternalsDescription.REPO: rdatat},
-                'simp_branch' : {ExternalsDescription.REQUIRED: True,
-                                 ExternalsDescription.PATH: 'simp_branch',
-                                 ExternalsDescription.EXTERNALS: EMPTY_STR,
-                                 ExternalsDescription.REPO: rdatab},
-                'simp_opt': {ExternalsDescription.REQUIRED: False,
-                             ExternalsDescription.PATH: 'simp_opt',
-                             ExternalsDescription.EXTERNALS: EMPTY_STR,
-                             ExternalsDescription.REPO: rdatat},
-                'mixed_req': {ExternalsDescription.REQUIRED: True,
-                              ExternalsDescription.PATH: 'mixed_req',
-                              ExternalsDescription.EXTERNALS: 'sub-ext.cfg',
-                              ExternalsDescription.REPO: rdatam}}
-
-        return desc
-
-    def test_cfg_v1_ok(self):
-        """Test that a correct cfg v1 object is created by create_externals_description
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.3')
-        ext = create_externals_description(self._config, model_format='cfg')
-        self.assertIsInstance(ext, ExternalsDescriptionConfigV1)
-
-    def test_cfg_v1_unknown_version(self):
-        """Test that a config file with unknown schema version is rejected by
-        create_externals_description.
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '100.0.3')
-        with self.assertRaises(RuntimeError):
-            create_externals_description(self._config, model_format='cfg')
-
-    def test_dict(self):
-        """Test that a correct cfg v1 object is created by create_externals_description
-
-        """
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL: '/path/to/repo',
-                 ExternalsDescription.TAG: 'tagv1',
-                }
-
-        desc = {
-            'test': {
-                ExternalsDescription.REQUIRED: False,
-                ExternalsDescription.PATH: '../fake',
-                ExternalsDescription.EXTERNALS: EMPTY_STR,
-                ExternalsDescription.REPO: rdata, },
-        }
-
-        ext = create_externals_description(desc, model_format='dict')
-        self.assertIsInstance(ext, ExternalsDescriptionDict)
-
-    def test_cfg_component_dict(self):
-        """Verify that create_externals_description works with a dictionary
-        """
-        # create the top level externals file
-        desc = self.setup_dict_config()
-        # Check external with all repos
-        external = create_externals_description(desc, model_format='dict')
-        self.assertIsInstance(external, ExternalsDescriptionDict)
-        self.assertTrue('simp_tag' in external)
-        self.assertTrue('simp_branch' in external)
-        self.assertTrue('simp_opt' in external)
-        self.assertTrue('mixed_req' in external)
-
-    def test_cfg_exclude_component_dict(self):
-        """Verify that exclude component checkout works with a dictionary
-        """
-        # create the top level externals file
-        desc = self.setup_dict_config()
-        # Test an excluded repo
-        external = create_externals_description(desc, model_format='dict',
-                                                exclude=['simp_tag',
-                                                         'simp_opt'])
-        self.assertIsInstance(external, ExternalsDescriptionDict)
-        self.assertFalse('simp_tag' in external)
-        self.assertTrue('simp_branch' in external)
-        self.assertFalse('simp_opt' in external)
-        self.assertTrue('mixed_req' in external)
-
-    def test_cfg_opt_component_dict(self):
-        """Verify that exclude component checkout works with a dictionary
-        """
-        # create the top level externals file
-        desc = self.setup_dict_config()
-        # Test an excluded repo
-        external = create_externals_description(desc, model_format='dict',
-                                                components=['simp_tag',
-                                                            'simp_opt'])
-        self.assertIsInstance(external, ExternalsDescriptionDict)
-        self.assertTrue('simp_tag' in external)
-        self.assertFalse('simp_branch' in external)
-        self.assertTrue('simp_opt' in external)
-        self.assertFalse('mixed_req' in external)
-
-    def test_cfg_unknown_version(self):
-        """Test that a runtime error is raised when an unknown file version is
-        received
-
-        """
-        self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '123.456.789')
-        with self.assertRaises(RuntimeError):
-            create_externals_description(self._config, model_format='cfg')
-
-    def test_cfg_unknown_format(self):
-        """Test that a runtime error is raised when an unknown format string is
-        received
-
-        """
-        with self.assertRaises(RuntimeError):
-            create_externals_description(self._config, model_format='unknown')
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_externals_status.py b/manage_externals/test/test_unit_externals_status.py
deleted file mode 100644
index f019514e9e..0000000000
--- a/manage_externals/test/test_unit_externals_status.py
+++ /dev/null
@@ -1,299 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for the manic external status reporting module.
-
-Note: this script assumes the path to the manic package is already in
-the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import unittest
-
-from manic.externals_status import ExternalStatus
-
-
-class TestStatusObject(unittest.TestCase):
-    """Verify that the Status object behaives as expected.
-    """
-
-    def test_exists_empty_all(self):
-        """If the repository sync-state is empty (doesn't exist), and there is no
-        clean state, then it is considered not to exist.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.EMPTY
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertFalse(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertFalse(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertFalse(exists)
-
-        # this state represtens an internal logic error in how the
-        # repo status was determined.
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        # this state represtens an internal logic error in how the
-        # repo status was determined.
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_default_all(self):
-        """If the repository sync-state is default, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.DEFAULT
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_unknown_all(self):
-        """If the repository sync-state is unknown, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_modified_all(self):
-        """If the repository sync-state is modified, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.MODEL_MODIFIED
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_exists_ok_all(self):
-        """If the repository sync-state is ok, then it is considered to exist
-        regardless of clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.STATUS_OK
-        stat.clean_state = ExternalStatus.DEFAULT
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        exists = stat.exists()
-        self.assertTrue(exists)
-
-    def test_update_ok_all(self):
-        """If the repository in-sync is ok, then it is safe to
-        update only if clean state is ok
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.STATUS_OK
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertTrue(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_modified_all(self):
-        """If the repository in-sync is modified, then it is safe to
-        update only if clean state is ok
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.MODEL_MODIFIED
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertTrue(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_unknown_all(self):
-        """If the repository in-sync is unknown, then it is not safe to
-        update, regardless of the clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_default_all(self):
-        """If the repository in-sync is default, then it is not safe to
-        update, regardless of the clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-    def test_update_empty_all(self):
-        """If the repository in-sync is empty, then it is not safe to
-        update, regardless of the clean state.
-
-        """
-        stat = ExternalStatus()
-        stat.sync_state = ExternalStatus.UNKNOWN
-        stat.clean_state = ExternalStatus.DEFAULT
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.EMPTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.UNKNOWN
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.STATUS_OK
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-        stat.clean_state = ExternalStatus.DIRTY
-        safe_to_update = stat.safe_to_update()
-        self.assertFalse(safe_to_update)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_repository.py b/manage_externals/test/test_unit_repository.py
deleted file mode 100644
index 1b93861834..0000000000
--- a/manage_externals/test/test_unit_repository.py
+++ /dev/null
@@ -1,208 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import unittest
-
-from manic.repository_factory import create_repository
-from manic.repository_git import GitRepository
-from manic.repository_svn import SvnRepository
-from manic.repository import Repository
-from manic.externals_description import ExternalsDescription
-from manic.global_constants import EMPTY_STR
-
-
-class TestCreateRepositoryDict(unittest.TestCase):
-    """Test the create_repository functionality to ensure it returns the
-    propper type of repository and errors for unknown repository
-    types.
-
-    """
-
-    def setUp(self):
-        """Common data needed for all tests in this class
-        """
-        self._name = 'test_name'
-        self._repo = {ExternalsDescription.PROTOCOL: None,
-                      ExternalsDescription.REPO_URL: 'junk_root',
-                      ExternalsDescription.TAG: 'junk_tag',
-                      ExternalsDescription.BRANCH: EMPTY_STR,
-                      ExternalsDescription.HASH: EMPTY_STR,
-                      ExternalsDescription.SPARSE: EMPTY_STR, }
-
-    def test_create_repo_git(self):
-        """Verify that several possible names for the 'git' protocol
-        create git repository objects.
-
-        """
-        protocols = ['git', 'GIT', 'Git', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            repo = create_repository(self._name, self._repo)
-            self.assertIsInstance(repo, GitRepository)
-
-    def test_create_repo_svn(self):
-        """Verify that several possible names for the 'svn' protocol
-        create svn repository objects.
-        """
-        protocols = ['svn', 'SVN', 'Svn', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            repo = create_repository(self._name, self._repo)
-            self.assertIsInstance(repo, SvnRepository)
-
-    def test_create_repo_externals_only(self):
-        """Verify that an externals only repo returns None.
-        """
-        protocols = ['externals_only', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            repo = create_repository(self._name, self._repo)
-            self.assertEqual(None, repo)
-
-    def test_create_repo_unsupported(self):
-        """Verify that an unsupported protocol generates a runtime error.
-        """
-        protocols = ['not_a_supported_protocol', ]
-        for protocol in protocols:
-            self._repo[ExternalsDescription.PROTOCOL] = protocol
-            with self.assertRaises(RuntimeError):
-                create_repository(self._name, self._repo)
-
-
-class TestRepository(unittest.TestCase):
-    """Test the externals description processing used to create the Repository
-    base class shared by protocol specific repository classes.
-
-    """
-
-    def test_tag(self):
-        """Test creation of a repository object with a tag
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        tag = 'test_tag'
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.BRANCH: EMPTY_STR,
-                     ExternalsDescription.HASH: EMPTY_STR,
-                     ExternalsDescription.SPARSE: EMPTY_STR, }
-        repo = Repository(name, repo_info)
-        print(repo.__dict__)
-        self.assertEqual(repo.tag(), tag)
-        self.assertEqual(repo.url(), url)
-
-    def test_branch(self):
-        """Test creation of a repository object with a branch
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = 'test_branch'
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: EMPTY_STR,
-                     ExternalsDescription.HASH: EMPTY_STR,
-                     ExternalsDescription.SPARSE: EMPTY_STR, }
-        repo = Repository(name, repo_info)
-        print(repo.__dict__)
-        self.assertEqual(repo.branch(), branch)
-        self.assertEqual(repo.url(), url)
-
-    def test_hash(self):
-        """Test creation of a repository object with a hash
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        ref = 'deadc0de'
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: EMPTY_STR,
-                     ExternalsDescription.TAG: EMPTY_STR,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        repo = Repository(name, repo_info)
-        print(repo.__dict__)
-        self.assertEqual(repo.hash(), ref)
-        self.assertEqual(repo.url(), url)
-
-    def test_tag_branch(self):
-        """Test creation of a repository object with a tag and branch raises a
-        runtimer error.
-
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = 'test_branch'
-        tag = 'test_tag'
-        ref = EMPTY_STR
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        with self.assertRaises(RuntimeError):
-            Repository(name, repo_info)
-
-    def test_tag_branch_hash(self):
-        """Test creation of a repository object with a tag, branch and hash raises a
-        runtimer error.
-
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = 'test_branch'
-        tag = 'test_tag'
-        ref = 'deadc0de'
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        with self.assertRaises(RuntimeError):
-            Repository(name, repo_info)
-
-    def test_no_tag_no_branch(self):
-        """Test creation of a repository object without a tag or branch raises a
-        runtimer error.
-
-        """
-        name = 'test_repo'
-        protocol = 'test_protocol'
-        url = 'test_url'
-        branch = EMPTY_STR
-        tag = EMPTY_STR
-        ref = EMPTY_STR
-        sparse = EMPTY_STR
-        repo_info = {ExternalsDescription.PROTOCOL: protocol,
-                     ExternalsDescription.REPO_URL: url,
-                     ExternalsDescription.BRANCH: branch,
-                     ExternalsDescription.TAG: tag,
-                     ExternalsDescription.HASH: ref,
-                     ExternalsDescription.SPARSE: sparse, }
-        with self.assertRaises(RuntimeError):
-            Repository(name, repo_info)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_repository_git.py b/manage_externals/test/test_unit_repository_git.py
deleted file mode 100644
index 1c01098acf..0000000000
--- a/manage_externals/test/test_unit_repository_git.py
+++ /dev/null
@@ -1,811 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-# pylint: disable=too-many-lines,protected-access
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import shutil
-import unittest
-
-from manic.repository_git import GitRepository
-from manic.externals_status import ExternalStatus
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.global_constants import EMPTY_STR
-
-# NOTE(bja, 2017-11) order is important here. origin should be a
-# subset of other to trap errors on processing remotes!
-GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM = '''
-upstream	/path/to/other/repo (fetch)
-upstream	/path/to/other/repo (push)
-other	/path/to/local/repo2 (fetch)
-other	/path/to/local/repo2 (push)
-origin	/path/to/local/repo (fetch)
-origin	/path/to/local/repo (push)
-'''
-
-
-class TestGitRepositoryCurrentRef(unittest.TestCase):
-    """test the current_ref command on a git repository
-    """
-
-    def setUp(self):
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG:
-                 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    #
-    # mock methods replacing git system calls
-    #
-    @staticmethod
-    def _git_current_branch(branch_found, branch_name):
-        """Return a function that takes the place of
-        repo._git_current_branch, which returns the given output."""
-        def my_git_current_branch(dirname):
-            """mock function that can take the place of repo._git_current_branch"""
-            return branch_found, branch_name
-        return my_git_current_branch
-
-    @staticmethod
-    def _git_current_tag(tag_found, tag_name):
-        """Return a function that takes the place of
-        repo._git_current_tag, which returns the given output."""
-        def my_git_current_tag(dirname):
-            """mock function that can take the place of repo._git_current_tag"""
-            return tag_found, tag_name
-        return my_git_current_tag
-
-    @staticmethod
-    def _git_current_hash(hash_found, hash_name):
-        """Return a function that takes the place of
-        repo._git_current_hash, which returns the given output."""
-        def my_git_current_hash(dirname):
-            """mock function that can take the place of repo._git_current_hash"""
-            return hash_found, hash_name
-        return my_git_current_hash
-
-    # ------------------------------------------------------------------------
-    # Begin tests
-    # ------------------------------------------------------------------------
-
-    def test_ref_branch(self):
-        """Test that we correctly identify we are on a branch
-        """
-        self._repo._git_current_branch = self._git_current_branch(
-            True, 'feature3')
-        self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag')
-        self._repo._git_current_hash = self._git_current_hash(True, 'abc123')
-        expected = 'foo_tag (branch feature3)'
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, expected)
-
-    def test_ref_detached_tag(self):
-        """Test that we correctly identify that the ref is detached at a tag
-        """
-        self._repo._git_current_branch = self._git_current_branch(False, '')
-        self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag')
-        self._repo._git_current_hash = self._git_current_hash(True, 'abc123')
-        expected = 'foo_tag'
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, expected)
-
-    def test_ref_detached_hash(self):
-        """Test that we can identify ref is detached at a hash
-
-        """
-        self._repo._git_current_branch = self._git_current_branch(False, '')
-        self._repo._git_current_tag = self._git_current_tag(False, '')
-        self._repo._git_current_hash = self._git_current_hash(True, 'abc123')
-        expected = 'abc123'
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, expected)
-
-    def test_ref_none(self):
-        """Test that we correctly identify that we're not in a git repo.
-        """
-        self._repo._git_current_branch = self._git_current_branch(False, '')
-        self._repo._git_current_tag = self._git_current_tag(False, '')
-        self._repo._git_current_hash = self._git_current_hash(False, '')
-        result = self._repo._current_ref(os.getcwd())
-        self.assertEqual(result, EMPTY_STR)
-
-
-class TestGitRepositoryCheckSync(unittest.TestCase):
-    """Test whether the GitRepository _check_sync_logic functionality is
-    correct.
-
-    Note: there are a lot of combinations of state:
-
-    - external description - tag, branch
-
-    - working copy
-      - doesn't exist (not checked out)
-      - exists, no git info - incorrect protocol, e.g. svn, or tarball?
-      - exists, git info
-        - as expected:
-        - different from expected:
-           - detached tag,
-           - detached hash,
-           - detached branch (compare remote and branch),
-           - tracking branch (compare remote and branch),
-             - same remote
-             - different remote
-           - untracked branch
-
-    Test list:
-      - doesn't exist
-      - exists no git info
-
-      - num_external * (working copy expected + num_working copy different)
-      - total tests = 16
-
-    """
-
-    # NOTE(bja, 2017-11) pylint complains about long method names, but
-    # it is hard to differentiate tests without making them more
-    # cryptic. Also complains about too many public methods, but it
-    # doesn't really make sense to break this up.
-    # pylint: disable=invalid-name,too-many-public-methods
-
-    TMP_FAKE_DIR = 'fake'
-    TMP_FAKE_GIT_DIR = os.path.join(TMP_FAKE_DIR, '.git')
-
-    def setUp(self):
-        """Setup reusable git repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG: 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: self.TMP_FAKE_DIR,
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-        # The unit tests here don't care about the result of
-        # _current_ref, but we replace it here so that we don't need to
-        # worry about calling a possibly slow and possibly
-        # error-producing command (since _current_ref calls various git
-        # functions):
-        self._repo._current_ref = self._current_ref_empty
-        self._create_tmp_git_dir()
-
-        # We have to override this class method rather than the self._repo
-        # instance method because it is called via
-        # GitRepository._remote_name_for_url, which is itself a @classmethod
-        # calls cls._git_remote_verbose().
-        self._orignal_git_remote_verbose = GitRepository._git_remote_verbose
-        GitRepository._git_remote_verbose = self._git_remote_origin_upstream        
-    def tearDown(self):
-        """Cleanup tmp stuff on the file system
-        """
-        self._remove_tmp_git_dir()
-
-        GitRepository._git_remote_verbose = self._orignal_git_remote_verbose
-
-    def _create_tmp_git_dir(self):
-        """Create a temporary fake git directory for testing purposes.
-        """
-        if not os.path.exists(self.TMP_FAKE_GIT_DIR):
-            os.makedirs(self.TMP_FAKE_GIT_DIR)
-
-    def _remove_tmp_git_dir(self):
-        """Remove the temporary fake git directory
-        """
-        if os.path.exists(self.TMP_FAKE_DIR):
-            shutil.rmtree(self.TMP_FAKE_DIR)
-
-    #
-    # mock methods replacing git system calls
-    #
-    @staticmethod
-    def _current_ref_empty(dirname):
-        """Return an empty string.
-
-        Drop-in for GitRepository._current_ref
-        """
-        return EMPTY_STR
-
-    @staticmethod
-    def _git_remote_origin_upstream(dirname):
-        """Return an info string that is a checkout hash.
-
-        Drop-in for GitRepository._git_remote_verbose.
-        """
-        return GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM
-
-    @staticmethod
-    def _git_current_hash(myhash):
-        """Return a function that takes the place of repo._git_current_hash,
-        which returns the given hash
-        """
-        def my_git_current_hash(dirname):
-            """mock function that can take the place of repo._git_current_hash"""
-            return 0, myhash
-        return my_git_current_hash
-
-    def _git_revparse_commit(self, expected_ref, mystatus, myhash):
-        """Return a function that takes the place of
-        repo._git_revparse_commit, which returns a tuple:
-        (mystatus, myhash).
-
-        Expects the passed-in ref to equal expected_ref
-
-        status = 0 implies success, non-zero implies failure
-        """
-        def my_git_revparse_commit(ref, dirname):
-            """mock function that can take the place of repo._git_revparse_commit"""
-            self.assertEqual(expected_ref, ref)
-            return mystatus, myhash
-        return my_git_revparse_commit
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where working copy doesn't exist or is invalid
-    #
-    # ----------------------------------------------------------------
-    def test_sync_dir_not_exist(self):
-        """Test that a directory that doesn't exist returns an error status
-
-        Note: the Repository classes should be prevented from ever
-        working on an empty directory by the _Source object.
-
-        """
-        stat = ExternalStatus()
-        self._repo._check_sync(stat, 'invalid_directory_name')
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_ERROR)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_dir_exist_no_git_info(self):
-        """Test that a non-existent git repo returns an unknown status
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 1, '')
-        self._repo._check_sync(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.UNKNOWN)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ------------------------------------------------------------------------
-    #
-    # Tests where version in configuration file is not a valid reference
-    #
-    # ------------------------------------------------------------------------
-
-    def test_sync_invalid_reference(self):
-        """Test that an invalid reference returns out-of-sync
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 1, '')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where external description specifies a tag
-    #
-    # ----------------------------------------------------------------
-    def test_sync_tag_on_same_hash(self):
-        """Test expect tag on same hash --> status ok
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_tag_on_different_hash(self):
-        """Test expect tag on a different hash --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = 'tag1'
-        self._repo._git_current_hash = self._git_current_hash('def456')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'tag1', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where external description specifies a hash
-    #
-    # ----------------------------------------------------------------
-    def test_sync_hash_on_same_hash(self):
-        """Test expect hash on same hash --> status ok
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = ''
-        self._repo._hash = 'abc'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'abc', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_hash_on_different_hash(self):
-        """Test expect hash on a different hash --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._tag = ''
-        self._repo._hash = 'abc'
-        self._repo._git_current_hash = self._git_current_hash('def456')
-        self._repo._git_revparse_commit = self._git_revparse_commit(
-            'abc', 0, 'abc123')
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    # ----------------------------------------------------------------
-    #
-    # Tests where external description specifies a branch
-    #
-    # ----------------------------------------------------------------
-    def test_sync_branch_on_same_hash(self):
-        """Test expect branch on same hash --> status ok
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('origin/feature-2', 0, 'abc123'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_branch_on_diff_hash(self):
-        """Test expect branch on diff hash --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('origin/feature-2', 0, 'def456'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_branch_diff_remote(self):
-        """Test _remote_name_for_url with a different remote
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._url = '/path/to/other/repo'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('upstream/feature-2', 0, 'def456'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        # The test passes if _git_revparse_commit is called with the
-        # expected argument
-
-    def test_sync_branch_diff_remote2(self):
-        """Test _remote_name_for_url with a different remote
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._url = '/path/to/local/repo2'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('other/feature-2', 0, 'def789'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        # The test passes if _git_revparse_commit is called with the
-        # expected argument
-
-    def test_sync_branch_on_unknown_remote(self):
-        """Test expect branch, but remote is unknown --> status modified
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature-2'
-        self._repo._tag = ''
-        self._repo._url = '/path/to/unknown/repo'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('unknown_remote/feature-2', 1, ''))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_sync_branch_on_untracked_local(self):
-        """Test expect branch, on untracked branch in local repo --> status ok
-
-        Setting the externals description to '.' indicates that the
-        user only wants to consider the current local repo state
-        without fetching from remotes. This is required to preserve
-        the current branch of a repository during an update.
-
-        """
-        stat = ExternalStatus()
-        self._repo._branch = 'feature3'
-        self._repo._tag = ''
-        self._repo._url = '.'
-        self._repo._git_current_hash = self._git_current_hash('abc123')
-        self._repo._git_revparse_commit = (
-            self._git_revparse_commit('feature3', 0, 'abc123'))
-        self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR)
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_sync should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-
-class TestGitStatusPorcelain(unittest.TestCase):
-    """Test parsing of output from git status --porcelain=v1 -z
-    """
-    # pylint: disable=C0103
-    GIT_STATUS_PORCELAIN_V1_ALL = (
-        r' D INSTALL\0MM Makefile\0M README.md\0R  cmakelists.txt\0'
-        r'CMakeLists.txt\0D  commit-message-template.txt\0A  stuff.txt\0'
-        r'?? junk.txt')
-
-    GIT_STATUS_PORCELAIN_CLEAN = r''
-
-    def test_porcelain_status_dirty(self):
-        """Verify that git status output is considered dirty when there are
-        listed files.
-
-        """
-        git_output = self.GIT_STATUS_PORCELAIN_V1_ALL
-        is_dirty = GitRepository._status_v1z_is_dirty(git_output)
-        self.assertTrue(is_dirty)
-
-    def test_porcelain_status_clean(self):
-        """Verify that git status output is considered clean when there are no
-        listed files.
-
-        """
-        git_output = self.GIT_STATUS_PORCELAIN_CLEAN
-        is_dirty = GitRepository._status_v1z_is_dirty(git_output)
-        self.assertFalse(is_dirty)
-
-
-class TestGitCreateRemoteName(unittest.TestCase):
-    """Test the create_remote_name method on the GitRepository class
-    """
-
-    def setUp(self):
-        """Common infrastructure for testing _create_remote_name
-        """
-        self._rdata = {ExternalsDescription.PROTOCOL: 'git',
-                       ExternalsDescription.REPO_URL:
-                       'empty',
-                       ExternalsDescription.TAG:
-                       'very_useful_tag',
-                       ExternalsDescription.BRANCH: EMPTY_STR,
-                       ExternalsDescription.HASH: EMPTY_STR,
-                       ExternalsDescription.SPARSE: EMPTY_STR, }
-        self._repo = GitRepository('test', self._rdata)
-
-    def test_remote_git_proto(self):
-        """Test remote with git protocol
-        """
-        self._repo._url = 'git@git.github.com:very_nice_org/useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'very_nice_org_useful_repo')
-
-    def test_remote_https_proto(self):
-        """Test remote with git protocol
-        """
-        self._repo._url = 'https://www.github.com/very_nice_org/useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'very_nice_org_useful_repo')
-
-    def test_remote_local_abs(self):
-        """Test remote with git protocol
-        """
-        self._repo._url = '/path/to/local/repositories/useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'repositories_useful_repo')
-
-    def test_remote_local_rel(self):
-        """Test remote with git protocol
-        """
-        os.environ['TEST_VAR'] = '/my/path/to/repos'
-        self._repo._url = '${TEST_VAR}/../../useful_repo'
-        remote_name = self._repo._create_remote_name()
-        self.assertEqual(remote_name, 'path_useful_repo')
-        del os.environ['TEST_VAR']
-
-
-class TestVerifyTag(unittest.TestCase):
-    """Test logic verifying that a tag exists and is unique
-
-    """
-
-    def setUp(self):
-        """Setup reusable git repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG: 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'tmp',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    @staticmethod
-    def _shell_true(*args, **kwargs):
-        return 0
-
-    @staticmethod
-    def _shell_false(*args, **kwargs):
-        return 1
-
-    @staticmethod
-    def _mock_revparse_commit(ref, dirname):
-        _ = ref
-        return (TestValidRef._shell_true, '97ebc0e0deadc0de')
-
-    @staticmethod
-    def _mock_revparse_commit_false(ref, dirname):
-        _ = ref
-        return (TestValidRef._shell_false, '97ebc0e0deadc0de')
-
-    def test_tag_not_tag_branch_commit(self):
-        """Verify a non-tag returns false
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_false
-        self._repo._tag = 'something'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_tag_not_tag(self):
-        """Verify a non-tag, untracked remote returns false
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_true
-        self._repo._git_lsremote_branch = self._shell_true
-        self._repo._git_revparse_commit = self._mock_revparse_commit_false
-        self._repo._tag = 'tag1'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_tag_indeterminant(self):
-        """Verify an indeterminant tag/branch returns false
-        """
-        self._repo._git_showref_tag = self._shell_true
-        self._repo._git_showref_branch = self._shell_true
-        self._repo._git_lsremote_branch = self._shell_true
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = 'something'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_tag_is_unique(self):
-        """Verify a unique tag match returns true
-        """
-        self._repo._git_showref_tag = self._shell_true
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = 'tag1'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertTrue(received)
-
-    def test_tag_is_not_hash(self):
-        """Verify a commit hash is not classified as a tag
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = '97ebc0e0'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-    def test_hash_is_commit(self):
-        """Verify a commit hash is not classified as a tag
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit
-        self._repo._tag = '97ebc0e0'
-        remote_name = 'origin'
-        received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name,
-                                                os.getcwd())
-        self.assertFalse(received)
-
-
-class TestValidRef(unittest.TestCase):
-    """Test logic verifying that a reference is a valid tag, branch or sha1
-
-    """
-
-    def setUp(self):
-        """Setup reusable git repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'git',
-                 ExternalsDescription.REPO_URL:
-                 '/path/to/local/repo',
-                 ExternalsDescription.TAG: 'tag1',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'tmp',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = GitRepository('test', repo)
-
-    @staticmethod
-    def _shell_true(url, remote=None):
-        _ = url
-        _ = remote
-        return 0
-
-    @staticmethod
-    def _shell_false(url, remote=None):
-        _ = url
-        _ = remote
-        return 1
-
-    @staticmethod
-    def _mock_revparse_commit_false(ref, dirname):
-        _ = ref
-        return (TestValidRef._shell_false, '')
-
-    @staticmethod
-    def _mock_revparse_commit_true(ref, dirname):
-        _ = ref
-        _ = dirname
-        return (TestValidRef._shell_true, '')
-
-    def test_valid_ref_is_invalid(self):
-        """Verify an invalid reference raises an exception
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_false
-        self._repo._tag = 'invalid_ref'
-        with self.assertRaises(RuntimeError):
-            self._repo._check_for_valid_ref(self._repo._tag,
-                                            remote_name=None,
-                                            dirname=os.getcwd())
-
-    def test_valid_tag(self):
-        """Verify a valid tag return true
-        """
-        self._repo._git_showref_tag = self._shell_true
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_true
-        self._repo._tag = 'tag1'
-        received = self._repo._check_for_valid_ref(self._repo._tag,
-                                                   remote_name=None,
-                                                   dirname=os.getcwd())
-        self.assertTrue(received)
-
-    def test_valid_branch(self):
-        """Verify a valid tag return true
-        """
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_true
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = self._mock_revparse_commit_true
-        self._repo._tag = 'tag1'
-        received = self._repo._check_for_valid_ref(self._repo._tag,
-                                                   remote_name=None,
-                                                   dirname=os.getcwd())
-        self.assertTrue(received)
-
-    def test_valid_hash(self):
-        """Verify a valid hash return true
-        """
-        def _mock_revparse_commit_true(ref, dirname):
-            _ = ref
-            return (0, '56cc0b539426eb26810af9e')
-
-        self._repo._git_showref_tag = self._shell_false
-        self._repo._git_showref_branch = self._shell_false
-        self._repo._git_lsremote_branch = self._shell_false
-        self._repo._git_revparse_commit = _mock_revparse_commit_true
-        self._repo._hash = '56cc0b5394'
-        received = self._repo._check_for_valid_ref(self._repo._hash,
-                                                   remote_name=None,
-                                                   dirname=os.getcwd())
-        self.assertTrue(received)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_repository_svn.py b/manage_externals/test/test_unit_repository_svn.py
deleted file mode 100755
index d9309df7f6..0000000000
--- a/manage_externals/test/test_unit_repository_svn.py
+++ /dev/null
@@ -1,501 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import unittest
-
-from manic.repository_svn import SvnRepository
-from manic.externals_status import ExternalStatus
-from manic.externals_description import ExternalsDescription
-from manic.externals_description import ExternalsDescriptionDict
-from manic.global_constants import EMPTY_STR
-
-# pylint: disable=W0212
-
-SVN_INFO_MOSART = """Path: components/mosart
-Working Copy Root Path: /Users/andreb/projects/ncar/git-conversion/clm-dev-experimental/components/mosart
-URL: https://svn-ccsm-models.cgd.ucar.edu/mosart/trunk_tags/mosart1_0_26
-Relative URL: ^/mosart/trunk_tags/mosart1_0_26
-Repository Root: https://svn-ccsm-models.cgd.ucar.edu
-Repository UUID: fe37f545-8307-0410-aea5-b40df96820b5
-Revision: 86711
-Node Kind: directory
-Schedule: normal
-Last Changed Author: erik
-Last Changed Rev: 86031
-Last Changed Date: 2017-07-07 12:28:10 -0600 (Fri, 07 Jul 2017)
-"""
-SVN_INFO_CISM = """
-Path: components/cism
-Working Copy Root Path: /Users/andreb/projects/ncar/git-conversion/clm-dev-experimental/components/cism
-URL: https://svn-ccsm-models.cgd.ucar.edu/glc/trunk_tags/cism2_1_37
-Relative URL: ^/glc/trunk_tags/cism2_1_37
-Repository Root: https://svn-ccsm-models.cgd.ucar.edu
-Repository UUID: fe37f545-8307-0410-aea5-b40df96820b5
-Revision: 86711
-Node Kind: directory
-Schedule: normal
-Last Changed Author: sacks
-Last Changed Rev: 85704
-Last Changed Date: 2017-06-15 05:59:28 -0600 (Thu, 15 Jun 2017)
-"""
-
-
-class TestSvnRepositoryCheckURL(unittest.TestCase):
-    """Verify that the svn_check_url function is working as expected.
-    """
-
-    def setUp(self):
-        """Setup reusable svn repository object
-        """
-        self._name = 'component'
-        rdata = {ExternalsDescription.PROTOCOL: 'svn',
-                 ExternalsDescription.REPO_URL:
-                     'https://svn-ccsm-models.cgd.ucar.edu',
-                 ExternalsDescription.TAG:
-                     'mosart/trunk_tags/mosart1_0_26',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: '',
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = SvnRepository('test', repo)
-
-    def test_check_url_same(self):
-        """Test that we correctly identify that the correct URL.
-        """
-        svn_output = SVN_INFO_MOSART
-        expected_url = self._repo.url()
-        result, current_version = \
-            self._repo._check_url(svn_output, expected_url)
-        self.assertEqual(result, ExternalStatus.STATUS_OK)
-        self.assertEqual(current_version, 'mosart/trunk_tags/mosart1_0_26')
-
-    def test_check_url_different(self):
-        """Test that we correctly reject an incorrect URL.
-        """
-        svn_output = SVN_INFO_CISM
-        expected_url = self._repo.url()
-        result, current_version = \
-            self._repo._check_url(svn_output, expected_url)
-        self.assertEqual(result, ExternalStatus.MODEL_MODIFIED)
-        self.assertEqual(current_version, 'glc/trunk_tags/cism2_1_37')
-
-    def test_check_url_none(self):
-        """Test that we can handle an empty string for output, e.g. not an svn
-        repo.
-
-        """
-        svn_output = EMPTY_STR
-        expected_url = self._repo.url()
-        result, current_version = \
-            self._repo._check_url(svn_output, expected_url)
-        self.assertEqual(result, ExternalStatus.UNKNOWN)
-        self.assertEqual(current_version, '')
-
-
-class TestSvnRepositoryCheckSync(unittest.TestCase):
-    """Test whether the SvnRepository svn_check_sync functionality is
-    correct.
-
-    """
-
-    def setUp(self):
-        """Setup reusable svn repository object
-        """
-        self._name = "component"
-        rdata = {ExternalsDescription.PROTOCOL: 'svn',
-                 ExternalsDescription.REPO_URL:
-                     'https://svn-ccsm-models.cgd.ucar.edu/',
-                 ExternalsDescription.TAG:
-                     'mosart/trunk_tags/mosart1_0_26',
-                 }
-
-        data = {self._name:
-                {
-                    ExternalsDescription.REQUIRED: False,
-                    ExternalsDescription.PATH: 'junk',
-                    ExternalsDescription.EXTERNALS: EMPTY_STR,
-                    ExternalsDescription.REPO: rdata,
-                },
-                }
-
-        model = ExternalsDescriptionDict(data)
-        repo = model[self._name][ExternalsDescription.REPO]
-        self._repo = SvnRepository('test', repo)
-
-    @staticmethod
-    def _svn_info_empty(*_):
-        """Return an empty info string. Simulates svn info failing.
-        """
-        return ''
-
-    @staticmethod
-    def _svn_info_synced(*_):
-        """Return an info sting that is synced with the setUp data
-        """
-        return SVN_INFO_MOSART
-
-    @staticmethod
-    def _svn_info_modified(*_):
-        """Return and info string that is modified from the setUp data
-        """
-        return SVN_INFO_CISM
-
-    def test_repo_dir_not_exist(self):
-        """Test that a directory that doesn't exist returns an error status
-
-        Note: the Repository classes should be prevented from ever
-        working on an empty directory by the _Source object.
-
-        """
-        stat = ExternalStatus()
-        self._repo._check_sync(stat, 'junk')
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_ERROR)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_repo_dir_exist_no_svn_info(self):
-        """Test that an empty info string returns an unknown status
-        """
-        stat = ExternalStatus()
-        # Now we over-ride the _svn_info method on the repo to return
-        # a known value without requiring access to svn.
-        self._repo._svn_info = self._svn_info_empty
-        self._repo._check_sync(stat, '.')
-        self.assertEqual(stat.sync_state, ExternalStatus.UNKNOWN)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_repo_dir_synced(self):
-        """Test that a valid info string that is synced to the repo in the
-        externals description returns an ok status.
-
-        """
-        stat = ExternalStatus()
-        # Now we over-ride the _svn_info method on the repo to return
-        # a known value without requiring access to svn.
-        self._repo._svn_info = self._svn_info_synced
-        self._repo._check_sync(stat, '.')
-        self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-    def test_repo_dir_modified(self):
-        """Test that a valid svn info string that is out of sync with the
-        externals description returns a modified status.
-
-        """
-        stat = ExternalStatus()
-        # Now we over-ride the _svn_info method on the repo to return
-        # a known value without requiring access to svn.
-        self._repo._svn_info = self._svn_info_modified
-        self._repo._check_sync(stat, '.')
-        self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED)
-        # check_dir should only modify the sync_state, not clean_state
-        self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT)
-
-
-class TestSVNStatusXML(unittest.TestCase):
-    """Test parsing of svn status xml output
-    """
-    SVN_STATUS_XML_DIRTY_ALL = '''
-<status>
-<target
-   path=".">
-<entry
-   path="ChangeLog">
-<wc-status
-   item="missing"
-   revision="86711"
-   props="none">
-<commit
-   revision="85703">
-<author>sacks</author>
-<date>2017-06-15T11:59:00.355419Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="README.parallelization">
-<wc-status
-   props="none"
-   item="modified"
-   revision="86711">
-<commit
-   revision="43811">
-<author>sacks</author>
-<date>2013-02-07T16:17:56.412878Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="SVN_EXTERNAL_DIRECTORIES">
-<wc-status
-   item="deleted"
-   revision="86711"
-   props="none">
-<commit
-   revision="84725">
-<author>sacks</author>
-<date>2017-05-01T16:48:27.893741Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="junk.txt">
-<wc-status
-   item="unversioned"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="stuff.txt">
-<wc-status
-   props="none"
-   item="added"
-   revision="-1">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_MISSING = '''
-<status>
-<target
-   path=".">
-<entry
-   path="ChangeLog">
-<wc-status
-   item="missing"
-   revision="86711"
-   props="none">
-<commit
-   revision="85703">
-<author>sacks</author>
-<date>2017-06-15T11:59:00.355419Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_MODIFIED = '''
-<status>
-<target
-   path=".">
-<entry
-   path="README.parallelization">
-<wc-status
-   props="none"
-   item="modified"
-   revision="86711">
-<commit
-   revision="43811">
-<author>sacks</author>
-<date>2013-02-07T16:17:56.412878Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_DELETED = '''
-<status>
-<target
-   path=".">
-<entry
-   path="SVN_EXTERNAL_DIRECTORIES">
-<wc-status
-   item="deleted"
-   revision="86711"
-   props="none">
-<commit
-   revision="84725">
-<author>sacks</author>
-<date>2017-05-01T16:48:27.893741Z</date>
-</commit>
-</wc-status>
-</entry>
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_UNVERSION = '''
-<status>
-<target
-   path=".">
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="junk.txt">
-<wc-status
-   item="unversioned"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_DIRTY_ADDED = '''
-<status>
-<target
-   path=".">
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="stuff.txt">
-<wc-status
-   props="none"
-   item="added"
-   revision="-1">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    SVN_STATUS_XML_CLEAN = '''
-<status>
-<target
-   path=".">
-<entry
-   path="glimmer-cism">
-<wc-status
-   item="external"
-   props="none">
-</wc-status>
-</entry>
-<entry
-   path="junk.txt">
-<wc-status
-   item="unversioned"
-   props="none">
-</wc-status>
-</entry>
-</target>
-</status>'''
-
-    def test_xml_status_dirty_missing(self):
-        """Verify that svn status output is consindered dirty when there is a
-        missing file.
-
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_MISSING
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_modified(self):
-        """Verify that svn status output is consindered dirty when there is a
-        modified file.
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_MODIFIED
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_deleted(self):
-        """Verify that svn status output is consindered dirty when there is a
-        deleted file.
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_DELETED
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_unversion(self):
-        """Verify that svn status output ignores unversioned files when making
-        the clean/dirty decision.
-
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_UNVERSION
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertFalse(is_dirty)
-
-    def test_xml_status_dirty_added(self):
-        """Verify that svn status output is consindered dirty when there is a
-        added file.
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_ADDED
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_all(self):
-        """Verify that svn status output is consindered dirty when there are
-        multiple dirty files..
-
-        """
-        svn_output = self.SVN_STATUS_XML_DIRTY_ALL
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertTrue(is_dirty)
-
-    def test_xml_status_dirty_clean(self):
-        """Verify that svn status output is consindered clean when there are
-        no 'dirty' files. This means accepting untracked and externals.
-
-        """
-        svn_output = self.SVN_STATUS_XML_CLEAN
-        is_dirty = SvnRepository.xml_status_is_dirty(
-            svn_output)
-        self.assertFalse(is_dirty)
-
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/manage_externals/test/test_unit_utils.py b/manage_externals/test/test_unit_utils.py
deleted file mode 100644
index 80e1636649..0000000000
--- a/manage_externals/test/test_unit_utils.py
+++ /dev/null
@@ -1,350 +0,0 @@
-#!/usr/bin/env python3
-
-"""Unit test driver for checkout_externals
-
-Note: this script assume the path to the checkout_externals.py module is
-already in the python path.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from __future__ import print_function
-
-import os
-import unittest
-
-from manic.utils import last_n_lines, indent_string
-from manic.utils import str_to_bool, execute_subprocess
-from manic.utils import is_remote_url, split_remote_url, expand_local_url
-
-
-class TestExecuteSubprocess(unittest.TestCase):
-    """Test the application logic of execute_subprocess wrapper
-    """
-
-    def test_exesub_return_stat_err(self):
-        """Test that execute_subprocess returns a status code when caller
-        requests and the executed subprocess fails.
-
-        """
-        cmd = ['false']
-        status = execute_subprocess(cmd, status_to_caller=True)
-        self.assertEqual(status, 1)
-
-    def test_exesub_return_stat_ok(self):
-        """Test that execute_subprocess returns a status code when caller
-        requests and the executed subprocess succeeds.
-
-        """
-        cmd = ['true']
-        status = execute_subprocess(cmd, status_to_caller=True)
-        self.assertEqual(status, 0)
-
-    def test_exesub_except_stat_err(self):
-        """Test that execute_subprocess raises an exception on error when
-        caller doesn't request return code
-
-        """
-        cmd = ['false']
-        with self.assertRaises(RuntimeError):
-            execute_subprocess(cmd, status_to_caller=False)
-
-
-class TestLastNLines(unittest.TestCase):
-    """Test the last_n_lines function.
-
-    """
-
-    def test_last_n_lines_short(self):
-        """With a message with <= n lines, result of last_n_lines should
-        just be the original message.
-
-        """
-        mystr = """three
-line
-string
-"""
-
-        mystr_truncated = last_n_lines(
-            mystr, 3, truncation_message='[truncated]')
-        self.assertEqual(mystr, mystr_truncated)
-
-    def test_last_n_lines_long(self):
-        """With a message with > n lines, result of last_n_lines should
-        be a truncated string.
-
-        """
-        mystr = """a
-big
-five
-line
-string
-"""
-        expected = """[truncated]
-five
-line
-string
-"""
-
-        mystr_truncated = last_n_lines(
-            mystr, 3, truncation_message='[truncated]')
-        self.assertEqual(expected, mystr_truncated)
-
-
-class TestIndentStr(unittest.TestCase):
-    """Test the indent_string function.
-
-    """
-
-    def test_indent_string_singleline(self):
-        """Test the indent_string function with a single-line string
-
-        """
-        mystr = 'foo'
-        result = indent_string(mystr, 4)
-        expected = '    foo'
-        self.assertEqual(expected, result)
-
-    def test_indent_string_multiline(self):
-        """Test the indent_string function with a multi-line string
-
-        """
-        mystr = """hello
-hi
-goodbye
-"""
-        result = indent_string(mystr, 2)
-        expected = """  hello
-  hi
-  goodbye
-"""
-        self.assertEqual(expected, result)
-
-
-class TestStrToBool(unittest.TestCase):
-    """Test the string to boolean conversion routine.
-
-    """
-
-    def test_case_insensitive_true(self):
-        """Verify that case insensitive variants of 'true' returns the True
-        boolean.
-
-        """
-        values = ['true', 'TRUE', 'True', 'tRuE', 't', 'T', ]
-        for value in values:
-            received = str_to_bool(value)
-            self.assertTrue(received)
-
-    def test_case_insensitive_false(self):
-        """Verify that case insensitive variants of 'false' returns the False
-        boolean.
-
-        """
-        values = ['false', 'FALSE', 'False', 'fAlSe', 'f', 'F', ]
-        for value in values:
-            received = str_to_bool(value)
-            self.assertFalse(received)
-
-    def test_invalid_str_error(self):
-        """Verify that a non-true/false string generates a runtime error.
-        """
-        values = ['not_true_or_false', 'A', '1', '0',
-                  'false_is_not_true', 'true_is_not_false']
-        for value in values:
-            with self.assertRaises(RuntimeError):
-                str_to_bool(value)
-
-
-class TestIsRemoteURL(unittest.TestCase):
-    """Crude url checking to determine if a url is local or remote.
-
-    """
-
-    def test_url_remote_git(self):
-        """verify that a remote git url is identified.
-        """
-        url = 'git@somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_remote_ssh(self):
-        """verify that a remote ssh url is identified.
-        """
-        url = 'ssh://user@somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_remote_http(self):
-        """verify that a remote http url is identified.
-        """
-        url = 'http://somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_remote_https(self):
-        """verify that a remote https url is identified.
-        """
-        url = 'https://somewhere'
-        is_remote = is_remote_url(url)
-        self.assertTrue(is_remote)
-
-    def test_url_local_user(self):
-        """verify that a local path with '~/path/to/repo' gets rejected
-
-        """
-        url = '~/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_var_curly(self):
-        """verify that a local path with env var '${HOME}' gets rejected
-        """
-        url = '${HOME}/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_var(self):
-        """verify that a local path with an env var '$HOME' gets rejected
-        """
-        url = '$HOME/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_abs(self):
-        """verify that a local abs path gets rejected
-        """
-        url = '/path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-    def test_url_local_rel(self):
-        """verify that a local relative path gets rejected
-        """
-        url = '../../path/to/repo'
-        is_remote = is_remote_url(url)
-        self.assertFalse(is_remote)
-
-
-class TestSplitRemoteURL(unittest.TestCase):
-    """Crude url checking to determine if a url is local or remote.
-
-    """
-
-    def test_url_remote_git(self):
-        """verify that a remote git url is identified.
-        """
-        url = 'git@somewhere.com:org/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, "org/repo")
-
-    def test_url_remote_ssh(self):
-        """verify that a remote ssh url is identified.
-        """
-        url = 'ssh://user@somewhere.com/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, 'somewhere.com/path/to/repo')
-
-    def test_url_remote_http(self):
-        """verify that a remote http url is identified.
-        """
-        url = 'http://somewhere.org/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, 'somewhere.org/path/to/repo')
-
-    def test_url_remote_https(self):
-        """verify that a remote http url is identified.
-        """
-        url = 'http://somewhere.gov/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, 'somewhere.gov/path/to/repo')
-
-    def test_url_local_url_unchanged(self):
-        """verify that a local path is unchanged
-
-        """
-        url = '/path/to/repo'
-        received = split_remote_url(url)
-        self.assertEqual(received, url)
-
-
-class TestExpandLocalURL(unittest.TestCase):
-    """Crude url checking to determine if a url is local or remote.
-
-    Remote should be unmodified.
-
-    Local, should perform user and variable expansion.
-
-    """
-
-    def test_url_local_user1(self):
-        """verify that a local path with '~/path/to/repo' gets expanded to an
-        absolute path.
-
-        NOTE(bja, 2017-11) we can't test for something like:
-        '~user/path/to/repo' because the user has to be in the local
-        machine password directory and we don't know a user name that
-        is valid on every system....?
-
-        """
-        field = 'test'
-        url = '~/path/to/repo'
-        received = expand_local_url(url, field)
-        print(received)
-        self.assertTrue(os.path.isabs(received))
-
-    def test_url_local_expand_curly(self):
-        """verify that a local path with '${HOME}' gets expanded to an absolute path.
-        """
-        field = 'test'
-        url = '${HOME}/path/to/repo'
-        received = expand_local_url(url, field)
-        self.assertTrue(os.path.isabs(received))
-
-    def test_url_local_expand_var(self):
-        """verify that a local path with '$HOME' gets expanded to an absolute path.
-        """
-        field = 'test'
-        url = '$HOME/path/to/repo'
-        received = expand_local_url(url, field)
-        self.assertTrue(os.path.isabs(received))
-
-    def test_url_local_env_missing(self):
-        """verify that a local path with env var that is missing gets left as-is
-
-        """
-        field = 'test'
-        url = '$TMP_VAR/path/to/repo'
-        received = expand_local_url(url, field)
-        print(received)
-        self.assertEqual(received, url)
-
-    def test_url_local_expand_env(self):
-        """verify that a local path with another env var gets expanded to an
-        absolute path.
-
-        """
-        field = 'test'
-        os.environ['TMP_VAR'] = '/some/absolute'
-        url = '$TMP_VAR/path/to/repo'
-        received = expand_local_url(url, field)
-        del os.environ['TMP_VAR']
-        print(received)
-        self.assertTrue(os.path.isabs(received))
-        self.assertEqual(received, '/some/absolute/path/to/repo')
-
-    def test_url_local_normalize_rel(self):
-        """verify that a local path with another env var gets expanded to an
-        absolute path.
-
-        """
-        field = 'test'
-        url = '/this/is/a/long/../path/to/a/repo'
-        received = expand_local_url(url, field)
-        print(received)
-        self.assertEqual(received, '/this/is/a/path/to/a/repo')
-
-
-if __name__ == '__main__':
-    unittest.main()

From 0f7d429f0071995504ef41a91215724c957e2fb6 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 27 May 2024 17:40:56 -0600
Subject: [PATCH 0336/1248] add submodules

---
 .gitignore           | 11 -----------
 .gitmodules          | 39 +++++++++++++++++++++++++++++++++++++++
 ccs_config           |  1 +
 cime                 |  1 +
 components/cdeps     |  1 +
 components/cism      |  1 +
 components/cmeps     |  1 +
 components/mizuRoute |  1 +
 components/mosart    |  1 +
 components/rtm       |  1 +
 doc/doc-builder      |  1 +
 libraries/mct        |  1 +
 libraries/parallelio |  1 +
 share                |  1 +
 src/fates            |  1 +
 15 files changed, 52 insertions(+), 11 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 ccs_config
 create mode 160000 cime
 create mode 160000 components/cdeps
 create mode 160000 components/cism
 create mode 160000 components/cmeps
 create mode 160000 components/mizuRoute
 create mode 160000 components/mosart
 create mode 160000 components/rtm
 create mode 160000 doc/doc-builder
 create mode 160000 libraries/mct
 create mode 160000 libraries/parallelio
 create mode 160000 share
 create mode 160000 src/fates

diff --git a/.gitignore b/.gitignore
index 163bfeda2d..a083a7853f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,14 +1,3 @@
-# directories checked out by manage_externals, and other files created
-# by manage_externals
-manage_externals.log
-ccs_config
-/src/fates/
-/cime/
-/components/
-/libraries/
-/share/
-/doc/doc-builder/
-
 # ignore svn directories
 **/.svn/**
 .svn/
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000..329ed2e748
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,39 @@
+[submodule "fates"]
+	path = src/fates
+	url = https://github.com/NGEET/fates
+[submodule "cism"]
+	path = components/cism
+	url = https://github.com/ESCOMP/CISM-wrapper
+[submodule "mosart"]
+	path = components/mosart
+	url = https://github.com/ESCOMP/MOSART
+[submodule "rtm"]
+	path = components/rtm
+	url = https://github.com/ESCOMP/RTM
+[submodule "mizuRoute"]
+	path = components/mizuRoute
+	url = https://github.com/ESCOMP/mizuRoute
+[submodule "ccs_config"]
+	path = ccs_config
+	url = https://github.com/ESMCI/ccs_config_cesm.git
+[submodule "cime"]
+	path = cime
+	url = https://github.com/ESMCI/cime
+[submodule "cmeps"]
+	path = components/cmeps
+	url = https://github.com/ESCOMP/CMEPS.git
+[submodule "cdeps"]
+	path = components/cdeps
+	url = https://github.com/ESCOMP/CDEPS.git
+[submodule "share"]
+	path = share
+	url = https://github.com/ESCOMP/CESM_share
+[submodule "mct"]
+	path = libraries/mct
+	url = https://github.com/MCSclimate/MCT
+[submodule "parallelio"]
+	path = libraries/parallelio
+	url = https://github.com/NCAR/ParallelIO
+[submodule "doc-builder"]
+	path = doc/doc-builder
+	url = https://github.com/ESMCI/doc-builder
diff --git a/ccs_config b/ccs_config
new file mode 160000
index 0000000000..f90e10502c
--- /dev/null
+++ b/ccs_config
@@ -0,0 +1 @@
+Subproject commit f90e10502c7246c2b45e373b7dd5e0da6cba0828
diff --git a/cime b/cime
new file mode 160000
index 0000000000..422ddaa770
--- /dev/null
+++ b/cime
@@ -0,0 +1 @@
+Subproject commit 422ddaa770a3cea6e83a60c9700ebce77acaceed
diff --git a/components/cdeps b/components/cdeps
new file mode 160000
index 0000000000..7a522c828c
--- /dev/null
+++ b/components/cdeps
@@ -0,0 +1 @@
+Subproject commit 7a522c828c32dc35777992653f281ec525509c4a
diff --git a/components/cism b/components/cism
new file mode 160000
index 0000000000..c05dd5c4fc
--- /dev/null
+++ b/components/cism
@@ -0,0 +1 @@
+Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928
diff --git a/components/cmeps b/components/cmeps
new file mode 160000
index 0000000000..6384ff4e4a
--- /dev/null
+++ b/components/cmeps
@@ -0,0 +1 @@
+Subproject commit 6384ff4e4a6bc82a678f9419a43ffbd5d53ac209
diff --git a/components/mizuRoute b/components/mizuRoute
new file mode 160000
index 0000000000..0a62ee6185
--- /dev/null
+++ b/components/mizuRoute
@@ -0,0 +1 @@
+Subproject commit 0a62ee6185bdc9b99cd88ed5f15ea850602c43a2
diff --git a/components/mosart b/components/mosart
new file mode 160000
index 0000000000..1c22a8c547
--- /dev/null
+++ b/components/mosart
@@ -0,0 +1 @@
+Subproject commit 1c22a8c5478b714cf5b7c54b3e5cf7bad09fd9b2
diff --git a/components/rtm b/components/rtm
new file mode 160000
index 0000000000..88503adbc2
--- /dev/null
+++ b/components/rtm
@@ -0,0 +1 @@
+Subproject commit 88503adbc275fb2ccbb6b598e460deaeb140e515
diff --git a/doc/doc-builder b/doc/doc-builder
new file mode 160000
index 0000000000..ab9bc93dd0
--- /dev/null
+++ b/doc/doc-builder
@@ -0,0 +1 @@
+Subproject commit ab9bc93dd09d0173f8097c7a18c7d061c1cd3b79
diff --git a/libraries/mct b/libraries/mct
new file mode 160000
index 0000000000..e36024c5dd
--- /dev/null
+++ b/libraries/mct
@@ -0,0 +1 @@
+Subproject commit e36024c5ddf482625ae6bd9474eff7d8f393f87c
diff --git a/libraries/parallelio b/libraries/parallelio
new file mode 160000
index 0000000000..6539ef05ae
--- /dev/null
+++ b/libraries/parallelio
@@ -0,0 +1 @@
+Subproject commit 6539ef05ae7584ec570a56fdab9f7dfb336c2b80
diff --git a/share b/share
new file mode 160000
index 0000000000..4b9dc4871a
--- /dev/null
+++ b/share
@@ -0,0 +1 @@
+Subproject commit 4b9dc4871a259f00f35bb47708d876cb7dcdf75c
diff --git a/src/fates b/src/fates
new file mode 160000
index 0000000000..f0185f7c70
--- /dev/null
+++ b/src/fates
@@ -0,0 +1 @@
+Subproject commit f0185f7c7033fa69c80d1ddb07cbcbf1f8be1adc

From aa544736634b4e095b691c2d5168dbd3c8de9cef Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 27 May 2024 17:43:00 -0600
Subject: [PATCH 0337/1248] update submodules

---
 .gitmodules                                   | 105 ++-
 .../git-fleximod/.github/workflows/pre-commit |  13 +
 .../.github/workflows/pytest.yaml             |  77 ++
 .lib/git-fleximod/.pre-commit-config.yaml     |  18 +
 .lib/git-fleximod/License                     |  20 +
 .lib/git-fleximod/README.md                   | 110 +++
 .lib/git-fleximod/doc/Makefile                |  20 +
 .lib/git-fleximod/doc/conf.py                 |  26 +
 .lib/git-fleximod/doc/index.rst               |  24 +
 .lib/git-fleximod/doc/make.bat                |  35 +
 .lib/git-fleximod/escomp_install              |  25 +
 .lib/git-fleximod/git_fleximod/__init__.py    |   0
 .lib/git-fleximod/git_fleximod/cli.py         | 119 +++
 .../git-fleximod/git_fleximod/git_fleximod.py | 601 +++++++++++++++
 .../git-fleximod/git_fleximod/gitinterface.py |  79 ++
 .lib/git-fleximod/git_fleximod/gitmodules.py  |  97 +++
 .../git-fleximod/git_fleximod/lstripreader.py |  43 ++
 .lib/git-fleximod/git_fleximod/metoflexi.py   | 236 ++++++
 .lib/git-fleximod/git_fleximod/utils.py       | 365 +++++++++
 .lib/git-fleximod/poetry.lock                 | 693 ++++++++++++++++++
 .lib/git-fleximod/pyproject.toml              |  41 ++
 .lib/git-fleximod/tbump.toml                  |  43 ++
 .lib/git-fleximod/tests/__init__.py           |   3 +
 .lib/git-fleximod/tests/conftest.py           | 138 ++++
 .lib/git-fleximod/tests/test_a_import.py      |   8 +
 .lib/git-fleximod/tests/test_b_update.py      |  26 +
 .lib/git-fleximod/tests/test_c_required.py    |  30 +
 .lib/git-fleximod/tests/test_d_complex.py     |  67 ++
 bin/git-fleximod                              |   8 +
 ccs_config                                    |   2 +-
 components/cdeps                              |   2 +-
 components/mizuRoute                          |   2 +-
 components/mosart                             |   2 +-
 libraries/mct                                 |   2 +-
 libraries/parallelio                          |   2 +-
 src/fates                                     |   2 +-
 36 files changed, 3050 insertions(+), 34 deletions(-)
 create mode 100644 .lib/git-fleximod/.github/workflows/pre-commit
 create mode 100644 .lib/git-fleximod/.github/workflows/pytest.yaml
 create mode 100644 .lib/git-fleximod/.pre-commit-config.yaml
 create mode 100644 .lib/git-fleximod/License
 create mode 100644 .lib/git-fleximod/README.md
 create mode 100644 .lib/git-fleximod/doc/Makefile
 create mode 100644 .lib/git-fleximod/doc/conf.py
 create mode 100644 .lib/git-fleximod/doc/index.rst
 create mode 100644 .lib/git-fleximod/doc/make.bat
 create mode 100644 .lib/git-fleximod/escomp_install
 create mode 100644 .lib/git-fleximod/git_fleximod/__init__.py
 create mode 100644 .lib/git-fleximod/git_fleximod/cli.py
 create mode 100755 .lib/git-fleximod/git_fleximod/git_fleximod.py
 create mode 100644 .lib/git-fleximod/git_fleximod/gitinterface.py
 create mode 100644 .lib/git-fleximod/git_fleximod/gitmodules.py
 create mode 100644 .lib/git-fleximod/git_fleximod/lstripreader.py
 create mode 100755 .lib/git-fleximod/git_fleximod/metoflexi.py
 create mode 100644 .lib/git-fleximod/git_fleximod/utils.py
 create mode 100644 .lib/git-fleximod/poetry.lock
 create mode 100644 .lib/git-fleximod/pyproject.toml
 create mode 100644 .lib/git-fleximod/tbump.toml
 create mode 100644 .lib/git-fleximod/tests/__init__.py
 create mode 100644 .lib/git-fleximod/tests/conftest.py
 create mode 100644 .lib/git-fleximod/tests/test_a_import.py
 create mode 100644 .lib/git-fleximod/tests/test_b_update.py
 create mode 100644 .lib/git-fleximod/tests/test_c_required.py
 create mode 100644 .lib/git-fleximod/tests/test_d_complex.py
 create mode 100755 bin/git-fleximod

diff --git a/.gitmodules b/.gitmodules
index 329ed2e748..699ad22969 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,39 +1,90 @@
 [submodule "fates"]
-	path = src/fates
-	url = https://github.com/NGEET/fates
+path = src/fates
+url = https://github.com/NGEET/fates
+fxtag = sci.1.73.0_api.35.0.0
+fxrequired = AlwaysRequired
+fxDONOTUSEurl = https://github.com/NCAR/fates-release
+
 [submodule "cism"]
-	path = components/cism
-	url = https://github.com/ESCOMP/CISM-wrapper
-[submodule "mosart"]
-	path = components/mosart
-	url = https://github.com/ESCOMP/MOSART
+path = components/cism
+url = https://github.com/ESCOMP/CISM-wrapper
+fxtag = cismwrap_2_2_001
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
+
 [submodule "rtm"]
-	path = components/rtm
-	url = https://github.com/ESCOMP/RTM
+path = components/rtm
+url = https://github.com/ESCOMP/RTM
+fxtag = rtm1_0_79
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/RTM
+
+[submodule "mosart"]
+path = components/mosart
+url = https://github.com/ESCOMP/MOSART
+fxtag = mosart1_0_49
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
+
 [submodule "mizuRoute"]
-	path = components/mizuRoute
-	url = https://github.com/ESCOMP/mizuRoute
+path = components/mizuRoute
+url = https://github.com/ESCOMP/mizuRoute
+fxtag = cesm-coupling.n02_v2.1.2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
+        
 [submodule "ccs_config"]
-	path = ccs_config
-	url = https://github.com/ESMCI/ccs_config_cesm.git
+path = ccs_config
+url = https://github.com/ESMCI/ccs_config_cesm.git
+fxtag = ccs_config_cesm0.0.106
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
+
 [submodule "cime"]
-	path = cime
-	url = https://github.com/ESMCI/cime
+path = cime
+url = https://github.com/ESMCI/cime
+fxtag = cime6.0.246
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESMCI/cime
+
 [submodule "cmeps"]
-	path = components/cmeps
-	url = https://github.com/ESCOMP/CMEPS.git
+path = components/cmeps
+url = https://github.com/ESCOMP/CMEPS.git
+fxtag = cmeps0.14.63
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
+
 [submodule "cdeps"]
-	path = components/cdeps
-	url = https://github.com/ESCOMP/CDEPS.git
+path = components/cdeps
+url = https://github.com/ESCOMP/CDEPS.git
+fxtag = cdeps1.0.34
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
+
 [submodule "share"]
-	path = share
-	url = https://github.com/ESCOMP/CESM_share
+path = share
+url = https://github.com/ESCOMP/CESM_share
+fxtag = share1.0.19
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
+
 [submodule "mct"]
-	path = libraries/mct
-	url = https://github.com/MCSclimate/MCT
+path = libraries/mct
+url = https://github.com/MCSclimate/MCT
+fxtag = MCT_2.11.0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/MCSclimate/MCT
+
 [submodule "parallelio"]
-	path = libraries/parallelio
-	url = https://github.com/NCAR/ParallelIO
+path = libraries/parallelio
+url = https://github.com/NCAR/ParallelIO
+fxtag = pio2_6_2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
+
 [submodule "doc-builder"]
-	path = doc/doc-builder
-	url = https://github.com/ESMCI/doc-builder
+path = doc/doc-builder
+url = https://github.com/ESMCI/doc-builder
+fxtag = v1.0.8
+fxrequired = ToplevelOptional
+fxDONOTUSEurl = https://github.com/ESMCI/doc-builder
diff --git a/.lib/git-fleximod/.github/workflows/pre-commit b/.lib/git-fleximod/.github/workflows/pre-commit
new file mode 100644
index 0000000000..1a6ad0082a
--- /dev/null
+++ b/.lib/git-fleximod/.github/workflows/pre-commit
@@ -0,0 +1,13 @@
+name: pre-commit
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml
new file mode 100644
index 0000000000..0868dd9a33
--- /dev/null
+++ b/.lib/git-fleximod/.github/workflows/pytest.yaml
@@ -0,0 +1,77 @@
+# Run this job on pushes to `main`, and for pull requests. If you don't specify
+# `branches: [main], then this actions runs _twice_ on pull requests, which is
+# annoying.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
+      # reference the matrixe python version here.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
+      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
+      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
+      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
+      # mildly cleaner by using an environment variable, but I don't really care.
+      - name: cache poetry install
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: poetry-1.7.1
+
+      # Install Poetry. You could do this manually, or there are several actions that do this.
+      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
+      # Poetry's default install script, which feels correct. I pin the Poetry version here
+      # because Poetry does occasionally change APIs between versions and I don't want my
+      # actions to break if it does.
+      #
+      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
+      # venv as a `.venv` in your testing directory, which allows the next step to easily
+      # cache it.
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.7.1
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
+      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
+      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
+      - name: cache deps
+        id: cache-deps
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+
+      # Install dependencies. `--no-root` means "install all dependencies but not the project
+      # itself", which is what you want to avoid caching _your_ code. The `if` statement
+      # ensures this only runs on a cache miss.
+      - run: poetry install --no-interaction --no-root
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+
+      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
+      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
+      # pyproject.toml and makes that if you add things like console-scripts at some point that
+      # they'll be installed and working.
+      - run: poetry install --no-interaction
+
+      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
+      # so this line is super-simple. But it could be as complex as you need.
+      - run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+          poetry run pytest
+
diff --git a/.lib/git-fleximod/.pre-commit-config.yaml b/.lib/git-fleximod/.pre-commit-config.yaml
new file mode 100644
index 0000000000..2f6089da72
--- /dev/null
+++ b/.lib/git-fleximod/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+exclude: ^utils/.*$
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/pylint
+    rev: v2.11.1
+    hooks:
+      - id: pylint
+        args:
+          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/.lib/git-fleximod/License b/.lib/git-fleximod/License
new file mode 100644
index 0000000000..2c6fe768c2
--- /dev/null
+++ b/.lib/git-fleximod/License
@@ -0,0 +1,20 @@
+Copyright 2024 National Center for Atmospheric Sciences (NCAR)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+“Software”), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/.lib/git-fleximod/README.md b/.lib/git-fleximod/README.md
new file mode 100644
index 0000000000..d1ef632f28
--- /dev/null
+++ b/.lib/git-fleximod/README.md
@@ -0,0 +1,110 @@
+# git-fleximod
+
+Flexible, Enhanced Submodule Management for Git
+
+## Overview
+
+Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
+
+## Installation
+
+#TODO    Install using pip:
+#        pip install git-fleximod
+  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
+
+## Usage
+
+    Basic Usage:
+        git fleximod <command> [options]
+    Available Commands:
+        status: Display the status of submodules.
+        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
+        test: Make sure that fxtags and submodule hashes are consistant,
+              make sure that official urls (as defined by fxDONOTUSEurl) are set
+              make sure that fxtags are defined for all submodules
+    Additional Options:
+        See git fleximod --help for more details.
+
+## Supported .gitmodules Variables
+
+    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxrequired: Mark a submodule's checkout behavior, with allowed values:
+      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
+      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - AlwaysRequired:       Always required (always checked out).
+      - AlwaysOptional:       Always optional (checked out with --optional flag).
+    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
+    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
+           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
+           changed by users.  Use the url variable to change to a fork if desired.
+
+## Sparse Checkouts
+
+    To enable sparse checkout for a submodule, set the fxsparse variable
+    in the .gitmodules file to the path of a file containing the desired
+    sparse checkout paths. Git-fleximod will automatically configure
+    sparse checkout based on this file when applicable commands are run.
+    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
+    for details on the format of this file.
+
+## Tests
+
+   The git fleximod test action is designed to be used by, for example, github workflows
+   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
+
+## Examples
+
+Here are some common usage examples:
+
+Update all submodules, including optional ones:
+```bash
+  git fleximod update --optional
+```
+
+Updating a specific submodule to the fxtag indicated in .gitmodules:
+
+```bash
+    git fleximod update submodule-name
+```
+Example .gitmodules entry:
+```ini, toml
+    [submodule "cosp2"]
+        path = src/physics/cosp2/src
+        url = https://github.com/CFMIP/COSPv2.0
+        fxsparse = ../.cosp_sparse_checkout
+        fxrequired = AlwaysRequired
+        fxtag = v2.1.4cesm
+```
+Explanation:
+
+This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
+should be checked out into the directory src/physics/cosp2/src
+relative to the .gitmodules directory.  It should be checked out from
+the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
+described in the file ../.cosp_sparse_checkout relative to the path
+directory.  It should be checked out anytime this .gitmodules entry is
+read.
+
+Additional example:
+```ini, toml
+    [submodule "cime"]
+        path = cime
+        url = https://github.com/jedwards4b/cime
+        fxrequired = ToplevelRequired
+        fxtag = cime6.0.198_rme01
+```
+
+Explanation:
+
+This entry indicates that the submodule cime should be checked out
+into a directory named cime at tag cime6.0.198_rme01 from the URL
+https://github.com/jedwards4b/cime.  This should only be done if
+the .gitmodules file is at the top level of the repository clone.
+
+## Contributing
+
+We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
+
+## License
+
+Git-fleximod is released under the MIT License.
diff --git a/.lib/git-fleximod/doc/Makefile b/.lib/git-fleximod/doc/Makefile
new file mode 100644
index 0000000000..d4bb2cbb9e
--- /dev/null
+++ b/.lib/git-fleximod/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/.lib/git-fleximod/doc/conf.py b/.lib/git-fleximod/doc/conf.py
new file mode 100644
index 0000000000..423099eec9
--- /dev/null
+++ b/.lib/git-fleximod/doc/conf.py
@@ -0,0 +1,26 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "git-fleximod"
+author = "Jim Edwards <jedwards@ucar.edu>"
+release = "0.4.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx_argparse_cli"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]
diff --git a/.lib/git-fleximod/doc/index.rst b/.lib/git-fleximod/doc/index.rst
new file mode 100644
index 0000000000..0f9c1a7f7e
--- /dev/null
+++ b/.lib/git-fleximod/doc/index.rst
@@ -0,0 +1,24 @@
+.. git-fleximod documentation master file, created by
+   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to git-fleximod's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+.. module:: sphinxcontrib.autoprogram
+.. sphinx_argparse_cli::
+   :module: git_fleximod.cli
+   :func: get_parser
+   :prog: git-fleximod
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/.lib/git-fleximod/doc/make.bat b/.lib/git-fleximod/doc/make.bat
new file mode 100644
index 0000000000..32bb24529f
--- /dev/null
+++ b/.lib/git-fleximod/doc/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/.lib/git-fleximod/escomp_install b/.lib/git-fleximod/escomp_install
new file mode 100644
index 0000000000..ae782e72a4
--- /dev/null
+++ b/.lib/git-fleximod/escomp_install
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# updates git-fleximod in an ESCOMP model
+# this script should be run from the model root directory, it expects
+# git-fleximod to already be installed with the script in bin
+# and the classes in lib/python/site-packages
+import sys
+import shutil
+import os
+
+from glob import iglob
+
+fleximod_root = sys.argv[1]
+fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
+if os.path.isfile(fleximod_path):
+   with open(fleximod_path,"r") as f:
+        fleximod = f.readlines()
+   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
+        for line in fleximod:
+            f.write(line)
+            if "import argparse" in line:
+               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
+
+   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
+       shutil.copy(file,
+        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/.lib/git-fleximod/git_fleximod/__init__.py b/.lib/git-fleximod/git_fleximod/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
new file mode 100644
index 0000000000..1fb959dad0
--- /dev/null
+++ b/.lib/git-fleximod/git_fleximod/cli.py
@@ -0,0 +1,119 @@
+from pathlib import Path
+import argparse
+
+__version__ = "0.7.4"
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return attempt
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    #
+    # user options
+    #
+    choices = ["update", "status", "test"]
+    parser.add_argument(
+        "action",
+        choices=choices,
+        default="update",
+        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
+    )
+
+    parser.add_argument(
+        "components",
+        nargs="*",
+        help="Specific component(s) to checkout. By default, "
+        "all required submodules are checked out.",
+    )
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--exclude",
+        nargs="*",
+        help="Component(s) listed in the gitmodules file which should be ignored.",
+    )
+    parser.add_argument(
+        "-f",
+        "--force",
+        action="store_true",
+        default=False,
+        help="Override cautions and update or checkout over locally modified repository.",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--optional",
+        action="store_true",
+        default=False,
+        help="By default only the required submodules "
+        "are checked out. This flag will also checkout the "
+        "optional submodules relative to the toplevel directory.",
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+
+    parser.add_argument(
+        "-V",
+        "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Print version and exit.",
+    )
+
+    #
+    # developer options
+    #
+    parser.add_argument(
+        "--backtrace",
+        action="store_true",
+        help="DEVELOPER: show exception backtraces as extra " "debugging output",
+    )
+
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
new file mode 100755
index 0000000000..103cc82a50
--- /dev/null
+++ b/.lib/git-fleximod/git_fleximod/git_fleximod.py
@@ -0,0 +1,601 @@
+#!/usr/bin/env python
+import sys
+
+MIN_PYTHON = (3, 7)
+if sys.version_info < MIN_PYTHON:
+    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
+
+import os
+import shutil
+import logging
+import textwrap
+from git_fleximod import utils
+from git_fleximod import cli
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from configparser import NoOptionError
+
+# logger variable is global
+logger = None
+
+
+def fxrequired_allowed_values():
+    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
+
+
+def commandline_arguments(args=None):
+    parser = cli.get_parser()
+
+    if args:
+        options = parser.parse_args(args)
+    else:
+        options = parser.parse_args()
+
+    # explicitly listing a component overrides the optional flag
+    if options.optional or options.components:
+        fxrequired = [
+            "ToplevelRequired",
+            "ToplevelOptional",
+            "AlwaysRequired",
+            "AlwaysOptional",
+        ]
+    else:
+        fxrequired = ["ToplevelRequired", "AlwaysRequired"]
+
+    action = options.action
+    if not action:
+        action = "update"
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    if hasattr(options, "version"):
+        exit()
+
+    return (
+        options.path,
+        options.gitmodules,
+        fxrequired,
+        options.components,
+        options.exclude,
+        options.force,
+        action,
+    )
+
+
+def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
+    """
+    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
+    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
+    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
+    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
+    and disk space consuming.
+
+    Parameters:
+    root_dir (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    url (str): The URL of the submodule.
+    path (str): The path to the submodule.
+    sparsefile (str): The sparse file for the submodule.
+    tag (str, optional): The tag to checkout. Defaults to "master".
+
+    Returns:
+    None
+    """
+    logger.info("Called sparse_checkout for {}".format(name))
+    rgit = GitInterface(root_dir, logger)
+    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+    if superroot:
+        gitroot = superroot.strip()
+    else:
+        gitroot = root_dir.strip()
+    assert os.path.isdir(os.path.join(gitroot, ".git"))
+    # first create the module directory
+    if not os.path.isdir(os.path.join(root_dir, path)):
+        os.makedirs(os.path.join(root_dir, path))
+
+    # initialize a new git repo and set the sparse checkout flag
+    sprep_repo = os.path.join(root_dir, path)
+    sprepo_git = GitInterface(sprep_repo, logger)
+    if os.path.exists(os.path.join(sprep_repo, ".git")):
+        try:
+            logger.info("Submodule {} found".format(name))
+            chk = sprepo_git.config_get_value("core", "sparseCheckout")
+            if chk == "true":
+                logger.info("Sparse submodule {} already checked out".format(name))
+                return
+        except NoOptionError:
+            logger.debug("Sparse submodule {} not present".format(name))
+        except Exception as e:
+            utils.fatal_error("Unexpected error {} occured.".format(e))
+
+    sprepo_git.config_set_value("core", "sparseCheckout", "true")
+
+    # set the repository remote
+
+    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
+    status = sprepo_git.git_operation("remote", "-v")
+    if url not in status:
+        sprepo_git.git_operation("remote", "add", "origin", url)
+
+    topgit = os.path.join(gitroot, ".git")
+
+    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
+        with open(os.path.join(root_dir, ".git")) as f:
+            gitpath = os.path.relpath(
+                os.path.join(root_dir, f.read().split()[1]),
+                start=os.path.join(root_dir, path),
+            )
+        topgit = os.path.join(gitpath, "modules")
+    else:
+        topgit = os.path.relpath(
+            os.path.join(root_dir, ".git", "modules"),
+            start=os.path.join(root_dir, path),
+        )
+
+    with utils.pushd(sprep_repo):
+        if not os.path.isdir(topgit):
+            os.makedirs(topgit)
+    topgit += os.sep + name
+
+    if os.path.isdir(os.path.join(root_dir, path, ".git")):
+        with utils.pushd(sprep_repo):
+            shutil.move(".git", topgit)
+            with open(".git", "w") as f:
+                f.write("gitdir: " + os.path.relpath(topgit))
+            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
+            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
+        if os.path.isfile(gitsparse):
+            logger.warning(
+                "submodule {} is already initialized {}".format(name, topgit)
+            )
+            return
+
+        with utils.pushd(sprep_repo):
+            shutil.copy(sparsefile, gitsparse)
+
+    # Finally checkout the repo
+    sprepo_git.git_operation("fetch", "origin", "--tags")
+    sprepo_git.git_operation("checkout", tag)
+
+    print(f"Successfully checked out {name:>20} at {tag}")
+    rgit.config_set_value(f'submodule "{name}"', "active", "true")
+    rgit.config_set_value(f'submodule "{name}"', "url", url)
+
+
+def single_submodule_checkout(
+    root, name, path, url=None, tag=None, force=False, optional=False
+):
+    """
+    This function checks out a single git submodule.
+
+    Parameters:
+    root (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    path (str): The path to the submodule.
+    url (str, optional): The URL of the submodule. Defaults to None.
+    tag (str, optional): The tag to checkout. Defaults to None.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+    optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
+    git = GitInterface(root, logger)
+    repodir = os.path.join(root, path)
+    logger.info("Checkout {} into {}/{}".format(name, root, path))
+    # if url is provided update to the new url
+    tmpurl = None
+    repo_exists = False
+    if os.path.exists(os.path.join(repodir, ".git")):
+        logger.info("Submodule {} already checked out".format(name))
+        repo_exists = True
+    # Look for a .gitmodules file in the newly checkedout repo
+    if not repo_exists and url:
+        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
+        # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
+        # opened with a GitModules object we don't need to worry about restoring the file here
+        # it will be done by the GitModules class
+        if url.startswith("git@"):
+            tmpurl = url
+            url = url.replace("git@github.com:", "https://github.com/")
+            git.git_operation("clone", url, path)
+            smgit = GitInterface(repodir, logger)
+            if not tag:
+                tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
+            smgit.git_operation("checkout", tag)
+            # Now need to move the .git dir to the submodule location
+            rootdotgit = os.path.join(root, ".git")
+            if os.path.isfile(rootdotgit):
+                with open(rootdotgit) as f:
+                    line = f.readline()
+                    if line.startswith("gitdir: "):
+                        rootdotgit = line[8:].rstrip()
+
+            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
+            if os.path.exists(newpath):
+                shutil.rmtree(os.path.join(repodir, ".git"))
+            else:
+                shutil.move(os.path.join(repodir, ".git"), newpath)
+
+            with open(os.path.join(repodir, ".git"), "w") as f:
+                f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
+                
+    if not os.path.exists(repodir):
+        parent = os.path.dirname(repodir)
+        if not os.path.isdir(parent):
+            os.makedirs(parent)
+        git.git_operation("submodule", "add", "--name", name, "--", url, path) 
+
+    if not repo_exists or not tmpurl:
+        git.git_operation("submodule", "update", "--init", "--", path)
+            
+    if os.path.exists(os.path.join(repodir, ".gitmodules")):
+        # recursively handle this checkout
+        print(f"Recursively checking out submodules of {name}")
+        gitmodules = GitModules(logger, confpath=repodir)
+        requiredlist = ["AlwaysRequired"]
+        if optional:
+            requiredlist.append("AlwaysOptional")
+        submodules_checkout(gitmodules, repodir, requiredlist, force=force)
+    if not os.path.exists(os.path.join(repodir, ".git")):
+        utils.fatal_error(
+            f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}"
+        )
+
+    if tmpurl:
+        print(git.git_operation("restore", ".gitmodules"))
+
+    return
+
+
+def submodules_status(gitmodules, root_dir, toplevel=False):
+    testfails = 0
+    localmods = 0
+    needsupdate = 0
+    for name in gitmodules.sections():
+        path = gitmodules.get(name, "path")
+        tag = gitmodules.get(name, "fxtag")
+        required = gitmodules.get(name, "fxrequired")
+        level = required and "Toplevel" in required
+        if not path:
+            utils.fatal_error("No path found in .gitmodules for {}".format(name))
+        newpath = os.path.join(root_dir, path)
+        logger.debug("newpath is {}".format(newpath))
+        if not os.path.exists(os.path.join(newpath, ".git")):
+            rootgit = GitInterface(root_dir, logger)
+            # submodule commands use path, not name
+            url = gitmodules.get(name, "url")
+            url = url.replace("git@github.com:", "https://github.com/")
+            tags = rootgit.git_operation("ls-remote", "--tags", url)
+            atag = None
+            needsupdate += 1
+            if not toplevel and level:
+                continue
+            for htag in tags.split("\n"):
+                if tag and tag in htag:
+                    atag = (htag.split()[1])[10:]
+                    break
+            if tag and tag == atag:
+                print(f"e {name:>20} not checked out, aligned at tag {tag}")
+            elif tag:
+                ahash = rootgit.git_operation(
+                    "submodule", "status", "{}".format(path)
+                ).rstrip()
+                ahash = ahash[1 : len(tag) + 1]
+                if tag == ahash:
+                    print(f"e {name:>20} not checked out, aligned at hash {ahash}")
+                else:
+                    print(
+                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
+                    )
+                    testfails += 1
+            else:
+                print(f"e {name:>20} has no fxtag defined in .gitmodules")
+                testfails += 1
+        else:
+            with utils.pushd(newpath):
+                git = GitInterface(newpath, logger)
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                ahash = git.git_operation("status").partition("\n")[0].split()[-1]
+                if tag and atag == tag:
+                    print(f"  {name:>20} at tag {tag}")
+                elif tag and ahash[: len(tag)] == tag:
+                    print(f"  {name:>20} at hash {ahash}")
+                elif atag == ahash:
+                    print(f"  {name:>20} at hash {ahash}")
+                elif tag:
+                    print(
+                        f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"
+                    )
+                    testfails += 1
+                    needsupdate += 1
+                else:
+                    print(
+                        f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
+                    )
+                    testfails += 1
+
+                status = git.git_operation("status", "--ignore-submodules")
+                if "nothing to commit" not in status:
+                    localmods = localmods + 1
+                    print("M" + textwrap.indent(status, "                      "))
+
+    return testfails, localmods, needsupdate
+
+
+def submodules_update(gitmodules, root_dir, requiredlist, force):
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+
+    if localmods and not force:
+        local_mods_output()
+        return
+    if needsupdate == 0:
+        return
+
+    for name in gitmodules.sections():
+        fxtag = gitmodules.get(name, "fxtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        logger.info(
+            "name={} path={} url={} fxtag={} requiredlist={}".format(
+                name, os.path.join(root_dir, path), url, fxtag, requiredlist
+            )
+        )
+        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
+        fxrequired = gitmodules.get(name, "fxrequired")
+        assert fxrequired in fxrequired_allowed_values()
+        rgit = GitInterface(root_dir, logger)
+        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+
+        fxsparse = gitmodules.get(name, "fxsparse")
+
+        if (
+            fxrequired
+            and (superroot and "Toplevel" in fxrequired)
+            or fxrequired not in requiredlist
+        ):
+            if "ToplevelOptional" == fxrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+        if fxsparse:
+            logger.debug(
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
+                )
+            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
+        else:
+            logger.info(
+                "Calling submodule_checkout({},{},{},{})".format(
+                    root_dir, name, path, url
+                )
+            )
+
+            single_submodule_checkout(
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional=("AlwaysOptional" in requiredlist),
+            )
+
+        if os.path.exists(os.path.join(path, ".git")):
+            submoddir = os.path.join(root_dir, path)
+            with utils.pushd(submoddir):
+                git = GitInterface(submoddir, logger)
+                # first make sure the url is correct
+                upstream = git.git_operation("ls-remote", "--get-url").rstrip()
+                newremote = "origin"
+                if upstream != url:
+                    # TODO - this needs to be a unique name
+                    remotes = git.git_operation("remote", "-v")
+                    if url in remotes:
+                        for line in remotes:
+                            if url in line and "fetch" in line:
+                                newremote = line.split()[0]
+                                break
+                    else:
+                        i = 0
+                        while newremote in remotes:
+                            i = i + 1
+                            newremote = f"newremote.{i:02d}"
+                        git.git_operation("remote", "add", newremote, url)
+
+                tags = git.git_operation("tag", "-l")
+                if fxtag and fxtag not in tags:
+                    git.git_operation("fetch", newremote, "--tags")
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                if fxtag and fxtag != atag:
+                    try:
+                        git.git_operation("checkout", fxtag)
+                        print(f"{name:>20} updated to {fxtag}")
+                    except Exception as error:
+                        print(error)
+                elif not fxtag:
+                    print(f"No fxtag found for submodule {name:>20}")
+                else:
+                    print(f"{name:>20} up to date.")
+
+
+def local_mods_output():
+    text = """\
+    The submodules labeled with 'M' above are not in a clean state.
+    The following are options for how to proceed:
+    (1) Go into each submodule which is not in a clean state and issue a 'git status'
+        Either revert or commit your changes so that the submodule is in a clean state.
+    (2) use the --force option to git-fleximod
+    (3) you can name the particular submodules to update using the git-fleximod command line
+    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
+        then rerun git-fleximod update.
+"""
+    print(text)
+
+
+# checkout is done by update if required so this function may be depricated
+def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
+    """
+    This function checks out all git submodules based on the provided parameters.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+    requiredlist (list): The list of required modules.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
+    print("")
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    if localmods and not force:
+        local_mods_output()
+        return
+    if not needsupdate:
+        return
+    for name in gitmodules.sections():
+        fxrequired = gitmodules.get(name, "fxrequired")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        fxtag = gitmodules.get(name, "fxtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        if fxrequired and fxrequired not in requiredlist:
+            if "Optional" in fxrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+
+        if fxsparse:
+            logger.debug(
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
+                )
+            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
+        else:
+            logger.debug(
+                "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
+            )
+            single_submodule_checkout(
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional="AlwaysOptional" in requiredlist,
+            )
+
+
+def submodules_test(gitmodules, root_dir):
+    """
+    This function tests the git submodules based on the provided parameters.
+
+    It first checks that fxtags are present and in sync with submodule hashes.
+    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
+    and that sparse checkout files exist.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+
+    Returns:
+    int: The number of test failures.
+    """
+    # First check that fxtags are present and in sync with submodule hashes
+    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    print("")
+    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
+    # and that sparse checkout files exist
+    for name in gitmodules.sections():
+        url = gitmodules.get(name, "url")
+        fxurl = gitmodules.get(name, "fxDONOTMODIFYurl")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        path = gitmodules.get(name, "path")
+        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
+        url = url[:-4] if url.endswith(".git") else url
+        if not fxurl or url.lower() != fxurl.lower():
+            print(f"{name:>20} url {url} not in sync with required {fxurl}")
+            testfails += 1
+        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
+            print(f"{name:>20} sparse checkout file {fxsparse} not found")
+            testfails += 1
+    return testfails + localmods + needsupdate
+
+
+def main():
+    (
+        root_dir,
+        file_name,
+        fxrequired,
+        includelist,
+        excludelist,
+        force,
+        action,
+    ) = commandline_arguments()
+    # Get a logger for the package
+    global logger
+    logger = logging.getLogger(__name__)
+
+    logger.info("action is {}".format(action))
+
+    if not os.path.isfile(os.path.join(root_dir, file_name)):
+        file_path = utils.find_upwards(root_dir, file_name)
+
+        if file_path is None:
+            utils.fatal_error(
+                "No {} found in {} or any of it's parents".format(file_name, root_dir)
+            )
+
+        root_dir = os.path.dirname(file_path)
+    logger.info(
+        "root_dir is {} includelist={} excludelist={}".format(
+            root_dir, includelist, excludelist
+        )
+    )
+    gitmodules = GitModules(
+        logger,
+        confpath=root_dir,
+        conffile=file_name,
+        includelist=includelist,
+        excludelist=excludelist,
+    )
+    if not gitmodules.sections():
+        sys.exit("No submodule components found")
+    retval = 0
+    if action == "update":
+        submodules_update(gitmodules, root_dir, fxrequired, force)
+    elif action == "status":
+        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
+        if tfails + lmods + updates > 0:
+            print(
+                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
+            )
+            if lmods > 0:
+                local_mods_output()
+    elif action == "test":
+        retval = submodules_test(gitmodules, root_dir)
+    else:
+        utils.fatal_error(f"unrecognized action request {action}")
+    return retval
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py
new file mode 100644
index 0000000000..93ae38ecde
--- /dev/null
+++ b/.lib/git-fleximod/git_fleximod/gitinterface.py
@@ -0,0 +1,79 @@
+import os
+import sys
+from . import utils
+from pathlib import Path
+
+class GitInterface:
+    def __init__(self, repo_path, logger):
+        logger.debug("Initialize GitInterface for {}".format(repo_path))
+        if isinstance(repo_path, str):
+            self.repo_path = Path(repo_path).resolve()
+        elif isinstance(repo_path, Path):
+            self.repo_path = repo_path.resolve()
+        else:
+            raise TypeError("repo_path must be a str or Path object")
+        self.logger = logger
+        try:
+            import git
+
+            self._use_module = True
+            try:
+                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
+            except git.exc.InvalidGitRepositoryError:
+                self.git = git
+                self._init_git_repo()
+            msg = "Using GitPython interface to git"
+        except ImportError:
+            self._use_module = False
+            if not (self.repo_path / ".git").exists():
+                self._init_git_repo()
+            msg = "Using shell interface to git"
+        self.logger.info(msg)
+
+    def _git_command(self, operation, *args):
+        self.logger.info(operation)
+        if self._use_module and operation != "submodule":
+            try:
+                return getattr(self.repo.git, operation)(*args)
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return ["git", "-C", str(self.repo_path), operation] + list(args)
+
+    def _init_git_repo(self):
+        if self._use_module:
+            self.repo = self.git.Repo.init(str(self.repo_path))
+        else:
+            command = ("git", "-C", str(self.repo_path), "init")
+            utils.execute_subprocess(command)
+
+    # pylint: disable=unused-argument
+    def git_operation(self, operation, *args, **kwargs):
+        command = self._git_command(operation, *args)
+        self.logger.info(command)
+        if isinstance(command, list):
+            try:
+                return utils.execute_subprocess(command, output_to_caller=True)
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return command
+
+    def config_get_value(self, section, name):
+        if self._use_module:
+            config = self.repo.config_reader()
+            return config.get_value(section, name)
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
+            output = utils.execute_subprocess(cmd, output_to_caller=True)
+            return output.strip()
+
+    def config_set_value(self, section, name, value):
+        if self._use_module:
+            with self.repo.config_writer() as writer:
+                writer.set_value(section, name, value)
+            writer.release()  # Ensure changes are saved
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
+            self.logger.info(cmd)
+            utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/.lib/git-fleximod/git_fleximod/gitmodules.py b/.lib/git-fleximod/git_fleximod/gitmodules.py
new file mode 100644
index 0000000000..68c82d066f
--- /dev/null
+++ b/.lib/git-fleximod/git_fleximod/gitmodules.py
@@ -0,0 +1,97 @@
+import shutil
+from pathlib import Path
+from configparser import RawConfigParser, ConfigParser
+from .lstripreader import LstripReader
+
+
+class GitModules(RawConfigParser):
+    def __init__(
+        self,
+        logger,
+        confpath=Path.cwd(),
+        conffile=".gitmodules",
+        includelist=None,
+        excludelist=None,
+    ):
+        """
+        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
+        conffile: Name of the configuration file (defaults to .gitmodules).
+        includelist: Optional list of submodules to include.
+        excludelist: Optional list of submodules to exclude.
+        """
+        self.logger = logger
+        self.logger.debug(
+            "Creating a GitModules object {} {} {} {}".format(
+                confpath, conffile, includelist, excludelist
+            )
+        )
+        super().__init__()
+        self.conf_file = (Path(confpath) / Path(conffile))
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
+        self.includelist = includelist
+        self.excludelist = excludelist
+        self.isdirty = False
+        
+    def reload(self):
+        self.clear()
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
+
+        
+    def set(self, name, option, value):
+        """
+        Sets a configuration value for a specific submodule:
+        Ensures the appropriate section exists for the submodule.
+        Calls the parent class's set method to store the value.
+        """
+        self.isdirty = True
+        self.logger.debug("set called {} {} {}".format(name, option, value))
+        section = f'submodule "{name}"'
+        if not self.has_section(section):
+            self.add_section(section)
+        super().set(section, option, str(value))
+
+    # pylint: disable=redefined-builtin, arguments-differ
+    def get(self, name, option, raw=False, vars=None, fallback=None):
+        """
+        Retrieves a configuration value for a specific submodule:
+        Uses the parent class's get method to access the value.
+        Handles potential errors if the section or option doesn't exist.
+        """
+        self.logger.debug("get called {} {}".format(name, option))
+        section = f'submodule "{name}"'
+        try:
+            return ConfigParser.get(
+                self, section, option, raw=raw, vars=vars, fallback=fallback
+            )
+        except ConfigParser.NoOptionError:
+            return None
+
+    def save(self):
+        if self.isdirty:
+            self.logger.info("Writing {}".format(self.conf_file))
+            with open(self.conf_file, "w") as fd:
+                self.write(fd)
+        self.isdirty = False
+        
+    def __del__(self):
+        self.save()
+
+    def sections(self):
+        """Strip the submodule part out of section and just use the name"""
+        self.logger.debug("calling GitModules sections iterator")
+        names = []
+        for section in ConfigParser.sections(self):
+            name = section[11:-1]
+            if self.includelist and name not in self.includelist:
+                continue
+            if self.excludelist and name in self.excludelist:
+                continue
+            names.append(name)
+        return names
+
+    def items(self, name, raw=False, vars=None):
+        self.logger.debug("calling GitModules items for {}".format(name))
+        section = f'submodule "{name}"'
+        return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/.lib/git-fleximod/git_fleximod/lstripreader.py b/.lib/git-fleximod/git_fleximod/lstripreader.py
new file mode 100644
index 0000000000..01d5580ee8
--- /dev/null
+++ b/.lib/git-fleximod/git_fleximod/lstripreader.py
@@ -0,0 +1,43 @@
+class LstripReader(object):
+    "LstripReader formats .gitmodules files to be acceptable for configparser"
+
+    def __init__(self, filename):
+        with open(filename, "r") as infile:
+            lines = infile.readlines()
+        self._lines = list()
+        self._num_lines = len(lines)
+        self._index = 0
+        for line in lines:
+            self._lines.append(line.lstrip())
+
+    def readlines(self):
+        """Return all the lines from this object's file"""
+        return self._lines
+
+    def readline(self, size=-1):
+        """Format and return the next line or raise StopIteration"""
+        try:
+            line = self.next()
+        except StopIteration:
+            line = ""
+
+        if (size > 0) and (len(line) < size):
+            return line[0:size]
+
+        return line
+
+    def __iter__(self):
+        """Begin an iteration"""
+        self._index = 0
+        return self
+
+    def next(self):
+        """Return the next line or raise StopIteration"""
+        if self._index >= self._num_lines:
+            raise StopIteration
+
+        self._index = self._index + 1
+        return self._lines[self._index - 1]
+
+    def __next__(self):
+        return self.next()
diff --git a/.lib/git-fleximod/git_fleximod/metoflexi.py b/.lib/git-fleximod/git_fleximod/metoflexi.py
new file mode 100755
index 0000000000..cc347db2dd
--- /dev/null
+++ b/.lib/git-fleximod/git_fleximod/metoflexi.py
@@ -0,0 +1,236 @@
+#!/usr/bin/env python
+from configparser import ConfigParser
+import sys
+import shutil
+from pathlib import Path
+import argparse
+import logging
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from git_fleximod import utils
+
+logger = None
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return d
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    parser.add_argument('-e', '--externals', nargs='?',
+                        default='Externals.cfg',
+                        help='The externals description filename. '
+                        'Default: %(default)s.')
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
+
+def commandline_arguments(args=None):
+    parser = get_parser()
+
+    options = parser.parse_args(args)
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    return(
+        options.path,
+        options.gitmodules,
+        options.externals
+        )
+
+class ExternalRepoTranslator:
+    """
+    Translates external repositories configured in an INI-style externals file.
+    """
+
+    def __init__(self, rootpath, gitmodules, externals):
+        self.rootpath = rootpath
+        if gitmodules:
+            self.gitmodules = GitModules(logger, confpath=rootpath)
+        self.externals = (rootpath / Path(externals)).resolve()
+        print(f"Translating {self.externals}")
+        self.git = GitInterface(rootpath, logger)
+        
+#    def __del__(self):
+#        if (self.rootpath / "save.gitignore"):
+            
+
+    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
+        """
+        Translates a single repository based on configuration details.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            tag (str): The tag to use for the external repository.
+            url (str): The URL of the external repository.
+            path (str): The relative path within the main repository for the external repository.
+            efile (str): The external file or file containing submodules.
+            hash_ (str): The commit hash to checkout (if applicable).
+            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
+            protocol (str): The protocol to use (e.g., 'git', 'http').
+        """
+        assert protocol != "svn", "SVN protocol is not currently supported"
+        print(f"Translating repository {section}")
+        if efile:
+            file_path = Path(path) / Path(efile)
+            newroot = (self.rootpath / file_path).parent.resolve()
+            if not newroot.exists():
+                newroot.mkdir(parents=True)
+            logger.info("Newroot is {}".format(newroot))
+            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
+            newt.translate_repo()
+        if protocol == "externals_only":
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+        else:
+            newpath = (self.rootpath / Path(path))
+            if newpath.exists():
+                shutil.rmtree(newpath)
+                logger.info("Creating directory {}".format(newpath))
+            newpath.mkdir(parents=True)
+            if tag:
+                logger.info("cloning {}".format(section))
+                try:
+                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+                except:
+                    self.git.git_operation("clone", url, path)
+                    with utils.pushd(newpath):
+                        ngit = GitInterface(newpath, logger)
+                        ngit.git_operation("checkout", tag)
+            if hash_:
+                self.git.git_operation("clone", url, path)
+                git = GitInterface(newpath, logger)
+                git.git_operation("fetch", "origin")
+                git.git_operation("checkout", hash_)
+            if sparse:
+                print("setting as sparse submodule {}".format(section))
+                sparsefile = (newpath / Path(sparse))
+                newfile = (newpath / ".git" / "info" / "sparse-checkout")
+                print(f"sparsefile {sparsefile} newfile {newfile}")
+                shutil.copy(sparsefile, newfile)
+        
+            logger.info("adding submodule {}".format(section))        
+            self.gitmodules.save()
+            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
+            self.git.git_operation("submodule","absorbgitdirs")
+            self.gitmodules.reload()
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+    
+        
+    def translate_repo(self):
+        """
+        Translates external repositories defined within an external file.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            external_file (str): The path to the external file containing repository definitions.
+        """
+        econfig = ConfigParser()
+        econfig.read((self.rootpath / Path(self.externals)))
+
+        for section in econfig.sections():
+            if section == "externals_description":
+                logger.info("skipping section {}".format(section))
+                return
+            logger.info("Translating section {}".format(section))
+            tag = econfig.get(section, "tag", raw=False, fallback=None)
+            url = econfig.get(section, "repo_url", raw=False, fallback=None)
+            path = econfig.get(section, "local_path", raw=False, fallback=None)
+            efile = econfig.get(section, "externals", raw=False, fallback=None)
+            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
+            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
+            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
+
+            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
+
+
+
+def _main():
+    rootpath, gitmodules, externals = commandline_arguments()
+    global logger
+    logger = logging.getLogger(__name__)
+    with utils.pushd(rootpath):
+        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
+        logger.info("Translating {}".format(rootpath))
+        t.translate_repo()
+
+        
+if __name__ == "__main__":
+    sys.exit(_main())
diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
new file mode 100644
index 0000000000..7cc1de38cc
--- /dev/null
+++ b/.lib/git-fleximod/git_fleximod/utils.py
@@ -0,0 +1,365 @@
+#!/usr/bin/env python3
+"""
+Common public utilities for manic package
+
+"""
+
+import logging
+import os
+import subprocess
+import sys
+from threading import Timer
+from pathlib import Path
+
+LOCAL_PATH_INDICATOR = "."
+# ---------------------------------------------------------------------
+#
+# functions to massage text for output and other useful utilities
+#
+# ---------------------------------------------------------------------
+from contextlib import contextmanager
+
+
+@contextmanager
+def pushd(new_dir):
+    """context for chdir. usage: with pushd(new_dir)"""
+    previous_dir = os.getcwd()
+    os.chdir(new_dir)
+    try:
+        yield
+    finally:
+        os.chdir(previous_dir)
+
+
+def log_process_output(output):
+    """Log each line of process output at debug level so it can be
+    filtered if necessary. By default, output is a single string, and
+    logging.debug(output) will only put log info heading on the first
+    line. This makes it hard to filter with grep.
+
+    """
+    output = output.split("\n")
+    for line in output:
+        logging.debug(line)
+
+
+def printlog(msg, **kwargs):
+    """Wrapper script around print to ensure that everything printed to
+    the screen also gets logged.
+
+    """
+    logging.info(msg)
+    if kwargs:
+        print(msg, **kwargs)
+    else:
+        print(msg)
+    sys.stdout.flush()
+
+
+def find_upwards(root_dir, filename):
+    """Find a file in root dir or any of it's parents"""
+    d = Path(root_dir)
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.exists():
+            return attempt
+        d = d.parent
+    return None
+
+
+def last_n_lines(the_string, n_lines, truncation_message=None):
+    """Returns the last n lines of the given string
+
+    Args:
+        the_string: str
+        n_lines: int
+        truncation_message: str, optional
+
+    Returns a string containing the last n lines of the_string
+
+    If truncation_message is provided, the returned string begins with
+    the given message if and only if the string is greater than n lines
+    to begin with.
+    """
+
+    lines = the_string.splitlines(True)
+    if len(lines) <= n_lines:
+        return_val = the_string
+    else:
+        lines_subset = lines[-n_lines:]
+        str_truncated = "".join(lines_subset)
+        if truncation_message:
+            str_truncated = truncation_message + "\n" + str_truncated
+        return_val = str_truncated
+
+    return return_val
+
+
+def indent_string(the_string, indent_level):
+    """Indents the given string by a given number of spaces
+
+    Args:
+       the_string: str
+       indent_level: int
+
+    Returns a new string that is the same as the_string, except that
+    each line is indented by 'indent_level' spaces.
+
+    In python3, this can be done with textwrap.indent.
+    """
+
+    lines = the_string.splitlines(True)
+    padding = " " * indent_level
+    lines_indented = [padding + line for line in lines]
+    return "".join(lines_indented)
+
+
+# ---------------------------------------------------------------------
+#
+# error handling
+#
+# ---------------------------------------------------------------------
+
+
+def fatal_error(message):
+    """
+    Error output function
+    """
+    logging.error(message)
+    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
+
+
+# ---------------------------------------------------------------------
+#
+# Data conversion / manipulation
+#
+# ---------------------------------------------------------------------
+def str_to_bool(bool_str):
+    """Convert a sting representation of as boolean into a true boolean.
+
+    Conversion should be case insensitive.
+    """
+    value = None
+    str_lower = bool_str.lower()
+    if str_lower in ("true", "t"):
+        value = True
+    elif str_lower in ("false", "f"):
+        value = False
+    if value is None:
+        msg = (
+            'ERROR: invalid boolean string value "{0}". '
+            'Must be "true" or "false"'.format(bool_str)
+        )
+        fatal_error(msg)
+    return value
+
+
+REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
+
+
+def is_remote_url(url):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    """
+    remote_url = False
+    for prefix in REMOTE_PREFIXES:
+        if url.startswith(prefix):
+            remote_url = True
+    return remote_url
+
+
+def split_remote_url(url):
+    """check if the user provided a local file path or a
+    remote. If remote, try to strip off protocol info.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        return url
+
+    for prefix in REMOTE_PREFIXES:
+        url = url.replace(prefix, "")
+
+    if "@" in url:
+        url = url.split("@")[1]
+
+    if ":" in url:
+        url = url.split(":")[1]
+
+    return url
+
+
+def expand_local_url(url, field):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
+    represent local copy only, don't work with the remotes.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        if url.strip() == LOCAL_PATH_INDICATOR:
+            pass
+        else:
+            url = os.path.expandvars(url)
+            url = os.path.expanduser(url)
+            if not os.path.isabs(url):
+                msg = (
+                    'WARNING: Externals description for "{0}" contains a '
+                    "url that is not remote and does not expand to an "
+                    "absolute path. Version control operations may "
+                    "fail.\n\nurl={1}".format(field, url)
+                )
+                printlog(msg)
+            else:
+                url = os.path.normpath(url)
+    return url
+
+
+# ---------------------------------------------------------------------
+#
+# subprocess
+#
+# ---------------------------------------------------------------------
+
+# Give the user a helpful message if we detect that a command seems to
+# be hanging.
+_HANGING_SEC = 300
+
+
+def _hanging_msg(working_directory, command):
+    print(
+        """
+
+Command '{command}'
+from directory {working_directory}
+has taken {hanging_sec} seconds. It may be hanging.
+
+The command will continue to run, but you may want to abort
+manage_externals with ^C and investigate. A possible cause of hangs is
+when svn or git require authentication to access a private
+repository. On some systems, svn and git requests for authentication
+information will not be displayed to the user. In this case, the program
+will appear to hang. Ensure you can run svn and git manually and access
+all repositories without entering your authentication information.
+
+""".format(
+            command=command,
+            working_directory=working_directory,
+            hanging_sec=_HANGING_SEC,
+        )
+    )
+
+
+def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
+    """Wrapper around subprocess.check_output to handle common
+    exceptions.
+
+    check_output runs a command with arguments and waits
+    for it to complete.
+
+    check_output raises an exception on a nonzero return code.  if
+    status_to_caller is true, execute_subprocess returns the subprocess
+    return code, otherwise execute_subprocess treats non-zero return
+    status as an error and raises an exception.
+
+    """
+    cwd = os.getcwd()
+    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
+    logging.info(msg)
+    commands_str = " ".join(str(element) for element in commands)
+    logging.info(commands_str)
+    return_to_caller = status_to_caller or output_to_caller
+    status = -1
+    output = ""
+    hanging_timer = Timer(
+        _HANGING_SEC,
+        _hanging_msg,
+        kwargs={"working_directory": cwd, "command": commands_str},
+    )
+    hanging_timer.start()
+    try:
+        output = subprocess.check_output(
+            commands, stderr=subprocess.STDOUT, universal_newlines=True
+        )
+        log_process_output(output)
+        status = 0
+    except OSError as error:
+        msg = failed_command_msg(
+            "Command execution failed. Does the executable exist?", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except ValueError as error:
+        msg = failed_command_msg(
+            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except subprocess.CalledProcessError as error:
+        # Only report the error if we are NOT returning to the
+        # caller. If we are returning to the caller, then it may be a
+        # simple status check. If returning, it is the callers
+        # responsibility determine if an error occurred and handle it
+        # appropriately.
+        if not return_to_caller:
+            msg_context = (
+                "Process did not run successfully; "
+                "returned status {0}".format(error.returncode)
+            )
+            msg = failed_command_msg(msg_context, commands, output=error.output)
+            logging.error(error)
+            logging.error(msg)
+            log_process_output(error.output)
+            fatal_error(msg)
+        status = error.returncode
+    finally:
+        hanging_timer.cancel()
+
+    if status_to_caller and output_to_caller:
+        ret_value = (status, output)
+    elif status_to_caller:
+        ret_value = status
+    elif output_to_caller:
+        ret_value = output
+    else:
+        ret_value = None
+
+    return ret_value
+
+
+def failed_command_msg(msg_context, command, output=None):
+    """Template for consistent error messages from subprocess calls.
+
+    If 'output' is given, it should provide the output from the failed
+    command
+    """
+
+    if output:
+        output_truncated = last_n_lines(
+            output, 20, truncation_message="[... Output truncated for brevity ...]"
+        )
+        errmsg = (
+            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
+        )
+    else:
+        errmsg = ""
+
+    command_str = " ".join(command)
+    errmsg += """In directory
+    {cwd}
+{context}:
+    {command}
+""".format(
+        cwd=os.getcwd(), context=msg_context, command=command_str
+    )
+
+    if output:
+        errmsg += "See above for output from failed command.\n"
+
+    return errmsg
diff --git a/.lib/git-fleximod/poetry.lock b/.lib/git-fleximod/poetry.lock
new file mode 100644
index 0000000000..b59ed3942c
--- /dev/null
+++ b/.lib/git-fleximod/poetry.lock
@@ -0,0 +1,693 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.dependencies]
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.2.2"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.3.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7.0"
+files = [
+    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
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+optional = false
+python-versions = ">=3.7"
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+description = "pytest: simple powerful testing with Python"
+optional = false
+python-versions = ">=3.8"
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+
+[package.extras]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+
+[[package]]
+name = "pytz"
+version = "2024.1"
+description = "World timezone definitions, modern and historical"
+optional = false
+python-versions = "*"
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+[[package]]
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+[package.extras]
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+
+[[package]]
+name = "smmap"
+version = "5.0.1"
+description = "A pure Python implementation of a sliding window memory map manager"
+optional = false
+python-versions = ">=3.7"
+files = [
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+[[package]]
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+version = "2.2.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+optional = false
+python-versions = "*"
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
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+[[package]]
+name = "sphinx"
+version = "5.3.0"
+description = "Python documentation generator"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "Sphinx-5.3.0.tar.gz", hash = "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"},
+    {file = "sphinx-5.3.0-py3-none-any.whl", hash = "sha256:060ca5c9f7ba57a08a1219e547b269fadf125ae25b06b9fa7f66768efb652d6d"},
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+[package.dependencies]
+alabaster = ">=0.7,<0.8"
+babel = ">=2.9"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.14,<0.20"
+imagesize = ">=1.3"
+importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
+Jinja2 = ">=3.0"
+packaging = ">=21.0"
+Pygments = ">=2.12"
+requests = ">=2.5.0"
+snowballstemmer = ">=2.0"
+sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
+sphinxcontrib-htmlhelp = ">=2.0.0"
+sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = ">=1.1.5"
+
+[package.extras]
+docs = ["sphinxcontrib-websupport"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
+test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
+
+[[package]]
+name = "sphinxcontrib-applehelp"
+version = "1.0.4"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
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+[package.extras]
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+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.2"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
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+[package.extras]
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+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.1"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
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+[[package]]
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+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
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+[[package]]
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+version = "1.0.3"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
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+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+optional = false
+python-versions = ">=3.5"
+files = [
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+test = ["pytest"]
+
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
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+[[package]]
+name = "urllib3"
+version = "2.2.0"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "urllib3-2.2.0-py3-none-any.whl", hash = "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"},
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+[package.extras]
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+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "wheel"
+version = "0.42.0"
+description = "A built-package format for Python"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "wheel-0.42.0-py3-none-any.whl", hash = "sha256:177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d"},
+    {file = "wheel-0.42.0.tar.gz", hash = "sha256:c45be39f7882c9d34243236f2d63cbd58039e360f85d0913425fbd7ceea617a8"},
+]
+
+[package.extras]
+test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
+
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.8"
+content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
new file mode 100644
index 0000000000..2484552e4f
--- /dev/null
+++ b/.lib/git-fleximod/pyproject.toml
@@ -0,0 +1,41 @@
+[tool.poetry]
+name = "git-fleximod"
+version = "0.7.4"
+description = "Extended support for git-submodule and git-sparse-checkout"
+authors = ["Jim Edwards <jedwards@ucar.edu>"]
+maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/jedwards4b/git-fleximod"
+keywords = ["git", "submodule", "sparse-checkout"]
+packages = [
+{ include = "git_fleximod"},
+{ include = "doc"},
+]
+
+[tool.poetry.scripts]
+git-fleximod = "git_fleximod.git_fleximod:main"
+me2flexi = "git_fleximod.metoflexi:_main"
+fsspec = "fsspec.fuse:main"
+
+[tool.poetry.dependencies]
+python = "^3.8"
+GitPython = "^3.1.0"
+sphinx = "^5.0.0"
+fsspec = "^2023.12.2"
+wheel = "^0.42.0"
+pytest = "^8.0.0"
+pyfakefs = "^5.3.5"
+
+[tool.poetry.urls]
+"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
+
+[tool.pytest.ini_options]
+markers = [
+        "skip_after_first: only run on first iteration"
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
new file mode 100644
index 0000000000..d4b8eaee11
--- /dev/null
+++ b/.lib/git-fleximod/tbump.toml
@@ -0,0 +1,43 @@
+# Uncomment this if your project is hosted on GitHub:
+github_url = "https://github.com/jedwards4b/git-fleximod/"
+
+[version]
+current = "0.7.4"
+
+# Example of a semver regexp.
+# Make sure this matches current_version before
+# using tbump
+regex = '''
+  (?P<major>\d+)
+  \.
+  (?P<minor>\d+)
+  \.
+  (?P<patch>\d+)
+  '''
+
+[git]
+message_template = "Bump to {new_version}"
+tag_template = "v{new_version}"
+
+# For each file to patch, add a [[file]] config
+# section containing the path of the file, relative to the
+# tbump.toml location.
+[[file]]
+src = "git_fleximod/cli.py"
+
+[[file]]
+src = "pyproject.toml"
+
+# You can specify a list of commands to
+# run after the files have been patched
+# and before the git commit is made
+
+#  [[before_commit]]
+#  name = "check changelog"
+#  cmd = "grep -q {new_version} Changelog.rst"
+
+# Or run some commands after the git tag and the branch
+# have been pushed:
+#  [[after_push]]
+#  name = "publish"
+#  cmd = "./publish.sh"
diff --git a/.lib/git-fleximod/tests/__init__.py b/.lib/git-fleximod/tests/__init__.py
new file mode 100644
index 0000000000..4d4c66c78e
--- /dev/null
+++ b/.lib/git-fleximod/tests/__init__.py
@@ -0,0 +1,3 @@
+import sys, os
+
+sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py
new file mode 100644
index 0000000000..942a0efb97
--- /dev/null
+++ b/.lib/git-fleximod/tests/conftest.py
@@ -0,0 +1,138 @@
+import pytest 
+from git_fleximod.gitinterface import GitInterface
+import os
+import subprocess
+import logging
+from pathlib import Path
+
+@pytest.fixture(scope='session')
+def logger():
+    logging.basicConfig(
+        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
+    )
+    logger = logging.getLogger(__name__)
+    return logger
+
+all_repos=[
+    {"subrepo_path": "modules/test",
+     "submodule_name": "test_submodule",
+     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_submodule at tag MPIserial_2.4.0",
+     "status3" : "test_submodule at tag MPIserial_2.4.0",
+     "status4" : "test_submodule at tag MPIserial_2.4.0",
+     "gitmodules_content" : """
+    [submodule "test_submodule"]
+    path = modules/test
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelRequired
+"""},
+    {"subrepo_path": "modules/test_optional",
+     "submodule_name": "test_optional",
+     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_optional at tag MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
+     "status4" : "test_optional at tag MPIserial_2.4.0",
+     "gitmodules_content": """
+     [submodule "test_optional"]
+    path = modules/test_optional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelOptional
+"""},
+    {"subrepo_path": "modules/test_alwaysoptional",
+     "submodule_name": "test_alwaysoptional",
+     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
+     "status2" : "test_alwaysoptional at hash e5cf35c",
+     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
+     "status4" : "test_alwaysoptional at hash e5cf35c",
+     "gitmodules_content": """
+    [submodule "test_alwaysoptional"]
+    path = modules/test_alwaysoptional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = e5cf35c
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysOptional
+"""},    
+    {"subrepo_path": "modules/test_sparse",
+     "submodule_name": "test_sparse",
+     "status1" : "test_sparse at tag MPIserial_2.5.0",
+     "status2" : "test_sparse at tag MPIserial_2.5.0",
+     "status3" : "test_sparse at tag MPIserial_2.5.0",
+     "status4" : "test_sparse at tag MPIserial_2.5.0",
+     "gitmodules_content": """
+    [submodule "test_sparse"]
+    path = modules/test_sparse
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.5.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysRequired
+    fxsparse = ../.sparse_file_list
+"""},
+]
+@pytest.fixture(params=all_repos)
+
+def shared_repos(request):
+    return request.param
+
+@pytest.fixture
+def get_all_repos():
+    return all_repos
+
+def write_sparse_checkout_file(fp):
+    sparse_content = """m4
+"""
+    fp.write_text(sparse_content)
+
+@pytest.fixture
+def test_repo(shared_repos, tmp_path, logger):
+    subrepo_path = shared_repos["subrepo_path"]
+    submodule_name = shared_repos["submodule_name"]
+    test_dir = tmp_path / "testrepo"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    assert test_dir.joinpath(".git").is_dir()
+    (test_dir / "modules").mkdir()
+    if "sparse" in submodule_name:
+        (test_dir / subrepo_path).mkdir()
+        # Add the sparse checkout file
+        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
+        gitp.git_operation("add","modules/.sparse_file_list")
+    else:
+        gitp = GitInterface(str(test_dir), logger)
+        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+        assert test_dir.joinpath(".gitmodules").is_file()
+        gitp.git_operation("add",subrepo_path)
+    gitp.git_operation("commit","-a","-m","\"add submod\"")
+    test_dir2 = tmp_path / "testrepo2"
+    gitp.git_operation("clone",test_dir,test_dir2)
+    return test_dir2    
+
+
+@pytest.fixture
+def complex_repo(tmp_path, logger):
+    test_dir = tmp_path / "testcomplex"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation("fetch", "origin", "main")
+    gitp.git_operation("checkout", "main")
+    return test_dir
+    
+@pytest.fixture
+def git_fleximod():
+    def _run_fleximod(path, args, input=None):
+        cmd = ["git", "fleximod"] + args.split()
+        result = subprocess.run(cmd, cwd=path, input=input, 
+                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
+                                text=True)
+        if result.returncode:
+            print(result.stdout)
+            print(result.stderr)
+        return result
+    return _run_fleximod
+
diff --git a/.lib/git-fleximod/tests/test_a_import.py b/.lib/git-fleximod/tests/test_a_import.py
new file mode 100644
index 0000000000..d5ca878de5
--- /dev/null
+++ b/.lib/git-fleximod/tests/test_a_import.py
@@ -0,0 +1,8 @@
+# pylint: disable=unused-import
+from git_fleximod import cli
+from git_fleximod import utils
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+
+def test_import():
+    print("here")
diff --git a/.lib/git-fleximod/tests/test_b_update.py b/.lib/git-fleximod/tests/test_b_update.py
new file mode 100644
index 0000000000..159f1cfae0
--- /dev/null
+++ b/.lib/git-fleximod/tests/test_b_update.py
@@ -0,0 +1,26 @@
+import pytest
+from pathlib import Path
+                
+def test_basic_checkout(git_fleximod, test_repo, shared_repos):
+    # Prepare a simple .gitmodules
+    gm = shared_repos['gitmodules_content']
+    file_path = (test_repo / ".gitmodules")
+    repo_name = shared_repos["submodule_name"]
+    repo_path = shared_repos["subrepo_path"]
+
+    file_path.write_text(gm)
+    
+    # Run the command
+    result = git_fleximod(test_repo, f"update {repo_name}")
+
+    # Assertions
+    assert result.returncode == 0 
+    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
+    if "sparse" in repo_name:
+        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
+        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
+    
+    status = git_fleximod(test_repo, f"status {repo_name}")
+        
+    assert shared_repos["status2"] in status.stdout
+        
diff --git a/.lib/git-fleximod/tests/test_c_required.py b/.lib/git-fleximod/tests/test_c_required.py
new file mode 100644
index 0000000000..89ab8d294d
--- /dev/null
+++ b/.lib/git-fleximod/tests/test_c_required.py
@@ -0,0 +1,30 @@
+import pytest
+from pathlib import Path
+                
+def test_required(git_fleximod, test_repo, shared_repos):
+    file_path = (test_repo / ".gitmodules")
+    gm = shared_repos["gitmodules_content"]
+    repo_name = shared_repos["submodule_name"]
+    if file_path.exists():
+        with file_path.open("r") as f:
+            gitmodules_content = f.read()
+            # add the entry if it does not exist
+            if repo_name not in gitmodules_content:
+                file_path.write_text(gitmodules_content+gm)
+            # or if it is incomplete
+            elif gm not in gitmodules_content:
+                file_path.write_text(gm)
+    else:
+        file_path.write_text(gm)
+    result = git_fleximod(test_repo, "update")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status3"] in status.stdout
+    status = git_fleximod(test_repo, f"update --optional")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
+    status = git_fleximod(test_repo, f"update {repo_name}")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
diff --git a/.lib/git-fleximod/tests/test_d_complex.py b/.lib/git-fleximod/tests/test_d_complex.py
new file mode 100644
index 0000000000..fdce516274
--- /dev/null
+++ b/.lib/git-fleximod/tests/test_d_complex.py
@@ -0,0 +1,67 @@
+import pytest
+from pathlib import Path
+from git_fleximod.gitinterface import GitInterface
+
+def test_complex_checkout(git_fleximod, complex_repo, logger):
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+    
+    # This should checkout and update test_submodule and complex_sub
+    result = git_fleximod(complex_repo, "update")    
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex")
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+    # update a single optional submodule
+
+    result = git_fleximod(complex_repo, "update ToplevelOptional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+
+
+    # Finally update optional
+    result = git_fleximod(complex_repo, "update --optional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
+    
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex" )
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+
diff --git a/bin/git-fleximod b/bin/git-fleximod
new file mode 100755
index 0000000000..f69ede1c22
--- /dev/null
+++ b/bin/git-fleximod
@@ -0,0 +1,8 @@
+#!/usr/bin/env python3
+import sys
+import os
+sys.path.insert(0,os.path.abspath(os.path.join(os.path.dirname(__file__),"..",".lib","git-fleximod")))
+from git_fleximod.git_fleximod import main
+
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/ccs_config b/ccs_config
index f90e10502c..2ff978f92a 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit f90e10502c7246c2b45e373b7dd5e0da6cba0828
+Subproject commit 2ff978f92a5ac9a6ab243e5c14d06a7e2d2f5799
diff --git a/components/cdeps b/components/cdeps
index 7a522c828c..7476950699 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit 7a522c828c32dc35777992653f281ec525509c4a
+Subproject commit 7476950699909813d1938a34bd8d71bf5bfbf1e9
diff --git a/components/mizuRoute b/components/mizuRoute
index 0a62ee6185..81c720c7ee 160000
--- a/components/mizuRoute
+++ b/components/mizuRoute
@@ -1 +1 @@
-Subproject commit 0a62ee6185bdc9b99cd88ed5f15ea850602c43a2
+Subproject commit 81c720c7ee51f9c69f2934f696078c42f4493565
diff --git a/components/mosart b/components/mosart
index 1c22a8c547..8c682b1b7f 160000
--- a/components/mosart
+++ b/components/mosart
@@ -1 +1 @@
-Subproject commit 1c22a8c5478b714cf5b7c54b3e5cf7bad09fd9b2
+Subproject commit 8c682b1b7f15d146816de302e0d359da3e957056
diff --git a/libraries/mct b/libraries/mct
index e36024c5dd..82b0071e69 160000
--- a/libraries/mct
+++ b/libraries/mct
@@ -1 +1 @@
-Subproject commit e36024c5ddf482625ae6bd9474eff7d8f393f87c
+Subproject commit 82b0071e69d14330b75d23b0bc68543ebea9aadc
diff --git a/libraries/parallelio b/libraries/parallelio
index 6539ef05ae..f52ade0756 160000
--- a/libraries/parallelio
+++ b/libraries/parallelio
@@ -1 +1 @@
-Subproject commit 6539ef05ae7584ec570a56fdab9f7dfb336c2b80
+Subproject commit f52ade075619b32fa141993b5665b0fe099befc2
diff --git a/src/fates b/src/fates
index f0185f7c70..adfa664806 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit f0185f7c7033fa69c80d1ddb07cbcbf1f8be1adc
+Subproject commit adfa6648063408d443f5cae671bd37f713d3e3e8

From 798d43c0fe673557b98dd7fd1eb614b205641db0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 28 May 2024 08:39:13 -0600
Subject: [PATCH 0338/1248] Add comment in lilacsmoke.py as per code review

---
 cime_config/SystemTests/lilacsmoke.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cime_config/SystemTests/lilacsmoke.py b/cime_config/SystemTests/lilacsmoke.py
index 366d5d1176..1287301ba2 100644
--- a/cime_config/SystemTests/lilacsmoke.py
+++ b/cime_config/SystemTests/lilacsmoke.py
@@ -407,6 +407,10 @@ def run_phase(self):
         # case.get_mpirun_cmd creates a command that runs the executable given by
         # case.run_exe. So it's important that (elsewhere in this test script) we create a
         # link pointing from that to the atm_driver.exe executable.
+        #
+        # 2024/5/28 slevis: We added the load_env here to replace the
+        # behavior of the PBS -V directive that was removed from
+        # /ccs_config/machines/config_batch.xml
         self._case.load_env(reset=True)
         lid = new_lid()
         os.environ["OMP_NUM_THREADS"] = str(self._case.thread_count)

From aaeae950ca98d3292e3a02eb95862e69e7783c40 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 28 May 2024 08:54:58 -0600
Subject: [PATCH 0339/1248] Updated ChangeLog and ChangeSum

---
 doc/ChangeLog | 26 +++-----------------------
 doc/ChangeSum |  2 +-
 2 files changed, 4 insertions(+), 24 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index d68ef323ac..e15c554f8f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.006
 Originator(s): slevis (Samuel Levis)
-Date: Tue 21 May 2024 02:59:05 PM MDT
+Date: Tue 28 May 2024 08:45:50 AM MDT
 One-line Summary: Update externals to cesm2_3_beta17, remove mct, retire /test/tools
 
 Purpose and description of changes
@@ -48,12 +48,6 @@ Changes to documentation:
 Substantial timing or memory changes:
  Not considered
 
-Notes of particular relevance for developers:
----------------------------------------------
-Changes to tests or testing:
- I added a long list of izumi nag debug tests to ExpectedFailures as per
- https://github.com/ESCOMP/CMEPS/pull/460
-
 Testing summary:
 ----------------
  [PASS means all tests PASS; OK means tests PASS other than expected fails.]
@@ -68,7 +62,7 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho -----
+    derecho ----- OK
     izumi ------- OK
 
   any other testing (give details below):
@@ -82,21 +76,7 @@ If the tag used for baseline comparisons was NOT the previous tag, note that her
 Answer changes
 --------------
 
-Changes answers relative to baseline:
-
-  [ If a tag changes answers relative to baseline comparison the
-    following should be filled in (otherwise remove this section).
-    And always remove these three lines and parts that don't apply. ]
-
-  Summarize any changes to answers, i.e.,
-    - what code configurations:
-    - what platforms/compilers:
-    - nature of change (roundoff; larger than roundoff/same climate; new climate):
-
-   If bitwise differences were observed, how did you show they were no worse
-   than roundoff? Roundoff differences means one or more lines of code change results
-   only by roundoff level (because order of operation changes for example). Roundoff
-   changes to state fields usually grow to greater than roundoff as the simulation progresses.
+Changes answers relative to baseline: NO
 
 Other details
 -------------
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 7f8cdaeead..77bc8a426d 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.006   slevis 05/21/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
+       ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems
        ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes
        ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev

From 62d8ad004e896037f04a626ac7c4fceee9ecf6b0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 28 May 2024 09:03:35 -0600
Subject: [PATCH 0340/1248] Update share in Externals.cfg

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index 70d103a94b..dac119c47c 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -63,7 +63,7 @@ externals =  Externals_CDEPS.cfg
 required = True
 
 [share]
-tag = share1.0.18
+tag = share1.0.19
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share

From 51d9f095ebe73eb5e1af0731cc85e36988b2b9b7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jan 2024 13:42:59 -0700
Subject: [PATCH 0341/1248] Break up a long line.

---
 src/main/clm_driver.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index 00a98e61b4..c4fa1b53f4 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -1078,7 +1078,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
           ! ============================================================================
           ! Update crop calendars
           ! ============================================================================
-          call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, filter_inactive_and_active(nc)%pcropp, crop_inst)
+          call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, &
+               filter_inactive_and_active(nc)%pcropp, crop_inst)
        end if
 
        ! ============================================================================

From c763d664f23d15cc44d7afbb807359eea6cde30e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jan 2024 13:45:32 -0700
Subject: [PATCH 0342/1248] use_cropcal_rx_cultivar_gdds not needed in
 CropPhenology().

---
 src/biogeochem/CNPhenologyMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index fffb19bc46..bf91532e5a 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -1808,7 +1808,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp                     , &
     use clm_varctl       , only : use_fertilizer 
     use clm_varctl       , only : use_c13, use_c14
     use clm_varcon       , only : c13ratio, c14ratio
-    use clm_varctl       , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams
+    use clm_varctl       , only : use_cropcal_rx_swindows, use_cropcal_streams
     !
     ! !ARGUMENTS:
     integer                        , intent(in)    :: num_pcropp       ! number of prog crop patches in filter

From 846f1cc0485e6f69682159d9c3a54b0cd6c8d941 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jan 2024 13:54:13 -0700
Subject: [PATCH 0343/1248] PlantCrop(): Be strict about PFT identification.

---
 src/biogeochem/CNPhenologyMod.F90 | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index bf91532e5a..09515042b8 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2679,8 +2679,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
          if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. &
                ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean) then
             gddmaturity(p) = min(gdd1020(p), hybgdd(ivt(p)))
-         end if
-         if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. &
+         else if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. &
                ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. &
                ivt(p) == nsugarcane .or. ivt(p) == nirrig_sugarcane .or. &
                ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
@@ -2689,11 +2688,13 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
             if (do_plant_normal) then
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
-         end if
-         if (ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
+         else if (ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
                ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. &
                ivt(p) == nrice   .or. ivt(p) == nirrig_rice) then
             gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p)))
+         else
+            write(iulog, *) 'ERROR: PlantCrop(): unrecognized ivt ',ivt(p)
+            call endrun(msg="Stopping")
          end if
 
       endif

From 5b056b744e64ac59aae5cbc44c99a1b3d9815f59 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jan 2024 14:07:42 -0700
Subject: [PATCH 0344/1248] PlantCrop: Get gdd20 before setting gddmaturity.

---
 src/biogeochem/CNPhenologyMod.F90 | 36 ++++++++++++++++++++++++-------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 09515042b8..efc581cffc 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2590,6 +2590,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
     ! LOCAL VARAIBLES:
     integer s              ! growing season index
     integer k              ! grain pool index
+    real(r8) gdd20         ! GDD*20 value for this crop type
     real(r8) gdd_target    ! cultivar GDD target this growing season
     real(r8) this_sowing_reason ! number representing sowing reason(s)
     logical did_rx_gdds    ! did this patch use a prescribed harvest requirement?
@@ -2668,6 +2669,26 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
          endif
       endif
 
+      ! which GDD*20 variable does this crop use?
+      if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. &
+            ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean) then
+         gdd20 = gdd1020(p)
+      else if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. &
+            ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. &
+            ivt(p) == nsugarcane .or. ivt(p) == nirrig_sugarcane .or. &
+            ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
+            ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then
+         gdd20 = gdd820(p)
+      else if (ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
+            ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat .or. &
+            ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. &
+            ivt(p) == nrice   .or. ivt(p) == nirrig_rice) then
+         gdd20 = gdd020(p)
+      else
+         write(iulog, *) 'ERROR: PlantCrop(): unrecognized ivt for gdd20: ',ivt(p)
+         call endrun(msg="Stopping")
+      end if
+
       ! set GDD target
       did_rx_gdds = .false.
       if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
@@ -2677,23 +2698,22 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
          gddmaturity(p) = hybgdd(ivt(p))
       else
          if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. &
-               ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean) then
-            gddmaturity(p) = min(gdd1020(p), hybgdd(ivt(p)))
+               ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean .or. &
+               ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
+               ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. &
+               ivt(p) == nrice   .or. ivt(p) == nirrig_rice) then
+            gddmaturity(p) = min(gdd20, hybgdd(ivt(p)))
          else if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. &
                ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. &
                ivt(p) == nsugarcane .or. ivt(p) == nirrig_sugarcane .or. &
                ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
                ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then
-            gddmaturity(p) = max(950._r8, min(gdd820(p)*0.85_r8, hybgdd(ivt(p))))
+            gddmaturity(p) = max(950._r8, min(gdd20*0.85_r8, hybgdd(ivt(p))))
             if (do_plant_normal) then
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
-         else if (ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
-               ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. &
-               ivt(p) == nrice   .or. ivt(p) == nirrig_rice) then
-            gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p)))
          else
-            write(iulog, *) 'ERROR: PlantCrop(): unrecognized ivt ',ivt(p)
+            write(iulog, *) 'ERROR: PlantCrop(): unrecognized ivt for GDD target: ',ivt(p)
             call endrun(msg="Stopping")
          end if
 

From 08906bb13054f32bb48e9a412beefd02bff9a3e2 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jan 2024 14:25:50 -0700
Subject: [PATCH 0345/1248] Correct a comment.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 0ea63f2c6d..23f00a1759 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -35,7 +35,7 @@ module cropcalStreamMod
   integer, allocatable        :: g_to_ig(:)         ! Array matching gridcell index to data index
   type(shr_strdata_type)      :: sdat_cropcal_swindow_start   ! sowing window start input data stream
   type(shr_strdata_type)      :: sdat_cropcal_swindow_end     ! sowing window end input data stream
-  type(shr_strdata_type)      :: sdat_cropcal_cultivar_gdds   ! sdate input data stream
+  type(shr_strdata_type)      :: sdat_cropcal_cultivar_gdds   ! maturity requirement input data stream
   character(len=CS), allocatable :: stream_varnames_sdate(:) ! used for both start and end dates
   character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:)
   integer                     :: ncft               ! Number of crop functional types (excl. generic crops)

From 6ef52cdc8a980d62a596e21d9e7e57878145a5bb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jan 2024 14:26:11 -0700
Subject: [PATCH 0346/1248] Remove a troubleshooting write to iulog.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 23f00a1759..75c3820e7e 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -490,7 +490,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst)
              call ESMF_Finalize(endflag=ESMF_END_ABORT)
           endif
        end do
-      write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file DONE'
    end if ! use_cropcal_rx_cultivar_gdds
 
    deallocate(dataptr2d_cultivar_gdds)

From 98f68e784fe4ab30fd559be0126cb847675b74fc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jan 2024 14:43:16 -0700
Subject: [PATCH 0347/1248] Optionally adjust rx maturity reqt based on recent
 climate.

---
 bld/CLMBuildNamelist.pm                       |   7 ++
 .../namelist_definition_ctsm.xml              |   5 +
 src/biogeochem/CNPhenologyMod.F90             |   6 +-
 src/biogeochem/CropType.F90                   |   2 +
 src/cpl/share_esmf/cropcalStreamMod.F90       | 113 +++++++++++++++++-
 src/main/clm_driver.F90                       |   2 +-
 src/main/clm_initializeMod.F90                |   2 +-
 src/main/clm_varctl.F90                       |   1 +
 8 files changed, 133 insertions(+), 5 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fb44023cd5..54752b6dbc 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4198,10 +4198,14 @@ sub setup_logic_cropcal_streams {
   my $swindow_start_file = $nl->get_value('stream_fldFileName_swindow_start') ;
   my $swindow_end_file = $nl->get_value('stream_fldFileName_swindow_end') ;
   my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ;
+  my $gdd20_baseline_file = $nl->get_value('stream_fldFileName_gdd20_baseline') ;
   my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ;
   if ( ($swindow_start_file eq '' and $swindow_start_file ne '') or ($swindow_start_file ne '' and $swindow_start_file eq '') ) {
     $log->fatal_error("When specifying sowing window dates, you must provide both swindow_start_file and swindow_end_file. To specify exact sowing dates, use the same file." );
   }
+  if ( $gdd_file eq '' and $gdd20_baseline_file ne '' ) {
+      $log->fatal_error("If not providing stream_fldFileName_cultivar_gdds, don't provide stream_fldFileName_gdd20_baseline");
+  }
   if ( $generate_crop_gdds eq '.true.' ) {
       if ( $use_mxmat eq '.true.' ) {
           $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" );
@@ -4215,6 +4219,9 @@ sub setup_logic_cropcal_streams {
       if ( $gdd_file ne '' ) {
           $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_cultivar_gdds")
       }
+      if ( $gdd20_baseline_file ne '' ) {
+          $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_gdd20_baseline")
+      }
   }
   if ( $mesh_file eq '' and ( $swindow_start_file ne '' or $gdd_file ne '' ) ) {
       $log->fatal_error("If prescribing crop sowing dates and/or maturity requirements, you must specify stream_meshfile_cropcal")
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 37c457141c..c88e987756 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1808,6 +1808,11 @@ Filename of input stream data for date (day of year) of end of sowing window. Ce
 Filename of input stream data for cultivar growing degree-day targets
 </entry>
 
+<entry id="stream_fldFileName_gdd20_baseline" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for baseline GDD20 values
+</entry>
+
 <entry id="stream_meshfile_cropcal" type="char*256" category="datasets"
        input_pathname="abs" group="cropcal_streams" valid_values="" >
 Filename of input stream data for crop calendar inputs
diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index efc581cffc..f1f2d5fcc0 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2559,7 +2559,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
 
     ! !USES:
     use clm_varctl       , only : use_c13, use_c14
-    use clm_varctl       , only : use_cropcal_rx_cultivar_gdds, use_cropcal_streams
+    use clm_varctl       , only : use_cropcal_rx_cultivar_gdds, use_cropcal_streams, adapt_cropcal_rx_cultivar_gdds
     use clm_varcon       , only : c13ratio, c14ratio
     use clm_varpar       , only : mxsowings
     use pftconMod        , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean
@@ -2694,6 +2694,10 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
       if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
          gddmaturity(p) = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p))
          did_rx_gdds = .true.
+         if (adapt_cropcal_rx_cultivar_gdds) then
+            gddmaturity(p) = gddmaturity(p) * gdd20 / crop_inst%gdd20_baseline_patch(p)
+            !TODO SSR: Set maximum gddmaturity
+         end if
       else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then
          gddmaturity(p) = hybgdd(ivt(p))
       else
diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index 760aa21b76..a7bccf1a73 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -52,6 +52,7 @@ module CropType
      integer , pointer :: rx_swindow_starts_thisyr_patch(:,:) ! all prescribed sowing window start dates for this patch this year (day of year) [patch, mxsowings]
      integer , pointer :: rx_swindow_ends_thisyr_patch  (:,:) ! all prescribed sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings]
+     real(r8), pointer :: gdd20_baseline_patch          (:)   ! GDD20 baseline for this patch (ddays) [patch]
      real(r8), pointer :: sdates_thisyr_patch     (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_starts_thisyr_patch(:,:) ! all sowing window start dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_ends_thisyr_patch  (:,:) ! all sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
@@ -235,6 +236,7 @@ subroutine InitAllocate(this, bounds)
     allocate(this%rx_swindow_starts_thisyr_patch(begp:endp,1:mxsowings)); this%rx_swindow_starts_thisyr_patch(:,:) = -1
     allocate(this%rx_swindow_ends_thisyr_patch(begp:endp,1:mxsowings))  ; this%rx_swindow_ends_thisyr_patch  (:,:) = -1
     allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval
+    allocate(this%gdd20_baseline_patch(begp:endp)) ; this%gdd20_baseline_patch(:) = spval
     allocate(this%sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%sdates_thisyr_patch(:,:) = spval
     allocate(this%swindow_starts_thisyr_patch(begp:endp,1:mxsowings)) ; this%swindow_starts_thisyr_patch(:,:) = spval
     allocate(this%swindow_ends_thisyr_patch  (begp:endp,1:mxsowings)) ; this%swindow_ends_thisyr_patch  (:,:) = spval
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 75c3820e7e..83f7fc0eb0 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -15,6 +15,7 @@ module cropcalStreamMod
   use abortutils       , only : endrun
   use clm_varctl       , only : iulog
   use clm_varctl       , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams
+  use clm_varctl       , only : adapt_cropcal_rx_cultivar_gdds
   use clm_varpar       , only : mxpft
   use clm_varpar       , only : mxsowings
   use perf_mod         , only : t_startf, t_stopf
@@ -36,13 +37,16 @@ module cropcalStreamMod
   type(shr_strdata_type)      :: sdat_cropcal_swindow_start   ! sowing window start input data stream
   type(shr_strdata_type)      :: sdat_cropcal_swindow_end     ! sowing window end input data stream
   type(shr_strdata_type)      :: sdat_cropcal_cultivar_gdds   ! maturity requirement input data stream
+  type(shr_strdata_type)      :: sdat_cropcal_gdd20_baseline  ! GDD20 baseline input data stream
   character(len=CS), allocatable :: stream_varnames_sdate(:) ! used for both start and end dates
   character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:)
+  character(len=CS), allocatable :: stream_varnames_gdd20_baseline(:)
   integer                     :: ncft               ! Number of crop functional types (excl. generic crops)
   logical                     :: allow_invalid_swindow_inputs ! Fall back on paramfile sowing windows in cases of invalid values in stream_fldFileName_swindow_start and _end?
   character(len=CL)       :: stream_fldFileName_swindow_start ! sowing window start stream filename to read
   character(len=CL)       :: stream_fldFileName_swindow_end   ! sowing window end stream filename to read
   character(len=CL)       :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read
+  character(len=CL)       :: stream_fldFileName_gdd20_baseline ! GDD20 baseline stream filename to read
 
   character(len=*), parameter :: sourcefile = &
        __FILE__
@@ -90,6 +94,7 @@ subroutine cropcal_init(bounds)
          stream_fldFileName_swindow_start, &
          stream_fldFileName_swindow_end,   &
          stream_fldFileName_cultivar_gdds, &
+         stream_fldFileName_gdd20_baseline, &
          stream_meshfile_cropcal
 
     ! Default values for namelist
@@ -101,14 +106,17 @@ subroutine cropcal_init(bounds)
     stream_fldFileName_swindow_start = ''
     stream_fldFileName_swindow_end   = ''
     stream_fldFileName_cultivar_gdds = ''
+    stream_fldFileName_gdd20_baseline = ''
     ! Will need modification to work with mxsowings > 1
     ncft = mxpft - npcropmin + 1 ! Ignores generic crops
     allocate(stream_varnames_sdate(ncft))
     allocate(stream_varnames_cultivar_gdds(ncft))
+    allocate(stream_varnames_gdd20_baseline(ncft))
     do n = 1,ncft
        ivt = npcropmin + n - 1
        write(stream_varnames_sdate(n),'(a,i0)') "sdate1_",ivt
        write(stream_varnames_cultivar_gdds(n),'(a,i0)') "gdd1_",ivt
+       write(stream_varnames_gdd20_baseline(n),'(a,i0)') "gdd20bl_",ivt
     end do
 
     ! Read cropcal_streams namelist
@@ -132,6 +140,7 @@ subroutine cropcal_init(bounds)
     call shr_mpi_bcast(stream_fldFileName_swindow_start, mpicom)
     call shr_mpi_bcast(stream_fldFileName_swindow_end  , mpicom)
     call shr_mpi_bcast(stream_fldFileName_cultivar_gdds, mpicom)
+    call shr_mpi_bcast(stream_fldFileName_gdd20_baseline, mpicom)
     call shr_mpi_bcast(stream_meshfile_cropcal    , mpicom)
 
     if (masterproc) then
@@ -144,10 +153,12 @@ subroutine cropcal_init(bounds)
        write(iulog,'(a,a)' ) '  stream_fldFileName_swindow_start   = ',trim(stream_fldFileName_swindow_start)
        write(iulog,'(a,a)' ) '  stream_fldFileName_swindow_end     = ',trim(stream_fldFileName_swindow_end)
        write(iulog,'(a,a)' ) '  stream_fldFileName_cultivar_gdds   = ',trim(stream_fldFileName_cultivar_gdds)
+       write(iulog,'(a,a)' ) '  stream_fldFileName_gdd20_baseline  = ',trim(stream_fldFileName_gdd20_baseline)
        write(iulog,'(a,a)' ) '  stream_meshfile_cropcal    = ',trim(stream_meshfile_cropcal)
        do n = 1,ncft
           write(iulog,'(a,a)' ) '  stream_varnames_sdate  = ',trim(stream_varnames_sdate(n))
           write(iulog,'(a,a)' ) '  stream_varnames_cultivar_gdds  = ',trim(stream_varnames_cultivar_gdds(n))
+          write(iulog,'(a,a)' ) '  stream_varnames_gdd20_baseline  = ',trim(stream_varnames_gdd20_baseline(n))
        end do
        write(iulog,*)
     endif
@@ -155,6 +166,7 @@ subroutine cropcal_init(bounds)
     ! CLMBuildNamelist checks that both start and end files are provided if either is
     use_cropcal_rx_swindows      = stream_fldFileName_swindow_start /= ''
     use_cropcal_rx_cultivar_gdds = stream_fldFileName_cultivar_gdds /= ''
+    adapt_cropcal_rx_cultivar_gdds = stream_fldFileName_gdd20_baseline /= ''
     use_cropcal_streams = use_cropcal_rx_swindows .or. use_cropcal_rx_cultivar_gdds
 
     if (use_cropcal_rx_swindows) then
@@ -242,6 +254,36 @@ subroutine cropcal_init(bounds)
        end if
     end if
 
+    ! Initialize the cdeps data type sdat_cropcal_gdd20_baseline
+    ! NOTE: stream_dtlimit 1.5 didn't work for some reason
+    !TODO SSR: Do not allow time axis length > 1
+    if (adapt_cropcal_rx_cultivar_gdds) then
+       call shr_strdata_init_from_inline(sdat_cropcal_gdd20_baseline,  &
+            my_task             = iam,                                &
+            logunit             = iulog,                              &
+            compname            = 'LND',                              &
+            model_clock         = model_clock,                        &
+            model_mesh          = mesh,                               &
+            stream_meshfile     = trim(stream_meshfile_cropcal),      &
+            stream_lev_dimname  = 'null',                             &
+            stream_mapalgo      = 'bilinear',                         &
+            stream_filenames    = (/trim(stream_fldFileName_gdd20_baseline)/), &
+            stream_fldlistFile  = stream_varnames_gdd20_baseline,     &
+            stream_fldListModel = stream_varnames_gdd20_baseline,     &
+            stream_yearFirst    = 2000,                               &
+            stream_yearLast     = 2000,                               &
+            stream_yearAlign    = 2000,                               &
+            stream_offset       = cropcal_offset,                     &
+            stream_taxmode      = 'extend',                           &
+            stream_dtlimit      = 1.0e30_r8,                          &
+            stream_tintalgo     = cropcal_tintalgo,                   &
+            stream_name         = 'GDD20 baseline data',              &
+            rc                  = rc)
+       if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+          call ESMF_Finalize(endflag=ESMF_END_ABORT)
+       end if
+    end if
+
   end subroutine cropcal_init
 
   !================================================================
@@ -285,6 +327,8 @@ subroutine cropcal_advance( bounds )
        end if
     end if
 
+    ! GDD20 baseline values do not have an associated time axis and thus will not be advanced here
+
     if ( .not. allocated(g_to_ig) )then
        allocate (g_to_ig(bounds%begg:bounds%endg) )
        ig = 0
@@ -298,7 +342,7 @@ end subroutine cropcal_advance
 
   !================================================================
 
-  subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst)
+  subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     !
     ! Interpolate data stream information for crop calendars.
     !
@@ -314,6 +358,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst)
     type(bounds_type)      , intent(in)    :: bounds
     integer                , intent(in)    :: num_pcropp        ! number of prog. crop patches in filter
     integer                , intent(in)    :: filter_pcropp(:)  ! filter for prognostic crop patches
+    logical                , intent(in)    :: init  ! is this being called as initialization?
     type(crop_type)        , intent(inout) :: crop_inst
     !
     ! !LOCAL VARIABLES:
@@ -327,9 +372,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst)
     real(r8), pointer :: dataptr1d_swindow_start(:)
     real(r8), pointer :: dataptr1d_swindow_end  (:)
     real(r8), pointer :: dataptr1d_cultivar_gdds(:)
+    real(r8), pointer :: dataptr1d_gdd20_baseline(:)
     real(r8), pointer :: dataptr2d_swindow_start(:,:)
     real(r8), pointer :: dataptr2d_swindow_end  (:,:)
     real(r8), pointer :: dataptr2d_cultivar_gdds(:,:)
+    real(r8), pointer :: dataptr2d_gdd20_baseline(:,:)
     !-----------------------------------------------------------------------
 
     associate( &
@@ -345,7 +392,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst)
     lsize = bounds%endg - bounds%begg + 1
 
     begp = bounds%begp
-    endp= bounds%endp
+    endp = bounds%endp
 
     dayspyr = get_curr_days_per_year()
 
@@ -494,6 +541,68 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst)
 
    deallocate(dataptr2d_cultivar_gdds)
 
+   allocate(dataptr2d_gdd20_baseline(lsize, ncft))
+   if (adapt_cropcal_rx_cultivar_gdds .and. init) then
+      ! Read GDD20 baselines from input files
+      ! Starting with npcropmin will skip generic crops
+      do n = 1, ncft
+         call dshr_fldbun_getFldPtr(sdat_cropcal_gdd20_baseline%pstrm(1)%fldbun_model, trim(stream_varnames_gdd20_baseline(n)), &
+              fldptr1=dataptr1d_gdd20_baseline,  rc=rc)
+         if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+            call ESMF_Finalize(endflag=ESMF_END_ABORT)
+         end if
+
+         ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
+         ! So an explicit loop is required here
+         do g = 1,lsize
+  
+            !  Ensure valid values
+            if (dataptr1d_gdd20_baseline(g) < 0 .or. dataptr1d_gdd20_baseline(g) > 1000000._r8) then
+               write(iulog, *) 'ERROR: invalid read-in gdd20_baseline value: ',dataptr1d_gdd20_baseline(g)
+               call ESMF_Finalize(endflag=ESMF_END_ABORT)
+            else if (dataptr1d_gdd20_baseline(g) == 0) then
+               write(iulog, *) 'ERROR: read-in gdd20_baseline value 0 will cause inf'
+               call ESMF_Finalize(endflag=ESMF_END_ABORT)
+            end if
+           
+            dataptr2d_gdd20_baseline(g,n) = dataptr1d_gdd20_baseline(g)
+         end do
+      end do
+  
+      ! Set gdd20_baseline_patch for each gridcell/patch combination
+      do fp = 1, num_pcropp
+         p = filter_pcropp(fp)
+
+         ivt = patch%itype(p)
+         ! Will skip generic crops
+         if (ivt >= npcropmin) then
+            n = ivt - npcropmin + 1
+
+            if (n > ncft) then
+                write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')'
+                call ESMF_Finalize(endflag=ESMF_END_ABORT)
+            end if
+
+            ! vegetated pft
+            ig = g_to_ig(patch%gridcell(p))
+
+            if (ig > lsize) then
+                write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')'
+                call ESMF_Finalize(endflag=ESMF_END_ABORT)
+            end if
+
+            crop_inst%gdd20_baseline_patch(p) = dataptr2d_gdd20_baseline(ig,n)
+  
+         else
+            write(iulog,'(a,i0)') 'cropcal_interp(), rx_gdd20_baseline: Crop patch has ivt ',ivt
+            call ESMF_Finalize(endflag=ESMF_END_ABORT)
+         endif
+      end do
+  end if ! adapt_cropcal_rx_cultivar_gdds
+
+  deallocate(dataptr2d_gdd20_baseline)
+
+
    end associate
 
   end subroutine cropcal_interp
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index c4fa1b53f4..2a3cef4b8b 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -1079,7 +1079,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
           ! Update crop calendars
           ! ============================================================================
           call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, &
-               filter_inactive_and_active(nc)%pcropp, crop_inst)
+               filter_inactive_and_active(nc)%pcropp, .false., crop_inst)
        end if
 
        ! ============================================================================
diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index 9bf0cc59a2..e8f70bdef8 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -667,7 +667,7 @@ subroutine initialize2(ni,nj)
       do nc = 1,nclumps
          call get_clump_bounds(nc, bounds_clump)
          call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, &
-              filter_inactive_and_active(nc)%pcropp, crop_inst)
+              filter_inactive_and_active(nc)%pcropp, .true., crop_inst)
       end do
       !$OMP END PARALLEL DO
     end if
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 7d0b2b55ad..fe67380fd2 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -391,6 +391,7 @@ module clm_varctl
   logical, public :: use_cropcal_streams = .false.
   logical, public :: use_cropcal_rx_swindows = .false.
   logical, public :: use_cropcal_rx_cultivar_gdds = .false.
+  logical, public :: adapt_cropcal_rx_cultivar_gdds = .false.
 
   !----------------------------------------------------------
   ! biomass heat storage switch

From b73bcfdd104d8d591afb41ef6d6c18398cf8ef69 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 23 May 2024 15:09:16 -0600
Subject: [PATCH 0348/1248] =?UTF-8?q?Don't=20adapt=20rx=20cultivar=20gdd?=
 =?UTF-8?q?=20reqts=20if=20baseline=20gdd20=20is=20=E2=89=A40.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/biogeochem/CNPhenologyMod.F90 | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index f1f2d5fcc0..cfeee0b867 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -143,6 +143,9 @@ module CNPhenologyMod
   logical,  public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing
   logical,  public :: use_mxmat = .true.           ! If true, ignore crop maximum growing season length
 
+  ! For use with adapt_cropcal_rx_cultivar_gdds .true.
+  real(r8), parameter :: min_gdd20_baseline = 0._r8  ! If gdd20_baseline_patch is ≤ this, do not consider baseline.
+
   ! Constants for seasonal decidious leaf onset and offset
   logical,  private :: onset_thresh_depends_on_veg     = .false. ! If onset threshold depends on vegetation type
   integer,  public, parameter :: critical_daylight_constant           = 1
@@ -2694,9 +2697,9 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
       if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
          gddmaturity(p) = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p))
          did_rx_gdds = .true.
-         if (adapt_cropcal_rx_cultivar_gdds) then
+         if (adapt_cropcal_rx_cultivar_gdds .and. crop_inst%gdd20_baseline_patch(p) > min_gdd20_baseline) then
             gddmaturity(p) = gddmaturity(p) * gdd20 / crop_inst%gdd20_baseline_patch(p)
-            !TODO SSR: Set maximum gddmaturity
+            !TODO SSR: Set maximum and minimum gddmaturity
          end if
       else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then
          gddmaturity(p) = hybgdd(ivt(p))

From 20f32c1d70d709a96416c70a1d143d142b52fecf Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 24 May 2024 12:45:18 -0600
Subject: [PATCH 0349/1248] Ignore 'invalid' values in
 stream_fldFileName_gdd20_baseline on read.

They're being handled in PlantCrop() instead.

(cherry picked from commit 045b3d72c54319769e50500b2bd445215e07446d)
---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 83f7fc0eb0..f60ab51000 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -555,16 +555,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
          ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
          ! So an explicit loop is required here
          do g = 1,lsize
-  
-            !  Ensure valid values
-            if (dataptr1d_gdd20_baseline(g) < 0 .or. dataptr1d_gdd20_baseline(g) > 1000000._r8) then
-               write(iulog, *) 'ERROR: invalid read-in gdd20_baseline value: ',dataptr1d_gdd20_baseline(g)
-               call ESMF_Finalize(endflag=ESMF_END_ABORT)
-            else if (dataptr1d_gdd20_baseline(g) == 0) then
-               write(iulog, *) 'ERROR: read-in gdd20_baseline value 0 will cause inf'
-               call ESMF_Finalize(endflag=ESMF_END_ABORT)
-            end if
-           
             dataptr2d_gdd20_baseline(g,n) = dataptr1d_gdd20_baseline(g)
          end do
       end do

From a7cd0573ddfdef805f97c1f9aba3083492515ca3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 24 May 2024 14:05:36 -0600
Subject: [PATCH 0350/1248] Add generate_gdd20_baseline tool.

(cherry picked from commit 3ae50b7402fb1e3580f11ba09883e9ddaa563fda)
---
 .../crop_calendars/generate_gdd20_baseline.py | 243 ++++++++++++++++++
 tools/crop_calendars/generate_gdd20_baseline  |  19 ++
 2 files changed, 262 insertions(+)
 create mode 100644 python/ctsm/crop_calendars/generate_gdd20_baseline.py
 create mode 100755 tools/crop_calendars/generate_gdd20_baseline

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
new file mode 100644
index 0000000000..d5cbd779e0
--- /dev/null
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -0,0 +1,243 @@
+"""
+Generate stream_fldFileName_gdd20_baseline file from CTSM outputs
+"""
+
+import sys
+import argparse
+import os
+import datetime as dt
+import numpy as np
+import xarray as xr
+import cftime
+
+# -- add python/ctsm  to path (needed if we want to run generate_gdd20_baseline stand-alone)
+_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir)
+sys.path.insert(1, _CTSM_PYTHON)
+
+# pylint: disable=wrong-import-position
+from ctsm.crop_calendars.import_ds import import_ds
+import ctsm.crop_calendars.cropcal_utils as utils
+
+VAR_LIST_IN = ["GDD0", "GDD8", "GDD10"]
+VAR_LIST_IN = [x + "20" for x in VAR_LIST_IN]  # TODO: Delete this once using the right variables
+MISSING_FILL = -1  # Something negative to ensure that gddmaturity never changes (see PlantCrop)
+STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
+                    # shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
+
+
+def _parse_args():
+    """
+    Set up and parse input arguments
+    """
+    parser = argparse.ArgumentParser(
+        description=(
+            "Given a list of CTSM history files, generate stream_fldFileName_gdd20_baseline input"
+            + "file from the GDD0, GDD8, and GDD10 variables."
+        )
+    )
+
+    # Required
+    parser.add_argument(
+        "-i",
+        "--input-files",
+        help="Space-separated string of CTSM history files",
+        type=str,
+        required=True,
+    )
+    parser.add_argument(
+        "-o",
+        "--output-file",
+        help="Path to which output file should be saved",
+        type=str,
+        required=True,
+    )
+    parser.add_argument(
+        "-a",
+        "--author",
+        help=(
+            "String to be saved in author attribute of output files."
+            + "E.g., 'Author Name (authorname@ucar.edu)'"
+        ),
+        type=str,
+        required=True,
+    )
+
+    # Optional
+    parser.add_argument(
+        "--overwrite",
+        help="Overwrite existing output file, if any",
+        action="store_true",
+    )
+
+    # Get arguments
+    args = parser.parse_args(sys.argv[1:])
+
+    # Check arguments
+    if os.path.exists(args.output_file) and not args.overwrite:
+        raise FileExistsError("Output file exists but --overwrite is not specified")
+
+    return args
+
+
+def _get_cft_list(crop_list):
+    """
+    Given a list of strings, return a list of CFT names that contain any of those strings.
+    Will include both irrigated and rainfed!
+
+    Args:
+        crop_list (list): List of crops to look for.
+                          E.g.: ["corn", "cotton"]
+
+    Returns:
+        cft_str_list: List of CFTs containing any of the crop names in crop_list.
+                      E.g.: ["tropical_corn", "irrigated_tropical_corn",
+                             "temperate_corn", "irrigated_temperate_corn",
+                             "cotton", "irrigated_cotton"]
+    """
+
+    mgdcrop_list = utils.define_mgdcrop_list()
+    cft_str_list = []
+    for crop_str in crop_list:
+        cft_str_list += [x for x in mgdcrop_list if crop_str in x]
+    return cft_str_list
+
+
+def _get_gddn_for_cft(cft_str):
+    """
+    Given a CFT name, return the GDDN variable it uses.
+
+    Args:
+        cft_str (str): E.g., "irrigated_temperate_corn"
+
+    Returns:
+        str or None: Name of variable to use (e.g., "GDD8"). If crop isn't yet handled, return None.
+    """
+
+    gddn = None
+
+    gdd0_list_str = ["wheat", "cotton", "rice"]
+    if cft_str in _get_cft_list(gdd0_list_str):
+        gddn = "GDD0"
+
+    gdd8_list_str = ["corn", "sugarcane", "miscanthus", "switchgrass"]
+    if cft_str in _get_cft_list(gdd8_list_str):
+        gddn = "GDD8"
+
+    gdd10_list_str = ["soybean"]
+    if cft_str in _get_cft_list(gdd10_list_str):
+        gddn = "GDD10"
+
+    # TODO: Delete this once using the right variables
+    if gddn is not None:
+        gddn += "20"
+
+    return gddn
+
+
+def _get_output_varname(cft_str):
+    cft_int = utils.vegtype_str2int(cft_str)[0]
+    return f"gdd20bl_{cft_int}"
+
+
+def _add_time_axis(da_in):
+    """
+    Adds a size-1 time axis to a DataArray. Needed because CDEPS streams code requires a time axis,
+    even if the data in question is not supposed to vary over time.
+
+    Args:
+        da_in (DataArray): xarray DataArray which needs a time axis added
+
+    Returns:
+        DataArray: da_in with a new 1-step time axis
+    """
+    this_date = np.array(cftime.DatetimeNoLeap(STREAM_YEAR, 1, 1, 0, 0, 0, 0, has_year_zero=True))
+    this_date = np.expand_dims(this_date, axis=0)
+    da_time = xr.DataArray(
+        data=this_date,
+        dims={"time": this_date},
+    )
+    da_out = da_in.expand_dims(time=da_time)
+    return da_out
+
+
+def generate_gdd20_baseline(input_files, output_file, author):
+    """
+    Generate stream_fldFileName_gdd20_baseline file from CTSM outputs
+    """
+
+    # Get input file list
+    input_files = input_files.split(sep=" ")
+    # Get unique values and sort
+    input_files = list(set(input_files))
+    input_files.sort()
+
+    # Import history files and ensure they have lat/lon dims
+    ds_in = import_ds(input_files, VAR_LIST_IN)
+    if not all(x in ds_in.dims for x in ["lat", "lon"]):
+        raise RuntimeError("Input files must have lat and lon dimensions")
+
+    # If needed, find mean over time
+    if "time" in ds_in.dims:
+        ds_in = ds_in.mean(dim="time", skipna=True)
+
+    # Set up a dummy DataArray to use for crops without an assigned GDDN variable
+    dummy_da = xr.DataArray(
+        data=MISSING_FILL * np.ones_like(ds_in[VAR_LIST_IN[0]].values),
+        dims=ds_in[VAR_LIST_IN[0]].dims,
+        coords=ds_in[VAR_LIST_IN[0]].coords,
+    )
+    dummy_da = _add_time_axis(dummy_da)
+
+    # Process all crops
+    ds_out = xr.Dataset(
+        data_vars=None,
+        attrs={
+            "author": author,
+            "created": dt.datetime.now().astimezone().isoformat(),
+        },
+    )
+    for cft_str in utils.define_mgdcrop_list():
+        cft_int = utils.vegtype_str2int(cft_str)[0]
+        print(f"{cft_str} ({cft_int})")
+
+        # Which GDDN history variable does this crop use? E.g., GDD0, GDD10
+        gddn = _get_gddn_for_cft(cft_str)
+
+        # Fill any missing values with MISSING_FILL. This will mean that gddmaturity in these cells
+        # never changes.
+        if gddn is None:
+            # Crop not handled yet? Fill it entirely with missing value
+            this_da = dummy_da
+            long_name = "Dummy GDD20"
+            print("   dummy GDD20")
+        else:
+            this_da = ds_in[gddn].fillna(MISSING_FILL)
+            this_da = _add_time_axis(this_da)
+            long_name = gddn
+            print(f"   {gddn}")
+
+        # Add attributes
+        this_da.attrs["long_name"] = long_name + f" baseline for {cft_str}"
+        this_da.attrs["units"] = "°C days"
+
+        # Copy that to ds_out
+        var_out = _get_output_varname(cft_str)
+        print(f"   Output variable {var_out}")
+        ds_out[var_out] = this_da
+
+    # Save
+    ds_out.to_netcdf(output_file)
+
+    print("Done!")
+
+
+def main():
+    """
+    main() function for calling generate_gdd20_baseline.py from command line.
+    """
+    args = _parse_args()
+    generate_gdd20_baseline(
+        args.input_files,
+        args.output_file,
+        args.author,
+    )
diff --git a/tools/crop_calendars/generate_gdd20_baseline b/tools/crop_calendars/generate_gdd20_baseline
new file mode 100755
index 0000000000..a0238c8d0f
--- /dev/null
+++ b/tools/crop_calendars/generate_gdd20_baseline
@@ -0,0 +1,19 @@
+#!/usr/bin/env python3
+"""
+For description and instructions, please see README.
+"""
+
+import os
+import sys
+
+_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                            os.pardir,
+                            os.pardir,
+                            'python')
+sys.path.insert(1, _CTSM_PYTHON)
+
+from ctsm.crop_calendars.generate_gdd20_baseline import main
+
+if __name__ == "__main__":
+    main()
+

From fd5f177131d63d39e79a13918390bdfb642d781e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 28 May 2024 11:27:09 -0600
Subject: [PATCH 0351/1248] Format generate_gdd20_baseline.py with black.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index d5cbd779e0..d28bfda0e7 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -22,7 +22,7 @@
 VAR_LIST_IN = [x + "20" for x in VAR_LIST_IN]  # TODO: Delete this once using the right variables
 MISSING_FILL = -1  # Something negative to ensure that gddmaturity never changes (see PlantCrop)
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
-                    # shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
+# shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
 
 
 def _parse_args():

From 5eafae73aeeaec3950123a955d9c781d3840e157 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 28 May 2024 11:28:14 -0600
Subject: [PATCH 0352/1248] Add previous commit to .git-blame-ignore-revs.

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index e769d3187c..2620839223 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -26,6 +26,7 @@ d866510188d26d51bcd6d37239283db690af7e82
 0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
+fd5f177131d63d39e79a13918390bdfb642d781e
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

From 348c39422bec5a28f99572bba353196d574491b5 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 28 May 2024 13:18:19 -0600
Subject: [PATCH 0353/1248] dmleung 28 May 2024: a small edit of DUSTMod.F90 to
 deal with the situation of dpfct_rock(p) = NaN, which likely causes the run
 to die when turning on debug mode

---
 src/biogeochem/DUSTMod.F90 | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index e1348b8ebf..ffe74e6861 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -673,7 +673,14 @@ subroutine DustEmission (bounds, &
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then ! if bare, uses rock drag partition factor
-                  frc_thr_rgh_fct = dpfct_rock(p)
+                  if (dpfct_rock(p) /= dpfct_rock(p)) then ! dmleung added 24 May 2024: dpfct_rock(p) could be NaN; CLM could run when DEBUG=FALSE in env_build.xml but dies when DEBUG=TRUE (usually when checking if wnd_frc_slt > wnd_frc_thr_slt_it and if numer/denom < 30._r8 below)
+                     !write(iulog,*) 'dpfct_rock(p) == NaN; dpfct_rock(p) = ', dpfct_rock(p)
+                     frc_thr_rgh_fct = 0.001_r8 ! Set drag partition effect to be a very small value (or zero) such that there is no emission whenever dpfct_rock(p) = NaN; dmleung 24 May 2024
+                  else
+                     !write(iulog,*) 'dpfct_rock(p) = ', dpfct_rock(p)
+                     frc_thr_rgh_fct = dpfct_rock(p)
+                  end if
+                  !frc_thr_rgh_fct = dpfct_rock(p) ! This should be the original code when dpfct_rock(p) has values everywhere
                else   ! if vegetation, uses vegetation drag partition factor
                   frc_thr_rgh_fct = ssr(p)  
                end if
@@ -681,7 +688,7 @@ subroutine DustEmission (bounds, &
                frc_thr_rgh_fct = 1.0_r8
             end if
 
-            wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt will be used in the dust emission equation
+            wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt is the drag-parition-modified wind speed and will be used in the dust emission equation below
 
             frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor
 
@@ -756,7 +763,7 @@ subroutine DustEmission (bounds, &
             numer = (u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p)))
             denom = (2.0_r8 * u_sd_slt(p)**2.0_r8)
             ! Truncate to zero if the expression inside exp is becoming too large
-            if ( numer/denom < 30._r8 )then
+            if ( numer/denom < 30._r8  .and. denom/=0.0_r8)then  ! set numer/denom to be < 30 given exp(30) below is already very large; also set denom to be non-zero (and denom should be autonamtically non-negative given the standard deviation u_sd_slt of the subtimestep wind fluctuation is non-negative)
                thr_crs_rate(p) = (exp((u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2.0_r8 * u_sd_slt(p)**2.0_r8)) + 1.0_r8)**(-1.0_r8)
             else
                thr_crs_rate(p) = 0.0_r8

From 26c1222668be7b2be11936d666be76916be1b751 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 28 May 2024 15:18:22 -0600
Subject: [PATCH 0354/1248] Update ChangeLog with latest info about tests

---
 doc/ChangeLog | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e15c554f8f..b2f14a2c01 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.006
 Originator(s): slevis (Samuel Levis)
-Date: Tue 28 May 2024 08:45:50 AM MDT
+Date: Tue 28 May 2024 03:14:18 PM MDT
 One-line Summary: Update externals to cesm2_3_beta17, remove mct, retire /test/tools
 
 Purpose and description of changes
@@ -68,15 +68,15 @@ Testing summary:
   any other testing (give details below):
 
   ctsm_sci
-     derecho ----
-
-If the tag used for baseline comparisons was NOT the previous tag, note that here:
+     derecho ---- OK
 
 
 Answer changes
 --------------
 
 Changes answers relative to baseline: NO
+ Except two derecho_nvhpc tests due to an update to the nvhpc compiler
+ as documented in the Pull Request listed a few lines down.
 
 Other details
 -------------

From f8eb462ca90c5d0d3edb122d0abeb0ce703ccb46 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 28 May 2024 17:36:41 -0600
Subject: [PATCH 0355/1248] dmleung added comments on the positive denom
 required for dust emission intermittency in DUSTMod.F90. 28 May 2024

---
 src/biogeochem/DUSTMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index ffe74e6861..b23a26b429 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -761,9 +761,9 @@ subroutine DustEmission (bounds, &
 
             ! threshold crossing rate
             numer = (u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p)))
-            denom = (2.0_r8 * u_sd_slt(p)**2.0_r8)
+            denom = (2.0_r8 * u_sd_slt(p)**2.0_r8) ! note that u_sd_slt should be always positive
             ! Truncate to zero if the expression inside exp is becoming too large
-            if ( numer/denom < 30._r8  .and. denom/=0.0_r8)then  ! set numer/denom to be < 30 given exp(30) below is already very large; also set denom to be non-zero (and denom should be autonamtically non-negative given the standard deviation u_sd_slt of the subtimestep wind fluctuation is non-negative)
+            if ( numer/denom < 30._r8 ) then  ! set numer/denom to be < 30 given exp(30) below is already very large; also denom itself should be non-zero and non-negative given the standard deviation (u_sd_slt) of the subtimestep wind fluctuation is non-negative. dmleung 28 May 2024
                thr_crs_rate(p) = (exp((u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2.0_r8 * u_sd_slt(p)**2.0_r8)) + 1.0_r8)**(-1.0_r8)
             else
                thr_crs_rate(p) = 0.0_r8

From 38d6888fd04cef4f2d507df99e9c4d1a3a16c4ac Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 07:50:21 -0600
Subject: [PATCH 0356/1248] Add testmods RxCropCals, RxCropCalsAdapt.

---
 .../testmods_dirs/clm/RxCropCals/include_user_mods        | 1 +
 .../testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm     | 8 ++++++++
 .../testmods_dirs/clm/RxCropCalsAdapt/include_user_mods   | 1 +
 .../testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm         | 3 +++
 4 files changed, 13 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCals/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCals/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCals/include_user_mods
new file mode 100644
index 0000000000..23ea3745e6
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCals/include_user_mods
@@ -0,0 +1 @@
+../crop
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
new file mode 100644
index 0000000000..9cbfea97f0
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
@@ -0,0 +1,8 @@
+
+! Sowing windows
+stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
+stream_fldFileName_swindow_end  = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
+stream_fldFileName_cultivar_gdds = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc'
+stream_year_first_cropcal = 2000
+stream_year_last_cropcal = 2000
+stream_meshfile_cropcal = '$DIN_LOC_ROOT/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
new file mode 100644
index 0000000000..88c9694365
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
@@ -0,0 +1 @@
+../RxCropCals
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm
new file mode 100644
index 0000000000..1bba9d2a89
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm
@@ -0,0 +1,3 @@
+
+! Eventually replace this with half-degree version in the proper place
+stream_fldFileName_gdd20_baseline = '/glade/u/home/samrabin/ctsm_scale-mat-reqs/tools/crop_calendars/test.nc'

From 5b40c489fcaa2650b02a3386b93e08e4b09e44b5 Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Wed, 29 May 2024 10:16:50 -0600
Subject: [PATCH 0357/1248] removed unnecessary zeroing calls for fates
 history, they are called internally now

---
 src/utils/clmfates_interfaceMod.F90 | 89 ++++++++++++++++++-----------
 1 file changed, 56 insertions(+), 33 deletions(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index fcd5cb5230..98845f8e62 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -135,6 +135,9 @@ module CLMFatesInterfaceMod
 
    use FatesInterfaceMod     , only : DetermineGridCellNeighbors
    use FatesIOVariableKindMod, only : group_dyna_simple, group_dyna_complx
+   use FatesIOVariableKindMod, only : group_hifr_simple, group_hifr_complx
+   use FatesIOVariableKindMod, only : group_nflx_simple, group_nflx_complx
+   use FatesIOVariableKindMod, only : group_hydr_simple, group_hydr_complx
    use FatesHistoryInterfaceMod, only : fates_hist
    use FatesRestartInterfaceMod, only : fates_restart_interface_type
 
@@ -1192,14 +1195,6 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
          call this%WrapUpdateFatesSeedInOut(bounds_clump)
       end if
 
-      ! ---------------------------------------------------------------------------------
-      ! Flush arrays to values defined by %flushval (see registry entry in
-      ! subroutine define_history_vars()
-      ! ---------------------------------------------------------------------------------
-      call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-
-      call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-
       ! ---------------------------------------------------------------------------------
       ! Part II: Call the FATES model now that input boundary conditions have been
       ! provided.
@@ -1970,23 +1965,38 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, &
                                                                 this%fates(nc)%sites, &
                                                                 this%fates(nc)%bc_out)
 
+
                ! ------------------------------------------------------------------------
-               ! Update history IO fields that depend on ecosystem dynamics
+               ! Flush FATES history variables.
+               ! The flushing process sets all columns outside of FATES perview to
+               ! the ignore value. This only needs to be done once, because FATES will
+               ! not overwright values outside the columns that it is in charge of.
                ! ------------------------------------------------------------------------
-               if(fates_history_dimlevel(2)>0) then
+
+               ! tbd: fates_hist%flush_all_hvars(nc)    
+               
+               if_dim1: if(fates_history_dimlevel(1)>0) then
+                  call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_simple)
+                  if (use_fates_planthydro) then
+                     call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_simple)
+                  end if
+                  if(fates_history_dimlevel(1)>1) then
+                     call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_complx)
+                     if (use_fates_planthydro) then
+                        call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_complx)
+                     end if
+                  end if
+               end if if_dim1
+               
+               if_dim2: if(fates_history_dimlevel(2)>0) then
                   call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-                  do s = 1,this%fates(nc)%nsites
-                     call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                          upfreq_in=group_dyna_simple)
-                  end do
+                  call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_simple)
                   if(fates_history_dimlevel(2)>1) then
                      call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-                     do s = 1,this%fates(nc)%nsites
-                        call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                             upfreq_in=group_dyna_complx)
-                     end do
+                     call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_complx)
                   end if
-               end if
+               end if if_dim2
+               
                call fates_hist%update_history_dyn( nc,                     &
                                                    this%fates(nc)%nsites,  &
                                                    this%fates(nc)%sites,   &
@@ -2164,22 +2174,38 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, &
                 soilbiogeochem_carbonflux_inst, .false.)
 
            ! ------------------------------------------------------------------------
-           ! Update history IO fields that depend on ecosystem dynamics
+           ! Flush and zero FATES history variables.
+           ! The flushing process sets all columns outside of FATES perview to
+           ! the ignore value. This only needs to be done once, because FATES will
+           ! not overwright values outside the columns that it is in charge of.
+           ! We also start off by setting all values on FATES columns to zero.
            ! ------------------------------------------------------------------------
-           if(fates_history_dimlevel(2)>0) then
+
+           ! tbd: fates_hist%flush_all_hvars(nc)
+           
+           if_dim1: if(fates_history_dimlevel(1)>0) then
+              call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_simple)
+              if (use_fates_planthydro) then
+                 call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_simple)
+              end if
+              if(fates_history_dimlevel(1)>1) then
+                 call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_complx)
+                 if (use_fates_planthydro) then
+                    call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_complx)
+                 end if
+              end if
+           end if if_dim1
+           
+           if_dim2: if(fates_history_dimlevel(2)>0) then
               call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-              do s = 1,this%fates(nc)%nsites
-                 call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                      upfreq_in=group_dyna_simple)
-              end do
+              call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_simple)
               if(fates_history_dimlevel(2)>1) then
                  call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-                 do s = 1,this%fates(nc)%nsites
-                    call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                         upfreq_in=group_dyna_complx)
-                 end do
+                 call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_complx)
               end if
-           end if
+           end if if_dim2
+
+           
            call fates_hist%update_history_dyn( nc,                     &
                 this%fates(nc)%nsites,                                  &
                 this%fates(nc)%sites,                                   &
@@ -3570,9 +3596,6 @@ subroutine wrap_hydraulics_drive(this, bounds_clump, nc, &
             this%fates(nc)%bc_out(s)%plant_stored_h2o_si
    end do
 
-
-   ! Update History Buffers that need to be updated after hydraulics calls
-
    call fates_hist%update_history_hydraulics(nc, &
          this%fates(nc)%nsites, &
          this%fates(nc)%sites, &

From 51079bfb92ca2d75a71cfee5679bbce40314eaae Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 May 2024 10:17:10 -0600
Subject: [PATCH 0358/1248] update run_sys_tests.py for fleximod

---
 python/ctsm/run_sys_tests.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py
index de93081504..ecea2342a7 100644
--- a/python/ctsm/run_sys_tests.py
+++ b/python/ctsm/run_sys_tests.py
@@ -576,12 +576,12 @@ def _record_git_status(testroot, retry, dry_run):
     if git_status.count("\n") == 1:
         # Only line in git status is the branch info
         output += "(clean sandbox)\n"
-    manic = os.path.join("manage_externals", "checkout_externals")
-    manage_externals_status = subprocess.check_output(
-        [manic, "--status", "--verbose"], cwd=ctsm_root, universal_newlines=True
+    fleximod = os.path.join("bin", "git-fleximod")
+    fleximod_status = subprocess.check_output(
+        [fleximod, "status"], cwd=ctsm_root, universal_newlines=True
     )
-    output += 72 * "-" + "\n" + "manage_externals status:" + "\n"
-    output += manage_externals_status
+    output += 72 * "-" + "\n" + "git-fleximod status:" + "\n"
+    output += fleximod_status
     output += 72 * "-" + "\n"
 
     print(output)

From 0537a6a32d586e62c237b6e2a6d645b7895bf76a Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 29 May 2024 11:23:15 -0600
Subject: [PATCH 0359/1248] add potential veg check to avoid accessing
 timeseries file

---
 src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 88 ++++++++++----------
 src/dyn_subgrid/dynSubgridDriverMod.F90      |  4 +-
 2 files changed, 48 insertions(+), 44 deletions(-)

diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
index f330ee2b78..d7c1063494 100644
--- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
+++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
@@ -107,6 +107,7 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename)
 
     ! !USES:
     use clm_varctl            , only : use_cn, use_fates_luh, fates_harvest_mode
+    use clm_varctl            , only : use_fates_potentialveg
     use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type
     use dynTimeInfoMod        , only : YEAR_POSITION_START_OF_TIMESTEP
     use dynTimeInfoMod        , only : YEAR_POSITION_END_OF_TIMESTEP
@@ -148,55 +149,58 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename)
     landuse_transitions = 0._r8
     landuse_harvest = 0._r8
 
-    if (use_fates_luh) then
+    ! Avoid initializing the landuse timeseries file if in fates potential vegetation mode
+    if (.not. use_fates_potentialveg) then
+       if (use_fates_luh) then
 
-       ! Generate the dyn_file_type object.
-       ! Start calls get_prev_date, whereas end calls get_curr_date
-       dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP)
+          ! Generate the dyn_file_type object.
+          ! Start calls get_prev_date, whereas end calls get_curr_date
+          dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP)
 
-       ! Get initial land use data from the fates luh2 timeseries dataset
-       num_points = (bounds%endg - bounds%begg + 1)
-       landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor?
-       do varnum = 1, num_landuse_transition_vars
-          landuse_transition_vars(varnum) = dyn_var_time_uninterp_type( &
-               dyn_file=dynFatesLandUse_file, varname=landuse_transition_varnames(varnum), &
-               dim1name=grlnd, conversion_factor=1.0_r8, &
-               do_check_sums_equal_1=.false., data_shape=landuse_shape)
-       end do
-       do varnum = 1, num_landuse_state_vars
-          landuse_state_vars(varnum) = dyn_var_time_uninterp_type( &
-               dyn_file=dynFatesLandUse_file, varname=landuse_state_varnames(varnum), &
-               dim1name=grlnd, conversion_factor=1.0_r8, &
-               do_check_sums_equal_1=.false., data_shape=landuse_shape)
-       end do
-
-       ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled
-       if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. &
-           trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then
-
-          ! change the harvest varnames being used depending on the mode selected
-          if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area ) then
-             landuse_harvest_varnames => landuse_harvest_area_varnames
-             landuse_harvest_units = landuse_harvest_area_units
-          elseif (trim(fates_harvest_mode) .eq. fates_harvest_luh_mass ) then
-             landuse_harvest_varnames => landuse_harvest_mass_varnames
-             landuse_harvest_units = landuse_harvest_mass_units
-          else
-             call endrun(msg=' undefined fates harvest mode selected'//errMsg(__FILE__, __LINE__))
-          end if
-
-          do varnum = 1, num_landuse_harvest_vars
-             landuse_harvest_vars(varnum) = dyn_var_time_uninterp_type( &
-                  dyn_file=dynFatesLandUse_file, varname=landuse_harvest_varnames(varnum), &
+          ! Get initial land use data from the fates luh2 timeseries dataset
+          num_points = (bounds%endg - bounds%begg + 1)
+          landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor?
+          do varnum = 1, num_landuse_transition_vars
+             landuse_transition_vars(varnum) = dyn_var_time_uninterp_type( &
+                  dyn_file=dynFatesLandUse_file, varname=landuse_transition_varnames(varnum), &
+                  dim1name=grlnd, conversion_factor=1.0_r8, &
+                  do_check_sums_equal_1=.false., data_shape=landuse_shape)
+          end do
+          do varnum = 1, num_landuse_state_vars
+             landuse_state_vars(varnum) = dyn_var_time_uninterp_type( &
+                  dyn_file=dynFatesLandUse_file, varname=landuse_state_varnames(varnum), &
                   dim1name=grlnd, conversion_factor=1.0_r8, &
                   do_check_sums_equal_1=.false., data_shape=landuse_shape)
           end do
+
+          ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled
+          if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. &
+              trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then
+
+             ! change the harvest varnames being used depending on the mode selected
+             if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area ) then
+                landuse_harvest_varnames => landuse_harvest_area_varnames
+                landuse_harvest_units = landuse_harvest_area_units
+             elseif (trim(fates_harvest_mode) .eq. fates_harvest_luh_mass ) then
+                landuse_harvest_varnames => landuse_harvest_mass_varnames
+                landuse_harvest_units = landuse_harvest_mass_units
+             else
+                call endrun(msg=' undefined fates harvest mode selected'//errMsg(__FILE__, __LINE__))
+             end if
+
+             do varnum = 1, num_landuse_harvest_vars
+                landuse_harvest_vars(varnum) = dyn_var_time_uninterp_type( &
+                     dyn_file=dynFatesLandUse_file, varname=landuse_harvest_varnames(varnum), &
+                     dim1name=grlnd, conversion_factor=1.0_r8, &
+                     do_check_sums_equal_1=.false., data_shape=landuse_shape)
+             end do
+          end if
        end if
-    end if
 
-    ! Since fates needs state data during initialization, make sure to call
-    ! the interpolation routine at the start
-    call dynFatesLandUseInterp(bounds,init_state=.true.)
+       ! Since fates needs state data during initialization, make sure to call
+       ! the interpolation routine at the start
+       call dynFatesLandUseInterp(bounds,init_state=.true.)
+    end if
 
   end subroutine dynFatesLandUseInit
 
diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90
index faef029b40..ea1210521d 100644
--- a/src/dyn_subgrid/dynSubgridDriverMod.F90
+++ b/src/dyn_subgrid/dynSubgridDriverMod.F90
@@ -206,7 +206,7 @@ subroutine dynSubgrid_driver(bounds_proc,
     ! OUTSIDE any loops over clumps in the driver.
     !
     ! !USES:
-    use clm_varctl              , only : use_cn, use_fates, use_fates_luh
+    use clm_varctl              , only : use_cn, use_fates, use_fates_luh, use_fates_potentialveg
     use dynInitColumnsMod       , only : initialize_new_columns
     use dynConsBiogeophysMod    , only : dyn_hwcontent_init, dyn_hwcontent_final
     use dynEDMod                , only : dyn_ED
@@ -295,7 +295,7 @@ subroutine dynSubgrid_driver(bounds_proc,
        call dynurban_interp(bounds_proc)
     end if
 
-    if (use_fates_luh) then
+    if (use_fates_luh .and. .not. use_fates_potentialveg) then
        call dynFatesLandUseInterp(bounds_proc)
     end if
 

From 317f77d7b692a58644e679d48c8f4ec026c8a697 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 11:30:54 -0600
Subject: [PATCH 0360/1248] Add cropcals_rx namelist boolean.

---
 bld/namelist_files/namelist_defaults_ctsm.xml   | 15 +++++++++++----
 bld/namelist_files/namelist_definition_ctsm.xml |  9 +++++++--
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 655e97c47c..08f67a2712 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1686,10 +1686,17 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <lai_mapalgo  hgrid="1x1_asphaltjungleNJ" >nn</lai_mapalgo>
 <lai_mapalgo  hgrid="5x5_amazon"          >nn</lai_mapalgo>
 
-<!-- crop calendar streams namelist defaults -->
-<stream_year_first_cropcal  >1850</stream_year_first_cropcal>
-<stream_year_last_cropcal   >2100</stream_year_last_cropcal>
-<model_year_align_cropcal   >1850</model_year_align_cropcal>
+<!-- crop calendars: default settings -->
+<cropcals_rx>.false.</cropcals_rx>
+<stream_year_first_cropcal  >2000</stream_year_first_cropcal>
+<stream_year_last_cropcal   >2000</stream_year_last_cropcal>
+<model_year_align_cropcal   >2000</model_year_align_cropcal>
+
+<!-- crop calendars: default input files -->
+<stream_fldFileName_swindow_start cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
+<stream_fldFileName_swindow_end cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
+<stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
+<stream_meshfile_cropcal cropcals_rx=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>
 
 <!-- lightning streams namelist defaults -->
 
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index c88e987756..366b7498e8 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1773,14 +1773,19 @@ Mapping method from LAI input file to the model resolution
 <!-- ========================================================================================  -->
 
 <!-- Crop calendars -->
+<entry id="cropcals_rx" type="logical" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Flag to enable prescribed crop calendars (sowing window dates and maturity requirement)
+</entry>
+
 <entry id="stream_year_first_cropcal" type="integer" category="datasets"
        group="cropcal_streams" valid_values="" >
-First year to loop over for crop calendar data
+First year to loop over for crop calendar data (not including gdd20_baseline file)
 </entry>
 
 <entry id="stream_year_last_cropcal" type="integer" category="datasets"
        group="cropcal_streams" valid_values="" >
-Last year to loop over for crop calendar data
+Last year to loop over for crop calendar data (not including gdd20_baseline file)
 </entry>
 
 <entry id="model_year_align_cropcal" type="integer" category="datasets"

From 81380ef7abb6820eb9a99078e0827ead84093e3c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 11:38:29 -0600
Subject: [PATCH 0361/1248] CLMBuildNamelist: Fix logic and message for check
 of sowing window start/end files.

---
 bld/CLMBuildNamelist.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 54752b6dbc..9753549db1 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4200,8 +4200,8 @@ sub setup_logic_cropcal_streams {
   my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ;
   my $gdd20_baseline_file = $nl->get_value('stream_fldFileName_gdd20_baseline') ;
   my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ;
-  if ( ($swindow_start_file eq '' and $swindow_start_file ne '') or ($swindow_start_file ne '' and $swindow_start_file eq '') ) {
-    $log->fatal_error("When specifying sowing window dates, you must provide both swindow_start_file and swindow_end_file. To specify exact sowing dates, use the same file." );
+  if ( ($swindow_start_file eq '' and $swindow_end_file ne '') or ($swindow_start_file ne '' and $swindow_end_file eq '') ) {
+    $log->fatal_error("When specifying sowing window dates, you must provide both stream_fldFileName_swindow_start and stream_fldFileName_swindow_end. To specify exact sowing dates, use the same file." );
   }
   if ( $gdd_file eq '' and $gdd20_baseline_file ne '' ) {
       $log->fatal_error("If not providing stream_fldFileName_cultivar_gdds, don't provide stream_fldFileName_gdd20_baseline");

From b19573466744c3426de70a1edbb9a3725821de67 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 11:42:11 -0600
Subject: [PATCH 0362/1248] CLMBuildNamelist: Use &string_is_undef_or_empty()
 instead of comparing to ''.

---
 bld/CLMBuildNamelist.pm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 9753549db1..833a254f1a 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4200,30 +4200,30 @@ sub setup_logic_cropcal_streams {
   my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ;
   my $gdd20_baseline_file = $nl->get_value('stream_fldFileName_gdd20_baseline') ;
   my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ;
-  if ( ($swindow_start_file eq '' and $swindow_end_file ne '') or ($swindow_start_file ne '' and $swindow_end_file eq '') ) {
+  if ( (&string_is_undef_or_empty($swindow_start_file) and !&string_is_undef_or_empty($swindow_end_file)) or (!&string_is_undef_or_empty($swindow_start_file) and &string_is_undef_or_empty($swindow_end_file)) ) {
     $log->fatal_error("When specifying sowing window dates, you must provide both stream_fldFileName_swindow_start and stream_fldFileName_swindow_end. To specify exact sowing dates, use the same file." );
   }
-  if ( $gdd_file eq '' and $gdd20_baseline_file ne '' ) {
+  if ( &string_is_undef_or_empty($gdd_file) and ! &string_is_undef_or_empty($gdd20_baseline_file) ) {
       $log->fatal_error("If not providing stream_fldFileName_cultivar_gdds, don't provide stream_fldFileName_gdd20_baseline");
   }
   if ( $generate_crop_gdds eq '.true.' ) {
       if ( $use_mxmat eq '.true.' ) {
           $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" );
       }
-      if ( $swindow_start_file eq '' or $swindow_end_file eq '' ) {
+      if ( &string_is_undef_or_empty($swindow_start_file) or &string_is_undef_or_empty($swindow_end_file) ) {
           $log->fatal_error("If generate_crop_gdds is true, you must specify stream_fldFileName_swindow_start and stream_fldFileName_swindow_end")
       }
       if ( $swindow_start_file ne $swindow_end_file ) {
           $log->fatal_error("If generate_crop_gdds is true, you must specify exact sowing dates by setting stream_fldFileName_swindow_start and stream_fldFileName_swindow_end to the same file")
       }
-      if ( $gdd_file ne '' ) {
+      if ( ! &string_is_undef_or_empty($gdd_file) ) {
           $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_cultivar_gdds")
       }
-      if ( $gdd20_baseline_file ne '' ) {
+      if ( ! &string_is_undef_or_empty($gdd20_baseline_file) ) {
           $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_gdd20_baseline")
       }
   }
-  if ( $mesh_file eq '' and ( $swindow_start_file ne '' or $gdd_file ne '' ) ) {
+  if ( &string_is_undef_or_empty($mesh_file) and ( ! &string_is_undef_or_empty($swindow_start_file) or ! &string_is_undef_or_empty($gdd_file) ) ) {
       $log->fatal_error("If prescribing crop sowing dates and/or maturity requirements, you must specify stream_meshfile_cropcal")
   }
 }

From 4b18a5bb159e1a98a5905ec939dffb5981e55185 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 11:48:50 -0600
Subject: [PATCH 0363/1248] CLMBuildNamelist: Use &value_is_true() instead of
 comparing to '.true.'

---
 bld/CLMBuildNamelist.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 833a254f1a..d35649bef4 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4206,8 +4206,8 @@ sub setup_logic_cropcal_streams {
   if ( &string_is_undef_or_empty($gdd_file) and ! &string_is_undef_or_empty($gdd20_baseline_file) ) {
       $log->fatal_error("If not providing stream_fldFileName_cultivar_gdds, don't provide stream_fldFileName_gdd20_baseline");
   }
-  if ( $generate_crop_gdds eq '.true.' ) {
-      if ( $use_mxmat eq '.true.' ) {
+  if ( &value_is_true($generate_crop_gdds) ) {
+      if ( &value_is_true($use_mxmat) ) {
           $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" );
       }
       if ( &string_is_undef_or_empty($swindow_start_file) or &string_is_undef_or_empty($swindow_end_file) ) {

From e76fbbc134ab5c4c6186f35732d11b46879a5a13 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 12:02:17 -0600
Subject: [PATCH 0364/1248] CLMBuildNamelist: Update
 setup_logic_cropcal_streams() with cropcals_rx.

---
 bld/CLMBuildNamelist.pm | 77 ++++++++++++++++++++++++++++-------------
 1 file changed, 53 insertions(+), 24 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index d35649bef4..aff46be3f0 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4172,41 +4172,73 @@ sub setup_logic_lai_streams {
 sub setup_logic_cropcal_streams {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  # Set first and last stream years
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal',
-              'sim_year'=>$nl_flags->{'sim_year'},
-              'sim_year_range'=>$nl_flags->{'sim_year_range'});
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal',
-              'sim_year'=>$nl_flags->{'sim_year'},
-              'sim_year_range'=>$nl_flags->{'sim_year_range'});
-
-  # Set align year, if first and last years are different
-  if ( $nl->get_value('stream_year_first_cropcal') !=
-      $nl->get_value('stream_year_last_cropcal') ) {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-                'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'},
-                'sim_year_range'=>$nl_flags->{'sim_year_range'});
-  }
-
   # Set up other crop calendar parameters
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcals_rx');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat');
 
-  # Option checks
-  my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ;
-  my $use_mxmat = $nl->get_value('use_mxmat') ;
+  # Add defaults if using prescribed crop calendars
+  my $cropcals_rx = $nl->get_value('cropcals_rx') ;
+  if ( &value_is_true($cropcals_rx) ) {
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_start');
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_end');
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds');
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal');
+  }
+
+  # Add defaults if using any potentially time-varying crop calendar input files
   my $swindow_start_file = $nl->get_value('stream_fldFileName_swindow_start') ;
   my $swindow_end_file = $nl->get_value('stream_fldFileName_swindow_end') ;
   my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ;
   my $gdd20_baseline_file = $nl->get_value('stream_fldFileName_gdd20_baseline') ;
   my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ;
-  if ( (&string_is_undef_or_empty($swindow_start_file) and !&string_is_undef_or_empty($swindow_end_file)) or (!&string_is_undef_or_empty($swindow_start_file) and &string_is_undef_or_empty($swindow_end_file)) ) {
-    $log->fatal_error("When specifying sowing window dates, you must provide both stream_fldFileName_swindow_start and stream_fldFileName_swindow_end. To specify exact sowing dates, use the same file." );
+  if ( !&string_is_undef_or_empty($swindow_start_file) or !&string_is_undef_or_empty($swindow_end_file) or !&string_is_undef_or_empty($gdd_file) or !&string_is_undef_or_empty($gdd20_baseline_file) or !&string_is_undef_or_empty($mesh_file)) {
+
+    # User gave an input file without specifying cropcals_rx = .true.
+    # Changing this means nothing to the code, but helps namelist make more sense
+    if ( ! &value_is_true($cropcals_rx) ){
+      $log->fatal_error("If providing any crop calendar input file(s), cropcals_rx must be true" );
+    }
+
+    # User provided an input file but set mesh file to empty
+    if ( &string_is_undef_or_empty($mesh_file) ) {
+      $log->fatal_error("If providing any crop calendar input file(s), you must provide stream_meshfile_cropcal" );
+    }
+
+    # Set first and last stream years
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal',
+                'sim_year'=>$nl_flags->{'sim_year'},
+                'sim_year_range'=>$nl_flags->{'sim_year_range'});
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal',
+                'sim_year'=>$nl_flags->{'sim_year'},
+                'sim_year_range'=>$nl_flags->{'sim_year_range'});
+
+    # Set align year, if first and last years are different
+    if ( $nl->get_value('stream_year_first_cropcal') !=
+        $nl->get_value('stream_year_last_cropcal') ) {
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+                  'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'},
+                  'sim_year_range'=>$nl_flags->{'sim_year_range'});
+    }
   }
+
+  # If running with prescribed crop calendars, certain files must be provided
+  my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ;
+  if ( &value_is_true($cropcals_rx) ) {
+    if ( &string_is_undef_or_empty($swindow_start_file) or &string_is_undef_or_empty($swindow_end_file) ) {
+      $log->fatal_error("If cropcals_rx is true, sowing window start and end files must be provided. To specify exact sowing dates, use the same file." );
+    }
+    if ( &string_is_undef_or_empty($gdd_file) and (! &value_is_true($generate_crop_gdds)) ){
+      $log->fatal_error("If cropcals_rx is true and generate_crop_gdds is false, maturity requirement file stream_fldFileName_cultivar_gdds must be provided" );
+    }
+  }
+
+  # Option checks
   if ( &string_is_undef_or_empty($gdd_file) and ! &string_is_undef_or_empty($gdd20_baseline_file) ) {
       $log->fatal_error("If not providing stream_fldFileName_cultivar_gdds, don't provide stream_fldFileName_gdd20_baseline");
   }
   if ( &value_is_true($generate_crop_gdds) ) {
+      my $use_mxmat = $nl->get_value('use_mxmat') ;
       if ( &value_is_true($use_mxmat) ) {
           $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" );
       }
@@ -4223,9 +4255,6 @@ sub setup_logic_cropcal_streams {
           $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_gdd20_baseline")
       }
   }
-  if ( &string_is_undef_or_empty($mesh_file) and ( ! &string_is_undef_or_empty($swindow_start_file) or ! &string_is_undef_or_empty($gdd_file) ) ) {
-      $log->fatal_error("If prescribing crop sowing dates and/or maturity requirements, you must specify stream_meshfile_cropcal")
-  }
 }
 
 #-------------------------------------------------------------------------------

From dbbd7954a9b5e9a38d0afe45648b19dd5597c4fe Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 29 May 2024 12:17:31 -0600
Subject: [PATCH 0365/1248] change fluh_timeseries to use an file with wider
 time range

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index fe34e9f4b8..37aff979f9 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1557,7 +1557,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- This one is just for testing until Issue #2304 is resolved -->
 <fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."
- >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
+ >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1650-2015_c240216.nc</fluh_timeseries>
 
 <!-- Fixation and Uptake of Nitrogen Model (FUN2.0) -->
 <use_fun                                                            >.false.</use_fun>

From 2848873409be7eddecb0f62326116afaf9a2e319 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 29 May 2024 12:18:24 -0600
Subject: [PATCH 0366/1248] fix pvt system test

---
 cime_config/SystemTests/pvt.py | 34 +++++++++++++++++++++++++++++++---
 1 file changed, 31 insertions(+), 3 deletions(-)

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
index 6b2a958eaa..05da935a0e 100644
--- a/cime_config/SystemTests/pvt.py
+++ b/cime_config/SystemTests/pvt.py
@@ -51,6 +51,11 @@ def run_phase(self):
         orig_casevar = self._case.get_value("CASE")
         caseroot = self._case.get_value("CASEROOT")
 
+        # Set the run start date based on the desired starting reference case year
+        refcase_year = 1700
+        stop_n_pveg = 5
+        startyear_pveg = refcase_year - stop_n_pveg
+
         # clone the main case to create spinup case
         logger.info("PVT log:  cloning setup")
         clone_path = "{}.potveg".format(caseroot)
@@ -65,10 +70,11 @@ def run_phase(self):
         self._set_active_case(clone)
 
         # set the clone case values
-        stop_n_pveg = 1
         with clone:
-            # clone.set_value("CLM_ACCELERATED_SPINUP", "on")
+            clone.set_value("CLM_ACCELERATED_SPINUP", "off")
             clone.set_value("STOP_N", stop_n_pveg)
+            clone.set_value("STOP_OPTION", "nyears")
+            clone.set_value("RUN_STARTDATE", "{}-01-01".format(startyear_pveg))
 
         # Modify the spin up case to use the potential vegetation mode.
         # Checks for incompatible cases and necessary mapping files are
@@ -93,11 +99,33 @@ def run_phase(self):
         os.chdir(caseroot)
         self._set_active_case(orig_case)
 
+        # Copy restart files from spin up to the transient case run directory
+        # obtain rpointer files and necessary restart files from short term archiving directory
+        rundir = self._case.get_value("RUNDIR")
+
+        refdate = str(refcase_year) + '-01-01-00000'
+        rest_path = os.path.join(dout_sr, "rest", "{}".format(refdate))
+
+        for item in glob.glob("{}/*{}*".format(rest_path, refdate)):
+            link_name = os.path.join(rundir, os.path.basename(item))
+            if os.path.islink(link_name) and os.readlink(link_name) == item:
+                # Link is already set up correctly: do nothing
+                # (os.symlink raises an exception if you try to replace an
+                # existing file)
+                pass
+            else:
+                os.symlink(item, link_name)
+
+        for item in glob.glob("{}/*rpointer*".format(rest_path)):
+            shutil.copy(item, rundir)
+
+        # Update run case settings
         self._case.set_value("CLM_ACCELERATED_SPINUP", "off")
         self._case.set_value("RUN_TYPE", "hybrid")
         self._case.set_value("GET_REFCASE", False)
         self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar))
-        self._case.set_value("RUN_REFDATE", "1700-01-01")
+        self._case.set_value("RUN_REFDATE", "{}-01-01".format(refcase_year))
+        self._case.set_value("RUN_STARTDATE", "{}-01-01".format(refcase_year))
         self._case.set_value("DOUT_S", False)
         self._case.flush()
 

From 6b550b1aa536fed46d197580614226e16691d1f8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 29 May 2024 14:03:29 -0600
Subject: [PATCH 0367/1248] Replace checkout_externals with git-fleximod in
 documentation

---
 .gitignore                                    |  6 ++--
 README                                        |  4 +--
 README_EXTERNALS.rst                          | 32 +++++++++----------
 bld/CLMBuildNamelist.pm                       |  2 +-
 doc/README.CHECKLIST.master_tags              |  6 ++--
 doc/build_docs                                |  2 +-
 doc/design/python_script_user_interface.rst   |  2 +-
 .../obtaining-and-building-ctsm.rst           |  6 ++--
 doc/source/lilac/specific-atm-models/wrf.rst  |  2 +-
 python/ctsm/site_and_regional/run_neon.py     |  2 +-
 tools/mksurfdata_esmf/README.md               |  2 +-
 11 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/.gitignore b/.gitignore
index 1da8072fed..6c8111525a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,6 @@
-# directories checked out by manage_externals, and other files created
-# by manage_externals
-manage_externals.log
+# directories checked out by git-fleximod, and other files created
+# by git-fleximod
+git-fleximod.log
 ccs_config
 /src/fates/
 /cime/
diff --git a/README b/README
index 18cc2b1458..97daae2d5a 100644
--- a/README
+++ b/README
@@ -50,7 +50,7 @@ lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for
 test -------------- CTSM Testing scripts for CTSM offline tools (deprecated)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
-manage_externals -- Script to manage the external source directories (deprecated)
+git-fleximod ------ Script to manage the external source directories
 py_env_create ----- Script to setup the python environment for CTSM python tools using conda
 python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts
 
@@ -75,7 +75,7 @@ Top level documentation ($CTSMROOT):
 README ------------------- This file
 README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git
 README.rst --------------- File that displays under the project in github
-README_EXTERNALS.rst ----- Information on how to work with manage_externals for CTSM (deprecated)
+README_EXTERNALS.rst ----- Information on how to work with git-fleximod for CTSM
 CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project
 Copyright ---------------- CESM Copyright file
 doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the
diff --git a/README_EXTERNALS.rst b/README_EXTERNALS.rst
index ed7a068991..22c56ee6f6 100644
--- a/README_EXTERNALS.rst
+++ b/README_EXTERNALS.rst
@@ -18,11 +18,11 @@ To obtain the CTSM code you need to do the following:
 
    This will create a directory ``my_ctsm_sandbox/`` in your current working directory.
 
-#. Run the script **manage_externals/checkout_externals**. ::
+#. Run **./bin/git-fleximod update**. ::
 
-      ./manage_externals/checkout_externals
+      ./bin/git-fleximod update
 
-   The **checkout_externals** script is a package manager that will
+   **git-fleximod** is a package manager that will
    populate the ctsm directory with the relevant versions of each of the
    components along with the CIME infrastructure code.
 
@@ -30,21 +30,21 @@ At this point you have a working version of CTSM.
 
 To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ .
 
-More details on checkout_externals
-----------------------------------
+More details on git-fleximod
+----------------------------
 
 The file **Externals.cfg** in your top-level CTSM directory tells
-**checkout_externals** which tag/branch of each component should be
+**git-fleximod** which tag/branch of each component should be
 brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**.
 
-NOTE: checkout_externals will always attempt
+NOTE: git-fleximod will always attempt
 to make the working copy exactly match the externals description. If
 you manually modify an external without updating Externals.cfg, e.g. switch
-to a different tag, then rerunning checkout_externals will switch you
+to a different tag, then rerunning git-fleximod will switch you
 back to the external described in Externals.cfg. See below
 documentation `Customizing your CTSM sandbox`_ for more details.
 
-**You need to rerun checkout_externals whenever Externals.cfg has
+**You need to rerun git-fleximod whenever Externals.cfg has
 changed** (unless you have already manually updated the relevant
 external(s) to have the correct branch/tag checked out). Common times
 when this is needed are:
@@ -54,17 +54,17 @@ when this is needed are:
 * After merging some other CTSM branch/tag into your currently
   checked-out branch
 
-**checkout_externals** must be run from the root of the source
+**git-fleximod** must be run from the root of the source
 tree. For example, if you cloned CTSM with::
 
   git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
 
-then you must run **checkout_externals** from
+then you must run **git-fleximod** from
 ``/path/to/my_ctsm_sandbox``.
 
-To see more details of **checkout_externals**, issue ::
+To see more details of **git-fleximod**, issue ::
 
-  ./manage_externals/checkout_externals --help
+  ./bin/git-fleximod --help
 
 Customizing your CTSM sandbox
 =============================
@@ -80,7 +80,7 @@ checked out ctsm1.0.0 but really wanted to have ctsm1.1.0;
 you would simply do the following::
 
   git checkout ctsm1.1.0
-  ./manage_externals/checkout_externals
+  ./bin/git-fleximod update
 
 You should **not** use this method if you have made any source code
 changes, or if you have any ongoing CTSM cases that were created from
@@ -107,11 +107,11 @@ Each entry specifies either a tag, a hash or a branch. To point to a new tag:
 
 #. Checkout the new component(s)::
 
-     ./manage_externals/checkout_externals
+     ./bin/git-fleximod update
 
 To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``.
 
-To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``manage_externals/checkout_externals`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.)
+To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod update`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.)
 
 Keep in mind that changing individual components from a tag may result
 in an invalid model (won't compile, won't run, not scientifically
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fb44023cd5..1371ea5c06 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -366,7 +366,7 @@ sub check_for_perl_utils {
     } else {
       die <<"EOF";
 ** Cannot find the root of the cime directory  enter it using the -cimeroot option
-   Did you run the checkout_externals scripts?
+   Did you run ./bin/git-fleximod update?
 EOF
     }
   }
diff --git a/doc/README.CHECKLIST.master_tags b/doc/README.CHECKLIST.master_tags
index ed7794130b..0da52acaaa 100644
--- a/doc/README.CHECKLIST.master_tags
+++ b/doc/README.CHECKLIST.master_tags
@@ -14,9 +14,9 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow
    2a -- run 'git pull' to pull in the latest version from GitHub
    2b -- run 'git status' and/or 'git diff' to make sure you don't have any uncommitted
          local changes
-   2c -- run './manage_externals/checkout_externals -S' to make sure all externals are
-         updated and don't have any uncommitted changes. (If any are marked with 's' in
-         the first column, run ./manage_externals/checkout_externals to update them.)
+   2c -- run './bin/git-fleximod status' to make sure all externals are
+         updated and don't have any uncommitted changes. If any are marked with 's' in
+         the first column, run './bin/git-fleximod update'.
 
 (3) Do all testing on your fork/feature-branch
 
diff --git a/doc/build_docs b/doc/build_docs
index a8e8099b60..45c7099ec5 100755
--- a/doc/build_docs
+++ b/doc/build_docs
@@ -6,5 +6,5 @@ if [ -f doc-builder/build_docs ]; then
     echo "Running: ./doc-builder/build_docs $@"
     ./doc-builder/build_docs "$@"
 else
-    echo "Obtain doc-builder by running ./manage_externals/checkout_externals -o from the top-level"
+    echo "Obtain doc-builder by running './bin/git-fleximod update --optional' from the top-level"
 fi
diff --git a/doc/design/python_script_user_interface.rst b/doc/design/python_script_user_interface.rst
index 87c1b3e8fc..d639117810 100644
--- a/doc/design/python_script_user_interface.rst
+++ b/doc/design/python_script_user_interface.rst
@@ -66,7 +66,7 @@ For logical flags, use a flag without an argument -- ``--feature`` for the case
 
 We try to follow the guide at the top of `Python's logging howto <https://docs.python.org/3/howto/logging.html>`_. In particular, print statements should be used for "console output for ordinary usage of a command line script or program"; ``logger.info`` or ``logger.debug`` should be used to "report events that occur during normal operation of a program (e.g. for status monitoring or fault investigation)", etc.
 
-The distinction between when to use print and when to use logging can admittedly be a bit subjective, as it comes down to the question of whether the given output is part of the fundamental operation of the script – i.e., part of what the script is designed to do is to give this output. For example, ``run_sys_tests`` prints a variety of information when it starts, particularly concerning the git and manage_externals status of the current repository. The rationale for using ``print`` statements for this is that we designed ``run_sys_tests`` to replace some of the repetitive items that we did whenever running the system tests. One of these items was running ``git status`` and ``./manage_externals/checkout_externals -S -v`` to check that the repository is in a clean state. Thus, in this case, our view is that the output from these commands is part of the fundamental purpose of ``run_sys_tests``: it is something we always want to see, and we feel that it is important for anyone running the system tests to review, and thus ``print`` statements are appropriate here.
+The distinction between when to use print and when to use logging can admittedly be a bit subjective, as it comes down to the question of whether the given output is part of the fundamental operation of the script – i.e., part of what the script is designed to do is to give this output. For example, ``run_sys_tests`` prints a variety of information when it starts, particularly concerning the git and git-fleximod status of the current repository. The rationale for using ``print`` statements for this is that we designed ``run_sys_tests`` to replace some of the repetitive items that we did whenever running the system tests. One of these items was running ``git status`` and ``./bin/git-fleximod status --verbose`` to check that the repository is in a clean state. Thus, in this case, our view is that the output from these commands is part of the fundamental purpose of ``run_sys_tests``: it is something we always want to see, and we feel that it is important for anyone running the system tests to review, and thus ``print`` statements are appropriate here.
 
 In general, ``print`` statements should be used sparingly, just for output that is important for the user to see. That said, users of CTSM scripts often expect more output than you would see from a typical Unix tool (where the philosophy is that there should be no output if everything worked correctly). Some examples of things that users of CTSM scripts typically want to see are:
 
diff --git a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
index c0e510c017..ef24e695b9 100644
--- a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
+++ b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
@@ -26,7 +26,7 @@ Obtain CTSM by running::
 
   git clone https://github.com/ESCOMP/CTSM.git
   cd CTSM
-  ./manage_externals/checkout_externals
+  ./bin/git-fleximod update
 
 Then build CTSM and its dependencies. On a machine that has been ported to CIME, the
 command will look like this (example given for NCAR's ``cheyenne`` machine)::
@@ -101,11 +101,11 @@ above<building-ctsm-and-lilac-prerequisites>`) can be obtained with::
 
   git clone https://github.com/ESCOMP/CTSM.git
   cd CTSM
-  ./manage_externals/checkout_externals
+  ./bin/git-fleximod update
 
 By default, this will put you on the ``master`` branch of CTSM, which is the main
 development branch. You can checkout a different branch or tag using ``git checkout``;
-**be sure to rerun** ``./manage_externals/checkout_externals`` **after doing so.**
+**be sure to rerun** ``./bin/git-fleximod update`` **after doing so.**
 
 For more details, see
 https://github.com/ESCOMP/CTSM/wiki/Quick-start-to-CTSM-development-with-git
diff --git a/doc/source/lilac/specific-atm-models/wrf.rst b/doc/source/lilac/specific-atm-models/wrf.rst
index 5d104778ec..ad85fee777 100644
--- a/doc/source/lilac/specific-atm-models/wrf.rst
+++ b/doc/source/lilac/specific-atm-models/wrf.rst
@@ -44,7 +44,7 @@ Clone the CTSM repository::
 
     git clone https://github.com/ESCOMP/CTSM.git
     cd CTSM
-    ./manage_externals/checkout_externals
+    ./bin/git-fleximod update
 
 .. _build-CTSM-and-dependencies:
 
diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py
index 4b0df2722d..3acbf435b1 100755
--- a/python/ctsm/site_and_regional/run_neon.py
+++ b/python/ctsm/site_and_regional/run_neon.py
@@ -41,7 +41,7 @@
 # - [ ] Case dependency and the ability to check case status
 # - [ ] If Case dependency works we don't need finidat given explicilty for post-ad and transient.
 
-# - [ ] checkout_externals instead of using env varaiable
+# - [ ] "./bin/git-fleximod update" instead of using env variable
 # - [ ] wget the fields available and run for those available
 
 # - [ ] Matrix spin-up if (SASU) Eric merged it in
diff --git a/tools/mksurfdata_esmf/README.md b/tools/mksurfdata_esmf/README.md
index 11cb69c681..3d19c88ff0 100644
--- a/tools/mksurfdata_esmf/README.md
+++ b/tools/mksurfdata_esmf/README.md
@@ -93,7 +93,7 @@ https://github.com/ESCOMP/CTSM/issues/2341
 
 ``` shell
 # Assuming pwd is the tools/mksurfdata_esmf directory
- ./manage_externals/checkout_externals # Assuming at the top level of the CTSM/CESM checkout
+ ./bin/git-fleximod update  # Assuming at the top level of the CTSM/CESM checkout
 ```
 
 This will bring in CIME and ccs_config which are required for building.

From 0f729d8edcec2fa97db471bb766cc8964b01ed81 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 14:16:45 -0600
Subject: [PATCH 0368/1248] Bugfix: cropcalStreamMod now handles cropcals_rx.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index f60ab51000..101ad9f2a4 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -47,6 +47,7 @@ module cropcalStreamMod
   character(len=CL)       :: stream_fldFileName_swindow_end   ! sowing window end stream filename to read
   character(len=CL)       :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read
   character(len=CL)       :: stream_fldFileName_gdd20_baseline ! GDD20 baseline stream filename to read
+  logical                 :: cropcals_rx ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
 
   character(len=*), parameter :: sourcefile = &
        __FILE__
@@ -95,7 +96,8 @@ subroutine cropcal_init(bounds)
          stream_fldFileName_swindow_end,   &
          stream_fldFileName_cultivar_gdds, &
          stream_fldFileName_gdd20_baseline, &
-         stream_meshfile_cropcal
+         stream_meshfile_cropcal, &
+         cropcals_rx
 
     ! Default values for namelist
     stream_year_first_cropcal  = 1      ! first year in stream to use

From 74411ea31189969410205a3edba96c14670a38f4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 14:17:05 -0600
Subject: [PATCH 0369/1248] Update RxCropCals testmod to use cropcals_rx true.

---
 .../testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm     | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
index 9cbfea97f0..8a0b4a91be 100644
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
@@ -1,8 +1,2 @@
 
-! Sowing windows
-stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
-stream_fldFileName_swindow_end  = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
-stream_fldFileName_cultivar_gdds = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc'
-stream_year_first_cropcal = 2000
-stream_year_last_cropcal = 2000
-stream_meshfile_cropcal = '$DIN_LOC_ROOT/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc'
+cropcals_rx = .true.

From 612962280d766d86497ae5747c10d8af33623121 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 29 May 2024 14:32:40 -0600
Subject: [PATCH 0370/1248] Restore .gitignore as it was

---
 .gitignore | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index 6c8111525a..1da8072fed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,6 @@
-# directories checked out by git-fleximod, and other files created
-# by git-fleximod
-git-fleximod.log
+# directories checked out by manage_externals, and other files created
+# by manage_externals
+manage_externals.log
 ccs_config
 /src/fates/
 /cime/

From 5a577cdf701d028393bacc12bfde1749c9a9a2d8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 29 May 2024 14:34:26 -0600
Subject: [PATCH 0371/1248] Delete README_EXTERNALS.rst to be like #2559

---
 README_EXTERNALS.rst | 132 -------------------------------------------
 1 file changed, 132 deletions(-)
 delete mode 100644 README_EXTERNALS.rst

diff --git a/README_EXTERNALS.rst b/README_EXTERNALS.rst
deleted file mode 100644
index 22c56ee6f6..0000000000
--- a/README_EXTERNALS.rst
+++ /dev/null
@@ -1,132 +0,0 @@
-Obtaining the full model code and associated scripting infrastructure
-=====================================================================
-
-[!CAUTION]
-This is deprecated and will be replaced with git submodules. See
-https://github.com/ESCOMP/CTSM/pull/2443
-
-
-CTSM is released via GitHub. You will need some familiarity with git in order
-to modify the code and commit these changes. However, to simply checkout and run the
-code, no git knowledge is required other than what is documented in the following steps.
-
-To obtain the CTSM code you need to do the following:
-
-#. Clone the repository. ::
-
-      git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
-
-   This will create a directory ``my_ctsm_sandbox/`` in your current working directory.
-
-#. Run **./bin/git-fleximod update**. ::
-
-      ./bin/git-fleximod update
-
-   **git-fleximod** is a package manager that will
-   populate the ctsm directory with the relevant versions of each of the
-   components along with the CIME infrastructure code.
-
-At this point you have a working version of CTSM.
-
-To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ .
-
-More details on git-fleximod
-----------------------------
-
-The file **Externals.cfg** in your top-level CTSM directory tells
-**git-fleximod** which tag/branch of each component should be
-brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**.
-
-NOTE: git-fleximod will always attempt
-to make the working copy exactly match the externals description. If
-you manually modify an external without updating Externals.cfg, e.g. switch
-to a different tag, then rerunning git-fleximod will switch you
-back to the external described in Externals.cfg. See below
-documentation `Customizing your CTSM sandbox`_ for more details.
-
-**You need to rerun git-fleximod whenever Externals.cfg has
-changed** (unless you have already manually updated the relevant
-external(s) to have the correct branch/tag checked out). Common times
-when this is needed are:
-
-* After checking out a new CTSM branch/tag
-
-* After merging some other CTSM branch/tag into your currently
-  checked-out branch
-
-**git-fleximod** must be run from the root of the source
-tree. For example, if you cloned CTSM with::
-
-  git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
-
-then you must run **git-fleximod** from
-``/path/to/my_ctsm_sandbox``.
-
-To see more details of **git-fleximod**, issue ::
-
-  ./bin/git-fleximod --help
-
-Customizing your CTSM sandbox
-=============================
-
-There are several use cases to consider when you want to customize or modify your CTSM sandbox.
-
-Switching to a different CTSM branch or tag
--------------------------------------------
-
-If you have already checked out a branch or tag and **HAVE NOT MADE ANY
-MODIFICATIONS** it is simple to change your sandbox. Say that you
-checked out ctsm1.0.0 but really wanted to have ctsm1.1.0;
-you would simply do the following::
-
-  git checkout ctsm1.1.0
-  ./bin/git-fleximod update
-
-You should **not** use this method if you have made any source code
-changes, or if you have any ongoing CTSM cases that were created from
-this sandbox. In these cases, it is often easiest to do a second **git
-clone**.
-
-Pointing to a different version of a component
-----------------------------------------------
-
-Each entry in **Externals.cfg** has the following form (we use CIME as an
-example below)::
-
-  [cime]
-  local_path = cime
-  protocol = git
-  repo_url = https://github.com/CESM-Development/cime
-  tag = cime5.4.0-alpha.20
-  required = True
-
-Each entry specifies either a tag, a hash or a branch. To point to a new tag:
-
-#. Modify the relevant entry/entries in **Externals.cfg** (e.g., changing
-   ``cime5.4.0-alpha.20`` to ``cime5.4.0-alpha.21`` above)
-
-#. Checkout the new component(s)::
-
-     ./bin/git-fleximod update
-
-To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``.
-
-To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod update`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.)
-
-Keep in mind that changing individual components from a tag may result
-in an invalid model (won't compile, won't run, not scientifically
-meaningful) and is unsupported.
-
-Committing your change to Externals.cfg
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-After making this change, it's a good idea to commit the change in your
-local CTSM git repository. First create a branch in your local
-repository, then commit it. (Unlike with subversion, branches are stored
-locally unless you explicitly push them up to GitHub. Feel free to
-create whatever local branches you'd like.) For example::
-
-  git checkout -b my_ctsm_branch
-  git add Externals.cfg
-  git commit -m "Update CIME to cime5.4.0-alpha.20"
-

From 61c97a13ebf81bb28f4bbac7aa1072c9f544c85b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 29 May 2024 15:27:22 -0600
Subject: [PATCH 0372/1248] Add dummy ./manage_externals/checkout_externals
 with ERROR message

---
 manage_externals/checkout_externals | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100755 manage_externals/checkout_externals

diff --git a/manage_externals/checkout_externals b/manage_externals/checkout_externals
new file mode 100755
index 0000000000..5f848f5da9
--- /dev/null
+++ b/manage_externals/checkout_externals
@@ -0,0 +1,3 @@
+echo "ERROR: Instead of ./manage_externals/checkout_externals"
+echo "please type './bin/git-fleximod update'"
+echo "For additional information, please type './bin/git-fleximod --help'"

From 9d1f88d15ac942cb7176b30bc48163ab6e5031fc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 15:30:41 -0600
Subject: [PATCH 0373/1248] Add RxCropCals and RxCropCalsAdapt tests to new
 suite crop_calendars.

---
 cime_config/testdefs/testlist_clm.xml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 9cfba6f5b3..bf763c4775 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3719,5 +3719,23 @@
     </options>
   </test>
 
+  <test name="SMS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCals">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:00:00</option>
+    </options>
+  </test>
+
+  <test name="ERS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdapt">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:00:00</option>
+    </options>
+  </test>
+
 
 </testlist>

From 7e5257a94efa920f7b608a97b041fef63b1d9aa7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 29 May 2024 16:12:06 -0600
Subject: [PATCH 0374/1248] Add cropcals_rx_adapt option.

---
 bld/CLMBuildNamelist.pm                       | 50 +++++++++++++++----
 bld/namelist_files/namelist_defaults_ctsm.xml |  6 +++
 .../namelist_definition_ctsm.xml              |  5 ++
 .../clm/RxCropCalsAdapt/user_nl_clm           |  4 +-
 src/cpl/share_esmf/cropcalStreamMod.F90       |  4 +-
 5 files changed, 55 insertions(+), 14 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index aff46be3f0..fc80379201 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4174,19 +4174,29 @@ sub setup_logic_cropcal_streams {
 
   # Set up other crop calendar parameters
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcals_rx');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcals_rx_adapt');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat');
 
-  # Add defaults if using prescribed crop calendars
+  # These can't both be true
   my $cropcals_rx = $nl->get_value('cropcals_rx') ;
-  if ( &value_is_true($cropcals_rx) ) {
+  my $cropcals_rx_adapt = $nl->get_value('cropcals_rx_adapt') ;
+  if (&value_is_true($cropcals_rx) and &value_is_true($cropcals_rx_adapt)) {
+    $log->fatal_error("cropcals_rx and cropcals_rx_adapt may not both be true" );
+  }
+
+  # Add defaults if using prescribed crop calendars
+  if ( &value_is_true($cropcals_rx) or &value_is_true($cropcals_rx_adapt) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_start');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_end');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal');
+    if ( &value_is_true($cropcals_rx_adapt) ) {
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline');
+    }
   }
 
-  # Add defaults if using any potentially time-varying crop calendar input files
+  # Add defaults if using any crop calendar input files
   my $swindow_start_file = $nl->get_value('stream_fldFileName_swindow_start') ;
   my $swindow_end_file = $nl->get_value('stream_fldFileName_swindow_end') ;
   my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ;
@@ -4194,10 +4204,20 @@ sub setup_logic_cropcal_streams {
   my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ;
   if ( !&string_is_undef_or_empty($swindow_start_file) or !&string_is_undef_or_empty($swindow_end_file) or !&string_is_undef_or_empty($gdd_file) or !&string_is_undef_or_empty($gdd20_baseline_file) or !&string_is_undef_or_empty($mesh_file)) {
 
-    # User gave an input file without specifying cropcals_rx = .true.
-    # Changing this means nothing to the code, but helps namelist make more sense
-    if ( ! &value_is_true($cropcals_rx) ){
-      $log->fatal_error("If providing any crop calendar input file(s), cropcals_rx must be true" );
+    # User gave an input file without specifying cropcals_rx or cropcals_rx_adapt = .true.
+    # Requiring this means nothing to the code, but helps namelist make more sense
+    if ( !&value_is_true($cropcals_rx) and !&value_is_true($cropcals_rx_adapt) ){
+      $log->fatal_error("If providing any crop calendar input file(s), cropcals_rx or cropcals_rx_adapt must be true" );
+    }
+
+    # User set cropcals_rx_adapt to true but set stream_fldFileName_gdd20_baseline to empty
+    if ( &value_is_true($cropcals_rx_adapt) and &string_is_undef_or_empty($gdd20_baseline_file) ) {
+      $log->fatal_error("If cropcals_rx_adapt is true, stream_fldFileName_gdd20_baseline must be provided" );
+    }
+
+    # cropcals_rx_adapt is false but user provided stream_fldFileName_gdd20_baseline
+    if ( !&value_is_true($cropcals_rx_adapt) and !&string_is_undef_or_empty($gdd20_baseline_file) ) {
+      $log->fatal_error("If stream_fldFileName_gdd20_baseline provided, cropcals_rx_adapt must be true" );
     }
 
     # User provided an input file but set mesh file to empty
@@ -4213,9 +4233,17 @@ sub setup_logic_cropcal_streams {
                 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
 
-    # Set align year, if first and last years are different
+    # Check/set things if first and last years are different
     if ( $nl->get_value('stream_year_first_cropcal') !=
         $nl->get_value('stream_year_last_cropcal') ) {
+
+      # Do not allow maturity requirements to change over time if stream_fldFileName_gdd20_baseline is provided. That would be nonsensical.
+      # Note that this restricts sowing windows from changing over time as well, because there are not separate stream_year settings for that.
+      if ( !&string_is_undef_or_empty($gdd20_baseline_file) ) {
+        $log->fatal_error("If cropcals_rx_adapt is true (i.e., stream_fldFileName_gdd20_baseline is provided), no crop calendar input is allowed to vary over time (i.e., stream_year_first_cropcal and stream_year_last_cropcal must be the same)." );
+      }
+
+      # Set align year
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
                   'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'},
                   'sim_year_range'=>$nl_flags->{'sim_year_range'});
@@ -4224,12 +4252,12 @@ sub setup_logic_cropcal_streams {
 
   # If running with prescribed crop calendars, certain files must be provided
   my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ;
-  if ( &value_is_true($cropcals_rx) ) {
+  if ( &value_is_true($cropcals_rx) or &value_is_true($cropcals_rx_adapt) ) {
     if ( &string_is_undef_or_empty($swindow_start_file) or &string_is_undef_or_empty($swindow_end_file) ) {
-      $log->fatal_error("If cropcals_rx is true, sowing window start and end files must be provided. To specify exact sowing dates, use the same file." );
+      $log->fatal_error("If cropcals_rx or cropcals_rx_adapt is true, sowing window start and end files must be provided. To specify exact sowing dates, use the same file." );
     }
     if ( &string_is_undef_or_empty($gdd_file) and (! &value_is_true($generate_crop_gdds)) ){
-      $log->fatal_error("If cropcals_rx is true and generate_crop_gdds is false, maturity requirement file stream_fldFileName_cultivar_gdds must be provided" );
+      $log->fatal_error("If cropcals_rx or cropcals_rx_adapt is true and generate_crop_gdds is false, maturity requirement file stream_fldFileName_cultivar_gdds must be provided" );
     }
   }
 
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 08f67a2712..85f37a22fd 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1688,6 +1688,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- crop calendars: default settings -->
 <cropcals_rx>.false.</cropcals_rx>
+<cropcals_rx_adapt>.false.</cropcals_rx_adapt>
 <stream_year_first_cropcal  >2000</stream_year_first_cropcal>
 <stream_year_last_cropcal   >2000</stream_year_last_cropcal>
 <model_year_align_cropcal   >2000</model_year_align_cropcal>
@@ -1697,6 +1698,11 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldFileName_swindow_end cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
 <stream_meshfile_cropcal cropcals_rx=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>
+<stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
+<stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
+<stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/testdata/gdd20baseline.tmp_dontupload.nc</stream_fldFileName_gdd20_baseline>
+<stream_meshfile_cropcal cropcals_rx_adapt=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>
 
 <!-- lightning streams namelist defaults -->
 
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 366b7498e8..f37ada6847 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1778,6 +1778,11 @@ Mapping method from LAI input file to the model resolution
 Flag to enable prescribed crop calendars (sowing window dates and maturity requirement)
 </entry>
 
+<entry id="cropcals_rx_adapt" type="logical" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Flag to enable prescribed crop calendars (sowing window dates and maturity requirement), with maturity requirement adaptive based on recent climate
+</entry>
+
 <entry id="stream_year_first_cropcal" type="integer" category="datasets"
        group="cropcal_streams" valid_values="" >
 First year to loop over for crop calendar data (not including gdd20_baseline file)
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm
index 1bba9d2a89..709c7221e0 100644
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm
@@ -1,3 +1,3 @@
 
-! Eventually replace this with half-degree version in the proper place
-stream_fldFileName_gdd20_baseline = '/glade/u/home/samrabin/ctsm_scale-mat-reqs/tools/crop_calendars/test.nc'
+cropcals_rx = .false.
+cropcals_rx_adapt = .true.
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 101ad9f2a4..3333b6cfdc 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -48,6 +48,7 @@ module cropcalStreamMod
   character(len=CL)       :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read
   character(len=CL)       :: stream_fldFileName_gdd20_baseline ! GDD20 baseline stream filename to read
   logical                 :: cropcals_rx ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
+  logical                 :: cropcals_rx_adapt ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
 
   character(len=*), parameter :: sourcefile = &
        __FILE__
@@ -97,7 +98,8 @@ subroutine cropcal_init(bounds)
          stream_fldFileName_cultivar_gdds, &
          stream_fldFileName_gdd20_baseline, &
          stream_meshfile_cropcal, &
-         cropcals_rx
+         cropcals_rx, &
+         cropcals_rx_adapt
 
     ! Default values for namelist
     stream_year_first_cropcal  = 1      ! first year in stream to use

From 709c3da94d1816b42268bf98a4b3d947bdc29a9d Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 29 May 2024 16:30:06 -0600
Subject: [PATCH 0375/1248] remove unnecessary import call

---
 cime_config/SystemTests/pvt.py              | 2 --
 cime_config/SystemTests/systemtest_utils.py | 5 ++---
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
index 05da935a0e..feef6cb04c 100644
--- a/cime_config/SystemTests/pvt.py
+++ b/cime_config/SystemTests/pvt.py
@@ -8,12 +8,10 @@
     - use CLM_ACCELERATED_SPINUP?
 2) run a transient landuse case with use_fates_lupft
     - start from the restart file generated in (1)
-
 """
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
-from systemtest_utils import find_user_nl_option
 import shutil, glob, os
 
 logger = logging.getLogger(__name__)
diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py
index 2591ac4223..c39f5171ba 100644
--- a/cime_config/SystemTests/systemtest_utils.py
+++ b/cime_config/SystemTests/systemtest_utils.py
@@ -85,9 +85,8 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path):
     except:
         print(f"ERROR trying to run {tool_name}.")
         raise
-"""
-Read a user_nl file and return the namelist option if found
-"""
+
+# Read a user_nl file and return the namelist option if found
 def find_user_nl_option(caseroot, component, namelist_option):
     
     # This is a copy of the CIME _get_list_of_user_nl_files

From 1ed3f1967ed4564e2809841ca8a99b09a479299f Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 29 May 2024 16:46:46 -0600
Subject: [PATCH 0376/1248] Replace cheyenne with derecho in a .rst file

---
 .../obtaining-and-building-ctsm.rst                    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
index ef24e695b9..907f63f211 100644
--- a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
+++ b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
@@ -29,9 +29,9 @@ Obtain CTSM by running::
   ./bin/git-fleximod update
 
 Then build CTSM and its dependencies. On a machine that has been ported to CIME, the
-command will look like this (example given for NCAR's ``cheyenne`` machine)::
+command will look like this (example given for NCAR's ``derecho`` machine)::
 
-  ./lilac/build_ctsm /glade/scratch/$USER/ctsm_build_dir --machine cheyenne --compiler intel
+  ./lilac/build_ctsm /glade/scratch/$USER/ctsm_build_dir --machine derecho --compiler intel
 
 and then, before building the atmosphere model::
 
@@ -145,13 +145,13 @@ the `CIME documentation`_.
 Building on a CIME-supported machine
 ------------------------------------
 
-If you are using a machine that has been ported to CIME_ (for example, NCAR's ``cheyenne``
+If you are using a machine that has been ported to CIME_ (for example, NCAR's ``derecho``
 machine), then you do not need to specify much information to ``build_ctsm``. In addition,
 in this case, CIME will load the appropriate modules and set the appropriate environment
 variables at build time, so you do not need to do anything to set up your environment
 ahead of time. **Building CTSM with LILAC requires ESMF. ESMF is currently an optional
 CIME dependency, so many CIME-ported machines do not provide information on an ESMF
-installation. NCAR's cheyenne machine DOES provide ESMF, but for other machines, you may
+installation. NCAR's derecho machine DOES provide ESMF, but for other machines, you may
 need to add this to your CIME port.**
 
 To build CTSM and its dependencies in this case, run::
@@ -231,7 +231,7 @@ Example usage for a Mac (a simple case) is::
 
   ./lilac/build_ctsm ~/ctsm_build_dir --os Darwin --compiler gnu --netcdf-path /usr/local --esmf-mkfile-path /Users/sacks/ESMF/esmf8.0.0/lib/libO/Darwin.gfortranclang.64.mpich3.default/esmf.mk --max-mpitasks-per-node 4 --no-pnetcdf
 
-Example usage for NCAR's ``cheyenne`` machine (a more complex case) is::
+Example usage for NCAR's ``derecho`` machine (a more complex case) is::
 
   module purge
   module load ncarenv/1.3 python/3.7.9 cmake intel/19.1.1 esmf_libs mkl

From 4f9db007afa9b3e1705c7bad78c2cc71714d9cd6 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 30 May 2024 11:51:36 -0600
Subject: [PATCH 0377/1248] Add "bin/" before git-fleximod in README
 documentation

---
 README | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README b/README
index 97daae2d5a..07d9c7b13d 100644
--- a/README
+++ b/README
@@ -50,7 +50,7 @@ lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for
 test -------------- CTSM Testing scripts for CTSM offline tools (deprecated)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
-git-fleximod ------ Script to manage the external source directories
+bin/git-fleximod -- Script to manage the external source directories
 py_env_create ----- Script to setup the python environment for CTSM python tools using conda
 python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts
 

From 8ac86a1f21704e952b5dbb753f51cb4ddcfd47f4 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 30 May 2024 12:10:04 -0600
Subject: [PATCH 0378/1248] Replacing README_EXTERNALS.rst with
 README_GITFLEXIMOD.rst

---
 README_GITFLEXIMOD.rst | 127 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 127 insertions(+)
 create mode 100644 README_GITFLEXIMOD.rst

diff --git a/README_GITFLEXIMOD.rst b/README_GITFLEXIMOD.rst
new file mode 100644
index 0000000000..f91ef30fae
--- /dev/null
+++ b/README_GITFLEXIMOD.rst
@@ -0,0 +1,127 @@
+Obtaining the full model code and associated scripting infrastructure
+=====================================================================
+
+CTSM is released via GitHub. You will need some familiarity with git in order
+to modify the code and commit these changes. However, to simply checkout and run the
+code, no git knowledge is required other than what is documented in the following steps.
+
+To obtain the CTSM code you need to do the following:
+
+#. Clone the repository. ::
+
+      git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
+
+   This will create a directory ``my_ctsm_sandbox/`` in your current working directory.
+
+#. Run **./bin/git-fleximod update**. ::
+
+      ./bin/git-fleximod update
+
+   **git-fleximod** is a package manager that will
+   populate the ctsm directory with the relevant versions of each of the
+   components along with the CIME infrastructure code.
+
+At this point you have a working version of CTSM.
+
+To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ .
+
+More details on git-fleximod
+----------------------------
+
+The file **Externals.cfg** in your top-level CTSM directory tells
+**git-fleximod** which tag/branch of each component should be
+brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**.
+
+NOTE: git-fleximod will always attempt
+to make the working copy exactly match the externals description. If
+you manually modify an external without updating Externals.cfg, e.g. switch
+to a different tag, then rerunning git-fleximod will switch you
+back to the external described in Externals.cfg. See below
+documentation `Customizing your CTSM sandbox`_ for more details.
+
+**You need to rerun git-fleximod whenever Externals.cfg has
+changed** (unless you have already manually updated the relevant
+external(s) to have the correct branch/tag checked out). Common times
+when this is needed are:
+
+* After checking out a new CTSM branch/tag
+
+* After merging some other CTSM branch/tag into your currently
+  checked-out branch
+
+**./bin/git-fleximod** must be run from the root of the source
+tree. For example, if you cloned CTSM with::
+
+  git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
+
+then you must run **./bin/git-fleximod** from
+``/path/to/my_ctsm_sandbox``.
+
+To see more details of **git-fleximod**, issue ::
+
+  ./bin/git-fleximod --help
+
+Customizing your CTSM sandbox
+=============================
+
+There are several use cases to consider when you want to customize or modify your CTSM sandbox.
+
+Switching to a different CTSM branch or tag
+-------------------------------------------
+
+If you have already checked out a branch or tag and **HAVE NOT MADE ANY
+MODIFICATIONS** it is simple to change your sandbox. Say that you
+checked out ctsm1.0.0 but really wanted to have ctsm1.1.0;
+you would simply do the following::
+
+  git checkout ctsm1.1.0
+  ./bin/git-fleximod
+
+You should **not** use this method if you have made any source code
+changes, or if you have any ongoing CTSM cases that were created from
+this sandbox. In these cases, it is often easiest to do a second **git
+clone**.
+
+Pointing to a different version of a component
+----------------------------------------------
+
+Each entry in **Externals.cfg** has the following form (we use CIME as an
+example below)::
+
+  [cime]
+  local_path = cime
+  protocol = git
+  repo_url = https://github.com/CESM-Development/cime
+  tag = cime5.4.0-alpha.20
+  required = True
+
+Each entry specifies either a tag, a hash or a branch. To point to a new tag:
+
+#. Modify the relevant entry/entries in **Externals.cfg** (e.g., changing
+   ``cime5.4.0-alpha.20`` to ``cime5.4.0-alpha.21`` above)
+
+#. Checkout the new component(s)::
+
+     ./bin/git-fleximod
+
+To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``.
+
+To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.)
+
+Keep in mind that changing individual components from a tag may result
+in an invalid model (won't compile, won't run, not scientifically
+meaningful) and is unsupported.
+
+Committing your change to Externals.cfg
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+After making this change, it's a good idea to commit the change in your
+local CTSM git repository. First create a branch in your local
+repository, then commit it. (Unlike with subversion, branches are stored
+locally unless you explicitly push them up to GitHub. Feel free to
+create whatever local branches you'd like.) For example::
+
+  git checkout -b my_ctsm_branch
+  git add Externals.cfg
+  git commit -m "Update CIME to cime5.4.0-alpha.20"
+

From 03762a081fd3f283c4ff1b9336fe14b7f71a051a Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 30 May 2024 16:08:27 -0600
Subject: [PATCH 0379/1248] Updates to README_GITFLEXIMOD.rst as per Jim's
 review

---
 README_GITFLEXIMOD.rst | 68 +++++++++++++++++-------------------------
 1 file changed, 28 insertions(+), 40 deletions(-)

diff --git a/README_GITFLEXIMOD.rst b/README_GITFLEXIMOD.rst
index f91ef30fae..ab8c412cee 100644
--- a/README_GITFLEXIMOD.rst
+++ b/README_GITFLEXIMOD.rst
@@ -15,11 +15,15 @@ To obtain the CTSM code you need to do the following:
 
 #. Run **./bin/git-fleximod update**. ::
 
+      cd my_ctsm_sandbox
       ./bin/git-fleximod update
+      ./bin/git-fleximod --help  # for a user's guide
 
    **git-fleximod** is a package manager that will
    populate the ctsm directory with the relevant versions of each of the
    components along with the CIME infrastructure code.
+   Additional documentation for git-fleximod appears here:
+   https://github.com/ESMCI/git-fleximod?tab=readme-ov-file#git-fleximod
 
 At this point you have a working version of CTSM.
 
@@ -28,18 +32,18 @@ To see full details of how to set up a case, compile and run, see the CIME docum
 More details on git-fleximod
 ----------------------------
 
-The file **Externals.cfg** in your top-level CTSM directory tells
+The file **.gitmodules** in your top-level CTSM directory tells
 **git-fleximod** which tag/branch of each component should be
-brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**.
+brought in to generate your sandbox.
 
-NOTE: git-fleximod will always attempt
-to make the working copy exactly match the externals description. If
-you manually modify an external without updating Externals.cfg, e.g. switch
-to a different tag, then rerunning git-fleximod will switch you
-back to the external described in Externals.cfg. See below
-documentation `Customizing your CTSM sandbox`_ for more details.
+NOTE: If you manually modify an external without updating .gitmodules,
+e.g. switch to a different tag, then rerunning git-fleximod will warn you of
+local changes you need to resolve.
+git-fleximod will not change a modified external back to what is specified in
+.gitmodules without the --force option.
+See below documentation `Customizing your CTSM sandbox`_ for more details.
 
-**You need to rerun git-fleximod whenever Externals.cfg has
+**You need to rerun git-fleximod whenever .gitmodules has
 changed** (unless you have already manually updated the relevant
 external(s) to have the correct branch/tag checked out). Common times
 when this is needed are:
@@ -49,18 +53,6 @@ when this is needed are:
 * After merging some other CTSM branch/tag into your currently
   checked-out branch
 
-**./bin/git-fleximod** must be run from the root of the source
-tree. For example, if you cloned CTSM with::
-
-  git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
-
-then you must run **./bin/git-fleximod** from
-``/path/to/my_ctsm_sandbox``.
-
-To see more details of **git-fleximod**, issue ::
-
-  ./bin/git-fleximod --help
-
 Customizing your CTSM sandbox
 =============================
 
@@ -75,7 +67,7 @@ checked out ctsm1.0.0 but really wanted to have ctsm1.1.0;
 you would simply do the following::
 
   git checkout ctsm1.1.0
-  ./bin/git-fleximod
+  ./bin/git-fleximod update
 
 You should **not** use this method if you have made any source code
 changes, or if you have any ongoing CTSM cases that were created from
@@ -85,35 +77,31 @@ clone**.
 Pointing to a different version of a component
 ----------------------------------------------
 
-Each entry in **Externals.cfg** has the following form (we use CIME as an
+Each entry in **.gitmodules** has the following form (we use CIME as an
 example below)::
 
-  [cime]
-  local_path = cime
-  protocol = git
-  repo_url = https://github.com/CESM-Development/cime
-  tag = cime5.4.0-alpha.20
-  required = True
+  [submodule "cime"]
+  path = cime
+  url = https://github.com/ESMCI/cime
+  fxtag = cime6.0.246
+  fxrequired = ToplevelRequired
+  fxDONOTUSEurl = https://github.com/ESMCI/cime
 
-Each entry specifies either a tag, a hash or a branch. To point to a new tag:
+Each entry specifies either a tag or a hash. To point to a new tag or hash:
 
-#. Modify the relevant entry/entries in **Externals.cfg** (e.g., changing
-   ``cime5.4.0-alpha.20`` to ``cime5.4.0-alpha.21`` above)
+#. Modify the relevant entry/entries in **.gitmodules** (e.g., changing
+   ``cime6.0.246`` to ``cime6.0.247`` above)
 
 #. Checkout the new component(s)::
 
-     ./bin/git-fleximod
-
-To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``.
-
-To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.)
+     ./bin/git-fleximod update <component>
 
 Keep in mind that changing individual components from a tag may result
 in an invalid model (won't compile, won't run, not scientifically
 meaningful) and is unsupported.
 
-Committing your change to Externals.cfg
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Committing your change to .gitmodules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 After making this change, it's a good idea to commit the change in your
 local CTSM git repository. First create a branch in your local
@@ -122,6 +110,6 @@ locally unless you explicitly push them up to GitHub. Feel free to
 create whatever local branches you'd like.) For example::
 
   git checkout -b my_ctsm_branch
-  git add Externals.cfg
+  git add .gitmodules
   git commit -m "Update CIME to cime5.4.0-alpha.20"
 

From 6fa0255660c848b4f49603511b1da79750b686c8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 30 May 2024 16:09:26 -0600
Subject: [PATCH 0380/1248] Jim's suggestions for
 doc/.../lilac/.../obtaining-and-building-ctsm.rst

---
 .../obtaining-and-building-ctsm.rst                   | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
index 907f63f211..fcd8235b62 100644
--- a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
+++ b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst
@@ -91,7 +91,7 @@ Building CTSM requires:
 
 - ESMF version 8 or later
 
-  - **ESMF is not needed in general for CTSM, but is needed for LILAC**
+  - **ESMF is needed for LILAC (and for CESM3 and later)**
 
 Obtaining CTSM
 ==============
@@ -149,10 +149,11 @@ If you are using a machine that has been ported to CIME_ (for example, NCAR's ``
 machine), then you do not need to specify much information to ``build_ctsm``. In addition,
 in this case, CIME will load the appropriate modules and set the appropriate environment
 variables at build time, so you do not need to do anything to set up your environment
-ahead of time. **Building CTSM with LILAC requires ESMF. ESMF is currently an optional
-CIME dependency, so many CIME-ported machines do not provide information on an ESMF
-installation. NCAR's derecho machine DOES provide ESMF, but for other machines, you may
-need to add this to your CIME port.**
+ahead of time. **Building CTSM with LILAC requires ESMF. ESMF is an optional
+CIME dependency before CESM3 and not optional for CESM3.
+NCAR's derecho machine DOES provide ESMF. For other machines, you may
+need to add this to your CIME port. Please see esmf.org for download and build
+instructions.**
 
 To build CTSM and its dependencies in this case, run::
 

From ae93d22bfee601a9fbe4561cedbd77945ab23bbf Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 30 May 2024 16:42:18 -0600
Subject: [PATCH 0381/1248] Remove cheyenne from testlis_clm.xml

---
 cime_config/testdefs/testlist_clm.xml | 651 +-------------------------
 1 file changed, 1 insertion(+), 650 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 9cfba6f5b3..1ac2334ba8 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -43,8 +43,6 @@
   </test>
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -259,24 +257,14 @@
 -->
   <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/vrtlay">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/SNICARFRC">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="SMS_D_Ld1_PS" grid="f09_g17" compset="I1850Clm50Sp" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -360,8 +348,6 @@
   </test>
   <test name="ERP_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50Sp" testmods="clm/prescribed">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
@@ -422,15 +408,6 @@
       <option name="comment">Do a test similar to FXHIST starting at a 2005 start date, will interpoalte from the 2003 IC file</option>
     </options>
   </test>
-  <test name="SMS_D_Ln9_P36x3" grid="f19_g17" compset="IHistClm50Sp" testmods="clm/waccmx_offline">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment">Run a transient case with standalone settings similar to the FXHIST waccm test</option>
-    </options>
-  </test>
   <test name="SMS_D_Ln9_P128x3" grid="f19_g17" compset="IHistClm50Sp" testmods="clm/waccmx_offline">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -440,14 +417,6 @@
       <option name="comment">Run a transient case with standalone settings similar to the FXHIST waccm test</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/cn_conly">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/cn_conly">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -456,14 +425,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/snowveg_norad">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/snowveg_norad">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -474,7 +435,6 @@
   </test>
   <test name="ERI_Ld9" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/drydepnomegan">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -483,8 +443,6 @@
   </test>
   <test name="ERI_Ld9" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -494,7 +452,6 @@
   </test>
   <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm50BgcCru" testmods="clm/nofire">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -512,7 +469,6 @@
   </test>
   <test name="ERI_C2_Ld9" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -539,8 +495,6 @@
   </test>
   <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -548,15 +502,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld3_P36x2" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld3_P64x2" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -568,7 +513,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_changeFlags">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -788,7 +732,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -798,7 +741,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/anoxia">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -808,7 +750,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/ciso_flexCN_FUN">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -817,8 +758,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/fire_emis">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="prebeta"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
@@ -828,7 +767,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm60Sp" testmods="clm/decStart">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -838,8 +776,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/reduceOutput">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -857,7 +793,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/vrtlay">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -866,8 +801,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50SpCru" testmods="clm/drydepnomegan">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="prebeta"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
@@ -877,7 +810,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm60Sp" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -922,15 +854,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment"  >Transient case with isotopes with a December start</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -940,15 +863,6 @@
       <option name="comment"  >Transient case with isotopes with a December start</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment"  >Transient case with isotopes with a December start, without Meier roughness</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -960,7 +874,6 @@
   </test>
   <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -984,17 +897,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="clm_short"/>
-      <machine name="cheyenne" compiler="gnu" category="clm_short"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1006,14 +908,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/coldStart">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/coldStart">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1022,15 +916,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/mimics">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/mimics">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -1058,14 +943,6 @@
       <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1074,14 +951,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1090,14 +959,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/luna">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/luna">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1106,15 +967,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1124,15 +976,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld30" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment"  >NOTE(bja, 201509) constrain_stress_deciduous_onset is on by default for clm50, but functionality is not exercised by nine day tests, Sean Swenson verified that it is active during 30 day tests.</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld30" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1142,15 +985,6 @@
       <option name="comment"  >NOTE(bja, 201509) constrain_stress_deciduous_onset is on by default for clm50, but functionality is not exercised by nine day tests, Sean Swenson verified that it is active during 30 day tests.</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld5" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/irrig_spunup">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Want ERP _D test with irrigation on</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld5" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/irrig_spunup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1160,15 +994,6 @@
       <option name="comment"  >Want ERP _D test with irrigation on</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCropRtm" testmods="clm/irrig_spunup">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Include an irrigation test with RTM to test irrigation-river feedbacks with that component</option>
-    </options>
-  </test>
   <test name="ERP_D_P64x2_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCropRtm" testmods="clm/irrig_spunup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1180,8 +1005,6 @@
   </test>
   <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCropRtm" testmods="rtm/rtmOnFloodOnEffvelOn">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
     </machines>
@@ -1201,7 +1024,6 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/drydepnomegan">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -1210,8 +1032,6 @@
   </test>
   <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1229,7 +1049,6 @@
   </test>
   <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/decStart">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -1286,15 +1105,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_Ly3_P72x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
-    </options>
-  </test>
   <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1306,7 +1116,6 @@
   </test>
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm45Bgc" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -1314,15 +1123,6 @@
       <option name="comment"  >include a Clm45 ERI test; also, want a debug test of I1850Clm45Bgc</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCru" testmods="clm/ciso">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
-      <machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCru" testmods="clm/ciso">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1333,14 +1133,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1349,15 +1141,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm45Sp" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a debug test of I2000Clm45Sp</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm45Sp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1367,15 +1150,6 @@
       <option name="comment"  >include a debug test of I2000Clm45Sp</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="IHistClm45BgcCru" testmods="clm/decStart">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a debug test of IHistClm45BgcCru</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="IHistClm45BgcCru" testmods="clm/decStart">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1387,23 +1161,12 @@
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm45Sp" testmods="clm/decStart">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P36x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">02:00:00</option>
-      <option name="tput_tolerance">0.5</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1414,16 +1177,6 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D" grid="f10_f10_mg37" compset="I2000Clm50SpRtmFl" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a debug test with flooding on</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D" grid="f10_f10_mg37" compset="I2000Clm50SpRtmFl" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1434,16 +1187,6 @@
       <option name="comment"  >include a debug test with flooding on</option>
     </options>
   </test>
-  <test name="ERP_P72x2_D_Ld5" grid="f19_g17_gris4" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_increase">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >cism is not answer preserving across processor changes, but short test length should be ok.</option>
-    </options>
-  </test>
   <test name="ERP_P256x2_D_Ld5" grid="f19_g17_gris4" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_increase">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1454,15 +1197,6 @@
       <option name="comment"  >cism is not answer preserving across processor changes, but short test length should be ok.</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="prealpha"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -1472,14 +1206,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_P180x2_D_Ld5" grid="f19_g17" compset="I2000Clm50Sp" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="SMS_P384x2_D_Ld5" grid="f19_g17" compset="I2000Clm50Sp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1489,15 +1215,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P72x2_Lm25" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/monthly">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >threaded ERP test for crop just over 2-years</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_Lm25" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/monthly">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1507,16 +1224,6 @@
       <option name="comment"  >threaded ERP test for crop just over 2-years</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/crop">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a debug test of I1850Clm45BgcCrop</option>
-      <option name="tput_tolerance">0.5</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/crop">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1527,14 +1234,6 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCru" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCru" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1543,15 +1242,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P72x2_Ly3" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/irrig_o3falk_reduceOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Want a multi-year global crop restart test; this was 5 years when we were doing cold start, but 3 years is probably sufficient given that we have spun-up crop initial conditions</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_Ly3" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/irrig_o3falk_reduceOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1561,16 +1251,6 @@
       <option name="comment"  >Want a multi-year global crop restart test; this was 5 years when we were doing cold start, but 3 years is probably sufficient given that we have spun-up crop initial conditions</option>
     </options>
   </test>
-  <test name="ERP_P72x2_Lm36" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/clm50cropIrrigMonth_interp">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Want a multi-year global crop restart test; this was 5 years when we were doing cold start, but 3 years is probably sufficient given that we have spun-up crop initial conditions</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_Lm36" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/clm50cropIrrigMonth_interp">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1581,16 +1261,6 @@
       <option name="comment"  >Want a multi-year global crop restart test; this was 5 years when we were doing cold start, but 3 years is probably sufficient given that we have spun-up crop initial conditions</option>
     </options>
   </test>
-  <test name="ERP_P72x2_Lm7" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/irrig_alternate_monthly">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm">
-        <options>
-          <option name="wallclock">00:30:00</option>
-          <option name="comment">Want an ERP test covering some non-default irrigation options. Long enough so that we're likely to exercise the various groundwater irrigation code.</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="ERP_P64x2_Lm7" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/irrig_alternate_monthly">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm">
@@ -1603,22 +1273,12 @@
   </test>
   <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/reseedresetsnow">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld10" grid="f10_f10_mg37" compset="IHistClm50SpG" testmods="clm/glcMEC_decrease">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Test transient PFTs (via HIST) in conjunction with changing glacier area. This test also covers the reset_dynbal_baselines option. CISM is not answer preserving across processor changes, but short test length should be OK.</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld10" grid="f10_f10_mg37" compset="IHistClm50SpG" testmods="clm/glcMEC_decrease">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1639,7 +1299,6 @@
   </test>
   <test name="ERS_D_Ld10" grid="f10_f10_mg37" compset="IHistClm50Sp" testmods="clm/collapse_pfts_78_to_16_decStart_f10">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1649,7 +1308,6 @@
   </test>
   <test name="SOILSTRUCTUD_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1659,7 +1317,6 @@
   </test>
   <test name="ERS_D_Ld12" grid="f10_f10_mg37" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_spunup_inc_dec_bgc">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1667,15 +1324,6 @@
       <option name="comment"  >Tests updates of BGC variables with increasing and decreasing glacier areas</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/extra_outputs">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Among other extra outputs, ensure that writing the list of all history fields to a separate file does not cause failure"</option>
-    </options>
-  </test>
   <test name="ERP_P64x2_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/extra_outputs">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -1687,10 +1335,6 @@
   </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="clm_short"/>
-      <machine name="cheyenne" compiler="gnu" category="clm_short"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_short"/>
@@ -1702,7 +1346,6 @@
   </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/clm50dynroots">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi"  compiler="intel" category="prebeta"/>
     </machines>
@@ -1712,7 +1355,6 @@
   </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/deepsoil_bedrock">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1721,7 +1363,6 @@
   </test>
   <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1730,8 +1371,6 @@
   </test>
   <test name="ERS_D_Ld6" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/clm50CMIP6frc">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1750,7 +1389,6 @@
   </test>
   <test name="ERS_Ld3_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/rad_hrly_light_res_half">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -1805,7 +1443,6 @@
   </test>
   <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1822,15 +1459,6 @@
       <option name="comment"  >restart is right before the transition from 100% nat veg to 100% crop</option>
     </options>
   </test>
-  <test name="ERS_Ly3_P72x2" grid="f10_f10_mg37" compset="IHistClm50BgcCropG" testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use glacier evolution with ERS test</option>
-    </options>
-  </test>
   <test name="ERS_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm50BgcCropG" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1840,15 +1468,6 @@
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use glacier evolution with ERS test</option>
     </options>
   </test>
-  <test name="ERS_Ly5_P144x1" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-      <option name="comment"  >Want a multi-year global test of transient crops; also want a multi-year transient restart test.  Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test</option>
-    </options>
-  </test>
   <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1858,15 +1477,6 @@
       <option name="comment"  >Want a multi-year global test of transient crops; also want a multi-year transient restart test.  Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test</option>
     </options>
   </test>
-  <test name="ERS_Ly5_P72x1" grid="f10_f10_mg37" compset="IHistClm45BgcCrop" testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">03:00:00</option>
-      <option name="comment"  >include a long Clm45 test, and include a production intel test of Clm45</option>
-    </options>
-  </test>
   <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm45BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1878,7 +1488,6 @@
   </test>
   <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1888,8 +1497,6 @@
   </test>
   <test name="SMS_D" grid="f10_f10_mg37" compset="I2000Clm60Bgc">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu"   category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu"   category="aux_clm"/>
     </machines>
@@ -1900,7 +1507,6 @@
   </test>
   <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm60Sp">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1931,7 +1537,6 @@
   </test>
   <test name="LII_D_Ld3_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1939,15 +1544,6 @@
       <option name="comment"  >Basic LII test, covering the standard range of subgrid heterogeneity - particularly, including crop. Uses a year-2000 restart file so that the restart file has non-zero product pools, so that we exercise the gridcell-level code in init_interp.</option>
     </options>
   </test>
-  <test name="LII2FINIDATAREAS_D_P72x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Exercise the init_interp_method='use_finidat_areas' option. See documentation at the top of the python script implementing this test for more details and rationale. This test requires a compatible finidat file (i.e., a file that can be used without interpolation). If no such file is available out-of-the-box, then the test will need to use a testmod that points to a compatible file.</option>
-    </options>
-  </test>
   <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -1959,7 +1555,6 @@
   </test>
   <test name="LVG_Ld5_D" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/no_vector_output">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1969,8 +1564,6 @@
   </test>
   <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_monthly">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
     </machines>
@@ -1981,8 +1574,6 @@
   </test>
   <test name="NCK_Ld1" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
@@ -1992,8 +1583,6 @@
   </test>
   <test name="PEM_D_Ld5" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
@@ -2010,16 +1599,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="PET_P36x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >The main purpose of this test is to test threading of init_interp, exercising the OpenMP directives in initInterp. (Note that ERP tests don't compare threaded vs. non-threaded runs of init_interp, since init_interp won't run in the restart case.) Note that this test will use init_interp as long as we don't have out-of-the-box initial conditions at f10 resolution. We could probably get a similar level of confidence in the threading directives by deleting this test and instead changing the LII test to use threading; the main loss would be that that wouldn't test threading combined with interpolating from one resolution to another, as this one does.</option>
-      <option name="tput_tolerance">0.5</option>
-    </options>
-  </test>
   <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -2033,7 +1612,6 @@
   <test name="SMS" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/crop">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="nvhpc" category="aux_clm"/>
       <machine name="derecho" compiler="nvhpc" category="aux_clm"/>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -2043,7 +1621,6 @@
   </test>
   <test name="SMS" grid="f45_f45_mg37" compset="I2000Clm60FatesSpRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
-      <machine name="cheyenne" compiler="nvhpc" category="aux_clm"/>
       <machine name="derecho" compiler="nvhpc" category="aux_clm"/>
     </machines>
     <options>
@@ -2053,8 +1630,6 @@
   </test>
   <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
@@ -2146,7 +1721,6 @@
   </test>
   <test name="SMS_Ln9" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2156,7 +1730,6 @@
   </test>
   <test name="SMS_Ln9" grid="ne30pg2_ne30pg2_mg17" compset="I2000Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2166,7 +1739,6 @@
   </test>
   <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I1850Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -2204,12 +1776,10 @@
   </test>
   <test name="SMS_D_Ld1_Mmpi-serial" grid="f45_f45_mg37" compset="I2000Clm50SpRs" testmods="clm/ptsRLA">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="izumi" compiler="gnu" category="prealpha"/>
       <machine name="izumi" compiler="nag" category="prealpha"/>
     </machines>
@@ -2225,16 +1795,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm45BgcCrop" testmods="clm/no_subgrid_fluxes">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">00:20:00</option>
-          <option name="comment">This covers some code that isn't covered by any existing tests (such as the oldhyd test), though the amount of additional code coverage is small, so we don't necessarily need to keep this test long-term.</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm45BgcCrop" testmods="clm/no_subgrid_fluxes">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm">
@@ -2255,10 +1815,6 @@
   </test>
   <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="clm_short"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
-      <machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_short"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -2270,9 +1826,6 @@
   </test>
   <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="prebeta"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
@@ -2283,7 +1836,6 @@
   </test>
   <test name="SMS_C2_D_Lh12" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/pauseResume">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2292,8 +1844,6 @@
   </test>
   <test name="DAE_C2_D_Lh12" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/DA_multidrv">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
     </machines>
@@ -2356,20 +1906,9 @@
     </options>
   </test>
 
-  <test name="ERS_P144x1_Lm25" grid="f10_f10_mg37" compset="I2000Clm60Fates" testmods="clm/FatesColdNoComp">
-       <machines>
-	 <!-- no izumi tests since this has a pe layout specific for cheyenne -->
-	 <machine name="cheyenne" compiler="intel"   category="aux_clm"/>
-	 <machine name="cheyenne" compiler="intel"   category="fates"/>
-       </machines>
-       <options>
-	 <option name="wallclock">00:60:00</option>
-	 <option name="comment"  >This is a long fates test on full dynamics. The 144 count is designed to minimize wall time.</option>
-       </options>
-  </test>
   <test name="ERS_P128x1_Lm25" grid="f10_f10_mg37" compset="I2000Clm60Fates" testmods="clm/FatesColdNoComp">
     <machines>
-      <!-- no izumi tests since this has a pe layout specific for cheyenne -->
+      <!-- no izumi tests since this has a pe layout specific for derecho -->
       <machine name="derecho" compiler="intel"   category="aux_clm"/>
       <machine name="derecho" compiler="intel"   category="fates"/>
     </machines>
@@ -2407,7 +1946,6 @@
   </test>
   <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2426,7 +1964,6 @@
   </test>
   <test name="ERS_Lm25" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/smallville_dynlakes_monthly">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -2436,7 +1973,6 @@
   </test>
   <test name="ERS_Lm25" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/smallville_dynurban_monthly">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -2456,7 +1992,6 @@
   </test>
   <test name="SMS_Ld1_PS" grid="f09_g17" compset="I2000Clm50BgcCru" testmods="clm/datm_bias_correct_cruv7">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -2482,7 +2017,6 @@
   </test>
   <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/till--clm/remove_residues">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -2492,7 +2026,6 @@
   </test>
   <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/crop">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2502,7 +2035,6 @@
   </test>
   <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic_interp">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2584,7 +2116,6 @@
   </test>
   <test name="SMS_Lm13_PS" grid="f19_g17" compset="I2000Clm60BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2594,8 +2125,6 @@
   </test>
   <test name="SMS_Lm37" grid="f10_f10_mg37" compset="I1850Clm50SpG" testmods="clm/glcMEC_long">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
     </machines>
@@ -2632,7 +2161,6 @@
   </test>
   <test name="ERP_D_Ld10" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/ADspinup">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2642,7 +2170,6 @@
   </test>
   <test name="SSP_D_Ld10" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/rtmColdSSP">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2651,7 +2178,6 @@
   </test>
   <test name="SSP_D_Ld4" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_rtmColdSSP">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2660,8 +2186,6 @@
   </test>
   <test name="SSP_Ld10" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/rtmColdSSP">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="prebeta"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -2690,7 +2214,6 @@
   </test>
   <test name="ERS_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
@@ -2700,7 +2223,6 @@
   </test>
   <test name="PEM_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
@@ -2710,7 +2232,6 @@
   </test>
   <test name="ERS_D_Ld15" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdTreeDamage">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -2740,7 +2261,6 @@
   </test>
   <test name="ERS_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2759,8 +2279,6 @@
   </test>
   <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Fates" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
@@ -2771,7 +2289,6 @@
   </test>
   <test name="ERS_Lm13" grid="f10_f10_mg37" compset="I2000Clm50Fates" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
@@ -2780,7 +2297,6 @@
   </test>
   <test name="ERS_Lm13" grid="f45_f45_mg37" compset="I2000Clm50Fates" testmods="clm/FatesColdNoComp">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -2790,7 +2306,6 @@
   <test name="ERS_D_Mmpi-serial_Ld5" grid="1x1_brazil" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -2799,8 +2314,6 @@
   </test>
   <test name="ERS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
@@ -2819,7 +2332,6 @@
   </test>
   <test name="ERS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2829,8 +2341,6 @@
   </test>
   <test name="SMS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm45Fates" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_cime_baselines"/>
     </machines>
@@ -2838,14 +2348,6 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="SMS_D_Lm6_P144x1" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-    </options>
-  </test>
   <test name="SMS_D_Lm6_P256x1" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -2856,12 +2358,9 @@
   </test>
   <test name="SMS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="prebeta"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
     <options>
@@ -2870,7 +2369,6 @@
   </test>
   <test name="SMS_Ld5_PS" grid="f19_g17" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -2879,7 +2377,6 @@
   </test>
   <test name="ERP_Ld9" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdAllVars">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2889,7 +2386,6 @@
   </test>
   <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I2000Clm45Fates" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2900,7 +2396,6 @@
   </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdFixedBiogeo">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2911,7 +2406,6 @@
   </test>
   <test name="SMS_Ld5" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2922,7 +2416,6 @@
   </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSizeAgeMort">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -2930,16 +2423,6 @@
       <option name="comment">30 day exact restart test activating FATES size and age mortality mode on an f45 grid.</option>
     </options>
   </test>
-  <test name="ERP_P72x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesRs" testmods="clm/mimicsFatesCold">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment">30 day exact restart test with threading, running FATES-MIMICS on an f45 grid.</option>
-    </options>
-  </test>
   <test name="ERP_P256x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesRs" testmods="clm/mimicsFatesCold">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -2972,18 +2455,6 @@
 
     </machines>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpBgcCropGswp" testmods="clm/default">
-    <machines>
-
-      <machine name="cheyenne" compiler="intel" category="aux_clm">
-        <options>
-          <option name="wallclock">00:30:00</option>
-          <option name="comment">A debug ERP test of the NWP configuration with active BGC and CROP.</option>
-        </options>
-      </machine>
-
-    </machines>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpBgcCropGswp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -2995,7 +2466,6 @@
   </test>
   <test name="LWISO_Ld10" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/coldStart">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -3003,18 +2473,6 @@
       <option name="comment">Ensure that turning on water tracers doesn't change answers. Cold start for now, until we can use initial conditions from a non-isotope case in an isotope case; once we can do that, this should be changed to not be cold start (e.g., 5-day decStart transient test: see also https://github.com/ESCOMP/ctsm/issues/495#issuecomment-516619853).</option>
     </options>
   </test>
-  <test name="ERP_P36x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpSpGswp" testmods="clm/default">
-    <machines>
-
-      <machine name="cheyenne" compiler="intel" category="aux_clm">
-        <options>
-          <option name="wallclock">00:30:00</option>
-          <option name="comment">Include a debug ERP test of the NWP configuration.</option>
-        </options>
-      </machine>
-
-    </machines>
-  </test>
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I2000Ctsm50NwpSpGswp" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -3027,7 +2485,6 @@
   </test>
   <test name="SMS_Ld1_PS" grid="nldas2_rnldas2_mnldas2" compset="I2000Ctsm50NwpSpNldas" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -3038,7 +2495,6 @@
   </test>
   <test name="SMS_Ld1_PS" grid="nldas2_rnldas2_mnldas2" compset="I2000Ctsm50NwpSpNldasRs" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -3048,7 +2504,6 @@
   </test>
   <test name="ERP_D_Ld3" grid="f19_g17" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -3056,15 +2511,6 @@
       <option name="comment">Short ERP debug FATES test for f19_g17 grid.</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f19_g17" compset="I2000Clm50FatesCru" testmods="clm/FatesCold">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment">Short ERP debug FATES test for f19_g17 grid with modified task layout.</option>
-    </options>
-  </test>
   <test name="ERP_D_P128x2_Ld3" grid="f19_g17" compset="I2000Clm50FatesCru" testmods="clm/FatesCold">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
@@ -3076,7 +2522,6 @@
   </test>
   <test name="ERP_Ld3" grid="f09_g17" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3087,7 +2532,6 @@
   </test>
   <test name="ERP_Ld9" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdAllVars">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3098,7 +2542,6 @@
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdPRT2">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
@@ -3110,7 +2553,6 @@
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLandUse">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
@@ -3121,7 +2563,6 @@
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
     </machines>
@@ -3131,8 +2572,6 @@
   </test>
   <test name="ERS_D_Ld3" grid="f19_g17" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
-      <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
@@ -3144,7 +2583,6 @@
   </test>
   <test name="ERS_D_Ld5" grid="f19_g17" compset="I2000Clm50BgcCru" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3155,7 +2593,6 @@
   </test>
   <test name="ERS_D_Mmpi-serial_Ld5" grid="1x1_brazil" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
@@ -3167,10 +2604,8 @@
   </test>
   <test name="ERS_Ld9" grid="f10_f10_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdCH4Off">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -3181,7 +2616,6 @@
   <test name="SMS_Lm3_D_Mmpi-serial" grid="1x1_brazil" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdHydro">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
     </machines>
@@ -3192,7 +2626,6 @@
   </test>
   <test name="ERS_D_Ld5" grid="1x1_brazil" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdHydro">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
@@ -3204,7 +2637,6 @@
   </test>
   <test name="ERS_Ld5" grid="f19_g17" compset="I2000Clm45Fates" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3215,7 +2647,6 @@
   </test>
   <test name="ERS_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/Fates">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3226,7 +2657,6 @@
   </test>
   <test name="ERS_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdNoFire">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3237,7 +2667,6 @@
   </test>
   <test name="ERS_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdST3">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3248,7 +2677,6 @@
   </test>
   <test name="ERS_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdPPhys">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -3258,7 +2686,6 @@
   </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdFixedBiogeo">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3268,7 +2695,6 @@
   </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdNoComp">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3278,7 +2704,6 @@
   </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdNoCompFixedBioGeo">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -3287,7 +2712,6 @@
   </test>
   <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
@@ -3298,7 +2722,6 @@
   </test>
   <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdDryDepSatPhen">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -3308,7 +2731,6 @@
   </test>
   <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdMeganSatPhen">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -3319,7 +2741,6 @@
 
   <test name="SMS_D_Ld3" grid="f09_g17" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen_prescribed">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
@@ -3329,7 +2750,6 @@
   </test>
   <test name="SMS_Lm1" grid="f45_f45_mg37" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdBasic">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -3339,7 +2759,6 @@
   </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3348,16 +2767,6 @@
       <option name="comment">30 day exact restart test for FATES fixed biogeography reduced complexity mode on an f45 grid.</option>
     </options>
   </test>
-  <test name="ERP_P36x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment">30 day exact restart test with threading for FATES fixed biogeography reduced complexity mode on an f45 grid.</option>
-    </options>
-  </test>
   <test name="ERP_P128x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
@@ -3370,7 +2779,6 @@
   </test>
   <test name="ERS_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLogging">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -3380,7 +2788,6 @@
   </test>
   <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdSizeAgeMort">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3391,7 +2798,6 @@
   </test>
   <test name="SMS_Lm6" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/Fates">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
@@ -3402,8 +2808,6 @@
   </test>
   <test name="SMS_Lm13" grid="1x1_brazil" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
-      <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
@@ -3414,7 +2818,6 @@
   </test>
   <test name="ERS_Lm12" grid="1x1_brazil" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesFireLightningPopDens">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
@@ -3424,9 +2827,6 @@
   </test>
   <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6waccm" testmods="clm/basic">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="prealpha"/>
-      <machine name="cheyenne" compiler="gnu" category="prebeta"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prealpha"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
@@ -3448,7 +2848,6 @@
   </test>
   <test name="SMS_Lm1_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/output_crop_highfreq">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -3458,11 +2857,8 @@
   </test>
   <test name="SMS_Ly1_Mmpi-serial" grid="1x1_brazil" compset="IHistClm60BgcQianRs" testmods="clm/output_bgc_highfreq">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-      <machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_cime_baselines"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3471,7 +2867,6 @@
   </test>
   <test name="SMS_Ld12_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm60SpRs" testmods="clm/output_sp_highfreq">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -3491,7 +2886,6 @@
   </test>
   <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm50BgcCrop">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -3539,8 +2933,6 @@
 
   <test name="LILACSMOKE_D_Ld2" grid="f10_f10_mg37" compset="I2000Ctsm50NwpSpAsRs" testmods="clm-lilac">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="clm_pymods"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_pymods"/>
     </machines>
@@ -3561,16 +2953,6 @@
     </options>
   </test>
 
-  <test name="LGRAIN2_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="LGRAIN2_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -3580,16 +2962,6 @@
       <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
     </options>
   </test>
-  <test name="LGRAIN2_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="LGRAIN2_Ly2_P128x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -3599,16 +2971,6 @@
       <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
     </options>
   </test>
-  <test name="LREPRSTRUCT_Ly1_P72x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="LREPRSTRUCT_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -3618,15 +2980,6 @@
       <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
     </options>
   </test>
-  <test name="LREPRSTRUCT_Ly2_P72x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
-    <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">02:00:00</option>
-      <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). Compared to the Clm50 test, this Clm45 test exercises code in NutrientCompetitionCLM45defaultMod and use_grainproduct false. Need two years because this test starts from a non-crop finidat, so there is no crop growth in the first year.</option>
-    </options>
-  </test>
   <test name="LREPRSTRUCT_Ly2_P128x1" grid="f10_f10_mg37" compset="I1850Clm45BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -3639,7 +2992,6 @@
 
   <test name="REUSEINITFILES_D_Ld1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -3650,7 +3002,6 @@
 
   <test name="FUNITCTSM_P1x1" grid="f10_f10_mg37" compset="I2000Clm50Sp">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>

From b25a02d904bf8cd010fb400b4b0181361f077d83 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:20:07 -0600
Subject: [PATCH 0382/1248] fix subtree add

---
 .../git-fleximod/.github/workflows/pre-commit |  13 -
 .../.github/workflows/pytest.yaml             |  77 --
 .lib/git-fleximod/.pre-commit-config.yaml     |  18 -
 .lib/git-fleximod/License                     |  20 -
 .lib/git-fleximod/README.md                   | 110 ---
 .lib/git-fleximod/doc/Makefile                |  20 -
 .lib/git-fleximod/doc/conf.py                 |  26 -
 .lib/git-fleximod/doc/index.rst               |  24 -
 .lib/git-fleximod/doc/make.bat                |  35 -
 .lib/git-fleximod/escomp_install              |  25 -
 .lib/git-fleximod/git_fleximod/__init__.py    |   0
 .lib/git-fleximod/git_fleximod/cli.py         | 119 ---
 .../git-fleximod/git_fleximod/git_fleximod.py | 601 ---------------
 .../git-fleximod/git_fleximod/gitinterface.py |  79 --
 .lib/git-fleximod/git_fleximod/gitmodules.py  |  97 ---
 .../git-fleximod/git_fleximod/lstripreader.py |  43 --
 .lib/git-fleximod/git_fleximod/metoflexi.py   | 236 ------
 .lib/git-fleximod/git_fleximod/utils.py       | 365 ---------
 .lib/git-fleximod/poetry.lock                 | 693 ------------------
 .lib/git-fleximod/pyproject.toml              |  41 --
 .lib/git-fleximod/tbump.toml                  |  43 --
 .lib/git-fleximod/tests/__init__.py           |   3 -
 .lib/git-fleximod/tests/conftest.py           | 138 ----
 .lib/git-fleximod/tests/test_a_import.py      |   8 -
 .lib/git-fleximod/tests/test_b_update.py      |  26 -
 .lib/git-fleximod/tests/test_c_required.py    |  30 -
 .lib/git-fleximod/tests/test_d_complex.py     |  67 --
 27 files changed, 2957 deletions(-)
 delete mode 100644 .lib/git-fleximod/.github/workflows/pre-commit
 delete mode 100644 .lib/git-fleximod/.github/workflows/pytest.yaml
 delete mode 100644 .lib/git-fleximod/.pre-commit-config.yaml
 delete mode 100644 .lib/git-fleximod/License
 delete mode 100644 .lib/git-fleximod/README.md
 delete mode 100644 .lib/git-fleximod/doc/Makefile
 delete mode 100644 .lib/git-fleximod/doc/conf.py
 delete mode 100644 .lib/git-fleximod/doc/index.rst
 delete mode 100644 .lib/git-fleximod/doc/make.bat
 delete mode 100644 .lib/git-fleximod/escomp_install
 delete mode 100644 .lib/git-fleximod/git_fleximod/__init__.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/cli.py
 delete mode 100755 .lib/git-fleximod/git_fleximod/git_fleximod.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/gitinterface.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/gitmodules.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/lstripreader.py
 delete mode 100755 .lib/git-fleximod/git_fleximod/metoflexi.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/utils.py
 delete mode 100644 .lib/git-fleximod/poetry.lock
 delete mode 100644 .lib/git-fleximod/pyproject.toml
 delete mode 100644 .lib/git-fleximod/tbump.toml
 delete mode 100644 .lib/git-fleximod/tests/__init__.py
 delete mode 100644 .lib/git-fleximod/tests/conftest.py
 delete mode 100644 .lib/git-fleximod/tests/test_a_import.py
 delete mode 100644 .lib/git-fleximod/tests/test_b_update.py
 delete mode 100644 .lib/git-fleximod/tests/test_c_required.py
 delete mode 100644 .lib/git-fleximod/tests/test_d_complex.py

diff --git a/.lib/git-fleximod/.github/workflows/pre-commit b/.lib/git-fleximod/.github/workflows/pre-commit
deleted file mode 100644
index 1a6ad0082a..0000000000
--- a/.lib/git-fleximod/.github/workflows/pre-commit
+++ /dev/null
@@ -1,13 +0,0 @@
-name: pre-commit
-on:
-  pull_request:
-  push:
-    branches: [main]
-
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: pre-commit/action@v3.0.0
diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml
deleted file mode 100644
index 0868dd9a33..0000000000
--- a/.lib/git-fleximod/.github/workflows/pytest.yaml
+++ /dev/null
@@ -1,77 +0,0 @@
-# Run this job on pushes to `main`, and for pull requests. If you don't specify
-# `branches: [main], then this actions runs _twice_ on pull requests, which is
-# annoying.
-
-on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
-      # reference the matrixe python version here.
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
-
-      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
-      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
-      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
-      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
-      # mildly cleaner by using an environment variable, but I don't really care.
-      - name: cache poetry install
-        uses: actions/cache@v4
-        with:
-          path: ~/.local
-          key: poetry-1.7.1
-
-      # Install Poetry. You could do this manually, or there are several actions that do this.
-      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
-      # Poetry's default install script, which feels correct. I pin the Poetry version here
-      # because Poetry does occasionally change APIs between versions and I don't want my
-      # actions to break if it does.
-      #
-      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
-      # venv as a `.venv` in your testing directory, which allows the next step to easily
-      # cache it.
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.7.1
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
-      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
-      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v4
-        with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-
-      # Install dependencies. `--no-root` means "install all dependencies but not the project
-      # itself", which is what you want to avoid caching _your_ code. The `if` statement
-      # ensures this only runs on a cache miss.
-      - run: poetry install --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-
-      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
-      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
-      # pyproject.toml and makes that if you add things like console-scripts at some point that
-      # they'll be installed and working.
-      - run: poetry install --no-interaction
-
-      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
-      # so this line is super-simple. But it could be as complex as you need.
-      - run: |
-          git config --global user.name "${GITHUB_ACTOR}"
-          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-          poetry run pytest
-
diff --git a/.lib/git-fleximod/.pre-commit-config.yaml b/.lib/git-fleximod/.pre-commit-config.yaml
deleted file mode 100644
index 2f6089da72..0000000000
--- a/.lib/git-fleximod/.pre-commit-config.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-exclude: ^utils/.*$
-
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
-    hooks:
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/pylint
-    rev: v2.11.1
-    hooks:
-      - id: pylint
-        args:
-          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/.lib/git-fleximod/License b/.lib/git-fleximod/License
deleted file mode 100644
index 2c6fe768c2..0000000000
--- a/.lib/git-fleximod/License
+++ /dev/null
@@ -1,20 +0,0 @@
-Copyright 2024 National Center for Atmospheric Sciences (NCAR)
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-“Software”), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/.lib/git-fleximod/README.md b/.lib/git-fleximod/README.md
deleted file mode 100644
index d1ef632f28..0000000000
--- a/.lib/git-fleximod/README.md
+++ /dev/null
@@ -1,110 +0,0 @@
-# git-fleximod
-
-Flexible, Enhanced Submodule Management for Git
-
-## Overview
-
-Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
-
-## Installation
-
-#TODO    Install using pip:
-#        pip install git-fleximod
-  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
-
-## Usage
-
-    Basic Usage:
-        git fleximod <command> [options]
-    Available Commands:
-        status: Display the status of submodules.
-        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
-        test: Make sure that fxtags and submodule hashes are consistant,
-              make sure that official urls (as defined by fxDONOTUSEurl) are set
-              make sure that fxtags are defined for all submodules
-    Additional Options:
-        See git fleximod --help for more details.
-
-## Supported .gitmodules Variables
-
-    fxtag: Specify a specific tag or branch to checkout for a submodule.
-    fxrequired: Mark a submodule's checkout behavior, with allowed values:
-      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
-      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
-      - AlwaysRequired:       Always required (always checked out).
-      - AlwaysOptional:       Always optional (checked out with --optional flag).
-    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
-    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
-           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
-           changed by users.  Use the url variable to change to a fork if desired.
-
-## Sparse Checkouts
-
-    To enable sparse checkout for a submodule, set the fxsparse variable
-    in the .gitmodules file to the path of a file containing the desired
-    sparse checkout paths. Git-fleximod will automatically configure
-    sparse checkout based on this file when applicable commands are run.
-    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
-    for details on the format of this file.
-
-## Tests
-
-   The git fleximod test action is designed to be used by, for example, github workflows
-   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
-
-## Examples
-
-Here are some common usage examples:
-
-Update all submodules, including optional ones:
-```bash
-  git fleximod update --optional
-```
-
-Updating a specific submodule to the fxtag indicated in .gitmodules:
-
-```bash
-    git fleximod update submodule-name
-```
-Example .gitmodules entry:
-```ini, toml
-    [submodule "cosp2"]
-        path = src/physics/cosp2/src
-        url = https://github.com/CFMIP/COSPv2.0
-        fxsparse = ../.cosp_sparse_checkout
-        fxrequired = AlwaysRequired
-        fxtag = v2.1.4cesm
-```
-Explanation:
-
-This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
-should be checked out into the directory src/physics/cosp2/src
-relative to the .gitmodules directory.  It should be checked out from
-the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
-described in the file ../.cosp_sparse_checkout relative to the path
-directory.  It should be checked out anytime this .gitmodules entry is
-read.
-
-Additional example:
-```ini, toml
-    [submodule "cime"]
-        path = cime
-        url = https://github.com/jedwards4b/cime
-        fxrequired = ToplevelRequired
-        fxtag = cime6.0.198_rme01
-```
-
-Explanation:
-
-This entry indicates that the submodule cime should be checked out
-into a directory named cime at tag cime6.0.198_rme01 from the URL
-https://github.com/jedwards4b/cime.  This should only be done if
-the .gitmodules file is at the top level of the repository clone.
-
-## Contributing
-
-We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
-
-## License
-
-Git-fleximod is released under the MIT License.
diff --git a/.lib/git-fleximod/doc/Makefile b/.lib/git-fleximod/doc/Makefile
deleted file mode 100644
index d4bb2cbb9e..0000000000
--- a/.lib/git-fleximod/doc/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/.lib/git-fleximod/doc/conf.py b/.lib/git-fleximod/doc/conf.py
deleted file mode 100644
index 423099eec9..0000000000
--- a/.lib/git-fleximod/doc/conf.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
-project = "git-fleximod"
-author = "Jim Edwards <jedwards@ucar.edu>"
-release = "0.4.0"
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
-extensions = ["sphinx_argparse_cli"]
-
-templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
-
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = "alabaster"
-html_static_path = ["_static"]
diff --git a/.lib/git-fleximod/doc/index.rst b/.lib/git-fleximod/doc/index.rst
deleted file mode 100644
index 0f9c1a7f7e..0000000000
--- a/.lib/git-fleximod/doc/index.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-.. git-fleximod documentation master file, created by
-   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to git-fleximod's documentation!
-========================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-.. module:: sphinxcontrib.autoprogram
-.. sphinx_argparse_cli::
-   :module: git_fleximod.cli
-   :func: get_parser
-   :prog: git-fleximod
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/.lib/git-fleximod/doc/make.bat b/.lib/git-fleximod/doc/make.bat
deleted file mode 100644
index 32bb24529f..0000000000
--- a/.lib/git-fleximod/doc/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/.lib/git-fleximod/escomp_install b/.lib/git-fleximod/escomp_install
deleted file mode 100644
index ae782e72a4..0000000000
--- a/.lib/git-fleximod/escomp_install
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python
-# updates git-fleximod in an ESCOMP model
-# this script should be run from the model root directory, it expects
-# git-fleximod to already be installed with the script in bin
-# and the classes in lib/python/site-packages
-import sys
-import shutil
-import os
-
-from glob import iglob
-
-fleximod_root = sys.argv[1]
-fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
-if os.path.isfile(fleximod_path):
-   with open(fleximod_path,"r") as f:
-        fleximod = f.readlines()
-   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
-        for line in fleximod:
-            f.write(line)
-            if "import argparse" in line:
-               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
-
-   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
-       shutil.copy(file,
-        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/.lib/git-fleximod/git_fleximod/__init__.py b/.lib/git-fleximod/git_fleximod/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
deleted file mode 100644
index 1fb959dad0..0000000000
--- a/.lib/git-fleximod/git_fleximod/cli.py
+++ /dev/null
@@ -1,119 +0,0 @@
-from pathlib import Path
-import argparse
-
-__version__ = "0.7.4"
-
-def find_root_dir(filename=".git"):
-    d = Path.cwd()
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.is_dir():
-            return attempt
-        d = d.parent
-    return None
-
-
-def get_parser():
-    description = """
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
-    """
-    parser = argparse.ArgumentParser(
-        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-    )
-
-    #
-    # user options
-    #
-    choices = ["update", "status", "test"]
-    parser.add_argument(
-        "action",
-        choices=choices,
-        default="update",
-        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
-    )
-
-    parser.add_argument(
-        "components",
-        nargs="*",
-        help="Specific component(s) to checkout. By default, "
-        "all required submodules are checked out.",
-    )
-
-    parser.add_argument(
-        "-C",
-        "--path",
-        default=find_root_dir(),
-        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
-    )
-
-    parser.add_argument(
-        "-g",
-        "--gitmodules",
-        nargs="?",
-        default=".gitmodules",
-        help="The submodule description filename. " "Default: %(default)s.",
-    )
-
-    parser.add_argument(
-        "-x",
-        "--exclude",
-        nargs="*",
-        help="Component(s) listed in the gitmodules file which should be ignored.",
-    )
-    parser.add_argument(
-        "-f",
-        "--force",
-        action="store_true",
-        default=False,
-        help="Override cautions and update or checkout over locally modified repository.",
-    )
-
-    parser.add_argument(
-        "-o",
-        "--optional",
-        action="store_true",
-        default=False,
-        help="By default only the required submodules "
-        "are checked out. This flag will also checkout the "
-        "optional submodules relative to the toplevel directory.",
-    )
-
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        action="count",
-        default=0,
-        help="Output additional information to "
-        "the screen and log file. This flag can be "
-        "used up to two times, increasing the "
-        "verbosity level each time.",
-    )
-
-    parser.add_argument(
-        "-V",
-        "--version",
-        action="version",
-        version=f"%(prog)s {__version__}",
-        help="Print version and exit.",
-    )
-
-    #
-    # developer options
-    #
-    parser.add_argument(
-        "--backtrace",
-        action="store_true",
-        help="DEVELOPER: show exception backtraces as extra " "debugging output",
-    )
-
-    parser.add_argument(
-        "-d",
-        "--debug",
-        action="store_true",
-        default=False,
-        help="DEVELOPER: output additional debugging "
-        "information to the screen and log file.",
-    )
-
-    return parser
diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
deleted file mode 100755
index 103cc82a50..0000000000
--- a/.lib/git-fleximod/git_fleximod/git_fleximod.py
+++ /dev/null
@@ -1,601 +0,0 @@
-#!/usr/bin/env python
-import sys
-
-MIN_PYTHON = (3, 7)
-if sys.version_info < MIN_PYTHON:
-    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
-
-import os
-import shutil
-import logging
-import textwrap
-from git_fleximod import utils
-from git_fleximod import cli
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-from configparser import NoOptionError
-
-# logger variable is global
-logger = None
-
-
-def fxrequired_allowed_values():
-    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
-
-
-def commandline_arguments(args=None):
-    parser = cli.get_parser()
-
-    if args:
-        options = parser.parse_args(args)
-    else:
-        options = parser.parse_args()
-
-    # explicitly listing a component overrides the optional flag
-    if options.optional or options.components:
-        fxrequired = [
-            "ToplevelRequired",
-            "ToplevelOptional",
-            "AlwaysRequired",
-            "AlwaysOptional",
-        ]
-    else:
-        fxrequired = ["ToplevelRequired", "AlwaysRequired"]
-
-    action = options.action
-    if not action:
-        action = "update"
-    handlers = [logging.StreamHandler()]
-
-    if options.debug:
-        try:
-            open("fleximod.log", "w")
-        except PermissionError:
-            sys.exit("ABORT: Could not write file fleximod.log")
-        level = logging.DEBUG
-        handlers.append(logging.FileHandler("fleximod.log"))
-    elif options.verbose:
-        level = logging.INFO
-    else:
-        level = logging.WARNING
-    # Configure the root logger
-    logging.basicConfig(
-        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
-    )
-
-    if hasattr(options, "version"):
-        exit()
-
-    return (
-        options.path,
-        options.gitmodules,
-        fxrequired,
-        options.components,
-        options.exclude,
-        options.force,
-        action,
-    )
-
-
-def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
-    """
-    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
-    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
-    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
-    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
-    and disk space consuming.
-
-    Parameters:
-    root_dir (str): The root directory for the git operation.
-    name (str): The name of the submodule.
-    url (str): The URL of the submodule.
-    path (str): The path to the submodule.
-    sparsefile (str): The sparse file for the submodule.
-    tag (str, optional): The tag to checkout. Defaults to "master".
-
-    Returns:
-    None
-    """
-    logger.info("Called sparse_checkout for {}".format(name))
-    rgit = GitInterface(root_dir, logger)
-    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
-    if superroot:
-        gitroot = superroot.strip()
-    else:
-        gitroot = root_dir.strip()
-    assert os.path.isdir(os.path.join(gitroot, ".git"))
-    # first create the module directory
-    if not os.path.isdir(os.path.join(root_dir, path)):
-        os.makedirs(os.path.join(root_dir, path))
-
-    # initialize a new git repo and set the sparse checkout flag
-    sprep_repo = os.path.join(root_dir, path)
-    sprepo_git = GitInterface(sprep_repo, logger)
-    if os.path.exists(os.path.join(sprep_repo, ".git")):
-        try:
-            logger.info("Submodule {} found".format(name))
-            chk = sprepo_git.config_get_value("core", "sparseCheckout")
-            if chk == "true":
-                logger.info("Sparse submodule {} already checked out".format(name))
-                return
-        except NoOptionError:
-            logger.debug("Sparse submodule {} not present".format(name))
-        except Exception as e:
-            utils.fatal_error("Unexpected error {} occured.".format(e))
-
-    sprepo_git.config_set_value("core", "sparseCheckout", "true")
-
-    # set the repository remote
-
-    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
-    status = sprepo_git.git_operation("remote", "-v")
-    if url not in status:
-        sprepo_git.git_operation("remote", "add", "origin", url)
-
-    topgit = os.path.join(gitroot, ".git")
-
-    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
-        with open(os.path.join(root_dir, ".git")) as f:
-            gitpath = os.path.relpath(
-                os.path.join(root_dir, f.read().split()[1]),
-                start=os.path.join(root_dir, path),
-            )
-        topgit = os.path.join(gitpath, "modules")
-    else:
-        topgit = os.path.relpath(
-            os.path.join(root_dir, ".git", "modules"),
-            start=os.path.join(root_dir, path),
-        )
-
-    with utils.pushd(sprep_repo):
-        if not os.path.isdir(topgit):
-            os.makedirs(topgit)
-    topgit += os.sep + name
-
-    if os.path.isdir(os.path.join(root_dir, path, ".git")):
-        with utils.pushd(sprep_repo):
-            shutil.move(".git", topgit)
-            with open(".git", "w") as f:
-                f.write("gitdir: " + os.path.relpath(topgit))
-            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
-            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
-        if os.path.isfile(gitsparse):
-            logger.warning(
-                "submodule {} is already initialized {}".format(name, topgit)
-            )
-            return
-
-        with utils.pushd(sprep_repo):
-            shutil.copy(sparsefile, gitsparse)
-
-    # Finally checkout the repo
-    sprepo_git.git_operation("fetch", "origin", "--tags")
-    sprepo_git.git_operation("checkout", tag)
-
-    print(f"Successfully checked out {name:>20} at {tag}")
-    rgit.config_set_value(f'submodule "{name}"', "active", "true")
-    rgit.config_set_value(f'submodule "{name}"', "url", url)
-
-
-def single_submodule_checkout(
-    root, name, path, url=None, tag=None, force=False, optional=False
-):
-    """
-    This function checks out a single git submodule.
-
-    Parameters:
-    root (str): The root directory for the git operation.
-    name (str): The name of the submodule.
-    path (str): The path to the submodule.
-    url (str, optional): The URL of the submodule. Defaults to None.
-    tag (str, optional): The tag to checkout. Defaults to None.
-    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
-    optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False.
-
-    Returns:
-    None
-    """
-    # function implementation...
-    git = GitInterface(root, logger)
-    repodir = os.path.join(root, path)
-    logger.info("Checkout {} into {}/{}".format(name, root, path))
-    # if url is provided update to the new url
-    tmpurl = None
-    repo_exists = False
-    if os.path.exists(os.path.join(repodir, ".git")):
-        logger.info("Submodule {} already checked out".format(name))
-        repo_exists = True
-    # Look for a .gitmodules file in the newly checkedout repo
-    if not repo_exists and url:
-        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
-        # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
-        # opened with a GitModules object we don't need to worry about restoring the file here
-        # it will be done by the GitModules class
-        if url.startswith("git@"):
-            tmpurl = url
-            url = url.replace("git@github.com:", "https://github.com/")
-            git.git_operation("clone", url, path)
-            smgit = GitInterface(repodir, logger)
-            if not tag:
-                tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
-            smgit.git_operation("checkout", tag)
-            # Now need to move the .git dir to the submodule location
-            rootdotgit = os.path.join(root, ".git")
-            if os.path.isfile(rootdotgit):
-                with open(rootdotgit) as f:
-                    line = f.readline()
-                    if line.startswith("gitdir: "):
-                        rootdotgit = line[8:].rstrip()
-
-            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
-            if os.path.exists(newpath):
-                shutil.rmtree(os.path.join(repodir, ".git"))
-            else:
-                shutil.move(os.path.join(repodir, ".git"), newpath)
-
-            with open(os.path.join(repodir, ".git"), "w") as f:
-                f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
-                
-    if not os.path.exists(repodir):
-        parent = os.path.dirname(repodir)
-        if not os.path.isdir(parent):
-            os.makedirs(parent)
-        git.git_operation("submodule", "add", "--name", name, "--", url, path) 
-
-    if not repo_exists or not tmpurl:
-        git.git_operation("submodule", "update", "--init", "--", path)
-            
-    if os.path.exists(os.path.join(repodir, ".gitmodules")):
-        # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name}")
-        gitmodules = GitModules(logger, confpath=repodir)
-        requiredlist = ["AlwaysRequired"]
-        if optional:
-            requiredlist.append("AlwaysOptional")
-        submodules_checkout(gitmodules, repodir, requiredlist, force=force)
-    if not os.path.exists(os.path.join(repodir, ".git")):
-        utils.fatal_error(
-            f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}"
-        )
-
-    if tmpurl:
-        print(git.git_operation("restore", ".gitmodules"))
-
-    return
-
-
-def submodules_status(gitmodules, root_dir, toplevel=False):
-    testfails = 0
-    localmods = 0
-    needsupdate = 0
-    for name in gitmodules.sections():
-        path = gitmodules.get(name, "path")
-        tag = gitmodules.get(name, "fxtag")
-        required = gitmodules.get(name, "fxrequired")
-        level = required and "Toplevel" in required
-        if not path:
-            utils.fatal_error("No path found in .gitmodules for {}".format(name))
-        newpath = os.path.join(root_dir, path)
-        logger.debug("newpath is {}".format(newpath))
-        if not os.path.exists(os.path.join(newpath, ".git")):
-            rootgit = GitInterface(root_dir, logger)
-            # submodule commands use path, not name
-            url = gitmodules.get(name, "url")
-            url = url.replace("git@github.com:", "https://github.com/")
-            tags = rootgit.git_operation("ls-remote", "--tags", url)
-            atag = None
-            needsupdate += 1
-            if not toplevel and level:
-                continue
-            for htag in tags.split("\n"):
-                if tag and tag in htag:
-                    atag = (htag.split()[1])[10:]
-                    break
-            if tag and tag == atag:
-                print(f"e {name:>20} not checked out, aligned at tag {tag}")
-            elif tag:
-                ahash = rootgit.git_operation(
-                    "submodule", "status", "{}".format(path)
-                ).rstrip()
-                ahash = ahash[1 : len(tag) + 1]
-                if tag == ahash:
-                    print(f"e {name:>20} not checked out, aligned at hash {ahash}")
-                else:
-                    print(
-                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
-                    )
-                    testfails += 1
-            else:
-                print(f"e {name:>20} has no fxtag defined in .gitmodules")
-                testfails += 1
-        else:
-            with utils.pushd(newpath):
-                git = GitInterface(newpath, logger)
-                atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                ahash = git.git_operation("status").partition("\n")[0].split()[-1]
-                if tag and atag == tag:
-                    print(f"  {name:>20} at tag {tag}")
-                elif tag and ahash[: len(tag)] == tag:
-                    print(f"  {name:>20} at hash {ahash}")
-                elif atag == ahash:
-                    print(f"  {name:>20} at hash {ahash}")
-                elif tag:
-                    print(
-                        f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"
-                    )
-                    testfails += 1
-                    needsupdate += 1
-                else:
-                    print(
-                        f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
-                    )
-                    testfails += 1
-
-                status = git.git_operation("status", "--ignore-submodules")
-                if "nothing to commit" not in status:
-                    localmods = localmods + 1
-                    print("M" + textwrap.indent(status, "                      "))
-
-    return testfails, localmods, needsupdate
-
-
-def submodules_update(gitmodules, root_dir, requiredlist, force):
-    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-
-    if localmods and not force:
-        local_mods_output()
-        return
-    if needsupdate == 0:
-        return
-
-    for name in gitmodules.sections():
-        fxtag = gitmodules.get(name, "fxtag")
-        path = gitmodules.get(name, "path")
-        url = gitmodules.get(name, "url")
-        logger.info(
-            "name={} path={} url={} fxtag={} requiredlist={}".format(
-                name, os.path.join(root_dir, path), url, fxtag, requiredlist
-            )
-        )
-        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
-        fxrequired = gitmodules.get(name, "fxrequired")
-        assert fxrequired in fxrequired_allowed_values()
-        rgit = GitInterface(root_dir, logger)
-        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
-
-        fxsparse = gitmodules.get(name, "fxsparse")
-
-        if (
-            fxrequired
-            and (superroot and "Toplevel" in fxrequired)
-            or fxrequired not in requiredlist
-        ):
-            if "ToplevelOptional" == fxrequired:
-                print("Skipping optional component {}".format(name))
-            continue
-        if fxsparse:
-            logger.debug(
-                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
-                    root_dir, name, url, path, fxsparse, fxtag
-                )
-            )
-            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
-        else:
-            logger.info(
-                "Calling submodule_checkout({},{},{},{})".format(
-                    root_dir, name, path, url
-                )
-            )
-
-            single_submodule_checkout(
-                root_dir,
-                name,
-                path,
-                url=url,
-                tag=fxtag,
-                force=force,
-                optional=("AlwaysOptional" in requiredlist),
-            )
-
-        if os.path.exists(os.path.join(path, ".git")):
-            submoddir = os.path.join(root_dir, path)
-            with utils.pushd(submoddir):
-                git = GitInterface(submoddir, logger)
-                # first make sure the url is correct
-                upstream = git.git_operation("ls-remote", "--get-url").rstrip()
-                newremote = "origin"
-                if upstream != url:
-                    # TODO - this needs to be a unique name
-                    remotes = git.git_operation("remote", "-v")
-                    if url in remotes:
-                        for line in remotes:
-                            if url in line and "fetch" in line:
-                                newremote = line.split()[0]
-                                break
-                    else:
-                        i = 0
-                        while newremote in remotes:
-                            i = i + 1
-                            newremote = f"newremote.{i:02d}"
-                        git.git_operation("remote", "add", newremote, url)
-
-                tags = git.git_operation("tag", "-l")
-                if fxtag and fxtag not in tags:
-                    git.git_operation("fetch", newremote, "--tags")
-                atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                if fxtag and fxtag != atag:
-                    try:
-                        git.git_operation("checkout", fxtag)
-                        print(f"{name:>20} updated to {fxtag}")
-                    except Exception as error:
-                        print(error)
-                elif not fxtag:
-                    print(f"No fxtag found for submodule {name:>20}")
-                else:
-                    print(f"{name:>20} up to date.")
-
-
-def local_mods_output():
-    text = """\
-    The submodules labeled with 'M' above are not in a clean state.
-    The following are options for how to proceed:
-    (1) Go into each submodule which is not in a clean state and issue a 'git status'
-        Either revert or commit your changes so that the submodule is in a clean state.
-    (2) use the --force option to git-fleximod
-    (3) you can name the particular submodules to update using the git-fleximod command line
-    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
-        then rerun git-fleximod update.
-"""
-    print(text)
-
-
-# checkout is done by update if required so this function may be depricated
-def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
-    """
-    This function checks out all git submodules based on the provided parameters.
-
-    Parameters:
-    gitmodules (ConfigParser): The gitmodules configuration.
-    root_dir (str): The root directory for the git operation.
-    requiredlist (list): The list of required modules.
-    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
-
-    Returns:
-    None
-    """
-    # function implementation...
-    print("")
-    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-    if localmods and not force:
-        local_mods_output()
-        return
-    if not needsupdate:
-        return
-    for name in gitmodules.sections():
-        fxrequired = gitmodules.get(name, "fxrequired")
-        fxsparse = gitmodules.get(name, "fxsparse")
-        fxtag = gitmodules.get(name, "fxtag")
-        path = gitmodules.get(name, "path")
-        url = gitmodules.get(name, "url")
-        if fxrequired and fxrequired not in requiredlist:
-            if "Optional" in fxrequired:
-                print("Skipping optional component {}".format(name))
-            continue
-
-        if fxsparse:
-            logger.debug(
-                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
-                    root_dir, name, url, path, fxsparse, fxtag
-                )
-            )
-            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
-        else:
-            logger.debug(
-                "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
-            )
-            single_submodule_checkout(
-                root_dir,
-                name,
-                path,
-                url=url,
-                tag=fxtag,
-                force=force,
-                optional="AlwaysOptional" in requiredlist,
-            )
-
-
-def submodules_test(gitmodules, root_dir):
-    """
-    This function tests the git submodules based on the provided parameters.
-
-    It first checks that fxtags are present and in sync with submodule hashes.
-    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
-    and that sparse checkout files exist.
-
-    Parameters:
-    gitmodules (ConfigParser): The gitmodules configuration.
-    root_dir (str): The root directory for the git operation.
-
-    Returns:
-    int: The number of test failures.
-    """
-    # First check that fxtags are present and in sync with submodule hashes
-    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-    print("")
-    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
-    # and that sparse checkout files exist
-    for name in gitmodules.sections():
-        url = gitmodules.get(name, "url")
-        fxurl = gitmodules.get(name, "fxDONOTMODIFYurl")
-        fxsparse = gitmodules.get(name, "fxsparse")
-        path = gitmodules.get(name, "path")
-        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
-        url = url[:-4] if url.endswith(".git") else url
-        if not fxurl or url.lower() != fxurl.lower():
-            print(f"{name:>20} url {url} not in sync with required {fxurl}")
-            testfails += 1
-        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
-            print(f"{name:>20} sparse checkout file {fxsparse} not found")
-            testfails += 1
-    return testfails + localmods + needsupdate
-
-
-def main():
-    (
-        root_dir,
-        file_name,
-        fxrequired,
-        includelist,
-        excludelist,
-        force,
-        action,
-    ) = commandline_arguments()
-    # Get a logger for the package
-    global logger
-    logger = logging.getLogger(__name__)
-
-    logger.info("action is {}".format(action))
-
-    if not os.path.isfile(os.path.join(root_dir, file_name)):
-        file_path = utils.find_upwards(root_dir, file_name)
-
-        if file_path is None:
-            utils.fatal_error(
-                "No {} found in {} or any of it's parents".format(file_name, root_dir)
-            )
-
-        root_dir = os.path.dirname(file_path)
-    logger.info(
-        "root_dir is {} includelist={} excludelist={}".format(
-            root_dir, includelist, excludelist
-        )
-    )
-    gitmodules = GitModules(
-        logger,
-        confpath=root_dir,
-        conffile=file_name,
-        includelist=includelist,
-        excludelist=excludelist,
-    )
-    if not gitmodules.sections():
-        sys.exit("No submodule components found")
-    retval = 0
-    if action == "update":
-        submodules_update(gitmodules, root_dir, fxrequired, force)
-    elif action == "status":
-        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
-        if tfails + lmods + updates > 0:
-            print(
-                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
-            )
-            if lmods > 0:
-                local_mods_output()
-    elif action == "test":
-        retval = submodules_test(gitmodules, root_dir)
-    else:
-        utils.fatal_error(f"unrecognized action request {action}")
-    return retval
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py
deleted file mode 100644
index 93ae38ecde..0000000000
--- a/.lib/git-fleximod/git_fleximod/gitinterface.py
+++ /dev/null
@@ -1,79 +0,0 @@
-import os
-import sys
-from . import utils
-from pathlib import Path
-
-class GitInterface:
-    def __init__(self, repo_path, logger):
-        logger.debug("Initialize GitInterface for {}".format(repo_path))
-        if isinstance(repo_path, str):
-            self.repo_path = Path(repo_path).resolve()
-        elif isinstance(repo_path, Path):
-            self.repo_path = repo_path.resolve()
-        else:
-            raise TypeError("repo_path must be a str or Path object")
-        self.logger = logger
-        try:
-            import git
-
-            self._use_module = True
-            try:
-                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
-            except git.exc.InvalidGitRepositoryError:
-                self.git = git
-                self._init_git_repo()
-            msg = "Using GitPython interface to git"
-        except ImportError:
-            self._use_module = False
-            if not (self.repo_path / ".git").exists():
-                self._init_git_repo()
-            msg = "Using shell interface to git"
-        self.logger.info(msg)
-
-    def _git_command(self, operation, *args):
-        self.logger.info(operation)
-        if self._use_module and operation != "submodule":
-            try:
-                return getattr(self.repo.git, operation)(*args)
-            except Exception as e:
-                sys.exit(e)
-        else:
-            return ["git", "-C", str(self.repo_path), operation] + list(args)
-
-    def _init_git_repo(self):
-        if self._use_module:
-            self.repo = self.git.Repo.init(str(self.repo_path))
-        else:
-            command = ("git", "-C", str(self.repo_path), "init")
-            utils.execute_subprocess(command)
-
-    # pylint: disable=unused-argument
-    def git_operation(self, operation, *args, **kwargs):
-        command = self._git_command(operation, *args)
-        self.logger.info(command)
-        if isinstance(command, list):
-            try:
-                return utils.execute_subprocess(command, output_to_caller=True)
-            except Exception as e:
-                sys.exit(e)
-        else:
-            return command
-
-    def config_get_value(self, section, name):
-        if self._use_module:
-            config = self.repo.config_reader()
-            return config.get_value(section, name)
-        else:
-            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
-            output = utils.execute_subprocess(cmd, output_to_caller=True)
-            return output.strip()
-
-    def config_set_value(self, section, name, value):
-        if self._use_module:
-            with self.repo.config_writer() as writer:
-                writer.set_value(section, name, value)
-            writer.release()  # Ensure changes are saved
-        else:
-            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
-            self.logger.info(cmd)
-            utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/.lib/git-fleximod/git_fleximod/gitmodules.py b/.lib/git-fleximod/git_fleximod/gitmodules.py
deleted file mode 100644
index 68c82d066f..0000000000
--- a/.lib/git-fleximod/git_fleximod/gitmodules.py
+++ /dev/null
@@ -1,97 +0,0 @@
-import shutil
-from pathlib import Path
-from configparser import RawConfigParser, ConfigParser
-from .lstripreader import LstripReader
-
-
-class GitModules(RawConfigParser):
-    def __init__(
-        self,
-        logger,
-        confpath=Path.cwd(),
-        conffile=".gitmodules",
-        includelist=None,
-        excludelist=None,
-    ):
-        """
-        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
-        conffile: Name of the configuration file (defaults to .gitmodules).
-        includelist: Optional list of submodules to include.
-        excludelist: Optional list of submodules to exclude.
-        """
-        self.logger = logger
-        self.logger.debug(
-            "Creating a GitModules object {} {} {} {}".format(
-                confpath, conffile, includelist, excludelist
-            )
-        )
-        super().__init__()
-        self.conf_file = (Path(confpath) / Path(conffile))
-        if self.conf_file.exists():
-            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
-        self.includelist = includelist
-        self.excludelist = excludelist
-        self.isdirty = False
-        
-    def reload(self):
-        self.clear()
-        if self.conf_file.exists():
-            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
-
-        
-    def set(self, name, option, value):
-        """
-        Sets a configuration value for a specific submodule:
-        Ensures the appropriate section exists for the submodule.
-        Calls the parent class's set method to store the value.
-        """
-        self.isdirty = True
-        self.logger.debug("set called {} {} {}".format(name, option, value))
-        section = f'submodule "{name}"'
-        if not self.has_section(section):
-            self.add_section(section)
-        super().set(section, option, str(value))
-
-    # pylint: disable=redefined-builtin, arguments-differ
-    def get(self, name, option, raw=False, vars=None, fallback=None):
-        """
-        Retrieves a configuration value for a specific submodule:
-        Uses the parent class's get method to access the value.
-        Handles potential errors if the section or option doesn't exist.
-        """
-        self.logger.debug("get called {} {}".format(name, option))
-        section = f'submodule "{name}"'
-        try:
-            return ConfigParser.get(
-                self, section, option, raw=raw, vars=vars, fallback=fallback
-            )
-        except ConfigParser.NoOptionError:
-            return None
-
-    def save(self):
-        if self.isdirty:
-            self.logger.info("Writing {}".format(self.conf_file))
-            with open(self.conf_file, "w") as fd:
-                self.write(fd)
-        self.isdirty = False
-        
-    def __del__(self):
-        self.save()
-
-    def sections(self):
-        """Strip the submodule part out of section and just use the name"""
-        self.logger.debug("calling GitModules sections iterator")
-        names = []
-        for section in ConfigParser.sections(self):
-            name = section[11:-1]
-            if self.includelist and name not in self.includelist:
-                continue
-            if self.excludelist and name in self.excludelist:
-                continue
-            names.append(name)
-        return names
-
-    def items(self, name, raw=False, vars=None):
-        self.logger.debug("calling GitModules items for {}".format(name))
-        section = f'submodule "{name}"'
-        return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/.lib/git-fleximod/git_fleximod/lstripreader.py b/.lib/git-fleximod/git_fleximod/lstripreader.py
deleted file mode 100644
index 01d5580ee8..0000000000
--- a/.lib/git-fleximod/git_fleximod/lstripreader.py
+++ /dev/null
@@ -1,43 +0,0 @@
-class LstripReader(object):
-    "LstripReader formats .gitmodules files to be acceptable for configparser"
-
-    def __init__(self, filename):
-        with open(filename, "r") as infile:
-            lines = infile.readlines()
-        self._lines = list()
-        self._num_lines = len(lines)
-        self._index = 0
-        for line in lines:
-            self._lines.append(line.lstrip())
-
-    def readlines(self):
-        """Return all the lines from this object's file"""
-        return self._lines
-
-    def readline(self, size=-1):
-        """Format and return the next line or raise StopIteration"""
-        try:
-            line = self.next()
-        except StopIteration:
-            line = ""
-
-        if (size > 0) and (len(line) < size):
-            return line[0:size]
-
-        return line
-
-    def __iter__(self):
-        """Begin an iteration"""
-        self._index = 0
-        return self
-
-    def next(self):
-        """Return the next line or raise StopIteration"""
-        if self._index >= self._num_lines:
-            raise StopIteration
-
-        self._index = self._index + 1
-        return self._lines[self._index - 1]
-
-    def __next__(self):
-        return self.next()
diff --git a/.lib/git-fleximod/git_fleximod/metoflexi.py b/.lib/git-fleximod/git_fleximod/metoflexi.py
deleted file mode 100755
index cc347db2dd..0000000000
--- a/.lib/git-fleximod/git_fleximod/metoflexi.py
+++ /dev/null
@@ -1,236 +0,0 @@
-#!/usr/bin/env python
-from configparser import ConfigParser
-import sys
-import shutil
-from pathlib import Path
-import argparse
-import logging
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-from git_fleximod import utils
-
-logger = None
-
-def find_root_dir(filename=".git"):
-    d = Path.cwd()
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.is_dir():
-            return d
-        d = d.parent
-    return None
-
-
-def get_parser():
-    description = """
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
-    """
-    parser = argparse.ArgumentParser(
-        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-    )
-
-    parser.add_argument('-e', '--externals', nargs='?',
-                        default='Externals.cfg',
-                        help='The externals description filename. '
-                        'Default: %(default)s.')
-
-    parser.add_argument(
-        "-C",
-        "--path",
-        default=find_root_dir(),
-        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
-    )
-
-    parser.add_argument(
-        "-g",
-        "--gitmodules",
-        nargs="?",
-        default=".gitmodules",
-        help="The submodule description filename. " "Default: %(default)s.",
-    )
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        action="count",
-        default=0,
-        help="Output additional information to "
-        "the screen and log file. This flag can be "
-        "used up to two times, increasing the "
-        "verbosity level each time.",
-    )
-    parser.add_argument(
-        "-d",
-        "--debug",
-        action="store_true",
-        default=False,
-        help="DEVELOPER: output additional debugging "
-        "information to the screen and log file.",
-    )
-
-    return parser
-
-def commandline_arguments(args=None):
-    parser = get_parser()
-
-    options = parser.parse_args(args)
-    handlers = [logging.StreamHandler()]
-
-    if options.debug:
-        try:
-            open("fleximod.log", "w")
-        except PermissionError:
-            sys.exit("ABORT: Could not write file fleximod.log")
-        level = logging.DEBUG
-        handlers.append(logging.FileHandler("fleximod.log"))
-    elif options.verbose:
-        level = logging.INFO
-    else:
-        level = logging.WARNING
-    # Configure the root logger
-    logging.basicConfig(
-        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
-    )
-
-    return(
-        options.path,
-        options.gitmodules,
-        options.externals
-        )
-
-class ExternalRepoTranslator:
-    """
-    Translates external repositories configured in an INI-style externals file.
-    """
-
-    def __init__(self, rootpath, gitmodules, externals):
-        self.rootpath = rootpath
-        if gitmodules:
-            self.gitmodules = GitModules(logger, confpath=rootpath)
-        self.externals = (rootpath / Path(externals)).resolve()
-        print(f"Translating {self.externals}")
-        self.git = GitInterface(rootpath, logger)
-        
-#    def __del__(self):
-#        if (self.rootpath / "save.gitignore"):
-            
-
-    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
-        """
-        Translates a single repository based on configuration details.
-
-        Args:
-            rootpath (str): Root path of the main repository.
-            gitmodules (str): Path to the .gitmodules file.
-            tag (str): The tag to use for the external repository.
-            url (str): The URL of the external repository.
-            path (str): The relative path within the main repository for the external repository.
-            efile (str): The external file or file containing submodules.
-            hash_ (str): The commit hash to checkout (if applicable).
-            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
-            protocol (str): The protocol to use (e.g., 'git', 'http').
-        """
-        assert protocol != "svn", "SVN protocol is not currently supported"
-        print(f"Translating repository {section}")
-        if efile:
-            file_path = Path(path) / Path(efile)
-            newroot = (self.rootpath / file_path).parent.resolve()
-            if not newroot.exists():
-                newroot.mkdir(parents=True)
-            logger.info("Newroot is {}".format(newroot))
-            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
-            newt.translate_repo()
-        if protocol == "externals_only":
-            if tag:
-                self.gitmodules.set(section, "fxtag", tag)
-            if hash_:
-                self.gitmodules.set(section, "fxtag", hash_)
-            
-            self.gitmodules.set(section, "fxDONOTUSEurl", url)
-            if sparse:
-                self.gitmodules.set(section, "fxsparse", sparse)
-            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-        else:
-            newpath = (self.rootpath / Path(path))
-            if newpath.exists():
-                shutil.rmtree(newpath)
-                logger.info("Creating directory {}".format(newpath))
-            newpath.mkdir(parents=True)
-            if tag:
-                logger.info("cloning {}".format(section))
-                try:
-                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
-                except:
-                    self.git.git_operation("clone", url, path)
-                    with utils.pushd(newpath):
-                        ngit = GitInterface(newpath, logger)
-                        ngit.git_operation("checkout", tag)
-            if hash_:
-                self.git.git_operation("clone", url, path)
-                git = GitInterface(newpath, logger)
-                git.git_operation("fetch", "origin")
-                git.git_operation("checkout", hash_)
-            if sparse:
-                print("setting as sparse submodule {}".format(section))
-                sparsefile = (newpath / Path(sparse))
-                newfile = (newpath / ".git" / "info" / "sparse-checkout")
-                print(f"sparsefile {sparsefile} newfile {newfile}")
-                shutil.copy(sparsefile, newfile)
-        
-            logger.info("adding submodule {}".format(section))        
-            self.gitmodules.save()
-            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
-            self.git.git_operation("submodule","absorbgitdirs")
-            self.gitmodules.reload()
-            if tag:
-                self.gitmodules.set(section, "fxtag", tag)
-            if hash_:
-                self.gitmodules.set(section, "fxtag", hash_)
-            
-            self.gitmodules.set(section, "fxDONOTUSEurl", url)
-            if sparse:
-                self.gitmodules.set(section, "fxsparse", sparse)
-            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-    
-        
-    def translate_repo(self):
-        """
-        Translates external repositories defined within an external file.
-
-        Args:
-            rootpath (str): Root path of the main repository.
-            gitmodules (str): Path to the .gitmodules file.
-            external_file (str): The path to the external file containing repository definitions.
-        """
-        econfig = ConfigParser()
-        econfig.read((self.rootpath / Path(self.externals)))
-
-        for section in econfig.sections():
-            if section == "externals_description":
-                logger.info("skipping section {}".format(section))
-                return
-            logger.info("Translating section {}".format(section))
-            tag = econfig.get(section, "tag", raw=False, fallback=None)
-            url = econfig.get(section, "repo_url", raw=False, fallback=None)
-            path = econfig.get(section, "local_path", raw=False, fallback=None)
-            efile = econfig.get(section, "externals", raw=False, fallback=None)
-            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
-            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
-            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
-
-            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
-
-
-
-def _main():
-    rootpath, gitmodules, externals = commandline_arguments()
-    global logger
-    logger = logging.getLogger(__name__)
-    with utils.pushd(rootpath):
-        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
-        logger.info("Translating {}".format(rootpath))
-        t.translate_repo()
-
-        
-if __name__ == "__main__":
-    sys.exit(_main())
diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
deleted file mode 100644
index 7cc1de38cc..0000000000
--- a/.lib/git-fleximod/git_fleximod/utils.py
+++ /dev/null
@@ -1,365 +0,0 @@
-#!/usr/bin/env python3
-"""
-Common public utilities for manic package
-
-"""
-
-import logging
-import os
-import subprocess
-import sys
-from threading import Timer
-from pathlib import Path
-
-LOCAL_PATH_INDICATOR = "."
-# ---------------------------------------------------------------------
-#
-# functions to massage text for output and other useful utilities
-#
-# ---------------------------------------------------------------------
-from contextlib import contextmanager
-
-
-@contextmanager
-def pushd(new_dir):
-    """context for chdir. usage: with pushd(new_dir)"""
-    previous_dir = os.getcwd()
-    os.chdir(new_dir)
-    try:
-        yield
-    finally:
-        os.chdir(previous_dir)
-
-
-def log_process_output(output):
-    """Log each line of process output at debug level so it can be
-    filtered if necessary. By default, output is a single string, and
-    logging.debug(output) will only put log info heading on the first
-    line. This makes it hard to filter with grep.
-
-    """
-    output = output.split("\n")
-    for line in output:
-        logging.debug(line)
-
-
-def printlog(msg, **kwargs):
-    """Wrapper script around print to ensure that everything printed to
-    the screen also gets logged.
-
-    """
-    logging.info(msg)
-    if kwargs:
-        print(msg, **kwargs)
-    else:
-        print(msg)
-    sys.stdout.flush()
-
-
-def find_upwards(root_dir, filename):
-    """Find a file in root dir or any of it's parents"""
-    d = Path(root_dir)
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.exists():
-            return attempt
-        d = d.parent
-    return None
-
-
-def last_n_lines(the_string, n_lines, truncation_message=None):
-    """Returns the last n lines of the given string
-
-    Args:
-        the_string: str
-        n_lines: int
-        truncation_message: str, optional
-
-    Returns a string containing the last n lines of the_string
-
-    If truncation_message is provided, the returned string begins with
-    the given message if and only if the string is greater than n lines
-    to begin with.
-    """
-
-    lines = the_string.splitlines(True)
-    if len(lines) <= n_lines:
-        return_val = the_string
-    else:
-        lines_subset = lines[-n_lines:]
-        str_truncated = "".join(lines_subset)
-        if truncation_message:
-            str_truncated = truncation_message + "\n" + str_truncated
-        return_val = str_truncated
-
-    return return_val
-
-
-def indent_string(the_string, indent_level):
-    """Indents the given string by a given number of spaces
-
-    Args:
-       the_string: str
-       indent_level: int
-
-    Returns a new string that is the same as the_string, except that
-    each line is indented by 'indent_level' spaces.
-
-    In python3, this can be done with textwrap.indent.
-    """
-
-    lines = the_string.splitlines(True)
-    padding = " " * indent_level
-    lines_indented = [padding + line for line in lines]
-    return "".join(lines_indented)
-
-
-# ---------------------------------------------------------------------
-#
-# error handling
-#
-# ---------------------------------------------------------------------
-
-
-def fatal_error(message):
-    """
-    Error output function
-    """
-    logging.error(message)
-    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
-
-
-# ---------------------------------------------------------------------
-#
-# Data conversion / manipulation
-#
-# ---------------------------------------------------------------------
-def str_to_bool(bool_str):
-    """Convert a sting representation of as boolean into a true boolean.
-
-    Conversion should be case insensitive.
-    """
-    value = None
-    str_lower = bool_str.lower()
-    if str_lower in ("true", "t"):
-        value = True
-    elif str_lower in ("false", "f"):
-        value = False
-    if value is None:
-        msg = (
-            'ERROR: invalid boolean string value "{0}". '
-            'Must be "true" or "false"'.format(bool_str)
-        )
-        fatal_error(msg)
-    return value
-
-
-REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
-
-
-def is_remote_url(url):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    """
-    remote_url = False
-    for prefix in REMOTE_PREFIXES:
-        if url.startswith(prefix):
-            remote_url = True
-    return remote_url
-
-
-def split_remote_url(url):
-    """check if the user provided a local file path or a
-    remote. If remote, try to strip off protocol info.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        return url
-
-    for prefix in REMOTE_PREFIXES:
-        url = url.replace(prefix, "")
-
-    if "@" in url:
-        url = url.split("@")[1]
-
-    if ":" in url:
-        url = url.split(":")[1]
-
-    return url
-
-
-def expand_local_url(url, field):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
-    represent local copy only, don't work with the remotes.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        if url.strip() == LOCAL_PATH_INDICATOR:
-            pass
-        else:
-            url = os.path.expandvars(url)
-            url = os.path.expanduser(url)
-            if not os.path.isabs(url):
-                msg = (
-                    'WARNING: Externals description for "{0}" contains a '
-                    "url that is not remote and does not expand to an "
-                    "absolute path. Version control operations may "
-                    "fail.\n\nurl={1}".format(field, url)
-                )
-                printlog(msg)
-            else:
-                url = os.path.normpath(url)
-    return url
-
-
-# ---------------------------------------------------------------------
-#
-# subprocess
-#
-# ---------------------------------------------------------------------
-
-# Give the user a helpful message if we detect that a command seems to
-# be hanging.
-_HANGING_SEC = 300
-
-
-def _hanging_msg(working_directory, command):
-    print(
-        """
-
-Command '{command}'
-from directory {working_directory}
-has taken {hanging_sec} seconds. It may be hanging.
-
-The command will continue to run, but you may want to abort
-manage_externals with ^C and investigate. A possible cause of hangs is
-when svn or git require authentication to access a private
-repository. On some systems, svn and git requests for authentication
-information will not be displayed to the user. In this case, the program
-will appear to hang. Ensure you can run svn and git manually and access
-all repositories without entering your authentication information.
-
-""".format(
-            command=command,
-            working_directory=working_directory,
-            hanging_sec=_HANGING_SEC,
-        )
-    )
-
-
-def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
-    """Wrapper around subprocess.check_output to handle common
-    exceptions.
-
-    check_output runs a command with arguments and waits
-    for it to complete.
-
-    check_output raises an exception on a nonzero return code.  if
-    status_to_caller is true, execute_subprocess returns the subprocess
-    return code, otherwise execute_subprocess treats non-zero return
-    status as an error and raises an exception.
-
-    """
-    cwd = os.getcwd()
-    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
-    logging.info(msg)
-    commands_str = " ".join(str(element) for element in commands)
-    logging.info(commands_str)
-    return_to_caller = status_to_caller or output_to_caller
-    status = -1
-    output = ""
-    hanging_timer = Timer(
-        _HANGING_SEC,
-        _hanging_msg,
-        kwargs={"working_directory": cwd, "command": commands_str},
-    )
-    hanging_timer.start()
-    try:
-        output = subprocess.check_output(
-            commands, stderr=subprocess.STDOUT, universal_newlines=True
-        )
-        log_process_output(output)
-        status = 0
-    except OSError as error:
-        msg = failed_command_msg(
-            "Command execution failed. Does the executable exist?", commands
-        )
-        logging.error(error)
-        fatal_error(msg)
-    except ValueError as error:
-        msg = failed_command_msg(
-            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
-        )
-        logging.error(error)
-        fatal_error(msg)
-    except subprocess.CalledProcessError as error:
-        # Only report the error if we are NOT returning to the
-        # caller. If we are returning to the caller, then it may be a
-        # simple status check. If returning, it is the callers
-        # responsibility determine if an error occurred and handle it
-        # appropriately.
-        if not return_to_caller:
-            msg_context = (
-                "Process did not run successfully; "
-                "returned status {0}".format(error.returncode)
-            )
-            msg = failed_command_msg(msg_context, commands, output=error.output)
-            logging.error(error)
-            logging.error(msg)
-            log_process_output(error.output)
-            fatal_error(msg)
-        status = error.returncode
-    finally:
-        hanging_timer.cancel()
-
-    if status_to_caller and output_to_caller:
-        ret_value = (status, output)
-    elif status_to_caller:
-        ret_value = status
-    elif output_to_caller:
-        ret_value = output
-    else:
-        ret_value = None
-
-    return ret_value
-
-
-def failed_command_msg(msg_context, command, output=None):
-    """Template for consistent error messages from subprocess calls.
-
-    If 'output' is given, it should provide the output from the failed
-    command
-    """
-
-    if output:
-        output_truncated = last_n_lines(
-            output, 20, truncation_message="[... Output truncated for brevity ...]"
-        )
-        errmsg = (
-            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
-        )
-    else:
-        errmsg = ""
-
-    command_str = " ".join(command)
-    errmsg += """In directory
-    {cwd}
-{context}:
-    {command}
-""".format(
-        cwd=os.getcwd(), context=msg_context, command=command_str
-    )
-
-    if output:
-        errmsg += "See above for output from failed command.\n"
-
-    return errmsg
diff --git a/.lib/git-fleximod/poetry.lock b/.lib/git-fleximod/poetry.lock
deleted file mode 100644
index b59ed3942c..0000000000
--- a/.lib/git-fleximod/poetry.lock
+++ /dev/null
@@ -1,693 +0,0 @@
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-    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
-    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
-]
-
-[package.extras]
-test = ["flake8", "mypy", "pytest"]
-
-[[package]]
-name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
-    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
-    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "tomli"
-version = "2.0.1"
-description = "A lil' TOML parser"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
-]
-
-[[package]]
-name = "urllib3"
-version = "2.2.0"
-description = "HTTP library with thread-safe connection pooling, file post, and more."
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "urllib3-2.2.0-py3-none-any.whl", hash = "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"},
-    {file = "urllib3-2.2.0.tar.gz", hash = "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20"},
-]
-
-[package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
-h2 = ["h2 (>=4,<5)"]
-socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-zstd = ["zstandard (>=0.18.0)"]
-
-[[package]]
-name = "wheel"
-version = "0.42.0"
-description = "A built-package format for Python"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "wheel-0.42.0-py3-none-any.whl", hash = "sha256:177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d"},
-    {file = "wheel-0.42.0.tar.gz", hash = "sha256:c45be39f7882c9d34243236f2d63cbd58039e360f85d0913425fbd7ceea617a8"},
-]
-
-[package.extras]
-test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
-
-[[package]]
-name = "zipp"
-version = "3.17.0"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
-
-[metadata]
-lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
deleted file mode 100644
index 2484552e4f..0000000000
--- a/.lib/git-fleximod/pyproject.toml
+++ /dev/null
@@ -1,41 +0,0 @@
-[tool.poetry]
-name = "git-fleximod"
-version = "0.7.4"
-description = "Extended support for git-submodule and git-sparse-checkout"
-authors = ["Jim Edwards <jedwards@ucar.edu>"]
-maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
-license = "MIT"
-readme = "README.md"
-homepage = "https://github.com/jedwards4b/git-fleximod"
-keywords = ["git", "submodule", "sparse-checkout"]
-packages = [
-{ include = "git_fleximod"},
-{ include = "doc"},
-]
-
-[tool.poetry.scripts]
-git-fleximod = "git_fleximod.git_fleximod:main"
-me2flexi = "git_fleximod.metoflexi:_main"
-fsspec = "fsspec.fuse:main"
-
-[tool.poetry.dependencies]
-python = "^3.8"
-GitPython = "^3.1.0"
-sphinx = "^5.0.0"
-fsspec = "^2023.12.2"
-wheel = "^0.42.0"
-pytest = "^8.0.0"
-pyfakefs = "^5.3.5"
-
-[tool.poetry.urls]
-"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
-
-[tool.pytest.ini_options]
-markers = [
-        "skip_after_first: only run on first iteration"
-]
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
deleted file mode 100644
index d4b8eaee11..0000000000
--- a/.lib/git-fleximod/tbump.toml
+++ /dev/null
@@ -1,43 +0,0 @@
-# Uncomment this if your project is hosted on GitHub:
-github_url = "https://github.com/jedwards4b/git-fleximod/"
-
-[version]
-current = "0.7.4"
-
-# Example of a semver regexp.
-# Make sure this matches current_version before
-# using tbump
-regex = '''
-  (?P<major>\d+)
-  \.
-  (?P<minor>\d+)
-  \.
-  (?P<patch>\d+)
-  '''
-
-[git]
-message_template = "Bump to {new_version}"
-tag_template = "v{new_version}"
-
-# For each file to patch, add a [[file]] config
-# section containing the path of the file, relative to the
-# tbump.toml location.
-[[file]]
-src = "git_fleximod/cli.py"
-
-[[file]]
-src = "pyproject.toml"
-
-# You can specify a list of commands to
-# run after the files have been patched
-# and before the git commit is made
-
-#  [[before_commit]]
-#  name = "check changelog"
-#  cmd = "grep -q {new_version} Changelog.rst"
-
-# Or run some commands after the git tag and the branch
-# have been pushed:
-#  [[after_push]]
-#  name = "publish"
-#  cmd = "./publish.sh"
diff --git a/.lib/git-fleximod/tests/__init__.py b/.lib/git-fleximod/tests/__init__.py
deleted file mode 100644
index 4d4c66c78e..0000000000
--- a/.lib/git-fleximod/tests/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-import sys, os
-
-sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py
deleted file mode 100644
index 942a0efb97..0000000000
--- a/.lib/git-fleximod/tests/conftest.py
+++ /dev/null
@@ -1,138 +0,0 @@
-import pytest 
-from git_fleximod.gitinterface import GitInterface
-import os
-import subprocess
-import logging
-from pathlib import Path
-
-@pytest.fixture(scope='session')
-def logger():
-    logging.basicConfig(
-        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
-    )
-    logger = logging.getLogger(__name__)
-    return logger
-
-all_repos=[
-    {"subrepo_path": "modules/test",
-     "submodule_name": "test_submodule",
-     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_submodule at tag MPIserial_2.4.0",
-     "status3" : "test_submodule at tag MPIserial_2.4.0",
-     "status4" : "test_submodule at tag MPIserial_2.4.0",
-     "gitmodules_content" : """
-    [submodule "test_submodule"]
-    path = modules/test
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.4.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelRequired
-"""},
-    {"subrepo_path": "modules/test_optional",
-     "submodule_name": "test_optional",
-     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
-     "status4" : "test_optional at tag MPIserial_2.4.0",
-     "gitmodules_content": """
-     [submodule "test_optional"]
-    path = modules/test_optional
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.4.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelOptional
-"""},
-    {"subrepo_path": "modules/test_alwaysoptional",
-     "submodule_name": "test_alwaysoptional",
-     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
-     "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
-     "status4" : "test_alwaysoptional at hash e5cf35c",
-     "gitmodules_content": """
-    [submodule "test_alwaysoptional"]
-    path = modules/test_alwaysoptional
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = e5cf35c
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = AlwaysOptional
-"""},    
-    {"subrepo_path": "modules/test_sparse",
-     "submodule_name": "test_sparse",
-     "status1" : "test_sparse at tag MPIserial_2.5.0",
-     "status2" : "test_sparse at tag MPIserial_2.5.0",
-     "status3" : "test_sparse at tag MPIserial_2.5.0",
-     "status4" : "test_sparse at tag MPIserial_2.5.0",
-     "gitmodules_content": """
-    [submodule "test_sparse"]
-    path = modules/test_sparse
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.5.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = AlwaysRequired
-    fxsparse = ../.sparse_file_list
-"""},
-]
-@pytest.fixture(params=all_repos)
-
-def shared_repos(request):
-    return request.param
-
-@pytest.fixture
-def get_all_repos():
-    return all_repos
-
-def write_sparse_checkout_file(fp):
-    sparse_content = """m4
-"""
-    fp.write_text(sparse_content)
-
-@pytest.fixture
-def test_repo(shared_repos, tmp_path, logger):
-    subrepo_path = shared_repos["subrepo_path"]
-    submodule_name = shared_repos["submodule_name"]
-    test_dir = tmp_path / "testrepo"
-    test_dir.mkdir()
-    str_path = str(test_dir)
-    gitp = GitInterface(str_path, logger)
-    assert test_dir.joinpath(".git").is_dir()
-    (test_dir / "modules").mkdir()
-    if "sparse" in submodule_name:
-        (test_dir / subrepo_path).mkdir()
-        # Add the sparse checkout file
-        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
-        gitp.git_operation("add","modules/.sparse_file_list")
-    else:
-        gitp = GitInterface(str(test_dir), logger)
-        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
-        assert test_dir.joinpath(".gitmodules").is_file()
-        gitp.git_operation("add",subrepo_path)
-    gitp.git_operation("commit","-a","-m","\"add submod\"")
-    test_dir2 = tmp_path / "testrepo2"
-    gitp.git_operation("clone",test_dir,test_dir2)
-    return test_dir2    
-
-
-@pytest.fixture
-def complex_repo(tmp_path, logger):
-    test_dir = tmp_path / "testcomplex"
-    test_dir.mkdir()
-    str_path = str(test_dir)
-    gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
-    gitp.git_operation("fetch", "origin", "main")
-    gitp.git_operation("checkout", "main")
-    return test_dir
-    
-@pytest.fixture
-def git_fleximod():
-    def _run_fleximod(path, args, input=None):
-        cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=path, input=input, 
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
-                                text=True)
-        if result.returncode:
-            print(result.stdout)
-            print(result.stderr)
-        return result
-    return _run_fleximod
-
diff --git a/.lib/git-fleximod/tests/test_a_import.py b/.lib/git-fleximod/tests/test_a_import.py
deleted file mode 100644
index d5ca878de5..0000000000
--- a/.lib/git-fleximod/tests/test_a_import.py
+++ /dev/null
@@ -1,8 +0,0 @@
-# pylint: disable=unused-import
-from git_fleximod import cli
-from git_fleximod import utils
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-
-def test_import():
-    print("here")
diff --git a/.lib/git-fleximod/tests/test_b_update.py b/.lib/git-fleximod/tests/test_b_update.py
deleted file mode 100644
index 159f1cfae0..0000000000
--- a/.lib/git-fleximod/tests/test_b_update.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import pytest
-from pathlib import Path
-                
-def test_basic_checkout(git_fleximod, test_repo, shared_repos):
-    # Prepare a simple .gitmodules
-    gm = shared_repos['gitmodules_content']
-    file_path = (test_repo / ".gitmodules")
-    repo_name = shared_repos["submodule_name"]
-    repo_path = shared_repos["subrepo_path"]
-
-    file_path.write_text(gm)
-    
-    # Run the command
-    result = git_fleximod(test_repo, f"update {repo_name}")
-
-    # Assertions
-    assert result.returncode == 0 
-    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
-    if "sparse" in repo_name:
-        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
-        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
-    
-    status = git_fleximod(test_repo, f"status {repo_name}")
-        
-    assert shared_repos["status2"] in status.stdout
-        
diff --git a/.lib/git-fleximod/tests/test_c_required.py b/.lib/git-fleximod/tests/test_c_required.py
deleted file mode 100644
index 89ab8d294d..0000000000
--- a/.lib/git-fleximod/tests/test_c_required.py
+++ /dev/null
@@ -1,30 +0,0 @@
-import pytest
-from pathlib import Path
-                
-def test_required(git_fleximod, test_repo, shared_repos):
-    file_path = (test_repo / ".gitmodules")
-    gm = shared_repos["gitmodules_content"]
-    repo_name = shared_repos["submodule_name"]
-    if file_path.exists():
-        with file_path.open("r") as f:
-            gitmodules_content = f.read()
-            # add the entry if it does not exist
-            if repo_name not in gitmodules_content:
-                file_path.write_text(gitmodules_content+gm)
-            # or if it is incomplete
-            elif gm not in gitmodules_content:
-                file_path.write_text(gm)
-    else:
-        file_path.write_text(gm)
-    result = git_fleximod(test_repo, "update")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status3"] in status.stdout
-    status = git_fleximod(test_repo, f"update --optional")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
-    status = git_fleximod(test_repo, f"update {repo_name}")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
diff --git a/.lib/git-fleximod/tests/test_d_complex.py b/.lib/git-fleximod/tests/test_d_complex.py
deleted file mode 100644
index fdce516274..0000000000
--- a/.lib/git-fleximod/tests/test_d_complex.py
+++ /dev/null
@@ -1,67 +0,0 @@
-import pytest
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
-
-def test_complex_checkout(git_fleximod, complex_repo, logger):
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
-    
-    # This should checkout and update test_submodule and complex_sub
-    result = git_fleximod(complex_repo, "update")    
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
-
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex")
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
-    # update a single optional submodule
-
-    result = git_fleximod(complex_repo, "update ToplevelOptional")
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
-
-
-    # Finally update optional
-    result = git_fleximod(complex_repo, "update --optional")
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
-    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
-    
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex" )
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
-

From eb94e4d298564d52197d9cf632d73ffad74c5f61 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 31 May 2024 10:20:12 -0600
Subject: [PATCH 0383/1248] Squashed '.lib/git-fleximod/' content from commit
 a354b0528

git-subtree-dir: .lib/git-fleximod
git-subtree-split: a354b0528228ac89ce103b3b42b2a203fe495ba5
---
 .github/workflows/pre-commit  |  13 +
 .github/workflows/pytest.yaml |  77 ++++
 .pre-commit-config.yaml       |  18 +
 License                       |  20 +
 README.md                     | 108 ++++++
 doc/Makefile                  |  20 +
 doc/conf.py                   |  26 ++
 doc/index.rst                 |  24 ++
 doc/make.bat                  |  35 ++
 escomp_install                |  25 ++
 git_fleximod/__init__.py      |   0
 git_fleximod/cli.py           | 129 +++++++
 git_fleximod/git_fleximod.py  | 605 +++++++++++++++++++++++++++++
 git_fleximod/gitinterface.py  |  79 ++++
 git_fleximod/gitmodules.py    |  97 +++++
 git_fleximod/lstripreader.py  |  43 +++
 git_fleximod/metoflexi.py     | 236 ++++++++++++
 git_fleximod/utils.py         | 365 ++++++++++++++++++
 poetry.lock                   | 693 ++++++++++++++++++++++++++++++++++
 pyproject.toml                |  41 ++
 tbump.toml                    |  43 +++
 tests/__init__.py             |   3 +
 tests/conftest.py             | 138 +++++++
 tests/test_a_import.py        |   8 +
 tests/test_b_update.py        |  26 ++
 tests/test_c_required.py      |  30 ++
 tests/test_d_complex.py       |  67 ++++
 27 files changed, 2969 insertions(+)
 create mode 100644 .github/workflows/pre-commit
 create mode 100644 .github/workflows/pytest.yaml
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 License
 create mode 100644 README.md
 create mode 100644 doc/Makefile
 create mode 100644 doc/conf.py
 create mode 100644 doc/index.rst
 create mode 100644 doc/make.bat
 create mode 100644 escomp_install
 create mode 100644 git_fleximod/__init__.py
 create mode 100644 git_fleximod/cli.py
 create mode 100755 git_fleximod/git_fleximod.py
 create mode 100644 git_fleximod/gitinterface.py
 create mode 100644 git_fleximod/gitmodules.py
 create mode 100644 git_fleximod/lstripreader.py
 create mode 100755 git_fleximod/metoflexi.py
 create mode 100644 git_fleximod/utils.py
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 create mode 100644 tbump.toml
 create mode 100644 tests/__init__.py
 create mode 100644 tests/conftest.py
 create mode 100644 tests/test_a_import.py
 create mode 100644 tests/test_b_update.py
 create mode 100644 tests/test_c_required.py
 create mode 100644 tests/test_d_complex.py

diff --git a/.github/workflows/pre-commit b/.github/workflows/pre-commit
new file mode 100644
index 0000000000..1a6ad0082a
--- /dev/null
+++ b/.github/workflows/pre-commit
@@ -0,0 +1,13 @@
+name: pre-commit
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
new file mode 100644
index 0000000000..0868dd9a33
--- /dev/null
+++ b/.github/workflows/pytest.yaml
@@ -0,0 +1,77 @@
+# Run this job on pushes to `main`, and for pull requests. If you don't specify
+# `branches: [main], then this actions runs _twice_ on pull requests, which is
+# annoying.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
+      # reference the matrixe python version here.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
+      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
+      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
+      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
+      # mildly cleaner by using an environment variable, but I don't really care.
+      - name: cache poetry install
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: poetry-1.7.1
+
+      # Install Poetry. You could do this manually, or there are several actions that do this.
+      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
+      # Poetry's default install script, which feels correct. I pin the Poetry version here
+      # because Poetry does occasionally change APIs between versions and I don't want my
+      # actions to break if it does.
+      #
+      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
+      # venv as a `.venv` in your testing directory, which allows the next step to easily
+      # cache it.
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.7.1
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
+      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
+      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
+      - name: cache deps
+        id: cache-deps
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+
+      # Install dependencies. `--no-root` means "install all dependencies but not the project
+      # itself", which is what you want to avoid caching _your_ code. The `if` statement
+      # ensures this only runs on a cache miss.
+      - run: poetry install --no-interaction --no-root
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+
+      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
+      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
+      # pyproject.toml and makes that if you add things like console-scripts at some point that
+      # they'll be installed and working.
+      - run: poetry install --no-interaction
+
+      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
+      # so this line is super-simple. But it could be as complex as you need.
+      - run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+          poetry run pytest
+
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000..2f6089da72
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+exclude: ^utils/.*$
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/pylint
+    rev: v2.11.1
+    hooks:
+      - id: pylint
+        args:
+          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/License b/License
new file mode 100644
index 0000000000..88bc22515e
--- /dev/null
+++ b/License
@@ -0,0 +1,20 @@
+Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+“Software”), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000..53917da400
--- /dev/null
+++ b/README.md
@@ -0,0 +1,108 @@
+# git-fleximod
+
+Flexible, Enhanced Submodule Management for Git
+
+## Overview
+
+Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
+
+## Installation
+
+  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
+
+## Usage
+
+    Basic Usage:
+        git fleximod <command> [options]
+    Available Commands:
+        status: Display the status of submodules.
+        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
+        test: Make sure that fxtags and submodule hashes are consistant,
+              make sure that official urls (as defined by fxDONOTUSEurl) are set
+              make sure that fxtags are defined for all submodules
+    Additional Options:
+        See git fleximod --help for more details.
+
+## Supported .gitmodules Variables
+
+    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxrequired: Mark a submodule's checkout behavior, with allowed values:
+      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
+      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - AlwaysRequired:       Always required (always checked out).
+      - AlwaysOptional:       Always optional (checked out with --optional flag).
+    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
+    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
+           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
+           changed by users.  Use the url variable to change to a fork if desired.
+
+## Sparse Checkouts
+
+    To enable sparse checkout for a submodule, set the fxsparse variable
+    in the .gitmodules file to the path of a file containing the desired
+    sparse checkout paths. Git-fleximod will automatically configure
+    sparse checkout based on this file when applicable commands are run.
+    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
+    for details on the format of this file.
+
+## Tests
+
+   The git fleximod test action is designed to be used by, for example, github workflows
+   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
+
+## Examples
+
+Here are some common usage examples:
+
+Update all submodules, including optional ones:
+```bash
+  git fleximod update --optional
+```
+
+Updating a specific submodule to the fxtag indicated in .gitmodules:
+
+```bash
+    git fleximod update submodule-name
+```
+Example .gitmodules entry:
+```ini, toml
+    [submodule "cosp2"]
+        path = src/physics/cosp2/src
+        url = https://github.com/CFMIP/COSPv2.0
+        fxsparse = ../.cosp_sparse_checkout
+        fxrequired = AlwaysRequired
+        fxtag = v2.1.4cesm
+```
+Explanation:
+
+This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
+should be checked out into the directory src/physics/cosp2/src
+relative to the .gitmodules directory.  It should be checked out from
+the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
+described in the file ../.cosp_sparse_checkout relative to the path
+directory.  It should be checked out anytime this .gitmodules entry is
+read.
+
+Additional example:
+```ini, toml
+    [submodule "cime"]
+        path = cime
+        url = https://github.com/jedwards4b/cime
+        fxrequired = ToplevelRequired
+        fxtag = cime6.0.198_rme01
+```
+
+Explanation:
+
+This entry indicates that the submodule cime should be checked out
+into a directory named cime at tag cime6.0.198_rme01 from the URL
+https://github.com/jedwards4b/cime.  This should only be done if
+the .gitmodules file is at the top level of the repository clone.
+
+## Contributing
+
+We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
+
+## License
+
+Git-fleximod is released under the MIT License.
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000000..d4bb2cbb9e
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000000..423099eec9
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,26 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "git-fleximod"
+author = "Jim Edwards <jedwards@ucar.edu>"
+release = "0.4.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx_argparse_cli"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000000..0f9c1a7f7e
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,24 @@
+.. git-fleximod documentation master file, created by
+   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to git-fleximod's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+.. module:: sphinxcontrib.autoprogram
+.. sphinx_argparse_cli::
+   :module: git_fleximod.cli
+   :func: get_parser
+   :prog: git-fleximod
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/doc/make.bat b/doc/make.bat
new file mode 100644
index 0000000000..32bb24529f
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/escomp_install b/escomp_install
new file mode 100644
index 0000000000..ae782e72a4
--- /dev/null
+++ b/escomp_install
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# updates git-fleximod in an ESCOMP model
+# this script should be run from the model root directory, it expects
+# git-fleximod to already be installed with the script in bin
+# and the classes in lib/python/site-packages
+import sys
+import shutil
+import os
+
+from glob import iglob
+
+fleximod_root = sys.argv[1]
+fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
+if os.path.isfile(fleximod_path):
+   with open(fleximod_path,"r") as f:
+        fleximod = f.readlines()
+   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
+        for line in fleximod:
+            f.write(line)
+            if "import argparse" in line:
+               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
+
+   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
+       shutil.copy(file,
+        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/git_fleximod/__init__.py b/git_fleximod/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
new file mode 100644
index 0000000000..4c3fb1a8f9
--- /dev/null
+++ b/git_fleximod/cli.py
@@ -0,0 +1,129 @@
+from pathlib import Path
+import argparse
+from git_fleximod import utils
+
+__version__ = "0.7.5"
+
+def find_root_dir(filename=".gitmodules"):
+    """ finds the highest directory in tree
+    which contains a file called filename """
+    d = Path.cwd()
+    root = Path(d.root)
+    dirlist = []
+    dl = d
+    while dl != root:
+        dirlist.append(dl)
+        dl = dl.parent
+    dirlist.append(root)
+    dirlist.reverse()
+
+    for dl in dirlist:
+        attempt = dl / filename
+        if attempt.is_file():
+            return str(dl)
+    utils.fatal_error("No .gitmodules found in directory tree")
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    #
+    # user options
+    #
+    choices = ["update", "status", "test"]
+    parser.add_argument(
+        "action",
+        choices=choices,
+        default="update",
+        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
+    )
+
+    parser.add_argument(
+        "components",
+        nargs="*",
+        help="Specific component(s) to checkout. By default, "
+        "all required submodules are checked out.",
+    )
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--exclude",
+        nargs="*",
+        help="Component(s) listed in the gitmodules file which should be ignored.",
+    )
+    parser.add_argument(
+        "-f",
+        "--force",
+        action="store_true",
+        default=False,
+        help="Override cautions and update or checkout over locally modified repository.",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--optional",
+        action="store_true",
+        default=False,
+        help="By default only the required submodules "
+        "are checked out. This flag will also checkout the "
+        "optional submodules relative to the toplevel directory.",
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+
+    parser.add_argument(
+        "-V",
+        "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Print version and exit.",
+    )
+
+    #
+    # developer options
+    #
+    parser.add_argument(
+        "--backtrace",
+        action="store_true",
+        help="DEVELOPER: show exception backtraces as extra " "debugging output",
+    )
+
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
new file mode 100755
index 0000000000..f080513a52
--- /dev/null
+++ b/git_fleximod/git_fleximod.py
@@ -0,0 +1,605 @@
+#!/usr/bin/env python
+import sys
+
+MIN_PYTHON = (3, 7)
+if sys.version_info < MIN_PYTHON:
+    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
+
+import os
+import shutil
+import logging
+import textwrap
+from git_fleximod import utils
+from git_fleximod import cli
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from configparser import NoOptionError
+
+# logger variable is global
+logger = None
+
+
+def fxrequired_allowed_values():
+    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
+
+
+def commandline_arguments(args=None):
+    parser = cli.get_parser()
+
+    if args:
+        options = parser.parse_args(args)
+    else:
+        options = parser.parse_args()
+
+    # explicitly listing a component overrides the optional flag
+    if options.optional or options.components:
+        fxrequired = [
+            "ToplevelRequired",
+            "ToplevelOptional",
+            "AlwaysRequired",
+            "AlwaysOptional",
+        ]
+    else:
+        fxrequired = ["ToplevelRequired", "AlwaysRequired"]
+
+    action = options.action
+    if not action:
+        action = "update"
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    if hasattr(options, "version"):
+        exit()
+
+    return (
+        options.path,
+        options.gitmodules,
+        fxrequired,
+        options.components,
+        options.exclude,
+        options.force,
+        action,
+    )
+
+
+def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
+    """
+    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
+    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
+    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
+    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
+    and disk space consuming.
+
+    Parameters:
+    root_dir (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    url (str): The URL of the submodule.
+    path (str): The path to the submodule.
+    sparsefile (str): The sparse file for the submodule.
+    tag (str, optional): The tag to checkout. Defaults to "master".
+
+    Returns:
+    None
+    """
+    logger.info("Called sparse_checkout for {}".format(name))
+    rgit = GitInterface(root_dir, logger)
+    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+    if superroot:
+        gitroot = superroot.strip()
+    else:
+        gitroot = root_dir.strip()
+    assert os.path.isdir(os.path.join(gitroot, ".git"))
+    # first create the module directory
+    if not os.path.isdir(os.path.join(root_dir, path)):
+        os.makedirs(os.path.join(root_dir, path))
+
+    # initialize a new git repo and set the sparse checkout flag
+    sprep_repo = os.path.join(root_dir, path)
+    sprepo_git = GitInterface(sprep_repo, logger)
+    if os.path.exists(os.path.join(sprep_repo, ".git")):
+        try:
+            logger.info("Submodule {} found".format(name))
+            chk = sprepo_git.config_get_value("core", "sparseCheckout")
+            if chk == "true":
+                logger.info("Sparse submodule {} already checked out".format(name))
+                return
+        except NoOptionError:
+            logger.debug("Sparse submodule {} not present".format(name))
+        except Exception as e:
+            utils.fatal_error("Unexpected error {} occured.".format(e))
+
+    sprepo_git.config_set_value("core", "sparseCheckout", "true")
+
+    # set the repository remote
+
+    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
+    status = sprepo_git.git_operation("remote", "-v")
+    if url not in status:
+        sprepo_git.git_operation("remote", "add", "origin", url)
+
+    topgit = os.path.join(gitroot, ".git")
+
+    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
+        with open(os.path.join(root_dir, ".git")) as f:
+            gitpath = os.path.relpath(
+                os.path.join(root_dir, f.read().split()[1]),
+                start=os.path.join(root_dir, path),
+            )
+        topgit = os.path.join(gitpath, "modules")
+    else:
+        topgit = os.path.relpath(
+            os.path.join(root_dir, ".git", "modules"),
+            start=os.path.join(root_dir, path),
+        )
+
+    with utils.pushd(sprep_repo):
+        if not os.path.isdir(topgit):
+            os.makedirs(topgit)
+    topgit += os.sep + name
+
+    if os.path.isdir(os.path.join(root_dir, path, ".git")):
+        with utils.pushd(sprep_repo):
+            shutil.move(".git", topgit)
+            with open(".git", "w") as f:
+                f.write("gitdir: " + os.path.relpath(topgit))
+            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
+            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
+        if os.path.isfile(gitsparse):
+            logger.warning(
+                "submodule {} is already initialized {}".format(name, topgit)
+            )
+            return
+
+        with utils.pushd(sprep_repo):
+            shutil.copy(sparsefile, gitsparse)
+
+    # Finally checkout the repo
+    sprepo_git.git_operation("fetch", "origin", "--tags")
+    sprepo_git.git_operation("checkout", tag)
+
+    print(f"Successfully checked out {name:>20} at {tag}")
+    rgit.config_set_value(f'submodule "{name}"', "active", "true")
+    rgit.config_set_value(f'submodule "{name}"', "url", url)
+
+
+def single_submodule_checkout(
+    root, name, path, url=None, tag=None, force=False, optional=False
+):
+    """
+    This function checks out a single git submodule.
+
+    Parameters:
+    root (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    path (str): The path to the submodule.
+    url (str, optional): The URL of the submodule. Defaults to None.
+    tag (str, optional): The tag to checkout. Defaults to None.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+    optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
+    git = GitInterface(root, logger)
+    repodir = os.path.join(root, path)
+    logger.info("Checkout {} into {}/{}".format(name, root, path))
+    # if url is provided update to the new url
+    tmpurl = None
+    repo_exists = False
+    if os.path.exists(os.path.join(repodir, ".git")):
+        logger.info("Submodule {} already checked out".format(name))
+        repo_exists = True
+    # Look for a .gitmodules file in the newly checkedout repo
+    if not repo_exists and url:
+        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
+        # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
+        # opened with a GitModules object we don't need to worry about restoring the file here
+        # it will be done by the GitModules class
+        if url.startswith("git@"):
+            tmpurl = url
+            url = url.replace("git@github.com:", "https://github.com/")
+            git.git_operation("clone", url, path)
+            smgit = GitInterface(repodir, logger)
+            if not tag:
+                tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
+            smgit.git_operation("checkout", tag)
+            # Now need to move the .git dir to the submodule location
+            rootdotgit = os.path.join(root, ".git")
+            if os.path.isfile(rootdotgit):
+                with open(rootdotgit) as f:
+                    line = f.readline()
+                    if line.startswith("gitdir: "):
+                        rootdotgit = line[8:].rstrip()
+
+            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
+            if os.path.exists(newpath):
+                shutil.rmtree(os.path.join(repodir, ".git"))
+            else:
+                shutil.move(os.path.join(repodir, ".git"), newpath)
+
+            with open(os.path.join(repodir, ".git"), "w") as f:
+                f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
+                
+    if not os.path.exists(repodir):
+        parent = os.path.dirname(repodir)
+        if not os.path.isdir(parent):
+            os.makedirs(parent)
+        git.git_operation("submodule", "add", "--name", name, "--", url, path) 
+
+    if not repo_exists or not tmpurl:
+        git.git_operation("submodule", "update", "--init", "--", path)
+            
+    if os.path.exists(os.path.join(repodir, ".gitmodules")):
+        # recursively handle this checkout
+        print(f"Recursively checking out submodules of {name}")
+        gitmodules = GitModules(logger, confpath=repodir)
+        requiredlist = ["AlwaysRequired"]
+        if optional:
+            requiredlist.append("AlwaysOptional")
+        submodules_checkout(gitmodules, repodir, requiredlist, force=force)
+    if not os.path.exists(os.path.join(repodir, ".git")):
+        utils.fatal_error(
+            f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}"
+        )
+
+    if tmpurl:
+        print(git.git_operation("restore", ".gitmodules"))
+
+    return
+
+
+def submodules_status(gitmodules, root_dir, toplevel=False):
+    testfails = 0
+    localmods = 0
+    needsupdate = 0
+    for name in gitmodules.sections():
+        path = gitmodules.get(name, "path")
+        tag = gitmodules.get(name, "fxtag")
+        required = gitmodules.get(name, "fxrequired")
+        level = required and "Toplevel" in required
+        if not path:
+            utils.fatal_error("No path found in .gitmodules for {}".format(name))
+        newpath = os.path.join(root_dir, path)
+        logger.debug("newpath is {}".format(newpath))
+        if not os.path.exists(os.path.join(newpath, ".git")):
+            rootgit = GitInterface(root_dir, logger)
+            # submodule commands use path, not name
+            url = gitmodules.get(name, "url")
+            url = url.replace("git@github.com:", "https://github.com/")
+            tags = rootgit.git_operation("ls-remote", "--tags", url)
+            atag = None
+            needsupdate += 1
+            if not toplevel and level:
+                continue
+            for htag in tags.split("\n"):
+                if tag and tag in htag:
+                    atag = (htag.split()[1])[10:]
+                    break
+            if tag and tag == atag:
+                print(f"e {name:>20} not checked out, aligned at tag {tag}")
+            elif tag:
+                ahash = rootgit.git_operation(
+                    "submodule", "status", "{}".format(path)
+                ).rstrip()
+                ahash = ahash[1 : len(tag) + 1]
+                if tag == ahash:
+                    print(f"e {name:>20} not checked out, aligned at hash {ahash}")
+                else:
+                    print(
+                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
+                    )
+                    testfails += 1
+            else:
+                print(f"e {name:>20} has no fxtag defined in .gitmodules")
+                testfails += 1
+        else:
+            with utils.pushd(newpath):
+                git = GitInterface(newpath, logger)
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                part =  git.git_operation("status").partition("\n")[0]
+                # fake hash to initialize
+                ahash = "xxxx"
+                if part:
+                    ahash = part.split()[-1]
+                if tag and atag == tag:
+                    print(f"  {name:>20} at tag {tag}")
+                elif tag and ahash[: len(tag)] == tag:
+                    print(f"  {name:>20} at hash {ahash}")
+                elif atag == ahash:
+                    print(f"  {name:>20} at hash {ahash}")
+                elif tag:
+                    print(
+                        f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"
+                    )
+                    testfails += 1
+                    needsupdate += 1
+                else:
+                    print(
+                        f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
+                    )
+                    testfails += 1
+
+                status = git.git_operation("status", "--ignore-submodules")
+                if "nothing to commit" not in status:
+                    localmods = localmods + 1
+                    print("M" + textwrap.indent(status, "                      "))
+
+    return testfails, localmods, needsupdate
+
+
+def submodules_update(gitmodules, root_dir, requiredlist, force):
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+
+    if localmods and not force:
+        local_mods_output()
+        return
+    if needsupdate == 0:
+        return
+
+    for name in gitmodules.sections():
+        fxtag = gitmodules.get(name, "fxtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        logger.info(
+            "name={} path={} url={} fxtag={} requiredlist={}".format(
+                name, os.path.join(root_dir, path), url, fxtag, requiredlist
+            )
+        )
+        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
+        fxrequired = gitmodules.get(name, "fxrequired")
+        assert fxrequired in fxrequired_allowed_values()
+        rgit = GitInterface(root_dir, logger)
+        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+
+        fxsparse = gitmodules.get(name, "fxsparse")
+
+        if (
+            fxrequired
+            and (superroot and "Toplevel" in fxrequired)
+            or fxrequired not in requiredlist
+        ):
+            if "ToplevelOptional" == fxrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+        if fxsparse:
+            logger.debug(
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
+                )
+            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
+        else:
+            logger.info(
+                "Calling submodule_checkout({},{},{},{})".format(
+                    root_dir, name, path, url
+                )
+            )
+
+            single_submodule_checkout(
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional=("AlwaysOptional" in requiredlist),
+            )
+
+        if os.path.exists(os.path.join(path, ".git")):
+            submoddir = os.path.join(root_dir, path)
+            with utils.pushd(submoddir):
+                git = GitInterface(submoddir, logger)
+                # first make sure the url is correct
+                upstream = git.git_operation("ls-remote", "--get-url").rstrip()
+                newremote = "origin"
+                if upstream != url:
+                    # TODO - this needs to be a unique name
+                    remotes = git.git_operation("remote", "-v")
+                    if url in remotes:
+                        for line in remotes:
+                            if url in line and "fetch" in line:
+                                newremote = line.split()[0]
+                                break
+                    else:
+                        i = 0
+                        while newremote in remotes:
+                            i = i + 1
+                            newremote = f"newremote.{i:02d}"
+                        git.git_operation("remote", "add", newremote, url)
+
+                tags = git.git_operation("tag", "-l")
+                if fxtag and fxtag not in tags:
+                    git.git_operation("fetch", newremote, "--tags")
+                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                if fxtag and fxtag != atag:
+                    try:
+                        git.git_operation("checkout", fxtag)
+                        print(f"{name:>20} updated to {fxtag}")
+                    except Exception as error:
+                        print(error)
+                elif not fxtag:
+                    print(f"No fxtag found for submodule {name:>20}")
+                else:
+                    print(f"{name:>20} up to date.")
+
+
+def local_mods_output():
+    text = """\
+    The submodules labeled with 'M' above are not in a clean state.
+    The following are options for how to proceed:
+    (1) Go into each submodule which is not in a clean state and issue a 'git status'
+        Either revert or commit your changes so that the submodule is in a clean state.
+    (2) use the --force option to git-fleximod
+    (3) you can name the particular submodules to update using the git-fleximod command line
+    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
+        then rerun git-fleximod update.
+"""
+    print(text)
+
+
+# checkout is done by update if required so this function may be depricated
+def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
+    """
+    This function checks out all git submodules based on the provided parameters.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+    requiredlist (list): The list of required modules.
+    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
+
+    Returns:
+    None
+    """
+    # function implementation...
+    print("")
+    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    if localmods and not force:
+        local_mods_output()
+        return
+    if not needsupdate:
+        return
+    for name in gitmodules.sections():
+        fxrequired = gitmodules.get(name, "fxrequired")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        fxtag = gitmodules.get(name, "fxtag")
+        path = gitmodules.get(name, "path")
+        url = gitmodules.get(name, "url")
+        if fxrequired and fxrequired not in requiredlist:
+            if "Optional" in fxrequired:
+                print("Skipping optional component {}".format(name))
+            continue
+
+        if fxsparse:
+            logger.debug(
+                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
+                    root_dir, name, url, path, fxsparse, fxtag
+                )
+            )
+            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
+        else:
+            logger.debug(
+                "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
+            )
+            single_submodule_checkout(
+                root_dir,
+                name,
+                path,
+                url=url,
+                tag=fxtag,
+                force=force,
+                optional="AlwaysOptional" in requiredlist,
+            )
+
+
+def submodules_test(gitmodules, root_dir):
+    """
+    This function tests the git submodules based on the provided parameters.
+
+    It first checks that fxtags are present and in sync with submodule hashes.
+    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
+    and that sparse checkout files exist.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+
+    Returns:
+    int: The number of test failures.
+    """
+    # First check that fxtags are present and in sync with submodule hashes
+    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    print("")
+    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
+    # and that sparse checkout files exist
+    for name in gitmodules.sections():
+        url = gitmodules.get(name, "url")
+        fxurl = gitmodules.get(name, "fxDONOTMODIFYurl")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        path = gitmodules.get(name, "path")
+        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
+        url = url[:-4] if url.endswith(".git") else url
+        if not fxurl or url.lower() != fxurl.lower():
+            print(f"{name:>20} url {url} not in sync with required {fxurl}")
+            testfails += 1
+        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
+            print(f"{name:>20} sparse checkout file {fxsparse} not found")
+            testfails += 1
+    return testfails + localmods + needsupdate
+
+
+def main():
+    (
+        root_dir,
+        file_name,
+        fxrequired,
+        includelist,
+        excludelist,
+        force,
+        action,
+    ) = commandline_arguments()
+    # Get a logger for the package
+    global logger
+    logger = logging.getLogger(__name__)
+
+    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
+    
+    if not os.path.isfile(os.path.join(root_dir, file_name)):
+        file_path = utils.find_upwards(root_dir, file_name)
+
+        if file_path is None:
+            utils.fatal_error(
+                "No {} found in {} or any of it's parents".format(file_name, root_dir)
+            )
+
+        root_dir = os.path.dirname(file_path)
+    logger.info(
+        "root_dir is {} includelist={} excludelist={}".format(
+            root_dir, includelist, excludelist
+        )
+    )
+    gitmodules = GitModules(
+        logger,
+        confpath=root_dir,
+        conffile=file_name,
+        includelist=includelist,
+        excludelist=excludelist,
+    )
+    if not gitmodules.sections():
+        sys.exit("No submodule components found")
+    retval = 0
+    if action == "update":
+        submodules_update(gitmodules, root_dir, fxrequired, force)
+    elif action == "status":
+        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
+        if tfails + lmods + updates > 0:
+            print(
+                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
+            )
+            if lmods > 0:
+                local_mods_output()
+    elif action == "test":
+        retval = submodules_test(gitmodules, root_dir)
+    else:
+        utils.fatal_error(f"unrecognized action request {action}")
+    return retval
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py
new file mode 100644
index 0000000000..93ae38ecde
--- /dev/null
+++ b/git_fleximod/gitinterface.py
@@ -0,0 +1,79 @@
+import os
+import sys
+from . import utils
+from pathlib import Path
+
+class GitInterface:
+    def __init__(self, repo_path, logger):
+        logger.debug("Initialize GitInterface for {}".format(repo_path))
+        if isinstance(repo_path, str):
+            self.repo_path = Path(repo_path).resolve()
+        elif isinstance(repo_path, Path):
+            self.repo_path = repo_path.resolve()
+        else:
+            raise TypeError("repo_path must be a str or Path object")
+        self.logger = logger
+        try:
+            import git
+
+            self._use_module = True
+            try:
+                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
+            except git.exc.InvalidGitRepositoryError:
+                self.git = git
+                self._init_git_repo()
+            msg = "Using GitPython interface to git"
+        except ImportError:
+            self._use_module = False
+            if not (self.repo_path / ".git").exists():
+                self._init_git_repo()
+            msg = "Using shell interface to git"
+        self.logger.info(msg)
+
+    def _git_command(self, operation, *args):
+        self.logger.info(operation)
+        if self._use_module and operation != "submodule":
+            try:
+                return getattr(self.repo.git, operation)(*args)
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return ["git", "-C", str(self.repo_path), operation] + list(args)
+
+    def _init_git_repo(self):
+        if self._use_module:
+            self.repo = self.git.Repo.init(str(self.repo_path))
+        else:
+            command = ("git", "-C", str(self.repo_path), "init")
+            utils.execute_subprocess(command)
+
+    # pylint: disable=unused-argument
+    def git_operation(self, operation, *args, **kwargs):
+        command = self._git_command(operation, *args)
+        self.logger.info(command)
+        if isinstance(command, list):
+            try:
+                return utils.execute_subprocess(command, output_to_caller=True)
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return command
+
+    def config_get_value(self, section, name):
+        if self._use_module:
+            config = self.repo.config_reader()
+            return config.get_value(section, name)
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
+            output = utils.execute_subprocess(cmd, output_to_caller=True)
+            return output.strip()
+
+    def config_set_value(self, section, name, value):
+        if self._use_module:
+            with self.repo.config_writer() as writer:
+                writer.set_value(section, name, value)
+            writer.release()  # Ensure changes are saved
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
+            self.logger.info(cmd)
+            utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py
new file mode 100644
index 0000000000..68c82d066f
--- /dev/null
+++ b/git_fleximod/gitmodules.py
@@ -0,0 +1,97 @@
+import shutil
+from pathlib import Path
+from configparser import RawConfigParser, ConfigParser
+from .lstripreader import LstripReader
+
+
+class GitModules(RawConfigParser):
+    def __init__(
+        self,
+        logger,
+        confpath=Path.cwd(),
+        conffile=".gitmodules",
+        includelist=None,
+        excludelist=None,
+    ):
+        """
+        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
+        conffile: Name of the configuration file (defaults to .gitmodules).
+        includelist: Optional list of submodules to include.
+        excludelist: Optional list of submodules to exclude.
+        """
+        self.logger = logger
+        self.logger.debug(
+            "Creating a GitModules object {} {} {} {}".format(
+                confpath, conffile, includelist, excludelist
+            )
+        )
+        super().__init__()
+        self.conf_file = (Path(confpath) / Path(conffile))
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
+        self.includelist = includelist
+        self.excludelist = excludelist
+        self.isdirty = False
+        
+    def reload(self):
+        self.clear()
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
+
+        
+    def set(self, name, option, value):
+        """
+        Sets a configuration value for a specific submodule:
+        Ensures the appropriate section exists for the submodule.
+        Calls the parent class's set method to store the value.
+        """
+        self.isdirty = True
+        self.logger.debug("set called {} {} {}".format(name, option, value))
+        section = f'submodule "{name}"'
+        if not self.has_section(section):
+            self.add_section(section)
+        super().set(section, option, str(value))
+
+    # pylint: disable=redefined-builtin, arguments-differ
+    def get(self, name, option, raw=False, vars=None, fallback=None):
+        """
+        Retrieves a configuration value for a specific submodule:
+        Uses the parent class's get method to access the value.
+        Handles potential errors if the section or option doesn't exist.
+        """
+        self.logger.debug("get called {} {}".format(name, option))
+        section = f'submodule "{name}"'
+        try:
+            return ConfigParser.get(
+                self, section, option, raw=raw, vars=vars, fallback=fallback
+            )
+        except ConfigParser.NoOptionError:
+            return None
+
+    def save(self):
+        if self.isdirty:
+            self.logger.info("Writing {}".format(self.conf_file))
+            with open(self.conf_file, "w") as fd:
+                self.write(fd)
+        self.isdirty = False
+        
+    def __del__(self):
+        self.save()
+
+    def sections(self):
+        """Strip the submodule part out of section and just use the name"""
+        self.logger.debug("calling GitModules sections iterator")
+        names = []
+        for section in ConfigParser.sections(self):
+            name = section[11:-1]
+            if self.includelist and name not in self.includelist:
+                continue
+            if self.excludelist and name in self.excludelist:
+                continue
+            names.append(name)
+        return names
+
+    def items(self, name, raw=False, vars=None):
+        self.logger.debug("calling GitModules items for {}".format(name))
+        section = f'submodule "{name}"'
+        return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/git_fleximod/lstripreader.py b/git_fleximod/lstripreader.py
new file mode 100644
index 0000000000..01d5580ee8
--- /dev/null
+++ b/git_fleximod/lstripreader.py
@@ -0,0 +1,43 @@
+class LstripReader(object):
+    "LstripReader formats .gitmodules files to be acceptable for configparser"
+
+    def __init__(self, filename):
+        with open(filename, "r") as infile:
+            lines = infile.readlines()
+        self._lines = list()
+        self._num_lines = len(lines)
+        self._index = 0
+        for line in lines:
+            self._lines.append(line.lstrip())
+
+    def readlines(self):
+        """Return all the lines from this object's file"""
+        return self._lines
+
+    def readline(self, size=-1):
+        """Format and return the next line or raise StopIteration"""
+        try:
+            line = self.next()
+        except StopIteration:
+            line = ""
+
+        if (size > 0) and (len(line) < size):
+            return line[0:size]
+
+        return line
+
+    def __iter__(self):
+        """Begin an iteration"""
+        self._index = 0
+        return self
+
+    def next(self):
+        """Return the next line or raise StopIteration"""
+        if self._index >= self._num_lines:
+            raise StopIteration
+
+        self._index = self._index + 1
+        return self._lines[self._index - 1]
+
+    def __next__(self):
+        return self.next()
diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
new file mode 100755
index 0000000000..cc347db2dd
--- /dev/null
+++ b/git_fleximod/metoflexi.py
@@ -0,0 +1,236 @@
+#!/usr/bin/env python
+from configparser import ConfigParser
+import sys
+import shutil
+from pathlib import Path
+import argparse
+import logging
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from git_fleximod import utils
+
+logger = None
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return d
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    parser.add_argument('-e', '--externals', nargs='?',
+                        default='Externals.cfg',
+                        help='The externals description filename. '
+                        'Default: %(default)s.')
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
+
+def commandline_arguments(args=None):
+    parser = get_parser()
+
+    options = parser.parse_args(args)
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    return(
+        options.path,
+        options.gitmodules,
+        options.externals
+        )
+
+class ExternalRepoTranslator:
+    """
+    Translates external repositories configured in an INI-style externals file.
+    """
+
+    def __init__(self, rootpath, gitmodules, externals):
+        self.rootpath = rootpath
+        if gitmodules:
+            self.gitmodules = GitModules(logger, confpath=rootpath)
+        self.externals = (rootpath / Path(externals)).resolve()
+        print(f"Translating {self.externals}")
+        self.git = GitInterface(rootpath, logger)
+        
+#    def __del__(self):
+#        if (self.rootpath / "save.gitignore"):
+            
+
+    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
+        """
+        Translates a single repository based on configuration details.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            tag (str): The tag to use for the external repository.
+            url (str): The URL of the external repository.
+            path (str): The relative path within the main repository for the external repository.
+            efile (str): The external file or file containing submodules.
+            hash_ (str): The commit hash to checkout (if applicable).
+            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
+            protocol (str): The protocol to use (e.g., 'git', 'http').
+        """
+        assert protocol != "svn", "SVN protocol is not currently supported"
+        print(f"Translating repository {section}")
+        if efile:
+            file_path = Path(path) / Path(efile)
+            newroot = (self.rootpath / file_path).parent.resolve()
+            if not newroot.exists():
+                newroot.mkdir(parents=True)
+            logger.info("Newroot is {}".format(newroot))
+            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
+            newt.translate_repo()
+        if protocol == "externals_only":
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+        else:
+            newpath = (self.rootpath / Path(path))
+            if newpath.exists():
+                shutil.rmtree(newpath)
+                logger.info("Creating directory {}".format(newpath))
+            newpath.mkdir(parents=True)
+            if tag:
+                logger.info("cloning {}".format(section))
+                try:
+                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+                except:
+                    self.git.git_operation("clone", url, path)
+                    with utils.pushd(newpath):
+                        ngit = GitInterface(newpath, logger)
+                        ngit.git_operation("checkout", tag)
+            if hash_:
+                self.git.git_operation("clone", url, path)
+                git = GitInterface(newpath, logger)
+                git.git_operation("fetch", "origin")
+                git.git_operation("checkout", hash_)
+            if sparse:
+                print("setting as sparse submodule {}".format(section))
+                sparsefile = (newpath / Path(sparse))
+                newfile = (newpath / ".git" / "info" / "sparse-checkout")
+                print(f"sparsefile {sparsefile} newfile {newfile}")
+                shutil.copy(sparsefile, newfile)
+        
+            logger.info("adding submodule {}".format(section))        
+            self.gitmodules.save()
+            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
+            self.git.git_operation("submodule","absorbgitdirs")
+            self.gitmodules.reload()
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+    
+        
+    def translate_repo(self):
+        """
+        Translates external repositories defined within an external file.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            external_file (str): The path to the external file containing repository definitions.
+        """
+        econfig = ConfigParser()
+        econfig.read((self.rootpath / Path(self.externals)))
+
+        for section in econfig.sections():
+            if section == "externals_description":
+                logger.info("skipping section {}".format(section))
+                return
+            logger.info("Translating section {}".format(section))
+            tag = econfig.get(section, "tag", raw=False, fallback=None)
+            url = econfig.get(section, "repo_url", raw=False, fallback=None)
+            path = econfig.get(section, "local_path", raw=False, fallback=None)
+            efile = econfig.get(section, "externals", raw=False, fallback=None)
+            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
+            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
+            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
+
+            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
+
+
+
+def _main():
+    rootpath, gitmodules, externals = commandline_arguments()
+    global logger
+    logger = logging.getLogger(__name__)
+    with utils.pushd(rootpath):
+        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
+        logger.info("Translating {}".format(rootpath))
+        t.translate_repo()
+
+        
+if __name__ == "__main__":
+    sys.exit(_main())
diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py
new file mode 100644
index 0000000000..7cc1de38cc
--- /dev/null
+++ b/git_fleximod/utils.py
@@ -0,0 +1,365 @@
+#!/usr/bin/env python3
+"""
+Common public utilities for manic package
+
+"""
+
+import logging
+import os
+import subprocess
+import sys
+from threading import Timer
+from pathlib import Path
+
+LOCAL_PATH_INDICATOR = "."
+# ---------------------------------------------------------------------
+#
+# functions to massage text for output and other useful utilities
+#
+# ---------------------------------------------------------------------
+from contextlib import contextmanager
+
+
+@contextmanager
+def pushd(new_dir):
+    """context for chdir. usage: with pushd(new_dir)"""
+    previous_dir = os.getcwd()
+    os.chdir(new_dir)
+    try:
+        yield
+    finally:
+        os.chdir(previous_dir)
+
+
+def log_process_output(output):
+    """Log each line of process output at debug level so it can be
+    filtered if necessary. By default, output is a single string, and
+    logging.debug(output) will only put log info heading on the first
+    line. This makes it hard to filter with grep.
+
+    """
+    output = output.split("\n")
+    for line in output:
+        logging.debug(line)
+
+
+def printlog(msg, **kwargs):
+    """Wrapper script around print to ensure that everything printed to
+    the screen also gets logged.
+
+    """
+    logging.info(msg)
+    if kwargs:
+        print(msg, **kwargs)
+    else:
+        print(msg)
+    sys.stdout.flush()
+
+
+def find_upwards(root_dir, filename):
+    """Find a file in root dir or any of it's parents"""
+    d = Path(root_dir)
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.exists():
+            return attempt
+        d = d.parent
+    return None
+
+
+def last_n_lines(the_string, n_lines, truncation_message=None):
+    """Returns the last n lines of the given string
+
+    Args:
+        the_string: str
+        n_lines: int
+        truncation_message: str, optional
+
+    Returns a string containing the last n lines of the_string
+
+    If truncation_message is provided, the returned string begins with
+    the given message if and only if the string is greater than n lines
+    to begin with.
+    """
+
+    lines = the_string.splitlines(True)
+    if len(lines) <= n_lines:
+        return_val = the_string
+    else:
+        lines_subset = lines[-n_lines:]
+        str_truncated = "".join(lines_subset)
+        if truncation_message:
+            str_truncated = truncation_message + "\n" + str_truncated
+        return_val = str_truncated
+
+    return return_val
+
+
+def indent_string(the_string, indent_level):
+    """Indents the given string by a given number of spaces
+
+    Args:
+       the_string: str
+       indent_level: int
+
+    Returns a new string that is the same as the_string, except that
+    each line is indented by 'indent_level' spaces.
+
+    In python3, this can be done with textwrap.indent.
+    """
+
+    lines = the_string.splitlines(True)
+    padding = " " * indent_level
+    lines_indented = [padding + line for line in lines]
+    return "".join(lines_indented)
+
+
+# ---------------------------------------------------------------------
+#
+# error handling
+#
+# ---------------------------------------------------------------------
+
+
+def fatal_error(message):
+    """
+    Error output function
+    """
+    logging.error(message)
+    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
+
+
+# ---------------------------------------------------------------------
+#
+# Data conversion / manipulation
+#
+# ---------------------------------------------------------------------
+def str_to_bool(bool_str):
+    """Convert a sting representation of as boolean into a true boolean.
+
+    Conversion should be case insensitive.
+    """
+    value = None
+    str_lower = bool_str.lower()
+    if str_lower in ("true", "t"):
+        value = True
+    elif str_lower in ("false", "f"):
+        value = False
+    if value is None:
+        msg = (
+            'ERROR: invalid boolean string value "{0}". '
+            'Must be "true" or "false"'.format(bool_str)
+        )
+        fatal_error(msg)
+    return value
+
+
+REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
+
+
+def is_remote_url(url):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    """
+    remote_url = False
+    for prefix in REMOTE_PREFIXES:
+        if url.startswith(prefix):
+            remote_url = True
+    return remote_url
+
+
+def split_remote_url(url):
+    """check if the user provided a local file path or a
+    remote. If remote, try to strip off protocol info.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        return url
+
+    for prefix in REMOTE_PREFIXES:
+        url = url.replace(prefix, "")
+
+    if "@" in url:
+        url = url.split("@")[1]
+
+    if ":" in url:
+        url = url.split(":")[1]
+
+    return url
+
+
+def expand_local_url(url, field):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
+    represent local copy only, don't work with the remotes.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        if url.strip() == LOCAL_PATH_INDICATOR:
+            pass
+        else:
+            url = os.path.expandvars(url)
+            url = os.path.expanduser(url)
+            if not os.path.isabs(url):
+                msg = (
+                    'WARNING: Externals description for "{0}" contains a '
+                    "url that is not remote and does not expand to an "
+                    "absolute path. Version control operations may "
+                    "fail.\n\nurl={1}".format(field, url)
+                )
+                printlog(msg)
+            else:
+                url = os.path.normpath(url)
+    return url
+
+
+# ---------------------------------------------------------------------
+#
+# subprocess
+#
+# ---------------------------------------------------------------------
+
+# Give the user a helpful message if we detect that a command seems to
+# be hanging.
+_HANGING_SEC = 300
+
+
+def _hanging_msg(working_directory, command):
+    print(
+        """
+
+Command '{command}'
+from directory {working_directory}
+has taken {hanging_sec} seconds. It may be hanging.
+
+The command will continue to run, but you may want to abort
+manage_externals with ^C and investigate. A possible cause of hangs is
+when svn or git require authentication to access a private
+repository. On some systems, svn and git requests for authentication
+information will not be displayed to the user. In this case, the program
+will appear to hang. Ensure you can run svn and git manually and access
+all repositories without entering your authentication information.
+
+""".format(
+            command=command,
+            working_directory=working_directory,
+            hanging_sec=_HANGING_SEC,
+        )
+    )
+
+
+def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
+    """Wrapper around subprocess.check_output to handle common
+    exceptions.
+
+    check_output runs a command with arguments and waits
+    for it to complete.
+
+    check_output raises an exception on a nonzero return code.  if
+    status_to_caller is true, execute_subprocess returns the subprocess
+    return code, otherwise execute_subprocess treats non-zero return
+    status as an error and raises an exception.
+
+    """
+    cwd = os.getcwd()
+    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
+    logging.info(msg)
+    commands_str = " ".join(str(element) for element in commands)
+    logging.info(commands_str)
+    return_to_caller = status_to_caller or output_to_caller
+    status = -1
+    output = ""
+    hanging_timer = Timer(
+        _HANGING_SEC,
+        _hanging_msg,
+        kwargs={"working_directory": cwd, "command": commands_str},
+    )
+    hanging_timer.start()
+    try:
+        output = subprocess.check_output(
+            commands, stderr=subprocess.STDOUT, universal_newlines=True
+        )
+        log_process_output(output)
+        status = 0
+    except OSError as error:
+        msg = failed_command_msg(
+            "Command execution failed. Does the executable exist?", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except ValueError as error:
+        msg = failed_command_msg(
+            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except subprocess.CalledProcessError as error:
+        # Only report the error if we are NOT returning to the
+        # caller. If we are returning to the caller, then it may be a
+        # simple status check. If returning, it is the callers
+        # responsibility determine if an error occurred and handle it
+        # appropriately.
+        if not return_to_caller:
+            msg_context = (
+                "Process did not run successfully; "
+                "returned status {0}".format(error.returncode)
+            )
+            msg = failed_command_msg(msg_context, commands, output=error.output)
+            logging.error(error)
+            logging.error(msg)
+            log_process_output(error.output)
+            fatal_error(msg)
+        status = error.returncode
+    finally:
+        hanging_timer.cancel()
+
+    if status_to_caller and output_to_caller:
+        ret_value = (status, output)
+    elif status_to_caller:
+        ret_value = status
+    elif output_to_caller:
+        ret_value = output
+    else:
+        ret_value = None
+
+    return ret_value
+
+
+def failed_command_msg(msg_context, command, output=None):
+    """Template for consistent error messages from subprocess calls.
+
+    If 'output' is given, it should provide the output from the failed
+    command
+    """
+
+    if output:
+        output_truncated = last_n_lines(
+            output, 20, truncation_message="[... Output truncated for brevity ...]"
+        )
+        errmsg = (
+            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
+        )
+    else:
+        errmsg = ""
+
+    command_str = " ".join(command)
+    errmsg += """In directory
+    {cwd}
+{context}:
+    {command}
+""".format(
+        cwd=os.getcwd(), context=msg_context, command=command_str
+    )
+
+    if output:
+        errmsg += "See above for output from failed command.\n"
+
+    return errmsg
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000000..b59ed3942c
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,693 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.dependencies]
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.2.2"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
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+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.3.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7.0"
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diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000..ac1684ea0f
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,41 @@
+[tool.poetry]
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+
+[tool.poetry.scripts]
+git-fleximod = "git_fleximod.git_fleximod:main"
+me2flexi = "git_fleximod.metoflexi:_main"
+fsspec = "fsspec.fuse:main"
+
+[tool.poetry.dependencies]
+python = "^3.8"
+GitPython = "^3.1.0"
+sphinx = "^5.0.0"
+fsspec = "^2023.12.2"
+wheel = "^0.42.0"
+pytest = "^8.0.0"
+pyfakefs = "^5.3.5"
+
+[tool.poetry.urls]
+"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
+
+[tool.pytest.ini_options]
+markers = [
+        "skip_after_first: only run on first iteration"
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
diff --git a/tbump.toml b/tbump.toml
new file mode 100644
index 0000000000..e644fc4d24
--- /dev/null
+++ b/tbump.toml
@@ -0,0 +1,43 @@
+# Uncomment this if your project is hosted on GitHub:
+github_url = "https://github.com/jedwards4b/git-fleximod/"
+
+[version]
+current = "0.7.5"
+
+# Example of a semver regexp.
+# Make sure this matches current_version before
+# using tbump
+regex = '''
+  (?P<major>\d+)
+  \.
+  (?P<minor>\d+)
+  \.
+  (?P<patch>\d+)
+  '''
+
+[git]
+message_template = "Bump to {new_version}"
+tag_template = "v{new_version}"
+
+# For each file to patch, add a [[file]] config
+# section containing the path of the file, relative to the
+# tbump.toml location.
+[[file]]
+src = "git_fleximod/cli.py"
+
+[[file]]
+src = "pyproject.toml"
+
+# You can specify a list of commands to
+# run after the files have been patched
+# and before the git commit is made
+
+#  [[before_commit]]
+#  name = "check changelog"
+#  cmd = "grep -q {new_version} Changelog.rst"
+
+# Or run some commands after the git tag and the branch
+# have been pushed:
+#  [[after_push]]
+#  name = "publish"
+#  cmd = "./publish.sh"
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000000..4d4c66c78e
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1,3 @@
+import sys, os
+
+sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000000..942a0efb97
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,138 @@
+import pytest 
+from git_fleximod.gitinterface import GitInterface
+import os
+import subprocess
+import logging
+from pathlib import Path
+
+@pytest.fixture(scope='session')
+def logger():
+    logging.basicConfig(
+        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
+    )
+    logger = logging.getLogger(__name__)
+    return logger
+
+all_repos=[
+    {"subrepo_path": "modules/test",
+     "submodule_name": "test_submodule",
+     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_submodule at tag MPIserial_2.4.0",
+     "status3" : "test_submodule at tag MPIserial_2.4.0",
+     "status4" : "test_submodule at tag MPIserial_2.4.0",
+     "gitmodules_content" : """
+    [submodule "test_submodule"]
+    path = modules/test
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelRequired
+"""},
+    {"subrepo_path": "modules/test_optional",
+     "submodule_name": "test_optional",
+     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_optional at tag MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
+     "status4" : "test_optional at tag MPIserial_2.4.0",
+     "gitmodules_content": """
+     [submodule "test_optional"]
+    path = modules/test_optional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelOptional
+"""},
+    {"subrepo_path": "modules/test_alwaysoptional",
+     "submodule_name": "test_alwaysoptional",
+     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
+     "status2" : "test_alwaysoptional at hash e5cf35c",
+     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
+     "status4" : "test_alwaysoptional at hash e5cf35c",
+     "gitmodules_content": """
+    [submodule "test_alwaysoptional"]
+    path = modules/test_alwaysoptional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = e5cf35c
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysOptional
+"""},    
+    {"subrepo_path": "modules/test_sparse",
+     "submodule_name": "test_sparse",
+     "status1" : "test_sparse at tag MPIserial_2.5.0",
+     "status2" : "test_sparse at tag MPIserial_2.5.0",
+     "status3" : "test_sparse at tag MPIserial_2.5.0",
+     "status4" : "test_sparse at tag MPIserial_2.5.0",
+     "gitmodules_content": """
+    [submodule "test_sparse"]
+    path = modules/test_sparse
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.5.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysRequired
+    fxsparse = ../.sparse_file_list
+"""},
+]
+@pytest.fixture(params=all_repos)
+
+def shared_repos(request):
+    return request.param
+
+@pytest.fixture
+def get_all_repos():
+    return all_repos
+
+def write_sparse_checkout_file(fp):
+    sparse_content = """m4
+"""
+    fp.write_text(sparse_content)
+
+@pytest.fixture
+def test_repo(shared_repos, tmp_path, logger):
+    subrepo_path = shared_repos["subrepo_path"]
+    submodule_name = shared_repos["submodule_name"]
+    test_dir = tmp_path / "testrepo"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    assert test_dir.joinpath(".git").is_dir()
+    (test_dir / "modules").mkdir()
+    if "sparse" in submodule_name:
+        (test_dir / subrepo_path).mkdir()
+        # Add the sparse checkout file
+        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
+        gitp.git_operation("add","modules/.sparse_file_list")
+    else:
+        gitp = GitInterface(str(test_dir), logger)
+        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+        assert test_dir.joinpath(".gitmodules").is_file()
+        gitp.git_operation("add",subrepo_path)
+    gitp.git_operation("commit","-a","-m","\"add submod\"")
+    test_dir2 = tmp_path / "testrepo2"
+    gitp.git_operation("clone",test_dir,test_dir2)
+    return test_dir2    
+
+
+@pytest.fixture
+def complex_repo(tmp_path, logger):
+    test_dir = tmp_path / "testcomplex"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation("fetch", "origin", "main")
+    gitp.git_operation("checkout", "main")
+    return test_dir
+    
+@pytest.fixture
+def git_fleximod():
+    def _run_fleximod(path, args, input=None):
+        cmd = ["git", "fleximod"] + args.split()
+        result = subprocess.run(cmd, cwd=path, input=input, 
+                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
+                                text=True)
+        if result.returncode:
+            print(result.stdout)
+            print(result.stderr)
+        return result
+    return _run_fleximod
+
diff --git a/tests/test_a_import.py b/tests/test_a_import.py
new file mode 100644
index 0000000000..d5ca878de5
--- /dev/null
+++ b/tests/test_a_import.py
@@ -0,0 +1,8 @@
+# pylint: disable=unused-import
+from git_fleximod import cli
+from git_fleximod import utils
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+
+def test_import():
+    print("here")
diff --git a/tests/test_b_update.py b/tests/test_b_update.py
new file mode 100644
index 0000000000..159f1cfae0
--- /dev/null
+++ b/tests/test_b_update.py
@@ -0,0 +1,26 @@
+import pytest
+from pathlib import Path
+                
+def test_basic_checkout(git_fleximod, test_repo, shared_repos):
+    # Prepare a simple .gitmodules
+    gm = shared_repos['gitmodules_content']
+    file_path = (test_repo / ".gitmodules")
+    repo_name = shared_repos["submodule_name"]
+    repo_path = shared_repos["subrepo_path"]
+
+    file_path.write_text(gm)
+    
+    # Run the command
+    result = git_fleximod(test_repo, f"update {repo_name}")
+
+    # Assertions
+    assert result.returncode == 0 
+    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
+    if "sparse" in repo_name:
+        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
+        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
+    
+    status = git_fleximod(test_repo, f"status {repo_name}")
+        
+    assert shared_repos["status2"] in status.stdout
+        
diff --git a/tests/test_c_required.py b/tests/test_c_required.py
new file mode 100644
index 0000000000..89ab8d294d
--- /dev/null
+++ b/tests/test_c_required.py
@@ -0,0 +1,30 @@
+import pytest
+from pathlib import Path
+                
+def test_required(git_fleximod, test_repo, shared_repos):
+    file_path = (test_repo / ".gitmodules")
+    gm = shared_repos["gitmodules_content"]
+    repo_name = shared_repos["submodule_name"]
+    if file_path.exists():
+        with file_path.open("r") as f:
+            gitmodules_content = f.read()
+            # add the entry if it does not exist
+            if repo_name not in gitmodules_content:
+                file_path.write_text(gitmodules_content+gm)
+            # or if it is incomplete
+            elif gm not in gitmodules_content:
+                file_path.write_text(gm)
+    else:
+        file_path.write_text(gm)
+    result = git_fleximod(test_repo, "update")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status3"] in status.stdout
+    status = git_fleximod(test_repo, f"update --optional")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
+    status = git_fleximod(test_repo, f"update {repo_name}")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
new file mode 100644
index 0000000000..fdce516274
--- /dev/null
+++ b/tests/test_d_complex.py
@@ -0,0 +1,67 @@
+import pytest
+from pathlib import Path
+from git_fleximod.gitinterface import GitInterface
+
+def test_complex_checkout(git_fleximod, complex_repo, logger):
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+    
+    # This should checkout and update test_submodule and complex_sub
+    result = git_fleximod(complex_repo, "update")    
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex")
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+    # update a single optional submodule
+
+    result = git_fleximod(complex_repo, "update ToplevelOptional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+
+
+    # Finally update optional
+    result = git_fleximod(complex_repo, "update --optional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag01" in status.stdout)
+    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
+    
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex" )
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+

From c834c30292c96bf27b63a78c0ce01be66c14f64d Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 31 May 2024 11:28:29 -0600
Subject: [PATCH 0384/1248] Draft of ChangeLog/ChageSum

---
 doc/ChangeLog | 96 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 97 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index b2f14a2c01..ee2e861be7 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,100 @@
 ===============================================================
+Tag name: ctsm5.2.007
+Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD)
+Date: Fri 31 May 2024 11:24:29 AM MDT
+One-line Summary: Rm manage_externals and update documentation accordingly
+
+Purpose and description of changes
+----------------------------------
+#2443 Jim replaced this PR with the next one
+#2559 Remove manage externals
+#2564 Replace checkout_externals with git-fleximod in documentation
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+Fixes #2537 Remove manage_externals stuff from run_sys_tests
+Fixes #2536 Update documentation for git-fleximod
+Fixes #2467 Remove references to cheyenne from the testlist
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+ ./manage_externals/checkout_externals
+ is replaced with
+ ./bin/git-fleximod
+
+Changes to documentation:
+ Accordingly
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+    [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python
+     code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system
+     tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in
+     either model output or namelists, is: create sym links pointing to the last tag's baseline directory,
+     named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT
+     doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to
+     separately run the clm_pymods test suite, and you can remove the following line.]
+
+    clm_pymods test suite on derecho - 
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ---- OK
+
+Answer changes
+--------------
+Changes answers relative to baseline: No
+
+Other details
+-------------
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+ JIM: What's the answer here?
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2443
+ https://github.com/ESCOMP/ctsm/pull/2559
+ https://github.com/ESCOMP/ctsm/pull/2564
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.006
 Originator(s): slevis (Samuel Levis)
 Date: Tue 28 May 2024 03:14:18 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 77bc8a426d..b3f1632571 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems
        ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes

From 5911cea434581d33f1a4892699f029c32132e63e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 31 May 2024 13:13:02 -0600
Subject: [PATCH 0385/1248] Move add_default() of model_year_align_cropcal to
 be with other year params.

---
 bld/CLMBuildNamelist.pm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fc80379201..bbe83a3dc5 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4225,13 +4225,16 @@ sub setup_logic_cropcal_streams {
       $log->fatal_error("If providing any crop calendar input file(s), you must provide stream_meshfile_cropcal" );
     }
 
-    # Set first and last stream years
+    # Set stream years
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal',
                 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal',
                 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_cropcal',
+                'sim_year'=>$nl_flags->{'sim_year'},
+                'sim_year_range'=>$nl_flags->{'sim_year_range'});
 
     # Check/set things if first and last years are different
     if ( $nl->get_value('stream_year_first_cropcal') !=
@@ -4242,11 +4245,6 @@ sub setup_logic_cropcal_streams {
       if ( !&string_is_undef_or_empty($gdd20_baseline_file) ) {
         $log->fatal_error("If cropcals_rx_adapt is true (i.e., stream_fldFileName_gdd20_baseline is provided), no crop calendar input is allowed to vary over time (i.e., stream_year_first_cropcal and stream_year_last_cropcal must be the same)." );
       }
-
-      # Set align year
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-                  'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'},
-                  'sim_year_range'=>$nl_flags->{'sim_year_range'});
     }
   }
 

From d89cb9d4bc3cd8ab5761d23cf398b9b682a047fa Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 31 May 2024 13:38:31 -0600
Subject: [PATCH 0386/1248] Split streams year params for swindows vs maturity
 reqts.

---
 bld/CLMBuildNamelist.pm                       | 29 +++++----
 bld/namelist_files/namelist_defaults_ctsm.xml |  9 ++-
 .../namelist_definition_ctsm.xml              | 27 ++++++--
 cime_config/SystemTests/rxcropmaturity.py     |  6 +-
 .../clm/sowingWindows/user_nl_clm             |  4 +-
 .../Running-with-custom-crop-calendars.rst    | 10 +--
 src/cpl/share_esmf/cropcalStreamMod.F90       | 63 ++++++++++++-------
 7 files changed, 93 insertions(+), 55 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index bbe83a3dc5..26725b7d96 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4226,25 +4226,30 @@ sub setup_logic_cropcal_streams {
     }
 
     # Set stream years
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal',
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal_swindows',
                 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal',
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal_swindows',
                 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_cropcal',
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_cropcal_swindows',
+                'sim_year'=>$nl_flags->{'sim_year'},
+                'sim_year_range'=>$nl_flags->{'sim_year_range'});
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal_cultivar_gdds',
+                'sim_year'=>$nl_flags->{'sim_year'},
+                'sim_year_range'=>$nl_flags->{'sim_year_range'});
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal_cultivar_gdds',
+                'sim_year'=>$nl_flags->{'sim_year'},
+                'sim_year_range'=>$nl_flags->{'sim_year_range'});
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_cropcal_cultivar_gdds',
                 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
 
-    # Check/set things if first and last years are different
-    if ( $nl->get_value('stream_year_first_cropcal') !=
-        $nl->get_value('stream_year_last_cropcal') ) {
-
-      # Do not allow maturity requirements to change over time if stream_fldFileName_gdd20_baseline is provided. That would be nonsensical.
-      # Note that this restricts sowing windows from changing over time as well, because there are not separate stream_year settings for that.
-      if ( !&string_is_undef_or_empty($gdd20_baseline_file) ) {
-        $log->fatal_error("If cropcals_rx_adapt is true (i.e., stream_fldFileName_gdd20_baseline is provided), no crop calendar input is allowed to vary over time (i.e., stream_year_first_cropcal and stream_year_last_cropcal must be the same)." );
-      }
+    # Do not allow maturity requirements to change over time if stream_fldFileName_gdd20_baseline is provided. That would be nonsensical.
+    if ( $nl->get_value('stream_year_first_cropcal_cultivar_gdds') !=
+        $nl->get_value('stream_year_last_cropcal_cultivar_gdds')
+        and !&string_is_undef_or_empty($gdd20_baseline_file) ) {
+      $log->fatal_error("If cropcals_rx_adapt is true (i.e., stream_fldFileName_gdd20_baseline is provided), baseline maturity requirements are allowed to vary over time (i.e., stream_year_first_cropcal_cultivar_gdds and stream_year_last_cropcal_cultivar_gdds must be the same)." );
     }
   }
 
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 85f37a22fd..da0a523adc 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1689,9 +1689,12 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- crop calendars: default settings -->
 <cropcals_rx>.false.</cropcals_rx>
 <cropcals_rx_adapt>.false.</cropcals_rx_adapt>
-<stream_year_first_cropcal  >2000</stream_year_first_cropcal>
-<stream_year_last_cropcal   >2000</stream_year_last_cropcal>
-<model_year_align_cropcal   >2000</model_year_align_cropcal>
+<stream_year_first_cropcal_swindows  >2000</stream_year_first_cropcal_swindows>
+<stream_year_last_cropcal_swindows   >2000</stream_year_last_cropcal_swindows>
+<model_year_align_cropcal_swindows   >2000</model_year_align_cropcal_swindows>
+<stream_year_first_cropcal_cultivar_gdds  >2000</stream_year_first_cropcal_cultivar_gdds>
+<stream_year_last_cropcal_cultivar_gdds   >2000</stream_year_last_cropcal_cultivar_gdds>
+<model_year_align_cropcal_cultivar_gdds   >2000</model_year_align_cropcal_cultivar_gdds>
 
 <!-- crop calendars: default input files -->
 <stream_fldFileName_swindow_start cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index f37ada6847..50e645519c 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1783,19 +1783,34 @@ Flag to enable prescribed crop calendars (sowing window dates and maturity requi
 Flag to enable prescribed crop calendars (sowing window dates and maturity requirement), with maturity requirement adaptive based on recent climate
 </entry>
 
-<entry id="stream_year_first_cropcal" type="integer" category="datasets"
+<entry id="stream_year_first_cropcal_swindows" type="integer" category="datasets"
        group="cropcal_streams" valid_values="" >
-First year to loop over for crop calendar data (not including gdd20_baseline file)
+First year to loop over for crop sowing windows
 </entry>
 
-<entry id="stream_year_last_cropcal" type="integer" category="datasets"
+<entry id="stream_year_last_cropcal_swindows" type="integer" category="datasets"
        group="cropcal_streams" valid_values="" >
-Last year to loop over for crop calendar data (not including gdd20_baseline file)
+Last year to loop over for crop sowing windows
 </entry>
 
-<entry id="model_year_align_cropcal" type="integer" category="datasets"
+<entry id="model_year_align_cropcal_swindows" type="integer" category="datasets"
        group="cropcal_streams" valid_values="" >
-Simulation year that aligns with stream_year_first_cropcal value
+Simulation year that aligns with stream_year_first_cropcal_swindows value
+</entry>
+
+<entry id="stream_year_first_cropcal_cultivar_gdds" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+First year to loop over for crop maturity requirements
+</entry>
+
+<entry id="stream_year_last_cropcal_cultivar_gdds" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Last year to loop over for crop maturity requirements
+</entry>
+
+<entry id="model_year_align_cropcal_cultivar_gdds" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Simulation year that aligns with stream_year_first_cropcal_cultivar_gdds value
 </entry>
 
 <entry id="allow_invalid_swindow_inputs" type="logical" category="datasets"
diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index acb63bb000..75fff8a0e0 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -360,9 +360,9 @@ def _modify_user_nl_allruns(self):
             "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
             "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
             "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
-            "stream_year_first_cropcal = 2000",
-            "stream_year_last_cropcal = 2000",
-            "model_year_align_cropcal = 2000",
+            "stream_year_first_cropcal_swindows = 2000",
+            "stream_year_last_cropcal_swindows = 2000",
+            "model_year_align_cropcal_swindows = 2000",
             " ",
             "! (h1) Annual outputs on sowing or harvest axis",
             "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'",
diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
index 03165bb306..545e5f6ebd 100644
--- a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
@@ -1,5 +1,5 @@
 stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
 stream_fldFileName_swindow_end = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
 stream_meshfile_cropcal = '$DIN_LOC_ROOT/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc'
-stream_year_first_cropcal = 2000
-stream_year_last_cropcal = 2000
+stream_year_first_cropcal_swindows = 2000
+stream_year_last_cropcal_swindows = 2000
diff --git a/doc/source/users_guide/running-special-cases/Running-with-custom-crop-calendars.rst b/doc/source/users_guide/running-special-cases/Running-with-custom-crop-calendars.rst
index b19ebcdb09..878cc0d353 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-custom-crop-calendars.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-custom-crop-calendars.rst
@@ -28,8 +28,8 @@ However, geographically- and temporally-varying maps can also be used to prescri
    stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc'
 
    ! First and last years on the sowing window datasets
-   stream_year_first_cropcal = 2000
-   stream_year_last_cropcal = 2000
+   stream_year_first_cropcal_swindows = 2000
+   stream_year_last_cropcal_swindows = 2000
 
 Sowing date
 -----------
@@ -39,7 +39,7 @@ Specific sowing *dates* can be prescribed for any crop in any gridcell by settin
 
 Maturity requirements
 ---------------------
-The heat unit accumulation required for a crop to reach maturity (and thus be harvested) is typically determined by a formula with crop-specific parameters that are specified on the parameter file. However, geographically- and temporally-varying maps of maturity requirement (in units of degree-days) can also be specified using the ``user_nl_clm`` input variable ``stream_fldFileName_cultivar_gdds``. (Note that ``stream_meshfile_cropcal``, ``stream_year_first_cropcal``, and ``stream_year_last_cropcal``---see above---are all also required.)
+The heat unit accumulation required for a crop to reach maturity (and thus be harvested) is typically determined by a formula with crop-specific parameters that are specified on the parameter file. However, geographically- and temporally-varying maps of maturity requirement (in units of degree-days) can also be specified using the ``user_nl_clm`` input variable ``stream_fldFileName_cultivar_gdds``. (Note that ``stream_meshfile_cropcal``, ``stream_year_first_cropcal_cultivar_gdds``, and ``stream_year_last_cropcal_cultivar_gdds``---see above---are all also required.)
 
 Generating maturity requirements
 --------------------------------
@@ -52,8 +52,8 @@ In a GDD-generating run, crops are planted on the specified sowing dates and are
    stream_fldFileName_swindow_start = '/path/to/sowing_date_file.nc'
    stream_fldFileName_swindow_end = '/path/to/sowing_date_file.nc'
    stream_meshfile_cropcal = '/path/to/mesh_file.nc'
-   stream_year_first_cropcal = YEAR
-   stream_year_last_cropcal = YEAR
+   stream_year_first_cropcal_swindows = YEAR
+   stream_year_last_cropcal_swindows = YEAR
 
    ! Special settings for "GDD-generating" run
    generate_crop_gdds = .true.
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 3333b6cfdc..8f444a0479 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -73,9 +73,12 @@ subroutine cropcal_init(bounds)
     !
     ! !LOCAL VARIABLES:
     integer                 :: i,n,ivt                    ! index
-    integer                 :: stream_year_first_cropcal  ! first year in crop calendar streams to use
-    integer                 :: stream_year_last_cropcal   ! last year in crop calendar streams to use
-    integer                 :: model_year_align_cropcal   ! align stream_year_first_cropcal with
+    integer                 :: stream_year_first_cropcal_swindows  ! first year in sowing window streams to use
+    integer                 :: stream_year_last_cropcal_swindows   ! last year in sowing window streams to use
+    integer                 :: model_year_align_cropcal_swindows   ! alignment year for sowing window streams
+    integer                 :: stream_year_first_cropcal_cultivar_gdds  ! first year in cultivar gdd stream to use
+    integer                 :: stream_year_last_cropcal_cultivar_gdds   ! last year in cultivar gdd stream to use
+    integer                 :: model_year_align_cropcal_cultivar_gdds   ! alignment year for cultivar gdd stream
     integer                 :: nu_nml                     ! unit for namelist file
     integer                 :: nml_error                  ! namelist i/o error flag
     character(len=CL)       :: stream_meshfile_cropcal    ! crop calendar stream meshfile
@@ -89,9 +92,12 @@ subroutine cropcal_init(bounds)
     ! deal with namelist variables here in init
     !
     namelist /cropcal_streams/         &
-         stream_year_first_cropcal,    &
-         stream_year_last_cropcal,     &
-         model_year_align_cropcal,     &
+         stream_year_first_cropcal_swindows, &
+         stream_year_last_cropcal_swindows,  &
+         model_year_align_cropcal_swindows,  &
+         stream_year_first_cropcal_cultivar_gdds, &
+         stream_year_last_cropcal_cultivar_gdds,  &
+         model_year_align_cropcal_cultivar_gdds,  &
          allow_invalid_swindow_inputs, &
          stream_fldFileName_swindow_start, &
          stream_fldFileName_swindow_end,   &
@@ -102,9 +108,12 @@ subroutine cropcal_init(bounds)
          cropcals_rx_adapt
 
     ! Default values for namelist
-    stream_year_first_cropcal  = 1      ! first year in stream to use
-    stream_year_last_cropcal   = 1      ! last  year in stream to use
-    model_year_align_cropcal   = 1      ! align stream_year_first_cropcal with this model year
+    stream_year_first_cropcal_swindows  = 1      ! first year in sowing window streams to use
+    stream_year_last_cropcal_swindows   = 1      ! last  year in sowing window streams to use
+    model_year_align_cropcal_swindows   = 1      ! alignment year for sowing window streams
+    stream_year_first_cropcal_cultivar_gdds  = 1 ! first year in cultivar gdd stream to use
+    stream_year_last_cropcal_cultivar_gdds   = 1 ! last  year in cultivar gdd stream to use
+    model_year_align_cropcal_cultivar_gdds   = 1 ! alignment year for cultivar gdd stream
     allow_invalid_swindow_inputs = .false.
     stream_meshfile_cropcal    = ''
     stream_fldFileName_swindow_start = ''
@@ -137,9 +146,12 @@ subroutine cropcal_init(bounds)
        end if
        close(nu_nml)
     endif
-    call shr_mpi_bcast(stream_year_first_cropcal  , mpicom)
-    call shr_mpi_bcast(stream_year_last_cropcal   , mpicom)
-    call shr_mpi_bcast(model_year_align_cropcal   , mpicom)
+    call shr_mpi_bcast(stream_year_first_cropcal_swindows  , mpicom)
+    call shr_mpi_bcast(stream_year_last_cropcal_swindows   , mpicom)
+    call shr_mpi_bcast(model_year_align_cropcal_swindows   , mpicom)
+    call shr_mpi_bcast(stream_year_first_cropcal_cultivar_gdds, mpicom)
+    call shr_mpi_bcast(stream_year_last_cropcal_cultivar_gdds , mpicom)
+    call shr_mpi_bcast(model_year_align_cropcal_cultivar_gdds , mpicom)
     call shr_mpi_bcast(allow_invalid_swindow_inputs, mpicom)
     call shr_mpi_bcast(stream_fldFileName_swindow_start, mpicom)
     call shr_mpi_bcast(stream_fldFileName_swindow_end  , mpicom)
@@ -150,9 +162,12 @@ subroutine cropcal_init(bounds)
     if (masterproc) then
        write(iulog,*)
        write(iulog,*) 'cropcal_stream settings:'
-       write(iulog,'(a,i8)') '  stream_year_first_cropcal  = ',stream_year_first_cropcal
-       write(iulog,'(a,i8)') '  stream_year_last_cropcal   = ',stream_year_last_cropcal
-       write(iulog,'(a,i8)') '  model_year_align_cropcal   = ',model_year_align_cropcal
+       write(iulog,'(a,i8)') '  stream_year_first_cropcal_swindows  = ',stream_year_first_cropcal_swindows
+       write(iulog,'(a,i8)') '  stream_year_last_cropcal_swindows   = ',stream_year_last_cropcal_swindows
+       write(iulog,'(a,i8)') '  model_year_align_cropcal_swindows   = ',model_year_align_cropcal_swindows
+       write(iulog,'(a,i8)') '  stream_year_first_cropcal_cultivar_gdds  = ',stream_year_first_cropcal_cultivar_gdds
+       write(iulog,'(a,i8)') '  stream_year_last_cropcal_cultivar_gdds   = ',stream_year_last_cropcal_cultivar_gdds
+       write(iulog,'(a,i8)') '  model_year_align_cropcal_cultivar_gdds   = ',model_year_align_cropcal_cultivar_gdds
        write(iulog,'(a,l1)') '  allow_invalid_swindow_inputs = ',allow_invalid_swindow_inputs
        write(iulog,'(a,a)' ) '  stream_fldFileName_swindow_start   = ',trim(stream_fldFileName_swindow_start)
        write(iulog,'(a,a)' ) '  stream_fldFileName_swindow_end     = ',trim(stream_fldFileName_swindow_end)
@@ -188,9 +203,9 @@ subroutine cropcal_init(bounds)
             stream_filenames    = (/trim(stream_fldFileName_swindow_start)/), &
             stream_fldlistFile  = stream_varnames_sdate,              &
             stream_fldListModel = stream_varnames_sdate,              &
-            stream_yearFirst    = stream_year_first_cropcal,          &
-            stream_yearLast     = stream_year_last_cropcal,           &
-            stream_yearAlign    = model_year_align_cropcal,           &
+            stream_yearFirst    = stream_year_first_cropcal_swindows, &
+            stream_yearLast     = stream_year_last_cropcal_swindows,  &
+            stream_yearAlign    = model_year_align_cropcal_swindows,           &
             stream_offset       = cropcal_offset,                     &
             stream_taxmode      = 'extend',                           &
             stream_dtlimit      = 1.0e30_r8,                          &
@@ -215,9 +230,9 @@ subroutine cropcal_init(bounds)
             stream_filenames    = (/trim(stream_fldFileName_swindow_end)/), &
             stream_fldlistFile  = stream_varnames_sdate,              &
             stream_fldListModel = stream_varnames_sdate,              &
-            stream_yearFirst    = stream_year_first_cropcal,          &
-            stream_yearLast     = stream_year_last_cropcal,           &
-            stream_yearAlign    = model_year_align_cropcal,           &
+            stream_yearFirst    = stream_year_first_cropcal_swindows, &
+            stream_yearLast     = stream_year_last_cropcal_swindows,  &
+            stream_yearAlign    = model_year_align_cropcal_swindows,  &
             stream_offset       = cropcal_offset,                     &
             stream_taxmode      = 'extend',                           &
             stream_dtlimit      = 1.0e30_r8,                          &
@@ -244,9 +259,9 @@ subroutine cropcal_init(bounds)
             stream_filenames    = (/trim(stream_fldFileName_cultivar_gdds)/), &
             stream_fldlistFile  = stream_varnames_cultivar_gdds,      &
             stream_fldListModel = stream_varnames_cultivar_gdds,      &
-            stream_yearFirst    = stream_year_first_cropcal,          &
-            stream_yearLast     = stream_year_last_cropcal,           &
-            stream_yearAlign    = model_year_align_cropcal,           &
+            stream_yearFirst    = stream_year_first_cropcal_cultivar_gdds,&
+            stream_yearLast     = stream_year_last_cropcal_cultivar_gdds, &
+            stream_yearAlign    = model_year_align_cropcal_cultivar_gdds, &
             stream_offset       = cropcal_offset,                     &
             stream_taxmode      = 'extend',                           &
             stream_dtlimit      = 1.0e30_r8,                          &

From 9a82a3fb531de7f1d31578f51091b700bccc3651 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 31 May 2024 13:54:53 -0600
Subject: [PATCH 0387/1248] Replace manage_externals with git-fleximod in an
 error message

---
 .lib/git-fleximod/git_fleximod/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
index 7cc1de38cc..64a2e70d98 100644
--- a/.lib/git-fleximod/git_fleximod/utils.py
+++ b/.lib/git-fleximod/git_fleximod/utils.py
@@ -241,7 +241,7 @@ def _hanging_msg(working_directory, command):
 has taken {hanging_sec} seconds. It may be hanging.
 
 The command will continue to run, but you may want to abort
-manage_externals with ^C and investigate. A possible cause of hangs is
+git-fleximod with ^C and investigate. A possible cause of hangs is
 when svn or git require authentication to access a private
 repository. On some systems, svn and git requests for authentication
 information will not be displayed to the user. In this case, the program

From eb27a2d79fd7d9d935b1ed9afc100fd5cefe1039 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 31 May 2024 13:55:29 -0600
Subject: [PATCH 0388/1248] Explain hard-coding of 2000 when reading GDD20
 baseline file.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 8f444a0479..413ddbefce 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -274,8 +274,9 @@ subroutine cropcal_init(bounds)
     end if
 
     ! Initialize the cdeps data type sdat_cropcal_gdd20_baseline
-    ! NOTE: stream_dtlimit 1.5 didn't work for some reason
-    !TODO SSR: Do not allow time axis length > 1
+    ! NOTE: Hard-coded to one particular year because it should NOT vary over time. Note that the
+    ! particular year chosen doesn't matter. Users can base their file on whatever baseline they
+    ! want; they just need to put 2000 on the time axis.
     if (adapt_cropcal_rx_cultivar_gdds) then
        call shr_strdata_init_from_inline(sdat_cropcal_gdd20_baseline,  &
             my_task             = iam,                                &

From c9020ec5320013121b84e4abc03bc0cf5bab2133 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 31 May 2024 13:57:53 -0600
Subject: [PATCH 0389/1248] Replace "externals directories" with "git
 submodules" in ChangeLogs

---
 doc/.ChangeLog_template | 2 +-
 doc/ChangeLog           | 9 ++++++---
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template
index f6a6dbd2f8..60a7f49288 100644
--- a/doc/.ChangeLog_template
+++ b/doc/.ChangeLog_template
@@ -157,7 +157,7 @@ Other details
 -------------
 [Remove any lines that don't apply. Remove entire section if nothing applies.]
 
-List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
 
 Pull Requests that document the changes (include PR ids):
 (https://github.com/ESCOMP/ctsm/pull)
diff --git a/doc/ChangeLog b/doc/ChangeLog
index ee2e861be7..8b6bb8f0d2 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.007
 Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD)
-Date: Fri 31 May 2024 11:24:29 AM MDT
+Date: Fri 31 May 2024 13:49:29 AM MDT
 One-line Summary: Rm manage_externals and update documentation accordingly
 
 Purpose and description of changes
@@ -85,8 +85,11 @@ Changes answers relative to baseline: No
 
 Other details
 -------------
-List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
- JIM: What's the answer here?
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ Comparing .gitmodules against Externals.cfg and Externals_CLM_cfg:
+ - cismwrap_2_2_001 from cismwrap_2_1_100
+ - cime6.0.246 from cime6.0.238_httpsbranch01
+ - cdeps1.0.34 from cdeps1.0.33
 
 Pull Requests that document the changes (include PR ids):
  https://github.com/ESCOMP/ctsm/pull/2443

From 34f2dd45ea32ea9e4a8d4e2c7d81f07806ca1710 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 31 May 2024 15:16:08 -0600
Subject: [PATCH 0390/1248] Make dns_aer a global constant

---
 src/biogeochem/DustEmisZender2003.F90 | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index 22bbbe0742..d17ebc8f1c 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -43,7 +43,7 @@ module DustEmisZender2003
   real(r8) , allocatable :: dmt_vwr(:) ![m] Mass-weighted mean diameter resolved
   real(r8) , allocatable :: stk_crc(:) ![frc] Correction to Stokes settling velocity
   real(r8) tmp1                        !Factor in saltation computation (named as in Charlie's code)
-  real(r8) dns_aer                     ![kg m-3] Aerosol density
+  real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density
   !
   ! !PUBLIC DATA TYPES:
   !
@@ -880,7 +880,6 @@ subroutine InitDustVars(this, bounds)
 
       gsd_anl = 2.0_r8      ! [frc] Geometric std dev PaG77 p. 2080 Table1
       ln_gsd = log(gsd_anl)
-      dns_aer = 2.5e+3_r8   ! [kg m-3] Aerosol density
 
       ! Set a fundamental statistic for each bin
 

From 75d7df65dc721083f19a92e801f883c6e4b5d8cb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 31 May 2024 15:07:12 -0600
Subject: [PATCH 0391/1248] Functionize UpdateAccVars_CropGDDs().

---
 src/biogeophys/TemperatureType.F90 | 121 ++++++++++++++++-------------
 1 file changed, 69 insertions(+), 52 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index ab310650c8..1b28b2e1aa 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -129,6 +129,7 @@ module TemperatureType
      procedure, public  :: InitAccBuffer
      procedure, public  :: InitAccVars
      procedure, public  :: UpdateAccVars
+     procedure, private :: UpdateAccVars_CropGDDs
 
   end type temperature_type
 
@@ -1357,6 +1358,71 @@ subroutine InitAccVars(this, bounds)
 
   end subroutine InitAccVars
 
+  subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, dtime, nstep, basetemp_int, gddx_patch)
+    !
+    ! USES
+    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
+    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    !
+    ! !ARGUMENTS
+    class(temperature_type) :: this
+    real(r8), intent(inout), pointer, dimension(:) :: rbufslp  ! temporary single level - pft level
+    integer, intent(in) :: begp, endp
+    integer, intent(in) :: month, day, secs, dtime, nstep
+    integer, intent(in) :: basetemp_int  ! Crop base temperature. Integer to avoid possible float weirdness
+    real(r8), intent(inout), pointer, dimension(:) :: gddx_patch  ! E.g., gdd0_patch
+    !
+    ! !LOCAL VARIABLES
+    real(r8) :: basetemp_r8  ! real(r8) version of basetemp for arithmetic
+    real(r8) :: max_accum    ! Maximum daily accumulation
+    character(8) :: field_name   ! E.g., GDD0
+    character(32) :: format_string
+    integer :: p, g
+
+    basetemp_r8 = real(basetemp_int, r8)
+
+    ! Get maximum daily accumulation
+    if (basetemp_int == 0) then
+       ! SSR 2024-05-31: I'm not sure why this was different for base temp 0, but I'm keeping it as I refactor into UpdateAccVars_CropGDDs()
+       max_accum = 26._r8
+    else
+       max_accum = 30._r8
+    end if
+
+    do p = begp,endp
+
+       ! Avoid unnecessary calculations over inactive points
+       if (.not. patch%active(p)) then
+          cycle
+       end if
+
+       g = patch%gridcell(p)
+       if (month==1 .and. day==1 .and. secs==dtime) then
+          rbufslp(p) = accumResetVal ! reset gdd
+       else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
+            ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
+          rbufslp(p) = max(0._r8, min(max_accum, &
+               this%t_ref2m_patch(p)-(SHR_CONST_TKFRZ + basetemp_r8))) * dtime/SHR_CONST_CDAY
+       else
+          rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
+       end if
+    end do
+
+    ! Get field name
+    if (basetemp_int < 10) then
+       format_string = "(A3,I1)"
+    else if (basetemp_int < 100) then
+       format_string = "(A3,I2)"
+    else
+       format_string = "(A3,I3)"
+    end if
+    write(field_name, format_string) "GDD",basetemp_int
+
+    ! Save
+    call update_accum_field  (trim(field_name), rbufslp, nstep)
+    call extract_accum_field (trim(field_name), gddx_patch, nstep)
+  end subroutine UpdateAccVars_CropGDDs
+
   !-----------------------------------------------------------------------
   subroutine UpdateAccVars (this, bounds)
     !
@@ -1538,63 +1604,14 @@ subroutine UpdateAccVars (this, bounds)
 
 
        ! Accumulate and extract GDD0
-
-       do p = begp,endp
-          ! Avoid unnecessary calculations over inactive points
-          if (patch%active(p)) then
-             g = patch%gridcell(p)
-             if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
-             else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
-                  ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
-                rbufslp(p) = max(0._r8, min(26._r8, this%t_ref2m_patch(p)-SHR_CONST_TKFRZ)) * dtime/SHR_CONST_CDAY
-             else
-                rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
-             end if
-          end if
-       end do
-       call update_accum_field  ('GDD0', rbufslp, nstep)
-       call extract_accum_field ('GDD0', this%gdd0_patch, nstep)
+       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 0, this%gdd0_patch)
 
        ! Accumulate and extract GDD8
-
-       do p = begp,endp
-          ! Avoid unnecessary calculations over inactive points
-          if (patch%active(p)) then
-             g = patch%gridcell(p)
-             if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
-             else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
-                  ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
-                rbufslp(p) = max(0._r8, min(30._r8, &
-                     this%t_ref2m_patch(p)-(SHR_CONST_TKFRZ + 8._r8))) * dtime/SHR_CONST_CDAY
-             else
-                rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
-             end if
-          end if
-       end do
-       call update_accum_field  ('GDD8', rbufslp, nstep)
-       call extract_accum_field ('GDD8', this%gdd8_patch, nstep)
+       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 8, this%gdd8_patch)
 
        ! Accumulate and extract GDD10
+       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 10, this%gdd10_patch)
 
-       do p = begp,endp
-          ! Avoid unnecessary calculations over inactive points
-          if (patch%active(p)) then
-             g = patch%gridcell(p)
-             if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
-             else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
-                  ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
-                rbufslp(p) = max(0._r8, min(30._r8, &
-                     this%t_ref2m_patch(p)-(SHR_CONST_TKFRZ + 10._r8))) * dtime/SHR_CONST_CDAY
-             else
-                rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
-             end if
-          end if
-       end do
-       call update_accum_field  ('GDD10', rbufslp, nstep)
-       call extract_accum_field ('GDD10', this%gdd10_patch, nstep)
 
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then

From 45aff290b33baed02b48b089858de6f0f4a89a74 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 31 May 2024 17:08:01 -0600
Subject: [PATCH 0392/1248] Optionally read/use gdd20 accum seasons from stream
 files.

---
 bld/CLMBuildNamelist.pm                       |  15 ++
 bld/namelist_files/namelist_defaults_ctsm.xml |   3 +
 .../namelist_definition_ctsm.xml              |  15 ++
 src/biogeochem/CropType.F90                   |   4 +
 src/biogeophys/TemperatureType.F90            |  54 +++--
 src/cpl/share_esmf/cropcalStreamMod.F90       | 198 ++++++++++++++++--
 src/main/clm_driver.F90                       |   2 +-
 7 files changed, 265 insertions(+), 26 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 26725b7d96..dddd17ced9 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4175,6 +4175,7 @@ sub setup_logic_cropcal_streams {
   # Set up other crop calendar parameters
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcals_rx');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcals_rx_adapt');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_gdd20_seasons');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat');
 
@@ -4185,6 +4186,20 @@ sub setup_logic_cropcal_streams {
     $log->fatal_error("cropcals_rx and cropcals_rx_adapt may not both be true" );
   }
 
+  # Add defaults if reading gdd20 seasons from stream files
+  my $stream_gdd20_seasons = $nl->get_value('stream_gdd20_seasons') ;
+  my $gdd20_season_start_file = $nl->get_value('stream_fldFileName_gdd20_season_start') ;
+  my $gdd20_season_end_file = $nl->get_value('stream_fldFileName_gdd20_season_end') ;
+  if ( &value_is_true($stream_gdd20_seasons)) {
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_season_start');
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_season_end');
+
+    # Check
+    if ( &string_is_undef_or_empty($gdd20_season_start_file) or &string_is_undef_or_empty($gdd20_season_end_file) ) {
+      $log->fatal_error("If stream_gdd20_seasons is true, gdd20 season start and end files must be provided." );
+    }
+  }
+
   # Add defaults if using prescribed crop calendars
   if ( &value_is_true($cropcals_rx) or &value_is_true($cropcals_rx_adapt) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_start');
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index da0a523adc..7e3ddb7c64 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1689,6 +1689,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- crop calendars: default settings -->
 <cropcals_rx>.false.</cropcals_rx>
 <cropcals_rx_adapt>.false.</cropcals_rx_adapt>
+<stream_gdd20_seasons>.false.</stream_gdd20_seasons>
 <stream_year_first_cropcal_swindows  >2000</stream_year_first_cropcal_swindows>
 <stream_year_last_cropcal_swindows   >2000</stream_year_last_cropcal_swindows>
 <model_year_align_cropcal_swindows   >2000</model_year_align_cropcal_swindows>
@@ -1705,6 +1706,8 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
 <stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/testdata/gdd20baseline.tmp_dontupload.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_start>
+<stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_end>
 <stream_meshfile_cropcal cropcals_rx_adapt=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>
 
 <!-- lightning streams namelist defaults -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 50e645519c..036b9aca72 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1838,6 +1838,21 @@ Filename of input stream data for cultivar growing degree-day targets
 Filename of input stream data for baseline GDD20 values
 </entry>
 
+<entry id="stream_fldFileName_gdd20_season_start" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for date (day of year) of start of gdd20 accumulation season.
+</entry>
+
+<entry id="stream_gdd20_seasons" type="logical" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Set this to true to read gdd20 accumulation season start and end dates from stream files, rather than using hard-coded hemisphere-specific "warm seasons."
+</entry>
+
+<entry id="stream_fldFileName_gdd20_season_end" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for date (day of year) of end of gdd20 accumulation season.
+</entry>
+
 <entry id="stream_meshfile_cropcal" type="char*256" category="datasets"
        input_pathname="abs" group="cropcal_streams" valid_values="" >
 Filename of input stream data for crop calendar inputs
diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index a7bccf1a73..04806f9349 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -53,6 +53,8 @@ module CropType
      integer , pointer :: rx_swindow_ends_thisyr_patch  (:,:) ! all prescribed sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings]
      real(r8), pointer :: gdd20_baseline_patch          (:)   ! GDD20 baseline for this patch (ddays) [patch]
+     integer , pointer :: gdd20_season_start_patch(:) ! gdd20 season start date for this patch (day of year) [patch]
+     integer , pointer :: gdd20_season_end_patch  (:) ! gdd20 season end   date for this patch (day of year) [patch]
      real(r8), pointer :: sdates_thisyr_patch     (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_starts_thisyr_patch(:,:) ! all sowing window start dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_ends_thisyr_patch  (:,:) ! all sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
@@ -237,6 +239,8 @@ subroutine InitAllocate(this, bounds)
     allocate(this%rx_swindow_ends_thisyr_patch(begp:endp,1:mxsowings))  ; this%rx_swindow_ends_thisyr_patch  (:,:) = -1
     allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval
     allocate(this%gdd20_baseline_patch(begp:endp)) ; this%gdd20_baseline_patch(:) = spval
+    allocate(this%gdd20_season_start_patch(begp:endp)); this%gdd20_season_start_patch(:) = -1
+    allocate(this%gdd20_season_end_patch(begp:endp))  ; this%gdd20_season_end_patch  (:) = -1
     allocate(this%sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%sdates_thisyr_patch(:,:) = spval
     allocate(this%swindow_starts_thisyr_patch(begp:endp,1:mxsowings)) ; this%swindow_starts_thisyr_patch(:,:) = spval
     allocate(this%swindow_ends_thisyr_patch  (begp:endp,1:mxsowings)) ; this%swindow_ends_thisyr_patch  (:,:) = spval
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 1b28b2e1aa..31fba16274 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1358,11 +1358,13 @@ subroutine InitAccVars(this, bounds)
 
   end subroutine InitAccVars
 
-  subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, dtime, nstep, basetemp_int, gddx_patch)
+  subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, dtime, nstep, basetemp_int, gddx_patch, crop_inst)
     !
     ! USES
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    use clm_time_manager , only : is_doy_in_interval
+    use CropType, only : crop_type
     !
     ! !ARGUMENTS
     class(temperature_type) :: this
@@ -1371,13 +1373,22 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     integer, intent(in) :: month, day, secs, dtime, nstep
     integer, intent(in) :: basetemp_int  ! Crop base temperature. Integer to avoid possible float weirdness
     real(r8), intent(inout), pointer, dimension(:) :: gddx_patch  ! E.g., gdd0_patch
+    type(crop_type), intent(inout) :: crop_inst
     !
     ! !LOCAL VARIABLES
     real(r8) :: basetemp_r8  ! real(r8) version of basetemp for arithmetic
     real(r8) :: max_accum    ! Maximum daily accumulation
     character(8) :: field_name   ! E.g., GDD0
     character(32) :: format_string
-    integer :: p, g
+    integer :: p
+    logical :: in_accumulation_season
+    real(r8) :: lat  ! latitude
+    integer :: gdd20_season_start, gdd20_season_end
+
+    associate( &
+     gdd20_season_starts => crop_inst%gdd20_season_start_patch, &
+     gdd20_season_ends   => crop_inst%gdd20_season_end_patch    &
+     )
 
     basetemp_r8 = real(basetemp_int, r8)
 
@@ -1396,15 +1407,28 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
           cycle
        end if
 
-       g = patch%gridcell(p)
+       ! Is this patch in its gdd20 accumulation season?
+       ! First, check based on latitude. This will be fallback if read-in gdd20 accumulation season is invalid.
+       lat = grc%latdeg(patch%gridcell(p))
+       in_accumulation_season = &
+          ((month > 3 .and. month < 10) .and. lat >= 0._r8) .or. &
+          ((month > 9 .or.  month < 4)  .and. lat <  0._r8)
+       ! Replace with read-in gdd20 accumulation season, if valid
+       ! (If these aren't being read in or they're invalid, they'll be -1)
+       gdd20_season_start = crop_inst%gdd20_season_start_patch(p)
+       gdd20_season_end = crop_inst%gdd20_season_end_patch(p)
+       if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
+          in_accumulation_season = is_doy_in_interval( &
+             gdd20_season_starts(p), gdd20_season_ends(p), day)
+       end if
+
        if (month==1 .and. day==1 .and. secs==dtime) then
           rbufslp(p) = accumResetVal ! reset gdd
-       else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
-            ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
+       else if (in_accumulation_season) then
           rbufslp(p) = max(0._r8, min(max_accum, &
                this%t_ref2m_patch(p)-(SHR_CONST_TKFRZ + basetemp_r8))) * dtime/SHR_CONST_CDAY
        else
-          rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
+          rbufslp(p) = 0._r8      ! keeps gdd unchanged outside accumulation season
        end if
     end do
 
@@ -1421,24 +1445,28 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     ! Save
     call update_accum_field  (trim(field_name), rbufslp, nstep)
     call extract_accum_field (trim(field_name), gddx_patch, nstep)
+
+    end associate
   end subroutine UpdateAccVars_CropGDDs
 
   !-----------------------------------------------------------------------
-  subroutine UpdateAccVars (this, bounds)
+  subroutine UpdateAccVars (this, bounds, crop_inst)
     !
     ! USES
-    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
+    use shr_const_mod    , only : SHR_CONST_TKFRZ
     use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date, is_end_curr_year
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    use accumulMod       , only : update_accum_field, extract_accum_field
     use CNSharedParamsMod, only : upper_soil_layer
+    use CropType         , only : crop_type
     !
     ! !ARGUMENTS:
     class(temperature_type)                :: this
     type(bounds_type)      , intent(in)    :: bounds
+    type(crop_type), intent(inout)         :: crop_inst
 
     !
     ! !LOCAL VARIABLES:
-    integer :: m,g,l,c,p                 ! indices
+    integer :: m,l,c,p                 ! indices
     integer :: ier                       ! error status
     integer :: dtime                     ! timestep size [seconds]
     integer :: nstep                     ! timestep number
@@ -1604,13 +1632,13 @@ subroutine UpdateAccVars (this, bounds)
 
 
        ! Accumulate and extract GDD0
-       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 0, this%gdd0_patch)
+       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 0, this%gdd0_patch, crop_inst)
 
        ! Accumulate and extract GDD8
-       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 8, this%gdd8_patch)
+       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 8, this%gdd8_patch, crop_inst)
 
        ! Accumulate and extract GDD10
-       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 10, this%gdd10_patch)
+       call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 10, this%gdd10_patch, crop_inst)
 
 
        ! Accumulate and extract running 20-year means
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 413ddbefce..8196ca1dfb 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -38,9 +38,12 @@ module cropcalStreamMod
   type(shr_strdata_type)      :: sdat_cropcal_swindow_end     ! sowing window end input data stream
   type(shr_strdata_type)      :: sdat_cropcal_cultivar_gdds   ! maturity requirement input data stream
   type(shr_strdata_type)      :: sdat_cropcal_gdd20_baseline  ! GDD20 baseline input data stream
+  type(shr_strdata_type)      :: sdat_cropcal_gdd20_season_start   ! gdd20 season start input data stream
+  type(shr_strdata_type)      :: sdat_cropcal_gdd20_season_end     ! gdd20 season end input data stream
   character(len=CS), allocatable :: stream_varnames_sdate(:) ! used for both start and end dates
   character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:)
   character(len=CS), allocatable :: stream_varnames_gdd20_baseline(:)
+  character(len=CS), allocatable :: stream_varnames_gdd20_season_enddate(:) ! start uses stream_varnames_sdate
   integer                     :: ncft               ! Number of crop functional types (excl. generic crops)
   logical                     :: allow_invalid_swindow_inputs ! Fall back on paramfile sowing windows in cases of invalid values in stream_fldFileName_swindow_start and _end?
   character(len=CL)       :: stream_fldFileName_swindow_start ! sowing window start stream filename to read
@@ -49,6 +52,10 @@ module cropcalStreamMod
   character(len=CL)       :: stream_fldFileName_gdd20_baseline ! GDD20 baseline stream filename to read
   logical                 :: cropcals_rx ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
   logical                 :: cropcals_rx_adapt ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
+  logical                 :: stream_gdd20_seasons  ! Read stream file for GDD20 accumulation seasons, instead of per-hemisphere periods
+  logical                     :: allow_invalid_gdd20_season_inputs ! Fall back on hemisphere "warm periods" in cases of invalid values in stream_fldFileName_gdd20_season_start and _end?
+  character(len=CL)       :: stream_fldFileName_gdd20_season_start ! Stream filename to read for start of gdd20 season
+  character(len=CL)       :: stream_fldFileName_gdd20_season_end ! Stream filename to read for end of gdd20 season
 
   character(len=*), parameter :: sourcefile = &
        __FILE__
@@ -105,7 +112,11 @@ subroutine cropcal_init(bounds)
          stream_fldFileName_gdd20_baseline, &
          stream_meshfile_cropcal, &
          cropcals_rx, &
-         cropcals_rx_adapt
+         cropcals_rx_adapt, &
+         stream_gdd20_seasons, &
+         allow_invalid_gdd20_season_inputs, &
+         stream_fldFileName_gdd20_season_start, &
+         stream_fldFileName_gdd20_season_end
 
     ! Default values for namelist
     stream_year_first_cropcal_swindows  = 1      ! first year in sowing window streams to use
@@ -120,16 +131,22 @@ subroutine cropcal_init(bounds)
     stream_fldFileName_swindow_end   = ''
     stream_fldFileName_cultivar_gdds = ''
     stream_fldFileName_gdd20_baseline = ''
+    stream_gdd20_seasons = .false.
+    allow_invalid_gdd20_season_inputs = .false.
+    stream_fldFileName_gdd20_season_start = ''
+    stream_fldFileName_gdd20_season_end = ''
     ! Will need modification to work with mxsowings > 1
     ncft = mxpft - npcropmin + 1 ! Ignores generic crops
     allocate(stream_varnames_sdate(ncft))
     allocate(stream_varnames_cultivar_gdds(ncft))
     allocate(stream_varnames_gdd20_baseline(ncft))
+    allocate(stream_varnames_gdd20_season_enddate(ncft))
     do n = 1,ncft
        ivt = npcropmin + n - 1
        write(stream_varnames_sdate(n),'(a,i0)') "sdate1_",ivt
        write(stream_varnames_cultivar_gdds(n),'(a,i0)') "gdd1_",ivt
        write(stream_varnames_gdd20_baseline(n),'(a,i0)') "gdd20bl_",ivt
+       write(stream_varnames_gdd20_season_enddate(n),'(a,i0)') "hdate1_",ivt
     end do
 
     ! Read cropcal_streams namelist
@@ -158,6 +175,10 @@ subroutine cropcal_init(bounds)
     call shr_mpi_bcast(stream_fldFileName_cultivar_gdds, mpicom)
     call shr_mpi_bcast(stream_fldFileName_gdd20_baseline, mpicom)
     call shr_mpi_bcast(stream_meshfile_cropcal    , mpicom)
+    call shr_mpi_bcast(stream_gdd20_seasons, mpicom)
+    call shr_mpi_bcast(allow_invalid_gdd20_season_inputs, mpicom)
+    call shr_mpi_bcast(stream_fldFileName_gdd20_season_start, mpicom)
+    call shr_mpi_bcast(stream_fldFileName_gdd20_season_end, mpicom)
 
     if (masterproc) then
        write(iulog,*)
@@ -174,9 +195,14 @@ subroutine cropcal_init(bounds)
        write(iulog,'(a,a)' ) '  stream_fldFileName_cultivar_gdds   = ',trim(stream_fldFileName_cultivar_gdds)
        write(iulog,'(a,a)' ) '  stream_fldFileName_gdd20_baseline  = ',trim(stream_fldFileName_gdd20_baseline)
        write(iulog,'(a,a)' ) '  stream_meshfile_cropcal    = ',trim(stream_meshfile_cropcal)
+       write(iulog,'(a,l1)') '  stream_gdd20_seasons  = ',stream_gdd20_seasons
+       write(iulog,'(a,l1)') '  allow_invalid_gdd20_season_inputs = ',allow_invalid_gdd20_season_inputs
+       write(iulog,'(a,a)' ) '  stream_fldFileName_gdd20_season_start  = ',stream_fldFileName_gdd20_season_start
+       write(iulog,'(a,a)' ) '  stream_fldFileName_gdd20_season_end    = ',stream_fldFileName_gdd20_season_end
        do n = 1,ncft
           write(iulog,'(a,a)' ) '  stream_varnames_sdate  = ',trim(stream_varnames_sdate(n))
           write(iulog,'(a,a)' ) '  stream_varnames_cultivar_gdds  = ',trim(stream_varnames_cultivar_gdds(n))
+          write(iulog,'(a,a)' ) '  stream_varnames_gdd20_season_enddate  = ',trim(stream_varnames_gdd20_season_enddate(n))
           write(iulog,'(a,a)' ) '  stream_varnames_gdd20_baseline  = ',trim(stream_varnames_gdd20_baseline(n))
        end do
        write(iulog,*)
@@ -304,6 +330,65 @@ subroutine cropcal_init(bounds)
        end if
     end if
 
+    if (stream_gdd20_seasons) then
+      ! Initialize the cdeps data type sdat_cropcal_gdd20_season_start
+      ! NOTE: Hard-coded to one particular year because it should NOT vary over time. Note that the
+      ! particular year chosen doesn't matter.
+      call shr_strdata_init_from_inline(sdat_cropcal_gdd20_season_start,  &
+           my_task             = iam,                                &
+           logunit             = iulog,                              &
+           compname            = 'LND',                              &
+           model_clock         = model_clock,                        &
+           model_mesh          = mesh,                               &
+           stream_meshfile     = trim(stream_meshfile_cropcal),      &
+           stream_lev_dimname  = 'null',                             &
+           stream_mapalgo      = trim(cropcal_mapalgo),              &
+           stream_filenames    = (/trim(stream_fldFileName_gdd20_season_start)/), &
+           stream_fldlistFile  = stream_varnames_sdate,              &
+           stream_fldListModel = stream_varnames_sdate,              &
+           stream_yearFirst    = 2000,                               &
+           stream_yearLast     = 2000,                               &
+           stream_yearAlign    = 2000,                               &
+           stream_offset       = cropcal_offset,                     &
+           stream_taxmode      = 'extend',                           &
+           stream_dtlimit      = 1.0e30_r8,                          &
+           stream_tintalgo     = cropcal_tintalgo,                   &
+           stream_name         = 'gdd20 season start data',         &
+           rc                  = rc)
+      if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+         call ESMF_Finalize(endflag=ESMF_END_ABORT)
+      end if
+
+      ! Initialize the cdeps data type sdat_cropcal_gdd20_season_end
+      ! NOTE: Hard-coded to one particular year because it should NOT vary over time. Note that the
+      ! particular year chosen doesn't matter.
+      call shr_strdata_init_from_inline(sdat_cropcal_gdd20_season_end,  &
+           my_task             = iam,                                &
+           logunit             = iulog,                              &
+           compname            = 'LND',                              &
+           model_clock         = model_clock,                        &
+           model_mesh          = mesh,                               &
+           stream_meshfile     = trim(stream_meshfile_cropcal),      &
+           stream_lev_dimname  = 'null',                             &
+           stream_mapalgo      = trim(cropcal_mapalgo),              &
+           stream_filenames    = (/trim(stream_fldFileName_gdd20_season_end)/), &
+           stream_fldlistFile  = stream_varnames_gdd20_season_enddate, &
+           stream_fldListModel = stream_varnames_gdd20_season_enddate, &
+           stream_yearFirst    = 2000,                               &
+           stream_yearLast     = 2000,                               &
+           stream_yearAlign    = 2000,                               &
+           stream_offset       = cropcal_offset,                     &
+           stream_taxmode      = 'extend',                           &
+           stream_dtlimit      = 1.0e30_r8,                          &
+           stream_tintalgo     = cropcal_tintalgo,                   &
+           stream_name         = 'gdd20 season start data',         &
+           rc                  = rc)
+      if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+         call ESMF_Finalize(endflag=ESMF_END_ABORT)
+      end if
+
+   end if
+
   end subroutine cropcal_init
 
   !================================================================
@@ -347,7 +432,10 @@ subroutine cropcal_advance( bounds )
        end if
     end if
 
-    ! GDD20 baseline values do not have an associated time axis and thus will not be advanced here
+    ! The following should not have an associated time axis and thus will not be advanced here:
+    ! - GDD20 baseline values
+    ! - GDD20 season start dates
+    ! - GDD20 season end dates
 
     if ( .not. allocated(g_to_ig) )then
        allocate (g_to_ig(bounds%begg:bounds%endg) )
@@ -393,15 +481,21 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     real(r8), pointer :: dataptr1d_swindow_end  (:)
     real(r8), pointer :: dataptr1d_cultivar_gdds(:)
     real(r8), pointer :: dataptr1d_gdd20_baseline(:)
+    real(r8), pointer :: dataptr1d_gdd20_season_start(:)
+    real(r8), pointer :: dataptr1d_gdd20_season_end  (:)
     real(r8), pointer :: dataptr2d_swindow_start(:,:)
     real(r8), pointer :: dataptr2d_swindow_end  (:,:)
     real(r8), pointer :: dataptr2d_cultivar_gdds(:,:)
     real(r8), pointer :: dataptr2d_gdd20_baseline(:,:)
+    real(r8), pointer :: dataptr2d_gdd20_season_start(:,:)
+    real(r8), pointer :: dataptr2d_gdd20_season_end  (:,:)
     !-----------------------------------------------------------------------
 
     associate( &
-         starts => crop_inst%rx_swindow_starts_thisyr_patch, &
-         ends   => crop_inst%rx_swindow_ends_thisyr_patch    &
+         swindow_starts => crop_inst%rx_swindow_starts_thisyr_patch, &
+         swindow_ends   => crop_inst%rx_swindow_ends_thisyr_patch,   &
+         gdd20_season_starts => crop_inst%gdd20_season_start_patch, &
+         gdd20_season_ends   => crop_inst%gdd20_season_end_patch    &
          )
 
     SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
@@ -459,8 +553,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
              n = ivt - npcropmin + 1
              ! vegetated pft
              ig = g_to_ig(patch%gridcell(p))
-             starts(p,1) = dataptr2d_swindow_start(ig,n)
-             ends(p,1)   = dataptr2d_swindow_end  (ig,n)
+             swindow_starts(p,1) = dataptr2d_swindow_start(ig,n)
+             swindow_ends(p,1)   = dataptr2d_swindow_end  (ig,n)
          else
              write(iulog,'(a,i0)') 'cropcal_interp(), prescribed sowing windows: Crop patch has ivt ',ivt
              call ESMF_Finalize(endflag=ESMF_END_ABORT)
@@ -469,23 +563,23 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
        ! Ensure that, if mxsowings > 1, sowing windows are ordered such that ENDS are monotonically increasing. This is necessary because of how get_swindow() works.
        if (mxsowings > 1) then
-           if (any(ends(begp:endp,2:mxsowings) <= ends(begp:endp,1:mxsowings-1) .and. &
-                   ends(begp:endp,2:mxsowings) >= 1)) then
+           if (any(swindow_ends(begp:endp,2:mxsowings) <= swindow_ends(begp:endp,1:mxsowings-1) .and. &
+                   swindow_ends(begp:endp,2:mxsowings) >= 1)) then
                write(iulog, *) 'Sowing window inputs must be ordered such that end dates are monotonically increasing.'
                call ESMF_Finalize(endflag=ESMF_END_ABORT)
            end if
        end if
 
        ! Handle invalid sowing window values
-       if (any(starts(begp:endp,:) < 1 .or. ends(begp:endp,:) < 1)) then 
+       if (any(swindow_starts(begp:endp,:) < 1 .or. swindow_ends(begp:endp,:) < 1)) then
            ! Fail if not allowing fallback to paramfile sowing windows
-           if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts(begp:endp,:) < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then
+           if ((.not. allow_invalid_swindow_inputs) .and. any(all(swindow_starts(begp:endp,:) < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then
                write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.'
                write(iulog, *) 'Affected crops:'
                do ivt = npcropmin, mxpft
                    do fp = 1, num_pcropp
                        p = filter_pcropp(fp)
-                       if (ivt == patch%itype(p) .and. patch%wtgcell(p) > 0._r8 .and. all(starts(p,:) < 1)) then
+                       if (ivt == patch%itype(p) .and. patch%wtgcell(p) > 0._r8 .and. all(swindow_starts(p,:) < 1)) then
                            write(iulog, *) '    ',pftname(ivt),'  (',ivt,')'
                            exit  ! Stop looking for patches of this type
                        end if
@@ -494,7 +588,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
                call ESMF_Finalize(endflag=ESMF_END_ABORT)
 
            ! Fail if a sowing window start date is prescribed without an end date (or vice versa)
-           else if (any((starts(begp:endp,:) >= 1 .and. ends(begp:endp,:) < 1) .or. (starts(begp:endp,:) < 1 .and. ends(begp:endp,:) >= 1))) then
+           else if (any((swindow_starts(begp:endp,:) >= 1 .and. swindow_ends(begp:endp,:) < 1) .or. (swindow_starts(begp:endp,:) < 1 .and. swindow_ends(begp:endp,:) >= 1))) then
                write(iulog, *) 'Every prescribed sowing window start date must have a corresponding end date.'
                call ESMF_Finalize(endflag=ESMF_END_ABORT)
            end if
@@ -613,6 +707,86 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
   deallocate(dataptr2d_gdd20_baseline)
 
 
+  ! Read prescribed gdd20 season start dates from input files
+  allocate(dataptr2d_gdd20_season_start(lsize, ncft))
+  dataptr2d_gdd20_season_start(:,:) = -1._r8
+  allocate(dataptr2d_gdd20_season_end  (lsize, ncft))
+  dataptr2d_gdd20_season_end(:,:) = -1._r8
+  if (stream_gdd20_seasons .and. init) then
+     ! Starting with npcropmin will skip generic crops
+     do n = 1, ncft
+        call dshr_fldbun_getFldPtr(sdat_cropcal_gdd20_season_start%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), &
+             fldptr1=dataptr1d_gdd20_season_start,  rc=rc)
+        if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+           call ESMF_Finalize(endflag=ESMF_END_ABORT)
+        end if
+        call dshr_fldbun_getFldPtr(sdat_cropcal_gdd20_season_end%pstrm(1)%fldbun_model, trim(stream_varnames_gdd20_season_enddate(n)), &
+             fldptr1=dataptr1d_gdd20_season_end,  rc=rc)
+        if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+           call ESMF_Finalize(endflag=ESMF_END_ABORT)
+        end if
+        ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
+        ! So an explicit loop is required here
+        do g = 1,lsize
+
+           ! If read-in value is invalid, set to -1. Will be handled later in this subroutine.
+           if (dataptr1d_gdd20_season_start(g) <= 0 .or. dataptr1d_gdd20_season_start(g) > 366 &
+               .or. dataptr1d_gdd20_season_end(g) <= 0 .or. dataptr1d_gdd20_season_end(g) > 366) then
+              dataptr1d_gdd20_season_start(g) = -1
+              dataptr1d_gdd20_season_end  (g) = -1
+           end if
+
+          dataptr2d_gdd20_season_start(g,n) = dataptr1d_gdd20_season_start(g)
+          dataptr2d_gdd20_season_end  (g,n) = dataptr1d_gdd20_season_end  (g)
+        end do
+     end do
+
+     ! Set gdd20 season for each gridcell/patch combination
+     do fp = 1, num_pcropp
+        p = filter_pcropp(fp)
+        ivt = patch%itype(p)
+        ! Will skip generic crops
+        if (ivt >= npcropmin) then
+           n = ivt - npcropmin + 1
+           ! vegetated pft
+           ig = g_to_ig(patch%gridcell(p))
+           gdd20_season_starts(p) = dataptr2d_gdd20_season_start(ig,n)
+           gdd20_season_ends(p)   = dataptr2d_gdd20_season_end  (ig,n)
+       else
+           write(iulog,'(a,i0)') 'cropcal_interp(), gdd20 seasons: Crop patch has ivt ',ivt
+           call ESMF_Finalize(endflag=ESMF_END_ABORT)
+        endif
+     end do
+
+     ! Handle invalid gdd20 season values
+     if (any(gdd20_season_starts(begp:endp) < 1 .or. gdd20_season_ends(begp:endp) < 1)) then
+         ! Fail if not allowing fallback to paramfile sowing windows
+         if ((.not. allow_invalid_gdd20_season_inputs) .and. any(gdd20_season_starts(begp:endp) < 1 .and. patch%wtgcell(begp:endp) > 0._r8 .and. patch%itype(begp:endp) >= npcropmin)) then
+             write(iulog, *) 'At least one crop in one gridcell has invalid gdd20 season start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_gdd20_season_inputs to .true.'
+             write(iulog, *) 'Affected crops:'
+             do ivt = npcropmin, mxpft
+                 do fp = 1, num_pcropp
+                     p = filter_pcropp(fp)
+                     if (ivt == patch%itype(p) .and. patch%wtgcell(p) > 0._r8 .and. gdd20_season_starts(p) < 1) then
+                         write(iulog, *) '    ',pftname(ivt),'  (',ivt,')'
+                         exit  ! Stop looking for patches of this type
+                     end if
+                 end do
+             end do
+             call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+         ! Fail if a gdd20 season start date is given without an end date (or vice versa)
+         else if (any((gdd20_season_starts(begp:endp) >= 1 .and. gdd20_season_ends(begp:endp) < 1) .or. (gdd20_season_starts(begp:endp) < 1 .and. gdd20_season_ends(begp:endp) >= 1))) then
+             write(iulog, *) 'Every gdd20 season start date must have a corresponding end date.'
+             call ESMF_Finalize(endflag=ESMF_END_ABORT)
+         end if
+     end if
+
+  end if ! stream_gdd20_seasons and init
+  deallocate(dataptr2d_gdd20_season_start)
+  deallocate(dataptr2d_gdd20_season_end)
+
+
    end associate
 
   end subroutine cropcal_interp
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index 2a3cef4b8b..e660ab9d8d 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -1374,7 +1374,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
 
        call atm2lnd_inst%UpdateAccVars(bounds_proc)
 
-       call temperature_inst%UpdateAccVars(bounds_proc)
+       call temperature_inst%UpdateAccVars(bounds_proc, crop_inst)
 
        call canopystate_inst%UpdateAccVars(bounds_proc)
 

From 0feff1f3d641ec47c616d41d8c6fe3e4b9208db1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 31 May 2024 18:26:51 -0600
Subject: [PATCH 0393/1248] Fix check of invalid swindow inputs.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 8196ca1dfb..4c4925f88e 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -573,7 +573,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
        ! Handle invalid sowing window values
        if (any(swindow_starts(begp:endp,:) < 1 .or. swindow_ends(begp:endp,:) < 1)) then
            ! Fail if not allowing fallback to paramfile sowing windows
-           if ((.not. allow_invalid_swindow_inputs) .and. any(all(swindow_starts(begp:endp,:) < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then
+           if ((.not. allow_invalid_swindow_inputs) .and. any(all(swindow_starts(begp:endp,:) < 1, dim=2) .and. patch%wtgcell(begp:endp) > 0._r8 .and. patch%itype(begp:endp) >= npcropmin)) then
                write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.'
                write(iulog, *) 'Affected crops:'
                do ivt = npcropmin, mxpft

From 3729b6db9f2139399618e39c4c48084144eecf12 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 31 May 2024 22:35:35 -0600
Subject: [PATCH 0394/1248] Add RxCropCalsAdaptGGCMI testmod and test.

---
 cime_config/testdefs/testlist_clm.xml                    | 9 +++++++++
 .../clm/RxCropCalsAdaptGGCMI/include_user_mods           | 1 +
 .../testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm   | 2 ++
 3 files changed, 12 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index bf763c4775..edb932d24e 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3737,5 +3737,14 @@
     </options>
   </test>
 
+  <test name="SMS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:00:00</option>
+    </options>
+  </test>
+
 
 </testlist>
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
new file mode 100644
index 0000000000..af5fe8591e
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
@@ -0,0 +1 @@
+../RxCropCalsAdapt
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
new file mode 100644
index 0000000000..fa0e4ec663
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
@@ -0,0 +1,2 @@
+
+stream_gdd20_seasons = .true.

From d020eada257e99055b2b90600f78c630286492c1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 09:10:40 -0600
Subject: [PATCH 0395/1248] Fix check that gdd20 season files are provided.

---
 bld/CLMBuildNamelist.pm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index dddd17ced9..d5c2ffd54f 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4188,14 +4188,17 @@ sub setup_logic_cropcal_streams {
 
   # Add defaults if reading gdd20 seasons from stream files
   my $stream_gdd20_seasons = $nl->get_value('stream_gdd20_seasons') ;
-  my $gdd20_season_start_file = $nl->get_value('stream_fldFileName_gdd20_season_start') ;
-  my $gdd20_season_end_file = $nl->get_value('stream_fldFileName_gdd20_season_end') ;
   if ( &value_is_true($stream_gdd20_seasons)) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_season_start');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_season_end');
 
     # Check
+    my $gdd20_season_start_file = $nl->get_value('stream_fldFileName_gdd20_season_start') ;
+    my $gdd20_season_end_file = $nl->get_value('stream_fldFileName_gdd20_season_end') ;
     if ( &string_is_undef_or_empty($gdd20_season_start_file) or &string_is_undef_or_empty($gdd20_season_end_file) ) {
+      $log->message($gdd20_season_start_file);
+      $log->message('abcd');
+      $log->message($gdd20_season_end_file);
       $log->fatal_error("If stream_gdd20_seasons is true, gdd20 season start and end files must be provided." );
     }
   }

From 42b0dbb9f7e02ab2138710904af129704867e466 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 09:11:09 -0600
Subject: [PATCH 0396/1248] Minor rearrangement in cropcal namelist definition.

---
 bld/namelist_files/namelist_definition_ctsm.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 036b9aca72..5b6dcef87e 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1838,16 +1838,16 @@ Filename of input stream data for cultivar growing degree-day targets
 Filename of input stream data for baseline GDD20 values
 </entry>
 
-<entry id="stream_fldFileName_gdd20_season_start" type="char*256(30)" category="datasets"
-       input_pathname="abs" group="cropcal_streams" valid_values="" >
-Filename of input stream data for date (day of year) of start of gdd20 accumulation season.
-</entry>
-
 <entry id="stream_gdd20_seasons" type="logical" category="datasets"
        group="cropcal_streams" valid_values="" >
 Set this to true to read gdd20 accumulation season start and end dates from stream files, rather than using hard-coded hemisphere-specific "warm seasons."
 </entry>
 
+<entry id="stream_fldFileName_gdd20_season_start" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for date (day of year) of start of gdd20 accumulation season.
+</entry>
+
 <entry id="stream_fldFileName_gdd20_season_end" type="char*256(30)" category="datasets"
        input_pathname="abs" group="cropcal_streams" valid_values="" >
 Filename of input stream data for date (day of year) of end of gdd20 accumulation season.

From 92555b9c394a4542ff7412335a459dfab57a8979 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 12:13:20 -0600
Subject: [PATCH 0397/1248] generate_gdd20_baseline.py now saves
 NETCDF3_CLASSIC.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index d28bfda0e7..7b5fd625d6 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -226,7 +226,7 @@ def generate_gdd20_baseline(input_files, output_file, author):
         ds_out[var_out] = this_da
 
     # Save
-    ds_out.to_netcdf(output_file)
+    ds_out.to_netcdf(output_file, format="NETCDF3_CLASSIC")
 
     print("Done!")
 

From 30eb31ce8e92a05bd104268e01e3d62b964ee486 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 12:16:49 -0600
Subject: [PATCH 0398/1248] Update default to point to classic version.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 7e3ddb7c64..2683c2e535 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1705,7 +1705,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
 <stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
-<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/testdata/gdd20baseline.tmp_dontupload.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/testdata/gdd20baseline.tmp_dontupload.classic.nc</stream_fldFileName_gdd20_baseline>
 <stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_start>
 <stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_end>
 <stream_meshfile_cropcal cropcals_rx_adapt=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>

From a6e2c1e23964b6e9c3bf35d1778a14187a0b62e9 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 12:59:29 -0600
Subject: [PATCH 0399/1248] Add allow_invalid_gdd20_season_inputs to namelist
 XML.

---
 bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 5b6dcef87e..675c912900 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1843,6 +1843,11 @@ Filename of input stream data for baseline GDD20 values
 Set this to true to read gdd20 accumulation season start and end dates from stream files, rather than using hard-coded hemisphere-specific "warm seasons."
 </entry>
 
+<entry id="allow_invalid_gdd20_season_inputs" type="logical" category="datasets"
+       group="cropcal_streams" valid_values="" >
+By default, a value in stream_fldFileName_gdd20_season_start or _end outside the range [1, 365] (or 366 in leap years) will cause the run to fail. Set this to .true. to instead have such cells fall back to the hard-coded hemisphere-specific "warm seasons."
+</entry>
+
 <entry id="stream_fldFileName_gdd20_season_start" type="char*256(30)" category="datasets"
        input_pathname="abs" group="cropcal_streams" valid_values="" >
 Filename of input stream data for date (day of year) of start of gdd20 accumulation season.

From 9f04d71e0ac7f5e4f0bcadd195281dfcc2134f81 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 13:22:59 -0600
Subject: [PATCH 0400/1248] Update missing values from
 generate_gdd20_baseline.py.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 7b5fd625d6..fd56d61550 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -20,7 +20,8 @@
 
 VAR_LIST_IN = ["GDD0", "GDD8", "GDD10"]
 VAR_LIST_IN = [x + "20" for x in VAR_LIST_IN]  # TODO: Delete this once using the right variables
-MISSING_FILL = -1  # Something negative to ensure that gddmaturity never changes (see PlantCrop)
+MISSING_FILL = -1  # Something impossible to ensure that you can mark it as a missing value, to be
+# bilinear-interpolated
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
 # shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
 
@@ -211,7 +212,8 @@ def generate_gdd20_baseline(input_files, output_file, author):
             long_name = "Dummy GDD20"
             print("   dummy GDD20")
         else:
-            this_da = ds_in[gddn].fillna(MISSING_FILL)
+            # this_da = ds_in[gddn].fillna(MISSING_FILL)
+            this_da = ds_in[gddn]
             this_da = _add_time_axis(this_da)
             long_name = gddn
             print(f"   {gddn}")
@@ -219,6 +221,7 @@ def generate_gdd20_baseline(input_files, output_file, author):
         # Add attributes
         this_da.attrs["long_name"] = long_name + f" baseline for {cft_str}"
         this_da.attrs["units"] = "°C days"
+        # this_da.attrs["_FillValue"] = MISSING_FILL
 
         # Copy that to ds_out
         var_out = _get_output_varname(cft_str)

From 625fd5e7b9eebc61bf8e93824e92a3079bf937cd Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 13:23:16 -0600
Subject: [PATCH 0401/1248] RxCropCalsAdaptGGCMI now uses
 allow_invalid_gdd20_season_inputs.

---
 .../testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
index fa0e4ec663..42e57a675c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
@@ -1,2 +1,4 @@
 
 stream_gdd20_seasons = .true.
+!TODO SSR: Try without this once you have half-degree inputs
+allow_invalid_gdd20_season_inputs = .true.

From 0156d1aa928f5bc002c1eb8508962138c76f4a1d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 13:25:02 -0600
Subject: [PATCH 0402/1248] Move hist_addfld1d() for GDD0 to be with its
 siblings.

---
 src/biogeophys/TemperatureType.F90 | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 31fba16274..89dfd11074 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -597,9 +597,7 @@ subroutine InitHistory(this, bounds, is_simple_buildtemp, is_prog_buildtemp )
        call hist_addfld1d (fname='GDD0', units='ddays', &
             avgflag='A', long_name='Growing degree days base  0C from planting', &
             ptr_patch=this%gdd0_patch, default='inactive')
-    end if
 
-    if (use_crop) then
        this%gdd8_patch(begp:endp) = spval
        call hist_addfld1d (fname='GDD8', units='ddays', &
             avgflag='A', long_name='Growing degree days base  8C from planting', &

From b7c34ffcd7b4421f5266051d3bb7aeef2f790744 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 13:34:16 -0600
Subject: [PATCH 0403/1248] Add max versions of GDD season accum outputs.

---
 src/biogeophys/TemperatureType.F90 | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 89dfd11074..f8d5206a1e 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -608,6 +608,21 @@ subroutine InitHistory(this, bounds, is_simple_buildtemp, is_prog_buildtemp )
             avgflag='A', long_name='Growing degree days base 10C from planting', &
             ptr_patch=this%gdd10_patch, default='inactive')
 
+       this%gdd0_patch(begp:endp) = spval
+       call hist_addfld1d (fname='GDD0X', units='ddays', &
+            avgflag='X', long_name='Growing degree days base  0C from planting, max', &
+            ptr_patch=this%gdd0_patch, default='inactive')
+
+       this%gdd8_patch(begp:endp) = spval
+       call hist_addfld1d (fname='GDD8X', units='ddays', &
+            avgflag='X', long_name='Growing degree days base  8C from planting, max', &
+            ptr_patch=this%gdd8_patch, default='inactive')
+
+       this%gdd10_patch(begp:endp) = spval
+       call hist_addfld1d (fname='GDD10X', units='ddays', &
+            avgflag='X', long_name='Growing degree days base 10C from planting, max', &
+            ptr_patch=this%gdd10_patch, default='inactive')
+
        this%gdd020_patch(begp:endp) = spval
        call hist_addfld1d (fname='GDD020', units='ddays', &
             avgflag='A', long_name='Twenty year average of growing degree days base  0C from planting', &

From 6fbb432e97389e4c0bde8aad7d8da77646c98936 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 1 Jun 2024 15:52:19 -0600
Subject: [PATCH 0404/1248] Move tmp1 to inside the dustemis type

---
 src/biogeochem/DustEmisZender2003.F90 | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index d17ebc8f1c..a2d4ed2d26 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -37,18 +37,18 @@ module DustEmisZender2003
   implicit none
   private
   !
-  ! !PUBLIC DATA:
+  ! !PRIVATE DATA:
   !
-  real(r8) , allocatable :: ovr_src_snk_mss(:,:)
+  real(r8) , allocatable :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin
   real(r8) , allocatable :: dmt_vwr(:) ![m] Mass-weighted mean diameter resolved
   real(r8) , allocatable :: stk_crc(:) ![frc] Correction to Stokes settling velocity
-  real(r8) tmp1                        !Factor in saltation computation (named as in Charlie's code)
   real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density
   !
   ! !PUBLIC DATA TYPES:
   !
   type, public :: dust_type
 
+     real(r8), private          :: tmp1                            ! Factor in saltation computation (named as in Charlie's code)
      real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) 
      real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:)   ! total dust flux into atmosphere
      real(r8), pointer, private :: vlc_trb_patch             (:,:) ! turbulent deposition velocity  (m/s) (ndst) 
@@ -293,7 +293,7 @@ subroutine GetConstVars(this, SaltationFactor )
     class(dust_type)  , intent(in)  :: this
     real(r8)          , intent(out) :: SaltationFactor
 
-    SaltationFactor = tmp1
+    SaltationFactor = this%tmp1
   end subroutine GetConstVars
 
   !------------------------------------------------------------------------
@@ -505,7 +505,7 @@ subroutine DustEmission (this, bounds, &
             !          subr. wnd_frc_thr_slt_get which computes dry threshold
             !          friction velocity for saltation
 
-            wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
+            wnd_frc_thr_slt = this%tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
 
             ! reset these variables which will be updated in the following if-block
 
@@ -846,7 +846,7 @@ subroutine InitDustVars(this, bounds)
 
       icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8))
       dns_fct = dns_slt * grav * dmt_slt_opt
-      tmp1 = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc)
+      this%tmp1 = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc)
 
       ! Introducing particle diameter. Needed by atm model and by dry dep model.
       ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl,

From 1cf137bf57ed63aa9f9716f6425917268e13e4e4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 1 Jun 2024 16:05:33 -0600
Subject: [PATCH 0405/1248] Move three module variables to inside the data type

---
 src/biogeochem/DustEmisZender2003.F90 | 54 +++++++++++++--------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index a2d4ed2d26..6adbac8521 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -39,15 +39,15 @@ module DustEmisZender2003
   !
   ! !PRIVATE DATA:
   !
-  real(r8) , allocatable :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin
-  real(r8) , allocatable :: dmt_vwr(:) ![m] Mass-weighted mean diameter resolved
-  real(r8) , allocatable :: stk_crc(:) ![frc] Correction to Stokes settling velocity
   real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density
   !
   ! !PUBLIC DATA TYPES:
   !
   type, public :: dust_type
 
+     real(r8) , allocatable, private :: ovr_src_snk_mss(:,:)       ! overlap factors between the source and sin
+     real(r8) , allocatable, private :: dmt_vwr(:)                 ! [m] Mass-weighted mean diameter resolved
+     real(r8) , allocatable, private :: stk_crc(:)                 ! [frc] Correction to Stokes settling velocity
      real(r8), private          :: tmp1                            ! Factor in saltation computation (named as in Charlie's code)
      real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) 
      real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:)   ! total dust flux into atmosphere
@@ -116,9 +116,9 @@ subroutine Clean(this)
    deallocate(this%vlc_trb_4_patch)
    deallocate(this%mbl_bsn_fct_col)
 
-   deallocate (ovr_src_snk_mss)
-   deallocate (dmt_vwr)
-   deallocate (stk_crc)
+   deallocate (this%ovr_src_snk_mss)
+   deallocate (this%dmt_vwr)
+   deallocate (this%stk_crc)
 
  end subroutine Clean
 
@@ -146,6 +146,11 @@ subroutine InitAllocate(this, bounds)
     allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
     allocate(this%mbl_bsn_fct_col           (begc:endc))        ; this%mbl_bsn_fct_col           (:)   = nan
 
+    allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst))           ; this%ovr_src_snk_mss           (:,:) = nan
+    allocate (this%dmt_vwr(ndst))                               ; this%dmt_vwr                   (:)   = nan
+    allocate (this%stk_crc(ndst))                               ; this%stk_crc                   (:)   = nan
+
+
   end subroutine InitAllocate
 
   !------------------------------------------------------------------------
@@ -564,7 +569,7 @@ subroutine DustEmission (this, bounds, &
             do fp = 1,num_nolakep
                p = filter_nolakep(fp)
                if (lnd_frc_mbl(p) > 0.0_r8) then
-                  flx_mss_vrt_dst(p,n) = flx_mss_vrt_dst(p,n) +  ovr_src_snk_mss(m,n) * flx_mss_vrt_dst_ttl(p)
+                  flx_mss_vrt_dst(p,n) = flx_mss_vrt_dst(p,n) +  this%ovr_src_snk_mss(m,n) * flx_mss_vrt_dst_ttl(p)
                end if
             end do
          end do
@@ -663,11 +668,11 @@ subroutine DustDryDep (this, bounds, &
 
             do m = 1, ndst
                slp_crc(p,m) = 1.0_r8 + 2.0_r8 * mfp_atm * &
-                    (1.257_r8+0.4_r8*exp(-1.1_r8*dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
-                    dmt_vwr(m)   ![frc] Slip correction factor SeP97 p. 464
-               vlc_grv(p,m) = (1.0_r8/18.0_r8) * dmt_vwr(m) * dmt_vwr(m) * dns_aer * &
+                    (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
+                    this%dmt_vwr(m)   ![frc] Slip correction factor SeP97 p. 464
+               vlc_grv(p,m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * &
                     grav * slp_crc(p,m) / vsc_dyn_atm(p)   ![m s-1] Stokes' settling velocity SeP97 p. 466
-               vlc_grv(p,m) = vlc_grv(p,m) * stk_crc(m)    ![m s-1] Correction to Stokes settling velocity
+               vlc_grv(p,m) = vlc_grv(p,m) * this%stk_crc(m)    ![m s-1] Correction to Stokes settling velocity
             end do
          end if
       end do
@@ -680,7 +685,7 @@ subroutine DustDryDep (this, bounds, &
 
                stk_nbr = vlc_grv(p,m) * fv(p) * fv(p) / (grav * vsc_knm_atm(p))  ![frc] SeP97 p.965
                dff_aer = SHR_CONST_BOLTZ * forc_t(c) * slp_crc(p,m) / &          ![m2 s-1]
-                    (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * dmt_vwr(m))          !SeP97 p.474
+                    (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * this%dmt_vwr(m))     !SeP97 p.474
                shm_nbr = vsc_knm_atm(p) / dff_aer                                ![frc] SeP97 p.972
                shm_nbr_xpn = shm_nbr_xpn_lnd                                     ![frc]
 
@@ -796,11 +801,6 @@ subroutine InitDustVars(this, bounds)
     real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles
     !------------------------------------------------------------------------
 
-      ! allocate module variable
-      allocate (ovr_src_snk_mss(dst_src_nbr,ndst))  
-      allocate (dmt_vwr(ndst))
-      allocate (stk_crc(ndst))
-
       ! allocate local variable
       allocate (dmt_vma_src(dst_src_nbr))  
       allocate (gsd_anl_src(dst_src_nbr))  
@@ -824,7 +824,7 @@ subroutine InitDustVars(this, bounds)
             lndminjovrdmdni = log(dmt_grd(n  )/dmt_vma_src(m))
             ovr_src_snk_frc = 0.5_r8 * (erf(lndmaxjovrdmdni/sqrt2lngsdi) - &
                  erf(lndminjovrdmdni/sqrt2lngsdi))
-            ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m)
+            this%ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m)
          end do
       end do
 
@@ -914,7 +914,7 @@ subroutine InitDustVars(this, bounds)
          end do
 
          lngsdsqrttwopi_rcp = 1.0_r8 / (ln_gsd*sqrt(2.0_r8*SHR_CONST_PI))
-         dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved
+         this%dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved
          vlm_rsl(n) = 0.0_r8 ! [m3 m-3] Volume concentration resolved
 
          do m = 1, sz_nbr
@@ -924,7 +924,7 @@ subroutine InitDustVars(this, bounds)
             lgn_dst = lngsdsqrttwopi_rcp * exp(-0.5_r8*tmp*tmp) / sz_ctr(m)
 
             ! Integrate moments of size distribution
-            dmt_vwr(n) = dmt_vwr(n) + sz_ctr(m) *                    &
+            this%dmt_vwr(n) = this%dmt_vwr(n) + sz_ctr(m) *                    &
                  SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume
                  lgn_dst * sz_dlt(m)                ![# m-3] Number concentrn
             vlm_rsl(n) = vlm_rsl(n) +                                &
@@ -933,7 +933,7 @@ subroutine InitDustVars(this, bounds)
 
          end do
 
-         dmt_vwr(n) = dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved
+         this%dmt_vwr(n) = this%dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved
 
       end do
 
@@ -952,9 +952,9 @@ subroutine InitDustVars(this, bounds)
 
       do m = 1, ndst
          slp_crc(m) = 1.0_r8 + 2.0_r8 * mfp_atm *                      &
-              (1.257_r8+0.4_r8*exp(-1.1_r8*dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
-              dmt_vwr(m)                      ! [frc] Slip correction factor SeP97 p.464
-         vlc_stk(m) = (1.0_r8/18.0_r8) * dmt_vwr(m) * dmt_vwr(m) * dns_aer * &
+              (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
+              this%dmt_vwr(m)                      ! [frc] Slip correction factor SeP97 p.464
+         vlc_stk(m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * &
               grav * slp_crc(m) / vsc_dyn_atm ! [m s-1] SeP97 p.466
       end do
 
@@ -979,7 +979,7 @@ subroutine InitDustVars(this, bounds)
 
             ! Save terminal velocity for convergence test
             vlc_grv_old = vlc_grv(m) ![m s-1]
-            ryn_nbr_grv(m) = vlc_grv(m) * dmt_vwr(m) / vsc_knm_atm !SeP97 p.460
+            ryn_nbr_grv(m) = vlc_grv(m) * this%dmt_vwr(m) / vsc_knm_atm !SeP97 p.460
 
             ! Update drag coefficient based on new Reynolds number
             if (ryn_nbr_grv(m) < 0.1_r8) then
@@ -1003,7 +1003,7 @@ subroutine InitDustVars(this, bounds)
             ! Update terminal velocity based on new Reynolds number and drag coeff
             ! [m s-1] Terminal veloc SeP97 p.467 (8.44)
 
-            vlc_grv(m) = sqrt(4.0_r8 * grav * dmt_vwr(m) * slp_crc(m) * dns_aer / &
+            vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / &
                  (3.0_r8*cff_drg_grv(m)*dns_mdp))   
             eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence
             if (itr_idx == 12) then
@@ -1027,7 +1027,7 @@ subroutine InitDustVars(this, bounds)
       ! actual settling velocities
 
       do m = 1, ndst
-         stk_crc(m) = vlc_grv(m) / vlc_stk(m)
+         this%stk_crc(m) = vlc_grv(m) / vlc_stk(m)
       end do
 
   end subroutine InitDustVars

From 17864ceae227f9a42dd724b58dacc5987bcef27f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 1 Jun 2024 16:13:08 -0600
Subject: [PATCH 0406/1248] Change name of tmp1 to saltation_factor

---
 src/biogeochem/DustEmisZender2003.F90 | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index 6adbac8521..db6f93581a 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -39,7 +39,7 @@ module DustEmisZender2003
   !
   ! !PRIVATE DATA:
   !
-  real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density
+  real(r8), parameter :: dns_aer = 2.5e+3_r8        ![kg m-3] Aerosol density
   !
   ! !PUBLIC DATA TYPES:
   !
@@ -48,7 +48,7 @@ module DustEmisZender2003
      real(r8) , allocatable, private :: ovr_src_snk_mss(:,:)       ! overlap factors between the source and sin
      real(r8) , allocatable, private :: dmt_vwr(:)                 ! [m] Mass-weighted mean diameter resolved
      real(r8) , allocatable, private :: stk_crc(:)                 ! [frc] Correction to Stokes settling velocity
-     real(r8), private          :: tmp1                            ! Factor in saltation computation (named as in Charlie's code)
+     real(r8), private          :: saltation_factor                ! Factor in saltation computation (named as in Charlie's code)
      real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) 
      real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:)   ! total dust flux into atmosphere
      real(r8), pointer, private :: vlc_trb_patch             (:,:) ! turbulent deposition velocity  (m/s) (ndst) 
@@ -298,7 +298,7 @@ subroutine GetConstVars(this, SaltationFactor )
     class(dust_type)  , intent(in)  :: this
     real(r8)          , intent(out) :: SaltationFactor
 
-    SaltationFactor = this%tmp1
+    SaltationFactor = this%saltation_factor
   end subroutine GetConstVars
 
   !------------------------------------------------------------------------
@@ -506,11 +506,11 @@ subroutine DustEmission (this, bounds, &
 
             ! the following lines come from subr. dst_mbl
             ! purpose: adjust threshold friction velocity to acct for moisture and
-            !          roughness. The ratio tmp1 / sqrt(forc_rho) comes from
+            !          roughness. The ratio saltation_factor / sqrt(forc_rho) comes from
             !          subr. wnd_frc_thr_slt_get which computes dry threshold
             !          friction velocity for saltation
 
-            wnd_frc_thr_slt = this%tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
+            wnd_frc_thr_slt = this%saltation_factor / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
 
             ! reset these variables which will be updated in the following if-block
 
@@ -733,7 +733,7 @@ subroutine InitDustVars(this, bounds)
      !
      ! Compute source efficiency factor from topography
      ! Initialize other variables used in subroutine Dust:
-     ! ovr_src_snk_mss(m,n) and tmp1.
+     ! ovr_src_snk_mss(m,n) and saltation_factor.
      ! Define particle diameter and density needed by atm model
      ! as well as by dry dep model
      ! Source: Paul Ginoux (for source efficiency factor)
@@ -829,7 +829,7 @@ subroutine InitDustVars(this, bounds)
       end do
 
       ! The following code from subroutine wnd_frc_thr_slt_get was placed 
-      ! here because tmp1 needs to be defined just once
+      ! here because saltation_factor needs to be defined just once
 
       ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8
 
@@ -846,7 +846,7 @@ subroutine InitDustVars(this, bounds)
 
       icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8))
       dns_fct = dns_slt * grav * dmt_slt_opt
-      this%tmp1 = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc)
+      this%saltation_factor = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc)
 
       ! Introducing particle diameter. Needed by atm model and by dry dep model.
       ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl,

From 535e2c5a43f309ea3bbe8eb851c963ee7cb33dcf Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 17:01:44 -0600
Subject: [PATCH 0407/1248] Even gdd20 files need to be advance()d.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 4c4925f88e..faa13b5fda 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -432,10 +432,26 @@ subroutine cropcal_advance( bounds )
        end if
     end if
 
-    ! The following should not have an associated time axis and thus will not be advanced here:
+    ! The following should not have an associated time axis, but still need to be here
     ! - GDD20 baseline values
     ! - GDD20 season start dates
     ! - GDD20 season end dates
+    if (adapt_cropcal_rx_cultivar_gdds) then
+       call shr_strdata_advance(sdat_cropcal_gdd20_baseline, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc)
+       if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+          call ESMF_Finalize(endflag=ESMF_END_ABORT)
+       end if
+    end if
+    if (stream_gdd20_seasons) then
+       call shr_strdata_advance(sdat_cropcal_gdd20_season_start, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc)
+       if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+          call ESMF_Finalize(endflag=ESMF_END_ABORT)
+       end if
+       call shr_strdata_advance(sdat_cropcal_gdd20_season_end, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc)
+       if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
+          call ESMF_Finalize(endflag=ESMF_END_ABORT)
+       end if
+    end if
 
     if ( .not. allocated(g_to_ig) )then
        allocate (g_to_ig(bounds%begg:bounds%endg) )

From 3e524db1aa4f34a70cd08c48c740c8c35033db9d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 17:03:43 -0600
Subject: [PATCH 0408/1248] generate_gdd20_baseline.py now saves to double
 instead of float.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index fd56d61550..8cf30bf44d 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -197,6 +197,7 @@ def generate_gdd20_baseline(input_files, output_file, author):
             "created": dt.datetime.now().astimezone().isoformat(),
         },
     )
+    encoding_dict = {}
     for cft_str in utils.define_mgdcrop_list():
         cft_int = utils.vegtype_str2int(cft_str)[0]
         print(f"{cft_str} ({cft_int})")
@@ -227,9 +228,10 @@ def generate_gdd20_baseline(input_files, output_file, author):
         var_out = _get_output_varname(cft_str)
         print(f"   Output variable {var_out}")
         ds_out[var_out] = this_da
+        encoding_dict[var_out] = {"dtype": "float64"}
 
     # Save
-    ds_out.to_netcdf(output_file, format="NETCDF3_CLASSIC")
+    ds_out.to_netcdf(output_file, format="NETCDF3_CLASSIC", encoding=encoding_dict)
 
     print("Done!")
 

From 18df6b4a04ac901737ccb5d9b806619e66ebe532 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sat, 1 Jun 2024 17:06:19 -0600
Subject: [PATCH 0409/1248] stream_fldFileName_gdd20_baseline now defaults to
 half-deg fake file.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 2683c2e535..bd5f7132ca 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1705,7 +1705,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
 <stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
-<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/testdata/gdd20baseline.tmp_dontupload.classic.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.nc</stream_fldFileName_gdd20_baseline>
 <stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_start>
 <stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_end>
 <stream_meshfile_cropcal cropcals_rx_adapt=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>

From a3feed96de079cdc04f42e60a5cfc4ff22959606 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 2 Jun 2024 08:25:06 -0600
Subject: [PATCH 0410/1248] Use fixed gdd20 baseline file.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index bd5f7132ca..8ed75be01a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1705,7 +1705,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
 <stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
-<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.nc</stream_fldFileName_gdd20_baseline>
 <stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_start>
 <stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_end>
 <stream_meshfile_cropcal cropcals_rx_adapt=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>

From 5144b36a7993ae6363bd8bb16b41219ed3e032ed Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 10:58:43 -0600
Subject: [PATCH 0411/1248] gdd20 baseline now interpolated w/
 nearest-neighbor. Revert this!

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index faa13b5fda..ce595c0d70 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -312,7 +312,7 @@ subroutine cropcal_init(bounds)
             model_mesh          = mesh,                               &
             stream_meshfile     = trim(stream_meshfile_cropcal),      &
             stream_lev_dimname  = 'null',                             &
-            stream_mapalgo      = 'bilinear',                         &
+            stream_mapalgo      = 'nn',                         &
             stream_filenames    = (/trim(stream_fldFileName_gdd20_baseline)/), &
             stream_fldlistFile  = stream_varnames_gdd20_baseline,     &
             stream_fldListModel = stream_varnames_gdd20_baseline,     &

From 90b938b5bbf8bc3e13d86e1211bb9519409b477d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 10:59:37 -0600
Subject: [PATCH 0412/1248] generate_gdd20_nbaseline: Use GDDNX.

---
 .../ctsm/crop_calendars/generate_gdd20_baseline.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 8cf30bf44d..7f60fb6a68 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -18,8 +18,7 @@
 from ctsm.crop_calendars.import_ds import import_ds
 import ctsm.crop_calendars.cropcal_utils as utils
 
-VAR_LIST_IN = ["GDD0", "GDD8", "GDD10"]
-VAR_LIST_IN = [x + "20" for x in VAR_LIST_IN]  # TODO: Delete this once using the right variables
+VAR_LIST_IN = ["GDD0X", "GDD8X", "GDD10X"]
 MISSING_FILL = -1  # Something impossible to ensure that you can mark it as a missing value, to be
 # bilinear-interpolated
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
@@ -111,26 +110,25 @@ def _get_gddn_for_cft(cft_str):
         cft_str (str): E.g., "irrigated_temperate_corn"
 
     Returns:
-        str or None: Name of variable to use (e.g., "GDD8"). If crop isn't yet handled, return None.
+        str or None: Name of variable to use (e.g., "GDD8X"). If crop isn't yet handled, return None.
     """
 
     gddn = None
 
     gdd0_list_str = ["wheat", "cotton", "rice"]
     if cft_str in _get_cft_list(gdd0_list_str):
-        gddn = "GDD0"
+        gddn = 0
 
     gdd8_list_str = ["corn", "sugarcane", "miscanthus", "switchgrass"]
     if cft_str in _get_cft_list(gdd8_list_str):
-        gddn = "GDD8"
+        gddn = 8
 
     gdd10_list_str = ["soybean"]
     if cft_str in _get_cft_list(gdd10_list_str):
-        gddn = "GDD10"
+        gddn = 10
 
-    # TODO: Delete this once using the right variables
     if gddn is not None:
-        gddn += "20"
+        gddn = f"GDD{gddn}X"
 
     return gddn
 

From e82679df56e1a514f28ee4a38ae4d9c9b581b120 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 11:25:37 -0600
Subject: [PATCH 0413/1248] generate_gdd20_baseline: Grid, if needed.

---
 .../ctsm/crop_calendars/generate_gdd20_baseline.py  | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 7f60fb6a68..71125e332d 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -17,8 +17,10 @@
 # pylint: disable=wrong-import-position
 from ctsm.crop_calendars.import_ds import import_ds
 import ctsm.crop_calendars.cropcal_utils as utils
+from ctsm.crop_calendars.grid_one_variable import grid_one_variable
 
 VAR_LIST_IN = ["GDD0X", "GDD8X", "GDD10X"]
+GRIDDING_VAR_LIST = ["patches1d_ixy", "patches1d_jxy", "lat", "lon"]
 MISSING_FILL = -1  # Something impossible to ensure that you can mark it as a missing value, to be
 # bilinear-interpolated
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
@@ -171,7 +173,7 @@ def generate_gdd20_baseline(input_files, output_file, author):
     input_files.sort()
 
     # Import history files and ensure they have lat/lon dims
-    ds_in = import_ds(input_files, VAR_LIST_IN)
+    ds_in = import_ds(input_files, VAR_LIST_IN + GRIDDING_VAR_LIST)
     if not all(x in ds_in.dims for x in ["lat", "lon"]):
         raise RuntimeError("Input files must have lat and lon dimensions")
 
@@ -188,8 +190,11 @@ def generate_gdd20_baseline(input_files, output_file, author):
     dummy_da = _add_time_axis(dummy_da)
 
     # Process all crops
+    data_var_dict = {}
+    for v in GRIDDING_VAR_LIST:
+        data_var_dict[v] = ds_in[v]
     ds_out = xr.Dataset(
-        data_vars=None,
+        data_vars=data_var_dict,
         attrs={
             "author": author,
             "created": dt.datetime.now().astimezone().isoformat(),
@@ -228,6 +233,10 @@ def generate_gdd20_baseline(input_files, output_file, author):
         ds_out[var_out] = this_da
         encoding_dict[var_out] = {"dtype": "float64"}
 
+        # Grid, if needed
+        if any(x not in this_da.dims for x in ["lat", "lon"]):
+            ds_out[var_out] = grid_one_variable(ds_out, var_out)
+
     # Save
     ds_out.to_netcdf(output_file, format="NETCDF3_CLASSIC", encoding=encoding_dict)
 

From 8b43fec5168d56df1b7c5ac6e22635d70024c3b0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 11:28:32 -0600
Subject: [PATCH 0414/1248] generate_gdd20_baseline: Improve long names.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 71125e332d..89a38a0a08 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -219,7 +219,7 @@ def generate_gdd20_baseline(input_files, output_file, author):
             # this_da = ds_in[gddn].fillna(MISSING_FILL)
             this_da = ds_in[gddn]
             this_da = _add_time_axis(this_da)
-            long_name = gddn
+            long_name = gddn.replace("X", "20")
             print(f"   {gddn}")
 
         # Add attributes

From dcacbd4003585edf1a8608bc9d70232285f01202 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 11:47:38 -0600
Subject: [PATCH 0415/1248] Minor cleanup in UpdateAccVars_CropGDDs.

---
 src/biogeophys/TemperatureType.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index f8d5206a1e..5ae0b7b20c 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1428,11 +1428,11 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
           ((month > 9 .or.  month < 4)  .and. lat <  0._r8)
        ! Replace with read-in gdd20 accumulation season, if valid
        ! (If these aren't being read in or they're invalid, they'll be -1)
-       gdd20_season_start = crop_inst%gdd20_season_start_patch(p)
-       gdd20_season_end = crop_inst%gdd20_season_end_patch(p)
+       gdd20_season_start = gdd20_season_starts(p)
+       gdd20_season_end = gdd20_season_ends(p)
        if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
           in_accumulation_season = is_doy_in_interval( &
-             gdd20_season_starts(p), gdd20_season_ends(p), day)
+          gdd20_season_start, gdd20_season_end, day)
        end if
 
        if (month==1 .and. day==1 .and. secs==dtime) then

From 2cf491da0127f1caeec5ae6d7152d637f2975599 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 11:53:44 -0600
Subject: [PATCH 0416/1248] Add outputs: GDD20_BASELINE,
 GDD20_SEASON_START/END.

---
 src/biogeochem/CropType.F90             | 28 +++++++++++++++++++++----
 src/biogeophys/TemperatureType.F90      |  5 +++--
 src/cpl/share_esmf/cropcalStreamMod.F90 | 18 ++++++++++------
 3 files changed, 39 insertions(+), 12 deletions(-)

diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index 04806f9349..fdfdaa05aa 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -53,8 +53,11 @@ module CropType
      integer , pointer :: rx_swindow_ends_thisyr_patch  (:,:) ! all prescribed sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings]
      real(r8), pointer :: gdd20_baseline_patch          (:)   ! GDD20 baseline for this patch (ddays) [patch]
-     integer , pointer :: gdd20_season_start_patch(:) ! gdd20 season start date for this patch (day of year) [patch]
-     integer , pointer :: gdd20_season_end_patch  (:) ! gdd20 season end   date for this patch (day of year) [patch]
+
+     ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+     real(r8), pointer :: gdd20_season_start_patch(:) ! gdd20 season start date for this patch (day of year) [patch]
+     real(r8), pointer :: gdd20_season_end_patch  (:) ! gdd20 season end   date for this patch (day of year) [patch]
+
      real(r8), pointer :: sdates_thisyr_patch     (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_starts_thisyr_patch(:,:) ! all sowing window start dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_ends_thisyr_patch  (:,:) ! all sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
@@ -239,8 +242,11 @@ subroutine InitAllocate(this, bounds)
     allocate(this%rx_swindow_ends_thisyr_patch(begp:endp,1:mxsowings))  ; this%rx_swindow_ends_thisyr_patch  (:,:) = -1
     allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval
     allocate(this%gdd20_baseline_patch(begp:endp)) ; this%gdd20_baseline_patch(:) = spval
-    allocate(this%gdd20_season_start_patch(begp:endp)); this%gdd20_season_start_patch(:) = -1
-    allocate(this%gdd20_season_end_patch(begp:endp))  ; this%gdd20_season_end_patch  (:) = -1
+
+    ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+    allocate(this%gdd20_season_start_patch(begp:endp)); this%gdd20_season_start_patch(:) = spval
+    allocate(this%gdd20_season_end_patch(begp:endp))  ; this%gdd20_season_end_patch  (:) = spval
+
     allocate(this%sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%sdates_thisyr_patch(:,:) = spval
     allocate(this%swindow_starts_thisyr_patch(begp:endp,1:mxsowings)) ; this%swindow_starts_thisyr_patch(:,:) = spval
     allocate(this%swindow_ends_thisyr_patch  (begp:endp,1:mxsowings)) ; this%swindow_ends_thisyr_patch  (:,:) = spval
@@ -364,6 +370,20 @@ subroutine InitHistory(this, bounds)
          avgflag='I', long_name='Reason for each crop harvest; should only be output annually', &
          ptr_patch=this%harvest_reason_thisyr_patch, default='inactive')
 
+    ! DEVELOPMENT ONLY; DELETE BEFORE MERGE
+    this%gdd20_baseline_patch(begp:endp) = spval
+    call hist_addfld1d (fname='GDD20_BASELINE', units='ddays', &
+         avgflag='A', long_name='Baseline mean growing-degree days accumulated during accumulation period (from input)', &
+         ptr_patch=this%gdd20_baseline_patch, default='inactive')
+    this%gdd20_season_start_patch(begp:endp) = spval
+    call hist_addfld1d (fname='GDD20_SEASON_START', units='day of year', &
+         avgflag='A', long_name='Start of the GDD20 accumulation season (from input)', &
+         ptr_patch=this%gdd20_season_start_patch, default='inactive')
+    this%gdd20_season_end_patch(begp:endp) = spval
+    call hist_addfld1d (fname='GDD20_SEASON_END', units='day of year', &
+         avgflag='A', long_name='End of the GDD20 accumulation season (from input)', &
+         ptr_patch=this%gdd20_season_end_patch, default='inactive')
+
   end subroutine InitHistory
 
   subroutine InitCold(this, bounds)
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 5ae0b7b20c..ae5703237e 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1428,8 +1428,9 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
           ((month > 9 .or.  month < 4)  .and. lat <  0._r8)
        ! Replace with read-in gdd20 accumulation season, if valid
        ! (If these aren't being read in or they're invalid, they'll be -1)
-       gdd20_season_start = gdd20_season_starts(p)
-       gdd20_season_end = gdd20_season_ends(p)
+       ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+       gdd20_season_start = int(gdd20_season_starts(p))
+       gdd20_season_end = int(gdd20_season_ends(p))
        if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
           in_accumulation_season = is_doy_in_interval( &
           gdd20_season_start, gdd20_season_end, day)
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index ce595c0d70..802b669905 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -766,8 +766,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
            n = ivt - npcropmin + 1
            ! vegetated pft
            ig = g_to_ig(patch%gridcell(p))
-           gdd20_season_starts(p) = dataptr2d_gdd20_season_start(ig,n)
-           gdd20_season_ends(p)   = dataptr2d_gdd20_season_end  (ig,n)
+
+           ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+           gdd20_season_starts(p) = real(dataptr2d_gdd20_season_start(ig,n), r8)
+           gdd20_season_ends(p)   = real(dataptr2d_gdd20_season_end  (ig,n), r8)
        else
            write(iulog,'(a,i0)') 'cropcal_interp(), gdd20 seasons: Crop patch has ivt ',ivt
            call ESMF_Finalize(endflag=ESMF_END_ABORT)
@@ -775,15 +777,18 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
      end do
 
      ! Handle invalid gdd20 season values
-     if (any(gdd20_season_starts(begp:endp) < 1 .or. gdd20_season_ends(begp:endp) < 1)) then
+     ! gdd20_season_starts and gdd20_season_ends REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+     if (any(gdd20_season_starts(begp:endp) < 1._r8 .or. gdd20_season_ends(begp:endp) < 1._r8)) then
          ! Fail if not allowing fallback to paramfile sowing windows
-         if ((.not. allow_invalid_gdd20_season_inputs) .and. any(gdd20_season_starts(begp:endp) < 1 .and. patch%wtgcell(begp:endp) > 0._r8 .and. patch%itype(begp:endp) >= npcropmin)) then
+         ! gdd20_season_starts REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+         if ((.not. allow_invalid_gdd20_season_inputs) .and. any(gdd20_season_starts(begp:endp) < 1._r8 .and. patch%wtgcell(begp:endp) > 0._r8 .and. patch%itype(begp:endp) >= npcropmin)) then
              write(iulog, *) 'At least one crop in one gridcell has invalid gdd20 season start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_gdd20_season_inputs to .true.'
              write(iulog, *) 'Affected crops:'
              do ivt = npcropmin, mxpft
                  do fp = 1, num_pcropp
                      p = filter_pcropp(fp)
-                     if (ivt == patch%itype(p) .and. patch%wtgcell(p) > 0._r8 .and. gdd20_season_starts(p) < 1) then
+                     ! gdd20_season_starts REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+                     if (ivt == patch%itype(p) .and. patch%wtgcell(p) > 0._r8 .and. gdd20_season_starts(p) < 1._r8) then
                          write(iulog, *) '    ',pftname(ivt),'  (',ivt,')'
                          exit  ! Stop looking for patches of this type
                      end if
@@ -792,7 +797,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
              call ESMF_Finalize(endflag=ESMF_END_ABORT)
 
          ! Fail if a gdd20 season start date is given without an end date (or vice versa)
-         else if (any((gdd20_season_starts(begp:endp) >= 1 .and. gdd20_season_ends(begp:endp) < 1) .or. (gdd20_season_starts(begp:endp) < 1 .and. gdd20_season_ends(begp:endp) >= 1))) then
+         ! gdd20_season_starts and gdd20_season_ends REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+         else if (any((gdd20_season_starts(begp:endp) >= 1._r8 .and. gdd20_season_ends(begp:endp) < 1._r8) .or. (gdd20_season_starts(begp:endp) < 1._r8 .and. gdd20_season_ends(begp:endp) >= 1._r8))) then
              write(iulog, *) 'Every gdd20 season start date must have a corresponding end date.'
              call ESMF_Finalize(endflag=ESMF_END_ABORT)
          end if

From 0083a08432859948707cf4e8e7b4937dc7f1d92c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 12:03:15 -0600
Subject: [PATCH 0417/1248] rxcropmaturity.py is now parent
 rxcropmaturityshared.py.

---
 ...ropmaturity.py => rxcropmaturityshared.py} | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)
 rename cime_config/SystemTests/{rxcropmaturity.py => rxcropmaturityshared.py} (97%)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturityshared.py
similarity index 97%
rename from cime_config/SystemTests/rxcropmaturity.py
rename to cime_config/SystemTests/rxcropmaturityshared.py
index 75fff8a0e0..f8e4b1c9bb 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -11,6 +11,10 @@
 code do the interpolation. However, that wouldn't act on harvest dates
 (which are needed for generate_gdds.py). I could have Python interpolate
 those, but this would cause a potential inconsistency.
+
+Note that this is just a parent class. The actual tests are RXCROPMATURITY and
+RXCROPMATURITY_SKIPRUN, the latter of which does everything except perform and 
+check the CTSM runs.
 """
 
 import os
@@ -25,7 +29,7 @@
 logger = logging.getLogger(__name__)
 
 
-class RXCROPMATURITY(SystemTestsCommon):
+class RXCROPMATURITYSHARED(SystemTestsCommon):
     def __init__(self, case):
         # initialize an object interface to the SMS system test
         SystemTestsCommon.__init__(self, case)
@@ -84,7 +88,7 @@ def __init__(self, case):
         # Which conda environment should we use?
         self._get_conda_env()
 
-    def run_phase(self):
+    def _run_phase(self, skip_run=False):
         # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
         # want to be saved as baseline.
 
@@ -146,9 +150,10 @@ def run_phase(self):
         # "No history files expected, set suffix=None to avoid compare error"
         # We *do* expect history files here, but anyway. This works.
         self._skip_pnl = False
-        self.run_indv(suffix=None, st_archive=True)
 
-        self._run_generate_gdds(case_gddgen)
+        if not skip_run:
+            self.run_indv(suffix=None, st_archive=True)
+            self._run_generate_gdds(case_gddgen)
 
         # -------------------------------------------------------------------
         # (3) Set up and perform Prescribed Calendars run
@@ -168,13 +173,15 @@ def run_phase(self):
             ]
         )
 
-        self.run_indv()
+        if not skip_run:
+            self.run_indv()
 
         # -------------------------------------------------------------------
         # (4) Check Prescribed Calendars run
         # -------------------------------------------------------------------
         logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
-        self._run_check_rxboth_run()
+        if not skip_run:
+            self._run_check_rxboth_run()
 
     # Get sowing and harvest dates for this resolution.
     def _get_rx_dates(self):

From f728f9676e5103298dd255fcec2a6796d22e0144 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 13:44:07 -0600
Subject: [PATCH 0418/1248] Added back RXCROPMATURITY.

---
 cime_config/SystemTests/rxcropmaturity.py | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 cime_config/SystemTests/rxcropmaturity.py

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
new file mode 100644
index 0000000000..3eadccfeb3
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -0,0 +1,5 @@
+from RXCROPMATURITYSHARED import RXCROPMATURITYSHARED
+
+class RXCROPMATURITY(RXCROPMATURITYSHARED):
+    def run_phase(self):
+        self._run_phase()
\ No newline at end of file

From e4b97a233cd722ab915a9b0be27f5ece509c8ca9 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 13:44:51 -0600
Subject: [PATCH 0419/1248] Add RXCROPMATURITYSKIPRUN.

---
 cime_config/SystemTests/rxcropmaturityskiprun.py |  6 ++++++
 cime_config/config_tests.xml                     | 10 ++++++++++
 2 files changed, 16 insertions(+)
 create mode 100644 cime_config/SystemTests/rxcropmaturityskiprun.py

diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py
new file mode 100644
index 0000000000..d52742f95a
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityskiprun.py
@@ -0,0 +1,6 @@
+print("pre-import")
+from RXCROPMATURITYSHARED import RXCROPMATURITYSHARED
+
+class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED):
+    def run_phase(self):
+        self._run_phase(skip_run=True)
\ No newline at end of file
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index c0b6afed9d..98434da10e 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -133,6 +133,16 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="RXCROPMATURITYSKIPRUN">
+    <DESC>As RXCROPMATURITY but don't actually run or postprocess; just setup</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

From b3b8e08acdcad393844207ac9e556bdee8b3ef08 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 3 Jun 2024 15:42:23 -0600
Subject: [PATCH 0420/1248] Add reference for ThresholdSoilMoist and add
 extended comments from Danny Leung from the Leung PR, actually use it in the
 code and make sure the unit test uses the new name

---
 .../DustEmis_test/test_DustEmisZender2003.pf  |  4 +-
 src/biogeophys/SoilStateInitTimeConstMod.F90  | 49 ++++++++++++++++---
 2 files changed, 45 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index c99f4bd97d..a7fea904c9 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -19,7 +19,7 @@ module test_DustEmisZender2003
   use WaterType, only : water_type
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
-  use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay
+  use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay
 
   implicit none
 
@@ -156,7 +156,7 @@ contains
        ! considered bedrock
        col%nbedrock(c) = nlevsoi
 
-       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay )
+       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
        this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
     end do
 
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 3b71efe103..0be54571e5 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -19,7 +19,7 @@ module SoilStateInitTimeConstMod
   public  :: readParams
 
   ! PRIVATE FUNCTIONS MADE PUBLIC Just for unit-testing:
-  public :: ThresholdSoilMoist
+  public :: ThresholdSoilMoistZender2003
   public :: ThresholdSoilMoistKok2014
   public :: MassFracClay
   !
@@ -707,8 +707,8 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     do c = begc,endc
        g = col%gridcell(c)
 
-       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8
-       soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
+       soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay3d(g,1) )
+       soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay3d(g,1) )
     end do
 
     ! --------------------------------------------------------------------
@@ -722,9 +722,31 @@ end subroutine SoilStateInitTimeConst
 
   !------------------------------------------------------------------------------
 
-  real(r8) function ThresholdSoilMoist( clay )
+  real(r8) function ThresholdSoilMoistZender2003( clay )
+  !------------------------------------------------------------------------------
+  !
   ! Calculate the threshold soil moisture needed for dust emission, based on clay content
-      use abortUtils    , only : endrun    
+  ! This was the original equation with a = 1 / (%clay) being the tuning factor for soil
+  ! moisture effect in Zender's 2003 dust emission scheme.
+  !
+  ! 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to
+  ! convert surface clay fraction from percentage to fraction.
+  !
+  !------------------------------------------------------------------------------
+  ! For future developments Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) o
+  ! dust emission scheme in the CESM will use Zender's tuning as well, which overall
+  ! encourages more dust emissions from seriamid and more marginal dust sources.
+  ! Another advantage of using this tuning factor instead of a = 1 is that the dust emission
+  ! threshold is linearly dependent on the clay fraction instead of parabolically dependent
+  ! on clay fraction as in the above line. This means that dust emission becomes a little
+  ! less sensitive to clay content (soil texture).
+  !
+  ! Also see the notes below for ThresholdSoilMoistKok2014.
+  !
+  ! Notes from: dmleung 19 Feb 2024.
+  !
+  !------------------------------------------------------------------------------
+      use abortUtils    , only : endrun
       use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
@@ -734,12 +756,27 @@ real(r8) function ThresholdSoilMoist( clay )
          return
       end if
       ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
-  end function ThresholdSoilMoist
+  end function ThresholdSoilMoistZender2003
 
   !------------------------------------------------------------------------------
 
   real(r8) function ThresholdSoilMoistKok2014( clay )
+  !------------------------------------------------------------------------------
   ! Calculate the threshold soil moisture needed for dust emission, based on clay content
+  !
+  ! The below calculates the threshold gravimetric water content for the dust emission
+  ! calculation in DustEmis. The equation comes from Eq. 14 of Fecan et al.
+  ! (1999; https://doi.org/10.1007/s00585-999-0149-7).
+  ! gwc_thr_col = 0.17*clay3d + 0.0014*(clay3d**2), and we only concern the topmost
+  ! soil layer.  Charlie Zender later on added a tuning factor (a) such that the
+  ! equation becomes gwc_thr_col = a*[0.17*clay3d + 0.0014*(clay3d**2)].
+  ! (Zender et al., 2003a; https://doi.org/10.1029/2002JD002775)
+  ! Kok et al. (2014a, b) chose to use a = 1. Resulting in this function
+  ! Charlie Zender (2003a) chose:  a = 1/clay3d, which gives the ThresholdSoilMoistZender2003
+  ! function above.
+  !
+  ! Notes from: dmleung 24 May 2024.
+  !------------------------------------------------------------------------------
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
       ThresholdSoilMoistKok2014 = 0.01_r8*(0.17_r8*clay + 0.0014_r8*clay*clay)

From afbdcbfd8517fbe951772c39bcb1f57da2abd24d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 3 Jun 2024 17:16:08 -0600
Subject: [PATCH 0421/1248] Squashed '.lib/git-fleximod/' changes from
 a354b0528..a34070be0

a34070be0 Bump to 0.7.6
9e5d5f72b Merge pull request #40 from ESMCI/fix/change_url
00b7b3817 some fixes when modifying url

git-subtree-dir: .lib/git-fleximod
git-subtree-split: a34070be02d10071b544be3839f6c9ed79662665
---
 git_fleximod/cli.py          |  2 +-
 git_fleximod/git_fleximod.py | 49 ++++++++++++++++++++----------------
 git_fleximod/gitmodules.py   |  2 +-
 pyproject.toml               |  2 +-
 tbump.toml                   |  2 +-
 5 files changed, 31 insertions(+), 26 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 4c3fb1a8f9..7d09abd83b 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.7.5"
+__version__ = "0.7.6"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index f080513a52..a003c0da8c 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -263,6 +263,21 @@ def single_submodule_checkout(
 
     return
 
+def add_remote(git, url):
+    remotes = git.git_operation("remote", "-v")
+    newremote = "newremote.00"
+    if url in remotes:
+        for line in remotes:
+            if url in line and "fetch" in line:
+                newremote = line.split()[0]
+                break
+    else:
+        i = 0
+        while "newremote" in remotes:
+            i = i + 1
+            newremote = f"newremote.{i:02d}"
+        git.git_operation("remote", "add", newremote, url)
+    return newremote
 
 def submodules_status(gitmodules, root_dir, toplevel=False):
     testfails = 0
@@ -271,6 +286,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
     for name in gitmodules.sections():
         path = gitmodules.get(name, "path")
         tag = gitmodules.get(name, "fxtag")
+        url = gitmodules.get(name, "url")
         required = gitmodules.get(name, "fxrequired")
         level = required and "Toplevel" in required
         if not path:
@@ -280,7 +296,6 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
         if not os.path.exists(os.path.join(newpath, ".git")):
             rootgit = GitInterface(root_dir, logger)
             # submodule commands use path, not name
-            url = gitmodules.get(name, "url")
             url = url.replace("git@github.com:", "https://github.com/")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
             atag = None
@@ -312,11 +327,11 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             with utils.pushd(newpath):
                 git = GitInterface(newpath, logger)
                 atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                part =  git.git_operation("status").partition("\n")[0]
-                # fake hash to initialize
-                ahash = "xxxx"
-                if part:
-                    ahash = part.split()[-1]
+                ahash =  git.git_operation("rev-list", "HEAD").partition("\n")[0]
+                rurl = git.git_operation("ls-remote","--get-url").rstrip()
+                if rurl != url:
+                    remote = add_remote(git, url)
+                    git.git_operation("fetch", remote)
                 if tag and atag == tag:
                     print(f"  {name:>20} at tag {tag}")
                 elif tag and ahash[: len(tag)] == tag:
@@ -335,7 +350,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                     )
                     testfails += 1
 
-                status = git.git_operation("status", "--ignore-submodules")
+                status = git.git_operation("status", "--ignore-submodules", "-uno")
                 if "nothing to commit" not in status:
                     localmods = localmods + 1
                     print("M" + textwrap.indent(status, "                      "))
@@ -357,11 +372,11 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
         path = gitmodules.get(name, "path")
         url = gitmodules.get(name, "url")
         logger.info(
-            "name={} path={} url={} fxtag={} requiredlist={}".format(
+            "name={} path={} url={} fxtag={} requiredlist={} ".format(
                 name, os.path.join(root_dir, path), url, fxtag, requiredlist
             )
         )
-        #        if not os.path.exists(os.path.join(root_dir,path, ".git")):
+
         fxrequired = gitmodules.get(name, "fxrequired")
         assert fxrequired in fxrequired_allowed_values()
         rgit = GitInterface(root_dir, logger)
@@ -409,19 +424,7 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 upstream = git.git_operation("ls-remote", "--get-url").rstrip()
                 newremote = "origin"
                 if upstream != url:
-                    # TODO - this needs to be a unique name
-                    remotes = git.git_operation("remote", "-v")
-                    if url in remotes:
-                        for line in remotes:
-                            if url in line and "fetch" in line:
-                                newremote = line.split()[0]
-                                break
-                    else:
-                        i = 0
-                        while newremote in remotes:
-                            i = i + 1
-                            newremote = f"newremote.{i:02d}"
-                        git.git_operation("remote", "add", newremote, url)
+                    add_remote(git, url)
 
                 tags = git.git_operation("tag", "-l")
                 if fxtag and fxtag not in tags:
@@ -439,6 +442,8 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                     print(f"{name:>20} up to date.")
 
 
+
+
 def local_mods_output():
     text = """\
     The submodules labeled with 'M' above are not in a clean state.
diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py
index 68c82d066f..7e4e05394a 100644
--- a/git_fleximod/gitmodules.py
+++ b/git_fleximod/gitmodules.py
@@ -59,7 +59,7 @@ def get(self, name, option, raw=False, vars=None, fallback=None):
         Uses the parent class's get method to access the value.
         Handles potential errors if the section or option doesn't exist.
         """
-        self.logger.debug("get called {} {}".format(name, option))
+        self.logger.debug("git get called {} {}".format(name, option))
         section = f'submodule "{name}"'
         try:
             return ConfigParser.get(
diff --git a/pyproject.toml b/pyproject.toml
index ac1684ea0f..3c70c6c9c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.5"
+version = "0.7.6"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index e644fc4d24..3854682df4 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.5"
+current = "0.7.6"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From 4a06a23d1b2bcab8e177f6ad57bb64e8bb4db1d6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 3 Jun 2024 22:55:25 -0600
Subject: [PATCH 0422/1248] Get unit tests to work again

---
 src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf    | 4 ++--
 src/biogeophys/SoilStateInitTimeConstMod.F90              | 4 ++--
 .../test_dust_soil_clay_functions.pf                      | 8 ++++----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
index b25ad5c44c..e60ec2cc7f 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
@@ -19,7 +19,7 @@ module test_DustEmisBase
   use WaterType, only : water_type
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
-  use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay
+  use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay
 
   implicit none
 
@@ -156,7 +156,7 @@ contains
        ! considered bedrock
        col%nbedrock(c) = nlevsoi
 
-       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay )
+       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
        this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
     end do
 
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 0be54571e5..e47577c9b9 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -751,11 +751,11 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
       if ( clay < 0.0_r8 .or. clay > 100.0_r8 )then
-         ThresholdSoilMoist = nan
+         ThresholdSoilMoistZender2003 = nan
          call endrun( 'Clay fraction is out of bounds (0 to 100)')
          return
       end if
-      ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
+      ThresholdSoilMoistZender2003 = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
   end function ThresholdSoilMoistZender2003
 
   !------------------------------------------------------------------------------
diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
index 0e4ac8b3db..5a8f858286 100644
--- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
@@ -33,10 +33,10 @@ contains
     real(r8) :: value
     character(len=100) :: expected_msg
 
-    value = ThresholdSoilMoist( -1.e-15_r8 )
+    value = ThresholdSoilMoistZender2003( -1.e-15_r8 )
     expected_msg = "ABORTED: Clay fraction is out of bounds (0 to 100)"
     @assertExceptionRaised(expected_msg)
-    value = ThresholdSoilMoist( 1._r8 + 1.-15_r8 )
+    value = ThresholdSoilMoistZender2003( 1._r8 + 1.-15_r8 )
     @assertExceptionRaised(expected_msg)
   end subroutine TestClayOutOfRangeThreshold
 
@@ -45,9 +45,9 @@ contains
     class(TestDustEmisSoilFunctions), intent(inout) :: this
     real(r8) :: value
 
-    value = ThresholdSoilMoist( 0.0_r8 )
+    value = ThresholdSoilMoistZender2003( 0.0_r8 )
     @assertEqual( value, 0.17_r8, tolerance=tol )
-    value = ThresholdSoilMoist( 100.0_r8 )
+    value = ThresholdSoilMoistZender2003( 100.0_r8 )
     @assertEqual( value, 0.31_r8, tolerance=tol )
   end subroutine TestThresholdValues
 

From 9d6901b5b5db6e18a1804f8a2ceef00761c659f7 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Tue, 4 Jun 2024 08:57:20 -0600
Subject: [PATCH 0423/1248] fix namelist logic

---
 bld/CLMBuildNamelist.pm | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 09b721a8f9..f739b033f8 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4588,14 +4588,20 @@ sub setup_logic_exice {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
   my $use_exice = $nl->get_value( 'use_excess_ice' );
   my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' );
-  # IF excess ice streams is on
-  if ( (not defined($use_exice_streams) && value_is_true($use_exice)) && ($nl_flags->{'clm_start_type'} == /cold/  || $nl_flags->{'clm_start_type'} == /arb_ic/ ) ) {
+  my $finidat = $nl->get_value('finidat');
+  # If coldstart and use_excess_ice is on:
+  if ( ( (not defined($use_exice_streams)) && value_is_true($use_exice) ) && string_is_undef_or_empty($finidat) ) {
    $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.true.');
-   $use_exice_streams = '.true.'
+   $use_exice_streams = '.true.';
+   # if excess ice is turned off
+   } elsif ( (not defined($use_exice_streams)) && (not value_is_true($use_exice)) ) {
+   $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.false.');
+   $use_exice_streams = '.false.';
    }
+  # If excess ice streams is on
   if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
      # Can only be true if excess ice is also on, otherwise fail
-     if (defined($use_exice) && not value_is_true($use_exice)) {
+     if ( defined($use_exice) && (not value_is_true($use_exice)) ) {
         $log->fatal_error("use_excess_ice_streams can NOT be TRUE when use_excess_ice is FALSE" );
      }
   # Otherwise if ice streams are off

From 7ff7d6a2a272297f4b3d4ae8cb0765ada163e33e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 4 Jun 2024 09:49:03 -0600
Subject: [PATCH 0424/1248] Spin off a base class and have the Zender2003 class
 extend it, unit tests working and passes

---
 src/biogeochem/CMakeLists.txt         |   1 +
 src/biogeochem/DustEmisBase.F90       | 740 ++++++++++++++++++++++++++
 src/biogeochem/DustEmisZender2003.F90 | 629 +---------------------
 3 files changed, 770 insertions(+), 600 deletions(-)
 create mode 100644 src/biogeochem/DustEmisBase.F90

diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt
index 0dd06ac09e..9824bcb072 100644
--- a/src/biogeochem/CMakeLists.txt
+++ b/src/biogeochem/CMakeLists.txt
@@ -6,6 +6,7 @@ list(APPEND clm_sources
   CNPhenologyMod.F90
   CNSpeciesMod.F90
   CNDVType.F90
+  DustEmisBase.F90
   DustEmisZender2003.F90
   CropReprPoolsMod.F90
   CropType.F90
diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
new file mode 100644
index 0000000000..11912096fd
--- /dev/null
+++ b/src/biogeochem/DustEmisBase.F90
@@ -0,0 +1,740 @@
+module DustEmisBase
+
+  !----------------------------------------------------------------------- 
+  ! !DESCRIPTION: 
+  ! Routines in this module calculate Dust mobilization and dry deposition for dust.
+  ! Simulates dust mobilization due to wind from the surface into the 
+  ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust 
+  ! emission (kg/m**2/s) [ + = to atm].
+  ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition 
+  ! velocity through the lowest atmospheric layer). CAM will calculate the settling 
+  ! velocity through the whole atmospheric column. The two calculations will determine 
+  ! the dust dry deposition flux to the surface.
+  !                              
+  ! !USES:
+  use shr_kind_mod         , only : r8 => shr_kind_r8 
+  use shr_log_mod          , only : errMsg => shr_log_errMsg
+  use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
+  use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr
+  use clm_varcon           , only : grav, spval
+  use landunit_varcon      , only : istcrop, istsoil
+  use clm_varctl           , only : iulog
+  use abortutils           , only : endrun
+  use decompMod            , only : bounds_type, subgrid_level_landunit, subgrid_level_patch
+  use atm2lndType          , only : atm2lnd_type
+  use SoilStateType        , only : soilstate_type
+  use CanopyStateType      , only : canopystate_type
+  use WaterStateBulkType       , only : waterstatebulk_type
+  use WaterDiagnosticBulkType       , only : waterdiagnosticbulk_type
+  use FrictionVelocityMod  , only : frictionvel_type
+  use LandunitType         , only : lun
+  use ColumnType           , only : col
+  use PatchType            , only : patch
+  use clm_varctl           , only : dust_emis_method
+  !  
+  ! !PUBLIC TYPES
+  implicit none
+  private
+  !
+  ! !PRIVATE DATA:
+  !
+  real(r8), parameter :: dns_aer = 2.5e+3_r8        ![kg m-3] Aerosol density
+  !
+  ! !PUBLIC DATA TYPES:
+  !
+  type, abstract, public :: dust_base_type
+
+     real(r8) , allocatable, public  :: ovr_src_snk_mss(:,:)       ! overlap factors between the source and sin
+     real(r8) , allocatable, private :: dmt_vwr(:)                 ! [m] Mass-weighted mean diameter resolved
+     real(r8) , allocatable, private :: stk_crc(:)                 ! [frc] Correction to Stokes settling velocity
+     real(r8), public           :: saltation_factor                ! Factor in saltation computation (named as in Charlie's code)
+     real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) 
+     real(r8), pointer, public  :: flx_mss_vrt_dst_tot_patch (:)   ! total dust flux into atmosphere
+     real(r8), pointer, private :: vlc_trb_patch             (:,:) ! turbulent deposition velocity  (m/s) (ndst) 
+     real(r8), pointer, private :: vlc_trb_1_patch           (:)   ! turbulent deposition velocity 1(m/s)
+     real(r8), pointer, private :: vlc_trb_2_patch           (:)   ! turbulent deposition velocity 2(m/s)
+     real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
+     real(r8), pointer, private :: vlc_trb_4_patch           (:)   ! turbulent deposition velocity 4(m/s)
+
+   contains
+
+     procedure , public   :: InitBase        ! Base object initiatlization (allows it to be extended)
+     procedure , public   :: Init => InitBase ! Initialization name used by callers
+     procedure(DustEmission_interface) , public, deferred  :: DustEmission    ! Dust mobilization
+     procedure , public   :: DustDryDep      ! Turbulent dry deposition for dust
+     procedure , public   :: WritePatchToLog ! Write information on the given patch to the log file
+     procedure , public   :: GetPatchVars    ! Get important variables on a given patch
+     procedure , public   :: GetConstVars    ! Get important constant variables
+     procedure , public   :: CleanBase       ! Base object deallocation (allows extension)
+     procedure , public   :: Clean => CleanBase ! Deallocation used by callers
+     procedure , private  :: InitAllocate 
+     procedure , private  :: InitHistory  
+     procedure , private  :: InitDustVars    ! Initialize variables used in DustEmission method
+
+  end type dust_base_type
+  !------------------------------------------------------------------------
+
+  abstract interface
+  !------------------------------------------------------------------------
+
+  subroutine DustEmission_interface (this, bounds, &
+       num_nolakep, filter_nolakep, &
+       atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, &
+       frictionvel_inst)
+    !
+    ! !DESCRIPTION: 
+    ! Dust mobilization. This code simulates dust mobilization due to wind
+    ! from the surface into the lowest atmospheric layer
+    ! On output flx_mss_vrt_dst(ndst) is the surface dust emission 
+    ! (kg/m**2/s) [ + = to atm]
+    !
+    ! !USES
+    use decompMod              , only : bounds_type
+    use atm2lndType            , only : atm2lnd_type
+    use SoilStateType          , only : soilstate_type
+    use CanopyStateType        , only : canopystate_type
+    use WaterStateBulkType     , only : waterstatebulk_type
+    use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
+    use FrictionVelocityMod    , only : frictionvel_type
+
+    import :: dust_base_type
+    !
+    ! !ARGUMENTS:
+    class (dust_base_type)                 :: this
+    type(bounds_type)      , intent(in)    :: bounds                      
+    integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
+    integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
+    type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
+    type(soilstate_type)   , intent(in)    :: soilstate_inst
+    type(canopystate_type) , intent(in)    :: canopystate_inst
+    type(waterstatebulk_type)  , intent(in)    :: waterstatebulk_inst
+    type(waterdiagnosticbulk_type)  , intent(in)    :: waterdiagnosticbulk_inst
+    type(frictionvel_type) , intent(in)    :: frictionvel_inst
+
+  end subroutine DustEmission_interface
+
+  end interface
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+contains
+
+  !------------------------------------------------------------------------
+  subroutine InitBase(this, bounds, NLFilename)
+
+   ! Base level initialization of this base object, this allows classes that extend
+   ! this base class to use this one and extend it with additional initialization
+    class(dust_base_type) :: this
+    type(bounds_type), intent(in) :: bounds  
+    character(len=*),  intent(in) :: NLFilename
+
+    call this%InitAllocate (bounds)
+    call this%InitHistory  (bounds)
+    call this%InitDustVars (bounds)
+
+  end subroutine InitBase
+
+  !------------------------------------------------------------------------
+  subroutine CleanBase(this)
+   !
+   ! Base level deallocation of this base object, this allows classes that extend
+   ! this base class to use this one and extend it with additional deallocation.
+   ! !ARGUMENTS:
+   class (dust_base_type) :: this
+   !
+   ! !LOCAL VARIABLES:
+   !------------------------------------------------------------------------
+
+   deallocate(this%flx_mss_vrt_dst_patch)
+   deallocate(this%flx_mss_vrt_dst_tot_patch)
+   deallocate(this%vlc_trb_patch)
+   deallocate(this%vlc_trb_1_patch)
+   deallocate(this%vlc_trb_2_patch)
+   deallocate(this%vlc_trb_3_patch)
+   deallocate(this%vlc_trb_4_patch)
+
+   deallocate (this%ovr_src_snk_mss)
+   deallocate (this%dmt_vwr)
+   deallocate (this%stk_crc)
+
+ end subroutine CleanBase
+
+  !------------------------------------------------------------------------
+  subroutine InitAllocate(this, bounds)
+    !
+    ! !ARGUMENTS:
+    class (dust_base_type) :: this
+    type(bounds_type), intent(in) :: bounds  
+    !
+    ! !LOCAL VARIABLES:
+    integer :: begp,endp
+    integer :: begc,endc
+    !------------------------------------------------------------------------
+
+    begp = bounds%begp ; endp = bounds%endp
+    begc = bounds%begc ; endc = bounds%endc
+
+    allocate(this%flx_mss_vrt_dst_patch     (begp:endp,1:ndst)) ; this%flx_mss_vrt_dst_patch     (:,:) = nan
+    allocate(this%flx_mss_vrt_dst_tot_patch (begp:endp))        ; this%flx_mss_vrt_dst_tot_patch (:)   = nan
+    allocate(this%vlc_trb_patch             (begp:endp,1:ndst)) ; this%vlc_trb_patch             (:,:) = nan
+    allocate(this%vlc_trb_1_patch           (begp:endp))        ; this%vlc_trb_1_patch           (:)   = nan
+    allocate(this%vlc_trb_2_patch           (begp:endp))        ; this%vlc_trb_2_patch           (:)   = nan 
+    allocate(this%vlc_trb_3_patch           (begp:endp))        ; this%vlc_trb_3_patch           (:)   = nan
+    allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
+
+    allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst))           ; this%ovr_src_snk_mss           (:,:) = nan
+    allocate (this%dmt_vwr(ndst))                               ; this%dmt_vwr                   (:)   = nan
+    allocate (this%stk_crc(ndst))                               ; this%stk_crc                   (:)   = nan
+
+
+  end subroutine InitAllocate
+
+  !------------------------------------------------------------------------
+  subroutine InitHistory(this, bounds)
+    !
+    ! !USES:
+    use histFileMod, only : hist_addfld1d
+    !
+    !
+    ! !ARGUMENTS:
+    class (dust_base_type) :: this
+    type(bounds_type), intent(in) :: bounds  
+    !
+    ! !LOCAL VARIABLES:
+    integer :: begp,endp
+    integer :: begc,endc
+    !------------------------------------------------------------------------
+
+    begp = bounds%begp; endp = bounds%endp
+    begc = bounds%begc; endc = bounds%endc
+
+    this%flx_mss_vrt_dst_tot_patch(begp:endp) = spval
+    call hist_addfld1d (fname='DSTFLXT', units='kg/m2/s',  &
+         avgflag='A', long_name='total surface dust emission', &
+         ptr_patch=this%flx_mss_vrt_dst_tot_patch, set_lake=0._r8, set_urb=0._r8)
+
+    this%vlc_trb_1_patch(begp:endp) = spval
+    call hist_addfld1d (fname='DPVLTRB1', units='m/s',  &
+         avgflag='A', long_name='turbulent deposition velocity 1', &
+         ptr_patch=this%vlc_trb_1_patch, default='inactive')
+
+    this%vlc_trb_2_patch(begp:endp) = spval
+    call hist_addfld1d (fname='DPVLTRB2', units='m/s',  &
+         avgflag='A', long_name='turbulent deposition velocity 2', &
+         ptr_patch=this%vlc_trb_2_patch, default='inactive')
+
+    this%vlc_trb_3_patch(begp:endp) = spval
+    call hist_addfld1d (fname='DPVLTRB3', units='m/s',  &
+         avgflag='A', long_name='turbulent deposition velocity 3', &
+         ptr_patch=this%vlc_trb_3_patch, default='inactive')
+
+    this%vlc_trb_4_patch(begp:endp) = spval
+    call hist_addfld1d (fname='DPVLTRB4', units='m/s',  &
+         avgflag='A', long_name='turbulent deposition velocity 4', &
+         ptr_patch=this%vlc_trb_4_patch, default='inactive')
+
+  end subroutine InitHistory
+
+    !-----------------------------------------------------------------------
+
+  subroutine WritePatchToLog(this, p)
+    !
+    ! !DESCRIPTION:
+    ! Write out information on dust emisisons for this patch to the log file
+    ! !ARGUMENTS:
+    class(dust_base_type), intent(in) :: this
+    integer         , intent(in) :: p      ! Patch to display
+
+    write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p)
+    write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p)
+    write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p)
+    write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p)
+    write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p)
+  end subroutine WritePatchToLog
+
+    !-----------------------------------------------------------------------
+
+  subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, &
+                          vlc_trb_2, vlc_trb_3, vlc_trb_4)
+   !
+   ! !DESCRIPTION:
+   ! Get important variables on the given patch
+   ! !ARGUMENTS:
+   class(dust_base_type)  , intent(in)  :: this
+   integer           , intent(in)  :: p      ! Patch to get
+   real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst)
+   real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot
+   real(r8), optional, intent(out) :: vlc_trb(ndst)
+   real(r8), optional, intent(out) :: vlc_trb_1
+   real(r8), optional, intent(out) :: vlc_trb_2
+   real(r8), optional, intent(out) :: vlc_trb_3
+   real(r8), optional, intent(out) :: vlc_trb_4
+
+   if ( present(flx_mss_vrt_dst    ) ) flx_mss_vrt_dst     = this%flx_mss_vrt_dst_patch(p,:)
+   if ( present(flx_mss_vrt_dst_tot) ) flx_mss_vrt_dst_tot = this%flx_mss_vrt_dst_tot_patch(p)
+   if ( present(vlc_trb  ) ) vlc_trb   = this%vlc_trb_patch(p,:)
+   if ( present(vlc_trb_1) ) vlc_trb_1 = this%vlc_trb_1_patch(p)
+   if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p)
+   if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p)
+   if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p)
+  end subroutine GetPatchVars
+
+    !-----------------------------------------------------------------------
+
+  subroutine GetConstVars(this, SaltationFactor )
+  !
+  ! !DESCRIPTION:
+  ! Get important constant variables
+  ! !ARGUMENTS:
+    class(dust_base_type)  , intent(in)  :: this
+    real(r8)          , intent(out) :: SaltationFactor
+
+    SaltationFactor = this%saltation_factor
+  end subroutine GetConstVars
+
+   !------------------------------------------------------------------------
+  subroutine DustDryDep (this, bounds, &
+       atm2lnd_inst, frictionvel_inst)
+    !
+    ! !DESCRIPTION: 
+    !
+    ! Determine Turbulent dry deposition for dust. Calculate the turbulent 
+    ! component of dust dry deposition, (the turbulent deposition velocity 
+    ! through the lowest atmospheric layer. CAM will calculate the settling 
+    ! velocity through the whole atmospheric column. The two calculations 
+    ! will determine the dust dry deposition flux to the surface.
+    ! Note: Same process should occur over oceans. For the coupled CESM,
+    ! we may find it more efficient to let CAM calculate the turbulent dep
+    ! velocity over all surfaces. This would require passing the
+    ! aerodynamic resistance, ram(1), and the friction velocity, fv, from
+    ! the land to the atmosphere component. In that case, dustini need not
+    ! calculate particle diamter (dmt_vwr) and particle density (dns_aer).
+    ! Source: C. Zender's dry deposition code
+    !
+    ! !USES
+    use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ
+    !
+    ! !ARGUMENTS:
+    class (dust_base_type)                      :: this
+    type(bounds_type)      , intent(in)    :: bounds 
+    type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
+    type(frictionvel_type) , intent(in)    :: frictionvel_inst
+    !
+    ! !LOCAL VARIABLES
+    integer  :: p,c,g,m,n                             ! indices
+    real(r8) :: vsc_dyn_atm(bounds%begp:bounds%endp)  ! [kg m-1 s-1] Dynamic viscosity of air
+    real(r8) :: vsc_knm_atm(bounds%begp:bounds%endp)  ! [m2 s-1] Kinematic viscosity of atmosphere
+    real(r8) :: shm_nbr_xpn                           ! [frc] Sfc-dep exponent for aerosol-diffusion dependence on Schmidt number
+    real(r8) :: shm_nbr                               ! [frc] Schmidt number
+    real(r8) :: stk_nbr                               ! [frc] Stokes number
+    real(r8) :: mfp_atm                               ! [m] Mean free path of air
+    real(r8) :: dff_aer                               ! [m2 s-1] Brownian diffusivity of particle
+    real(r8) :: rss_trb                               ! [s m-1] Resistance to turbulent deposition
+    real(r8) :: slp_crc(bounds%begp:bounds%endp,ndst) ! [frc] Slip correction factor
+    real(r8) :: vlc_grv(bounds%begp:bounds%endp,ndst) ! [m s-1] Settling velocity
+    real(r8) :: rss_lmn(bounds%begp:bounds%endp,ndst) ! [s m-1] Quasi-laminar layer resistance
+    real(r8) :: tmp                                   ! temporary 
+    real(r8), parameter::shm_nbr_xpn_lnd=-2._r8/3._r8 ![frc] shm_nbr_xpn over land
+    !------------------------------------------------------------------------
+
+    associate(                                                   & 
+         forc_pbot =>    atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8)  (:)   ]  atm pressure (Pa)                                 
+         forc_rho  =>    atm2lnd_inst%forc_rho_downscaled_col  , & ! Input:  [real(r8)  (:)   ]  atm density (kg/m**3)                             
+         forc_t    =>    atm2lnd_inst%forc_t_downscaled_col    , & ! Input:  [real(r8)  (:)   ]  atm temperature (K)                               
+         
+         ram1      =>    frictionvel_inst%ram1_patch           , & ! Input:  [real(r8)  (:)   ]  aerodynamical resistance (s/m)                    
+         fv        =>    frictionvel_inst%fv_patch             , & ! Input:  [real(r8)  (:)   ]  friction velocity (m/s)                           
+         
+         vlc_trb   =>    this%vlc_trb_patch                   , & ! Output:  [real(r8) (:,:) ]  Turbulent deposn velocity (m/s)                 
+         vlc_trb_1 =>    this%vlc_trb_1_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 1                   
+         vlc_trb_2 =>    this%vlc_trb_2_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 2                   
+         vlc_trb_3 =>    this%vlc_trb_3_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 3                   
+         vlc_trb_4 =>    this%vlc_trb_4_patch                   & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 4                   
+         )
+
+      do p = bounds%begp,bounds%endp
+         if (patch%active(p)) then
+            g = patch%gridcell(p)
+            c = patch%column(p)
+
+            ! from subroutine dst_dps_dry (consider adding sanity checks from line 212)
+            ! when code asks to use midlayer density, pressure, temperature,
+            ! I use the data coming in from the atmosphere, ie forc_t, forc_pbot, forc_rho
+
+            ! Quasi-laminar layer resistance: call rss_lmn_get
+            ! Size-independent thermokinetic properties
+
+            vsc_dyn_atm(p) = 1.72e-5_r8 * ((forc_t(c)/273.0_r8)**1.5_r8) * 393.0_r8 / &
+                 (forc_t(c)+120.0_r8)      ![kg m-1 s-1] RoY94 p. 102
+            mfp_atm = 2.0_r8 * vsc_dyn_atm(p) / &   ![m] SeP97 p. 455
+                 (forc_pbot(c)*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*forc_t(c))))
+            vsc_knm_atm(p) = vsc_dyn_atm(p) / forc_rho(c) ![m2 s-1] Kinematic viscosity of air
+
+            do m = 1, ndst
+               slp_crc(p,m) = 1.0_r8 + 2.0_r8 * mfp_atm * &
+                    (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
+                    this%dmt_vwr(m)   ![frc] Slip correction factor SeP97 p. 464
+               vlc_grv(p,m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * &
+                    grav * slp_crc(p,m) / vsc_dyn_atm(p)   ![m s-1] Stokes' settling velocity SeP97 p. 466
+               vlc_grv(p,m) = vlc_grv(p,m) * this%stk_crc(m)    ![m s-1] Correction to Stokes settling velocity
+            end do
+         end if
+      end do
+
+      do m = 1, ndst
+         do p = bounds%begp,bounds%endp
+            if (patch%active(p)) then
+               g = patch%gridcell(p)
+               c = patch%column(p)
+
+               stk_nbr = vlc_grv(p,m) * fv(p) * fv(p) / (grav * vsc_knm_atm(p))  ![frc] SeP97 p.965
+               dff_aer = SHR_CONST_BOLTZ * forc_t(c) * slp_crc(p,m) / &          ![m2 s-1]
+                    (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * this%dmt_vwr(m))     !SeP97 p.474
+               shm_nbr = vsc_knm_atm(p) / dff_aer                                ![frc] SeP97 p.972
+               shm_nbr_xpn = shm_nbr_xpn_lnd                                     ![frc]
+
+               ! fxm: Turning this on dramatically reduces
+               ! deposition velocity in low wind regimes
+               ! Schmidt number exponent is -2/3 over solid surfaces and
+               ! -1/2 over liquid surfaces SlS80 p. 1014
+               ! if (oro(i)==0.0) shm_nbr_xpn=shm_nbr_xpn_ocn else shm_nbr_xpn=shm_nbr_xpn_lnd
+               ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # 
+
+               tmp = shm_nbr**shm_nbr_xpn + 10.0_r8**(-3.0_r8/stk_nbr)
+               rss_lmn(p,m) = 1.0_r8 / (tmp * fv(p)) ![s m-1] SeP97 p.972,965
+            end if
+         end do
+      end do
+
+      ! Lowest layer: Turbulent deposition (CAM will calc. gravitational dep)
+
+      do m = 1, ndst
+         do p = bounds%begp,bounds%endp
+            if (patch%active(p)) then
+               rss_trb = ram1(p) + rss_lmn(p,m) + ram1(p) * rss_lmn(p,m) * vlc_grv(p,m) ![s m-1]
+               vlc_trb(p,m) = 1.0_r8 / rss_trb                                          ![m s-1]
+            end if
+         end do
+      end do
+
+      do p = bounds%begp,bounds%endp
+         if (patch%active(p)) then
+            vlc_trb_1(p) = vlc_trb(p,1)
+            vlc_trb_2(p) = vlc_trb(p,2)
+            vlc_trb_3(p) = vlc_trb(p,3)
+            vlc_trb_4(p) = vlc_trb(p,4)
+         end if
+      end do
+
+    end associate
+
+  end subroutine DustDryDep
+
+   !------------------------------------------------------------------------
+   subroutine InitDustVars(this, bounds)
+     !
+     ! !DESCRIPTION: 
+     !
+     ! Compute source efficiency factor from topography
+     ! Initialize other variables used in subroutine Dust:
+     ! ovr_src_snk_mss(m,n) and saltation_factor.
+     ! Define particle diameter and density needed by atm model
+     ! as well as by dry dep model
+     ! Source: Paul Ginoux (for source efficiency factor)
+     ! Modifications by C. Zender and later by S. Levis
+     ! Rest of subroutine from C. Zender's dust model
+     !
+     ! !USES
+     use shr_const_mod , only: SHR_CONST_PI, SHR_CONST_RDAIR
+     use shr_spfn_mod  , only: erf => shr_spfn_erf
+     use decompMod     , only : get_proc_bounds
+     !
+     ! !ARGUMENTS:
+     class(dust_base_type)  :: this
+     type(bounds_type), intent(in) :: bounds  
+     !
+     ! !LOCAL VARIABLES
+    integer  :: fc,c,l,m,n              ! indices
+    real(r8) :: ovr_src_snk_frc
+    real(r8) :: sqrt2lngsdi             ! [frc] Factor in erf argument
+    real(r8) :: lndmaxjovrdmdni         ! [frc] Factor in erf argument
+    real(r8) :: lndminjovrdmdni         ! [frc] Factor in erf argument
+    real(r8) :: ryn_nbr_frc_thr_prx_opt ! [frc] Threshold friction Reynolds number approximation for optimal size
+    real(r8) :: ryn_nbr_frc_thr_opt_fnc ! [frc] Threshold friction Reynolds factor for saltation calculation
+    real(r8) :: icf_fct                 ! Interpartical cohesive forces factor for saltation calc
+    real(r8) :: dns_fct                 ! Density ratio factor for saltation calculation
+    real(r8) :: dmt_min(ndst)           ! [m] Size grid minimum
+    real(r8) :: dmt_max(ndst)           ! [m] Size grid maximum
+    real(r8) :: dmt_ctr(ndst)           ! [m] Diameter at bin center
+    real(r8) :: dmt_dlt(ndst)           ! [m] Width of size bin
+    real(r8) :: slp_crc(ndst)           ! [frc] Slip correction factor
+    real(r8) :: vlm_rsl(ndst)           ! [m3 m-3] Volume concentration resolved
+    real(r8) :: vlc_stk(ndst)           ! [m s-1] Stokes settling velocity
+    real(r8) :: vlc_grv(ndst)           ! [m s-1] Settling velocity
+    real(r8) :: ryn_nbr_grv(ndst)       ! [frc] Reynolds number at terminal velocity
+    real(r8) :: cff_drg_grv(ndst)       ! [frc] Drag coefficient at terminal velocity
+    real(r8) :: tmp                     ! temporary 
+    real(r8) :: ln_gsd                  ! [frc] ln(gsd)
+    real(r8) :: gsd_anl                 ! [frc] Geometric standard deviation
+    real(r8) :: dmt_vma                 ! [m] Mass median diameter analytic She84 p.75 Tabl.1
+    real(r8) :: dmt_nma                 ! [m] Number median particle diameter
+    real(r8) :: lgn_dst                 ! Lognormal distribution at sz_ctr
+    real(r8) :: eps_max                 ! [frc] Relative accuracy for convergence
+    real(r8) :: eps_crr                 ! [frc] Current relative accuracy
+    real(r8) :: itr_idx                 ! [idx] Counting index
+    real(r8) :: dns_mdp                 ! [kg m-3] Midlayer density
+    real(r8) :: mfp_atm                 ! [m] Mean free path of air
+    real(r8) :: vsc_dyn_atm             ! [kg m-1 s-1] Dynamic viscosity of air
+    real(r8) :: vsc_knm_atm             ! [kg m-1 s-1] Kinematic viscosity of air
+    real(r8) :: vlc_grv_old             ! [m s-1] Previous gravitational settling velocity
+    real(r8) :: series_ratio            ! Factor for logarithmic grid
+    real(r8) :: lngsdsqrttwopi_rcp      ! Factor in lognormal distribution
+    real(r8) :: sz_min(sz_nbr)          ! [m] Size Bin minima
+    real(r8) :: sz_max(sz_nbr)          ! [m] Size Bin maxima
+    real(r8) :: sz_ctr(sz_nbr)          ! [m] Size Bin centers
+    real(r8) :: sz_dlt(sz_nbr)          ! [m] Size Bin widths
+    
+    ! constants
+    real(r8), allocatable :: dmt_vma_src(:) ! [m] Mass median diameter       BSM96 p. 73 Table 2
+    real(r8), allocatable :: gsd_anl_src(:) ! [frc] Geometric std deviation  BSM96 p. 73 Table 2
+    real(r8), allocatable :: mss_frc_src(:) ! [frc] Mass fraction            BSM96 p. 73 Table 2
+
+    real(r8) :: dmt_grd(5) =                  &     ! [m] Particle diameter grid
+         (/ 0.1e-6_r8, 1.0e-6_r8, 2.5e-6_r8, 5.0e-6_r8, 10.0e-6_r8 /)
+    real(r8), parameter :: dmt_slt_opt = 75.0e-6_r8    ! [m] Optim diam for saltation
+    real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles
+    !------------------------------------------------------------------------
+
+      ! allocate local variable
+      allocate (dmt_vma_src(dst_src_nbr))  
+      allocate (gsd_anl_src(dst_src_nbr))  
+      allocate (mss_frc_src(dst_src_nbr))  
+
+      dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /)        
+      gsd_anl_src(:) = (/ 2.10_r8     , 1.90_r8    , 1.60_r8     /)        
+      mss_frc_src(:) = (/ 0.036_r8    , 0.957_r8   , 0.007_r8 /)                  
+
+      ! the following comes from (1) szdstlgn.F subroutine ovr_src_snk_frc_get
+      !                      and (2) dstszdst.F subroutine dst_szdst_ini
+      ! purpose(1): given one set (the "source") of lognormal distributions,
+      !             and one set of bin boundaries (the "sink"), compute and return
+      !             the overlap factors between the source and sink distributions
+      ! purpose(2): set important statistics of size distributions
+
+      do m = 1, dst_src_nbr
+         sqrt2lngsdi = sqrt(2.0_r8) * log(gsd_anl_src(m))
+         do n = 1, ndst
+            lndmaxjovrdmdni = log(dmt_grd(n+1)/dmt_vma_src(m))
+            lndminjovrdmdni = log(dmt_grd(n  )/dmt_vma_src(m))
+            ovr_src_snk_frc = 0.5_r8 * (erf(lndmaxjovrdmdni/sqrt2lngsdi) - &
+                 erf(lndminjovrdmdni/sqrt2lngsdi))
+            this%ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m)
+         end do
+      end do
+
+      ! The following code from subroutine wnd_frc_thr_slt_get was placed 
+      ! here because saltation_factor needs to be defined just once
+
+      ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8
+
+      if (ryn_nbr_frc_thr_prx_opt < 0.03_r8) then
+         write(iulog,*) 'dstmbl: ryn_nbr_frc_thr_prx_opt < 0.03'
+         call endrun(msg=errMsg(sourcefile, __LINE__))
+      else if (ryn_nbr_frc_thr_prx_opt < 10.0_r8) then
+         ryn_nbr_frc_thr_opt_fnc = -1.0_r8 + 1.928_r8 * (ryn_nbr_frc_thr_prx_opt**0.0922_r8)
+         ryn_nbr_frc_thr_opt_fnc = 0.1291_r8 * 0.1291_r8 / ryn_nbr_frc_thr_opt_fnc
+      else
+         ryn_nbr_frc_thr_opt_fnc = 1.0_r8 - 0.0858_r8 * exp(-0.0617_r8*(ryn_nbr_frc_thr_prx_opt-10.0_r8))
+         ryn_nbr_frc_thr_opt_fnc = 0.120_r8 * 0.120_r8 * ryn_nbr_frc_thr_opt_fnc * ryn_nbr_frc_thr_opt_fnc
+      end if
+
+      icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8))
+      dns_fct = dns_slt * grav * dmt_slt_opt
+      this%saltation_factor = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc)
+
+      ! Introducing particle diameter. Needed by atm model and by dry dep model.
+      ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl,
+      ! grd_mk (dstpsd.F90) and subroutine lgn_evl (psdlgn.F90)
+
+      ! Charlie allows logarithmic or linear option for size distribution
+      ! however, he hardwires the distribution to logarithmic in his code
+      ! therefore, I take his logarithmic code only
+      ! furthermore, if dst_nbr == 4, he overrides the automatic grid calculation
+      ! he currently works with dst_nbr = 4, so I only take the relevant code
+      ! if ndst ever becomes different from 4, must add call grd_mk (dstpsd.F90)
+      ! as done in subroutine dst_psd_ini
+      ! note that here ndst = dst_nbr
+
+      ! Override automatic grid with preset grid if available
+
+      if (ndst == 4) then
+         do n = 1, ndst
+            dmt_min(n) = dmt_grd(n)                       ![m] Max diameter in bin
+            dmt_max(n) = dmt_grd(n+1)                     ![m] Min diameter in bin
+            dmt_ctr(n) = 0.5_r8 * (dmt_min(n)+dmt_max(n)) ![m] Diameter at bin ctr
+            dmt_dlt(n) = dmt_max(n)-dmt_min(n)            ![m] Width of size bin
+         end do
+      else
+         write(iulog,*) 'Dustini error: ndst must equal to 4 with current code'
+         call endrun(msg=errMsg(sourcefile, __LINE__))
+         !see more comments above end if ndst == 4
+      end if
+
+      ! Bin physical properties
+
+      gsd_anl = 2.0_r8      ! [frc] Geometric std dev PaG77 p. 2080 Table1
+      ln_gsd = log(gsd_anl)
+
+      ! Set a fundamental statistic for each bin
+
+      dmt_vma = 3.5000e-6_r8 ! [m] Mass median diameter analytic She84 p.75 Table1
+
+      ! Compute analytic size statistics
+      ! Convert mass median diameter to number median diameter (call vma2nma)
+
+      dmt_nma = dmt_vma * exp(-3.0_r8*ln_gsd*ln_gsd) ! [m]
+
+      ! Compute resolved size statistics for each size distribution
+      ! In C. Zender's code call dst_sz_rsl
+
+      do n = 1, ndst
+
+         series_ratio = (dmt_max(n)/dmt_min(n))**(1.0_r8/sz_nbr)
+         sz_min(1) = dmt_min(n)
+         do m = 2, sz_nbr                            ! Loop starts at 2
+            sz_min(m) = sz_min(m-1) * series_ratio
+         end do
+
+         ! Derived grid values
+         do m = 1, sz_nbr-1                          ! Loop ends at sz_nbr-1
+            sz_max(m) = sz_min(m+1)                  ! [m]
+         end do
+         sz_max(sz_nbr) = dmt_max(n)                 ! [m]
+
+         ! Final derived grid values
+         do m = 1, sz_nbr
+            sz_ctr(m) = 0.5_r8 * (sz_min(m)+sz_max(m))
+            sz_dlt(m) = sz_max(m)-sz_min(m)
+         end do
+
+         lngsdsqrttwopi_rcp = 1.0_r8 / (ln_gsd*sqrt(2.0_r8*SHR_CONST_PI))
+         this%dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved
+         vlm_rsl(n) = 0.0_r8 ! [m3 m-3] Volume concentration resolved
+
+         do m = 1, sz_nbr
+
+            ! Evaluate lognormal distribution for these sizes (call lgn_evl)
+            tmp = log(sz_ctr(m)/dmt_nma) / ln_gsd
+            lgn_dst = lngsdsqrttwopi_rcp * exp(-0.5_r8*tmp*tmp) / sz_ctr(m)
+
+            ! Integrate moments of size distribution
+            this%dmt_vwr(n) = this%dmt_vwr(n) + sz_ctr(m) *                    &
+                 SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume
+                 lgn_dst * sz_dlt(m)                ![# m-3] Number concentrn
+            vlm_rsl(n) = vlm_rsl(n) +                                &
+                 SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume
+                 lgn_dst * sz_dlt(m)                ![# m-3] Number concentrn
+
+         end do
+
+         this%dmt_vwr(n) = this%dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved
+
+      end do
+
+      ! calculate correction to Stokes' settling velocity (subroutine stk_crc_get)
+
+      eps_max = 1.0e-4_r8
+      dns_mdp = 100000._r8 / (295.0_r8*SHR_CONST_RDAIR) ![kg m-3] const prs_mdp & tpt_vrt
+
+      ! Size-independent thermokinetic properties
+
+      vsc_dyn_atm = 1.72e-5_r8 * ((295.0_r8/273.0_r8)**1.5_r8) * 393.0_r8 / &
+           (295.0_r8+120.0_r8)      ![kg m-1 s-1] RoY94 p.102 tpt_mdp=295.0
+      mfp_atm = 2.0_r8 * vsc_dyn_atm / &  !SeP97 p. 455 constant prs_mdp, tpt_mdp
+           (100000._r8*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*295.0_r8)))
+      vsc_knm_atm = vsc_dyn_atm / dns_mdp ![m2 s-1] Kinematic viscosity of air
+
+      do m = 1, ndst
+         slp_crc(m) = 1.0_r8 + 2.0_r8 * mfp_atm *                      &
+              (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
+              this%dmt_vwr(m)                      ! [frc] Slip correction factor SeP97 p.464
+         vlc_stk(m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * &
+              grav * slp_crc(m) / vsc_dyn_atm ! [m s-1] SeP97 p.466
+      end do
+
+      ! For Reynolds number flows Re < 0.1 Stokes' velocity is valid for
+      ! vlc_grv SeP97 p. 466 (8.42). For larger Re, inertial effects become
+      ! important and empirical drag coefficients must be employed
+      ! Implicit equation for Re, Cd, and Vt is SeP97 p. 467 (8.44)
+      ! Using Stokes' velocity rather than iterative solution with empirical
+      ! drag coefficient causes 60% errors for D = 200 um SeP97 p. 468
+
+      ! Iterative solution for drag coefficient, Reynolds number, and terminal veloc
+      do m = 1, ndst
+
+         ! Initialize accuracy and counter
+         eps_crr = eps_max + 1.0_r8  ![frc] Current relative accuracy
+         itr_idx = 0                 ![idx] Counting index
+
+         ! Initial guess for vlc_grv is exact for Re < 0.1
+         vlc_grv(m) = vlc_stk(m)     ![m s-1]
+
+         do while(eps_crr > eps_max)
+
+            ! Save terminal velocity for convergence test
+            vlc_grv_old = vlc_grv(m) ![m s-1]
+            ryn_nbr_grv(m) = vlc_grv(m) * this%dmt_vwr(m) / vsc_knm_atm !SeP97 p.460
+
+            ! Update drag coefficient based on new Reynolds number
+            if (ryn_nbr_grv(m) < 0.1_r8) then
+               cff_drg_grv(m) = 24.0_r8 / ryn_nbr_grv(m) !Stokes' law Sep97 p.463 (8.32)
+            else if (ryn_nbr_grv(m) < 2.0_r8) then
+               cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) *    &
+                    (1.0_r8 + 3.0_r8*ryn_nbr_grv(m)/16.0_r8 + &
+                    9.0_r8*ryn_nbr_grv(m)*ryn_nbr_grv(m)*     &
+                    log(2.0_r8*ryn_nbr_grv(m))/160.0_r8)        !Sep97 p.463 (8.32)
+            else if (ryn_nbr_grv(m) < 500.0_r8) then
+               cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) * &
+                    (1.0_r8 + 0.15_r8*ryn_nbr_grv(m)**0.687_r8) !Sep97 p.463 (8.32)
+            else if (ryn_nbr_grv(m) < 2.0e5_r8) then
+               cff_drg_grv(m) = 0.44_r8                         !Sep97 p.463 (8.32)
+            else
+               write(iulog,'(a,es9.2)') "ryn_nbr_grv(m) = ",ryn_nbr_grv(m)
+               write(iulog,*)'Dustini error: Reynolds number too large in stk_crc_get()'
+               call endrun(msg=errMsg(sourcefile, __LINE__))
+            end if
+
+            ! Update terminal velocity based on new Reynolds number and drag coeff
+            ! [m s-1] Terminal veloc SeP97 p.467 (8.44)
+
+            vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / &
+                 (3.0_r8*cff_drg_grv(m)*dns_mdp))   
+            eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence
+            if (itr_idx == 12) then
+               ! Numerical pingpong may occur when Re = 0.1, 2.0, or 500.0
+               ! due to discontinuities in derivative of drag coefficient
+               vlc_grv(m) = 0.5_r8 * (vlc_grv(m)+vlc_grv_old)  ! [m s-1]
+            end if
+            if (itr_idx > 20) then
+               write(iulog,*) 'Dustini error: Terminal velocity not converging ',&
+                    ' in stk_crc_get(), breaking loop...'
+               goto 100                                        !to next iteration
+            end if
+            itr_idx = itr_idx + 1
+
+         end do                                                !end while
+
+100      continue   !Label to jump to when iteration does not converge
+      end do   !end loop over size
+
+      ! Compute factors to convert Stokes' settling velocities to
+      ! actual settling velocities
+
+      do m = 1, ndst
+         this%stk_crc(m) = vlc_grv(m) / vlc_stk(m)
+      end do
+
+  end subroutine InitDustVars
+
+end module DustEmisBase
diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index db6f93581a..442fddbedf 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -15,12 +15,12 @@ module DustEmisZender2003
   use shr_kind_mod         , only : r8 => shr_kind_r8 
   use shr_log_mod          , only : errMsg => shr_log_errMsg
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
-  use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr
+  use clm_varpar           , only : dst_src_nbr, ndst
   use clm_varcon           , only : grav, spval
   use landunit_varcon      , only : istcrop, istsoil
   use clm_varctl           , only : iulog
   use abortutils           , only : endrun
-  use decompMod            , only : bounds_type, subgrid_level_landunit, subgrid_level_patch
+  use decompMod            , only : bounds_type, subgrid_level_landunit
   use atm2lndType          , only : atm2lnd_type
   use SoilStateType        , only : soilstate_type
   use CanopyStateType      , only : canopystate_type
@@ -28,9 +28,9 @@ module DustEmisZender2003
   use WaterDiagnosticBulkType       , only : waterdiagnosticbulk_type
   use FrictionVelocityMod  , only : frictionvel_type
   use LandunitType         , only : lun
-  use ColumnType           , only : col
   use PatchType            , only : patch
   use ZenderSoilErodStreamType,  only : soil_erod_stream_type
+  use DustEmisBase         , only : dust_base_type
   use clm_varctl           , only : dust_emis_method
   !  
   ! !PUBLIC TYPES
@@ -39,39 +39,22 @@ module DustEmisZender2003
   !
   ! !PRIVATE DATA:
   !
-  real(r8), parameter :: dns_aer = 2.5e+3_r8        ![kg m-3] Aerosol density
   !
   ! !PUBLIC DATA TYPES:
   !
-  type, public :: dust_type
-
-     real(r8) , allocatable, private :: ovr_src_snk_mss(:,:)       ! overlap factors between the source and sin
-     real(r8) , allocatable, private :: dmt_vwr(:)                 ! [m] Mass-weighted mean diameter resolved
-     real(r8) , allocatable, private :: stk_crc(:)                 ! [frc] Correction to Stokes settling velocity
-     real(r8), private          :: saltation_factor                ! Factor in saltation computation (named as in Charlie's code)
-     real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) 
-     real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:)   ! total dust flux into atmosphere
-     real(r8), pointer, private :: vlc_trb_patch             (:,:) ! turbulent deposition velocity  (m/s) (ndst) 
-     real(r8), pointer, private :: vlc_trb_1_patch           (:)   ! turbulent deposition velocity 1(m/s)
-     real(r8), pointer, private :: vlc_trb_2_patch           (:)   ! turbulent deposition velocity 2(m/s)
-     real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
-     real(r8), pointer, private :: vlc_trb_4_patch           (:)   ! turbulent deposition velocity 4(m/s)
+  type, public, extends(dust_base_type) :: dust_type
+
+     real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! [dimensionless] basin factor, or soil rodibility, time-constant
      type(soil_erod_stream_type), private :: soil_erod_stream      ! Zender soil erodibility stream data
-     real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! [dimensionless] basin factor, or soil erodibility, time-constant
 
    contains
 
-     procedure , public  :: Init
+     procedure , public  :: Init => InitZender2003
      procedure , public  :: DustEmission    ! Dust mobilization
-     procedure , public  :: DustDryDep      ! Turbulent dry deposition for dust
-     procedure , public  :: WritePatchToLog ! Write information on the given patch to the log file
-     procedure , public  :: GetPatchVars    ! Get important variables on a given patch
-     procedure , public  :: GetConstVars    ! Get important constant variables
-     procedure , public  :: Clean           ! Deallocate data 
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory  
+     procedure , public  :: Clean => CleanZender2003
+     procedure , private :: InitAllocate    ! Allocate data
+     procedure , private :: InitHistory     ! History initialization
      procedure , private :: InitCold     
-     procedure , private :: InitDustVars    ! Initialize variables used in DustEmission method
 
   end type dust_type
   !------------------------------------------------------------------------
@@ -82,76 +65,52 @@ module DustEmisZender2003
 contains
 
   !------------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
+  subroutine InitZender2003(this, bounds, NLFilename)
 
+   ! Initialization for this extended class, calling base level initiation and adding to it
     class(dust_type) :: this
     type(bounds_type), intent(in) :: bounds  
     character(len=*),  intent(in) :: NLFilename
 
     call this%soil_erod_stream%Init( bounds, NLFilename )
+    call this%InitBase(bounds, NLFilename)
     call this%InitAllocate (bounds)
     call this%InitHistory  (bounds)
     call this%InitCold     (bounds)
-    call this%InitDustVars (bounds)
-
-  end subroutine Init
-
 
+  end subroutine InitZender2003
 
   !------------------------------------------------------------------------
-  subroutine Clean(this)
+  subroutine InitAllocate(this, bounds)
    !
    ! !ARGUMENTS:
    class (dust_type) :: this
+   type(bounds_type), intent(in) :: bounds  
    !
    ! !LOCAL VARIABLES:
+   integer :: begc,endc
    !------------------------------------------------------------------------
 
-   deallocate(this%flx_mss_vrt_dst_patch)
-   deallocate(this%flx_mss_vrt_dst_tot_patch)
-   deallocate(this%vlc_trb_patch)
-   deallocate(this%vlc_trb_1_patch)
-   deallocate(this%vlc_trb_2_patch)
-   deallocate(this%vlc_trb_3_patch)
-   deallocate(this%vlc_trb_4_patch)
-   deallocate(this%mbl_bsn_fct_col)
+   begc = bounds%begc ; endc = bounds%endc
 
-   deallocate (this%ovr_src_snk_mss)
-   deallocate (this%dmt_vwr)
-   deallocate (this%stk_crc)
+   allocate(this%mbl_bsn_fct_col           (begc:endc))        ; this%mbl_bsn_fct_col           (:)   = nan
 
- end subroutine Clean
+ end subroutine InitAllocate
 
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
+   !------------------------------------------------------------------------
+  subroutine CleanZender2003(this)
     !
+    ! Deallocation for this extended class, calling base level deallocation and adding to it
     ! !ARGUMENTS:
     class (dust_type) :: this
-    type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
-    integer :: begp,endp
-    integer :: begc,endc
     !------------------------------------------------------------------------
 
-    begp = bounds%begp ; endp = bounds%endp
-    begc = bounds%begc ; endc = bounds%endc
+    call this%CleanBase()
+    deallocate(this%mbl_bsn_fct_col)
 
-    allocate(this%flx_mss_vrt_dst_patch     (begp:endp,1:ndst)) ; this%flx_mss_vrt_dst_patch     (:,:) = nan
-    allocate(this%flx_mss_vrt_dst_tot_patch (begp:endp))        ; this%flx_mss_vrt_dst_tot_patch (:)   = nan
-    allocate(this%vlc_trb_patch             (begp:endp,1:ndst)) ; this%vlc_trb_patch             (:,:) = nan
-    allocate(this%vlc_trb_1_patch           (begp:endp))        ; this%vlc_trb_1_patch           (:)   = nan
-    allocate(this%vlc_trb_2_patch           (begp:endp))        ; this%vlc_trb_2_patch           (:)   = nan 
-    allocate(this%vlc_trb_3_patch           (begp:endp))        ; this%vlc_trb_3_patch           (:)   = nan
-    allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
-    allocate(this%mbl_bsn_fct_col           (begc:endc))        ; this%mbl_bsn_fct_col           (:)   = nan
-
-    allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst))           ; this%ovr_src_snk_mss           (:,:) = nan
-    allocate (this%dmt_vwr(ndst))                               ; this%dmt_vwr                   (:)   = nan
-    allocate (this%stk_crc(ndst))                               ; this%stk_crc                   (:)   = nan
-
-
-  end subroutine InitAllocate
+  end subroutine CleanZender2003
 
   !------------------------------------------------------------------------
   subroutine InitHistory(this, bounds)
@@ -165,45 +124,16 @@ subroutine InitHistory(this, bounds)
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
-    integer :: begp,endp
     integer :: begc,endc
     !------------------------------------------------------------------------
 
-    begp = bounds%begp; endp = bounds%endp
     begc = bounds%begc; endc = bounds%endc
 
-    this%flx_mss_vrt_dst_tot_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DSTFLXT', units='kg/m2/s',  &
-         avgflag='A', long_name='total surface dust emission', &
-         ptr_patch=this%flx_mss_vrt_dst_tot_patch, set_lake=0._r8, set_urb=0._r8)
-
-    this%vlc_trb_1_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB1', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 1', &
-         ptr_patch=this%vlc_trb_1_patch, default='inactive')
-
-    this%vlc_trb_2_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB2', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 2', &
-         ptr_patch=this%vlc_trb_2_patch, default='inactive')
-
-    this%vlc_trb_3_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB3', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 3', &
-         ptr_patch=this%vlc_trb_3_patch, default='inactive')
-
-    this%vlc_trb_4_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB4', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 4', &
-         ptr_patch=this%vlc_trb_4_patch, default='inactive')
-
-    if (dust_emis_method == 'Zender_2003') then
-       if ( this%soil_erod_stream%UseStreams() )then
-          this%mbl_bsn_fct_col(begc:endc) = spval
-          call hist_addfld1d (fname='LND_MBL', units='fraction',  &
+    if ( this%soil_erod_stream%UseStreams() )then
+       this%mbl_bsn_fct_col(begc:endc) = spval
+       call hist_addfld1d (fname='LND_MBL', units='fraction',  &
                avgflag='A', long_name='Soil erodibility factor', &
                ptr_col=this%mbl_bsn_fct_col, default='inactive')
-       end if
     end if
 
   end subroutine InitHistory
@@ -244,63 +174,6 @@ subroutine InitCold(this, bounds)
 
   end subroutine InitCold
 
-    !-----------------------------------------------------------------------
-
-  subroutine WritePatchToLog(this, p)
-    !
-    ! !DESCRIPTION:
-    ! Write out information on dust emisisons for this patch to the log file
-    ! !ARGUMENTS:
-    class(dust_type), intent(in) :: this
-    integer         , intent(in) :: p      ! Patch to display
-
-    write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p)
-    write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p)
-    write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p)
-    write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p)
-    write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p)
-  end subroutine WritePatchToLog
-
-    !-----------------------------------------------------------------------
-
-  subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, &
-                          vlc_trb_2, vlc_trb_3, vlc_trb_4)
-   !
-   ! !DESCRIPTION:
-   ! Get important variables on the given patch
-   ! !ARGUMENTS:
-   class(dust_type)  , intent(in)  :: this
-   integer           , intent(in)  :: p      ! Patch to get
-   real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst)
-   real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot
-   real(r8), optional, intent(out) :: vlc_trb(ndst)
-   real(r8), optional, intent(out) :: vlc_trb_1
-   real(r8), optional, intent(out) :: vlc_trb_2
-   real(r8), optional, intent(out) :: vlc_trb_3
-   real(r8), optional, intent(out) :: vlc_trb_4
-
-   if ( present(flx_mss_vrt_dst    ) ) flx_mss_vrt_dst     = this%flx_mss_vrt_dst_patch(p,:)
-   if ( present(flx_mss_vrt_dst_tot) ) flx_mss_vrt_dst_tot = this%flx_mss_vrt_dst_tot_patch(p)
-   if ( present(vlc_trb  ) ) vlc_trb   = this%vlc_trb_patch(p,:)
-   if ( present(vlc_trb_1) ) vlc_trb_1 = this%vlc_trb_1_patch(p)
-   if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p)
-   if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p)
-   if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p)
-  end subroutine GetPatchVars
-
-    !-----------------------------------------------------------------------
-
-  subroutine GetConstVars(this, SaltationFactor )
-  !
-  ! !DESCRIPTION:
-  ! Get important constant variables
-  ! !ARGUMENTS:
-    class(dust_type)  , intent(in)  :: this
-    real(r8)          , intent(out) :: SaltationFactor
-
-    SaltationFactor = this%saltation_factor
-  end subroutine GetConstVars
-
   !------------------------------------------------------------------------
   subroutine DustEmission (this, bounds, &
        num_nolakep, filter_nolakep, &
@@ -588,448 +461,4 @@ subroutine DustEmission (this, bounds, &
 
   end subroutine DustEmission
 
-   !------------------------------------------------------------------------
-  subroutine DustDryDep (this, bounds, &
-       atm2lnd_inst, frictionvel_inst)
-    !
-    ! !DESCRIPTION: 
-    !
-    ! Determine Turbulent dry deposition for dust. Calculate the turbulent 
-    ! component of dust dry deposition, (the turbulent deposition velocity 
-    ! through the lowest atmospheric layer. CAM will calculate the settling 
-    ! velocity through the whole atmospheric column. The two calculations 
-    ! will determine the dust dry deposition flux to the surface.
-    ! Note: Same process should occur over oceans. For the coupled CESM,
-    ! we may find it more efficient to let CAM calculate the turbulent dep
-    ! velocity over all surfaces. This would require passing the
-    ! aerodynamic resistance, ram(1), and the friction velocity, fv, from
-    ! the land to the atmosphere component. In that case, dustini need not
-    ! calculate particle diamter (dmt_vwr) and particle density (dns_aer).
-    ! Source: C. Zender's dry deposition code
-    !
-    ! !USES
-    use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ
-    !
-    ! !ARGUMENTS:
-    class (dust_type)                      :: this
-    type(bounds_type)      , intent(in)    :: bounds 
-    type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
-    type(frictionvel_type) , intent(in)    :: frictionvel_inst
-    !
-    ! !LOCAL VARIABLES
-    integer  :: p,c,g,m,n                             ! indices
-    real(r8) :: vsc_dyn_atm(bounds%begp:bounds%endp)  ! [kg m-1 s-1] Dynamic viscosity of air
-    real(r8) :: vsc_knm_atm(bounds%begp:bounds%endp)  ! [m2 s-1] Kinematic viscosity of atmosphere
-    real(r8) :: shm_nbr_xpn                           ! [frc] Sfc-dep exponent for aerosol-diffusion dependence on Schmidt number
-    real(r8) :: shm_nbr                               ! [frc] Schmidt number
-    real(r8) :: stk_nbr                               ! [frc] Stokes number
-    real(r8) :: mfp_atm                               ! [m] Mean free path of air
-    real(r8) :: dff_aer                               ! [m2 s-1] Brownian diffusivity of particle
-    real(r8) :: rss_trb                               ! [s m-1] Resistance to turbulent deposition
-    real(r8) :: slp_crc(bounds%begp:bounds%endp,ndst) ! [frc] Slip correction factor
-    real(r8) :: vlc_grv(bounds%begp:bounds%endp,ndst) ! [m s-1] Settling velocity
-    real(r8) :: rss_lmn(bounds%begp:bounds%endp,ndst) ! [s m-1] Quasi-laminar layer resistance
-    real(r8) :: tmp                                   ! temporary 
-    real(r8), parameter::shm_nbr_xpn_lnd=-2._r8/3._r8 ![frc] shm_nbr_xpn over land
-    !------------------------------------------------------------------------
-
-    associate(                                                   & 
-         forc_pbot =>    atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8)  (:)   ]  atm pressure (Pa)                                 
-         forc_rho  =>    atm2lnd_inst%forc_rho_downscaled_col  , & ! Input:  [real(r8)  (:)   ]  atm density (kg/m**3)                             
-         forc_t    =>    atm2lnd_inst%forc_t_downscaled_col    , & ! Input:  [real(r8)  (:)   ]  atm temperature (K)                               
-         
-         ram1      =>    frictionvel_inst%ram1_patch           , & ! Input:  [real(r8)  (:)   ]  aerodynamical resistance (s/m)                    
-         fv        =>    frictionvel_inst%fv_patch             , & ! Input:  [real(r8)  (:)   ]  friction velocity (m/s)                           
-         
-         vlc_trb   =>    this%vlc_trb_patch                   , & ! Output:  [real(r8) (:,:) ]  Turbulent deposn velocity (m/s)                 
-         vlc_trb_1 =>    this%vlc_trb_1_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 1                   
-         vlc_trb_2 =>    this%vlc_trb_2_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 2                   
-         vlc_trb_3 =>    this%vlc_trb_3_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 3                   
-         vlc_trb_4 =>    this%vlc_trb_4_patch                   & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 4                   
-         )
-
-      do p = bounds%begp,bounds%endp
-         if (patch%active(p)) then
-            g = patch%gridcell(p)
-            c = patch%column(p)
-
-            ! from subroutine dst_dps_dry (consider adding sanity checks from line 212)
-            ! when code asks to use midlayer density, pressure, temperature,
-            ! I use the data coming in from the atmosphere, ie forc_t, forc_pbot, forc_rho
-
-            ! Quasi-laminar layer resistance: call rss_lmn_get
-            ! Size-independent thermokinetic properties
-
-            vsc_dyn_atm(p) = 1.72e-5_r8 * ((forc_t(c)/273.0_r8)**1.5_r8) * 393.0_r8 / &
-                 (forc_t(c)+120.0_r8)      ![kg m-1 s-1] RoY94 p. 102
-            mfp_atm = 2.0_r8 * vsc_dyn_atm(p) / &   ![m] SeP97 p. 455
-                 (forc_pbot(c)*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*forc_t(c))))
-            vsc_knm_atm(p) = vsc_dyn_atm(p) / forc_rho(c) ![m2 s-1] Kinematic viscosity of air
-
-            do m = 1, ndst
-               slp_crc(p,m) = 1.0_r8 + 2.0_r8 * mfp_atm * &
-                    (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
-                    this%dmt_vwr(m)   ![frc] Slip correction factor SeP97 p. 464
-               vlc_grv(p,m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * &
-                    grav * slp_crc(p,m) / vsc_dyn_atm(p)   ![m s-1] Stokes' settling velocity SeP97 p. 466
-               vlc_grv(p,m) = vlc_grv(p,m) * this%stk_crc(m)    ![m s-1] Correction to Stokes settling velocity
-            end do
-         end if
-      end do
-
-      do m = 1, ndst
-         do p = bounds%begp,bounds%endp
-            if (patch%active(p)) then
-               g = patch%gridcell(p)
-               c = patch%column(p)
-
-               stk_nbr = vlc_grv(p,m) * fv(p) * fv(p) / (grav * vsc_knm_atm(p))  ![frc] SeP97 p.965
-               dff_aer = SHR_CONST_BOLTZ * forc_t(c) * slp_crc(p,m) / &          ![m2 s-1]
-                    (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * this%dmt_vwr(m))     !SeP97 p.474
-               shm_nbr = vsc_knm_atm(p) / dff_aer                                ![frc] SeP97 p.972
-               shm_nbr_xpn = shm_nbr_xpn_lnd                                     ![frc]
-
-               ! fxm: Turning this on dramatically reduces
-               ! deposition velocity in low wind regimes
-               ! Schmidt number exponent is -2/3 over solid surfaces and
-               ! -1/2 over liquid surfaces SlS80 p. 1014
-               ! if (oro(i)==0.0) shm_nbr_xpn=shm_nbr_xpn_ocn else shm_nbr_xpn=shm_nbr_xpn_lnd
-               ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # 
-
-               tmp = shm_nbr**shm_nbr_xpn + 10.0_r8**(-3.0_r8/stk_nbr)
-               rss_lmn(p,m) = 1.0_r8 / (tmp * fv(p)) ![s m-1] SeP97 p.972,965
-            end if
-         end do
-      end do
-
-      ! Lowest layer: Turbulent deposition (CAM will calc. gravitational dep)
-
-      do m = 1, ndst
-         do p = bounds%begp,bounds%endp
-            if (patch%active(p)) then
-               rss_trb = ram1(p) + rss_lmn(p,m) + ram1(p) * rss_lmn(p,m) * vlc_grv(p,m) ![s m-1]
-               vlc_trb(p,m) = 1.0_r8 / rss_trb                                          ![m s-1]
-            end if
-         end do
-      end do
-
-      do p = bounds%begp,bounds%endp
-         if (patch%active(p)) then
-            vlc_trb_1(p) = vlc_trb(p,1)
-            vlc_trb_2(p) = vlc_trb(p,2)
-            vlc_trb_3(p) = vlc_trb(p,3)
-            vlc_trb_4(p) = vlc_trb(p,4)
-         end if
-      end do
-
-    end associate
-
-  end subroutine DustDryDep
-
-   !------------------------------------------------------------------------
-   subroutine InitDustVars(this, bounds)
-     !
-     ! !DESCRIPTION: 
-     !
-     ! Compute source efficiency factor from topography
-     ! Initialize other variables used in subroutine Dust:
-     ! ovr_src_snk_mss(m,n) and saltation_factor.
-     ! Define particle diameter and density needed by atm model
-     ! as well as by dry dep model
-     ! Source: Paul Ginoux (for source efficiency factor)
-     ! Modifications by C. Zender and later by S. Levis
-     ! Rest of subroutine from C. Zender's dust model
-     !
-     ! !USES
-     use shr_const_mod , only: SHR_CONST_PI, SHR_CONST_RDAIR
-     use shr_spfn_mod  , only: erf => shr_spfn_erf
-     use decompMod     , only : get_proc_bounds
-     !
-     ! !ARGUMENTS:
-     class(dust_type)  :: this
-     type(bounds_type), intent(in) :: bounds  
-     !
-     ! !LOCAL VARIABLES
-    integer  :: fc,c,l,m,n              ! indices
-    real(r8) :: ovr_src_snk_frc
-    real(r8) :: sqrt2lngsdi             ! [frc] Factor in erf argument
-    real(r8) :: lndmaxjovrdmdni         ! [frc] Factor in erf argument
-    real(r8) :: lndminjovrdmdni         ! [frc] Factor in erf argument
-    real(r8) :: ryn_nbr_frc_thr_prx_opt ! [frc] Threshold friction Reynolds number approximation for optimal size
-    real(r8) :: ryn_nbr_frc_thr_opt_fnc ! [frc] Threshold friction Reynolds factor for saltation calculation
-    real(r8) :: icf_fct                 ! Interpartical cohesive forces factor for saltation calc
-    real(r8) :: dns_fct                 ! Density ratio factor for saltation calculation
-    real(r8) :: dmt_min(ndst)           ! [m] Size grid minimum
-    real(r8) :: dmt_max(ndst)           ! [m] Size grid maximum
-    real(r8) :: dmt_ctr(ndst)           ! [m] Diameter at bin center
-    real(r8) :: dmt_dlt(ndst)           ! [m] Width of size bin
-    real(r8) :: slp_crc(ndst)           ! [frc] Slip correction factor
-    real(r8) :: vlm_rsl(ndst)           ! [m3 m-3] Volume concentration resolved
-    real(r8) :: vlc_stk(ndst)           ! [m s-1] Stokes settling velocity
-    real(r8) :: vlc_grv(ndst)           ! [m s-1] Settling velocity
-    real(r8) :: ryn_nbr_grv(ndst)       ! [frc] Reynolds number at terminal velocity
-    real(r8) :: cff_drg_grv(ndst)       ! [frc] Drag coefficient at terminal velocity
-    real(r8) :: tmp                     ! temporary 
-    real(r8) :: ln_gsd                  ! [frc] ln(gsd)
-    real(r8) :: gsd_anl                 ! [frc] Geometric standard deviation
-    real(r8) :: dmt_vma                 ! [m] Mass median diameter analytic She84 p.75 Tabl.1
-    real(r8) :: dmt_nma                 ! [m] Number median particle diameter
-    real(r8) :: lgn_dst                 ! Lognormal distribution at sz_ctr
-    real(r8) :: eps_max                 ! [frc] Relative accuracy for convergence
-    real(r8) :: eps_crr                 ! [frc] Current relative accuracy
-    real(r8) :: itr_idx                 ! [idx] Counting index
-    real(r8) :: dns_mdp                 ! [kg m-3] Midlayer density
-    real(r8) :: mfp_atm                 ! [m] Mean free path of air
-    real(r8) :: vsc_dyn_atm             ! [kg m-1 s-1] Dynamic viscosity of air
-    real(r8) :: vsc_knm_atm             ! [kg m-1 s-1] Kinematic viscosity of air
-    real(r8) :: vlc_grv_old             ! [m s-1] Previous gravitational settling velocity
-    real(r8) :: series_ratio            ! Factor for logarithmic grid
-    real(r8) :: lngsdsqrttwopi_rcp      ! Factor in lognormal distribution
-    real(r8) :: sz_min(sz_nbr)          ! [m] Size Bin minima
-    real(r8) :: sz_max(sz_nbr)          ! [m] Size Bin maxima
-    real(r8) :: sz_ctr(sz_nbr)          ! [m] Size Bin centers
-    real(r8) :: sz_dlt(sz_nbr)          ! [m] Size Bin widths
-    
-    ! constants
-    real(r8), allocatable :: dmt_vma_src(:) ! [m] Mass median diameter       BSM96 p. 73 Table 2
-    real(r8), allocatable :: gsd_anl_src(:) ! [frc] Geometric std deviation  BSM96 p. 73 Table 2
-    real(r8), allocatable :: mss_frc_src(:) ! [frc] Mass fraction            BSM96 p. 73 Table 2
-
-    real(r8) :: dmt_grd(5) =                  &     ! [m] Particle diameter grid
-         (/ 0.1e-6_r8, 1.0e-6_r8, 2.5e-6_r8, 5.0e-6_r8, 10.0e-6_r8 /)
-    real(r8), parameter :: dmt_slt_opt = 75.0e-6_r8    ! [m] Optim diam for saltation
-    real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles
-    !------------------------------------------------------------------------
-
-      ! allocate local variable
-      allocate (dmt_vma_src(dst_src_nbr))  
-      allocate (gsd_anl_src(dst_src_nbr))  
-      allocate (mss_frc_src(dst_src_nbr))  
-
-      dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /)        
-      gsd_anl_src(:) = (/ 2.10_r8     , 1.90_r8    , 1.60_r8     /)        
-      mss_frc_src(:) = (/ 0.036_r8    , 0.957_r8   , 0.007_r8 /)                  
-
-      ! the following comes from (1) szdstlgn.F subroutine ovr_src_snk_frc_get
-      !                      and (2) dstszdst.F subroutine dst_szdst_ini
-      ! purpose(1): given one set (the "source") of lognormal distributions,
-      !             and one set of bin boundaries (the "sink"), compute and return
-      !             the overlap factors between the source and sink distributions
-      ! purpose(2): set important statistics of size distributions
-
-      do m = 1, dst_src_nbr
-         sqrt2lngsdi = sqrt(2.0_r8) * log(gsd_anl_src(m))
-         do n = 1, ndst
-            lndmaxjovrdmdni = log(dmt_grd(n+1)/dmt_vma_src(m))
-            lndminjovrdmdni = log(dmt_grd(n  )/dmt_vma_src(m))
-            ovr_src_snk_frc = 0.5_r8 * (erf(lndmaxjovrdmdni/sqrt2lngsdi) - &
-                 erf(lndminjovrdmdni/sqrt2lngsdi))
-            this%ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m)
-         end do
-      end do
-
-      ! The following code from subroutine wnd_frc_thr_slt_get was placed 
-      ! here because saltation_factor needs to be defined just once
-
-      ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8
-
-      if (ryn_nbr_frc_thr_prx_opt < 0.03_r8) then
-         write(iulog,*) 'dstmbl: ryn_nbr_frc_thr_prx_opt < 0.03'
-         call endrun(msg=errMsg(sourcefile, __LINE__))
-      else if (ryn_nbr_frc_thr_prx_opt < 10.0_r8) then
-         ryn_nbr_frc_thr_opt_fnc = -1.0_r8 + 1.928_r8 * (ryn_nbr_frc_thr_prx_opt**0.0922_r8)
-         ryn_nbr_frc_thr_opt_fnc = 0.1291_r8 * 0.1291_r8 / ryn_nbr_frc_thr_opt_fnc
-      else
-         ryn_nbr_frc_thr_opt_fnc = 1.0_r8 - 0.0858_r8 * exp(-0.0617_r8*(ryn_nbr_frc_thr_prx_opt-10.0_r8))
-         ryn_nbr_frc_thr_opt_fnc = 0.120_r8 * 0.120_r8 * ryn_nbr_frc_thr_opt_fnc * ryn_nbr_frc_thr_opt_fnc
-      end if
-
-      icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8))
-      dns_fct = dns_slt * grav * dmt_slt_opt
-      this%saltation_factor = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc)
-
-      ! Introducing particle diameter. Needed by atm model and by dry dep model.
-      ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl,
-      ! grd_mk (dstpsd.F90) and subroutine lgn_evl (psdlgn.F90)
-
-      ! Charlie allows logarithmic or linear option for size distribution
-      ! however, he hardwires the distribution to logarithmic in his code
-      ! therefore, I take his logarithmic code only
-      ! furthermore, if dst_nbr == 4, he overrides the automatic grid calculation
-      ! he currently works with dst_nbr = 4, so I only take the relevant code
-      ! if ndst ever becomes different from 4, must add call grd_mk (dstpsd.F90)
-      ! as done in subroutine dst_psd_ini
-      ! note that here ndst = dst_nbr
-
-      ! Override automatic grid with preset grid if available
-
-      if (ndst == 4) then
-         do n = 1, ndst
-            dmt_min(n) = dmt_grd(n)                       ![m] Max diameter in bin
-            dmt_max(n) = dmt_grd(n+1)                     ![m] Min diameter in bin
-            dmt_ctr(n) = 0.5_r8 * (dmt_min(n)+dmt_max(n)) ![m] Diameter at bin ctr
-            dmt_dlt(n) = dmt_max(n)-dmt_min(n)            ![m] Width of size bin
-         end do
-      else
-         write(iulog,*) 'Dustini error: ndst must equal to 4 with current code'
-         call endrun(msg=errMsg(sourcefile, __LINE__))
-         !see more comments above end if ndst == 4
-      end if
-
-      ! Bin physical properties
-
-      gsd_anl = 2.0_r8      ! [frc] Geometric std dev PaG77 p. 2080 Table1
-      ln_gsd = log(gsd_anl)
-
-      ! Set a fundamental statistic for each bin
-
-      dmt_vma = 3.5000e-6_r8 ! [m] Mass median diameter analytic She84 p.75 Table1
-
-      ! Compute analytic size statistics
-      ! Convert mass median diameter to number median diameter (call vma2nma)
-
-      dmt_nma = dmt_vma * exp(-3.0_r8*ln_gsd*ln_gsd) ! [m]
-
-      ! Compute resolved size statistics for each size distribution
-      ! In C. Zender's code call dst_sz_rsl
-
-      do n = 1, ndst
-
-         series_ratio = (dmt_max(n)/dmt_min(n))**(1.0_r8/sz_nbr)
-         sz_min(1) = dmt_min(n)
-         do m = 2, sz_nbr                            ! Loop starts at 2
-            sz_min(m) = sz_min(m-1) * series_ratio
-         end do
-
-         ! Derived grid values
-         do m = 1, sz_nbr-1                          ! Loop ends at sz_nbr-1
-            sz_max(m) = sz_min(m+1)                  ! [m]
-         end do
-         sz_max(sz_nbr) = dmt_max(n)                 ! [m]
-
-         ! Final derived grid values
-         do m = 1, sz_nbr
-            sz_ctr(m) = 0.5_r8 * (sz_min(m)+sz_max(m))
-            sz_dlt(m) = sz_max(m)-sz_min(m)
-         end do
-
-         lngsdsqrttwopi_rcp = 1.0_r8 / (ln_gsd*sqrt(2.0_r8*SHR_CONST_PI))
-         this%dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved
-         vlm_rsl(n) = 0.0_r8 ! [m3 m-3] Volume concentration resolved
-
-         do m = 1, sz_nbr
-
-            ! Evaluate lognormal distribution for these sizes (call lgn_evl)
-            tmp = log(sz_ctr(m)/dmt_nma) / ln_gsd
-            lgn_dst = lngsdsqrttwopi_rcp * exp(-0.5_r8*tmp*tmp) / sz_ctr(m)
-
-            ! Integrate moments of size distribution
-            this%dmt_vwr(n) = this%dmt_vwr(n) + sz_ctr(m) *                    &
-                 SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume
-                 lgn_dst * sz_dlt(m)                ![# m-3] Number concentrn
-            vlm_rsl(n) = vlm_rsl(n) +                                &
-                 SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume
-                 lgn_dst * sz_dlt(m)                ![# m-3] Number concentrn
-
-         end do
-
-         this%dmt_vwr(n) = this%dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved
-
-      end do
-
-      ! calculate correction to Stokes' settling velocity (subroutine stk_crc_get)
-
-      eps_max = 1.0e-4_r8
-      dns_mdp = 100000._r8 / (295.0_r8*SHR_CONST_RDAIR) ![kg m-3] const prs_mdp & tpt_vrt
-
-      ! Size-independent thermokinetic properties
-
-      vsc_dyn_atm = 1.72e-5_r8 * ((295.0_r8/273.0_r8)**1.5_r8) * 393.0_r8 / &
-           (295.0_r8+120.0_r8)      ![kg m-1 s-1] RoY94 p.102 tpt_mdp=295.0
-      mfp_atm = 2.0_r8 * vsc_dyn_atm / &  !SeP97 p. 455 constant prs_mdp, tpt_mdp
-           (100000._r8*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*295.0_r8)))
-      vsc_knm_atm = vsc_dyn_atm / dns_mdp ![m2 s-1] Kinematic viscosity of air
-
-      do m = 1, ndst
-         slp_crc(m) = 1.0_r8 + 2.0_r8 * mfp_atm *                      &
-              (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
-              this%dmt_vwr(m)                      ! [frc] Slip correction factor SeP97 p.464
-         vlc_stk(m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * &
-              grav * slp_crc(m) / vsc_dyn_atm ! [m s-1] SeP97 p.466
-      end do
-
-      ! For Reynolds number flows Re < 0.1 Stokes' velocity is valid for
-      ! vlc_grv SeP97 p. 466 (8.42). For larger Re, inertial effects become
-      ! important and empirical drag coefficients must be employed
-      ! Implicit equation for Re, Cd, and Vt is SeP97 p. 467 (8.44)
-      ! Using Stokes' velocity rather than iterative solution with empirical
-      ! drag coefficient causes 60% errors for D = 200 um SeP97 p. 468
-
-      ! Iterative solution for drag coefficient, Reynolds number, and terminal veloc
-      do m = 1, ndst
-
-         ! Initialize accuracy and counter
-         eps_crr = eps_max + 1.0_r8  ![frc] Current relative accuracy
-         itr_idx = 0                 ![idx] Counting index
-
-         ! Initial guess for vlc_grv is exact for Re < 0.1
-         vlc_grv(m) = vlc_stk(m)     ![m s-1]
-
-         do while(eps_crr > eps_max)
-
-            ! Save terminal velocity for convergence test
-            vlc_grv_old = vlc_grv(m) ![m s-1]
-            ryn_nbr_grv(m) = vlc_grv(m) * this%dmt_vwr(m) / vsc_knm_atm !SeP97 p.460
-
-            ! Update drag coefficient based on new Reynolds number
-            if (ryn_nbr_grv(m) < 0.1_r8) then
-               cff_drg_grv(m) = 24.0_r8 / ryn_nbr_grv(m) !Stokes' law Sep97 p.463 (8.32)
-            else if (ryn_nbr_grv(m) < 2.0_r8) then
-               cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) *    &
-                    (1.0_r8 + 3.0_r8*ryn_nbr_grv(m)/16.0_r8 + &
-                    9.0_r8*ryn_nbr_grv(m)*ryn_nbr_grv(m)*     &
-                    log(2.0_r8*ryn_nbr_grv(m))/160.0_r8)        !Sep97 p.463 (8.32)
-            else if (ryn_nbr_grv(m) < 500.0_r8) then
-               cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) * &
-                    (1.0_r8 + 0.15_r8*ryn_nbr_grv(m)**0.687_r8) !Sep97 p.463 (8.32)
-            else if (ryn_nbr_grv(m) < 2.0e5_r8) then
-               cff_drg_grv(m) = 0.44_r8                         !Sep97 p.463 (8.32)
-            else
-               write(iulog,'(a,es9.2)') "ryn_nbr_grv(m) = ",ryn_nbr_grv(m)
-               write(iulog,*)'Dustini error: Reynolds number too large in stk_crc_get()'
-               call endrun(msg=errMsg(sourcefile, __LINE__))
-            end if
-
-            ! Update terminal velocity based on new Reynolds number and drag coeff
-            ! [m s-1] Terminal veloc SeP97 p.467 (8.44)
-
-            vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / &
-                 (3.0_r8*cff_drg_grv(m)*dns_mdp))   
-            eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence
-            if (itr_idx == 12) then
-               ! Numerical pingpong may occur when Re = 0.1, 2.0, or 500.0
-               ! due to discontinuities in derivative of drag coefficient
-               vlc_grv(m) = 0.5_r8 * (vlc_grv(m)+vlc_grv_old)  ! [m s-1]
-            end if
-            if (itr_idx > 20) then
-               write(iulog,*) 'Dustini error: Terminal velocity not converging ',&
-                    ' in stk_crc_get(), breaking loop...'
-               goto 100                                        !to next iteration
-            end if
-            itr_idx = itr_idx + 1
-
-         end do                                                !end while
-
-100      continue   !Label to jump to when iteration does not converge
-      end do   !end loop over size
-
-      ! Compute factors to convert Stokes' settling velocities to
-      ! actual settling velocities
-
-      do m = 1, ndst
-         this%stk_crc(m) = vlc_grv(m) / vlc_stk(m)
-      end do
-
-  end subroutine InitDustVars
-
 end module DustEmisZender2003

From 3a28c670f08099bcf9d205f6d5bf25c20ec633ac Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 17:14:06 -0600
Subject: [PATCH 0425/1248] UpdateAccVars_CropGDDs: Only check gdd20 seasons if
 no NaNs/Infs.

---
 src/biogeophys/TemperatureType.F90 | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index ae5703237e..69dbf3251d 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1426,14 +1426,16 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
        in_accumulation_season = &
           ((month > 3 .and. month < 10) .and. lat >= 0._r8) .or. &
           ((month > 9 .or.  month < 4)  .and. lat <  0._r8)
-       ! Replace with read-in gdd20 accumulation season, if valid
+       ! Replace with read-in gdd20 accumulation season, if needed and valid
        ! (If these aren't being read in or they're invalid, they'll be -1)
-       ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
-       gdd20_season_start = int(gdd20_season_starts(p))
-       gdd20_season_end = int(gdd20_season_ends(p))
-       if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
-          in_accumulation_season = is_doy_in_interval( &
-          gdd20_season_start, gdd20_season_end, day)
+       if (gdd20_season_starts(p)==gdd20_season_starts(p) .and. gdd20_season_ends(p)==gdd20_season_ends(p) .and. gdd20_season_starts(p)<=366 .and. gdd20_season_ends(p)<=366) then
+          ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
+          gdd20_season_start = int(gdd20_season_starts(p))
+          gdd20_season_end = int(gdd20_season_ends(p))
+          if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
+             in_accumulation_season = is_doy_in_interval( &
+             gdd20_season_start, gdd20_season_end, day)
+          end if
        end if
 
        if (month==1 .and. day==1 .and. secs==dtime) then

From dcbc90ede272bff5daad2c05f9f267c8607491ec Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 4 Jun 2024 11:29:38 -0600
Subject: [PATCH 0426/1248] Add TemperatureType restart var to flush GDD20s.

---
 src/biogeophys/TemperatureType.F90      | 41 ++++++++++++++++++++++---
 src/cpl/share_esmf/cropcalStreamMod.F90 |  2 +-
 src/main/clm_varctl.F90                 |  1 +
 3 files changed, 39 insertions(+), 5 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 69dbf3251d..5fda936169 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -8,6 +8,7 @@ module TemperatureType
   use decompMod       , only : bounds_type
   use abortutils      , only : endrun
   use clm_varctl      , only : use_cndv, iulog, use_luna, use_crop, use_biomass_heat_storage
+  use clm_varctl      , only : stream_gdd20_seasons
   use clm_varpar      , only : nlevsno, nlevgrnd, nlevlak, nlevurb, nlevmaxurbgrnd
   use clm_varcon      , only : spval, ispval
   use GridcellType    , only : grc
@@ -94,6 +95,7 @@ module TemperatureType
      real(r8), pointer :: gdd020_patch            (:)   ! patch 20-year average of gdd0                     (ddays)
      real(r8), pointer :: gdd820_patch            (:)   ! patch 20-year average of gdd8                     (ddays)
      real(r8), pointer :: gdd1020_patch           (:)   ! patch 20-year average of gdd10                    (ddays)
+     logical           :: flush_gdd20 = .false.         ! whether accumulated GDD20s need to be flushed
 
      ! Heat content
      real(r8), pointer :: beta_col                 (:)   ! coefficient of convective velocity [-]
@@ -895,7 +897,7 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     use shr_log_mod     , only : errMsg => shr_log_errMsg
     use spmdMod         , only : masterproc
     use abortutils      , only : endrun
-    use ncdio_pio       , only : file_desc_t, ncd_double, ncd_int
+    use ncdio_pio       , only : file_desc_t, ncd_double, ncd_int, ncd_log
     use restUtilMod
     !
     ! !ARGUMENTS:
@@ -907,8 +909,9 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     logical          , intent(in)    :: is_prog_buildtemp    ! Prognostic building temp is being used
     !
     ! !LOCAL VARIABLES:
-    integer :: j,c       ! indices
+    integer :: j,c,p     ! indices
     logical :: readvar   ! determine if variable is on initial file
+    integer, pointer :: logical_as_int(:) ! used for saving/reading logicals
     !-----------------------------------------------------------------------
 
     call restartvar(ncid=ncid, flag=flag, varname='T_SOISNO', xtype=ncd_double,   &
@@ -1133,6 +1136,29 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
        end if
     end if
 
+    if (use_crop .and. stream_gdd20_seasons) then
+       allocate(logical_as_int(1))
+       if (flag == 'write') then
+          if (this%flush_gdd20) then
+             logical_as_int(1) = 1
+          else
+             logical_as_int(1) = 0
+          end if
+       end if
+       call restartvar(ncid=ncid, flag=flag,  varname='flush_gdd20', xtype=ncd_log,  &
+            dim1name='pft', &
+            long_name='Flag indicating that GDD20 values need to be flushed', &
+            units='none', interpinic_flag='interp', readvar=readvar, data=logical_as_int)
+       if (flag == 'read') then
+          if (readvar .and. logical_as_int(1) == 0) then
+             this%flush_gdd20 = .false.
+          else
+             this%flush_gdd20 = .true.
+          end if
+       end if
+       deallocate(logical_as_int)
+    end if
+
 
   end subroutine Restart
 
@@ -1428,7 +1454,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
           ((month > 9 .or.  month < 4)  .and. lat <  0._r8)
        ! Replace with read-in gdd20 accumulation season, if needed and valid
        ! (If these aren't being read in or they're invalid, they'll be -1)
-       if (gdd20_season_starts(p)==gdd20_season_starts(p) .and. gdd20_season_ends(p)==gdd20_season_ends(p) .and. gdd20_season_starts(p)<=366 .and. gdd20_season_ends(p)<=366) then
+       if (stream_gdd20_seasons) then
           ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
           gdd20_season_start = int(gdd20_season_starts(p))
           gdd20_season_end = int(gdd20_season_ends(p))
@@ -1471,7 +1497,7 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
     ! USES
     use shr_const_mod    , only : SHR_CONST_TKFRZ
     use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date, is_end_curr_year
-    use accumulMod       , only : update_accum_field, extract_accum_field
+    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
     use CNSharedParamsMod, only : upper_soil_layer
     use CropType         , only : crop_type
     !
@@ -1659,6 +1685,13 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
 
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then
+          ! Flush, if needed
+          if (this%flush_gdd20) then
+              this%gdd020_patch(begp:endp) = accumResetVal
+              this%gdd820_patch(begp:endp) = accumResetVal
+              this%gdd1020_patch(begp:endp) = accumResetVal
+              this%flush_gdd20 = .false.
+          end if
           call update_accum_field  ('GDD020', this%gdd0_patch, nstep)
           call extract_accum_field ('GDD020', this%gdd020_patch, nstep)
           call update_accum_field  ('GDD820', this%gdd8_patch, nstep)
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 802b669905..80314ee947 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -16,6 +16,7 @@ module cropcalStreamMod
   use clm_varctl       , only : iulog
   use clm_varctl       , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams
   use clm_varctl       , only : adapt_cropcal_rx_cultivar_gdds
+  use clm_varctl       , only : stream_gdd20_seasons
   use clm_varpar       , only : mxpft
   use clm_varpar       , only : mxsowings
   use perf_mod         , only : t_startf, t_stopf
@@ -52,7 +53,6 @@ module cropcalStreamMod
   character(len=CL)       :: stream_fldFileName_gdd20_baseline ! GDD20 baseline stream filename to read
   logical                 :: cropcals_rx ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
   logical                 :: cropcals_rx_adapt ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
-  logical                 :: stream_gdd20_seasons  ! Read stream file for GDD20 accumulation seasons, instead of per-hemisphere periods
   logical                     :: allow_invalid_gdd20_season_inputs ! Fall back on hemisphere "warm periods" in cases of invalid values in stream_fldFileName_gdd20_season_start and _end?
   character(len=CL)       :: stream_fldFileName_gdd20_season_start ! Stream filename to read for start of gdd20 season
   character(len=CL)       :: stream_fldFileName_gdd20_season_end ! Stream filename to read for end of gdd20 season
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index fe67380fd2..43bab01d24 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -392,6 +392,7 @@ module clm_varctl
   logical, public :: use_cropcal_rx_swindows = .false.
   logical, public :: use_cropcal_rx_cultivar_gdds = .false.
   logical, public :: adapt_cropcal_rx_cultivar_gdds = .false.
+  logical, public :: stream_gdd20_seasons = .false.
 
   !----------------------------------------------------------
   ! biomass heat storage switch

From 982ef9a8ea135e47ccfec9d1088d5a6b8d06259e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 4 Jun 2024 11:31:37 -0600
Subject: [PATCH 0427/1248] Fixes to imports in RXCROPMATURITY(SKIPRUN).

---
 cime_config/SystemTests/rxcropmaturity.py        | 2 +-
 cime_config/SystemTests/rxcropmaturityskiprun.py | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 3eadccfeb3..206476f051 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -1,4 +1,4 @@
-from RXCROPMATURITYSHARED import RXCROPMATURITYSHARED
+from rxcropmaturityshared import RXCROPMATURITYSHARED
 
 class RXCROPMATURITY(RXCROPMATURITYSHARED):
     def run_phase(self):
diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py
index d52742f95a..343ef5860f 100644
--- a/cime_config/SystemTests/rxcropmaturityskiprun.py
+++ b/cime_config/SystemTests/rxcropmaturityskiprun.py
@@ -1,5 +1,4 @@
-print("pre-import")
-from RXCROPMATURITYSHARED import RXCROPMATURITYSHARED
+from rxcropmaturityshared import RXCROPMATURITYSHARED
 
 class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED):
     def run_phase(self):

From aed9d31c060ce247a3c7dd29ccf138552e56a1f4 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 4 Jun 2024 10:40:46 -0700
Subject: [PATCH 0428/1248] remove hydro tests that are now passing per
 NGEET/FATES#1164

---
 cime_config/testdefs/ExpectedTestFails.xml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 23e481222b..2d59568602 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -190,20 +190,6 @@
     </phase>
   </test>
 
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdHydro">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2373</issue>
-    </phase>
-  </test>
-
-  <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdHydro">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>FATES#701</issue>
-    </phase>
-  </test>
-
   <test name="ERP_P256x2_Ld30.f45_f45_mg37.I2000Clm60FatesRs.derecho_intel.clm-mimicsFatesCold">
     <phase name="RUN">
       <status>FAIL</status>

From 086e218d184abeed37dbc7fc5fc2a8bdf246d92e Mon Sep 17 00:00:00 2001
From: HuiWangWanderInGitHub <wanghuigis2013@gmail.com>
Date: Tue, 4 Jun 2024 13:17:21 -0600
Subject: [PATCH 0429/1248] Updates from Arctic isoprene research

---
 src/biogeochem/VOCEmissionMod.F90 | 44 ++++++++++++++++++++++---------
 1 file changed, 31 insertions(+), 13 deletions(-)

diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
index a4bd9dc4d2..84de85031a 100644
--- a/src/biogeochem/VOCEmissionMod.F90
+++ b/src/biogeochem/VOCEmissionMod.F90
@@ -84,15 +84,10 @@ module VOCEmissionMod
   !------------------------------------------------------------------------
   subroutine Init(this, bounds)
 
-    use clm_varctl     , only : use_fates, use_fates_sp
     class(vocemis_type) :: this
     type(bounds_type), intent(in)    :: bounds  
 
     if ( shr_megan_mechcomps_n > 0) then
-       if ( use_fates .and. (.not. use_fates_sp) ) then
-           call endrun( msg='ERROR: MEGAN currently does NOT work with FATES outside of FATES-SP mode (see github issue #115)'//&
-                     errMsg(sourcefile, __LINE__))
-       end if
        call this%InitAllocate(bounds) 
        call this%InitHistory(bounds)
        call this%InitCold(bounds)
@@ -485,7 +480,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
          !h2osoi_vol   => waterstate_inst%h2osoi_vol_col        , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (m3/m3)                   
          !h2osoi_ice   => waterstate_inst%h2osoi_ice_col        , & ! Input:  [real(r8) (:,:) ]  ice soil content (kg/m3)                        
          
-         forc_solad    => atm2lnd_inst%forc_solad_downscaled_col, & ! Input:  [real(r8) (:,:) ]  direct beam radiation (visible only)            
+         forc_solad    => atm2lnd_inst%forc_solad_grc           , & ! Input:  [real(r8) (:,:) ]  direct beam radiation (visible only)            
          forc_solai    => atm2lnd_inst%forc_solai_grc           , & ! Input:  [real(r8) (:,:) ]  diffuse radiation     (visible only)            
          forc_pbot     => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8) (:)   ]  downscaled atmospheric pressure (Pa)                          
          forc_pco2     => atm2lnd_inst%forc_pco2_grc            , & ! Input:  [real(r8) (:)   ]  partial pressure co2 (Pa)                                             
@@ -557,7 +552,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
           ! Calculate PAR: multiply w/m2 by 4.6 to get umol/m2/s for par (added 8/14/02)
           !------------------------
           ! SUN:
-          par_sun    = (forc_solad(c,1)  + fsun(p)    * forc_solai(g,1))  * 4.6_r8
+          par_sun    = (forc_solad(g,1)  + fsun(p)    * forc_solai(g,1))  * 4.6_r8
           par24_sun  = (forc_solad24(p)  + fsun24(p)  * forc_solai24(p))  * 4.6_r8
           par240_sun = (forc_solad240(p) + fsun240(p) * forc_solai240(p)) * 4.6_r8
 
@@ -599,14 +594,14 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
 
              ! Activity factor for T
              gamma_t = get_gamma_T(t_veg240(p), t_veg24(p),t_veg(p), ct1(class_num), ct2(class_num),&
-                                   betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt)
+                                   betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt, patch%itype(p))
 
              ! Activity factor for Leaf Age
              gamma_a = get_gamma_A(patch%itype(p), elai240(p),elai(p),class_num)
 
              ! Activity factor for CO2 (only for isoprene)
              if (trim(meg_cmp%name) == 'isoprene') then 
-                co2_ppmv = 1.e6_r8*forc_pco2(g)/forc_pbot(c)
+                co2_ppmv = 1.e6*forc_pco2(g)/forc_pbot(c)
                 gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv)
              else
                 gamma_c = 1._r8
@@ -891,10 +886,14 @@ function get_gamma_SM(clayfrac_in, sandfrac_in, h2osoi_vol_in, h2osoi_ice_in, dz
   end function get_gamma_SM
   
   !-----------------------------------------------------------------------
-  function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in, LDF_in, Ceo_in, Eopt, topt)
+  function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in, LDF_in, Ceo_in, Eopt, topt, ivt_in)
 
     ! Activity factor for temperature 
     !--------------------------------
+    ! May 24, 2024 Hui updated the temperature response curves of isoprene for 
+    ! Boreal Broadleaf Deciduous Shrub and Arctic C3 grass based on 
+    ! Wang et al., 2024 (GRL) and Wang et al., 2024 (Nature Communications)
+    !--------------------------------
     ! Calculate both a light-dependent fraction as in Guenther et al., 2006 for isoprene
     ! of a max saturation type form. Also caculate a light-independent fraction of the
     ! form of an exponential. Final activity factor depends on light dependent fraction
@@ -902,6 +901,7 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     !
     ! !ARGUMENTS:
     implicit none
+    integer,intent(in)  :: ivt_in
     real(r8),intent(in) :: t_veg240_in
     real(r8),intent(in) :: t_veg24_in
     real(r8),intent(in) :: t_veg_in
@@ -917,7 +917,8 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     real(r8) :: get_gamma_T
     real(r8) :: gamma_t_LDF             ! activity factor for temperature
     real(r8) :: gamma_t_LIF             ! activity factor for temperature
-    real(r8) :: x                       ! temporary 
+    real(r8) :: x                       ! temporary i
+    real(r8) :: bet_arc_c3
     real(r8), parameter :: co1 = 313._r8                   ! empirical coefficient
     real(r8), parameter :: co2 = 0.6_r8                    ! empirical coefficient
     real(r8), parameter :: co4 = 0.05_r8                   ! empirical coefficient
@@ -933,13 +934,30 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     if ( (t_veg240_in > 0.0_r8) .and. (t_veg240_in < 1.e30_r8) ) then 
        ! topt and Eopt from eq 8 and 9:
        topt = co1 + (co2 * (t_veg240_in-tstd0))
-       Eopt = Ceo_in * exp (co4 * (t_veg24_in-tstd0)) * exp(co4 * (t_veg240_in -tstd0))
+       if ( (ivt_in == nbrdlf_dcd_brl_shrub) ) then  ! boreal-shrub
+       ! coming from BEAR-oNS campaign willows results
+             Eopt = 7.9 * exp (0.217_r8 * (t_veg24_in-273.15_r8-24.0_r8))
+       else if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
+             Eopt = exp(0.12*(t_veg240_in-288.15_r8))
+       else
+             Eopt = Ceo_in * exp (co4 * (t_veg24_in-tstd0)) * exp(co4 * (t_veg240_in -tstd0))
+       endif
+
     else
        topt = topt_fix
        Eopt = Eopt_fix
     endif
     x = ( (1._r8/topt) - (1._r8/(t_veg_in)) ) / ct3
-    gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x)/(ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
+    ! for the boreal grass from BEAR-oNS campaign
+    if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
+        bet_arc_c3  = 95+9.49*exp(0.53*(288.15_r8-t_veg240_in))
+        if (bet_arc_c3 .gt. 300) then
+            bet_arc_c3 = 300
+        endif
+        gamma_t_LDF = Eopt * exp(bet_arc_c3*((1/303.15_r8 - 1.0_r8/(t_veg_in))/ct3))
+    else
+        gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x)/(ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
+    endif
     
     
     ! Light independent fraction (of exp(beta T) form)

From 5431850c991fbed4a2c7e3ac7d9f321e7d907ed0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 4 Jun 2024 15:57:53 -0600
Subject: [PATCH 0430/1248] Add cime_config/usermods_dirs/NEON/NIWO/user_nl_clm
 for tests to pass

---
 cime_config/usermods_dirs/NEON/NIWO/user_nl_clm | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 cime_config/usermods_dirs/NEON/NIWO/user_nl_clm

diff --git a/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm b/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm
new file mode 100644
index 0000000000..cf427d738b
--- /dev/null
+++ b/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm
@@ -0,0 +1,8 @@
+! 20240604 slevis introduced this file to bypass test failures in the
+! cnmatrix branch (so cnmatrix on by default) with two izumi tests:
+! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO--clm-matrixcnOn
+! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO
+! when the tests point to the default finidat, as documented in this post:
+! https://github.com/ESCOMP/CTSM/pull/640#issuecomment-2143101361
+use_init_interp = .true.
+finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc'

From 0edef8a33450154a60d0d50af5419dc57e5c0996 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 4 Jun 2024 16:00:30 -0600
Subject: [PATCH 0431/1248] Update ntests in
 bld/unit_testers/build-namelist_test.pl

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 152430d514..28a2392736 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3357;
+my $ntests = 3283;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2045;

From 1a49e547ba3c48fa483f9ae81a8f05adcd6b888c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 4 Jun 2024 16:01:28 -0600
Subject: [PATCH 0432/1248] Reformatting by "make run-black"

---
 cime_config/SystemTests/sspmatrixcn.py | 20 +++++---------------
 cime_config/buildnml                   | 24 ++++++------------------
 2 files changed, 11 insertions(+), 33 deletions(-)

diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py
index 37d4154121..f4a09a277e 100644
--- a/cime_config/SystemTests/sspmatrixcn.py
+++ b/cime_config/SystemTests/sspmatrixcn.py
@@ -163,28 +163,18 @@ def append_user_nl(self, caseroot, n=0):
         self.check_n(n)
         # For all set output to yearly
         contents_to_append = "hist_nhtfrq = -8760"
-        contents_to_append = (
-            contents_to_append + ", hist_mfilt = " + str(self.nyr_forcing)
-        )
+        contents_to_append = contents_to_append + ", hist_mfilt = " + str(self.nyr_forcing)
         # For all but last step turn extra matrix output to off
         b4last = self.n_steps() - 1
         if n < b4last:
-            contents_to_append = (
-                contents_to_append + ", hist_wrt_matrixcn_diag = .False."
-            )
+            contents_to_append = contents_to_append + ", hist_wrt_matrixcn_diag = .False."
         # For matrix spinup steps, set the matrix spinup and other variables associated with it
         if self.spin[n] == "sasu":
-            contents_to_append = (
-                contents_to_append + ", nyr_forcing = " + str(self.nyr_forcing)
-            )
+            contents_to_append = contents_to_append + ", nyr_forcing = " + str(self.nyr_forcing)
             if self.sasu[n] != -999:
-                contents_to_append = (
-                    contents_to_append + ", nyr_sasu = " + str(self.sasu[n])
-                )
+                contents_to_append = contents_to_append + ", nyr_sasu = " + str(self.sasu[n])
             if self.iloop[n] != -999:
-                contents_to_append = (
-                    contents_to_append + ", iloop_avg = " + str(self.iloop[n])
-                )
+                contents_to_append = contents_to_append + ", iloop_avg = " + str(self.iloop[n])
 
         # For cold start, run with matrix off
         if self.cold[n]:
diff --git a/cime_config/buildnml b/cime_config/buildnml
index 9be7c447fb..3eb45dff31 100755
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,9 +182,7 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -283,17 +281,13 @@ def buildnml(case, caseroot, compname):
         if (yr_start != None) and (yr_end != None):
             nyr = yr_end - yr_start + 1
             if (yr_end <= 0) or (yr_start <= 0):
-                logger.error(
-                    "ERROR: Year start and end are both negative and should not be"
-                )
+                logger.error("ERROR: Year start and end are both negative and should not be")
             clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts)
         else:
             logger.warning(
                 "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model"
             )
-            logger.warning(
-                "         as it expects regular atmosphere forcing that is cycled over"
-            )
+            logger.warning("         as it expects regular atmosphere forcing that is cycled over")
 
     infile = os.path.join(ctsmconf, "namelist")
 
@@ -307,9 +301,7 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
 
     # -----------------------------------------------------
     # Clear out old data
@@ -372,9 +364,7 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning(
-                    "WARNING: Could NOT find a start file to use using" + clm_startfile
-                )
+                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -385,9 +375,7 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(
-            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
-        )
+        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From dd6a5a434b95e70e85814812089fd78ee0216c2f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 4 Jun 2024 16:04:07 -0600
Subject: [PATCH 0433/1248] Change occurances of dust_type with
 dust_emis_zender2003_type with VS code

---
 src/biogeochem/DustEmisZender2003.F90            | 16 ++++++++--------
 .../test/DustEmis_test/test_DustEmisBase.pf      |  2 +-
 .../DustEmis_test/test_DustEmisZender2003.pf     |  2 +-
 src/main/clm_instMod.F90                         |  4 ++--
 src/main/lnd2atmMod.F90                          |  4 ++--
 5 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index 442fddbedf..e67bd43e1b 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -42,7 +42,7 @@ module DustEmisZender2003
   !
   ! !PUBLIC DATA TYPES:
   !
-  type, public, extends(dust_base_type) :: dust_type
+  type, public, extends(dust_base_type) :: dust_emis_zender2003_type
 
      real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! [dimensionless] basin factor, or soil rodibility, time-constant
      type(soil_erod_stream_type), private :: soil_erod_stream      ! Zender soil erodibility stream data
@@ -56,7 +56,7 @@ module DustEmisZender2003
      procedure , private :: InitHistory     ! History initialization
      procedure , private :: InitCold     
 
-  end type dust_type
+  end type dust_emis_zender2003_type
   !------------------------------------------------------------------------
 
   character(len=*), parameter, private :: sourcefile = &
@@ -68,7 +68,7 @@ module DustEmisZender2003
   subroutine InitZender2003(this, bounds, NLFilename)
 
    ! Initialization for this extended class, calling base level initiation and adding to it
-    class(dust_type) :: this
+    class(dust_emis_zender2003_type) :: this
     type(bounds_type), intent(in) :: bounds  
     character(len=*),  intent(in) :: NLFilename
 
@@ -84,7 +84,7 @@ end subroutine InitZender2003
   subroutine InitAllocate(this, bounds)
    !
    ! !ARGUMENTS:
-   class (dust_type) :: this
+   class (dust_emis_zender2003_type) :: this
    type(bounds_type), intent(in) :: bounds  
    !
    ! !LOCAL VARIABLES:
@@ -102,7 +102,7 @@ subroutine CleanZender2003(this)
     !
     ! Deallocation for this extended class, calling base level deallocation and adding to it
     ! !ARGUMENTS:
-    class (dust_type) :: this
+    class (dust_emis_zender2003_type) :: this
     !
     ! !LOCAL VARIABLES:
     !------------------------------------------------------------------------
@@ -120,7 +120,7 @@ subroutine InitHistory(this, bounds)
     !
     !
     ! !ARGUMENTS:
-    class (dust_type) :: this
+    class (dust_emis_zender2003_type) :: this
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
@@ -142,7 +142,7 @@ end subroutine InitHistory
   subroutine InitCold(this, bounds)
     !
     ! !ARGUMENTS:
-    class (dust_type) :: this
+    class (dust_emis_zender2003_type) :: this
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
@@ -192,7 +192,7 @@ subroutine DustEmission (this, bounds, &
     use subgridaveMod, only : p2g
     !
     ! !ARGUMENTS:
-    class (dust_type)                      :: this
+    class (dust_emis_zender2003_type)                      :: this
     type(bounds_type)      , intent(in)    :: bounds                      
     integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
     integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
index e60ec2cc7f..cf8df87d64 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
@@ -27,7 +27,7 @@ module test_DustEmisBase
 
   @TestCase
   type, extends(TestCase) :: TestDustEmisBase
-     type(dust_type) :: dust_emis
+     type(dust_emis_zender2003_type) :: dust_emis
      integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
      integer :: num_nolakep              ! number of patches in non-lake filter
      type(atm2lnd_type) :: atm2lnd_inst
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index a7fea904c9..1168200cfe 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -27,7 +27,7 @@ module test_DustEmisZender2003
 
   @TestCase
   type, extends(TestCase) :: TestDustEmisZender2003
-     type(dust_type) :: dust_emis
+     type(dust_emis_zender2003_type) :: dust_emis
      integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
      integer :: num_nolakep              ! number of patches in non-lake filter
      type(atm2lnd_type) :: atm2lnd_inst
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index f11805a755..c3ea8a68b3 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -45,7 +45,7 @@ module clm_instMod
   use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
   use CropType                        , only : crop_type
   use DryDepVelocity                  , only : drydepvel_type
-  use DustEmisZender2003                         , only : dust_type
+  use DustEmisZender2003                         , only : dust_emis_zender2003_type
   use EnergyFluxType                  , only : energyflux_type
   use FrictionVelocityMod             , only : frictionvel_type
   use GlacierSurfaceMassBalanceMod    , only : glacier_smb_type
@@ -151,7 +151,7 @@ module clm_instMod
   ! General biogeochem types
   type(ch4_type)      , public            :: ch4_inst
   type(crop_type)     , public            :: crop_inst
-  type(dust_type)     , public            :: dust_inst
+  type(dust_emis_zender2003_type)     , public            :: dust_inst
   type(vocemis_type)  , public            :: vocemis_inst
   type(fireemis_type) , public            :: fireemis_inst
   type(drydepvel_type), public            :: drydepvel_inst
diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90
index b91feaabf9..e6b1bb43f0 100644
--- a/src/main/lnd2atmMod.F90
+++ b/src/main/lnd2atmMod.F90
@@ -20,7 +20,7 @@ module lnd2atmMod
   use lnd2atmType          , only : lnd2atm_type
   use atm2lndType          , only : atm2lnd_type
   use ch4Mod               , only : ch4_type
-  use DustEmisZender2003              , only : dust_type
+  use DustEmisZender2003              , only : dust_emis_zender2003_type
   use DryDepVelocity       , only : drydepvel_type
   use VocEmissionMod       , only : vocemis_type
   use CNFireEmissionsMod   , only : fireemis_type
@@ -173,7 +173,7 @@ subroutine lnd2atm(bounds, &
     type(drydepvel_type)        , intent(in)    :: drydepvel_inst
     type(vocemis_type)          , intent(in)    :: vocemis_inst
     type(fireemis_type)         , intent(in)    :: fireemis_inst
-    type(dust_type)             , intent(in)    :: dust_inst
+    type(dust_emis_zender2003_type)             , intent(in)    :: dust_inst
     type(ch4_type)              , intent(in)    :: ch4_inst
     type(glc_behavior_type)     , intent(in)    :: glc_behavior
     type(lnd2atm_type)          , intent(inout) :: lnd2atm_inst

From 66e1c3d6dd330accc670b8ea281e43e938d2018d Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 4 Jun 2024 16:05:05 -0600
Subject: [PATCH 0434/1248] Update .git-blame-ignore-revs

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index c62b279ba0..bc3600b925 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -47,3 +47,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 6c6f57e948bfa31e60b383536cc21663fedb8b70
 9660667b1267dcd4150889f5f39db540158be74a
 665cf86102e09b4c4c5a140700676dca23bc55a9
+1a49e547ba3c48fa483f9ae81a8f05adcd6b888c

From e0cbd401b56a466676beceedd2796abd813a6272 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 4 Jun 2024 16:17:57 -0600
Subject: [PATCH 0435/1248] Update dust_base_type to dust_emis_base_type

---
 src/biogeochem/DustEmisBase.F90       | 26 +++++++++++++-------------
 src/biogeochem/DustEmisZender2003.F90 |  4 ++--
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
index 11912096fd..adf2716f8a 100644
--- a/src/biogeochem/DustEmisBase.F90
+++ b/src/biogeochem/DustEmisBase.F90
@@ -42,7 +42,7 @@ module DustEmisBase
   !
   ! !PUBLIC DATA TYPES:
   !
-  type, abstract, public :: dust_base_type
+  type, abstract, public :: dust_emis_base_type
 
      real(r8) , allocatable, public  :: ovr_src_snk_mss(:,:)       ! overlap factors between the source and sin
      real(r8) , allocatable, private :: dmt_vwr(:)                 ! [m] Mass-weighted mean diameter resolved
@@ -71,7 +71,7 @@ module DustEmisBase
      procedure , private  :: InitHistory  
      procedure , private  :: InitDustVars    ! Initialize variables used in DustEmission method
 
-  end type dust_base_type
+  end type dust_emis_base_type
   !------------------------------------------------------------------------
 
   abstract interface
@@ -97,10 +97,10 @@ subroutine DustEmission_interface (this, bounds, &
     use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
     use FrictionVelocityMod    , only : frictionvel_type
 
-    import :: dust_base_type
+    import :: dust_emis_base_type
     !
     ! !ARGUMENTS:
-    class (dust_base_type)                 :: this
+    class (dust_emis_base_type)                 :: this
     type(bounds_type)      , intent(in)    :: bounds                      
     integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
     integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
@@ -125,7 +125,7 @@ subroutine InitBase(this, bounds, NLFilename)
 
    ! Base level initialization of this base object, this allows classes that extend
    ! this base class to use this one and extend it with additional initialization
-    class(dust_base_type) :: this
+    class(dust_emis_base_type) :: this
     type(bounds_type), intent(in) :: bounds  
     character(len=*),  intent(in) :: NLFilename
 
@@ -141,7 +141,7 @@ subroutine CleanBase(this)
    ! Base level deallocation of this base object, this allows classes that extend
    ! this base class to use this one and extend it with additional deallocation.
    ! !ARGUMENTS:
-   class (dust_base_type) :: this
+   class (dust_emis_base_type) :: this
    !
    ! !LOCAL VARIABLES:
    !------------------------------------------------------------------------
@@ -164,7 +164,7 @@ end subroutine CleanBase
   subroutine InitAllocate(this, bounds)
     !
     ! !ARGUMENTS:
-    class (dust_base_type) :: this
+    class (dust_emis_base_type) :: this
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
@@ -198,7 +198,7 @@ subroutine InitHistory(this, bounds)
     !
     !
     ! !ARGUMENTS:
-    class (dust_base_type) :: this
+    class (dust_emis_base_type) :: this
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
@@ -243,7 +243,7 @@ subroutine WritePatchToLog(this, p)
     ! !DESCRIPTION:
     ! Write out information on dust emisisons for this patch to the log file
     ! !ARGUMENTS:
-    class(dust_base_type), intent(in) :: this
+    class(dust_emis_base_type), intent(in) :: this
     integer         , intent(in) :: p      ! Patch to display
 
     write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p)
@@ -261,7 +261,7 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb,
    ! !DESCRIPTION:
    ! Get important variables on the given patch
    ! !ARGUMENTS:
-   class(dust_base_type)  , intent(in)  :: this
+   class(dust_emis_base_type)  , intent(in)  :: this
    integer           , intent(in)  :: p      ! Patch to get
    real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst)
    real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot
@@ -287,7 +287,7 @@ subroutine GetConstVars(this, SaltationFactor )
   ! !DESCRIPTION:
   ! Get important constant variables
   ! !ARGUMENTS:
-    class(dust_base_type)  , intent(in)  :: this
+    class(dust_emis_base_type)  , intent(in)  :: this
     real(r8)          , intent(out) :: SaltationFactor
 
     SaltationFactor = this%saltation_factor
@@ -316,7 +316,7 @@ subroutine DustDryDep (this, bounds, &
     use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ
     !
     ! !ARGUMENTS:
-    class (dust_base_type)                      :: this
+    class (dust_emis_base_type)                      :: this
     type(bounds_type)      , intent(in)    :: bounds 
     type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
     type(frictionvel_type) , intent(in)    :: frictionvel_inst
@@ -451,7 +451,7 @@ subroutine InitDustVars(this, bounds)
      use decompMod     , only : get_proc_bounds
      !
      ! !ARGUMENTS:
-     class(dust_base_type)  :: this
+     class(dust_emis_base_type)  :: this
      type(bounds_type), intent(in) :: bounds  
      !
      ! !LOCAL VARIABLES
diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index e67bd43e1b..fa2a96b7e0 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -30,7 +30,7 @@ module DustEmisZender2003
   use LandunitType         , only : lun
   use PatchType            , only : patch
   use ZenderSoilErodStreamType,  only : soil_erod_stream_type
-  use DustEmisBase         , only : dust_base_type
+  use DustEmisBase         , only : dust_emis_base_type
   use clm_varctl           , only : dust_emis_method
   !  
   ! !PUBLIC TYPES
@@ -42,7 +42,7 @@ module DustEmisZender2003
   !
   ! !PUBLIC DATA TYPES:
   !
-  type, public, extends(dust_base_type) :: dust_emis_zender2003_type
+  type, public, extends(dust_emis_base_type) :: dust_emis_zender2003_type
 
      real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! [dimensionless] basin factor, or soil rodibility, time-constant
      type(soil_erod_stream_type), private :: soil_erod_stream      ! Zender soil erodibility stream data

From e1db253814ba944935d0a571c5b17b29010f1090 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 4 Jun 2024 16:16:26 -0600
Subject: [PATCH 0436/1248] Add reset option to update_accum_field_runmean().

---
 src/main/accumulMod.F90 | 59 +++++++++++++++++++++++++++++++++++------
 1 file changed, 51 insertions(+), 8 deletions(-)

diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index e328632501..883aa9063b 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -102,13 +102,14 @@ subroutine extract_accum_field_interface(this, level, nstep, field)
        real(r8), intent(inout) :: field(:) ! field values for current time step
      end subroutine extract_accum_field_interface
 
-     subroutine update_accum_field_interface(this, level, nstep, field)
+     subroutine update_accum_field_interface(this, level, nstep, field, reset)
        use shr_kind_mod, only: r8 => shr_kind_r8
        import :: accum_field
        class(accum_field), intent(in) :: this
        integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
        integer, intent(in) :: nstep      ! timestep index
        real(r8), intent(in) :: field(:)  ! field values for current time step
+       logical, optional, intent(in) :: reset  ! whether to reset accumulator
      end subroutine update_accum_field_interface
   end interface
 
@@ -487,7 +488,7 @@ subroutine extract_accum_field_timeavg(this, level, nstep, field)
   end subroutine extract_accum_field_timeavg
 
   !------------------------------------------------------------------------
-  subroutine update_accum_field_sl (name, field, nstep)
+  subroutine update_accum_field_sl (name, field, nstep, reset_in)
     !
     ! !DESCRIPTION:
     ! Accumulate single level field over specified time interval.
@@ -501,14 +502,22 @@ subroutine update_accum_field_sl (name, field, nstep)
     character(len=*), intent(in) :: name     !field name
     real(r8), pointer, dimension(:) :: field !field values for current time step
     integer , intent(in) :: nstep            !time step index
+    logical, optional, intent(in) :: reset_in  ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: nf     ! field index
     integer :: numlev ! number of vertical levels
+    logical :: reset
 
     character(len=*), parameter :: subname = 'update_accum_field_sl'
     !------------------------------------------------------------------------
 
+    if (present(reset_in)) then
+       reset = reset_in
+    else
+       reset = .false.
+    end if
+
     call find_field(field_name=name, caller_name=subname, field_index=nf)
 
     numlev = accum(nf)%numlev
@@ -517,12 +526,13 @@ subroutine update_accum_field_sl (name, field, nstep)
     call accum(nf)%update_accum_field_func( &
          level = 1, &
          nstep = nstep, &
-         field = field)
+         field = field, &
+         reset = reset)
 
   end subroutine update_accum_field_sl
 
   !------------------------------------------------------------------------
-  subroutine update_accum_field_ml (name, field, nstep)
+  subroutine update_accum_field_ml (name, field, nstep, reset_in)
     !
     ! !DESCRIPTION:
     ! Accumulate multi level field over specified time interval.
@@ -535,14 +545,22 @@ subroutine update_accum_field_ml (name, field, nstep)
     character(len=*), intent(in) :: name       !field name
     real(r8), pointer, dimension(:,:) :: field !field values for current time step
     integer , intent(in) :: nstep              !time step index
+    logical, optional, intent(in) :: reset_in  ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: j,nf            !indices
     integer :: numlev          !number of vertical levels
+    logical :: reset
 
     character(len=*), parameter :: subname = 'update_accum_field_ml'
     !------------------------------------------------------------------------
 
+    if (present(reset_in)) then
+       reset = reset_in
+    else
+       reset = .false.
+    end if
+
     call find_field(field_name=name, caller_name=subname, field_index=nf)
 
     numlev = accum(nf)%numlev
@@ -552,13 +570,14 @@ subroutine update_accum_field_ml (name, field, nstep)
        call accum(nf)%update_accum_field_func( &
             level = j, &
             nstep = nstep, &
-            field = field(:,j))
+            field = field(:,j), &
+            reset = reset)
     end do
 
   end subroutine update_accum_field_ml
 
   !-----------------------------------------------------------------------
-  subroutine update_accum_field_timeavg(this, level, nstep, field)
+  subroutine update_accum_field_timeavg(this, level, nstep, field, reset)
     !
     ! !DESCRIPTION:
     ! Update values for one level of the given timeavg field
@@ -568,6 +587,7 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
     integer, intent(in) :: nstep      ! timestep index
     real(r8), intent(in) :: field(:)  ! field values for current time step
+    logical, intent(in)  :: reset     ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
@@ -580,6 +600,11 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     endi = this%end1d
     SHR_ASSERT_FL((size(field) == endi-begi+1), sourcefile, __LINE__)
 
+    if (reset) then
+       write(iulog,*) trim(subname), 'ERROR: field name ',trim(this%name),' may not use reset=.true.'
+       call endrun('Unhandled use of reset=.true. for ',subname)
+    end if
+
     ! time average field: reset every accumulation period; normalize at end of
     ! accumulation period
 
@@ -611,7 +636,7 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
   end subroutine update_accum_field_timeavg
 
   !-----------------------------------------------------------------------
-  subroutine update_accum_field_runmean(this, level, nstep, field)
+  subroutine update_accum_field_runmean(this, level, nstep, field, reset)
     !
     ! !DESCRIPTION:
     ! Update values for one level of the given runmean field
@@ -621,6 +646,7 @@ subroutine update_accum_field_runmean(this, level, nstep, field)
     integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
     integer, intent(in) :: nstep      ! timestep index
     real(r8), intent(in) :: field(:)  ! field values for current time step
+    logical, intent(in)  :: reset     ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
@@ -635,7 +661,18 @@ subroutine update_accum_field_runmean(this, level, nstep, field)
     SHR_ASSERT_FL((size(field) == endi-begi+1), sourcefile, __LINE__)
 
     do k = begi,endi
+       ! Whether or not this patch/landunit/etc. is active, mark it for reset. Don't actually reset it now, because it might become active again (and thus, its value might be needed) before it has another chance to get reset.
+       if (reset) then
+          this%nsteps(k,level) = -1
+       end if
+
        if (this%active(k)) then
+          ! Negative nsteps means this was marked as needing to be reset
+          if (this%nsteps(k,level) < 0) then
+             this%val(k,level) = 0._r8
+             this%nsteps(k,level) = 0
+          end if
+
           kf = k - begi + 1
           this%nsteps(k,level) = this%nsteps(k,level) + 1
           ! Cap nsteps at 'period' - partly to avoid overflow, but also because it doesn't
@@ -653,7 +690,7 @@ subroutine update_accum_field_runmean(this, level, nstep, field)
   end subroutine update_accum_field_runmean
 
   !-----------------------------------------------------------------------
-  subroutine update_accum_field_runaccum(this, level, nstep, field)
+  subroutine update_accum_field_runaccum(this, level, nstep, field, reset)
     !
     ! !DESCRIPTION:
     ! Update values for one level of the given runaccum field
@@ -663,6 +700,7 @@ subroutine update_accum_field_runaccum(this, level, nstep, field)
     integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
     integer, intent(in) :: nstep      ! timestep index
     real(r8), intent(in) :: field(:)  ! field values for current time step
+    logical, intent(in)  :: reset     ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
@@ -675,6 +713,11 @@ subroutine update_accum_field_runaccum(this, level, nstep, field)
     endi = this%end1d
     SHR_ASSERT_FL((size(field) == endi-begi+1), sourcefile, __LINE__)
 
+    if (reset) then
+       write(iulog,*) trim(subname), 'ERROR: field name ',trim(this%name),' may not use reset=.true.; set value to -99999 instead'
+       call endrun('Unhandled use of reset=.true. for ',subname)
+    end if
+
     !running accumulation field; reset at trigger -99999
 
     do k = begi,endi

From da722568a24220ce5bd128e081a4acc2c46e0e6b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 4 Jun 2024 16:22:39 -0600
Subject: [PATCH 0437/1248] Update dust emission calls to OO format, now a case
 passes: SMS_D.f10_f10_mg37.I2000Clm60Bgc.derecho_intel

---
 src/main/clm_driver.F90 | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index f9db72e0ed..b6dacf3866 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -62,7 +62,6 @@ module clm_driver
   use ndepStreamMod          , only : ndep_interp
   use cropcalStreamMod       , only : cropcal_advance, cropcal_interp
   use ch4Mod                 , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check
-  use DustEmisZender2003                , only : DustDryDep, DustEmission
   use VOCEmissionMod         , only : VOCEmission
   !
   use filterMod              , only : setFilters
@@ -806,15 +805,15 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
        call t_startf('bgc')
 
        ! Dust mobilization (C. Zender's modified codes)
-       call DustEmission(bounds_clump,                                       &
+       call dust_inst%DustEmission(bounds_clump,                                       &
             filter(nc)%num_nolakep, filter(nc)%nolakep,                      &
             atm2lnd_inst, soilstate_inst, canopystate_inst, &
             water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, &
-            frictionvel_inst, dust_inst)
+            frictionvel_inst)
 
        ! Dust dry deposition (C. Zender's modified codes)
-       call DustDryDep(bounds_clump, &
-            atm2lnd_inst, frictionvel_inst, dust_inst)
+       call dust_inst%DustDryDep(bounds_clump, &
+            atm2lnd_inst, frictionvel_inst)
 
        ! VOC emission (A. Guenther's MEGAN (2006) model)
        call VOCEmission(bounds_clump,                                         &

From af0e12d2593fbd0a468d7ea65ac3761fcc771f2c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 4 Jun 2024 16:23:55 -0600
Subject: [PATCH 0438/1248] Actually flush GDD20 variables.

---
 src/biogeophys/TemperatureType.F90 | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 5fda936169..c71b5d64aa 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1497,7 +1497,7 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
     ! USES
     use shr_const_mod    , only : SHR_CONST_TKFRZ
     use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date, is_end_curr_year
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    use accumulMod       , only : update_accum_field, extract_accum_field
     use CNSharedParamsMod, only : upper_soil_layer
     use CropType         , only : crop_type
     !
@@ -1685,19 +1685,13 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
 
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then
-          ! Flush, if needed
-          if (this%flush_gdd20) then
-              this%gdd020_patch(begp:endp) = accumResetVal
-              this%gdd820_patch(begp:endp) = accumResetVal
-              this%gdd1020_patch(begp:endp) = accumResetVal
-              this%flush_gdd20 = .false.
-          end if
-          call update_accum_field  ('GDD020', this%gdd0_patch, nstep)
+          call update_accum_field  ('GDD020', this%gdd0_patch, nstep, this%flush_gdd20)
           call extract_accum_field ('GDD020', this%gdd020_patch, nstep)
-          call update_accum_field  ('GDD820', this%gdd8_patch, nstep)
+          call update_accum_field  ('GDD820', this%gdd8_patch, nstep, this%flush_gdd20)
           call extract_accum_field ('GDD820', this%gdd820_patch, nstep)
-          call update_accum_field  ('GDD1020', this%gdd10_patch, nstep)
+          call update_accum_field  ('GDD1020', this%gdd10_patch, nstep, this%flush_gdd20)
           call extract_accum_field ('GDD1020', this%gdd1020_patch, nstep)
+          this%flush_gdd20 = .false.
        end if
 
     end if

From c6060dba9dd6298f1c274b33e5f4e75b14b53cdd Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 4 Jun 2024 16:46:35 -0600
Subject: [PATCH 0439/1248] Some whitespace formatting changes

---
 src/biogeochem/DustEmisBase.F90       | 193 +++++++++++++-------------
 src/biogeochem/DustEmisZender2003.F90 | 100 +++++++------
 2 files changed, 152 insertions(+), 141 deletions(-)

diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
index adf2716f8a..6fb1066607 100644
--- a/src/biogeochem/DustEmisBase.F90
+++ b/src/biogeochem/DustEmisBase.F90
@@ -1,18 +1,18 @@
 module DustEmisBase
 
-  !----------------------------------------------------------------------- 
-  ! !DESCRIPTION: 
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
   ! Routines in this module calculate Dust mobilization and dry deposition for dust.
-  ! Simulates dust mobilization due to wind from the surface into the 
-  ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust 
+  ! Simulates dust mobilization due to wind from the surface into the
+  ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust
   ! emission (kg/m**2/s) [ + = to atm].
-  ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition 
-  ! velocity through the lowest atmospheric layer). CAM will calculate the settling 
-  ! velocity through the whole atmospheric column. The two calculations will determine 
+  ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition
+  ! velocity through the lowest atmospheric layer). CAM will calculate the settling
+  ! velocity through the whole atmospheric column. The two calculations will determine
   ! the dust dry deposition flux to the surface.
-  !                              
+  !
   ! !USES:
-  use shr_kind_mod         , only : r8 => shr_kind_r8 
+  use shr_kind_mod         , only : r8 => shr_kind_r8
   use shr_log_mod          , only : errMsg => shr_log_errMsg
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
   use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr
@@ -24,14 +24,14 @@ module DustEmisBase
   use atm2lndType          , only : atm2lnd_type
   use SoilStateType        , only : soilstate_type
   use CanopyStateType      , only : canopystate_type
-  use WaterStateBulkType       , only : waterstatebulk_type
-  use WaterDiagnosticBulkType       , only : waterdiagnosticbulk_type
+  use WaterStateBulkType   , only : waterstatebulk_type
+  use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
   use FrictionVelocityMod  , only : frictionvel_type
   use LandunitType         , only : lun
   use ColumnType           , only : col
   use PatchType            , only : patch
   use clm_varctl           , only : dust_emis_method
-  !  
+  !
   ! !PUBLIC TYPES
   implicit none
   private
@@ -48,9 +48,9 @@ module DustEmisBase
      real(r8) , allocatable, private :: dmt_vwr(:)                 ! [m] Mass-weighted mean diameter resolved
      real(r8) , allocatable, private :: stk_crc(:)                 ! [frc] Correction to Stokes settling velocity
      real(r8), public           :: saltation_factor                ! Factor in saltation computation (named as in Charlie's code)
-     real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) 
+     real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst)
      real(r8), pointer, public  :: flx_mss_vrt_dst_tot_patch (:)   ! total dust flux into atmosphere
-     real(r8), pointer, private :: vlc_trb_patch             (:,:) ! turbulent deposition velocity  (m/s) (ndst) 
+     real(r8), pointer, private :: vlc_trb_patch             (:,:) ! turbulent deposition velocity  (m/s) (ndst)
      real(r8), pointer, private :: vlc_trb_1_patch           (:)   ! turbulent deposition velocity 1(m/s)
      real(r8), pointer, private :: vlc_trb_2_patch           (:)   ! turbulent deposition velocity 2(m/s)
      real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
@@ -67,8 +67,8 @@ module DustEmisBase
      procedure , public   :: GetConstVars    ! Get important constant variables
      procedure , public   :: CleanBase       ! Base object deallocation (allows extension)
      procedure , public   :: Clean => CleanBase ! Deallocation used by callers
-     procedure , private  :: InitAllocate 
-     procedure , private  :: InitHistory  
+     procedure , private  :: InitAllocate
+     procedure , private  :: InitHistory
      procedure , private  :: InitDustVars    ! Initialize variables used in DustEmission method
 
   end type dust_emis_base_type
@@ -77,41 +77,41 @@ module DustEmisBase
   abstract interface
   !------------------------------------------------------------------------
 
-  subroutine DustEmission_interface (this, bounds, &
-       num_nolakep, filter_nolakep, &
-       atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, &
-       frictionvel_inst)
-    !
-    ! !DESCRIPTION: 
-    ! Dust mobilization. This code simulates dust mobilization due to wind
-    ! from the surface into the lowest atmospheric layer
-    ! On output flx_mss_vrt_dst(ndst) is the surface dust emission 
-    ! (kg/m**2/s) [ + = to atm]
-    !
-    ! !USES
-    use decompMod              , only : bounds_type
-    use atm2lndType            , only : atm2lnd_type
-    use SoilStateType          , only : soilstate_type
-    use CanopyStateType        , only : canopystate_type
-    use WaterStateBulkType     , only : waterstatebulk_type
-    use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
-    use FrictionVelocityMod    , only : frictionvel_type
-
-    import :: dust_emis_base_type
-    !
-    ! !ARGUMENTS:
-    class (dust_emis_base_type)                 :: this
-    type(bounds_type)      , intent(in)    :: bounds                      
-    integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
-    integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
-    type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
-    type(soilstate_type)   , intent(in)    :: soilstate_inst
-    type(canopystate_type) , intent(in)    :: canopystate_inst
-    type(waterstatebulk_type)  , intent(in)    :: waterstatebulk_inst
-    type(waterdiagnosticbulk_type)  , intent(in)    :: waterdiagnosticbulk_inst
-    type(frictionvel_type) , intent(in)    :: frictionvel_inst
-
-  end subroutine DustEmission_interface
+   subroutine DustEmission_interface (this, bounds, &
+         num_nolakep, filter_nolakep, &
+         atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, &
+         frictionvel_inst)
+      !
+      ! !DESCRIPTION:
+      ! Dust mobilization. This code simulates dust mobilization due to wind
+      ! from the surface into the lowest atmospheric layer
+      ! On output flx_mss_vrt_dst(ndst) is the surface dust emission
+      ! (kg/m**2/s) [ + = to atm]
+      !
+      ! !USES
+      use decompMod              , only : bounds_type
+      use atm2lndType            , only : atm2lnd_type
+      use SoilStateType          , only : soilstate_type
+      use CanopyStateType        , only : canopystate_type
+      use WaterStateBulkType     , only : waterstatebulk_type
+      use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
+      use FrictionVelocityMod    , only : frictionvel_type
+
+      import :: dust_emis_base_type
+      !
+      ! !ARGUMENTS:
+      class (dust_emis_base_type)            :: this
+      type(bounds_type)      , intent(in)    :: bounds
+      integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
+      integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
+      type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
+      type(soilstate_type)   , intent(in)    :: soilstate_inst
+      type(canopystate_type) , intent(in)    :: canopystate_inst
+      type(waterstatebulk_type)  , intent(in)    :: waterstatebulk_inst
+      type(waterdiagnosticbulk_type)  , intent(in)    :: waterdiagnosticbulk_inst
+      type(frictionvel_type) , intent(in)    :: frictionvel_inst
+
+   end subroutine DustEmission_interface
 
   end interface
 
@@ -126,7 +126,7 @@ subroutine InitBase(this, bounds, NLFilename)
    ! Base level initialization of this base object, this allows classes that extend
    ! this base class to use this one and extend it with additional initialization
     class(dust_emis_base_type) :: this
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds
     character(len=*),  intent(in) :: NLFilename
 
     call this%InitAllocate (bounds)
@@ -158,14 +158,14 @@ subroutine CleanBase(this)
    deallocate (this%dmt_vwr)
    deallocate (this%stk_crc)
 
- end subroutine CleanBase
+  end subroutine CleanBase
 
   !------------------------------------------------------------------------
   subroutine InitAllocate(this, bounds)
     !
     ! !ARGUMENTS:
     class (dust_emis_base_type) :: this
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
     integer :: begp,endp
@@ -179,7 +179,7 @@ subroutine InitAllocate(this, bounds)
     allocate(this%flx_mss_vrt_dst_tot_patch (begp:endp))        ; this%flx_mss_vrt_dst_tot_patch (:)   = nan
     allocate(this%vlc_trb_patch             (begp:endp,1:ndst)) ; this%vlc_trb_patch             (:,:) = nan
     allocate(this%vlc_trb_1_patch           (begp:endp))        ; this%vlc_trb_1_patch           (:)   = nan
-    allocate(this%vlc_trb_2_patch           (begp:endp))        ; this%vlc_trb_2_patch           (:)   = nan 
+    allocate(this%vlc_trb_2_patch           (begp:endp))        ; this%vlc_trb_2_patch           (:)   = nan
     allocate(this%vlc_trb_3_patch           (begp:endp))        ; this%vlc_trb_3_patch           (:)   = nan
     allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
 
@@ -187,7 +187,6 @@ subroutine InitAllocate(this, bounds)
     allocate (this%dmt_vwr(ndst))                               ; this%dmt_vwr                   (:)   = nan
     allocate (this%stk_crc(ndst))                               ; this%stk_crc                   (:)   = nan
 
-
   end subroutine InitAllocate
 
   !------------------------------------------------------------------------
@@ -199,7 +198,7 @@ subroutine InitHistory(this, bounds)
     !
     ! !ARGUMENTS:
     class (dust_emis_base_type) :: this
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
     integer :: begp,endp
@@ -236,7 +235,7 @@ subroutine InitHistory(this, bounds)
 
   end subroutine InitHistory
 
-    !-----------------------------------------------------------------------
+  !-----------------------------------------------------------------------
 
   subroutine WritePatchToLog(this, p)
     !
@@ -280,7 +279,7 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb,
    if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p)
   end subroutine GetPatchVars
 
-    !-----------------------------------------------------------------------
+  !-----------------------------------------------------------------------
 
   subroutine GetConstVars(this, SaltationFactor )
   !
@@ -293,16 +292,17 @@ subroutine GetConstVars(this, SaltationFactor )
     SaltationFactor = this%saltation_factor
   end subroutine GetConstVars
 
-   !------------------------------------------------------------------------
+  !------------------------------------------------------------------------
+
   subroutine DustDryDep (this, bounds, &
        atm2lnd_inst, frictionvel_inst)
     !
-    ! !DESCRIPTION: 
+    ! !DESCRIPTION:
     !
-    ! Determine Turbulent dry deposition for dust. Calculate the turbulent 
-    ! component of dust dry deposition, (the turbulent deposition velocity 
-    ! through the lowest atmospheric layer. CAM will calculate the settling 
-    ! velocity through the whole atmospheric column. The two calculations 
+    ! Determine Turbulent dry deposition for dust. Calculate the turbulent
+    ! component of dust dry deposition, (the turbulent deposition velocity
+    ! through the lowest atmospheric layer. CAM will calculate the settling
+    ! velocity through the whole atmospheric column. The two calculations
     ! will determine the dust dry deposition flux to the surface.
     ! Note: Same process should occur over oceans. For the coupled CESM,
     ! we may find it more efficient to let CAM calculate the turbulent dep
@@ -317,7 +317,7 @@ subroutine DustDryDep (this, bounds, &
     !
     ! !ARGUMENTS:
     class (dust_emis_base_type)                      :: this
-    type(bounds_type)      , intent(in)    :: bounds 
+    type(bounds_type)      , intent(in)    :: bounds
     type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
     type(frictionvel_type) , intent(in)    :: frictionvel_inst
     !
@@ -334,23 +334,23 @@ subroutine DustDryDep (this, bounds, &
     real(r8) :: slp_crc(bounds%begp:bounds%endp,ndst) ! [frc] Slip correction factor
     real(r8) :: vlc_grv(bounds%begp:bounds%endp,ndst) ! [m s-1] Settling velocity
     real(r8) :: rss_lmn(bounds%begp:bounds%endp,ndst) ! [s m-1] Quasi-laminar layer resistance
-    real(r8) :: tmp                                   ! temporary 
+    real(r8) :: tmp                                   ! temporary
     real(r8), parameter::shm_nbr_xpn_lnd=-2._r8/3._r8 ![frc] shm_nbr_xpn over land
     !------------------------------------------------------------------------
 
-    associate(                                                   & 
-         forc_pbot =>    atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8)  (:)   ]  atm pressure (Pa)                                 
-         forc_rho  =>    atm2lnd_inst%forc_rho_downscaled_col  , & ! Input:  [real(r8)  (:)   ]  atm density (kg/m**3)                             
-         forc_t    =>    atm2lnd_inst%forc_t_downscaled_col    , & ! Input:  [real(r8)  (:)   ]  atm temperature (K)                               
-         
-         ram1      =>    frictionvel_inst%ram1_patch           , & ! Input:  [real(r8)  (:)   ]  aerodynamical resistance (s/m)                    
-         fv        =>    frictionvel_inst%fv_patch             , & ! Input:  [real(r8)  (:)   ]  friction velocity (m/s)                           
-         
-         vlc_trb   =>    this%vlc_trb_patch                   , & ! Output:  [real(r8) (:,:) ]  Turbulent deposn velocity (m/s)                 
-         vlc_trb_1 =>    this%vlc_trb_1_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 1                   
-         vlc_trb_2 =>    this%vlc_trb_2_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 2                   
-         vlc_trb_3 =>    this%vlc_trb_3_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 3                   
-         vlc_trb_4 =>    this%vlc_trb_4_patch                   & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 4                   
+    associate(                                                   &
+         forc_pbot =>    atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8)  (:)   ]  atm pressure (Pa)
+         forc_rho  =>    atm2lnd_inst%forc_rho_downscaled_col  , & ! Input:  [real(r8)  (:)   ]  atm density (kg/m**3)
+         forc_t    =>    atm2lnd_inst%forc_t_downscaled_col    , & ! Input:  [real(r8)  (:)   ]  atm temperature (K)
+
+         ram1      =>    frictionvel_inst%ram1_patch           , & ! Input:  [real(r8)  (:)   ]  aerodynamical resistance (s/m)
+         fv        =>    frictionvel_inst%fv_patch             , & ! Input:  [real(r8)  (:)   ]  friction velocity (m/s)
+
+         vlc_trb   =>    this%vlc_trb_patch                   , & ! Output:  [real(r8) (:,:) ]  Turbulent deposn velocity (m/s)
+         vlc_trb_1 =>    this%vlc_trb_1_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 1
+         vlc_trb_2 =>    this%vlc_trb_2_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 2
+         vlc_trb_3 =>    this%vlc_trb_3_patch                 , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 3
+         vlc_trb_4 =>    this%vlc_trb_4_patch                   & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 4
          )
 
       do p = bounds%begp,bounds%endp
@@ -399,7 +399,7 @@ subroutine DustDryDep (this, bounds, &
                ! Schmidt number exponent is -2/3 over solid surfaces and
                ! -1/2 over liquid surfaces SlS80 p. 1014
                ! if (oro(i)==0.0) shm_nbr_xpn=shm_nbr_xpn_ocn else shm_nbr_xpn=shm_nbr_xpn_lnd
-               ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # 
+               ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt #
 
                tmp = shm_nbr**shm_nbr_xpn + 10.0_r8**(-3.0_r8/stk_nbr)
                rss_lmn(p,m) = 1.0_r8 / (tmp * fv(p)) ![s m-1] SeP97 p.972,965
@@ -431,10 +431,11 @@ subroutine DustDryDep (this, bounds, &
 
   end subroutine DustDryDep
 
-   !------------------------------------------------------------------------
-   subroutine InitDustVars(this, bounds)
+  !------------------------------------------------------------------------
+
+  subroutine InitDustVars(this, bounds)
      !
-     ! !DESCRIPTION: 
+     ! !DESCRIPTION:
      !
      ! Compute source efficiency factor from topography
      ! Initialize other variables used in subroutine Dust:
@@ -452,7 +453,7 @@ subroutine InitDustVars(this, bounds)
      !
      ! !ARGUMENTS:
      class(dust_emis_base_type)  :: this
-     type(bounds_type), intent(in) :: bounds  
+     type(bounds_type), intent(in) :: bounds
      !
      ! !LOCAL VARIABLES
     integer  :: fc,c,l,m,n              ! indices
@@ -474,7 +475,7 @@ subroutine InitDustVars(this, bounds)
     real(r8) :: vlc_grv(ndst)           ! [m s-1] Settling velocity
     real(r8) :: ryn_nbr_grv(ndst)       ! [frc] Reynolds number at terminal velocity
     real(r8) :: cff_drg_grv(ndst)       ! [frc] Drag coefficient at terminal velocity
-    real(r8) :: tmp                     ! temporary 
+    real(r8) :: tmp                     ! temporary
     real(r8) :: ln_gsd                  ! [frc] ln(gsd)
     real(r8) :: gsd_anl                 ! [frc] Geometric standard deviation
     real(r8) :: dmt_vma                 ! [m] Mass median diameter analytic She84 p.75 Tabl.1
@@ -494,7 +495,7 @@ subroutine InitDustVars(this, bounds)
     real(r8) :: sz_max(sz_nbr)          ! [m] Size Bin maxima
     real(r8) :: sz_ctr(sz_nbr)          ! [m] Size Bin centers
     real(r8) :: sz_dlt(sz_nbr)          ! [m] Size Bin widths
-    
+
     ! constants
     real(r8), allocatable :: dmt_vma_src(:) ! [m] Mass median diameter       BSM96 p. 73 Table 2
     real(r8), allocatable :: gsd_anl_src(:) ! [frc] Geometric std deviation  BSM96 p. 73 Table 2
@@ -507,13 +508,13 @@ subroutine InitDustVars(this, bounds)
     !------------------------------------------------------------------------
 
       ! allocate local variable
-      allocate (dmt_vma_src(dst_src_nbr))  
-      allocate (gsd_anl_src(dst_src_nbr))  
-      allocate (mss_frc_src(dst_src_nbr))  
+      allocate (dmt_vma_src(dst_src_nbr))
+      allocate (gsd_anl_src(dst_src_nbr))
+      allocate (mss_frc_src(dst_src_nbr))
 
-      dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /)        
-      gsd_anl_src(:) = (/ 2.10_r8     , 1.90_r8    , 1.60_r8     /)        
-      mss_frc_src(:) = (/ 0.036_r8    , 0.957_r8   , 0.007_r8 /)                  
+      dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /)
+      gsd_anl_src(:) = (/ 2.10_r8     , 1.90_r8    , 1.60_r8     /)
+      mss_frc_src(:) = (/ 0.036_r8    , 0.957_r8   , 0.007_r8 /)
 
       ! the following comes from (1) szdstlgn.F subroutine ovr_src_snk_frc_get
       !                      and (2) dstszdst.F subroutine dst_szdst_ini
@@ -533,7 +534,7 @@ subroutine InitDustVars(this, bounds)
          end do
       end do
 
-      ! The following code from subroutine wnd_frc_thr_slt_get was placed 
+      ! The following code from subroutine wnd_frc_thr_slt_get was placed
       ! here because saltation_factor needs to be defined just once
 
       ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8
@@ -709,7 +710,7 @@ subroutine InitDustVars(this, bounds)
             ! [m s-1] Terminal veloc SeP97 p.467 (8.44)
 
             vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / &
-                 (3.0_r8*cff_drg_grv(m)*dns_mdp))   
+                 (3.0_r8*cff_drg_grv(m)*dns_mdp))
             eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence
             if (itr_idx == 12) then
                ! Numerical pingpong may occur when Re = 0.1, 2.0, or 500.0
@@ -737,4 +738,6 @@ subroutine InitDustVars(this, bounds)
 
   end subroutine InitDustVars
 
+  !------------------------------------------------------------------------
+
 end module DustEmisBase
diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index fa2a96b7e0..bebbc7ff30 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -1,18 +1,18 @@
 module DustEmisZender2003
 
-  !----------------------------------------------------------------------- 
-  ! !DESCRIPTION: 
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
   ! Routines in this module calculate Dust mobilization and dry deposition for dust.
-  ! Simulates dust mobilization due to wind from the surface into the 
-  ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust 
+  ! Simulates dust mobilization due to wind from the surface into the
+  ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust
   ! emission (kg/m**2/s) [ + = to atm].
-  ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition 
-  ! velocity through the lowest atmospheric layer). CAM will calculate the settling 
-  ! velocity through the whole atmospheric column. The two calculations will determine 
+  ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition
+  ! velocity through the lowest atmospheric layer). CAM will calculate the settling
+  ! velocity through the whole atmospheric column. The two calculations will determine
   ! the dust dry deposition flux to the surface.
-  !                              
+  !
   ! !USES:
-  use shr_kind_mod         , only : r8 => shr_kind_r8 
+  use shr_kind_mod         , only : r8 => shr_kind_r8
   use shr_log_mod          , only : errMsg => shr_log_errMsg
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
   use clm_varpar           , only : dst_src_nbr, ndst
@@ -32,7 +32,7 @@ module DustEmisZender2003
   use ZenderSoilErodStreamType,  only : soil_erod_stream_type
   use DustEmisBase         , only : dust_emis_base_type
   use clm_varctl           , only : dust_emis_method
-  !  
+  !
   ! !PUBLIC TYPES
   implicit none
   private
@@ -54,7 +54,7 @@ module DustEmisZender2003
      procedure , public  :: Clean => CleanZender2003
      procedure , private :: InitAllocate    ! Allocate data
      procedure , private :: InitHistory     ! History initialization
-     procedure , private :: InitCold     
+     procedure , private :: InitCold
 
   end type dust_emis_zender2003_type
   !------------------------------------------------------------------------
@@ -65,11 +65,12 @@ module DustEmisZender2003
 contains
 
   !------------------------------------------------------------------------
+
   subroutine InitZender2003(this, bounds, NLFilename)
 
    ! Initialization for this extended class, calling base level initiation and adding to it
     class(dust_emis_zender2003_type) :: this
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds
     character(len=*),  intent(in) :: NLFilename
 
     call this%soil_erod_stream%Init( bounds, NLFilename )
@@ -81,11 +82,12 @@ subroutine InitZender2003(this, bounds, NLFilename)
   end subroutine InitZender2003
 
   !------------------------------------------------------------------------
+
   subroutine InitAllocate(this, bounds)
    !
    ! !ARGUMENTS:
    class (dust_emis_zender2003_type) :: this
-   type(bounds_type), intent(in) :: bounds  
+   type(bounds_type), intent(in) :: bounds
    !
    ! !LOCAL VARIABLES:
    integer :: begc,endc
@@ -95,9 +97,10 @@ subroutine InitAllocate(this, bounds)
 
    allocate(this%mbl_bsn_fct_col           (begc:endc))        ; this%mbl_bsn_fct_col           (:)   = nan
 
- end subroutine InitAllocate
+  end subroutine InitAllocate
+
+  !------------------------------------------------------------------------
 
-   !------------------------------------------------------------------------
   subroutine CleanZender2003(this)
     !
     ! Deallocation for this extended class, calling base level deallocation and adding to it
@@ -113,6 +116,7 @@ subroutine CleanZender2003(this)
   end subroutine CleanZender2003
 
   !------------------------------------------------------------------------
+
   subroutine InitHistory(this, bounds)
     !
     ! !USES:
@@ -121,7 +125,7 @@ subroutine InitHistory(this, bounds)
     !
     ! !ARGUMENTS:
     class (dust_emis_zender2003_type) :: this
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
     integer :: begc,endc
@@ -139,11 +143,12 @@ subroutine InitHistory(this, bounds)
   end subroutine InitHistory
 
   !-----------------------------------------------------------------------
+
   subroutine InitCold(this, bounds)
     !
     ! !ARGUMENTS:
     class (dust_emis_zender2003_type) :: this
-    type(bounds_type), intent(in) :: bounds  
+    type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
     integer :: c,l
@@ -175,15 +180,16 @@ subroutine InitCold(this, bounds)
   end subroutine InitCold
 
   !------------------------------------------------------------------------
+
   subroutine DustEmission (this, bounds, &
        num_nolakep, filter_nolakep, &
        atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, &
        frictionvel_inst)
     !
-    ! !DESCRIPTION: 
+    ! !DESCRIPTION:
     ! Dust mobilization. This code simulates dust mobilization due to wind
     ! from the surface into the lowest atmospheric layer
-    ! On output flx_mss_vrt_dst(ndst) is the surface dust emission 
+    ! On output flx_mss_vrt_dst(ndst) is the surface dust emission
     ! (kg/m**2/s) [ + = to atm]
     ! Source: C. Zender's dust model
     !
@@ -192,8 +198,8 @@ subroutine DustEmission (this, bounds, &
     use subgridaveMod, only : p2g
     !
     ! !ARGUMENTS:
-    class (dust_emis_zender2003_type)                      :: this
-    type(bounds_type)      , intent(in)    :: bounds                      
+    class (dust_emis_zender2003_type)      :: this
+    type(bounds_type)      , intent(in)    :: bounds
     integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
     integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
     type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
@@ -226,7 +232,7 @@ subroutine DustEmission (this, bounds, &
     real(r8) :: sumwt(bounds%begl:bounds%endl) ! sum of weights
     logical  :: found                          ! temporary for error check
     integer  :: index
-    !    
+    !
     ! constants
     !
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
@@ -235,26 +241,26 @@ subroutine DustEmission (this, bounds, &
     character(len=*),parameter :: subname = 'DUSTEmission'
     !------------------------------------------------------------------------
 
-    associate(                                                         & 
-         forc_rho            => atm2lnd_inst%forc_rho_downscaled_col , & ! Input:  [real(r8) (:)   ]  downscaled density (kg/m**3)                                 
-         
+    associate(                                                         &
+         forc_rho            => atm2lnd_inst%forc_rho_downscaled_col , & ! Input:  [real(r8) (:)   ]  downscaled density (kg/m**3)
+
          gwc_thr             => soilstate_inst%gwc_thr_col           , & ! Input:  [real(r8) (:)   ]  threshold gravimetric soil moisture based on clay content
-         mss_frc_cly_vld     => soilstate_inst%mss_frc_cly_vld_col   , & ! Input:  [real(r8) (:)   ]  [frc] Mass fraction clay limited to 0.20          
-         watsat              => soilstate_inst%watsat_col            , & ! Input:  [real(r8) (:,:) ]  saturated volumetric soil water                 
-         
-         tlai                => canopystate_inst%tlai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided leaf area index, no burying by snow     
-         tsai                => canopystate_inst%tsai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided stem area index, no burying by snow     
-         
-         frac_sno            => waterdiagnosticbulk_inst%frac_sno_col         , & ! Input:  [real(r8) (:)   ]  fraction of ground covered by snow (0 to 1)       
-         h2osoi_vol          => waterstatebulk_inst%h2osoi_vol_col       , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (0<=h2osoi_vol<=watsat)   
-         h2osoi_liq          => waterstatebulk_inst%h2osoi_liq_col       , & ! Input:  [real(r8) (:,:) ]  liquid soil water (kg/m2)                       
-         h2osoi_ice          => waterstatebulk_inst%h2osoi_ice_col       , & ! Input:  [real(r8) (:,:) ]  frozen soil water (kg/m2)                       
-         
-         fv                  => frictionvel_inst%fv_patch            , & ! Input:  [real(r8) (:)   ]  friction velocity (m/s) (for dust model)          
-         u10                 => frictionvel_inst%u10_patch           , & ! Input:  [real(r8) (:)   ]  10-m wind (m/s) (created for dust model)          
-         
+         mss_frc_cly_vld     => soilstate_inst%mss_frc_cly_vld_col   , & ! Input:  [real(r8) (:)   ]  [frc] Mass fraction clay limited to 0.20
+         watsat              => soilstate_inst%watsat_col            , & ! Input:  [real(r8) (:,:) ]  saturated volumetric soil water
+
+         tlai                => canopystate_inst%tlai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided leaf area index, no burying by snow
+         tsai                => canopystate_inst%tsai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided stem area index, no burying by snow
+
+         frac_sno            => waterdiagnosticbulk_inst%frac_sno_col         , & ! Input:  [real(r8) (:)   ]  fraction of ground covered by snow (0 to 1)
+         h2osoi_vol          => waterstatebulk_inst%h2osoi_vol_col       , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (0<=h2osoi_vol<=watsat)
+         h2osoi_liq          => waterstatebulk_inst%h2osoi_liq_col       , & ! Input:  [real(r8) (:,:) ]  liquid soil water (kg/m2)
+         h2osoi_ice          => waterstatebulk_inst%h2osoi_ice_col       , & ! Input:  [real(r8) (:,:) ]  frozen soil water (kg/m2)
+
+         fv                  => frictionvel_inst%fv_patch            , & ! Input:  [real(r8) (:)   ]  friction velocity (m/s) (for dust model)
+         u10                 => frictionvel_inst%u10_patch           , & ! Input:  [real(r8) (:)   ]  10-m wind (m/s) (created for dust model)
+
          mbl_bsn_fct         => this%mbl_bsn_fct_col                 , & ! Input:  [real(r8) (:)   ]  basin factor
-         flx_mss_vrt_dst     => this%flx_mss_vrt_dst_patch           , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
+         flx_mss_vrt_dst     => this%flx_mss_vrt_dst_patch           , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)
          flx_mss_vrt_dst_tot => this%flx_mss_vrt_dst_tot_patch         & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
          )
 
@@ -315,8 +321,8 @@ subroutine DustEmission (this, bounds, &
                lnd_frc_mbl(p) = 0.0_r8
             endif
             lnd_frc_mbl(p) = lnd_frc_mbl(p) * (1.0_r8 - frac_sno(c))
-         else          
-            lnd_frc_mbl(p) = 0.0_r8   
+         else
+            lnd_frc_mbl(p) = 0.0_r8
          end if
       end do
 
@@ -349,7 +355,7 @@ subroutine DustEmission (this, bounds, &
          l = patch%landunit(p)
          g = patch%gridcell(p)
 
-         ! only perform the following calculations if lnd_frc_mbl is non-zero 
+         ! only perform the following calculations if lnd_frc_mbl is non-zero
 
          if (lnd_frc_mbl(p) > 0.0_r8) then
 
@@ -396,7 +402,7 @@ subroutine DustEmission (this, bounds, &
 
             wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)
 
-            ! the following if-block comes from subr. wnd_frc_slt_get 
+            ! the following if-block comes from subr. wnd_frc_slt_get
             ! purpose: compute the saltating friction velocity
             ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
 
@@ -416,7 +422,7 @@ subroutine DustEmission (this, bounds, &
 
                ! the following loop originates from subr. dst_mbl
                ! purpose: apply land sfc and veg limitations and global tuning factor
-               ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect 
+               ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect
                ! of frozen soil
 
                flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * mbl_bsn_fct(c) * &
@@ -461,4 +467,6 @@ subroutine DustEmission (this, bounds, &
 
   end subroutine DustEmission
 
-end module DustEmisZender2003
+  !------------------------------------------------------------------------
+
+end module DustEmisZender2003
\ No newline at end of file

From ccb4f1e3b5d80068225512ac188a275f38807970 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 4 Jun 2024 16:59:43 -0600
Subject: [PATCH 0440/1248] Remove test_DustEmisBase.pf as it wasn't doing
 anything, I had trouble trying to make it a base class of the Zender Test
 case and get that to both build and run in the unit testing, so remove for
 now

---
 .../test/DustEmis_test/CMakeLists.txt         |   1 -
 .../test/DustEmis_test/test_DustEmisBase.pf   | 298 ------------------
 2 files changed, 299 deletions(-)
 delete mode 100644 src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf

diff --git a/src/biogeochem/test/DustEmis_test/CMakeLists.txt b/src/biogeochem/test/DustEmis_test/CMakeLists.txt
index 49e3c16391..9239d16e22 100644
--- a/src/biogeochem/test/DustEmis_test/CMakeLists.txt
+++ b/src/biogeochem/test/DustEmis_test/CMakeLists.txt
@@ -1,5 +1,4 @@
 set (pfunit_sources
-  test_DustEmisBase.pf
   test_DustEmisZender2003.pf)
 
 add_pfunit_ctest(DustEmis
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
deleted file mode 100644
index cf8df87d64..0000000000
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf
+++ /dev/null
@@ -1,298 +0,0 @@
-module test_DustEmisBase
-
-  ! Tests of DustEmisBase
-
-  use funit
-  use unittestSubgridMod
-  use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
-  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
-  use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
-  use clm_varcon, only : clm_varcon_init, clm_varcon_clean
-  use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean
-  use DustEmisZender2003
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use unittestFilterBuilderMod, only : filter_from_range
-  use atm2lndType, only : atm2lnd_type, atm2lnd_params_type
-  use SoilStateType, only : soilstate_type
-  use CanopyStateType, only : canopystate_type
-  use TemperatureType, only : temperature_type
-  use WaterType, only : water_type
-  use FrictionVelocityMod, only : frictionvel_type
-  use unittestWaterTypeFactory, only : unittest_water_type_factory_type
-  use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay
-
-  implicit none
-
-  real(r8), parameter :: tol = 1.e-18_r8
-
-  @TestCase
-  type, extends(TestCase) :: TestDustEmisBase
-     type(dust_emis_zender2003_type) :: dust_emis
-     integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
-     integer :: num_nolakep              ! number of patches in non-lake filter
-     type(atm2lnd_type) :: atm2lnd_inst
-     type(soilstate_type) :: soilstate_inst
-     type(canopystate_type) :: canopystate_inst
-     type(temperature_type) :: temperature_inst
-     type(unittest_water_type_factory_type) :: water_factory
-     type(water_type) :: water_inst
-     type(frictionvel_type) :: frictionvel_inst
-   contains
-     procedure :: setUp
-     procedure :: tearDown
-     procedure :: setupEnvironment
-     procedure :: create_atm2lnd
-     procedure :: create_fv
-     procedure :: print_values
-     procedure :: validate_patch
-  end type TestDustEmisBase
-
-contains
-
-  !-----------------------------------------------------------------------
-
-  subroutine setUp(this)
-    use ColumnType, only : col
-    class(TestDustEmisBase), intent(inout) :: this
-
-    character(len=5) :: NLFilename = 'none'
-    real(r8), allocatable :: snow_depth_col(:)
-    real(r8), allocatable :: urb_em(:)
-    integer :: begl, endl, begc, endc
-    integer :: c
-    type(atm2lnd_params_type) :: atm2lnd_params
-
-    soil_layerstruct_predefined = '20SL_8.5m'
-    create_crop_landunit = .true.
-    use_crop = .false.
-    call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
-    call clm_varcon_init( is_simple_buildtemp=.true.)
-    call this%water_factory%init()
-    call this%water_factory%setup_before_subgrid( &
-        my_nlevsoi = nlevsoi, &
-        nlevgrnd_additional = nlevgrnd - nlevsoi, &
-        my_nlevsno = 3)
-    call setup_single_veg_patch( pft_type=0 )
-    begl = bounds%begl
-    endl = bounds%endl
-    begc = bounds%begc
-    endc = bounds%endc
-    allocate( urb_em(begl:endl) )
-
-    call this%dust_emis%Init( bounds, NLFilename )
-    call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
-    atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
-                                          glcmec_downscale_longwave = .false., &
-                                          lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
-    )
-    allocate (snow_depth_col(begc:endc))
-    snow_depth_col(begc:endc) = 0.0_r8
-    call SnowHydrologySetControlForTesting()
-    call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc))
-    call this%water_factory%setup_after_subgrid(snl = 3)
-    call this%soilstate_inst%Init(bounds)
-    do c = begc, endc
-       this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1)
-    end do
-    call this%setupEnvironment( )
-    call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
-    call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
-    call this%canopystate_inst%SetNMLForTesting()
-    call this%canopystate_inst%Init(bounds)
-    call this%frictionvel_inst%InitForTesting(bounds)
-    urb_em(begl:endl) = 0.99_r8
-    call this%temperature_inst%Init(bounds,           &
-                               em_roof_lun=urb_em(begl:endl), &
-                               em_wall_lun=urb_em(begl:endl), &
-                               em_improad_lun=urb_em(begl:endl), &
-                               em_perroad_lun=urb_em(begl:endl), &
-                               is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
-    deallocate (snow_depth_col )
-    deallocate( urb_em )
-  end subroutine setUp
-
-  !-----------------------------------------------------------------------
-
-  subroutine tearDown(this)
-    class(TestDustEmisBase), intent(inout) :: this
-
-    call this%dust_emis%Clean()
-    call this%water_factory%teardown(this%water_inst)
-    call SnowHydrologyClean()
-    call unittest_subgrid_teardown()
-    call this%atm2lnd_inst%Clean()
-    call clm_varcon_clean()
-    deallocate( this%filter_nolakep )
-  end subroutine tearDown
-
-  !-----------------------------------------------------------------------
-
-  subroutine setupEnvironment(this)
-    !
-    ! !DESCRIPTION:
-    ! Sets up the external environment used by Dust emissions - i.e., things accessed via
-    ! 'use' statements.
-    !
-    ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has
-    ! been completed.
-    !
-    use ColumnType, only : col
-    use GridcellType, only : grc
-    class(TestDustEmisBase), intent(in) :: this
-    !
-    integer :: c,j
-    real(r8), parameter :: clay = 10.0_r8
-
-    !-----------------------------------------------------------------------
-    col%dz(:,1:nlevgrnd) = 1.0_r8
-    do j = 1, nlevgrnd
-       do c = bounds%begc, bounds%endc
-          col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j)
-       end do
-    end do
-
-    do c = bounds%begc, bounds%endc
-       ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are
-       ! considered bedrock
-       col%nbedrock(c) = nlevsoi
-
-       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
-       this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
-    end do
-
-
-    ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager)
-    grc%londeg(:) = 0.0_r8
-
-    grc%area(:) = 10.0_r8
-
-  end subroutine setupEnvironment
-
-  !-----------------------------------------------------------------------
-
-  subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho )
-    ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets
-    ! forcing fields based on inputs. Excluded inputs are given a default value
-    class(TestDustEmisBase), intent(inout) :: this
-    real(r8), intent(in), optional :: forc_t(:)
-    real(r8), intent(in), optional :: forc_pbot(:)
-    real(r8), intent(in), optional :: forc_rho(:)
-
-    real(r8), parameter :: forc_t_default = 301._r8
-    real(r8), parameter :: forc_pbot_default = 100000._r8
-    real(r8), parameter :: forc_rho_default = 1.1_r8
-    ! ------------------------------------------------------------------------
-
-    if (present(forc_t)) then
-       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:)
-    else
-       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default
-    end if
-
-    if (present(forc_pbot)) then
-       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:)
-    else
-       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default
-    end if
-
-    if (present(forc_rho)) then
-       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:)
-    else
-       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default
-    end if
-
-  end subroutine create_atm2lnd
-
-  !-----------------------------------------------------------------------
-
-  subroutine create_fv(this, fv, u10, ram1)
-    ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
-    ! fields based on inputs. Excluded inputs are given a default value
-    class(TestDustEmisBase), intent(inout) :: this
-    real(r8), intent(in), optional :: fv
-    real(r8), intent(in), optional :: u10
-    real(r8), intent(in), optional :: ram1
-
-    real(r8), parameter :: fv_default = 2.0_r8
-    real(r8), parameter :: u10_default = 4._r8
-    real(r8), parameter :: ram1_default = 200._r8
-    ! ------------------------------------------------------------------------
-
-    if (present(fv)) then
-       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv
-    else
-       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default
-    end if
-
-    if (present(u10)) then
-       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10
-    else
-       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default
-    end if
-
-    if (present(ram1)) then
-       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1
-    else
-       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default
-    end if
-
-  end subroutine create_fv
-
-  subroutine print_values(this)
-    use LandunitType, only : lun
-    use PatchType, only : patch
-    class(TestDustEmisBase), intent(inout) :: this
-    real(r8) :: SaltationFactor
-    integer :: p, c, l
-
-    call this%dust_emis%GetConstVars( SaltationFactor )
-    do l = bounds%begl, bounds%endl
-       print *, 'landunit type= ', lun%itype(l)
-    end do
-    do c = bounds%begc, bounds%endc
-       print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1)
-       print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1)
-       print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c)
-       print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c)
-       print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c))
-    end do
-    do p = bounds%begp, bounds%endp
-       print *, 'patch type= ', patch%itype(p)
-       print *, 'patch weight= ', patch%wtgcell(p)
-       print *, 'patch active= ', patch%active(p)
-       print *, 'tlai = ', this%canopystate_inst%tlai_patch(p)
-       print *, 'tsai = ', this%canopystate_inst%tsai_patch(p)
-       c = patch%column(p)
-       print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) &
-                                     / this%frictionvel_inst%fv_patch(p)
-       call this%dust_emis%WritePatchToLog( p )
-    end do
-  end subroutine print_values
-
-  !-----------------------------------------------------------------------
-  subroutine validate_patch(this, p)
-    class(TestDustEmisBase), intent(inout) :: this
-    integer, intent(in) :: p
-
-    real(r8) :: flx_mss_vrt_dst(ndst)
-    real(r8) :: flx_mss_vrt_dst_tot
-    real(r8) :: vlc_trb(ndst)
-    real(r8) :: vlc_trb_1
-    real(r8) :: vlc_trb_2
-    real(r8) :: vlc_trb_3
-    real(r8) :: vlc_trb_4
-
-    call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, &
-             flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, &
-             vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
-             vlc_trb_4=vlc_trb_4 )
-    @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot )
-    @assertEqual( vlc_trb(1), vlc_trb_1)
-    @assertEqual( vlc_trb(2), vlc_trb_2)
-    @assertEqual( vlc_trb(3), vlc_trb_3)
-    @assertEqual( vlc_trb(4), vlc_trb_4)
-  end subroutine validate_patch
-
-  !-----------------------------------------------------------------------
-
-end module test_DustEmisBase

From d101b25e174d1bffe43f6f6e97d6efc209a62a03 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 4 Jun 2024 18:17:23 -0600
Subject: [PATCH 0441/1248] Make a validate function for dust emission part of
 the dust_emis base class

---
 src/biogeochem/DustEmisBase.F90               | 47 +++++++++++++++++++
 .../DustEmis_test/test_DustEmisZender2003.pf  | 18 +------
 2 files changed, 48 insertions(+), 17 deletions(-)

diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
index 6fb1066607..dbc5729403 100644
--- a/src/biogeochem/DustEmisBase.F90
+++ b/src/biogeochem/DustEmisBase.F90
@@ -61,6 +61,7 @@ module DustEmisBase
      procedure , public   :: InitBase        ! Base object initiatlization (allows it to be extended)
      procedure , public   :: Init => InitBase ! Initialization name used by callers
      procedure(DustEmission_interface) , public, deferred  :: DustEmission    ! Dust mobilization
+     procedure , public   :: CheckDustEmisIsValid ! Check that the dust emission type is valid
      procedure , public   :: DustDryDep      ! Turbulent dry deposition for dust
      procedure , public   :: WritePatchToLog ! Write information on the given patch to the log file
      procedure , public   :: GetPatchVars    ! Get important variables on a given patch
@@ -279,6 +280,52 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb,
    if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p)
   end subroutine GetPatchVars
 
+  !------------------------------------------------------------------------
+  subroutine CheckDustEmisIsValid( this, p )
+   ! Check that dust emission state for this patch is valid
+   ! This means ensuring that total dust is the sum of all the dust bins
+   ! And that dry deposition for each dust bins agrees with the array of all
+   class(dust_emis_base_type) :: this
+   integer         , intent(in) :: p      ! Patch to display
+   integer :: i
+
+   if ( abs(sum(this%flx_mss_vrt_dst_patch(p,:)) - this%flx_mss_vrt_dst_tot_patch(p)) > 0.0_r8 )then
+      write(iulog,*) 'sum(flx_mss_vrt_dst(:)) /=flx_mss_vrt_dst_tot for p = ', p, &
+                     errMsg(sourcefile, __LINE__)
+      call endrun(msg="Sum over dust bins does NOT equal total dust")
+      return
+   end if
+   i = 1
+   if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_1_patch(p) )then
+      write(iulog,*) 'vlc_trb(i)) /= glc_trb for p = ', p, 'dust bin = ', i, &
+                     errMsg(sourcefile, __LINE__)
+      call endrun(msg="Dry deposition for dust bin not equal to the array bin for it")
+      return
+   end if
+   i = 2
+   if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_2_patch(p) )then
+      write(iulog,*) 'vlc_trb(i) /= glc_trb for p = ', p, 'dust bin = ', i, &
+                     errMsg(sourcefile, __LINE__)
+      call endrun(msg="Dry deposition for dust bin not equal to the array bin for it")
+      return
+   end if
+   i = 3
+   if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_3_patch(p) )then
+      write(iulog,*) 'vlc_trb(i)) /= glc_trb for p = ', p, 'dust bin = ', i, &
+                     errMsg(sourcefile, __LINE__)
+      call endrun(msg="Dry deposition for dust bin not equal to the array bin for it")
+      return
+   end if
+   i = 4
+   if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_4_patch(p) )then
+      write(iulog,*) 'vlc_trb(i)) /= glc_trb for p = ', p, 'dust bin = ', i, &
+                     errMsg(sourcefile, __LINE__)
+      call endrun(msg="Dry deposition for dust bin not equal to the array bin for it")
+      return
+   end if
+
+  end subroutine CheckDustEmisIsValid
+
   !-----------------------------------------------------------------------
 
   subroutine GetConstVars(this, SaltationFactor )
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 1168200cfe..7ba4e4b63e 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -274,23 +274,7 @@ contains
     class(TestDustEmisZender2003), intent(inout) :: this
     integer, intent(in) :: p
 
-    real(r8) :: flx_mss_vrt_dst(ndst)
-    real(r8) :: flx_mss_vrt_dst_tot
-    real(r8) :: vlc_trb(ndst)
-    real(r8) :: vlc_trb_1
-    real(r8) :: vlc_trb_2
-    real(r8) :: vlc_trb_3
-    real(r8) :: vlc_trb_4
-
-    call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, &
-             flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, &
-             vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
-             vlc_trb_4=vlc_trb_4 )
-    @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot )
-    @assertEqual( vlc_trb(1), vlc_trb_1)
-    @assertEqual( vlc_trb(2), vlc_trb_2)
-    @assertEqual( vlc_trb(3), vlc_trb_3)
-    @assertEqual( vlc_trb(4), vlc_trb_4)
+    call this%dust_emis%CheckDustEmisIsValid( p )
   end subroutine validate_patch
 
   !-----------------------------------------------------------------------

From a54623b85c6fe44958eaa972330fba1a052832ac Mon Sep 17 00:00:00 2001
From: HuiWangWanderInGitHub <wanghuigis2013@gmail.com>
Date: Wed, 5 Jun 2024 01:12:44 -0600
Subject: [PATCH 0442/1248] Add the drought part

---
 src/biogeochem/VOCEmissionMod.F90 | 178 ++++++++++++++++++------------
 src/main/clm_driver.F90           |   4 +-
 2 files changed, 107 insertions(+), 75 deletions(-)

diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
index 84de85031a..9833fe3de9 100644
--- a/src/biogeochem/VOCEmissionMod.F90
+++ b/src/biogeochem/VOCEmissionMod.F90
@@ -30,6 +30,7 @@ module VOCEmissionMod
   use SolarAbsorbedType  , only : solarabs_type
   use TemperatureType    , only : temperature_type
   use PatchType          , only : patch                
+  use EnergyFluxType     , only : energyflux_type
   !
   implicit none
   private 
@@ -84,10 +85,15 @@ module VOCEmissionMod
   !------------------------------------------------------------------------
   subroutine Init(this, bounds)
 
+    use clm_varctl     , only : use_fates, use_fates_sp
     class(vocemis_type) :: this
     type(bounds_type), intent(in)    :: bounds  
 
     if ( shr_megan_mechcomps_n > 0) then
+       if ( use_fates .and. (.not. use_fates_sp) ) then
+           call endrun( msg='ERROR: MEGAN currently does NOT work with FATES outside of FATES-SP mode (see github issue #115)'//&
+                     errMsg(sourcefile, __LINE__))
+       end if
        call this%InitAllocate(bounds) 
        call this%InitHistory(bounds)
        call this%InitCold(bounds)
@@ -373,7 +379,7 @@ end subroutine InitCold
   !-----------------------------------------------------------------------
   subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
        atm2lnd_inst, canopystate_inst, photosyns_inst, temperature_inst, &
-       vocemis_inst)
+       vocemis_inst, energyflux_inst)
     !
     ! ! NEW DESCRIPTION
     ! Volatile organic compound emission
@@ -417,6 +423,8 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
     type(photosyns_type)   , intent(in)    :: photosyns_inst
     type(temperature_type) , intent(in)    :: temperature_inst
     type(vocemis_type)     , intent(inout) :: vocemis_inst
+    !by Hui,
+    type(energyflux_type)  , intent(in)    :: energyflux_inst
     !
     ! !REVISION HISTORY:
     ! 4/29/11: Colette L. Heald: expand MEGAN to 20 compound classes
@@ -479,8 +487,9 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
          !sucsat       => soilstate_inst%sucsat_col             , & ! Input:  [real(r8) (:,:) ]  minimum soil suction (mm) (nlevgrnd)            
          !h2osoi_vol   => waterstate_inst%h2osoi_vol_col        , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (m3/m3)                   
          !h2osoi_ice   => waterstate_inst%h2osoi_ice_col        , & ! Input:  [real(r8) (:,:) ]  ice soil content (kg/m3)                        
+         btran         => energyflux_inst%btran_patch           , & ! Input: [real(r8) (:)    ]  transpiration wetness factor (0 to 1)
          
-         forc_solad    => atm2lnd_inst%forc_solad_grc           , & ! Input:  [real(r8) (:,:) ]  direct beam radiation (visible only)            
+         forc_solad    => atm2lnd_inst%forc_solad_downscaled_col, & ! Input:  [real(r8) (:,:) ]  direct beam radiation (visible only)            
          forc_solai    => atm2lnd_inst%forc_solai_grc           , & ! Input:  [real(r8) (:,:) ]  diffuse radiation     (visible only)            
          forc_pbot     => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8) (:)   ]  downscaled atmospheric pressure (Pa)                          
          forc_pco2     => atm2lnd_inst%forc_pco2_grc            , & ! Input:  [real(r8) (:)   ]  partial pressure co2 (Pa)                                             
@@ -552,7 +561,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
           ! Calculate PAR: multiply w/m2 by 4.6 to get umol/m2/s for par (added 8/14/02)
           !------------------------
           ! SUN:
-          par_sun    = (forc_solad(g,1)  + fsun(p)    * forc_solai(g,1))  * 4.6_r8
+          par_sun    = (forc_solad(c,1)  + fsun(p)    * forc_solai(g,1))  * 4.6_r8
           par24_sun  = (forc_solad24(p)  + fsun24(p)  * forc_solai24(p))  * 4.6_r8
           par240_sun = (forc_solad240(p) + fsun240(p) * forc_solai240(p)) * 4.6_r8
 
@@ -564,10 +573,12 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
           ! Activity factor for LAI (Guenther et al., 2006): all species
           gamma_l = get_gamma_L(fsun240(p), elai(p))
 
+          !gamma_sm = 1.0_r8
+          !Impact of soil moisture on isoprene emission
+          gamma_sm = get_gamma_SM(btran(p))
           ! Activity factor for soil moisture: all species (commented out for now)
           !          gamma_sm = get_gamma_SM(clayfrac(p), sandfrac(p), h2osoi_vol(c,:), h2osoi_ice(c,:), &
           !               col%dz(c,:), soilstate_inst%bsw_col(c,:), watsat(c,:), sucsat(c,:), root_depth(patch%itype(p)))
-          gamma_sm = 1.0_r8
 
           ! Loop through VOCs for light, temperature and leaf age activity factor & apply
           ! all final activity factors to baseline emission factors
@@ -601,7 +612,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
 
              ! Activity factor for CO2 (only for isoprene)
              if (trim(meg_cmp%name) == 'isoprene') then 
-                co2_ppmv = 1.e6*forc_pco2(g)/forc_pbot(c)
+                co2_ppmv = 1.e6_r8*forc_pco2(g)/forc_pbot(c)
                 gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv)
              else
                 gamma_c = 1._r8
@@ -813,77 +824,98 @@ function get_gamma_L(fsun240_in,elai_in)
   end function get_gamma_L
 
   !-----------------------------------------------------------------------
-  function get_gamma_SM(clayfrac_in, sandfrac_in, h2osoi_vol_in, h2osoi_ice_in, dz_in, &
-       bsw_in, watsat_in, sucsat_in, root_depth_in)
-    !
-    ! Activity factor for soil moisture (Guenther et al., 2006): all species
-    !----------------------------------
-    ! Calculate the mean scaling factor throughout the root depth.
-    ! wilting point potential is in units of matric potential (mm) 
-    ! (1 J/Kg = 0.001 MPa, approx = 0.1 m)
-    ! convert to volumetric soil water using equation 7.118 of the CLM4 Technical Note
-    !
-    ! !USES:
-    use clm_varcon , only : denice
-    use clm_varpar , only : nlevsoi
-    !
-    ! !ARGUMENTS:
+  function get_gamma_SM(btran_in)
+    !---------------------------------------
+    ! May 22, 2024
+    ! Activity factor for soil moisture of Isoprene (Wang et al., 2022, JAMES)
+    ! It is based on eq. (11) in the paper. Because the temperature response
+    ! of isoprene has been explicitly included in CLM; 
+    !ARGUMENTS:
     implicit none
-    real(r8),intent(in) :: clayfrac_in
-    real(r8),intent(in) :: sandfrac_in
-    real(r8),intent(in) :: h2osoi_vol_in(nlevsoi)
-    real(r8),intent(in) :: h2osoi_ice_in(nlevsoi)
-    real(r8),intent(in) :: dz_in(nlevsoi)
-    real(r8),intent(in) :: bsw_in(nlevsoi)
-    real(r8),intent(in) :: watsat_in(nlevsoi)
-    real(r8),intent(in) :: sucsat_in(nlevsoi)
-    real(r8),intent(in) :: root_depth_in
-    !
-    ! !LOCAL VARIABLES:
+    real(r8),intent(in) :: btran_in
+    
+    !!!------- the drought algorithm--------
+    real(r8), parameter :: a1 = -7.4463      
+    real(r8), parameter :: b1 = 3.2552       
     real(r8)            :: get_gamma_SM
-    integer  :: j
-    real(r8) :: nl                      ! temporary number of soil levels
-    real(r8) :: theta_ice               ! water content in ice in m3/m3
-    real(r8) :: wilt                    ! wilting point in m3/m3
-    real(r8) :: theta1                  ! temporary
-    real(r8), parameter :: deltheta1=0.06_r8               ! empirical coefficient
-    real(r8), parameter :: smpmax = 2.57e5_r8              ! maximum soil matrix potential
-    !-----------------------------------------------------------------------
-
-    if ((clayfrac_in > 0) .and. (sandfrac_in > 0)) then 
-       get_gamma_SM = 0._r8
-       nl=0._r8
-       
-       do j = 1,nlevsoi
-          if  (sum(dz_in(1:j)) < root_depth_in)  then
-             theta_ice = h2osoi_ice_in(j)/(dz_in(j)*denice)
-             wilt = ((smpmax/sucsat_in(j))**(-1._r8/bsw_in(j))) * (watsat_in(j) - theta_ice)
-             theta1 = wilt + deltheta1
-             if (h2osoi_vol_in(j) >= theta1) then 
-                get_gamma_SM = get_gamma_SM + 1._r8
-             else if ( (h2osoi_vol_in(j) > wilt) .and. (h2osoi_vol_in(j) < theta1) ) then
-                get_gamma_SM = get_gamma_SM + ( h2osoi_vol_in(j) - wilt ) / deltheta1
+             if (btran_in >= 1.) then
+                get_gamma_SM = 1
              else
-                get_gamma_SM = get_gamma_SM + 0._r8
-             end if
-             nl=nl+1._r8
-          end if
-       end do
-       
-       if (nl > 0._r8) then
-          get_gamma_SM = get_gamma_SM/nl
-       endif
-
-       if (get_gamma_SM > 1.0_r8) then 
-          write(iulog,*) 'healdSM > 1: gamma_SM, nl', get_gamma_SM, nl
-          get_gamma_SM=1.0_r8
-       endif
-
-    else
-       get_gamma_SM = 1.0_r8
-    end if
-
+                get_gamma_SM = 1/(1+b1*exp(a1*(btran_in-0.2)))
+             endif 
   end function get_gamma_SM
+ 
+  !function get_gamma_SM(clayfrac_in, sandfrac_in, h2osoi_vol_in, h2osoi_ice_in, dz_in, &
+  !     bsw_in, watsat_in, sucsat_in, root_depth_in)
+  !  !
+  !  ! Activity factor for soil moisture (Guenther et al., 2006): all species
+  !  !----------------------------------
+  !  ! Calculate the mean scaling factor throughout the root depth.
+  !  ! wilting point potential is in units of matric potential (mm) 
+  !  ! (1 J/Kg = 0.001 MPa, approx = 0.1 m)
+  !  ! convert to volumetric soil water using equation 7.118 of the CLM4 Technical Note
+  !  !
+  !  ! !USES:
+  !  use clm_varcon , only : denice
+  !  use clm_varpar , only : nlevsoi
+  !  !
+  !  ! !ARGUMENTS:
+  !  implicit none
+  !  real(r8),intent(in) :: clayfrac_in
+  !  real(r8),intent(in) :: sandfrac_in
+  !  real(r8),intent(in) :: h2osoi_vol_in(nlevsoi)
+  !  real(r8),intent(in) :: h2osoi_ice_in(nlevsoi)
+  !  real(r8),intent(in) :: dz_in(nlevsoi)
+  !  real(r8),intent(in) :: bsw_in(nlevsoi)
+  !  real(r8),intent(in) :: watsat_in(nlevsoi)
+  !  real(r8),intent(in) :: sucsat_in(nlevsoi)
+  !  real(r8),intent(in) :: root_depth_in
+  !  !
+  !  ! !LOCAL VARIABLES:
+  !  real(r8)            :: get_gamma_SM
+  !  integer  :: j
+  !  real(r8) :: nl                      ! temporary number of soil levels
+  !  real(r8) :: theta_ice               ! water content in ice in m3/m3
+  !  real(r8) :: wilt                    ! wilting point in m3/m3
+  !  real(r8) :: theta1                  ! temporary
+  !  real(r8), parameter :: deltheta1=0.06_r8               ! empirical coefficient
+  !  real(r8), parameter :: smpmax = 2.57e5_r8              ! maximum soil matrix potential
+  !  !-----------------------------------------------------------------------
+
+  !  if ((clayfrac_in > 0) .and. (sandfrac_in > 0)) then 
+  !     get_gamma_SM = 0._r8
+  !     nl=0._r8
+  !     
+  !     do j = 1,nlevsoi
+  !        if  (sum(dz_in(1:j)) < root_depth_in)  then
+  !           theta_ice = h2osoi_ice_in(j)/(dz_in(j)*denice)
+  !           wilt = ((smpmax/sucsat_in(j))**(-1._r8/bsw_in(j))) * (watsat_in(j) - theta_ice)
+  !           theta1 = wilt + deltheta1
+  !           if (h2osoi_vol_in(j) >= theta1) then 
+  !              get_gamma_SM = get_gamma_SM + 1._r8
+  !           else if ( (h2osoi_vol_in(j) > wilt) .and. (h2osoi_vol_in(j) < theta1) ) then
+  !              get_gamma_SM = get_gamma_SM + ( h2osoi_vol_in(j) - wilt ) / deltheta1
+  !           else
+  !              get_gamma_SM = get_gamma_SM + 0._r8
+  !           end if
+  !           nl=nl+1._r8
+  !        end if
+  !     end do
+  !     
+  !     if (nl > 0._r8) then
+  !        get_gamma_SM = get_gamma_SM/nl
+  !     endif
+
+  !     if (get_gamma_SM > 1.0_r8) then 
+  !        write(iulog,*) 'healdSM > 1: gamma_SM, nl', get_gamma_SM, nl
+  !        get_gamma_SM=1.0_r8
+  !     endif
+
+  !  else
+  !     get_gamma_SM = 1.0_r8
+  !  end if
+
+  !end function get_gamma_SM
   
   !-----------------------------------------------------------------------
   function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in, LDF_in, Ceo_in, Eopt, topt, ivt_in)
@@ -934,7 +966,7 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     if ( (t_veg240_in > 0.0_r8) .and. (t_veg240_in < 1.e30_r8) ) then 
        ! topt and Eopt from eq 8 and 9:
        topt = co1 + (co2 * (t_veg240_in-tstd0))
-       if ( (ivt_in == nbrdlf_dcd_brl_shrub) ) then  ! boreal-shrub
+       if ( (ivt_in == nbrdlf_dcd_brl_shrub) ) then  ! boreal-deciduous-shrub
        ! coming from BEAR-oNS campaign willows results
              Eopt = 7.9 * exp (0.217_r8 * (t_veg24_in-273.15_r8-24.0_r8))
        else if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index 00a98e61b4..99883d5241 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -816,11 +816,11 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
        call DustDryDep(bounds_clump, &
             atm2lnd_inst, frictionvel_inst, dust_inst)
 
-       ! VOC emission (A. Guenther's MEGAN (2006) model)
+       ! VOC emission (A. Guenther's MEGAN (2006) model; Wang et al., 2022, 2024a, 2024b)
        call VOCEmission(bounds_clump,                                         &
                filter(nc)%num_soilp, filter(nc)%soilp,                           &
                atm2lnd_inst, canopystate_inst, photosyns_inst, temperature_inst, &
-               vocemis_inst)
+               vocemis_inst, energyflux_inst)
 
        call t_stopf('bgc')
 

From 573feef24051536230a03c4c3de99730cd33c322 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 5 Jun 2024 10:03:45 -0600
Subject: [PATCH 0443/1248] Restore this back to ctsm5.1.dev166 to make merging
 easier

---
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 3c8945e9d2..9122b56890 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -369,7 +369,6 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
 
     call ncd_pio_closefile(ncid)
 
-
     ! --------------------------------------------------------------------
     ! get original soil depths to be used in interpolation of sand and clay
     ! --------------------------------------------------------------------
@@ -703,12 +702,7 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     do c = begc,endc
        g = col%gridcell(c)
 
-       ! dmleung++ added 24 May 2024: The below calculates the threshold gravimetric water content for the dust emission calculation in DUSTMod.F90. The equation comes from Eq. 14 of Fecan et al. (1999; https://doi.org/10.1007/s00585-999-0149-7).
-       !gwc_thr_col = 0.17*clay3d + 0.0014*(clay3d**2), and we only concern the topmost soil layer. 
-       ! Charlie Zender later on added a tuning factor (a) such that the equation becomes gwc_thr_col = a*[0.17*clay3d + 0.0014*(clay3d**2)]. (Zender et al., 2003a; https://doi.org/10.1029/2002JD002775)
-       ! There are different options: E.g., a = 1 gives the first line below. E.g., Kok et al. (2014a, b) chose to use a = 1. A second choice is proposed by Charlie Zender (2003a):  a = 1/clay3d, which gives the second line below. 
-       !soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Jasper Kok et al. (2014) modified the equation of soil moisture effect for dust emissions using a tuning factor of a = 1. 0.01 is to convert the threshold gravimetric soil moisture from % to fraction. Danny M. Leung et al. (2023) followed K14 and used this equation for offline dust emission calculations using MERRA-2 met fields. Later, Leung et al. (2024) changed to a = 2 for CESM2 simulations. However, Danny Leung later (Dec 2023) decided to revert to Zender's choice and use a = 1 / (clay3d), which overall encourages more dust emissions from seriamid and more marginal dust sources. This note should probably be on the CLM tech note since dmleung has made a different decision for CESM than his own paper. dmleung added this detailed comment on 19 Feb 2024; edited 24 May 2024.
-       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with a = 1 / (%clay) being the tuning factor for soil moisture effect in Zender's dust emission scheme. Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) dust emission scheme in the CESM will use Zender's tuning of a = 1 / (%clay), which overall encourages more dust emissions from seriamid and more marginal dust sources. Another advantage of using this tuning factor instead of a = 1 is that the dust emission threshold is linearly dependent on the clay fraction instead of parabolically dependent on clay fraction as in the above line. This means that dust emission becomes a little less sensitive to clay content (soil texture). 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to convert surface clay fraction from percentage to fraction. dmleung added this detailed comment on 19 Feb 2024.
+       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8
        soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
     end do
 

From 19cc5562ddc2a090654a9e3a3092d2cb1a0b2be8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 5 Jun 2024 10:21:32 -0600
Subject: [PATCH 0444/1248] Change prigentroughnessstream_type to use snake
 case with VS code

---
 src/biogeochem/DUSTMod.F90                        |  6 +++---
 src/cpl/share_esmf/PrigentRoughnessStreamType.F90 | 12 ++++++------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index b23a26b429..dc99a5d6bb 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -32,7 +32,7 @@ module DUSTMod
   use ColumnType           , only : col
   use PatchType            , only : patch
   use pftconMod            , only : noveg
-  use PrigentRoughnessStreamType    , only : prigentroughnessstream_type
+  use PrigentRoughnessStreamType    , only : prigent_roughness_stream_type
   !  
   ! !PUBLIC TYPES
   implicit none
@@ -85,7 +85,7 @@ module DUSTMod
      real(r8), pointer, private :: vai_Okin_patch             (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin drag partition
      real(r8), pointer, private :: frc_thr_rghn_fct_patch    (:)   ! [dimless] hybrid drag partition (or called roughness) factor
      real(r8), pointer, private :: wnd_frc_thr_std_patch     (:)   ! standardized fluid threshold friction velocity (m/s)
-     type(prigentroughnessstream_type), private :: prigent_roughness_stream      ! Prigent roughness stream data
+     type(prigent_roughness_stream_type), private :: prigent_roughness_stream      ! Prigent roughness stream data
      real(r8), pointer, private :: dpfct_rock_patch          (:)   ! [fraction] rock drag partition factor, time-constant
    contains
 
@@ -1296,7 +1296,7 @@ subroutine CalcDragPartition(this, bounds, prigent_roughness_stream )
     implicit none
     class(dust_type) , intent(inout) :: this
     type(bounds_type), intent(in) :: bounds
-    type(prigentroughnessstream_type), intent(in) :: prigent_roughness_stream
+    type(prigent_roughness_stream_type), intent(in) :: prigent_roughness_stream
     !
     ! !LOCAL VARIABLES:
     integer  :: g, p, fp, l    ! Indices
diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 6287b5f552..ae5f88946a 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -19,7 +19,7 @@ module PrigentRoughnessStreamType
   implicit none
   private
 
-  type, public :: prigentroughnessstream_type
+  type, public :: prigent_roughness_stream_type
      real(r8), pointer, public :: prigent_rghn  (:)         ! Prigent et al. (1997) roughness length (m)
   contains
 
@@ -31,7 +31,7 @@ module PrigentRoughnessStreamType
       ! !PRIVATE MEMBER FUNCTIONS:
       procedure, private :: InitAllocate   ! Allocate data
 
-  end type prigentroughnessstream_type
+  end type prigent_roughness_stream_type
 
   ! ! PRIVATE DATA:
   type, private :: streamcontrol_type
@@ -66,7 +66,7 @@ subroutine Init(this, bounds, NLFilename)
    !
    ! arguments
    implicit none
-   class(prigentroughnessstream_type) :: this
+   class(prigent_roughness_stream_type) :: this
    type(bounds_type), intent(in)   :: bounds
    character(len=*),  intent(in)   :: NLFilename   ! Namelist filename
    !
@@ -172,7 +172,7 @@ logical function UseStreams(this)
     !
     ! !ARGUMENTS:
     implicit none
-    class(prigentroughnessstream_type) :: this
+    class(prigent_roughness_stream_type) :: this
     !
     character(len=*), parameter :: subname = 'PrigentRoughnessStream::UseStreams'
     !
@@ -196,7 +196,7 @@ logical function IsStreamInit(this)
     !
     ! !ARGUMENTS:
     implicit none
-    class(prigentroughnessstream_type) :: this
+    class(prigent_roughness_stream_type) :: this
     !
     character(len=*), parameter :: subname = 'PrigentRoughnessStream::IsStreamInit'
     !
@@ -221,7 +221,7 @@ subroutine InitAllocate(this, bounds)
     !
     ! !ARGUMENTS:
     implicit none
-    class(prigentroughnessstream_type) :: this
+    class(prigent_roughness_stream_type) :: this
     type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:

From 65646fc25f4e563e822b9f79842ba4360e098fb9 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 5 Jun 2024 10:50:45 -0600
Subject: [PATCH 0445/1248] Remove uneeded code only needed for Zender's scheme

---
 src/biogeochem/DUSTMod.F90 | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index dc99a5d6bb..513114b012 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -373,7 +373,6 @@ subroutine DustEmission (bounds, &
     real(r8) :: flx_mss_vrt_dst_ttl(bounds%begp:bounds%endp)
     real(r8) :: frc_thr_wet_fct
     real(r8) :: frc_thr_rgh_fct
-    real(r8) :: wnd_rfr_thr_slt
     real(r8) :: wnd_frc_slt
     real(r8) :: lnd_frc_mbl(bounds%begp:bounds%endp)
     real(r8) :: bd
@@ -399,7 +398,6 @@ subroutine DustEmission (bounds, &
     !
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
-    !real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
     character(len=*),parameter :: subname = 'DUSTEmission'
     real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests 1, and Zender's scheme uses 0.3
     real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient
@@ -713,11 +711,6 @@ subroutine DustEmission (bounds, &
             flx_mss_hrz_slt_ttl = 0.0_r8
             flx_mss_vrt_dst_ttl(p) = 0.0_r8
 
-            ! the following line comes from subr. dst_mbl
-            ! purpose: threshold saltation wind speed
-
-            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)     ! use if we want the default Z03 scheme; for Leung 2023 this is not needed
-
             ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
             ! purpose: compute vertically integrated streamwise mass flux of particles
 

From c90fa866fcd81ca2664ea4ec29a1ea3e2bf823e2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 5 Jun 2024 13:16:48 -0600
Subject: [PATCH 0446/1248] Just fix a few typos

---
 src/biogeochem/DUSTMod.F90 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 513114b012..3cbd292611 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -588,7 +588,7 @@ subroutine DustEmission (bounds, &
          !####################################################################################################
          ! calculate soil moisture effect for dust emission threshold
          ! following Fecan, Marticorena et al. (1999)
-         ! also see Zender et al. (2003) for DEAD emission scheme and Kok et al. (2014b) for K14 emission scheme in CESM
+         ! also see Zender et al. (2003) for DUST emission scheme and Kok et al. (2014b) for K14 emission scheme in CESM
          bd = (1._r8-watsat(c,1))*dns_slt      ![kg m-3] Bulk density of dry surface soil (dmleung changed from 2700 to dns_slt, soil particle density, on 16 Feb 2024. Note that dns_slt=2650 kg m-3 so the value is changed by a tiny bit from 2700 to 2650. dns_slt has been here for many years so dns_slt should be used here instead of explicitly typing the value out. dmleung 16 Feb 2024)
 
          ! use emission threshold to calculate standardized threshold and dust emission coefficient
@@ -699,7 +699,7 @@ subroutine DustEmission (bounds, &
 
          ! save soil friction velocity and roughness effect before the if-statement
          wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect
-         ! 20 Feb 2024: dmleung notes that Leung does not consider the Owen's effect. This is Jasper Kok's decision. The Owen's effect should be in Zender's DEAD emission scheme.
+         ! 20 Feb 2024: dmleung notes that Leung does not consider the Owen's effect. This is Jasper Kok's decision. The Owen's effect should be in Zender's DUST emission scheme.
 
          ! save land mobile fraction
          lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement
@@ -719,8 +719,8 @@ subroutine DustEmission (bounds, &
                !################### for Leung et al. (2023) ################################################
                !################ uncomment the below block if want to use Leung's scheme ###################
 
-               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
-               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
+               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission equation for emission flux
+               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission equation for emission flux
 
                ! account for bare soil fraction, frozen soil fraction, and apply global tuning parameter (Kok et al. 2014)
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * lnd_frc_mbl(p) * C_tune * liqfrac

From 0f511eed129f00561af2611925de6463615ca696 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 5 Jun 2024 19:02:58 -0600
Subject: [PATCH 0447/1248] Change dust_inst to dust_emis_inst with VS code,
 unit test and a case works

---
 src/biogeochem/CNVegetationFacade.F90 | 2 +-
 src/main/clm_driver.F90               | 6 +++---
 src/main/clm_instMod.F90              | 4 ++--
 src/main/lnd2atmMod.F90               | 6 +++---
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90
index 61e2e9cf91..f42cf17d68 100644
--- a/src/biogeochem/CNVegetationFacade.F90
+++ b/src/biogeochem/CNVegetationFacade.F90
@@ -147,7 +147,7 @@ module CNVegetationFacade
      ! - ch4_inst
      !   - probably not: really seems to belong in soilbiogeochem
      ! - crop_inst
-     ! - dust_inst
+     ! - dust_emis_inst
      ! - vocemis_inst
      ! - fireemis_inst
      ! - drydepvel_inst
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index b6dacf3866..c1845d0de6 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -805,14 +805,14 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
        call t_startf('bgc')
 
        ! Dust mobilization (C. Zender's modified codes)
-       call dust_inst%DustEmission(bounds_clump,                                       &
+       call dust_emis_inst%DustEmission(bounds_clump,                                       &
             filter(nc)%num_nolakep, filter(nc)%nolakep,                      &
             atm2lnd_inst, soilstate_inst, canopystate_inst, &
             water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, &
             frictionvel_inst)
 
        ! Dust dry deposition (C. Zender's modified codes)
-       call dust_inst%DustDryDep(bounds_clump, &
+       call dust_emis_inst%DustDryDep(bounds_clump, &
             atm2lnd_inst, frictionvel_inst)
 
        ! VOC emission (A. Guenther's MEGAN (2006) model)
@@ -1307,7 +1307,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
          atm2lnd_inst, surfalb_inst, temperature_inst, frictionvel_inst, &
          water_inst, &
          energyflux_inst, solarabs_inst, drydepvel_inst,       &
-         vocemis_inst, fireemis_inst, dust_inst, ch4_inst, glc_behavior, &
+         vocemis_inst, fireemis_inst, dust_emis_inst, ch4_inst, glc_behavior, &
          lnd2atm_inst, &
          net_carbon_exchange_grc = net_carbon_exchange_grc(bounds_proc%begg:bounds_proc%endg))
     deallocate(net_carbon_exchange_grc)
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index c3ea8a68b3..9e187f639c 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -151,7 +151,7 @@ module clm_instMod
   ! General biogeochem types
   type(ch4_type)      , public            :: ch4_inst
   type(crop_type)     , public            :: crop_inst
-  type(dust_emis_zender2003_type)     , public            :: dust_inst
+  type(dust_emis_zender2003_type)     , public            :: dust_emis_inst
   type(vocemis_type)  , public            :: vocemis_inst
   type(fireemis_type) , public            :: fireemis_inst
   type(drydepvel_type), public            :: drydepvel_inst
@@ -350,7 +350,7 @@ subroutine clm_instInit(bounds)
 
     call surfrad_inst%Init(bounds)
 
-    call dust_inst%Init(bounds, NLFilename)
+    call dust_emis_inst%Init(bounds, NLFilename)
 
     allocate(scf_method, source = CreateAndInitSnowCoverFraction( &
          snow_cover_fraction_method = snow_cover_fraction_method, &
diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90
index e6b1bb43f0..71f55b3b05 100644
--- a/src/main/lnd2atmMod.F90
+++ b/src/main/lnd2atmMod.F90
@@ -150,7 +150,7 @@ subroutine lnd2atm(bounds, &
        atm2lnd_inst, surfalb_inst, temperature_inst, frictionvel_inst, &
        water_inst, &
        energyflux_inst, solarabs_inst, drydepvel_inst,  &
-       vocemis_inst, fireemis_inst, dust_inst, ch4_inst, glc_behavior, &
+       vocemis_inst, fireemis_inst, dust_emis_inst, ch4_inst, glc_behavior, &
        lnd2atm_inst, &
        net_carbon_exchange_grc)
     !
@@ -173,7 +173,7 @@ subroutine lnd2atm(bounds, &
     type(drydepvel_type)        , intent(in)    :: drydepvel_inst
     type(vocemis_type)          , intent(in)    :: vocemis_inst
     type(fireemis_type)         , intent(in)    :: fireemis_inst
-    type(dust_emis_zender2003_type)             , intent(in)    :: dust_inst
+    type(dust_emis_zender2003_type)             , intent(in)    :: dust_emis_inst
     type(ch4_type)              , intent(in)    :: ch4_inst
     type(glc_behavior_type)     , intent(in)    :: glc_behavior
     type(lnd2atm_type)          , intent(inout) :: lnd2atm_inst
@@ -332,7 +332,7 @@ subroutine lnd2atm(bounds, &
 
     ! dust emission flux
     call p2g(bounds, ndst, &
-         dust_inst%flx_mss_vrt_dst_patch(bounds%begp:bounds%endp, :), &
+         dust_emis_inst%flx_mss_vrt_dst_patch(bounds%begp:bounds%endp, :), &
          lnd2atm_inst%flxdst_grc        (bounds%begg:bounds%endg, :), &
          p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
 

From a30a975a28d654ae1b9dd9e8f2368d1682ed6076 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 4 Jun 2024 12:44:15 -0600
Subject: [PATCH 0448/1248] Update RXCROPMATURITY* namelists.

---
 cime_config/SystemTests/rxcropmaturityshared.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
index f8e4b1c9bb..cc4282f5c5 100644
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -118,6 +118,7 @@ def _run_phase(self, skip_run=False):
         self._append_to_user_nl_clm(
             [
                 "generate_crop_gdds = .true.",
+                "stream_fldFileName_cultivar_gdds = ''"
                 "use_mxmat = .false.",
                 " ",
                 "! (h2) Daily outputs for GDD generation and figure-making",
@@ -364,6 +365,7 @@ def _run_check_rxboth_run(self):
 
     def _modify_user_nl_allruns(self):
         nl_additions = [
+            "cropcals_rx = .true."
             "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
             "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
             "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),

From 0bdd55a66dcf55c038615c8bc1552336a669fcd2 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 4 Jun 2024 12:59:10 -0600
Subject: [PATCH 0449/1248] RXCROPMATURITYSKIPRUN now sets BUILD_COMPLETE=TRUE.
 Works!

---
 cime_config/SystemTests/rxcropmaturityskiprun.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py
index 343ef5860f..7fd217c4ff 100644
--- a/cime_config/SystemTests/rxcropmaturityskiprun.py
+++ b/cime_config/SystemTests/rxcropmaturityskiprun.py
@@ -1,5 +1,9 @@
 from rxcropmaturityshared import RXCROPMATURITYSHARED
 
 class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED):
+    def build_indv(self, sharedlib_only=False, model_only=False):
+        self._case.set_value("BUILD_COMPLETE", "TRUE")
+
+
     def run_phase(self):
         self._run_phase(skip_run=True)
\ No newline at end of file

From e890670c2b60c682a57918fec92c9edb4428d7b9 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 6 Jun 2024 15:16:04 -0600
Subject: [PATCH 0450/1248] Revert "Actually flush GDD20 variables."

This reverts commit af0e12d2593fbd0a468d7ea65ac3761fcc771f2c.
---
 src/biogeophys/TemperatureType.F90 | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index c71b5d64aa..5fda936169 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1497,7 +1497,7 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
     ! USES
     use shr_const_mod    , only : SHR_CONST_TKFRZ
     use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date, is_end_curr_year
-    use accumulMod       , only : update_accum_field, extract_accum_field
+    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
     use CNSharedParamsMod, only : upper_soil_layer
     use CropType         , only : crop_type
     !
@@ -1685,13 +1685,19 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
 
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then
-          call update_accum_field  ('GDD020', this%gdd0_patch, nstep, this%flush_gdd20)
+          ! Flush, if needed
+          if (this%flush_gdd20) then
+              this%gdd020_patch(begp:endp) = accumResetVal
+              this%gdd820_patch(begp:endp) = accumResetVal
+              this%gdd1020_patch(begp:endp) = accumResetVal
+              this%flush_gdd20 = .false.
+          end if
+          call update_accum_field  ('GDD020', this%gdd0_patch, nstep)
           call extract_accum_field ('GDD020', this%gdd020_patch, nstep)
-          call update_accum_field  ('GDD820', this%gdd8_patch, nstep, this%flush_gdd20)
+          call update_accum_field  ('GDD820', this%gdd8_patch, nstep)
           call extract_accum_field ('GDD820', this%gdd820_patch, nstep)
-          call update_accum_field  ('GDD1020', this%gdd10_patch, nstep, this%flush_gdd20)
+          call update_accum_field  ('GDD1020', this%gdd10_patch, nstep)
           call extract_accum_field ('GDD1020', this%gdd1020_patch, nstep)
-          this%flush_gdd20 = .false.
        end if
 
     end if

From 4fb19c8f9fb6870f2a8f9de7cea83081d285b340 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 6 Jun 2024 15:16:16 -0600
Subject: [PATCH 0451/1248] Revert "Add reset option to
 update_accum_field_runmean()."

This reverts commit e1db253814ba944935d0a571c5b17b29010f1090.
---
 src/main/accumulMod.F90 | 59 ++++++-----------------------------------
 1 file changed, 8 insertions(+), 51 deletions(-)

diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index 883aa9063b..e328632501 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -102,14 +102,13 @@ subroutine extract_accum_field_interface(this, level, nstep, field)
        real(r8), intent(inout) :: field(:) ! field values for current time step
      end subroutine extract_accum_field_interface
 
-     subroutine update_accum_field_interface(this, level, nstep, field, reset)
+     subroutine update_accum_field_interface(this, level, nstep, field)
        use shr_kind_mod, only: r8 => shr_kind_r8
        import :: accum_field
        class(accum_field), intent(in) :: this
        integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
        integer, intent(in) :: nstep      ! timestep index
        real(r8), intent(in) :: field(:)  ! field values for current time step
-       logical, optional, intent(in) :: reset  ! whether to reset accumulator
      end subroutine update_accum_field_interface
   end interface
 
@@ -488,7 +487,7 @@ subroutine extract_accum_field_timeavg(this, level, nstep, field)
   end subroutine extract_accum_field_timeavg
 
   !------------------------------------------------------------------------
-  subroutine update_accum_field_sl (name, field, nstep, reset_in)
+  subroutine update_accum_field_sl (name, field, nstep)
     !
     ! !DESCRIPTION:
     ! Accumulate single level field over specified time interval.
@@ -502,22 +501,14 @@ subroutine update_accum_field_sl (name, field, nstep, reset_in)
     character(len=*), intent(in) :: name     !field name
     real(r8), pointer, dimension(:) :: field !field values for current time step
     integer , intent(in) :: nstep            !time step index
-    logical, optional, intent(in) :: reset_in  ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: nf     ! field index
     integer :: numlev ! number of vertical levels
-    logical :: reset
 
     character(len=*), parameter :: subname = 'update_accum_field_sl'
     !------------------------------------------------------------------------
 
-    if (present(reset_in)) then
-       reset = reset_in
-    else
-       reset = .false.
-    end if
-
     call find_field(field_name=name, caller_name=subname, field_index=nf)
 
     numlev = accum(nf)%numlev
@@ -526,13 +517,12 @@ subroutine update_accum_field_sl (name, field, nstep, reset_in)
     call accum(nf)%update_accum_field_func( &
          level = 1, &
          nstep = nstep, &
-         field = field, &
-         reset = reset)
+         field = field)
 
   end subroutine update_accum_field_sl
 
   !------------------------------------------------------------------------
-  subroutine update_accum_field_ml (name, field, nstep, reset_in)
+  subroutine update_accum_field_ml (name, field, nstep)
     !
     ! !DESCRIPTION:
     ! Accumulate multi level field over specified time interval.
@@ -545,22 +535,14 @@ subroutine update_accum_field_ml (name, field, nstep, reset_in)
     character(len=*), intent(in) :: name       !field name
     real(r8), pointer, dimension(:,:) :: field !field values for current time step
     integer , intent(in) :: nstep              !time step index
-    logical, optional, intent(in) :: reset_in  ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: j,nf            !indices
     integer :: numlev          !number of vertical levels
-    logical :: reset
 
     character(len=*), parameter :: subname = 'update_accum_field_ml'
     !------------------------------------------------------------------------
 
-    if (present(reset_in)) then
-       reset = reset_in
-    else
-       reset = .false.
-    end if
-
     call find_field(field_name=name, caller_name=subname, field_index=nf)
 
     numlev = accum(nf)%numlev
@@ -570,14 +552,13 @@ subroutine update_accum_field_ml (name, field, nstep, reset_in)
        call accum(nf)%update_accum_field_func( &
             level = j, &
             nstep = nstep, &
-            field = field(:,j), &
-            reset = reset)
+            field = field(:,j))
     end do
 
   end subroutine update_accum_field_ml
 
   !-----------------------------------------------------------------------
-  subroutine update_accum_field_timeavg(this, level, nstep, field, reset)
+  subroutine update_accum_field_timeavg(this, level, nstep, field)
     !
     ! !DESCRIPTION:
     ! Update values for one level of the given timeavg field
@@ -587,7 +568,6 @@ subroutine update_accum_field_timeavg(this, level, nstep, field, reset)
     integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
     integer, intent(in) :: nstep      ! timestep index
     real(r8), intent(in) :: field(:)  ! field values for current time step
-    logical, intent(in)  :: reset     ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
@@ -600,11 +580,6 @@ subroutine update_accum_field_timeavg(this, level, nstep, field, reset)
     endi = this%end1d
     SHR_ASSERT_FL((size(field) == endi-begi+1), sourcefile, __LINE__)
 
-    if (reset) then
-       write(iulog,*) trim(subname), 'ERROR: field name ',trim(this%name),' may not use reset=.true.'
-       call endrun('Unhandled use of reset=.true. for ',subname)
-    end if
-
     ! time average field: reset every accumulation period; normalize at end of
     ! accumulation period
 
@@ -636,7 +611,7 @@ subroutine update_accum_field_timeavg(this, level, nstep, field, reset)
   end subroutine update_accum_field_timeavg
 
   !-----------------------------------------------------------------------
-  subroutine update_accum_field_runmean(this, level, nstep, field, reset)
+  subroutine update_accum_field_runmean(this, level, nstep, field)
     !
     ! !DESCRIPTION:
     ! Update values for one level of the given runmean field
@@ -646,7 +621,6 @@ subroutine update_accum_field_runmean(this, level, nstep, field, reset)
     integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
     integer, intent(in) :: nstep      ! timestep index
     real(r8), intent(in) :: field(:)  ! field values for current time step
-    logical, intent(in)  :: reset     ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
@@ -661,18 +635,7 @@ subroutine update_accum_field_runmean(this, level, nstep, field, reset)
     SHR_ASSERT_FL((size(field) == endi-begi+1), sourcefile, __LINE__)
 
     do k = begi,endi
-       ! Whether or not this patch/landunit/etc. is active, mark it for reset. Don't actually reset it now, because it might become active again (and thus, its value might be needed) before it has another chance to get reset.
-       if (reset) then
-          this%nsteps(k,level) = -1
-       end if
-
        if (this%active(k)) then
-          ! Negative nsteps means this was marked as needing to be reset
-          if (this%nsteps(k,level) < 0) then
-             this%val(k,level) = 0._r8
-             this%nsteps(k,level) = 0
-          end if
-
           kf = k - begi + 1
           this%nsteps(k,level) = this%nsteps(k,level) + 1
           ! Cap nsteps at 'period' - partly to avoid overflow, but also because it doesn't
@@ -690,7 +653,7 @@ subroutine update_accum_field_runmean(this, level, nstep, field, reset)
   end subroutine update_accum_field_runmean
 
   !-----------------------------------------------------------------------
-  subroutine update_accum_field_runaccum(this, level, nstep, field, reset)
+  subroutine update_accum_field_runaccum(this, level, nstep, field)
     !
     ! !DESCRIPTION:
     ! Update values for one level of the given runaccum field
@@ -700,7 +663,6 @@ subroutine update_accum_field_runaccum(this, level, nstep, field, reset)
     integer, intent(in) :: level      ! level index to update (1 for a 1-d field)
     integer, intent(in) :: nstep      ! timestep index
     real(r8), intent(in) :: field(:)  ! field values for current time step
-    logical, intent(in)  :: reset     ! whether to reset accumulator
     !
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
@@ -713,11 +675,6 @@ subroutine update_accum_field_runaccum(this, level, nstep, field, reset)
     endi = this%end1d
     SHR_ASSERT_FL((size(field) == endi-begi+1), sourcefile, __LINE__)
 
-    if (reset) then
-       write(iulog,*) trim(subname), 'ERROR: field name ',trim(this%name),' may not use reset=.true.; set value to -99999 instead'
-       call endrun('Unhandled use of reset=.true. for ',subname)
-    end if
-
     !running accumulation field; reset at trigger -99999
 
     do k = begi,endi

From 135131361b8f0e291767fc897f561da4f191b9d6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 5 Jun 2024 12:04:37 -0600
Subject: [PATCH 0452/1248] Remove unused 'use' of accumResetVal from
 EnergyFluxType UpdateAccVars().

---
 src/biogeophys/EnergyFluxType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/EnergyFluxType.F90 b/src/biogeophys/EnergyFluxType.F90
index 2e709596a1..16929d9708 100644
--- a/src/biogeophys/EnergyFluxType.F90
+++ b/src/biogeophys/EnergyFluxType.F90
@@ -988,7 +988,7 @@ subroutine UpdateAccVars (this, bounds)
     !
     ! USES
     use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    use accumulMod       , only : update_accum_field, extract_accum_field
     use abortutils       , only : endrun
     !
     ! !ARGUMENTS:

From 7364ad6b4f2e520f7eb980f227e8a248a8f0a618 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 5 Jun 2024 15:14:19 -0600
Subject: [PATCH 0453/1248] All accumulator types can now be manually reset.

Previously it was just runaccum, which would reset a point-level if that point-level had the value -99999._r8. That's potentially unsafe, since theoretically it could be a valid value. This behavior has now been replaced by looking for a .true. value for the point-level in the new "reset" array.

Accumulator types timeavg and runmean can also look at "reset" for a manual reset. These types were not able to be manually reset before. Note that these have some different reset behavior compared to runaccum: Whereas runaccum can't reset and update in the same call of its update_accum_field() subroutine, timeavg and runmean can (and do).

runmean's behavior is also a bit different from the others in that it will "remember" reset requests that occurred when a point was inactive. The others already had reset blocks that were embedded in a check of "active," so that behavior is preserved for them.

All existing unit tests pass. No new unit tests have been added yet.
---
 src/biogeochem/CNDVType.F90                | 15 ++--
 src/biogeochem/CropType.F90                |  7 +-
 src/biogeophys/TemperatureType.F90         |  8 +-
 src/main/accumulMod.F90                    | 91 +++++++++++++++++++---
 src/main/test/accumul_test/test_accumul.pf | 34 ++++++--
 5 files changed, 123 insertions(+), 32 deletions(-)

diff --git a/src/biogeochem/CNDVType.F90 b/src/biogeochem/CNDVType.F90
index 19a0f64f7d..21921f7cbd 100644
--- a/src/biogeochem/CNDVType.F90
+++ b/src/biogeochem/CNDVType.F90
@@ -439,7 +439,7 @@ subroutine UpdateAccVars(this, bounds, t_a10_patch, t_ref2m_patch)
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use clm_time_manager , only : get_step_size, get_nstep, get_curr_date
     use pftconMod        , only : ndllf_dcd_brl_tree
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    use accumulMod       , only : update_accum_field, extract_accum_field, markreset_accum_field
     !
     ! !ARGUMENTS:
     class(dgvs_type)  , intent(inout) :: this
@@ -493,8 +493,11 @@ subroutine UpdateAccVars(this, bounds, t_a10_patch, t_ref2m_patch)
        rbufslp(p) = max(0._r8, &
             (t_a10_patch(p) - SHR_CONST_TKFRZ - dgv_ecophyscon%twmax(ndllf_dcd_brl_tree)) &
             * dtime/SHR_CONST_CDAY)
-       if (month==1 .and. day==1 .and. secs==int(dtime)) rbufslp(p) = accumResetVal
     end do
+    if (month==1 .and. day==1 .and. secs==int(dtime)) then
+       ! Reset annually
+       call markreset_accum_field('AGDD')
+    end if
     call update_accum_field  ('AGDDTW', rbufslp, nstep)
     call extract_accum_field ('AGDDTW', this%agddtw_patch, nstep)
 
@@ -503,11 +506,11 @@ subroutine UpdateAccVars(this, bounds, t_a10_patch, t_ref2m_patch)
     do p = begp,endp
        rbufslp(p) = max(0.0_r8, &
             (t_ref2m_patch(p) - (SHR_CONST_TKFRZ + 5.0_r8)) * dtime/SHR_CONST_CDAY)
-       !
-       ! Fix (for bug 1858) from Sam Levis to reset the annual AGDD variable
-       ! 
-       if (month==1 .and. day==1 .and. secs==int(dtime)) rbufslp(p) = accumResetVal
     end do
+    if (month==1 .and. day==1 .and. secs==int(dtime)) then
+       ! Reset annually
+       call markreset_accum_field('AGDD')
+    end if
     call update_accum_field  ('AGDD', rbufslp, nstep)
     call extract_accum_field ('AGDD', this%agdd_patch, nstep)
 
diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index 760aa21b76..9d58a031fa 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -772,7 +772,7 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col)
     ! Should only be called if use_crop is true.
     !
     ! !USES:
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    use accumulMod       , only : update_accum_field, extract_accum_field, markreset_accum_field
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use clm_time_manager , only : get_step_size, get_nstep
     use clm_varpar       , only : nlevsno, nlevmaxurbgrnd
@@ -848,7 +848,8 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col)
              rbufslp(p) = rbufslp(p) * this%vf_patch(p)
           end if
        else
-          rbufslp(p) = accumResetVal
+          call markreset_accum_field('HUI', p)
+          call markreset_accum_field('GDDACCUM', p)
        end if
     end do
     call update_accum_field  ('HUI', rbufslp, nstep)
@@ -872,7 +873,7 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col)
              rbufslp(p) = rbufslp(p) * this%vf_patch(p)
           end if
        else
-          rbufslp(p) = accumResetVal
+          call markreset_accum_field('GDDTSOI', p)
        end if
     end do
     call update_accum_field  ('GDDTSOI', rbufslp, nstep)
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index ab310650c8..c9909e82d3 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1363,7 +1363,7 @@ subroutine UpdateAccVars (this, bounds)
     ! USES
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date, is_end_curr_year
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
+    use accumulMod       , only : update_accum_field, extract_accum_field, markreset_accum_field
     use CNSharedParamsMod, only : upper_soil_layer
     !
     ! !ARGUMENTS:
@@ -1544,7 +1544,7 @@ subroutine UpdateAccVars (this, bounds)
           if (patch%active(p)) then
              g = patch%gridcell(p)
              if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
+                call markreset_accum_field('GDD0', p)  ! reset gdd
              else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
                   ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
                 rbufslp(p) = max(0._r8, min(26._r8, this%t_ref2m_patch(p)-SHR_CONST_TKFRZ)) * dtime/SHR_CONST_CDAY
@@ -1563,7 +1563,7 @@ subroutine UpdateAccVars (this, bounds)
           if (patch%active(p)) then
              g = patch%gridcell(p)
              if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
+                call markreset_accum_field('GDD8', p)  ! reset gdd
              else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
                   ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
                 rbufslp(p) = max(0._r8, min(30._r8, &
@@ -1583,7 +1583,7 @@ subroutine UpdateAccVars (this, bounds)
           if (patch%active(p)) then
              g = patch%gridcell(p)
              if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
+                call markreset_accum_field('GDD10', p)  ! reset gdd
              else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
                   ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
                 rbufslp(p) = max(0._r8, min(30._r8, &
diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index e328632501..8c3f7ed9e4 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -40,6 +40,7 @@ module accumulMod
   public :: print_accum_fields   ! Print info about accumulator fields
   public :: extract_accum_field  ! Extracts the current value of an accumulator field
   public :: update_accum_field   ! Update the current value of an accumulator field
+  public :: markreset_accum_field  ! Mark (value(s) in) an accumulator field as needing to be reset
   public :: clean_accum_fields   ! Deallocate space and reset accum fields list
 
   interface extract_accum_field
@@ -76,6 +77,7 @@ module accumulMod
      logical, pointer   :: active(:)!whether each point (patch, column, etc.) is active
      real(r8)           :: initval  !initial value of accumulated field
      real(r8), pointer  :: val(:,:) !accumulated field
+     logical , pointer  :: reset(:,:) !whether accumulated field needs to be reset
      integer            :: period   !field accumulation period (in model time steps)
      logical            :: scale_by_thickness  ! true/false flag to scale vertically interpolated variable by soil thickness or not
      character(len=128) :: old_name !previous name of variable (may be present in restart files)
@@ -112,8 +114,6 @@ subroutine update_accum_field_interface(this, level, nstep, field)
      end subroutine update_accum_field_interface
   end interface
 
-  real(r8), parameter, public :: accumResetVal = -99999._r8 ! used to do an annual reset ( put in for bug 1858)
-
   integer, parameter :: ACCTYPE_TIMEAVG  = 1
   integer, parameter :: ACCTYPE_RUNMEAN  = 2
   integer, parameter :: ACCTYPE_RUNACCUM = 3
@@ -295,6 +295,9 @@ subroutine init_accum_field (name, units, desc, &
     end if
     accum(nf)%val(beg1d:end1d,1:numlev) = init_value
 
+    allocate(accum(nf)%reset(beg1d:end1d,numlev))
+    accum(nf)%reset(beg1d:end1d,1:numlev) = .false.
+
     allocate(accum(nf)%nsteps(beg1d:end1d,numlev))
     accum(nf)%nsteps(beg1d:end1d,1:numlev) = 0
 
@@ -572,6 +575,7 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
     integer :: k, kf
+    logical :: time_to_reset
 
     character(len=*), parameter :: subname = 'update_accum_field_timeavg'
     !-----------------------------------------------------------------------
@@ -583,14 +587,17 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     ! time average field: reset every accumulation period; normalize at end of
     ! accumulation period
 
-    if ((mod(nstep,this%period) == 1 .or. this%period == 1) .and. (nstep /= 0))then
-       do k = begi,endi
-          if (this%active(k)) then
-             this%val(k,level) = 0._r8
-             this%nsteps(k,level) = 0
-          end if
-       end do
-    end if
+    time_to_reset = (mod(nstep,this%period) == 1 .or. this%period == 1) .and. nstep /= 0
+    do k = begi,endi
+       if (this%active(k) .and. (time_to_reset .or. this%reset(k,level))) then
+          this%val(k,level) = 0._r8
+          this%nsteps(k,level) = 0
+          this%reset(k,level) = .false.
+       end if
+    end do
+
+    ! Ignore reset requests that occurred when patch was inactive
+    this%reset(begi:endi,level) = .false.
 
     do k = begi,endi
        if (this%active(k)) then
@@ -636,6 +643,13 @@ subroutine update_accum_field_runmean(this, level, nstep, field)
 
     do k = begi,endi
        if (this%active(k)) then
+          if (this%reset(k,level)) then
+             this%nsteps(k,level) = 0
+             this%val(k,level) = this%initval
+             this%reset(k,level) = .false.
+             ! SSR 2024-06-05: Note that, unlike other accumulator types, runmean preserves reset
+             ! requests that occurred when the patch was inactive.
+          end if
           kf = k - begi + 1
           this%nsteps(k,level) = this%nsteps(k,level) + 1
           ! Cap nsteps at 'period' - partly to avoid overflow, but also because it doesn't
@@ -680,20 +694,73 @@ subroutine update_accum_field_runaccum(this, level, nstep, field)
     do k = begi,endi
        if (this%active(k)) then
           kf = k - begi + 1
-          if (nint(field(kf)) == -99999) then
+          if (this%reset(k,level)) then
+             ! SSR 2024-06-05: Note that, unlike the other accumulator types, runaccum can not
+             ! reset AND update in the same call of its update_accum_field subroutine.
              this%val(k,level) = 0._r8
              this%nsteps(k,level) = 0
+             this%reset(k,level) = .false.
           else
              this%val(k,level) = &
                   min(max(this%val(k,level) + field(kf), 0._r8), 99999._r8)
              this%nsteps(k,level) = this%nsteps(k,level) + 1
           end if
-       end if
+      end if
     end do
 
+    ! Ignore reset requests that occurred when patch was inactive
+    this%reset(begi:endi,level) = .false.
+
   end subroutine update_accum_field_runaccum
 
 
+  !-----------------------------------------------------------------------
+  subroutine markreset_accum_field(name, kf, level)
+    !
+    ! !DESCRIPTION:
+    ! Mark accumulator values as needing to be reset. Note that resetting happens in
+    ! update_accum_field subroutines.
+    !
+    ! !ARGUMENTS:
+    character(len=*),  intent(in)  :: name  ! field name
+    integer, optional, intent(in)  :: kf    ! point index to update (in field, not accumulator's val)
+    integer, optional, intent(in)  :: level ! level index to update (in accumulator's val; 1 for a 1-d field)
+    !
+    ! !LOCAL VARIABLES:
+    integer :: nf          ! field index within the accum(nf) array
+    integer :: begi, endi  ! subgrid beginning, ending indices
+    integer :: k           ! index in accumulator's beg1d:end1d
+    integer :: numlev      ! number of levels in this accumulator
+
+    character(len=*), parameter :: subname = 'markreset_accum_field'
+    !-----------------------------------------------------------------------
+
+    call find_field(field_name=name, caller_name=subname, field_index=nf)
+    begi = accum(nf)%beg1d
+    endi = accum(nf)%end1d
+    numlev = accum(nf)%numlev
+
+    if (present(kf)) then
+       k = kf + begi - 1
+       SHR_ASSERT_FL(k >= begi .and. k <= endi, sourcefile, __LINE__)
+       if (present(level)) then
+          ! Reset one level of a single point
+          accum(nf)%reset(k,level) = .true.
+       else
+          ! Reset all levels of a single point
+          accum(nf)%reset(k,1:numlev) = .true.
+       end if
+    else if (present(level)) then
+       ! Reset one level of all points
+       accum(nf)%reset(begi:endi,level) = .true.
+    else
+       ! Reset all levels of all points
+       accum(nf)%reset(begi:endi,1:numlev) = .true.
+    end if
+
+  end subroutine markreset_accum_field
+
+
   !------------------------------------------------------------------------
   subroutine accumulRest( ncid, flag )
     !
diff --git a/src/main/test/accumul_test/test_accumul.pf b/src/main/test/accumul_test/test_accumul.pf
index 15d2e7403e..3c8e2a531d 100644
--- a/src/main/test/accumul_test/test_accumul.pf
+++ b/src/main/test/accumul_test/test_accumul.pf
@@ -99,7 +99,7 @@ contains
   end subroutine init_ml_patch_field
 
   subroutine update_and_extract_sl_patch_field(this, fieldname, values, val_output, &
-       pactive, timestep_start)
+       pactive, timestep_start, reset)
     ! Calls update_accum_field once for each value in 'values', assuming that the values
     ! come once per timestep. For the first call, all input values are set equal to
     ! values(1); for the second call, all input values are set equal to values(2); etc.
@@ -122,17 +122,24 @@ contains
     ! If present, this specifies the starting nstep value. If absent, we start with 1.
     integer, optional, intent(in) :: timestep_start
 
+    ! If present, same size as 'values', indicating whether each should be associated with a reset
+    logical, optional, intent(in) :: reset(:)
+
     integer :: n_timesteps
     integer :: timestep
     integer :: timestep_offset
     real(r8), pointer :: vals_input(:)
     real(r8), pointer :: vals_output(:)
     logical, allocatable :: l_pactive(:)  ! local version of pactive
+    logical, allocatable :: l_reset(:)    ! local version of reset
 
     n_timesteps = size(values)
     if (present(pactive)) then
        @assertEqual(n_timesteps, size(pactive))
     end if
+    if (present(reset)) then
+       @assertEqual(n_timesteps, size(reset))
+    end if
 
     allocate(l_pactive(n_timesteps))
     if (present(pactive)) then
@@ -147,11 +154,21 @@ contains
        timestep_offset = 0
     end if
 
+    allocate(l_reset(n_timesteps))
+    if (present(reset)) then
+       l_reset(:) = reset(:)
+    else
+       l_reset(:) = .false.
+    end if
+
     allocate(vals_input(bounds%begp:bounds%endp))
     allocate(vals_output(bounds%begp:bounds%endp))
     do timestep = 1, n_timesteps
        vals_input(:) = values(timestep)
        patch%active(bounds%begp) = l_pactive(timestep)
+       if (l_reset(timestep)) then
+          call markreset_accum_field(fieldname)
+       end if
        call update_accum_field(fieldname, vals_input, timestep+timestep_offset)
     end do
     call extract_accum_field(fieldname, vals_output, n_timesteps+timestep_offset)
@@ -599,7 +616,8 @@ contains
     class(TestAccumul), intent(inout) :: this
     character(len=*), parameter :: fieldname = 'foo'
     integer, parameter :: accum_period = 3  ! irrelevant for this type
-    real(r8), parameter :: values(5) = [11._r8, 12._r8, accumResetVal, 13._r8, 24._r8]
+    real(r8), parameter :: values(5) = [11._r8,  12._r8,  -99999._r8, 13._r8,  24._r8]
+    logical , parameter :: reset(5)  = [.false., .false., .true.,     .false., .false.]
     real(r8) :: val_output
     real(r8) :: expected
 
@@ -609,7 +627,7 @@ contains
          accum_period = accum_period)
 
     ! Exercise
-    call this%update_and_extract_sl_patch_field(fieldname, values, val_output)
+    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, reset=reset)
 
     ! Verify
     expected = sum(values(4:5))
@@ -626,7 +644,8 @@ contains
     class(TestAccumul), intent(inout) :: this
     character(len=*), parameter :: fieldname = 'foo'
     integer, parameter :: accum_period = 3  ! irrelevant for this type
-    real(r8), parameter :: values(5) = [11._r8,  accumResetVal, 12._r8,  13._r8, 24._r8]
+    real(r8), parameter :: values(5) = [11._r8,  -99999._r8, 12._r8,  13._r8,  24._r8]
+    logical , parameter :: reset(5)  = [.false., .true.,     .false., .false., .false.]
     logical, parameter :: pactive(5) = [.false., .false.,       .false., .true., .true.]
     real(r8) :: val_output
     real(r8) :: expected
@@ -649,7 +668,7 @@ contains
     ! Test runaccum with a point that starts active, becomes inactive, then later becomes
     ! active again.
     !
-    ! Should ignore values and accumResetVal in the inactive steps.
+    ! Should ignore values and reset request in the inactive steps.
     !
     ! Also, should continue where it left off - i.e., including the values accumulated
     ! when it was first active. This may or may not be the ideal behavior; we can change
@@ -657,7 +676,8 @@ contains
     class(TestAccumul), intent(inout) :: this
     character(len=*), parameter :: fieldname = 'foo'
     integer, parameter :: accum_period = 3  ! irrelevant for this type
-    real(r8), parameter :: values(5) = [11._r8,  accumResetVal, 12._r8,  17._r8, 24._r8]
+    real(r8), parameter :: values(5) = [11._r8,  -99999._r8, 12._r8,  17._r8,  24._r8]
+    logical , parameter :: reset(5)  = [.false., .true.,     .false., .false., .false.]
     logical, parameter :: pactive(5) = [.true., .false.,       .false., .true., .true.]
     real(r8) :: val_output
     real(r8) :: expected
@@ -668,7 +688,7 @@ contains
          accum_period = accum_period)
 
     ! Exercise
-    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, pactive=pactive)
+    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, pactive=pactive, reset=reset)
 
     ! Verify
     expected = values(1) + values(4) + values(5)

From 9e39acc5e50073273781af3e57cb8a70a39ecda1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 5 Jun 2024 16:29:24 -0600
Subject: [PATCH 0454/1248] Added reset tests for timeavg and runmean. Former
 not working.

---
 src/main/test/accumul_test/test_accumul.pf | 98 ++++++++++++++++++++++
 1 file changed, 98 insertions(+)

diff --git a/src/main/test/accumul_test/test_accumul.pf b/src/main/test/accumul_test/test_accumul.pf
index 3c8e2a531d..f2315cf815 100644
--- a/src/main/test/accumul_test/test_accumul.pf
+++ b/src/main/test/accumul_test/test_accumul.pf
@@ -274,6 +274,30 @@ contains
     @assertEqual(expected, val_output, tolerance=tol)
   end subroutine timeavg_basic
 
+  @Test
+  subroutine timeavg_reset(this)
+    ! Test reset of timeavg field
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: accum_period = 3
+    real(r8), parameter :: values(accum_period+1) = [11._r8, 12._r8, 13._r8, 14._r8]
+    logical, parameter :: reset(accum_period+1) = [.false., .true., .false., .false.]
+    real(r8) :: val_output
+    real(r8) :: expected
+
+    ! Setup
+    call setup_single_veg_patch(pft_type=1)
+    call this%init_sl_patch_field(name=fieldname, accum_type='timeavg', &
+         accum_period = accum_period)
+
+    ! Exercise
+    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, reset=reset)
+
+    ! Verify
+    expected = sum(values(2:4))/accum_period
+    @assertEqual(expected, val_output, tolerance=tol)
+  end subroutine timeavg_reset
+
   @Test
   subroutine timeavg_wrongTime(this)
     ! Test a timeavg field when it's the wrong time for producing an average
@@ -320,6 +344,32 @@ contains
     @assertEqual(expected, val_output, tolerance=tol)
   end subroutine timeavg_onlyLatestPeriod
 
+  @Test
+  subroutine timeavg_onlyLatestPeriod_redundantReset(this)
+    ! Manually requesting a reset when one was going to happen anyway should have no effect.
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: accum_period = 3
+    real(r8), parameter :: values(accum_period*2) = &
+         [11._r8, 12._r8, 13._r8, 21._r8, 22._r8, 23._r8]
+    logical, parameter :: reset(accum_period*2) = &
+         [.false., .false., .false., .true., .false., .false.]
+    real(r8) :: val_output
+    real(r8) :: expected
+
+    ! Setup
+    call setup_single_veg_patch(pft_type=1)
+    call this%init_sl_patch_field(name=fieldname, accum_type='timeavg', &
+         accum_period = accum_period)
+
+    ! Exercise
+    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, reset=reset)
+
+    ! Verify
+    expected = sum(values(accum_period+1:2*accum_period))/accum_period
+    @assertEqual(expected, val_output, tolerance=tol)
+  end subroutine timeavg_onlyLatestPeriod_redundantReset
+
   @Test
   subroutine timeavg_newlyActive(this)
     ! For timeavg: If a point becomes active in the middle of a period, then it should
@@ -522,6 +572,54 @@ contains
     @assertEqual(expected_ts5, val_output, tolerance=tol)
   end subroutine runmean_afterPeriod
 
+  @Test
+  subroutine runmean_afterPeriod_reset(this)
+    ! Test runmean accumulation after accum_period is reached, with a reset
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: accum_period = 3
+    real(r8), parameter :: values(5) = [11._r8,  22._r8,  43._r8,  110._r8, 17._r8]
+    logical,  parameter :: reset(5)  = [.false., .false., .false., .true.,  .false.]
+    real(r8) :: val_output
+    real(r8) :: expected_ts5
+
+    ! Setup
+    call setup_single_veg_patch(pft_type=1)
+    call this%init_sl_patch_field(name=fieldname, accum_type='runmean', &
+         accum_period = accum_period)
+
+    ! Exercise
+    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, reset=reset)
+
+    ! Verify
+    expected_ts5 = (values(4) + values(5)) / 2._r8
+    @assertEqual(expected_ts5, val_output, tolerance=tol)
+  end subroutine runmean_afterPeriod_reset
+
+  @Test
+  subroutine runmean_afterPeriod_resetWhileInactive(this)
+    ! Test runmean accumulation after accum_period is reached, with a reset while the patch was inactive. Unlike the other accumulator types, runmean should preserve this reset request and apply it when the patch is active again. This may or may not be the ideal behavior; we can change this if some other
+    ! behavior would be better in this situation.
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: accum_period = 3
+    real(r8), parameter :: values(5)  = [11._r8,  22._r8,  43._r8,  110._r8, 17._r8]
+    logical,  parameter :: pactive(5) = [.true.,  .true.,  .true.,  .false., .true.]
+    logical,  parameter :: reset(5)   = [.false., .false., .false., .true.,  .false.]
+    real(r8) :: val_output
+
+    ! Setup
+    call setup_single_veg_patch(pft_type=1)
+    call this%init_sl_patch_field(name=fieldname, accum_type='runmean', &
+         accum_period = accum_period)
+
+    ! Exercise
+    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, pactive=pactive, reset=reset)
+
+    ! Verify
+    @assertEqual(values(5), val_output, tolerance=tol)
+  end subroutine runmean_afterPeriod_resetWhileInactive
+
   @Test
   subroutine runmean_newlyActive(this)
     ! For runmean: If a point recently became active, its running mean should only

From 1ef5a74c7dadc53e85667e5eab30c366dd44bfb2 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 5 Jun 2024 16:29:42 -0600
Subject: [PATCH 0455/1248] Fix reset behavior for timeavg. Tests now working.

---
 src/main/accumulMod.F90 | 55 ++++++++++++++++++++++++++---------------
 1 file changed, 35 insertions(+), 20 deletions(-)

diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index 8c3f7ed9e4..63ea1777dc 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -87,6 +87,8 @@ module accumulMod
      ! different reset points for different levels.
      integer, pointer   :: nsteps(:,:)!number of steps each point has accumulated, since last reset time
 
+     integer, pointer   :: nresets(:,:)!number of times a reset has been requested (not including timeavg getting reset at end of period)
+
      ! NOTE(wjs, 2017-12-03) We should convert this to fully object-oriented (with
      ! inheritance / polymorphism). For now, in the interest of time, I'm going with a
      ! semi-object-oriented solution of using procedure pointers.
@@ -301,6 +303,9 @@ subroutine init_accum_field (name, units, desc, &
     allocate(accum(nf)%nsteps(beg1d:end1d,numlev))
     accum(nf)%nsteps(beg1d:end1d,1:numlev) = 0
 
+    allocate(accum(nf)%nresets(beg1d:end1d,numlev))
+    accum(nf)%nresets(beg1d:end1d,1:numlev) = 0
+
   end subroutine init_accum_field
 
   !------------------------------------------------------------------------
@@ -467,6 +472,7 @@ subroutine extract_accum_field_timeavg(this, level, nstep, field)
     ! !LOCAL VARIABLES:
     integer :: begi,endi         !subgrid beginning,ending indices
     integer :: k, kf
+    integer :: effective_nstep  ! Timestep accounting for resets
 
     character(len=*), parameter :: subname = 'extract_accum_field_basic'
     !-----------------------------------------------------------------------
@@ -475,17 +481,15 @@ subroutine extract_accum_field_timeavg(this, level, nstep, field)
     endi = this%end1d
     SHR_ASSERT_FL((size(field) == endi-begi+1), sourcefile, __LINE__)
 
-    if (mod(nstep,this%period) == 0) then
-       do k = begi, endi
-          kf = k - begi + 1
+    do k = begi, endi
+       kf = k - begi + 1
+       effective_nstep = nstep - this%nresets(k,level)
+       if (mod(effective_nstep,this%period) == 0) then
           field(kf) = this%val(k,level)
-       end do
-    else
-       do k = begi, endi
-          kf = k - begi + 1
+       else
           field(kf) = spval
-       end do
-    end if
+       end if
+    end do
 
   end subroutine extract_accum_field_timeavg
 
@@ -576,6 +580,7 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     integer :: begi,endi         !subgrid beginning,ending indices
     integer :: k, kf
     logical :: time_to_reset
+    integer :: effective_nstep  ! Timestep accounting for resets
 
     character(len=*), parameter :: subname = 'update_accum_field_timeavg'
     !-----------------------------------------------------------------------
@@ -587,11 +592,15 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     ! time average field: reset every accumulation period; normalize at end of
     ! accumulation period
 
-    time_to_reset = (mod(nstep,this%period) == 1 .or. this%period == 1) .and. nstep /= 0
     do k = begi,endi
+       effective_nstep = nstep - this%nresets(k,level)
+       time_to_reset = (mod(effective_nstep,this%period) == 1 .or. this%period == 1) .and. effective_nstep /= 0
        if (this%active(k) .and. (time_to_reset .or. this%reset(k,level))) then
           this%val(k,level) = 0._r8
           this%nsteps(k,level) = 0
+          if (this%reset(k,level) .and. .not. time_to_reset) then
+             this%nresets(k,level) = this%nresets(k,level) + 1
+          end if
           this%reset(k,level) = .false.
        end if
     end do
@@ -607,13 +616,12 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
        end if
     end do
 
-    if (mod(nstep,this%period) == 0) then
-       do k = begi,endi
-          if (this%active(k)) then
-             this%val(k,level) = this%val(k,level) / this%nsteps(k,level)
-          end if
-       end do
-    end if
+    do k = begi,endi
+       effective_nstep = nstep - this%nresets(k,level)
+       if (this%active(k) .and. mod(effective_nstep,this%period) == 0) then
+          this%val(k,level) = this%val(k,level) / this%nsteps(k,level)
+       end if
+    end do
 
   end subroutine update_accum_field_timeavg
 
@@ -647,8 +655,6 @@ subroutine update_accum_field_runmean(this, level, nstep, field)
              this%nsteps(k,level) = 0
              this%val(k,level) = this%initval
              this%reset(k,level) = .false.
-             ! SSR 2024-06-05: Note that, unlike other accumulator types, runmean preserves reset
-             ! requests that occurred when the patch was inactive.
           end if
           kf = k - begi + 1
           this%nsteps(k,level) = this%nsteps(k,level) + 1
@@ -663,7 +669,10 @@ subroutine update_accum_field_runmean(this, level, nstep, field)
                ((accper-1)*this%val(k,level) + field(kf)) / accper
        end if
     end do
-       
+
+    ! SSR 2024-06-05: Note that, unlike other accumulator types, runmean preserves reset requests
+    ! that occurred when the patch was inactive.
+
   end subroutine update_accum_field_runmean
 
   !-----------------------------------------------------------------------
@@ -853,9 +862,15 @@ subroutine clean_accum_fields
        if (associated(accum(i)%val)) then
           deallocate(accum(i)%val)
        end if
+       if (associated(accum(i)%reset)) then
+          deallocate(accum(i)%reset)
+       end if
        if (associated(accum(i)%nsteps)) then
           deallocate(accum(i)%nsteps)
        end if
+       if (associated(accum(i)%nresets)) then
+          deallocate(accum(i)%nresets)
+       end if
     end do
 
     naccflds = 0

From 2123b15cf8a8a41e4c9339d48709c7b3ad7ee69f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 6 Jun 2024 12:23:28 -0600
Subject: [PATCH 0456/1248] Added unit tests for markreset_accum_field().

---
 src/main/accumulMod.F90                    |  27 +++
 src/main/test/accumul_test/test_accumul.pf | 211 ++++++++++++++++++++-
 2 files changed, 237 insertions(+), 1 deletion(-)

diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index 63ea1777dc..d1cca206a9 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -41,6 +41,7 @@ module accumulMod
   public :: extract_accum_field  ! Extracts the current value of an accumulator field
   public :: update_accum_field   ! Update the current value of an accumulator field
   public :: markreset_accum_field  ! Mark (value(s) in) an accumulator field as needing to be reset
+  public :: get_accum_reset      ! Get reset array of accumulator
   public :: clean_accum_fields   ! Deallocate space and reset accum fields list
 
   interface extract_accum_field
@@ -770,6 +771,32 @@ subroutine markreset_accum_field(name, kf, level)
   end subroutine markreset_accum_field
 
 
+  !-----------------------------------------------------------------------
+  function get_accum_reset(name) result(reset)
+   !
+   ! !DESCRIPTION:
+   ! Get reset array for an accumulator
+   !
+   ! !ARGUMENTS:
+   character(len=*),  intent(in)  :: name  ! field name
+   !
+   ! !RESULT:
+   logical, pointer :: reset(:,:)
+   !
+   ! !LOCAL VARIABLES:
+   integer :: nf          ! field index within the accum(nf) array
+
+   character(len=*), parameter :: subname = 'get_reset'
+   !-----------------------------------------------------------------------
+
+   call find_field(field_name=name, caller_name=subname, field_index=nf)
+
+   allocate(reset(size(accum(nf)%reset, dim=1), size(accum(nf)%reset, dim=2)))
+   reset(:,:) = accum(nf)%reset
+
+  end function get_accum_reset
+
+
   !------------------------------------------------------------------------
   subroutine accumulRest( ncid, flag )
     !
diff --git a/src/main/test/accumul_test/test_accumul.pf b/src/main/test/accumul_test/test_accumul.pf
index f2315cf815..cd3d086ecd 100644
--- a/src/main/test/accumul_test/test_accumul.pf
+++ b/src/main/test/accumul_test/test_accumul.pf
@@ -5,7 +5,7 @@ module test_accumul
   use funit
   use accumulMod
   use unittestSubgridMod
-  use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
+  use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch, setup_n_veg_patches
   use shr_kind_mod , only : r8 => shr_kind_r8
   use clm_varcon, only : spval
   use PatchType, only : patch
@@ -19,6 +19,7 @@ module test_accumul
      procedure :: tearDown
      procedure :: init_sl_patch_field
      procedure :: init_ml_patch_field
+     procedure :: init_ml_mpatch_field
      procedure :: update_and_extract_sl_patch_field
      procedure :: update_and_extract_ml_patch_field
   end type TestAccumul
@@ -98,6 +99,36 @@ contains
          scale_by_thickness = .false.)
   end subroutine init_ml_patch_field
 
+  subroutine init_ml_mpatch_field(this, name, accum_type, accum_period, nlev, init_value)
+     ! Call init_accum_field for a multi-level, multi-patch field
+     class(TestAccumul), intent(in) :: this
+     character(len=*), intent(in) :: name
+     character(len=*), intent(in) :: accum_type ! timeavg, runmean, runaccum
+     integer, intent(in) :: accum_period
+     integer, intent(in) :: nlev
+     real(r8), intent(in), optional :: init_value ! if absent, use 0
+
+     real(r8) :: l_init_value
+
+     if (present(init_value)) then
+        l_init_value = init_value
+     else
+        l_init_value = 0._r8
+     end if
+
+     call init_accum_field(&
+          name = name, &
+          units = 'none', &
+          desc = 'no desc', &
+          accum_type = accum_type, &
+          accum_period = accum_period, &
+          numlev = nlev, &
+          subgrid_type = 'pft', &
+          init_value = l_init_value, &
+          type2d = 'patch', &
+          scale_by_thickness = .false.)
+   end subroutine init_ml_mpatch_field
+
   subroutine update_and_extract_sl_patch_field(this, fieldname, values, val_output, &
        pactive, timestep_start, reset)
     ! Calls update_accum_field once for each value in 'values', assuming that the values
@@ -836,4 +867,182 @@ contains
     @assertEqual(expected2, val_output2, tolerance=tol)
   end subroutine multipleFields
 
+  ! ------------------------------------------------------------------------
+  ! Tests of markreset_accum_field()
+  ! ------------------------------------------------------------------------
+
+  @Test
+  subroutine markreset_nopoints_nolevels(this)
+    ! Make sure that NOT calling markreset_accum_field() means no point-levels are marked for reset.
+    !
+    ! Note that type of accumulator and values don't matter.
+
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: npatches = 2
+    integer, parameter :: nlevels = 5
+    real(r8), parameter :: pwtcol(npatches) = [0.5, 0.5]
+    integer, parameter :: pft_type(npatches) = [1, 2]
+    integer, parameter :: accum_period = 3
+    integer, parameter :: expected(npatches, nlevels) = transpose(reshape([ &
+         0, 0, 0, 0, 0, &
+         0, 0, 0, 0, 0 &
+         ], [nlevels, npatches]))
+    logical :: reset_output(npatches, nlevels)
+    integer :: reset_output_int(npatches, nlevels)
+    integer :: l, p
+
+    ! Setup
+    call setup_n_veg_patches(pwtcol, pft_type)
+    call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+         accum_period = accum_period, nlev=nlevels)
+
+    ! Exercise
+    reset_output = get_accum_reset(fieldname)
+
+    ! Verify
+    do l = 1,nlevels
+       do p = 1,npatches
+          if (reset_output(p,l)) then
+             reset_output_int(p,l) = 1
+          else
+             reset_output_int(p,l) = 0
+          end if
+       end do
+    end do
+    @assertEqual(expected, reset_output_int)
+  end subroutine markreset_nopoints_nolevels
+
+  @Test
+  subroutine markreset_1point_nolevels(this)
+    ! Make sure that calling markreset_accum_field() with kf but no level works right (marks
+    ! all levels of that patch for reset).
+    ! Note that type of accumulator and values don't matter.
+
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: npatches = 2
+    integer, parameter :: nlevels = 5
+    real(r8), parameter :: pwtcol(npatches) = [0.5, 0.5]
+    integer, parameter :: pft_type(npatches) = [1, 2]
+    integer, parameter :: accum_period = 3
+    integer, parameter :: expected(npatches, nlevels) = transpose(reshape([ &
+         1, 1, 1, 1, 1, &
+         0, 0, 0, 0, 0 &
+         ], [nlevels, npatches]))
+    logical :: reset_output(npatches, nlevels)
+    integer :: reset_output_int(npatches, nlevels)
+    integer :: l, p
+
+    ! Setup
+    call setup_n_veg_patches(pwtcol, pft_type)
+    call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+         accum_period = accum_period, nlev=nlevels)
+
+    ! Exercise
+    call markreset_accum_field(fieldname, kf=1)
+    reset_output = get_accum_reset(fieldname)
+
+    ! Verify
+    do l = 1,nlevels
+       do p = 1,npatches
+          if (reset_output(p,l)) then
+             reset_output_int(p,l) = 1
+          else
+             reset_output_int(p,l) = 0
+          end if
+       end do
+    end do
+    @assertEqual(expected, reset_output_int)
+  end subroutine markreset_1point_nolevels
+
+  @Test
+  subroutine markreset_allpoints_1level(this)
+    ! Make sure that calling markreset_accum_field() with level but no kf works right (marks that
+    ! level for reset for all points).
+    !
+    ! Note that type of accumulator and values don't matter.
+
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: npatches = 2
+    integer, parameter :: nlevels = 5
+    real(r8), parameter :: pwtcol(npatches) = [0.5, 0.5]
+    integer, parameter :: pft_type(npatches) = [1, 2]
+    integer, parameter :: accum_period = 3
+    integer, parameter :: expected(npatches, nlevels) = transpose(reshape([ &
+         0, 0, 1, 0, 0, &
+         0, 0, 1, 0, 0 &
+         ], [nlevels, npatches]))
+    logical :: reset_output(npatches, nlevels)
+    integer :: reset_output_int(npatches, nlevels)
+    integer :: l, p
+
+    ! Setup
+    call setup_n_veg_patches(pwtcol, pft_type)
+    call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+         accum_period = accum_period, nlev=nlevels)
+
+    ! Exercise
+    call markreset_accum_field(fieldname, level=3)
+    reset_output = get_accum_reset(fieldname)
+
+    ! Verify
+    do l = 1,nlevels
+       do p = 1,npatches
+          if (reset_output(p,l)) then
+             reset_output_int(p,l) = 1
+          else
+             reset_output_int(p,l) = 0
+          end if
+       end do
+    end do
+    @assertEqual(expected, reset_output_int)
+end subroutine markreset_allpoints_1level
+
+@Test
+subroutine markreset_allpoints_alllevels(this)
+  ! Make sure that calling markreset_accum_field() with neither kf nor level works right (marks
+  ! all for reset).
+  !
+  ! Note that type of accumulator and values don't matter.
+
+  class(TestAccumul), intent(inout) :: this
+  character(len=*), parameter :: fieldname = 'foo'
+  integer, parameter :: npatches = 2
+  integer, parameter :: nlevels = 5
+  real(r8), parameter :: pwtcol(npatches) = [0.5, 0.5]
+  integer, parameter :: pft_type(npatches) = [1, 2]
+  integer, parameter :: accum_period = 3
+  integer, parameter :: expected(npatches, nlevels) = transpose(reshape([ &
+       1, 1, 1, 1, 1, &
+       1, 1, 1, 1, 1 &
+       ], [nlevels, npatches]))
+  logical :: reset_output(npatches, nlevels)
+  integer :: reset_output_int(npatches, nlevels)
+  integer :: l, p
+
+  ! Setup
+  call setup_n_veg_patches(pwtcol, pft_type)
+  call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+       accum_period = accum_period, nlev=nlevels)
+
+  ! Exercise
+  call markreset_accum_field(fieldname)
+  reset_output = get_accum_reset(fieldname)
+
+  ! Verify
+  do l = 1,nlevels
+     do p = 1,npatches
+        if (reset_output(p,l)) then
+           reset_output_int(p,l) = 1
+        else
+           reset_output_int(p,l) = 0
+        end if
+     end do
+  end do
+  @assertEqual(expected, reset_output_int)
+end subroutine markreset_allpoints_alllevels
+
+
 end module test_accumul

From 94cbf03fbcf680db69858197daa33f33fc50d7d4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 6 Jun 2024 15:45:53 -0600
Subject: [PATCH 0457/1248] Reset timeavg and runaccum accumulators to initval,
 not 0.

Fixes ESCOMP/CTSM#2584.
---
 src/main/accumulMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index d1cca206a9..1ee0b4dae7 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -597,7 +597,7 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
        effective_nstep = nstep - this%nresets(k,level)
        time_to_reset = (mod(effective_nstep,this%period) == 1 .or. this%period == 1) .and. effective_nstep /= 0
        if (this%active(k) .and. (time_to_reset .or. this%reset(k,level))) then
-          this%val(k,level) = 0._r8
+          this%val(k,level) = this%initval
           this%nsteps(k,level) = 0
           if (this%reset(k,level) .and. .not. time_to_reset) then
              this%nresets(k,level) = this%nresets(k,level) + 1
@@ -708,7 +708,7 @@ subroutine update_accum_field_runaccum(this, level, nstep, field)
              ! SSR 2024-06-05: Note that, unlike the other accumulator types, runaccum can not
              ! reset AND update in the same call of its update_accum_field subroutine.
              this%val(k,level) = 0._r8
-             this%nsteps(k,level) = 0
+             this%nsteps(k,level) = this%initval
              this%reset(k,level) = .false.
           else
              this%val(k,level) = &

From f8302705e25e062699fa2a08e387471e57c316e0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 6 Jun 2024 16:05:41 -0600
Subject: [PATCH 0458/1248] Update GDD20 flushing to use
 markreset_accum_field().

---
 src/biogeophys/TemperatureType.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 08d3e8cd57..1f6d0958c6 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1687,9 +1687,9 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
        if (is_end_curr_year()) then
           ! Flush, if needed
           if (this%flush_gdd20) then
-              this%gdd020_patch(begp:endp) = accumResetVal
-              this%gdd820_patch(begp:endp) = accumResetVal
-              this%gdd1020_patch(begp:endp) = accumResetVal
+              call markreset_accum_field('GDD020')
+              call markreset_accum_field('GDD820')
+              call markreset_accum_field('GDD1020')
               this%flush_gdd20 = .false.
           end if
           call update_accum_field  ('GDD020', this%gdd0_patch, nstep)

From 46862cc47510f3b4f4b376ab64f436f668c9d788 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 7 Jun 2024 00:11:41 -0600
Subject: [PATCH 0459/1248] Add a barebones dust emission factory module to
 create a dust emission class object to be used depending on the namelist
 option, need to add documentation to it

---
 src/biogeochem/CMakeLists.txt                 |  1 +
 src/biogeochem/DustEmisFactory.F90            | 51 +++++++++++++++++++
 src/biogeochem/DustEmisZender2003.F90         | 14 +++++
 .../DustEmis_test/test_DustEmisZender2003.pf  |  6 ++-
 src/main/clm_instMod.F90                      |  7 +--
 src/main/lnd2atmMod.F90                       |  4 +-
 6 files changed, 76 insertions(+), 7 deletions(-)
 create mode 100644 src/biogeochem/DustEmisFactory.F90

diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt
index 9824bcb072..50eb64cdb7 100644
--- a/src/biogeochem/CMakeLists.txt
+++ b/src/biogeochem/CMakeLists.txt
@@ -8,6 +8,7 @@ list(APPEND clm_sources
   CNDVType.F90
   DustEmisBase.F90
   DustEmisZender2003.F90
+  DustEmisFactory.F90
   CropReprPoolsMod.F90
   CropType.F90
   CNVegStateType.F90
diff --git a/src/biogeochem/DustEmisFactory.F90 b/src/biogeochem/DustEmisFactory.F90
new file mode 100644
index 0000000000..29787c1855
--- /dev/null
+++ b/src/biogeochem/DustEmisFactory.F90
@@ -0,0 +1,51 @@
+module DustEmisFactory
+
+    use abortutils   , only : endrun
+    use shr_log_mod  , only : errMsg => shr_log_errMsg
+    use clm_varctl   , only : iulog
+
+    implicit none
+    save
+    private
+    !
+    public :: create_dust_emissions  ! create an object of class dust_emis_base
+
+    character(len=*), parameter, private :: sourcefile = &
+        __FILE__
+
+contains
+
+    function create_dust_emissions(bounds, NLFilename) result(dust_emis)
+        use DustEmisBase      , only : dust_emis_base_type
+        use DustEmisZender2003, only : dust_emis_zender2003_type
+        use clm_varctl        , only : dust_emis_method
+        use decompMod         , only : bounds_type
+        use shr_kind_mod      , only : CL => shr_kind_cl
+        implicit none
+        class(dust_emis_base_type), allocatable :: dust_emis
+        type(bounds_type), intent(in) :: bounds
+        character(len=*),  intent(in) :: NLFilename
+        character(len=CL) :: method
+
+        method = dust_emis_method
+
+        select case ( trim(method) )
+
+        case( "Zender_2003" )
+           allocate(dust_emis, source=dust_emis_zender2003_type() )
+        
+        ! This will be added when the Leung2023 comes in
+        !case( "Leung_2023" )
+        !  allocate(dust_emis, source=dust_emis_zender2003_type() )
+        case default
+           write(iulog,*) 'ERROR: unknown dust_emis_method: ', method, &
+                           errMsg(sourcefile, __LINE__)
+           call endrun( "Unrecognized dust_emis_method"  )
+
+        end select
+
+        call dust_emis%Init(bounds, NLFilename)
+
+    end function create_dust_emissions
+
+end module DustEmisFactory
\ No newline at end of file
diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index bebbc7ff30..e3c4d4115e 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -57,6 +57,11 @@ module DustEmisZender2003
      procedure , private :: InitCold
 
   end type dust_emis_zender2003_type
+
+  interface dust_emis_zender2003_type
+     ! initialize a new dust emission object
+      module procedure constructor
+  end interface dust_emis_zender2003_type
   !------------------------------------------------------------------------
 
   character(len=*), parameter, private :: sourcefile = &
@@ -64,6 +69,15 @@ module DustEmisZender2003
 
 contains
 
+  !-----------------------------------------------------------------------
+  type(dust_emis_zender2003_type) function constructor()
+  !
+  ! Creates a dust emission object for Zender-2003 type
+  ! For now this is just a placeholder
+  !-----------------------------------------------------------------------
+
+  end function constructor
+
   !------------------------------------------------------------------------
 
   subroutine InitZender2003(this, bounds, NLFilename)
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 7ba4e4b63e..4df64c7da3 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -9,6 +9,7 @@ module test_DustEmisZender2003
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
   use clm_varcon, only : clm_varcon_init, clm_varcon_clean
   use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean
+  use DustEmisBase
   use DustEmisZender2003
   use shr_kind_mod , only : r8 => shr_kind_r8
   use unittestFilterBuilderMod, only : filter_from_range
@@ -20,6 +21,7 @@ module test_DustEmisZender2003
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
   use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay
+  use DustEmisFactory, only : create_dust_emissions
 
   implicit none
 
@@ -27,7 +29,7 @@ module test_DustEmisZender2003
 
   @TestCase
   type, extends(TestCase) :: TestDustEmisZender2003
-     type(dust_emis_zender2003_type) :: dust_emis
+     class(dust_emis_base_type), allocatable :: dust_emis
      integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
      integer :: num_nolakep              ! number of patches in non-lake filter
      type(atm2lnd_type) :: atm2lnd_inst
@@ -79,7 +81,7 @@ contains
     endc = bounds%endc
     allocate( urb_em(begl:endl) )
 
-    call this%dust_emis%Init( bounds, NLFilename )
+    allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))
     call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
     atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
                                           glcmec_downscale_longwave = .false., &
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index 9e187f639c..ab690a92a6 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -45,7 +45,7 @@ module clm_instMod
   use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
   use CropType                        , only : crop_type
   use DryDepVelocity                  , only : drydepvel_type
-  use DustEmisZender2003                         , only : dust_emis_zender2003_type
+  use DustEmisBase                    , only : dust_emis_base_type
   use EnergyFluxType                  , only : energyflux_type
   use FrictionVelocityMod             , only : frictionvel_type
   use GlacierSurfaceMassBalanceMod    , only : glacier_smb_type
@@ -151,7 +151,7 @@ module clm_instMod
   ! General biogeochem types
   type(ch4_type)      , public            :: ch4_inst
   type(crop_type)     , public            :: crop_inst
-  type(dust_emis_zender2003_type)     , public            :: dust_emis_inst
+  class(dust_emis_base_type), public, allocatable :: dust_emis_inst
   type(vocemis_type)  , public            :: vocemis_inst
   type(fireemis_type) , public            :: fireemis_inst
   type(drydepvel_type), public            :: drydepvel_inst
@@ -203,6 +203,7 @@ subroutine clm_instInit(bounds)
     use clm_varctl                         , only : use_hillslope
     use HillslopeHydrologyMod              , only : SetHillslopeSoilThickness
     use initVerticalMod                    , only : setSoilLayerClass
+    use DustEmisFactory                    , only : create_dust_emissions
     !
     ! !ARGUMENTS    
     type(bounds_type), intent(in) :: bounds  ! processor bounds
@@ -350,7 +351,7 @@ subroutine clm_instInit(bounds)
 
     call surfrad_inst%Init(bounds)
 
-    call dust_emis_inst%Init(bounds, NLFilename)
+    allocate(dust_emis_inst, source = create_dust_emissions(bounds, NLFilename))
 
     allocate(scf_method, source = CreateAndInitSnowCoverFraction( &
          snow_cover_fraction_method = snow_cover_fraction_method, &
diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90
index 71f55b3b05..503f4b9585 100644
--- a/src/main/lnd2atmMod.F90
+++ b/src/main/lnd2atmMod.F90
@@ -20,7 +20,7 @@ module lnd2atmMod
   use lnd2atmType          , only : lnd2atm_type
   use atm2lndType          , only : atm2lnd_type
   use ch4Mod               , only : ch4_type
-  use DustEmisZender2003              , only : dust_emis_zender2003_type
+  use DustEmisBase         , only : dust_emis_base_type
   use DryDepVelocity       , only : drydepvel_type
   use VocEmissionMod       , only : vocemis_type
   use CNFireEmissionsMod   , only : fireemis_type
@@ -173,7 +173,7 @@ subroutine lnd2atm(bounds, &
     type(drydepvel_type)        , intent(in)    :: drydepvel_inst
     type(vocemis_type)          , intent(in)    :: vocemis_inst
     type(fireemis_type)         , intent(in)    :: fireemis_inst
-    type(dust_emis_zender2003_type)             , intent(in)    :: dust_emis_inst
+    class(dust_emis_base_type)  , intent(in)    :: dust_emis_inst
     type(ch4_type)              , intent(in)    :: ch4_inst
     type(glc_behavior_type)     , intent(in)    :: glc_behavior
     type(lnd2atm_type)          , intent(inout) :: lnd2atm_inst

From 906a39ea2acdfdf0b05743c16a54dd8fd700561a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 7 Jun 2024 11:22:48 -0600
Subject: [PATCH 0460/1248] Whitespace fix.

---
 src/main/accumulMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index 1ee0b4dae7..7be5d5b87b 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -715,7 +715,7 @@ subroutine update_accum_field_runaccum(this, level, nstep, field)
                   min(max(this%val(k,level) + field(kf), 0._r8), 99999._r8)
              this%nsteps(k,level) = this%nsteps(k,level) + 1
           end if
-      end if
+       end if
     end do
 
     ! Ignore reset requests that occurred when patch was inactive

From 4a4e5efdd469d6b29408b28a38a737ebb3682b7a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 7 Jun 2024 11:29:11 -0600
Subject: [PATCH 0461/1248] Replace init_ml_mpatch_field with a change in
 init_ml_patch_field.

---
 src/main/test/accumul_test/test_accumul.pf | 41 +++-------------------
 1 file changed, 5 insertions(+), 36 deletions(-)

diff --git a/src/main/test/accumul_test/test_accumul.pf b/src/main/test/accumul_test/test_accumul.pf
index cd3d086ecd..3d791dc664 100644
--- a/src/main/test/accumul_test/test_accumul.pf
+++ b/src/main/test/accumul_test/test_accumul.pf
@@ -19,7 +19,6 @@ module test_accumul
      procedure :: tearDown
      procedure :: init_sl_patch_field
      procedure :: init_ml_patch_field
-     procedure :: init_ml_mpatch_field
      procedure :: update_and_extract_sl_patch_field
      procedure :: update_and_extract_ml_patch_field
   end type TestAccumul
@@ -95,40 +94,10 @@ contains
          numlev = nlev, &
          subgrid_type = 'pft', &
          init_value = l_init_value, &
-         type2d = 'irrelevant', &  ! type2d just needed for restart
+         type2d = 'patch', &  ! Irrelevant for one-patch fields, but some tests have more than one
          scale_by_thickness = .false.)
   end subroutine init_ml_patch_field
 
-  subroutine init_ml_mpatch_field(this, name, accum_type, accum_period, nlev, init_value)
-     ! Call init_accum_field for a multi-level, multi-patch field
-     class(TestAccumul), intent(in) :: this
-     character(len=*), intent(in) :: name
-     character(len=*), intent(in) :: accum_type ! timeavg, runmean, runaccum
-     integer, intent(in) :: accum_period
-     integer, intent(in) :: nlev
-     real(r8), intent(in), optional :: init_value ! if absent, use 0
-
-     real(r8) :: l_init_value
-
-     if (present(init_value)) then
-        l_init_value = init_value
-     else
-        l_init_value = 0._r8
-     end if
-
-     call init_accum_field(&
-          name = name, &
-          units = 'none', &
-          desc = 'no desc', &
-          accum_type = accum_type, &
-          accum_period = accum_period, &
-          numlev = nlev, &
-          subgrid_type = 'pft', &
-          init_value = l_init_value, &
-          type2d = 'patch', &
-          scale_by_thickness = .false.)
-   end subroutine init_ml_mpatch_field
-
   subroutine update_and_extract_sl_patch_field(this, fieldname, values, val_output, &
        pactive, timestep_start, reset)
     ! Calls update_accum_field once for each value in 'values', assuming that the values
@@ -894,7 +863,7 @@ contains
 
     ! Setup
     call setup_n_veg_patches(pwtcol, pft_type)
-    call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+    call this%init_ml_patch_field(name=fieldname, accum_type='timeavg', &
          accum_period = accum_period, nlev=nlevels)
 
     ! Exercise
@@ -936,7 +905,7 @@ contains
 
     ! Setup
     call setup_n_veg_patches(pwtcol, pft_type)
-    call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+    call this%init_ml_patch_field(name=fieldname, accum_type='timeavg', &
          accum_period = accum_period, nlev=nlevels)
 
     ! Exercise
@@ -980,7 +949,7 @@ contains
 
     ! Setup
     call setup_n_veg_patches(pwtcol, pft_type)
-    call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+    call this%init_ml_patch_field(name=fieldname, accum_type='timeavg', &
          accum_period = accum_period, nlev=nlevels)
 
     ! Exercise
@@ -1024,7 +993,7 @@ subroutine markreset_allpoints_alllevels(this)
 
   ! Setup
   call setup_n_veg_patches(pwtcol, pft_type)
-  call this%init_ml_mpatch_field(name=fieldname, accum_type='timeavg', &
+  call this%init_ml_patch_field(name=fieldname, accum_type='timeavg', &
        accum_period = accum_period, nlev=nlevels)
 
   ! Exercise

From 8035a772d8cb938e91cae9fa0a9301270b100fdf Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 7 Jun 2024 11:33:25 -0600
Subject: [PATCH 0462/1248] test_accumul: Replace logical->int loops with
 one-line merge().

---
 src/main/test/accumul_test/test_accumul.pf | 40 +++-------------------
 1 file changed, 4 insertions(+), 36 deletions(-)

diff --git a/src/main/test/accumul_test/test_accumul.pf b/src/main/test/accumul_test/test_accumul.pf
index 3d791dc664..b140366077 100644
--- a/src/main/test/accumul_test/test_accumul.pf
+++ b/src/main/test/accumul_test/test_accumul.pf
@@ -870,15 +870,7 @@ contains
     reset_output = get_accum_reset(fieldname)
 
     ! Verify
-    do l = 1,nlevels
-       do p = 1,npatches
-          if (reset_output(p,l)) then
-             reset_output_int(p,l) = 1
-          else
-             reset_output_int(p,l) = 0
-          end if
-       end do
-    end do
+    reset_output_int = merge(1, 0, reset_output)
     @assertEqual(expected, reset_output_int)
   end subroutine markreset_nopoints_nolevels
 
@@ -913,15 +905,7 @@ contains
     reset_output = get_accum_reset(fieldname)
 
     ! Verify
-    do l = 1,nlevels
-       do p = 1,npatches
-          if (reset_output(p,l)) then
-             reset_output_int(p,l) = 1
-          else
-             reset_output_int(p,l) = 0
-          end if
-       end do
-    end do
+    reset_output_int = merge(1, 0, reset_output)
     @assertEqual(expected, reset_output_int)
   end subroutine markreset_1point_nolevels
 
@@ -957,15 +941,7 @@ contains
     reset_output = get_accum_reset(fieldname)
 
     ! Verify
-    do l = 1,nlevels
-       do p = 1,npatches
-          if (reset_output(p,l)) then
-             reset_output_int(p,l) = 1
-          else
-             reset_output_int(p,l) = 0
-          end if
-       end do
-    end do
+    reset_output_int = merge(1, 0, reset_output)
     @assertEqual(expected, reset_output_int)
 end subroutine markreset_allpoints_1level
 
@@ -1001,15 +977,7 @@ subroutine markreset_allpoints_alllevels(this)
   reset_output = get_accum_reset(fieldname)
 
   ! Verify
-  do l = 1,nlevels
-     do p = 1,npatches
-        if (reset_output(p,l)) then
-           reset_output_int(p,l) = 1
-        else
-           reset_output_int(p,l) = 0
-        end if
-     end do
-  end do
+  reset_output_int = merge(1, 0, reset_output)
   @assertEqual(expected, reset_output_int)
 end subroutine markreset_allpoints_alllevels
 

From 669fe21c3164298d641fbb7a79dbf076a8a313ec Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 7 Jun 2024 11:37:16 -0600
Subject: [PATCH 0463/1248] test_accumul: Add test of timeavg reset 2 days
 after period start. Fails.

---
 src/main/test/accumul_test/test_accumul.pf | 30 +++++++++++++++++++---
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/src/main/test/accumul_test/test_accumul.pf b/src/main/test/accumul_test/test_accumul.pf
index b140366077..423a0aea18 100644
--- a/src/main/test/accumul_test/test_accumul.pf
+++ b/src/main/test/accumul_test/test_accumul.pf
@@ -275,8 +275,8 @@ contains
   end subroutine timeavg_basic
 
   @Test
-  subroutine timeavg_reset(this)
-    ! Test reset of timeavg field
+  subroutine timeavg_reset1(this)
+    ! Test reset of timeavg field 1 day after period start
     class(TestAccumul), intent(inout) :: this
     character(len=*), parameter :: fieldname = 'foo'
     integer, parameter :: accum_period = 3
@@ -296,7 +296,31 @@ contains
     ! Verify
     expected = sum(values(2:4))/accum_period
     @assertEqual(expected, val_output, tolerance=tol)
-  end subroutine timeavg_reset
+  end subroutine timeavg_reset1
+
+  @Test
+  subroutine timeavg_reset2(this)
+    ! Test reset of timeavg field 2 days after period start
+    class(TestAccumul), intent(inout) :: this
+    character(len=*), parameter :: fieldname = 'foo'
+    integer, parameter :: accum_period = 3
+    real(r8), parameter :: values(accum_period+2) = [11._r8, 12._r8, 13._r8, 14._r8, 15._r8]
+    logical, parameter :: reset(accum_period+2) = [.false., .false., .true., .false., .false.]
+    real(r8) :: val_output
+    real(r8) :: expected
+
+    ! Setup
+    call setup_single_veg_patch(pft_type=1)
+    call this%init_sl_patch_field(name=fieldname, accum_type='timeavg', &
+         accum_period = accum_period)
+
+    ! Exercise
+    call this%update_and_extract_sl_patch_field(fieldname, values, val_output, reset=reset)
+
+    ! Verify
+    expected = sum(values(3:5))/accum_period
+    @assertEqual(expected, val_output, tolerance=tol)
+  end subroutine timeavg_reset2
 
   @Test
   subroutine timeavg_wrongTime(this)

From d82be2c32dbde8cde0637871114b4a44cd2894fb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 7 Jun 2024 11:42:39 -0600
Subject: [PATCH 0464/1248] accumulMod bugfix: Use ndays_reset_shifted instead
 of nresets. Tests pass.

---
 src/main/accumulMod.F90 | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/main/accumulMod.F90 b/src/main/accumulMod.F90
index 7be5d5b87b..0c2462c1f8 100644
--- a/src/main/accumulMod.F90
+++ b/src/main/accumulMod.F90
@@ -88,7 +88,7 @@ module accumulMod
      ! different reset points for different levels.
      integer, pointer   :: nsteps(:,:)!number of steps each point has accumulated, since last reset time
 
-     integer, pointer   :: nresets(:,:)!number of times a reset has been requested (not including timeavg getting reset at end of period)
+     integer, pointer   :: ndays_reset_shifted(:,:)!accumulated number of days that resetting timeavg field has moved it out of sync with model timestep
 
      ! NOTE(wjs, 2017-12-03) We should convert this to fully object-oriented (with
      ! inheritance / polymorphism). For now, in the interest of time, I'm going with a
@@ -304,8 +304,8 @@ subroutine init_accum_field (name, units, desc, &
     allocate(accum(nf)%nsteps(beg1d:end1d,numlev))
     accum(nf)%nsteps(beg1d:end1d,1:numlev) = 0
 
-    allocate(accum(nf)%nresets(beg1d:end1d,numlev))
-    accum(nf)%nresets(beg1d:end1d,1:numlev) = 0
+    allocate(accum(nf)%ndays_reset_shifted(beg1d:end1d,numlev))
+    accum(nf)%ndays_reset_shifted(beg1d:end1d,1:numlev) = 0
 
   end subroutine init_accum_field
 
@@ -484,7 +484,7 @@ subroutine extract_accum_field_timeavg(this, level, nstep, field)
 
     do k = begi, endi
        kf = k - begi + 1
-       effective_nstep = nstep - this%nresets(k,level)
+       effective_nstep = nstep - this%ndays_reset_shifted(k,level)
        if (mod(effective_nstep,this%period) == 0) then
           field(kf) = this%val(k,level)
        else
@@ -594,14 +594,14 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     ! accumulation period
 
     do k = begi,endi
-       effective_nstep = nstep - this%nresets(k,level)
+       effective_nstep = nstep - this%ndays_reset_shifted(k,level)
        time_to_reset = (mod(effective_nstep,this%period) == 1 .or. this%period == 1) .and. effective_nstep /= 0
        if (this%active(k) .and. (time_to_reset .or. this%reset(k,level))) then
-          this%val(k,level) = this%initval
-          this%nsteps(k,level) = 0
           if (this%reset(k,level) .and. .not. time_to_reset) then
-             this%nresets(k,level) = this%nresets(k,level) + 1
+             this%ndays_reset_shifted(k,level) = this%ndays_reset_shifted(k,level) + this%nsteps(k,level)
           end if
+          this%val(k,level) = this%initval
+          this%nsteps(k,level) = 0
           this%reset(k,level) = .false.
        end if
     end do
@@ -618,7 +618,7 @@ subroutine update_accum_field_timeavg(this, level, nstep, field)
     end do
 
     do k = begi,endi
-       effective_nstep = nstep - this%nresets(k,level)
+       effective_nstep = nstep - this%ndays_reset_shifted(k,level)
        if (this%active(k) .and. mod(effective_nstep,this%period) == 0) then
           this%val(k,level) = this%val(k,level) / this%nsteps(k,level)
        end if
@@ -895,8 +895,8 @@ subroutine clean_accum_fields
        if (associated(accum(i)%nsteps)) then
           deallocate(accum(i)%nsteps)
        end if
-       if (associated(accum(i)%nresets)) then
-          deallocate(accum(i)%nresets)
+       if (associated(accum(i)%ndays_reset_shifted)) then
+          deallocate(accum(i)%ndays_reset_shifted)
        end if
     end do
 

From 7024437f8dddf7342547fa03f85148a0163b9d4a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 7 Jun 2024 11:44:46 -0600
Subject: [PATCH 0465/1248] Bugfix: Was resetting AGDD instead of AGDDTW.

---
 src/biogeochem/CNDVType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CNDVType.F90 b/src/biogeochem/CNDVType.F90
index 21921f7cbd..5130c0b085 100644
--- a/src/biogeochem/CNDVType.F90
+++ b/src/biogeochem/CNDVType.F90
@@ -496,7 +496,7 @@ subroutine UpdateAccVars(this, bounds, t_a10_patch, t_ref2m_patch)
     end do
     if (month==1 .and. day==1 .and. secs==int(dtime)) then
        ! Reset annually
-       call markreset_accum_field('AGDD')
+       call markreset_accum_field('AGDDTW')
     end if
     call update_accum_field  ('AGDDTW', rbufslp, nstep)
     call extract_accum_field ('AGDDTW', this%agddtw_patch, nstep)

From f5585268babcf413787fe7608fd58204a1bc458a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 7 Jun 2024 11:51:23 -0600
Subject: [PATCH 0466/1248] Add comments warning against wrapping runaccum
 do-loops in checks for reset.

---
 src/biogeochem/CNDVType.F90        | 6 ++++++
 src/biogeophys/TemperatureType.F90 | 9 +++++++++
 2 files changed, 15 insertions(+)

diff --git a/src/biogeochem/CNDVType.F90 b/src/biogeochem/CNDVType.F90
index 5130c0b085..fb6b3d9753 100644
--- a/src/biogeochem/CNDVType.F90
+++ b/src/biogeochem/CNDVType.F90
@@ -489,6 +489,9 @@ subroutine UpdateAccVars(this, bounds, t_a10_patch, t_ref2m_patch)
     ! Accumulate and extract AGDDTW (gdd base twmax, which is 23 deg C
     ! for boreal woody patches)
     
+    ! SSR 2024-06-07: Don't wrap this do-loop in an "if it's not time to reset." Behavior would
+    ! be identical for now, but if "missed update" behavior is fixed (see ESCOMP/CTSM#2585), you
+    ! would end up updating AGDDTW with uninitialized values.
     do p = begp,endp
        rbufslp(p) = max(0._r8, &
             (t_a10_patch(p) - SHR_CONST_TKFRZ - dgv_ecophyscon%twmax(ndllf_dcd_brl_tree)) &
@@ -503,6 +506,9 @@ subroutine UpdateAccVars(this, bounds, t_a10_patch, t_ref2m_patch)
 
     ! Accumulate and extract AGDD
 
+    ! SSR 2024-06-07: Don't wrap this do-loop in an "if it's not time to reset." Behavior would
+    ! be identical for now, but if "missed update" behavior is fixed (see ESCOMP/CTSM#2585), you
+    ! would end up updating AGDD with uninitialized values.
     do p = begp,endp
        rbufslp(p) = max(0.0_r8, &
             (t_ref2m_patch(p) - (SHR_CONST_TKFRZ + 5.0_r8)) * dtime/SHR_CONST_CDAY)
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index c9909e82d3..0144f1ef18 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1539,6 +1539,9 @@ subroutine UpdateAccVars (this, bounds)
 
        ! Accumulate and extract GDD0
 
+       ! SSR 2024-06-07: Don't wrap this do-loop in an "if it's not time to reset." Behavior would
+       ! be identical for now, but if "missed update" behavior is fixed (see ESCOMP/CTSM#2585), you
+       ! would end up updating GDD0 with uninitialized values.
        do p = begp,endp
           ! Avoid unnecessary calculations over inactive points
           if (patch%active(p)) then
@@ -1558,6 +1561,9 @@ subroutine UpdateAccVars (this, bounds)
 
        ! Accumulate and extract GDD8
 
+       ! SSR 2024-06-07: Don't wrap this do-loop in an "if it's not time to reset." Behavior would
+       ! be identical for now, but if "missed update" behavior is fixed (see ESCOMP/CTSM#2585), you
+       ! would end up updating GDD8 with uninitialized values.
        do p = begp,endp
           ! Avoid unnecessary calculations over inactive points
           if (patch%active(p)) then
@@ -1578,6 +1584,9 @@ subroutine UpdateAccVars (this, bounds)
 
        ! Accumulate and extract GDD10
 
+       ! SSR 2024-06-07: Don't wrap this do-loop in an "if it's not time to reset." Behavior would
+       ! be identical for now, but if "missed update" behavior is fixed (see ESCOMP/CTSM#2585), you
+       ! would end up updating GDD10 with uninitialized values.
        do p = begp,endp
           ! Avoid unnecessary calculations over inactive points
           if (patch%active(p)) then

From 779c9b51b15f6e0c7663df72590d4d5e36654e38 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 7 Jun 2024 12:07:37 -0600
Subject: [PATCH 0467/1248] Squashed '.lib/git-fleximod/' changes from
 a34070be0..4ff1e98de

4ff1e98de Merge tag 'v0.7.7' into tmp-release
87640adf4 Bump to 0.7.7
c124dc590 Merge pull request #43 from ESMCI/fix/root_dir
3ff935b83 update tests
0593149d3 one more improvement
d95f5d61b fix status issue
c304487af update complex test

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 4ff1e98de895eb146de451e6d676ecc78d224662
---
 git_fleximod/cli.py          |  4 ++--
 git_fleximod/git_fleximod.py | 22 +++++++++++++++++-----
 pyproject.toml               |  2 +-
 tbump.toml                   |  2 +-
 tests/conftest.py            |  4 ++--
 tests/test_d_complex.py      | 13 ++++++-------
 6 files changed, 29 insertions(+), 18 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 7d09abd83b..bc099fcbc0 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.7.6"
+__version__ = "0.7.7"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
@@ -21,7 +21,7 @@ def find_root_dir(filename=".gitmodules"):
         attempt = dl / filename
         if attempt.is_file():
             return str(dl)
-    utils.fatal_error("No .gitmodules found in directory tree")
+    return None
 
 
 def get_parser():
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index a003c0da8c..ca5f90622d 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -298,15 +298,25 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
             # submodule commands use path, not name
             url = url.replace("git@github.com:", "https://github.com/")
             tags = rootgit.git_operation("ls-remote", "--tags", url)
+            result = rootgit.git_operation("submodule","status",newpath).split()
+            ahash = None
+            if result:
+                ahash = result[0][1:]
+            hhash = None
             atag = None
             needsupdate += 1
             if not toplevel and level:
                 continue
             for htag in tags.split("\n"):
-                if tag and tag in htag:
+                if htag.endswith('^{}'):
+                    htag = htag[:-3]
+                if ahash and not atag and ahash in htag:
                     atag = (htag.split()[1])[10:]
+                if tag and not hhash and htag.endswith(tag):
+                    hhash = htag.split()[0]
+                if hhash and atag:
                     break
-            if tag and tag == atag:
+            if tag and (ahash == hhash or atag == tag):
                 print(f"e {name:>20} not checked out, aligned at tag {tag}")
             elif tag:
                 ahash = rootgit.git_operation(
@@ -565,10 +575,12 @@ def main():
 
     logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
     
-    if not os.path.isfile(os.path.join(root_dir, file_name)):
-        file_path = utils.find_upwards(root_dir, file_name)
+    if not root_dir or not os.path.isfile(os.path.join(root_dir, file_name)):
+        if root_dir:
+            file_path = utils.find_upwards(root_dir, file_name)
 
-        if file_path is None:
+        if root_dir is None or file_path is None:
+            root_dir = "."
             utils.fatal_error(
                 "No {} found in {} or any of it's parents".format(file_name, root_dir)
             )
diff --git a/pyproject.toml b/pyproject.toml
index 3c70c6c9c7..a316914bf5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.6"
+version = "0.7.7"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index 3854682df4..c22637ccda 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.6"
+current = "0.7.7"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before
diff --git a/tests/conftest.py b/tests/conftest.py
index 942a0efb97..1cc008eb1d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -32,7 +32,7 @@ def logger():
      "submodule_name": "test_optional",
      "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0",
      "status4" : "test_optional at tag MPIserial_2.4.0",
      "gitmodules_content": """
      [submodule "test_optional"]
@@ -46,7 +46,7 @@ def logger():
      "submodule_name": "test_alwaysoptional",
      "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
      "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0",
+     "status3" : "out of sync at tag None, expected tag is e5cf35c",
      "status4" : "test_alwaysoptional at hash e5cf35c",
      "gitmodules_content": """
     [submodule "test_alwaysoptional"]
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
index fdce516274..edde7d816d 100644
--- a/tests/test_d_complex.py
+++ b/tests/test_d_complex.py
@@ -7,8 +7,8 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, aligned at tag testtag01" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
+    assert("Complex not checked out, aligned at tag testtag02" in status.stdout)
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
     
     # This should checkout and update test_submodule and complex_sub
     result = git_fleximod(complex_repo, "update")    
@@ -18,7 +18,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
 
     # now check the complex_sub
     root = (complex_repo / "modules" / "complex")
@@ -39,9 +39,8 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
-    assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout)
-
+    assert("Complex at tag testtag02" in status.stdout)
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
 
     # Finally update optional
     result = git_fleximod(complex_repo, "update --optional")
@@ -51,7 +50,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert("ToplevelOptional at tag v5.3.2" in status.stdout)
     assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
     assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag01" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
     assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
     
     # now check the complex_sub

From 5eadc60c32d65b359fddee5947ffed57cdc02da8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 7 Jun 2024 13:18:22 -0600
Subject: [PATCH 0468/1248] Tweak the documenation a bit

---
 .gitignore                                    |  4 ---
 README                                        |  2 +-
 README_GITFLEXIMOD.rst                        | 31 ++++++++++---------
 cime_config/testdefs/ExpectedTestFails.xml    |  2 +-
 cime_config/testdefs/testlist_clm.xml         |  2 +-
 .../PLUMBER2/defaults/user_nl_datm_streams    |  2 +-
 doc/README.CHECKLIST.master_tags              |  4 +--
 python/ctsm/run_sys_tests.py                  |  6 ++--
 ...st_unit_gen_mksurfdata_jobscript_single.py |  2 +-
 tools/mksurfdata_esmf/README.md               |  2 +-
 10 files changed, 28 insertions(+), 29 deletions(-)

diff --git a/.gitignore b/.gitignore
index a083a7853f..27823e7f54 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,3 @@
-# ignore svn directories
-**/.svn/**
-.svn/
-
 # netcdf files
 *.nc
 # but don't ignore netcdf files here:
diff --git a/README b/README
index 4d33638e7e..8b4e15e557 100644
--- a/README
+++ b/README
@@ -49,7 +49,7 @@ src --------------- CTSM Source code.
 lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
-bin/git-fleximod -- Script to manage the external source directories
+bin/git-fleximod -- Script to manage the needed sub-component source directories (handled with git submodule)
 py_env_create ----- Script to setup the python environment for CTSM python tools using conda
 python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts
 
diff --git a/README_GITFLEXIMOD.rst b/README_GITFLEXIMOD.rst
index ab8c412cee..de6bbf392f 100644
--- a/README_GITFLEXIMOD.rst
+++ b/README_GITFLEXIMOD.rst
@@ -9,7 +9,7 @@ To obtain the CTSM code you need to do the following:
 
 #. Clone the repository. ::
 
-      git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
+      git clone https://github.com/ESCOMP/CTSM.git my_ctsm_sandbox
 
    This will create a directory ``my_ctsm_sandbox/`` in your current working directory.
 
@@ -25,6 +25,10 @@ To obtain the CTSM code you need to do the following:
    Additional documentation for git-fleximod appears here:
    https://github.com/ESMCI/git-fleximod?tab=readme-ov-file#git-fleximod
 
+"components" here refers to seperate git repositories for seperable parts of 
+the code (such as the MOSART or mizuRoute river models). Because they are
+managed with "submodule" in git hereafter we will refer to them as "submodule(s)".
+
 At this point you have a working version of CTSM.
 
 To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ .
@@ -33,19 +37,19 @@ More details on git-fleximod
 ----------------------------
 
 The file **.gitmodules** in your top-level CTSM directory tells
-**git-fleximod** which tag/branch of each component should be
-brought in to generate your sandbox.
+**git-fleximod** which tag/branch of each submodule
+should be brought in to generate your sandbox.
 
-NOTE: If you manually modify an external without updating .gitmodules,
+NOTE: If you manually modify a submodule without updating .gitmodules,
 e.g. switch to a different tag, then rerunning git-fleximod will warn you of
 local changes you need to resolve.
-git-fleximod will not change a modified external back to what is specified in
+git-fleximod will not change a modified submodule back to what is specified in
 .gitmodules without the --force option.
 See below documentation `Customizing your CTSM sandbox`_ for more details.
 
 **You need to rerun git-fleximod whenever .gitmodules has
 changed** (unless you have already manually updated the relevant
-external(s) to have the correct branch/tag checked out). Common times
+submodule(s) to have the correct branch/tag checked out). Common times
 when this is needed are:
 
 * After checking out a new CTSM branch/tag
@@ -74,7 +78,7 @@ changes, or if you have any ongoing CTSM cases that were created from
 this sandbox. In these cases, it is often easiest to do a second **git
 clone**.
 
-Pointing to a different version of a component
+Pointing to a different version of a submodule
 ----------------------------------------------
 
 Each entry in **.gitmodules** has the following form (we use CIME as an
@@ -92,11 +96,11 @@ Each entry specifies either a tag or a hash. To point to a new tag or hash:
 #. Modify the relevant entry/entries in **.gitmodules** (e.g., changing
    ``cime6.0.246`` to ``cime6.0.247`` above)
 
-#. Checkout the new component(s)::
+#. Checkout the new submodule(s)::
 
-     ./bin/git-fleximod update <component>
+     ./bin/git-fleximod update <submodule>
 
-Keep in mind that changing individual components from a tag may result
+Keep in mind that changing individual submodule from a tag may result
 in an invalid model (won't compile, won't run, not scientifically
 meaningful) and is unsupported.
 
@@ -105,11 +109,10 @@ Committing your change to .gitmodules
 
 After making this change, it's a good idea to commit the change in your
 local CTSM git repository. First create a branch in your local
-repository, then commit it. (Unlike with subversion, branches are stored
-locally unless you explicitly push them up to GitHub. Feel free to
-create whatever local branches you'd like.) For example::
+repository, then commit it.  Feel free to create whatever local branches
+you'd like in git. For example::
 
   git checkout -b my_ctsm_branch
   git add .gitmodules
-  git commit -m "Update CIME to cime5.4.0-alpha.20"
+  git commit -m "Update CIME to cime6.0.247"
 
diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 23e481222b..8b898a0627 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -272,7 +272,7 @@
     </phase>
   </test>
 
-  <!-- Other external test list failures (MOSART, RTM, etc. -->
+  <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 
   <test name="SMS_Lh3.f10_f10_mg37.I2000Clm51Sp.derecho_intel.mosart-clmAccelSpinupIgnoreWarn">
     <phase name="CREATE_NEWCASE">
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 1ac2334ba8..b40f00d5a6 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2913,7 +2913,7 @@
       <machine name="derecho" compiler="intel" category="prealpha">
         <options>
           <option name="wallclock">00:40:00</option>
-          <option name="comment">Run prealpha for this test as mksurfdata_esmf is tightly coupled to externals and we want to catch issues with externals for it ASAP.</option>
+          <option name="comment">Run prealpha for this test as mksurfdata_esmf is tightly coupled to submodule updates and we want to catch issues with submodules for it ASAP.</option>
         </options>
       </machine>
     </machines>
diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams
index 35071ff415..29a8c675ac 100644
--- a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams
+++ b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams
@@ -21,7 +21,7 @@
 !   foo:year_first = 1950
 ! would change the stream year_first stream_entry to 1950 for the foo stream block
 !------------------------------------------------------------------------
-! This will come out when cdeps externals are updated
+! This will come out when the cdeps submodule are updated
 CLM_USRDAT.PLUMBER2:datavars = ZBOT     Sa_z, \
         TBOT     Sa_tbot, \
         QBOT     Sa_shum, \
diff --git a/doc/README.CHECKLIST.master_tags b/doc/README.CHECKLIST.master_tags
index 0da52acaaa..51386c4238 100644
--- a/doc/README.CHECKLIST.master_tags
+++ b/doc/README.CHECKLIST.master_tags
@@ -14,7 +14,7 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow
    2a -- run 'git pull' to pull in the latest version from GitHub
    2b -- run 'git status' and/or 'git diff' to make sure you don't have any uncommitted
          local changes
-   2c -- run './bin/git-fleximod status' to make sure all externals are
+   2c -- run './bin/git-fleximod status' to make sure all submodules are
          updated and don't have any uncommitted changes. If any are marked with 's' in
          the first column, run './bin/git-fleximod update'.
 
@@ -26,7 +26,7 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow
         $EDITOR cime_config/testdefs/ExpectedTestFails.xml
    3c -- make sure you understand any changes to the baselines -- to document in ChangeLog
    3d -- Check the log file for run_sys_tests (../run_sys_test.log), to make sure that 
-         externals are correct (see 2c above)
+         submodules are correct (see 2c above)
 
 (4) Use diff and status to make sure any new files are in the repo and only the correct
     changes are on the branch
diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py
index ecea2342a7..f5a7ed04dc 100644
--- a/python/ctsm/run_sys_tests.py
+++ b/python/ctsm/run_sys_tests.py
@@ -124,7 +124,7 @@ def run_sys_tests(
     cime_path (str): path to root of cime
     skip_testroot_creation (bool): if True, assume the testroot directory has already been
         created, so don't try to recreate it or re-make the link to it
-    skip_git_status (bool): if True, skip printing git and manage_externals status
+    skip_git_status (bool): if True, skip printing git and git-fleximod status
     dry_run (bool): if True, print commands to be run but don't run them
     suite_name (str): name of test suite/category to run
     testfile (str): path to file containing list of tests to run
@@ -476,11 +476,11 @@ def _commandline_args():
     parser.add_argument(
         "--skip-git-status",
         action="store_true",
-        help="Skip printing git and manage_externals status,\n"
+        help="Skip printing git and git-fleximod status,\n"
         "both to screen and to the SRCROOT_GIT_STATUS file in TESTROOT.\n"
         "This printing can often be helpful, but this option can be used to\n"
         "avoid extraneous output, to reduce the time needed to run this script,\n"
-        "or if git or manage_externals are currently broken in your sandbox.\n",
+        "or if git or git-fleximod are currently broken in your sandbox.\n",
     )
 
     parser.add_argument(
diff --git a/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py b/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py
index 5038c6b3e1..8b8e2df32a 100755
--- a/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py
+++ b/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py
@@ -136,7 +136,7 @@ def test_simple_derecho_args(self):
     def test_derecho_mpirun(self):
         """
         test derecho mpirun. This would've helped caught a problem we ran into
-        It will also be helpful when externals are updated to guide to solutions
+        It will also be helpful when sumodules are updated to guide to solutions
         to problems
         """
         machine = "derecho"
diff --git a/tools/mksurfdata_esmf/README.md b/tools/mksurfdata_esmf/README.md
index 3d19c88ff0..a9c0b80de6 100644
--- a/tools/mksurfdata_esmf/README.md
+++ b/tools/mksurfdata_esmf/README.md
@@ -41,7 +41,7 @@ In addition for the build: python, bash-shell, CMake and GNU-Make are required
 These libraries need to be built such that they can all work together in the
 same executable. Hence, the above order may be required in building them.
 
-CTSM externals that are required are: cime and ccs_config. See [Building](#building-the-executable) on getting
+CTSM submodules that are required are: cime and ccs_config. See [Building](#building-the-executable) on getting
 those. A python environment that includes particular packages is also required
 we demonstrate how to use the ctsm_pylib environment that we support in CTSM.
 

From e65c2034682afd9e5024361415c9002f8d82ca60 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 7 Jun 2024 13:49:07 -0600
Subject: [PATCH 0469/1248] Start the changelog

---
 doc/ChangeLog | 90 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 91 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8b6bb8f0d2..4600af34be 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,94 @@
 ===============================================================
+Tag name: ctsm5.2.008
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Fri 07 Jun 2024 01:23:07 PM MDT
+One-line Summary: Another update of git-fleximod
+
+Purpose and description of changes
+----------------------------------
+
+Just update the gitfleximod subtree to v0.7.7. This fixes an issue in identifying that a tag is out of sync in a submodule.
+An issue about recursion on a submodule. Allows untracked files, and fixes a MS Window Memory error.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed:
+  Fixes #2591 -- Start using submodule rather than external
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+   doc-builder checkout seems to be required to use "git commit ." at the top level
+
+Changes to documentation:
+   Tweak some of the documentation around git-fleximod and use submodule rather than external.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+
+Testing summary: minimual
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho -
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    (any machine) -
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho -----
+    izumi -------
+
+  any other testing (give details below):
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   git-fleximod subtree updated
+
+Pull Requests that document the changes (include PR ids):
+  #2577 -- Update git-fleximod
+(https://github.com/ESCOMP/ctsm/pull)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.007
 Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD)
 Date: Fri 31 May 2024 13:49:29 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index b3f1632571..275c4a5cfa 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.008     erik 06/07/2024 Another update of git-fleximod
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems

From dfebe5fdbdce10ba25cbdc6419c95f41f82f3848 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Fri, 7 Jun 2024 14:08:42 -0600
Subject: [PATCH 0470/1248] Remove user_nl_clm (added in 5431850) and replace 2
 NIWO tests with HARV

---
 cime_config/testdefs/ExpectedTestFails.xml      | 17 +----------------
 cime_config/testdefs/testlist_clm.xml           |  6 +++---
 cime_config/usermods_dirs/NEON/NIWO/user_nl_clm |  8 --------
 3 files changed, 4 insertions(+), 27 deletions(-)
 delete mode 100644 cime_config/usermods_dirs/NEON/NIWO/user_nl_clm

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 03f60ad824..5968e73760 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -78,15 +78,11 @@
     </phase>
   </test>
 
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-default--clm-NEON-NIWO">
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-default--clm-NEON-HARV">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
       <issue>#2310</issue>
     </phase>
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
   </test>
   
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-NEON-MOAB--clm-PRISM">
@@ -100,17 +96,6 @@
     </phase>
   </test>
   
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
-    <phase name="SHAREDLIB_BUILD">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
-  </test>
-  
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 782af8bc34..9a2390bd58 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2257,7 +2257,7 @@
       <option name="comment">Want to keep a little single-point testing on HPC machines</option>
     </options>
   </test>
-  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/NIWO">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/HARV">
     <machines>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
@@ -2268,7 +2268,7 @@
       <option name="comment"  >Add at least one test of a NEON site</option>
     </options>
   </test>
-  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/NIWO--clm/matrixcnOn">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/HARV--clm/matrixcnOn">
     <machines>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
@@ -2276,7 +2276,7 @@
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="tput_tolerance">0.5</option>
-      <option name="comment"  >Repeat SMS_Ld10_D_Mmpi-serial...NIWO test with matrixcnOn</option>
+      <option name="comment"  >Repeat SMS_Ld10_D_Mmpi-serial...HARV test with matrixcnOn</option>
     </options>
   </test>
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60SpRs" testmods="clm/default--clm/NEON/TOOL">
diff --git a/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm b/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm
deleted file mode 100644
index cf427d738b..0000000000
--- a/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm
+++ /dev/null
@@ -1,8 +0,0 @@
-! 20240604 slevis introduced this file to bypass test failures in the
-! cnmatrix branch (so cnmatrix on by default) with two izumi tests:
-! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO--clm-matrixcnOn
-! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO
-! when the tests point to the default finidat, as documented in this post:
-! https://github.com/ESCOMP/CTSM/pull/640#issuecomment-2143101361
-use_init_interp = .true.
-finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc'

From 3041578054a85aba53840a421987cce6b9c4b887 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 10 Jun 2024 09:53:12 -0600
Subject: [PATCH 0471/1248] Move stream_gdd20_seasons stuff to controlMod.

---
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 src/cpl/share_esmf/cropcalStreamMod.F90         | 3 ---
 src/main/controlMod.F90                         | 4 +++-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 675c912900..b510b14ccb 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1839,7 +1839,7 @@ Filename of input stream data for baseline GDD20 values
 </entry>
 
 <entry id="stream_gdd20_seasons" type="logical" category="datasets"
-       group="cropcal_streams" valid_values="" >
+       group="clm_inparm" valid_values="" >
 Set this to true to read gdd20 accumulation season start and end dates from stream files, rather than using hard-coded hemisphere-specific "warm seasons."
 </entry>
 
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 80314ee947..939ef67c91 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -113,7 +113,6 @@ subroutine cropcal_init(bounds)
          stream_meshfile_cropcal, &
          cropcals_rx, &
          cropcals_rx_adapt, &
-         stream_gdd20_seasons, &
          allow_invalid_gdd20_season_inputs, &
          stream_fldFileName_gdd20_season_start, &
          stream_fldFileName_gdd20_season_end
@@ -131,7 +130,6 @@ subroutine cropcal_init(bounds)
     stream_fldFileName_swindow_end   = ''
     stream_fldFileName_cultivar_gdds = ''
     stream_fldFileName_gdd20_baseline = ''
-    stream_gdd20_seasons = .false.
     allow_invalid_gdd20_season_inputs = .false.
     stream_fldFileName_gdd20_season_start = ''
     stream_fldFileName_gdd20_season_end = ''
@@ -175,7 +173,6 @@ subroutine cropcal_init(bounds)
     call shr_mpi_bcast(stream_fldFileName_cultivar_gdds, mpicom)
     call shr_mpi_bcast(stream_fldFileName_gdd20_baseline, mpicom)
     call shr_mpi_bcast(stream_meshfile_cropcal    , mpicom)
-    call shr_mpi_bcast(stream_gdd20_seasons, mpicom)
     call shr_mpi_bcast(allow_invalid_gdd20_season_inputs, mpicom)
     call shr_mpi_bcast(stream_fldFileName_gdd20_season_start, mpicom)
     call shr_mpi_bcast(stream_fldFileName_gdd20_season_end, mpicom)
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 46d9e9958a..aabe753769 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -302,7 +302,7 @@ subroutine control_init(dtime)
          use_lch4, use_nitrif_denitrif, use_extralakelayers, &
          use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, &
          use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, &
-         use_nguardrail, crop_residue_removal_frac
+         use_nguardrail, crop_residue_removal_frac, stream_gdd20_seasons
 
     ! SNICAR
     namelist /clm_inparm/ &
@@ -711,6 +711,7 @@ subroutine control_spmd()
     call mpi_bcast (use_cndv, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_nguardrail, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_crop, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (stream_gdd20_seasons, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fertilizer, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_grainproduct, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (crop_residue_removal_frac, 1, MPI_REAL8, 0, mpicom, ier)
@@ -983,6 +984,7 @@ subroutine control_print ()
     write(iulog,*) '    use_cn = ', use_cn
     write(iulog,*) '    use_cndv = ', use_cndv
     write(iulog,*) '    use_crop = ', use_crop
+    write(iulog,*) '    stream_gdd20_seasons = ', stream_gdd20_seasons
     write(iulog,*) '    use_fertilizer = ', use_fertilizer
     write(iulog,*) '    use_grainproduct = ', use_grainproduct
     write(iulog,*) '    crop_residue_removal_frac = ', crop_residue_removal_frac

From 801fa0149668da07902da55ba14c217c30c2a08d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 10 Jun 2024 10:45:00 -0600
Subject: [PATCH 0472/1248] CLMBuildNamelist: Always set
 stream_meshfile_cropcal.

---
 bld/CLMBuildNamelist.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index d5c2ffd54f..8bffec0d46 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4178,6 +4178,7 @@ sub setup_logic_cropcal_streams {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_gdd20_seasons');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal');
 
   # These can't both be true
   my $cropcals_rx = $nl->get_value('cropcals_rx') ;
@@ -4208,7 +4209,6 @@ sub setup_logic_cropcal_streams {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_start');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_end');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal');
     if ( &value_is_true($cropcals_rx_adapt) ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline');
     }
@@ -4220,7 +4220,7 @@ sub setup_logic_cropcal_streams {
   my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ;
   my $gdd20_baseline_file = $nl->get_value('stream_fldFileName_gdd20_baseline') ;
   my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ;
-  if ( !&string_is_undef_or_empty($swindow_start_file) or !&string_is_undef_or_empty($swindow_end_file) or !&string_is_undef_or_empty($gdd_file) or !&string_is_undef_or_empty($gdd20_baseline_file) or !&string_is_undef_or_empty($mesh_file)) {
+  if ( !&string_is_undef_or_empty($swindow_start_file) or !&string_is_undef_or_empty($swindow_end_file) or !&string_is_undef_or_empty($gdd_file) or !&string_is_undef_or_empty($gdd20_baseline_file)) {
 
     # User gave an input file without specifying cropcals_rx or cropcals_rx_adapt = .true.
     # Requiring this means nothing to the code, but helps namelist make more sense

From dcff4f8eb9217ad9ad340957ddf7d5f01698c8dc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 10 Jun 2024 11:10:32 -0600
Subject: [PATCH 0473/1248] Set gdd20 season start/end NaNs to -1.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 939ef67c91..0a04278aa9 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -744,7 +744,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
            ! If read-in value is invalid, set to -1. Will be handled later in this subroutine.
            if (dataptr1d_gdd20_season_start(g) <= 0 .or. dataptr1d_gdd20_season_start(g) > 366 &
-               .or. dataptr1d_gdd20_season_end(g) <= 0 .or. dataptr1d_gdd20_season_end(g) > 366) then
+               .or. dataptr1d_gdd20_season_end(g) <= 0 .or. dataptr1d_gdd20_season_end(g) > 366 &
+               .or. dataptr1d_gdd20_season_start(g) /= dataptr1d_gdd20_season_start(g) &
+               .or. dataptr1d_gdd20_season_end(g) /= dataptr1d_gdd20_season_end(g)) then
               dataptr1d_gdd20_season_start(g) = -1
               dataptr1d_gdd20_season_end  (g) = -1
            end if

From fbe292d49b348ee0649527497b86ab8810222361 Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Mon, 10 Jun 2024 11:34:50 -0600
Subject: [PATCH 0474/1248] removing c13 from allvars until it is fixed

---
 .../testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
index a426c775b0..92434df000 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
@@ -26,7 +26,7 @@ hist_fincl1       = 'FATES_TLONGTERM',
 'FATES_MORTALITY_CROWNSCORCH_SZPF','FATES_MORTALITY_CAMBIALBURN_SZPF','FATES_MORTALITY_TERMINATION_SZPF',
 'FATES_MORTALITY_LOGGING_SZPF','FATES_MORTALITY_FREEZING_SZPF','FATES_MORTALITY_SENESCENCE_SZPF',
 'FATES_MORTALITY_AGESCEN_SZPF','FATES_MORTALITY_AGESCEN_ACPF','FATES_MORTALITY_CANOPY_SZPF',
-'FATES_M3_MORTALITY_CANOPY_SZPF','FATES_M3_MORTALITY_USTORY_SZPF','FATES_C13DISC_SZPF',
+'FATES_M3_MORTALITY_CANOPY_SZPF','FATES_M3_MORTALITY_USTORY_SZPF',
 'FATES_STOREC_CANOPY_SZPF','FATES_LEAFC_CANOPY_SZPF','FATES_LAI_CANOPY_SZPF','FATES_CROWNAREA_CANOPY_SZPF',
 'FATES_CROWNAREA_USTORY_SZPF','FATES_NPLANT_CANOPY_SZPF','FATES_MORTALITY_USTORY_SZPF','FATES_STOREC_USTORY_SZPF',
 'FATES_LEAFC_USTORY_SZPF','FATES_LAI_USTORY_SZPF','FATES_NPLANT_USTORY_SZPF','FATES_CWD_ABOVEGROUND_DC',

From be904a7da1b5ee182f2dde09c3efa50f69d43dc1 Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Mon, 10 Jun 2024 11:39:32 -0600
Subject: [PATCH 0475/1248] using flush_allvars

---
 src/utils/clmfates_interfaceMod.F90 | 49 ++---------------------------
 1 file changed, 2 insertions(+), 47 deletions(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 98845f8e62..a405850004 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -1973,29 +1973,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, &
                ! not overwright values outside the columns that it is in charge of.
                ! ------------------------------------------------------------------------
 
-               ! tbd: fates_hist%flush_all_hvars(nc)    
-               
-               if_dim1: if(fates_history_dimlevel(1)>0) then
-                  call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_simple)
-                  if (use_fates_planthydro) then
-                     call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_simple)
-                  end if
-                  if(fates_history_dimlevel(1)>1) then
-                     call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_complx)
-                     if (use_fates_planthydro) then
-                        call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_complx)
-                     end if
-                  end if
-               end if if_dim1
-               
-               if_dim2: if(fates_history_dimlevel(2)>0) then
-                  call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-                  call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_simple)
-                  if(fates_history_dimlevel(2)>1) then
-                     call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-                     call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_complx)
-                  end if
-               end if if_dim2
+               call fates_hist%flush_all_hvars(nc)    
                
                call fates_hist%update_history_dyn( nc,                     &
                                                    this%fates(nc)%nsites,  &
@@ -2181,30 +2159,7 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, &
            ! We also start off by setting all values on FATES columns to zero.
            ! ------------------------------------------------------------------------
 
-           ! tbd: fates_hist%flush_all_hvars(nc)
-           
-           if_dim1: if(fates_history_dimlevel(1)>0) then
-              call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_simple)
-              if (use_fates_planthydro) then
-                 call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_simple)
-              end if
-              if(fates_history_dimlevel(1)>1) then
-                 call fates_hist%flush_hvars(nc,upfreq_in=group_hifr_complx)
-                 if (use_fates_planthydro) then
-                    call fates_hist%flush_hvars(nc,upfreq_in=group_hydr_complx)
-                 end if
-              end if
-           end if if_dim1
-           
-           if_dim2: if(fates_history_dimlevel(2)>0) then
-              call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-              call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_simple)
-              if(fates_history_dimlevel(2)>1) then
-                 call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-                 call fates_hist%flush_hvars(nc,upfreq_in=group_nflx_complx)
-              end if
-           end if if_dim2
-
+           call fates_hist%flush_all_hvars(nc)
            
            call fates_hist%update_history_dyn( nc,                     &
                 this%fates(nc)%nsites,                                  &

From 34d7be9d8a8d5355a709a67871f4d38e0e2f14ca Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Mon, 10 Jun 2024 11:40:26 -0600
Subject: [PATCH 0476/1248] removing unused use statements

---
 src/utils/clmfates_interfaceMod.F90 | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index a405850004..e97d9b3e37 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -134,10 +134,6 @@ module CLMFatesInterfaceMod
    use FatesParametersInterface, only : fates_parameters_type
 
    use FatesInterfaceMod     , only : DetermineGridCellNeighbors
-   use FatesIOVariableKindMod, only : group_dyna_simple, group_dyna_complx
-   use FatesIOVariableKindMod, only : group_hifr_simple, group_hifr_complx
-   use FatesIOVariableKindMod, only : group_nflx_simple, group_nflx_complx
-   use FatesIOVariableKindMod, only : group_hydr_simple, group_hydr_complx
    use FatesHistoryInterfaceMod, only : fates_hist
    use FatesRestartInterfaceMod, only : fates_restart_interface_type
 

From c4ef0e73c4139e485d10303a1b19d58ef7be145b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 10 Jun 2024 11:54:12 -0600
Subject: [PATCH 0477/1248] UpdateAccVars_CropGDDs: Skip non-crops.

---
 src/biogeophys/TemperatureType.F90 | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 1f6d0958c6..1e60293fe3 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1403,6 +1403,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use accumulMod       , only : update_accum_field, extract_accum_field, markreset_accum_field
     use clm_time_manager , only : is_doy_in_interval
+    use pftconMod        , only : npcropmin
     use CropType, only : crop_type
     !
     ! !ARGUMENTS
@@ -1420,6 +1421,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     character(8) :: field_name   ! E.g., GDD0
     character(32) :: format_string
     integer :: p
+    integer :: ivt  ! vegetation type
     logical :: in_accumulation_season
     real(r8) :: lat  ! latitude
     integer :: gdd20_season_start, gdd20_season_end
@@ -1451,8 +1453,9 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
 
     do p = begp,endp
 
-       ! Avoid unnecessary calculations over inactive points
-       if (.not. patch%active(p)) then
+       ! Avoid unnecessary calculations over inactive points and non-crops
+       ivt = patch%itype(p)
+       if (ivt < npcropmin .or. .not. patch%active(p)) then
           cycle
        end if
 

From b90789ba3d6a6f675e706bb26efa346e03d17ea2 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 10 Jun 2024 11:55:58 -0600
Subject: [PATCH 0478/1248] use_cropcal_streams now includes gdd20 dates.

---
 src/biogeochem/CNPhenologyMod.F90       |  8 ++++----
 src/cpl/share_esmf/cropcalStreamMod.F90 | 10 ++++++++--
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index cfeee0b867..b0cc280e7e 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -1811,7 +1811,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp                     , &
     use clm_varctl       , only : use_fertilizer 
     use clm_varctl       , only : use_c13, use_c14
     use clm_varcon       , only : c13ratio, c14ratio
-    use clm_varctl       , only : use_cropcal_rx_swindows, use_cropcal_streams
+    use clm_varctl       , only : use_cropcal_rx_swindows
     !
     ! !ARGUMENTS:
     integer                        , intent(in)    :: num_pcropp       ! number of prog crop patches in filter
@@ -2245,7 +2245,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp                     , &
                 do_harvest = .true.
                 fake_harvest = .true.
                 harvest_reason = HARVEST_REASON_SOWNBADDEC31
-            else if (use_cropcal_streams .and. do_plant .and. .not. did_plant) then
+            else if (use_cropcal_rx_swindows .and. do_plant .and. .not. did_plant) then
                 ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested.
                 do_harvest = .true.
                 harvest_reason = HARVEST_REASON_SOWTODAY
@@ -2562,7 +2562,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
 
     ! !USES:
     use clm_varctl       , only : use_c13, use_c14
-    use clm_varctl       , only : use_cropcal_rx_cultivar_gdds, use_cropcal_streams, adapt_cropcal_rx_cultivar_gdds
+    use clm_varctl       , only : use_cropcal_rx_cultivar_gdds, adapt_cropcal_rx_cultivar_gdds
     use clm_varcon       , only : c13ratio, c14ratio
     use clm_varpar       , only : mxsowings
     use pftconMod        , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean
@@ -2726,7 +2726,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
 
       endif
 
-      if (use_cropcal_streams .and. gddmaturity(p) < min_gddmaturity) then
+      if (use_cropcal_rx_cultivar_gdds .and. gddmaturity(p) < min_gddmaturity) then
           if (did_rx_gdds) then
               write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')'
           endif
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 0a04278aa9..a352c7af97 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -209,9 +209,11 @@ subroutine cropcal_init(bounds)
     use_cropcal_rx_swindows      = stream_fldFileName_swindow_start /= ''
     use_cropcal_rx_cultivar_gdds = stream_fldFileName_cultivar_gdds /= ''
     adapt_cropcal_rx_cultivar_gdds = stream_fldFileName_gdd20_baseline /= ''
-    use_cropcal_streams = use_cropcal_rx_swindows .or. use_cropcal_rx_cultivar_gdds
+    use_cropcal_streams = .false.  ! Will be set to true if any file is read
 
     if (use_cropcal_rx_swindows) then
+       use_cropcal_streams = .true.
+
        ! Initialize the cdeps data type sdat_cropcal_swindow_start
        ! NOTE: stream_dtlimit 1.5 didn't work for some reason
        call shr_strdata_init_from_inline(sdat_cropcal_swindow_start,  &
@@ -270,6 +272,7 @@ subroutine cropcal_init(bounds)
     ! Initialize the cdeps data type sdat_cropcal_cultivar_gdds
     ! NOTE: stream_dtlimit 1.5 didn't work for some reason
     if (use_cropcal_rx_cultivar_gdds) then
+       use_cropcal_streams = .true.
        call shr_strdata_init_from_inline(sdat_cropcal_cultivar_gdds,  &
             my_task             = iam,                                &
             logunit             = iulog,                              &
@@ -301,6 +304,7 @@ subroutine cropcal_init(bounds)
     ! particular year chosen doesn't matter. Users can base their file on whatever baseline they
     ! want; they just need to put 2000 on the time axis.
     if (adapt_cropcal_rx_cultivar_gdds) then
+       use_cropcal_streams = .true.
        call shr_strdata_init_from_inline(sdat_cropcal_gdd20_baseline,  &
             my_task             = iam,                                &
             logunit             = iulog,                              &
@@ -328,7 +332,9 @@ subroutine cropcal_init(bounds)
     end if
 
     if (stream_gdd20_seasons) then
-      ! Initialize the cdeps data type sdat_cropcal_gdd20_season_start
+       use_cropcal_streams = .true.
+
+       ! Initialize the cdeps data type sdat_cropcal_gdd20_season_start
       ! NOTE: Hard-coded to one particular year because it should NOT vary over time. Note that the
       ! particular year chosen doesn't matter.
       call shr_strdata_init_from_inline(sdat_cropcal_gdd20_season_start,  &

From 0ffbd07da2c02561bfbcdbf6048c85547575159e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 10 Jun 2024 12:02:46 -0600
Subject: [PATCH 0479/1248] Handle invalid gdd20_season_start and _end
 separately.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index a352c7af97..69c529be24 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -750,10 +750,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
            ! If read-in value is invalid, set to -1. Will be handled later in this subroutine.
            if (dataptr1d_gdd20_season_start(g) <= 0 .or. dataptr1d_gdd20_season_start(g) > 366 &
-               .or. dataptr1d_gdd20_season_end(g) <= 0 .or. dataptr1d_gdd20_season_end(g) > 366 &
-               .or. dataptr1d_gdd20_season_start(g) /= dataptr1d_gdd20_season_start(g) &
-               .or. dataptr1d_gdd20_season_end(g) /= dataptr1d_gdd20_season_end(g)) then
+               .or. dataptr1d_gdd20_season_start(g) /= dataptr1d_gdd20_season_start(g)) then
               dataptr1d_gdd20_season_start(g) = -1
+           end if
+           if (dataptr1d_gdd20_season_end(g) <= 0 .or. dataptr1d_gdd20_season_end(g) > 366 &
+               .or. dataptr1d_gdd20_season_end(g) /= dataptr1d_gdd20_season_end(g)) then
               dataptr1d_gdd20_season_end  (g) = -1
            end if
 

From 2ebe85d51e44503c1e33c42635bbddc16488048f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 11 Jun 2024 11:46:28 -0600
Subject: [PATCH 0480/1248] Fix restartvar() for flush_gdd20.

---
 src/biogeophys/TemperatureType.F90 | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 1e60293fe3..831c99d9bf 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -911,7 +911,7 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     ! !LOCAL VARIABLES:
     integer :: j,c,p     ! indices
     logical :: readvar   ! determine if variable is on initial file
-    integer, pointer :: logical_as_int(:) ! used for saving/reading logicals
+    integer :: idata
     !-----------------------------------------------------------------------
 
     call restartvar(ncid=ncid, flag=flag, varname='T_SOISNO', xtype=ncd_double,   &
@@ -1137,26 +1137,23 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     end if
 
     if (use_crop .and. stream_gdd20_seasons) then
-       allocate(logical_as_int(1))
        if (flag == 'write') then
           if (this%flush_gdd20) then
-             logical_as_int(1) = 1
+             idata = 1
           else
-             logical_as_int(1) = 0
+             idata = 0
           end if
        end if
-       call restartvar(ncid=ncid, flag=flag,  varname='flush_gdd20', xtype=ncd_log,  &
-            dim1name='pft', &
+       call restartvar(ncid=ncid, flag=flag,  varname='flush_gdd20', xtype=ncd_int,  &
             long_name='Flag indicating that GDD20 values need to be flushed', &
-            units='none', interpinic_flag='interp', readvar=readvar, data=logical_as_int)
+            units='none', interpinic_flag='copy', readvar=readvar, data=idata)
        if (flag == 'read') then
-          if (readvar .and. logical_as_int(1) == 0) then
+          if (readvar .and. idata == 0) then
              this%flush_gdd20 = .false.
           else
              this%flush_gdd20 = .true.
           end if
        end if
-       deallocate(logical_as_int)
     end if
 
 

From 628be7bd39fb48acab7a456504be05c424f4510f Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 11 Jun 2024 12:20:30 -0700
Subject: [PATCH 0481/1248] temporarily update fates to point to latest pull
 request commit hash

---
 .gitmodules | 4 ++--
 src/fates   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 699ad22969..5b679e62bf 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,7 +1,7 @@
 [submodule "fates"]
 path = src/fates
-url = https://github.com/NGEET/fates
-fxtag = sci.1.73.0_api.35.0.0
+url = https://github.com/ckoven/fates
+fxtag = 4b018eade498d063b21dddf26f77c9658ff80261
 fxrequired = AlwaysRequired
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
 
diff --git a/src/fates b/src/fates
index adfa664806..4b018eade4 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit adfa6648063408d443f5cae671bd37f713d3e3e8
+Subproject commit 4b018eade498d063b21dddf26f77c9658ff80261

From e9531dee57adcf9d997eb703a544e5c3656d99b0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 10:44:46 -0600
Subject: [PATCH 0482/1248] Add RXCROPMATURITYSKIPBUILD test.

---
 cime_config/SystemTests/rxcropmaturityskipbuild.py |  9 +++++++++
 cime_config/config_tests.xml                       | 10 ++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 cime_config/SystemTests/rxcropmaturityskipbuild.py

diff --git a/cime_config/SystemTests/rxcropmaturityskipbuild.py b/cime_config/SystemTests/rxcropmaturityskipbuild.py
new file mode 100644
index 0000000000..4c3a69fb47
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityskipbuild.py
@@ -0,0 +1,9 @@
+from rxcropmaturityshared import RXCROPMATURITYSHARED
+
+class RXCROPMATURITYSKIPBUILD(RXCROPMATURITYSHARED):
+    def build_indv(self, sharedlib_only=False, model_only=False):
+        self._case.set_value("BUILD_COMPLETE", "TRUE")
+
+
+    def run_phase(self):
+        self._run_phase(skip_run=False)
\ No newline at end of file
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index 98434da10e..115f4c0e89 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -143,6 +143,16 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="RXCROPMATURITYSKIPBUILD">
+    <DESC>As RXCROPMATURITY but don't actually build; just setup and then start "run." Will fail when run start is requested, but should successfully test preprocessing.</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

From 4144ac99d4a1e1457b36a6cb12ca2adc00dc5dc4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 10:47:09 -0600
Subject: [PATCH 0483/1248] RXCROPMATURITY: copy .env_mach_specific.sh to
 gddgen dir.

---
 cime_config/SystemTests/rxcropmaturityshared.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
index cc4282f5c5..0811b5bc69 100644
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -138,6 +138,12 @@ def _run_phase(self, skip_run=False):
             # Download files from the server, if needed
             case_gddgen.check_all_input_data()
 
+            # Copy needed file from original to gddgen directory
+            shutil.copyfile(
+                os.path.join(caseroot, ".env_mach_specific.sh"),
+                os.path.join(self._path_gddgen, ".env_mach_specific.sh"),
+            )
+
             # Make custom version of surface file
             logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
             self._run_fsurdat_modifier()

From 9f0b7ba69ca23aa3b8b8f7ad228d318422d47dc1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 11:47:38 -0600
Subject: [PATCH 0484/1248] Add missing commas to RXCROPMATURITYSHARED.

---
 .../SystemTests/rxcropmaturityshared.py       | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
index 0811b5bc69..7fa3a2f1bd 100644
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -118,7 +118,7 @@ def _run_phase(self, skip_run=False):
         self._append_to_user_nl_clm(
             [
                 "generate_crop_gdds = .true.",
-                "stream_fldFileName_cultivar_gdds = ''"
+                "stream_fldFileName_cultivar_gdds = ''",
                 "use_mxmat = .false.",
                 " ",
                 "! (h2) Daily outputs for GDD generation and figure-making",
@@ -299,16 +299,16 @@ def _run_fsurdat_modifier(self):
                 tool_path,
             )
 
-        # Modify namelist
-        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
-        self._append_to_user_nl_clm(
-            [
-                "fsurdat = '{}'".format(self._fsurdat_out),
-                "do_transient_crops = .false.",
-                "flanduse_timeseries = ''",
-                "use_init_interp = .true.",
-            ]
-        )
+        # # Modify namelist
+        # logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
+        # self._append_to_user_nl_clm(
+        #     [
+        #         "fsurdat = '{}'".format(self._fsurdat_out),
+        #         "do_transient_crops = .false.",
+        #         "flanduse_timeseries = ''",
+        #         "use_init_interp = .true.",
+        #     ]
+        # )
 
     def _create_config_file_evenlysplitcrop(self):
         """
@@ -371,7 +371,7 @@ def _run_check_rxboth_run(self):
 
     def _modify_user_nl_allruns(self):
         nl_additions = [
-            "cropcals_rx = .true."
+            "cropcals_rx = .true.",
             "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
             "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
             "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),

From 874520649f0e015b5abfcf455d82262c6e860887 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 13:52:23 -0600
Subject: [PATCH 0485/1248] PlantCrop: Error if gddmaturity(p) <
 min_gddmaturity but use_cropcal_rx_cultivar_gdds false.

---
 src/biogeochem/CNPhenologyMod.F90 | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index b0cc280e7e..46d155d2d4 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2726,12 +2726,17 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
 
       endif
 
-      if (use_cropcal_rx_cultivar_gdds .and. gddmaturity(p) < min_gddmaturity) then
-          if (did_rx_gdds) then
-              write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')'
-          endif
-          gddmaturity(p) = min_gddmaturity
-      endif
+      if (gddmaturity(p) < min_gddmaturity) then
+         if (use_cropcal_rx_cultivar_gdds) then
+             if (did_rx_gdds) then
+                 write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')'
+             end if
+             gddmaturity(p) = min_gddmaturity
+         else
+            write(iulog, *) 'ERROR: PlantCrop(): gddmaturity < minimum for ivt ',ivt(p)
+            call endrun(msg="Stopping")
+         end if
+      end if
 
       ! Initialize allocation coefficients.
       ! Because crops have no live carbon pools when planted but not emerged, this shouldn't

From 62bcd0bbba8af0c2ec4d50f27f16383bb1fad316 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 14:03:21 -0600
Subject: [PATCH 0486/1248] Add some printout in PlantCrop().

---
 src/biogeochem/CNPhenologyMod.F90 | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 46d155d2d4..c85cbc609f 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2694,21 +2694,27 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
 
       ! set GDD target
       did_rx_gdds = .false.
+      write(iulog, *) 'ssr PlantCrop point A'
       if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
+         write(iulog, *) 'ssr PlantCrop point B'
          gddmaturity(p) = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p))
          did_rx_gdds = .true.
          if (adapt_cropcal_rx_cultivar_gdds .and. crop_inst%gdd20_baseline_patch(p) > min_gdd20_baseline) then
+            write(iulog, *) 'ssr PlantCrop point C'
             gddmaturity(p) = gddmaturity(p) * gdd20 / crop_inst%gdd20_baseline_patch(p)
             !TODO SSR: Set maximum and minimum gddmaturity
          end if
       else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then
+         write(iulog, *) 'ssr PlantCrop point D'
          gddmaturity(p) = hybgdd(ivt(p))
       else
+         write(iulog, *) 'ssr PlantCrop gdd20 = ',gdd20
          if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. &
                ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean .or. &
                ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
                ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. &
                ivt(p) == nrice   .or. ivt(p) == nirrig_rice) then
+            write(iulog, *) 'ssr PlantCrop point E'
             gddmaturity(p) = min(gdd20, hybgdd(ivt(p)))
          else if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. &
                ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. &
@@ -2716,7 +2722,9 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
                ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
                ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then
             gddmaturity(p) = max(950._r8, min(gdd20*0.85_r8, hybgdd(ivt(p))))
+            write(iulog, *) 'ssr PlantCrop point F'
             if (do_plant_normal) then
+               write(iulog, *) 'ssr PlantCrop point G'
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
          else

From 9cd2b221358b542b9b4c44098d64c4ca6775e790 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 14:15:56 -0600
Subject: [PATCH 0487/1248] Add printout of cropcal_stream DERIVED settings.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 69c529be24..e48fa2b6aa 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -392,6 +392,16 @@ subroutine cropcal_init(bounds)
 
    end if
 
+   if (masterproc) then
+      write(iulog,*)
+      write(iulog,*) 'cropcal_stream DERIVED settings:'
+      write(iulog,'(a,l1)') '  use_cropcal_rx_swindows  = ',use_cropcal_rx_swindows
+      write(iulog,'(a,l1)') '  use_cropcal_rx_cultivar_gdds   = ',use_cropcal_rx_cultivar_gdds
+      write(iulog,'(a,l1)') '  adapt_cropcal_rx_cultivar_gdds   = ',adapt_cropcal_rx_cultivar_gdds
+      write(iulog,'(a,l1)') '  use_cropcal_streams  = ',use_cropcal_streams
+      write(iulog,*)
+   endif
+
   end subroutine cropcal_init
 
   !================================================================

From a8923bf354318dbfd6f565333927e6f83f50985c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 14:18:14 -0600
Subject: [PATCH 0488/1248] Add printout when flushing GDD20s.

---
 src/biogeophys/TemperatureType.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 831c99d9bf..b31ccd9119 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1687,6 +1687,7 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
        if (is_end_curr_year()) then
           ! Flush, if needed
           if (this%flush_gdd20) then
+              write(iulog, *) 'Flushing GDD20 variables'
               call markreset_accum_field('GDD020')
               call markreset_accum_field('GDD820')
               call markreset_accum_field('GDD1020')

From f2518b611408c12ae262c1b71b9b0a128196c934 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 15:05:50 -0600
Subject: [PATCH 0489/1248] PlantCrop: GDD-gen runs get gddmaturity 1e36.

---
 src/biogeochem/CNPhenologyMod.F90 | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index c85cbc609f..70669ac955 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2695,7 +2695,11 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
       ! set GDD target
       did_rx_gdds = .false.
       write(iulog, *) 'ssr PlantCrop point A'
-      if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
+      if (generate_crop_gdds) then
+         write(iulog, *) 'ssr PlantCrop point AA'
+         ! Value mostly doesn't matter; it just needs to be large enough to avoid divide-by-zero errors.
+         gddmaturity(p) = 1.e36_r8
+      else if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
          write(iulog, *) 'ssr PlantCrop point B'
          gddmaturity(p) = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p))
          did_rx_gdds = .true.

From c4aa93ba0d084081a1733c6df9842fd632117a44 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 15:21:24 -0600
Subject: [PATCH 0490/1248] PlantCrop: Remove troubleshooting printout.

---
 src/biogeochem/CNPhenologyMod.F90 | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 70669ac955..41d4107f3f 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2694,31 +2694,24 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
 
       ! set GDD target
       did_rx_gdds = .false.
-      write(iulog, *) 'ssr PlantCrop point A'
       if (generate_crop_gdds) then
-         write(iulog, *) 'ssr PlantCrop point AA'
          ! Value mostly doesn't matter; it just needs to be large enough to avoid divide-by-zero errors.
          gddmaturity(p) = 1.e36_r8
       else if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
-         write(iulog, *) 'ssr PlantCrop point B'
          gddmaturity(p) = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p))
          did_rx_gdds = .true.
          if (adapt_cropcal_rx_cultivar_gdds .and. crop_inst%gdd20_baseline_patch(p) > min_gdd20_baseline) then
-            write(iulog, *) 'ssr PlantCrop point C'
             gddmaturity(p) = gddmaturity(p) * gdd20 / crop_inst%gdd20_baseline_patch(p)
             !TODO SSR: Set maximum and minimum gddmaturity
          end if
       else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then
-         write(iulog, *) 'ssr PlantCrop point D'
          gddmaturity(p) = hybgdd(ivt(p))
       else
-         write(iulog, *) 'ssr PlantCrop gdd20 = ',gdd20
          if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. &
                ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean .or. &
                ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
                ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. &
                ivt(p) == nrice   .or. ivt(p) == nirrig_rice) then
-            write(iulog, *) 'ssr PlantCrop point E'
             gddmaturity(p) = min(gdd20, hybgdd(ivt(p)))
          else if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. &
                ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. &
@@ -2726,13 +2719,10 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
                ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
                ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then
             gddmaturity(p) = max(950._r8, min(gdd20*0.85_r8, hybgdd(ivt(p))))
-            write(iulog, *) 'ssr PlantCrop point F'
             if (do_plant_normal) then
-               write(iulog, *) 'ssr PlantCrop point G'
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
          else
-            write(iulog, *) 'ERROR: PlantCrop(): unrecognized ivt for GDD target: ',ivt(p)
             call endrun(msg="Stopping")
          end if
 

From fb478a1de763892c6fb9e260094b156f11e86020 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 15:46:26 -0600
Subject: [PATCH 0491/1248] rxcropmaturityshared: Restore 'modify user_nl
 files: new fsurdat.'

---
 .../SystemTests/rxcropmaturityshared.py       | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
index 7fa3a2f1bd..8a944efdf9 100644
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -299,16 +299,16 @@ def _run_fsurdat_modifier(self):
                 tool_path,
             )
 
-        # # Modify namelist
-        # logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
-        # self._append_to_user_nl_clm(
-        #     [
-        #         "fsurdat = '{}'".format(self._fsurdat_out),
-        #         "do_transient_crops = .false.",
-        #         "flanduse_timeseries = ''",
-        #         "use_init_interp = .true.",
-        #     ]
-        # )
+        # Modify namelist
+        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
+        self._append_to_user_nl_clm(
+            [
+                "fsurdat = '{}'".format(self._fsurdat_out),
+                "do_transient_crops = .false.",
+                "flanduse_timeseries = ''",
+                "use_init_interp = .true.",
+            ]
+        )
 
     def _create_config_file_evenlysplitcrop(self):
         """

From 57daeec4a7a649623d9fe5368899a465f44401dd Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 17:06:01 -0600
Subject: [PATCH 0492/1248] Add manual flush_gdd20 option.

---
 bld/CLMBuildNamelist.pm                         | 1 +
 bld/namelist_files/namelist_defaults_ctsm.xml   | 1 +
 bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++
 src/biogeophys/TemperatureType.F90              | 5 +++--
 src/main/clm_varctl.F90                         | 1 +
 src/main/controlMod.F90                         | 4 +++-
 6 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 8bffec0d46..7fb613c36d 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4176,6 +4176,7 @@ sub setup_logic_cropcal_streams {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcals_rx');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcals_rx_adapt');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_gdd20_seasons');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'flush_gdd20');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal');
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 8ed75be01a..7503957e7d 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1690,6 +1690,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <cropcals_rx>.false.</cropcals_rx>
 <cropcals_rx_adapt>.false.</cropcals_rx_adapt>
 <stream_gdd20_seasons>.false.</stream_gdd20_seasons>
+<flush_gdd20>.false.</flush_gdd20>
 <stream_year_first_cropcal_swindows  >2000</stream_year_first_cropcal_swindows>
 <stream_year_last_cropcal_swindows   >2000</stream_year_last_cropcal_swindows>
 <model_year_align_cropcal_swindows   >2000</model_year_align_cropcal_swindows>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index b510b14ccb..31ce220d9c 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1843,6 +1843,11 @@ Filename of input stream data for baseline GDD20 values
 Set this to true to read gdd20 accumulation season start and end dates from stream files, rather than using hard-coded hemisphere-specific "warm seasons."
 </entry>
 
+<entry id="flush_gdd20" type="logical" category="datasets"
+       group="clm_inparm" valid_values="" >
+Set this to true to flush the accumulated GDD20 variables as soon as possible.
+</entry>
+
 <entry id="allow_invalid_gdd20_season_inputs" type="logical" category="datasets"
        group="cropcal_streams" valid_values="" >
 By default, a value in stream_fldFileName_gdd20_season_start or _end outside the range [1, 365] (or 366 in leap years) will cause the run to fail. Set this to .true. to instead have such cells fall back to the hard-coded hemisphere-specific "warm seasons."
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index b31ccd9119..4fd5bfcbe6 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -8,7 +8,7 @@ module TemperatureType
   use decompMod       , only : bounds_type
   use abortutils      , only : endrun
   use clm_varctl      , only : use_cndv, iulog, use_luna, use_crop, use_biomass_heat_storage
-  use clm_varctl      , only : stream_gdd20_seasons
+  use clm_varctl      , only : stream_gdd20_seasons, flush_gdd20
   use clm_varpar      , only : nlevsno, nlevgrnd, nlevlak, nlevurb, nlevmaxurbgrnd
   use clm_varcon      , only : spval, ispval
   use GridcellType    , only : grc
@@ -1686,12 +1686,13 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then
           ! Flush, if needed
-          if (this%flush_gdd20) then
+          if (flush_gdd20 .or. this%flush_gdd20) then
               write(iulog, *) 'Flushing GDD20 variables'
               call markreset_accum_field('GDD020')
               call markreset_accum_field('GDD820')
               call markreset_accum_field('GDD1020')
               this%flush_gdd20 = .false.
+              flush_gdd20 = .false.
           end if
           call update_accum_field  ('GDD020', this%gdd0_patch, nstep)
           call extract_accum_field ('GDD020', this%gdd020_patch, nstep)
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 43bab01d24..a1ca2fd3f7 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -393,6 +393,7 @@ module clm_varctl
   logical, public :: use_cropcal_rx_cultivar_gdds = .false.
   logical, public :: adapt_cropcal_rx_cultivar_gdds = .false.
   logical, public :: stream_gdd20_seasons = .false.
+  logical, public :: flush_gdd20 = .false.
 
   !----------------------------------------------------------
   ! biomass heat storage switch
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index aabe753769..98e0d1afac 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -302,7 +302,7 @@ subroutine control_init(dtime)
          use_lch4, use_nitrif_denitrif, use_extralakelayers, &
          use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, &
          use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, &
-         use_nguardrail, crop_residue_removal_frac, stream_gdd20_seasons
+         use_nguardrail, crop_residue_removal_frac, stream_gdd20_seasons, flush_gdd20
 
     ! SNICAR
     namelist /clm_inparm/ &
@@ -712,6 +712,7 @@ subroutine control_spmd()
     call mpi_bcast (use_nguardrail, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_crop, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (stream_gdd20_seasons, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (flush_gdd20, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fertilizer, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_grainproduct, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (crop_residue_removal_frac, 1, MPI_REAL8, 0, mpicom, ier)
@@ -985,6 +986,7 @@ subroutine control_print ()
     write(iulog,*) '    use_cndv = ', use_cndv
     write(iulog,*) '    use_crop = ', use_crop
     write(iulog,*) '    stream_gdd20_seasons = ', stream_gdd20_seasons
+    write(iulog,*) '    flush_gdd20 = ', flush_gdd20
     write(iulog,*) '    use_fertilizer = ', use_fertilizer
     write(iulog,*) '    use_grainproduct = ', use_grainproduct
     write(iulog,*) '    crop_residue_removal_frac = ', crop_residue_removal_frac

From 9010346b61198738b4843402124d5729a38f8363 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 17:27:27 -0600
Subject: [PATCH 0493/1248] Error if gdd20_season_start or _end > 366.

---
 src/biogeophys/TemperatureType.F90 | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 4fd5bfcbe6..6f6a3309c1 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1469,6 +1469,12 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
           gdd20_season_start = int(gdd20_season_starts(p))
           gdd20_season_end = int(gdd20_season_ends(p))
           if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
+             if (gdd20_season_start > 366 .or. gdd20_season_end > 366) then
+                write(iulog,*) 'invalid gdd20 season!'
+                write(iulog,*) '               start: ',gdd20_season_start
+                write(iulog,*) '                 end: ',gdd20_season_end
+                call endrun(msg=errMsg(sourcefile, __LINE__))
+             end if
              in_accumulation_season = is_doy_in_interval( &
              gdd20_season_start, gdd20_season_end, day)
           end if

From c2f52d19f48f98d97183d447a77b7947b4ab3051 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 13 Jun 2024 13:02:09 -0600
Subject: [PATCH 0494/1248] Squashed '.lib/git-fleximod/' changes from
 4ff1e98de..25ccc15de

25ccc15de Merge tag 'v0.7.8' into tmp-release
8eae7e3fb Bump to 0.7.8
34daa0657 Merge pull request #46 from ESMCI/add_optional_keyword
af12c80ca fix spelling
7ea36dc44 remove manage_externals error
2ede18208 add optional to status output

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 25ccc15de3b2e62554243300e69d44df69a65305
---
 git_fleximod/cli.py          |  4 ++--
 git_fleximod/git_fleximod.py | 10 ++++++----
 git_fleximod/utils.py        | 12 ++++++------
 pyproject.toml               |  2 +-
 tbump.toml                   |  2 +-
 tests/conftest.py            |  2 +-
 6 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index bc099fcbc0..a15a226de4 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.7.7"
+__version__ = "0.7.8"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
@@ -26,7 +26,7 @@ def find_root_dir(filename=".gitmodules"):
 
 def get_parser():
     description = """
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models
     """
     parser = argparse.ArgumentParser(
         description=description, formatter_class=argparse.RawDescriptionHelpFormatter
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index ca5f90622d..e1b8f484a5 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -304,6 +304,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                 ahash = result[0][1:]
             hhash = None
             atag = None
+            
             needsupdate += 1
             if not toplevel and level:
                 continue
@@ -316,22 +317,23 @@ def submodules_status(gitmodules, root_dir, toplevel=False):
                     hhash = htag.split()[0]
                 if hhash and atag:
                     break
+            optional = " (optional)" if required and "Optional" in required else ""
             if tag and (ahash == hhash or atag == tag):
-                print(f"e {name:>20} not checked out, aligned at tag {tag}")
+                print(f"e {name:>20} not checked out, aligned at tag {tag}{optional}")
             elif tag:
                 ahash = rootgit.git_operation(
                     "submodule", "status", "{}".format(path)
                 ).rstrip()
                 ahash = ahash[1 : len(tag) + 1]
                 if tag == ahash:
-                    print(f"e {name:>20} not checked out, aligned at hash {ahash}")
+                    print(f"e {name:>20} not checked out, aligned at hash {ahash}{optional}")
                 else:
                     print(
-                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}"
+                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}{optional}"
                     )
                     testfails += 1
             else:
-                print(f"e {name:>20} has no fxtag defined in .gitmodules")
+                print(f"e {name:>20} has no fxtag defined in .gitmodules{optional}")
                 testfails += 1
         else:
             with utils.pushd(newpath):
diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py
index 7cc1de38cc..1a2d5ccf2f 100644
--- a/git_fleximod/utils.py
+++ b/git_fleximod/utils.py
@@ -241,12 +241,12 @@ def _hanging_msg(working_directory, command):
 has taken {hanging_sec} seconds. It may be hanging.
 
 The command will continue to run, but you may want to abort
-manage_externals with ^C and investigate. A possible cause of hangs is
-when svn or git require authentication to access a private
-repository. On some systems, svn and git requests for authentication
-information will not be displayed to the user. In this case, the program
-will appear to hang. Ensure you can run svn and git manually and access
-all repositories without entering your authentication information.
+git-fleximod with ^C and investigate. A possible cause of hangs is git
+requires authentication to access a private repository. On some
+systems, git requests for authentication information will not
+be displayed to the user. In this case, the program will appear to
+hang. Ensure you can run git manually and access all
+repositories without entering your authentication information.
 
 """.format(
             command=command,
diff --git a/pyproject.toml b/pyproject.toml
index a316914bf5..5b1332549c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.7.7"
+version = "0.7.8"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index c22637ccda..c4f7ac96ea 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.7.7"
+current = "0.7.8"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before
diff --git a/tests/conftest.py b/tests/conftest.py
index 1cc008eb1d..65ee85d23d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -32,7 +32,7 @@ def logger():
      "submodule_name": "test_optional",
      "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0 (optional)",
      "status4" : "test_optional at tag MPIserial_2.4.0",
      "gitmodules_content": """
      [submodule "test_optional"]

From 4deb704ebbfdb2accb099d79f58680c0f8fa4906 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 13 Jun 2024 13:14:02 -0600
Subject: [PATCH 0495/1248] Update changelog a bit

---
 doc/ChangeLog | 21 ++++++++++-----------
 doc/ChangeSum |  2 +-
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 4600af34be..984d6c1c2b 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,14 +1,15 @@
 ===============================================================
 Tag name: ctsm5.2.008
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
-Date: Fri 07 Jun 2024 01:23:07 PM MDT
+Date: Thu 13 Jun 2024 01:13:24 PM MDT
 One-line Summary: Another update of git-fleximod
 
 Purpose and description of changes
 ----------------------------------
 
-Just update the gitfleximod subtree to v0.7.7. This fixes an issue in identifying that a tag is out of sync in a submodule.
-An issue about recursion on a submodule. Allows untracked files, and fixes a MS Window Memory error.
+Just update the gitfleximod subtree to v0.7.8. This fixes an issue in identifying that a tag is out of sync in a submodule.
+An issue about recursion on a submodule. Allows untracked files, and fixes a MS Window Memory error. And
+also git-fleximod status marks optional submodules, which helps explain why they are marked as not-checked out.
 
 
 Significant changes to scientifically-supported configurations
@@ -39,7 +40,7 @@ List of CTSM issues fixed:
 Notes of particular relevance for users
 ---------------------------------------
 Caveats for users (e.g., need to interpolate initial conditions):
-   doc-builder checkout seems to be required to use "git commit ." at the top level
+   doc-builder checkout requires use of "git commit ." at the top level
 
 Changes to documentation:
    Tweak some of the documentation around git-fleximod and use submodule rather than external.
@@ -50,25 +51,23 @@ NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the
 [Remove any lines that don't apply. Remove entire section if nothing applies.]
 
 
-Testing summary: minimual
+Testing summary: regular
 ----------------
 
  [PASS means all tests PASS; OK means tests PASS other than expected fails.]
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho -
+    derecho - PASS
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
-    (any machine) -
+    derecho - PASS
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho -----
-    izumi -------
-
-  any other testing (give details below):
+    derecho ----- OK
+    izumi ------- OK
 
 If the tag used for baseline comparisons was NOT the previous tag, note that here:
 
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 275c4a5cfa..145279cdf6 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.008     erik 06/07/2024 Another update of git-fleximod
+       ctsm5.2.008     erik 06/13/2024 Another update of git-fleximod
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems

From 3b6a8ce43e53d83122eee01fc00f5533edc57466 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 13 Jun 2024 13:21:57 -0600
Subject: [PATCH 0496/1248] UpdateAccVars_CropGDDs bugfix: Use day of year, not
 day of month.

---
 src/biogeophys/TemperatureType.F90 | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 6f6a3309c1..23fda977dd 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1399,7 +1399,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     ! USES
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use accumulMod       , only : update_accum_field, extract_accum_field, markreset_accum_field
-    use clm_time_manager , only : is_doy_in_interval
+    use clm_time_manager , only : is_doy_in_interval, get_curr_calday
     use pftconMod        , only : npcropmin
     use CropType, only : crop_type
     !
@@ -1422,6 +1422,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     logical :: in_accumulation_season
     real(r8) :: lat  ! latitude
     integer :: gdd20_season_start, gdd20_season_end
+    integer :: jday  ! Julian day of year (1, ..., 366)
 
     associate( &
      gdd20_season_starts => crop_inst%gdd20_season_start_patch, &
@@ -1430,6 +1431,11 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
 
     basetemp_r8 = real(basetemp_int, r8)
 
+    ! SSR 2024-06-13: This should probably be _prev_. Keeping it _curr_ for now for consistency with
+    ! parent subroutine UpdateAccVars(), which uses get_curr_date() to get the month/day/etc. values
+    ! that are passed into this subroutine.
+    jday = int(get_curr_calday())
+
     ! Get maximum daily accumulation
     if (basetemp_int == 0) then
        ! SSR 2024-05-31: I'm not sure why this was different for base temp 0, but I'm keeping it as I refactor into UpdateAccVars_CropGDDs()
@@ -1476,7 +1482,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
                 call endrun(msg=errMsg(sourcefile, __LINE__))
              end if
              in_accumulation_season = is_doy_in_interval( &
-             gdd20_season_start, gdd20_season_end, day)
+             gdd20_season_start, gdd20_season_end, jday)
           end if
        end if
 
@@ -1534,6 +1540,7 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
 
     dtime = get_step_size()
     nstep = get_nstep()
+    ! SSR 2024-06-13: This should probably be changed to _prev_
     call get_curr_date (year, month, day, secs)
 
     ! Allocate needed dynamic memory for single level pft field
@@ -1677,8 +1684,6 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
        call update_accum_field  ('TDM10', rbufslp, nstep)
        call extract_accum_field ('TDM10', this%t_a10min_patch, nstep)
 
-
-
        ! Accumulate and extract GDD0
        call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 0, this%gdd0_patch, crop_inst)
 
@@ -1688,7 +1693,6 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
        ! Accumulate and extract GDD10
        call this%UpdateAccVars_CropGDDs(rbufslp, begp, endp, month, day, secs, dtime, nstep, 10, this%gdd10_patch, crop_inst)
 
-
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then
           ! Flush, if needed

From e947ea3017667327a671adce10942ec2b31c3d3f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 13 Jun 2024 14:27:41 -0600
Subject: [PATCH 0497/1248] Explicitly allocate arrays to start at 1, since
 izumi_gnu seems to need that

---
 src/biogeochem/DustEmisBase.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
index dbc5729403..ef509add06 100644
--- a/src/biogeochem/DustEmisBase.F90
+++ b/src/biogeochem/DustEmisBase.F90
@@ -184,9 +184,9 @@ subroutine InitAllocate(this, bounds)
     allocate(this%vlc_trb_3_patch           (begp:endp))        ; this%vlc_trb_3_patch           (:)   = nan
     allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
 
-    allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst))           ; this%ovr_src_snk_mss           (:,:) = nan
-    allocate (this%dmt_vwr(ndst))                               ; this%dmt_vwr                   (:)   = nan
-    allocate (this%stk_crc(ndst))                               ; this%stk_crc                   (:)   = nan
+    allocate (this%ovr_src_snk_mss(1:dst_src_nbr,1:ndst))       ; this%ovr_src_snk_mss           (:,:) = nan
+    allocate (this%dmt_vwr(1:ndst))                             ; this%dmt_vwr                   (:)   = nan
+    allocate (this%stk_crc(1:ndst))                             ; this%stk_crc                   (:)   = nan
 
   end subroutine InitAllocate
 

From 97b95e9b266bed49c0f9bfe7016b81c0b3b05dda Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 13 Jun 2024 14:10:25 -0600
Subject: [PATCH 0498/1248] Add Cidadinho test site.

---
 Externals.cfg                                 |  4 +--
 bld/CLMBuildNamelist.pm                       |  5 ++--
 bld/namelist_files/namelist_defaults_ctsm.xml |  7 ++++-
 .../namelist_defaults_overall.xml             |  2 ++
 bld/unit_testers/build-namelist_test.pl       | 30 ++++++++++---------
 tools/mksurfdata_esmf/Makefile                | 11 +++++--
 6 files changed, 38 insertions(+), 21 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 185f412cab..49cfd25962 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -34,9 +34,9 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.92
+hash = 75847d58bac1149adcb8d9b40181df631c273e19
 protocol = git
-repo_url = https://github.com/ESMCI/ccs_config_cesm.git
+repo_url = https://github.com/samsrabin/ccs_config_cesm.git
 local_path = ccs_config
 required = True
 
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 7fb613c36d..ad110b017e 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1842,9 +1842,10 @@ sub setup_logic_site_specific {
      $nl->set_variable_value($group, $var, $val);
   }
 
-  if ($nl_flags->{'res'} eq "1x1_smallvilleIA") {
+  my $res = $nl_flags->{'res'};
+  if ($res eq "1x1_smallvilleIA" or $res eq "1x1_cidadinhoBR") {
     if (! &value_is_true($nl_flags->{'use_cn'}) || ! &value_is_true($nl_flags->{'use_crop'})) {
-      $log->fatal_error("1x1_smallvilleIA grids must use a compset with CN and CROP turned on.");
+      $log->fatal_error("${res} grids must use a compset with CN and CROP turned on.");
     }
   }
 
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 7503957e7d..ae9f9dee6a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1406,6 +1406,8 @@ lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_C96_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240221.nc</fsurdat>
+<fsurdat hgrid="1x1_cidadinhoBR" sim_year="2000" >
+lnd/clm2/surfdata_esmf/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240613.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_brazil_hist_1850_78pfts_c240221.nc</fsurdat>
 
@@ -1477,11 +1479,14 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 
-<!-- Note that this transient file only goes up to year 1855.
+<!-- Note that these transient files only go up to year 1855.
      This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
 <flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_c240221.nc</flanduse_timeseries>
 
+<!-- Cidadinho test site has no transient data. -->
+<flanduse_timeseries hgrid="1x1_cidadinhoBR" sim_year_range="1850-2000"></flanduse_timeseries>
+
 <!-- Future scenarios - landuse time series files with crop on -->
 
 <!-- SSP1-RCP2.6 - relative to {csmdata}) -->
diff --git a/bld/namelist_files/namelist_defaults_overall.xml b/bld/namelist_files/namelist_defaults_overall.xml
index 479b2a02b7..5b7ae1bdd9 100644
--- a/bld/namelist_files/namelist_defaults_overall.xml
+++ b/bld/namelist_files/namelist_defaults_overall.xml
@@ -62,6 +62,7 @@ determine default values for namelists.
 <res sitespf_pt="1x1_urbanc_alpha"   >1x1_urbanc_alpha</res>
 <res sitespf_pt="1x1_numaIA"         >1x1_numaIA</res>
 <res sitespf_pt="1x1_smallvilleIA"   >1x1_smallvilleIA</res>
+<res sitespf_pt="1x1_cidadinhoBR"    >1x1_cidadinhoBR</res>
 
 <!-- Default simulation year -->
 <sim_year>2000</sim_year>
@@ -110,6 +111,7 @@ determine default values for namelists.
 <mask hgrid="1x1_urbanc_alpha"    >test</mask>
 <mask hgrid="1x1_numaIA"          >navy</mask>
 <mask hgrid="1x1_smallvilleIA"    >test</mask>
+<mask hgrid="1x1_cidadinhoBR"     >test</mask>
 <mask                             >gx1v7</mask>
 
 <!-- Default glacier model options -->
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index b0ddb1e448..5c8aa3468d 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1590,21 +1590,23 @@ sub cat_and_create_namelistinfile {
 print "==================================================\n";
 
 # Check for crop resolutions
-my $crop1850_res = "1x1_smallvilleIA";
-$options = "-bgc bgc -crop -res $crop1850_res -use_case 1850_control -envxml_dir .";
-&make_env_run();
-eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
-is( $@, '', "$options" );
-$cfiles->checkfilesexist( "$options", $mode );
-$cfiles->shownmldiff( "default", "standard" );
-if ( defined($opts{'compare'}) ) {
-   $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-   $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
-}
-if ( defined($opts{'generate'}) ) {
-   $cfiles->copyfiles( "$options", $mode );
+my @crop1850_res = ( "1x1_smallvilleIA", "1x1_cidadinhoBR" );
+foreach my $res ( @crop1850_res ) {
+   $options = "-bgc bgc -crop -res $res -use_case 1850_control -envxml_dir .";
+   &make_env_run();
+   eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
+   is( $@, '', "$options" );
+   $cfiles->checkfilesexist( "$options", $mode );
+   $cfiles->shownmldiff( "default", "standard" );
+   if ( defined($opts{'compare'}) ) {
+      $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+      $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+   }
+   if ( defined($opts{'generate'}) ) {
+      $cfiles->copyfiles( "$options", $mode );
+   }
+   &cleanup();
 }
-&cleanup();
 
 my @crop_res = ( "1x1_numaIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne3np4.pg3", "ne30np4", "ne30np4.pg3", "C96", "mpasa120" );
 foreach my $res ( @crop_res ) {
diff --git a/tools/mksurfdata_esmf/Makefile b/tools/mksurfdata_esmf/Makefile
index d8bacdc5dd..c344843d06 100644
--- a/tools/mksurfdata_esmf/Makefile
+++ b/tools/mksurfdata_esmf/Makefile
@@ -54,7 +54,10 @@ SUBSETDATA_POINT_URBAN = $(SUBSETDATA_POINT) --include-nonveg
 # Subset data sites...
 SUBSETDATA_1X1_BRAZIL := --lat -7 --lon -55 --site 1x1_brazil
 SUBSETDATA_1X1_NUMAIA := --lat 40.6878 --lon 267.0228 --site 1x1_numaIA
-SUBSETDATA_1X1_SMALL  := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA \
+SUBSETDATA_1X1_SMALL_IA  := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA \
+		--dompft 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 \
+		--pctpft 6.5 1.5 1.6 1.7 1.8 1.9 1.5 1.6 1.7 1.8 1.9 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5
+SUBSETDATA_1X1_SMALL_BR  := --lat -12.9952 --lon 305.3233 --site 1x1_cidadinhoBR \
 		--dompft 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 \
 		--pctpft 6.5 1.5 1.6 1.7 1.8 1.9 1.5 1.6 1.7 1.8 1.9 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5
 # NOTE: The 1850 smallvilleIA site is constructed to start with 100% natural vegetation, so we can test transition to crops
@@ -112,6 +115,7 @@ all-subset : \
 	1x1-smallville-present \
 	1x1-smallville-1850 \
 	1x1-smallville-transient \
+	1x1-cidadinho-present \
 	urban
 
 DEBUG:
@@ -239,7 +243,7 @@ crop-global-hist-ne30 : FORCE
 	$(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA)
 
 1x1-smallville-present : FORCE
-	$(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL)
+	$(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL_IA)
 
 # Note that the smallville 1850 dataset is entirely natural vegetation. This
 # facilitates testing a transient case that starts with no crop, and then later
@@ -254,6 +258,9 @@ crop-global-hist-ne30 : FORCE
 	$(SUBSETDATA_POINT) --create-landuse $(SUBSETDATA_1X1_SMALLTRANSIENT)
 	../modify_input_files/modify_smallville.sh
 
+1x1-cidadinho-present : FORCE
+	$(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL_BR)
+
 #
 # Crop with future scenarios
 #

From d33ef3e5b3e695a627fa23dd4d56e85686794c2c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 3 Jun 2024 12:03:15 -0600
Subject: [PATCH 0499/1248] Add partial versions of RXCROPMATURITY test.

Useful for troubleshooting:
* RXCROPMATURITYSKIPRUN skips the build and run phases.
* RXCROPMATURITYSKIPBUILD just skips the build phase. It still does the run phase so as to test everything before actual run submission.
---
 cime_config/SystemTests/rxcropmaturity.py     | 444 +----------------
 .../SystemTests/rxcropmaturityshared.py       | 451 ++++++++++++++++++
 .../SystemTests/rxcropmaturityskipbuild.py    |   9 +
 .../SystemTests/rxcropmaturityskiprun.py      |   9 +
 cime_config/config_tests.xml                  |  20 +
 5 files changed, 492 insertions(+), 441 deletions(-)
 create mode 100644 cime_config/SystemTests/rxcropmaturityshared.py
 create mode 100644 cime_config/SystemTests/rxcropmaturityskipbuild.py
 create mode 100644 cime_config/SystemTests/rxcropmaturityskiprun.py

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index acb63bb000..12ec608898 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -1,444 +1,6 @@
-"""
-CTSM-specific test that first performs a GDD-generating run, then calls
-Python code to generate the maturity requirement file. This is then used
-in a sowing+maturity forced run, which finally is tested to ensure
-correct behavior.
+from rxcropmaturityshared import RXCROPMATURITYSHARED
 
-Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually,
-this test should be able to generate its own files at whatever resolution it's
-called at. Well, really, the ultimate goal would be to give CLM the files
-at the original resolution (for GGCMI phase 3, 0.5°) and have the stream
-code do the interpolation. However, that wouldn't act on harvest dates
-(which are needed for generate_gdds.py). I could have Python interpolate
-those, but this would cause a potential inconsistency.
-"""
-
-import os
-import re
-import systemtest_utils as stu
-import subprocess
-from CIME.SystemTests.system_tests_common import SystemTestsCommon
-from CIME.XML.standard_module_setup import *
-from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
-import shutil, glob
-
-logger = logging.getLogger(__name__)
-
-
-class RXCROPMATURITY(SystemTestsCommon):
-    def __init__(self, case):
-        # initialize an object interface to the SMS system test
-        SystemTestsCommon.__init__(self, case)
-
-        # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
-        stop_n = self._case.get_value("STOP_N")
-        stop_option = self._case.get_value("STOP_OPTION")
-        stop_n_orig = stop_n
-        stop_option_orig = stop_option
-        if "nsecond" in stop_option:
-            stop_n /= 60
-            stop_option = "nminutes"
-        if "nminute" in stop_option:
-            stop_n /= 60
-            stop_option = "nhours"
-        if "nhour" in stop_option:
-            stop_n /= 24
-            stop_option = "ndays"
-        if "nday" in stop_option:
-            stop_n /= 365
-            stop_option = "nyears"
-        if "nmonth" in stop_option:
-            stop_n /= 12
-            stop_option = "nyears"
-        error_message = None
-        if "nyear" not in stop_option:
-            error_message = (
-                f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), "
-                + "nhour(s), nday(s), nmonth(s), or nyear(s)"
-            )
-        elif stop_n < 5:
-            error_message = (
-                "RXCROPMATURITY must be run for at least 5 years; you requested "
-                + f"{stop_n_orig} {stop_option_orig[1:]}"
-            )
-        if error_message is not None:
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Get the number of complete years that will be run
-        self._run_Nyears = int(stop_n)
-
-        # Only allow RXCROPMATURITY to be called with test cropMonthOutput
-        casebaseid = self._case.get_value("CASEBASEID")
-        if casebaseid.split("-")[-1] != "cropMonthOutput":
-            error_message = (
-                "Only call RXCROPMATURITY with test cropMonthOutput "
-                + "to avoid potentially huge sets of daily outputs."
-            )
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Get files with prescribed sowing and harvest dates
-        self._get_rx_dates()
-
-        # Which conda environment should we use?
-        self._get_conda_env()
 
+class RXCROPMATURITY(RXCROPMATURITYSHARED):
     def run_phase(self):
-        # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
-        # want to be saved as baseline.
-
-        # -------------------------------------------------------------------
-        # (1) Set up GDD-generating run
-        # -------------------------------------------------------------------
-        # Create clone to be GDD-Generating case
-        logger.info("RXCROPMATURITY log:  cloning setup")
-        case_rxboth = self._case
-        caseroot = self._case.get_value("CASEROOT")
-        clone_path = f"{caseroot}.gddgen"
-        self._path_gddgen = clone_path
-        if os.path.exists(self._path_gddgen):
-            shutil.rmtree(self._path_gddgen)
-        logger.info("RXCROPMATURITY log:  cloning")
-        case_gddgen = self._case.create_clone(clone_path, keepexe=True)
-        logger.info("RXCROPMATURITY log:  done cloning")
-
-        os.chdir(self._path_gddgen)
-        self._set_active_case(case_gddgen)
-
-        # Set up stuff that applies to both tests
-        self._setup_all()
-
-        # Add stuff specific to GDD-Generating run
-        logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
-        self._append_to_user_nl_clm(
-            [
-                "generate_crop_gdds = .true.",
-                "use_mxmat = .false.",
-                " ",
-                "! (h2) Daily outputs for GDD generation and figure-making",
-                "hist_fincl3 = 'GDDACCUM', 'GDDHARV'",
-                "hist_nhtfrq(3) = -24",
-                "hist_mfilt(3) = 365",
-                "hist_type1d_pertape(3) = 'PFTS'",
-                "hist_dov2xy(3) = .false.",
-            ]
-        )
-
-        # If flanduse_timeseries is defined, we need to make a static version for this test. This
-        # should have every crop in most of the world.
-        self._get_flanduse_timeseries_in(case_gddgen)
-        if self._flanduse_timeseries_in is not None:
-
-            # Download files from the server, if needed
-            case_gddgen.check_all_input_data()
-
-            # Make custom version of surface file
-            logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
-            self._run_fsurdat_modifier()
-
-        # -------------------------------------------------------------------
-        # (2) Perform GDD-generating run and generate prescribed GDDs file
-        # -------------------------------------------------------------------
-        logger.info("RXCROPMATURITY log:  Start GDD-Generating run")
-
-        # As per SSP test:
-        # "No history files expected, set suffix=None to avoid compare error"
-        # We *do* expect history files here, but anyway. This works.
-        self._skip_pnl = False
-        self.run_indv(suffix=None, st_archive=True)
-
-        self._run_generate_gdds(case_gddgen)
-
-        # -------------------------------------------------------------------
-        # (3) Set up and perform Prescribed Calendars run
-        # -------------------------------------------------------------------
-        os.chdir(caseroot)
-        self._set_active_case(case_rxboth)
-
-        # Set up stuff that applies to both tests
-        self._setup_all()
-
-        # Add stuff specific to Prescribed Calendars run
-        logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
-        self._append_to_user_nl_clm(
-            [
-                "generate_crop_gdds = .false.",
-                f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'",
-            ]
-        )
-
-        self.run_indv()
-
-        # -------------------------------------------------------------------
-        # (4) Check Prescribed Calendars run
-        # -------------------------------------------------------------------
-        logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
-        self._run_check_rxboth_run()
-
-    # Get sowing and harvest dates for this resolution.
-    def _get_rx_dates(self):
-        # Eventually, I want to remove these hard-coded resolutions so that this test can generate
-        # its own sowing and harvest date files at whatever resolution is requested.
-        lnd_grid = self._case.get_value("LND_GRID")
-        input_data_root = self._case.get_value("DIN_LOC_ROOT")
-        processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed"
-        if lnd_grid == "10x15":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
-            )
-        elif lnd_grid == "1.9x2.5":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
-            )
-        elif lnd_grid == "0.9x1.25":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc",
-            )
-        else:
-            error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Ensure files exist
-        error_message = None
-        if not os.path.exists(self._sdatefile):
-            error_message = f"ERROR: Sowing date file not found: {self._sdatefile}"
-        elif not os.path.exists(self._hdatefile):
-            error_message = f"ERROR: Harvest date file not found: {self._sdatefile}"
-        if error_message is not None:
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-    def _setup_all(self):
-        logger.info("RXCROPMATURITY log:  _setup_all start")
-
-        # Get some info
-        self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND")
-        run_startdate = self._case.get_value("RUN_STARTDATE")
-        self._run_startyear = int(run_startdate.split("-")[0])
-
-        # Set sowing dates file (and other crop calendar settings) for all runs
-        logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
-        self._modify_user_nl_allruns()
-        logger.info("RXCROPMATURITY log:  _setup_all done")
-
-    # Make a surface dataset that has every crop in every gridcell
-    def _run_fsurdat_modifier(self):
-
-        # fsurdat should be defined. Where is it?
-        self._fsurdat_in = None
-        with open(self._lnd_in_path, "r") as lnd_in:
-            for line in lnd_in:
-                fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line)
-                if fsurdat_in:
-                    self._fsurdat_in = fsurdat_in.group(1)
-                    break
-        if self._fsurdat_in is None:
-            error_message = "fsurdat not defined"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Where we will save the fsurdat version for this test
-        path, ext = os.path.splitext(self._fsurdat_in)
-        dir_in, filename_in_noext = os.path.split(path)
-        self._fsurdat_out = os.path.join(
-            self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}"
-        )
-
-        # Make fsurdat for this test, if not already done
-        if not os.path.exists(self._fsurdat_out):
-            tool_path = os.path.join(
-                self._ctsm_root,
-                "tools",
-                "modify_input_files",
-                "fsurdat_modifier",
-            )
-
-            # Create configuration file for fsurdat_modifier
-            self._cfg_path = os.path.join(
-                self._path_gddgen,
-                "modify_fsurdat_allcropseverywhere.cfg",
-            )
-            self._create_config_file_evenlysplitcrop()
-
-            command = f"python3 {tool_path} {self._cfg_path} "
-            stu.run_python_script(
-                self._get_caseroot(),
-                self._this_conda_env,
-                command,
-                tool_path,
-            )
-
-        # Modify namelist
-        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
-        self._append_to_user_nl_clm(
-            [
-                "fsurdat = '{}'".format(self._fsurdat_out),
-                "do_transient_crops = .false.",
-                "flanduse_timeseries = ''",
-                "use_init_interp = .true.",
-            ]
-        )
-
-    def _create_config_file_evenlysplitcrop(self):
-        """
-        Open the new and the template .cfg files
-        Loop line by line through the template .cfg file
-        When string matches, replace that line's content
-        """
-        cfg_template_path = os.path.join(
-            self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg"
-        )
-
-        with open(self._cfg_path, "w", encoding="utf-8") as cfg_out:
-            # Copy template, replacing some lines
-            with open(cfg_template_path, "r", encoding="utf-8") as cfg_in:
-                for line in cfg_in:
-                    if re.match(r" *evenly_split_cropland *=", line):
-                        line = f"evenly_split_cropland = True"
-                    elif re.match(r" *fsurdat_in *=", line):
-                        line = f"fsurdat_in = {self._fsurdat_in}"
-                    elif re.match(r" *fsurdat_out *=", line):
-                        line = f"fsurdat_out = {self._fsurdat_out}"
-                    elif re.match(r" *process_subgrid_section *=", line):
-                        line = f"process_subgrid_section = True"
-                    cfg_out.write(line)
-
-            # Add new lines
-            cfg_out.write("\n")
-            cfg_out.write("[modify_fsurdat_subgrid_fractions]\n")
-            cfg_out.write("PCT_CROP    = 100.0\n")
-            cfg_out.write("PCT_NATVEG  = 0.0\n")
-            cfg_out.write("PCT_GLACIER = 0.0\n")
-            cfg_out.write("PCT_WETLAND = 0.0\n")
-            cfg_out.write("PCT_LAKE    = 0.0\n")
-            cfg_out.write("PCT_OCEAN   = 0.0\n")
-            cfg_out.write("PCT_URBAN   = 0.0 0.0 0.0\n")
-
-    def _run_check_rxboth_run(self):
-
-        output_dir = os.path.join(self._get_caseroot(), "run")
-        first_usable_year = self._run_startyear + 2
-        last_usable_year = self._run_startyear + self._run_Nyears - 2
-
-        tool_path = os.path.join(
-            self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py"
-        )
-        command = (
-            f"python3 {tool_path} "
-            + f"--directory {output_dir} "
-            + f"-y1 {first_usable_year} "
-            + f"-yN {last_usable_year} "
-            + f"--rx-sdates-file {self._sdatefile} "
-            + f"--rx-gdds-file {self._gdds_file} "
-        )
-        stu.run_python_script(
-            self._get_caseroot(),
-            self._this_conda_env,
-            command,
-            tool_path,
-        )
-
-    def _modify_user_nl_allruns(self):
-        nl_additions = [
-            "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
-            "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
-            "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
-            "stream_year_first_cropcal = 2000",
-            "stream_year_last_cropcal = 2000",
-            "model_year_align_cropcal = 2000",
-            " ",
-            "! (h1) Annual outputs on sowing or harvest axis",
-            "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'",
-            "hist_nhtfrq(2) = 17520",
-            "hist_mfilt(2) = 999",
-            "hist_type1d_pertape(2) = 'PFTS'",
-            "hist_dov2xy(2) = .false.",
-        ]
-        self._append_to_user_nl_clm(nl_additions)
-
-    def _run_generate_gdds(self, case_gddgen):
-        self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out")
-        os.makedirs(self._generate_gdds_dir)
-
-        # Get arguments to generate_gdds.py
-        dout_sr = case_gddgen.get_value("DOUT_S_ROOT")
-        input_dir = os.path.join(dout_sr, "lnd", "hist")
-        first_season = self._run_startyear + 2
-        last_season = self._run_startyear + self._run_Nyears - 2
-        sdates_file = self._sdatefile
-        hdates_file = self._hdatefile
-
-        # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds.
-        tool_path = os.path.join(
-            self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py"
-        )
-        command = " ".join(
-            [
-                f"python3 {tool_path}",
-                f"--input-dir {input_dir}",
-                f"--first-season {first_season}",
-                f"--last-season {last_season}",
-                f"--sdates-file {sdates_file}",
-                f"--hdates-file {hdates_file}",
-                f"--output-dir generate_gdds_out",
-                f"--skip-crops miscanthus,irrigated_miscanthus",
-            ]
-        )
-        stu.run_python_script(
-            self._get_caseroot(),
-            self._this_conda_env,
-            command,
-            tool_path,
-        )
-
-        # Where were the prescribed maturity requirements saved?
-        generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc"))
-        if len(generated_gdd_files) != 1:
-            error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-        self._gdds_file = generated_gdd_files[0]
-
-    def _get_conda_env(self):
-        conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot())
-
-        # If npl conda environment is available, use that (It has dask, which
-        # enables chunking, which makes reading daily 1-degree netCDF files
-        # much more efficient.
-        if "npl " in os.popen(conda_setup_commands + "conda env list").read():
-            self._this_conda_env = "npl"
-        else:
-            self._this_conda_env = "ctsm_pylib"
-
-    def _append_to_user_nl_clm(self, additions):
-        caseroot = self._get_caseroot()
-        append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions)
-
-    # Is flanduse_timeseries defined? If so, where is it?
-    def _get_flanduse_timeseries_in(self, case):
-        case.create_namelists(component="lnd")
-        self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in")
-        self._flanduse_timeseries_in = None
-        with open(self._lnd_in_path, "r") as lnd_in:
-            for line in lnd_in:
-                flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line)
-                if flanduse_timeseries_in:
-                    self._flanduse_timeseries_in = flanduse_timeseries_in.group(1)
-                    break
+        self._run_phase()
diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
new file mode 100644
index 0000000000..6b3a3191de
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -0,0 +1,451 @@
+"""
+CTSM-specific test that first performs a GDD-generating run, then calls
+Python code to generate the maturity requirement file. This is then used
+in a sowing+maturity forced run, which finally is tested to ensure
+correct behavior.
+
+Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually,
+this test should be able to generate its own files at whatever resolution it's
+called at. Well, really, the ultimate goal would be to give CLM the files
+at the original resolution (for GGCMI phase 3, 0.5°) and have the stream
+code do the interpolation. However, that wouldn't act on harvest dates
+(which are needed for generate_gdds.py). I could have Python interpolate
+those, but this would cause a potential inconsistency.
+
+Note that this is just a parent class. The actual tests are RXCROPMATURITY and
+RXCROPMATURITY_SKIPRUN, the latter of which does everything except perform and 
+check the CTSM runs.
+"""
+
+import os
+import re
+import systemtest_utils as stu
+import subprocess
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+from CIME.XML.standard_module_setup import *
+from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
+import shutil, glob
+
+logger = logging.getLogger(__name__)
+
+
+class RXCROPMATURITYSHARED(SystemTestsCommon):
+    def __init__(self, case):
+        # initialize an object interface to the SMS system test
+        SystemTestsCommon.__init__(self, case)
+
+        # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
+        stop_n = self._case.get_value("STOP_N")
+        stop_option = self._case.get_value("STOP_OPTION")
+        stop_n_orig = stop_n
+        stop_option_orig = stop_option
+        if "nsecond" in stop_option:
+            stop_n /= 60
+            stop_option = "nminutes"
+        if "nminute" in stop_option:
+            stop_n /= 60
+            stop_option = "nhours"
+        if "nhour" in stop_option:
+            stop_n /= 24
+            stop_option = "ndays"
+        if "nday" in stop_option:
+            stop_n /= 365
+            stop_option = "nyears"
+        if "nmonth" in stop_option:
+            stop_n /= 12
+            stop_option = "nyears"
+        error_message = None
+        if "nyear" not in stop_option:
+            error_message = (
+                f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), "
+                + "nhour(s), nday(s), nmonth(s), or nyear(s)"
+            )
+        elif stop_n < 5:
+            error_message = (
+                "RXCROPMATURITY must be run for at least 5 years; you requested "
+                + f"{stop_n_orig} {stop_option_orig[1:]}"
+            )
+        if error_message is not None:
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Get the number of complete years that will be run
+        self._run_Nyears = int(stop_n)
+
+        # Only allow RXCROPMATURITY to be called with test cropMonthOutput
+        casebaseid = self._case.get_value("CASEBASEID")
+        if casebaseid.split("-")[-1] != "cropMonthOutput":
+            error_message = (
+                "Only call RXCROPMATURITY with test cropMonthOutput "
+                + "to avoid potentially huge sets of daily outputs."
+            )
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Get files with prescribed sowing and harvest dates
+        self._get_rx_dates()
+
+        # Which conda environment should we use?
+        self._get_conda_env()
+
+    def _run_phase(self, skip_run=False):
+        # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
+        # want to be saved as baseline.
+
+        # -------------------------------------------------------------------
+        # (1) Set up GDD-generating run
+        # -------------------------------------------------------------------
+        # Create clone to be GDD-Generating case
+        logger.info("RXCROPMATURITY log:  cloning setup")
+        case_rxboth = self._case
+        caseroot = self._case.get_value("CASEROOT")
+        clone_path = f"{caseroot}.gddgen"
+        self._path_gddgen = clone_path
+        if os.path.exists(self._path_gddgen):
+            shutil.rmtree(self._path_gddgen)
+        logger.info("RXCROPMATURITY log:  cloning")
+        case_gddgen = self._case.create_clone(clone_path, keepexe=True)
+        logger.info("RXCROPMATURITY log:  done cloning")
+
+        os.chdir(self._path_gddgen)
+        self._set_active_case(case_gddgen)
+
+        # Set up stuff that applies to both tests
+        self._setup_all()
+
+        # Add stuff specific to GDD-Generating run
+        logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
+        self._append_to_user_nl_clm(
+            [
+                "generate_crop_gdds = .true.",
+                "use_mxmat = .false.",
+                " ",
+                "! (h2) Daily outputs for GDD generation and figure-making",
+                "hist_fincl3 = 'GDDACCUM', 'GDDHARV'",
+                "hist_nhtfrq(3) = -24",
+                "hist_mfilt(3) = 365",
+                "hist_type1d_pertape(3) = 'PFTS'",
+                "hist_dov2xy(3) = .false.",
+            ]
+        )
+
+        # If flanduse_timeseries is defined, we need to make a static version for this test. This
+        # should have every crop in most of the world.
+        self._get_flanduse_timeseries_in(case_gddgen)
+        if self._flanduse_timeseries_in is not None:
+
+            # Download files from the server, if needed
+            case_gddgen.check_all_input_data()
+
+            # Make custom version of surface file
+            logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
+            self._run_fsurdat_modifier()
+
+        # -------------------------------------------------------------------
+        # (2) Perform GDD-generating run and generate prescribed GDDs file
+        # -------------------------------------------------------------------
+        logger.info("RXCROPMATURITY log:  Start GDD-Generating run")
+
+        # As per SSP test:
+        # "No history files expected, set suffix=None to avoid compare error"
+        # We *do* expect history files here, but anyway. This works.
+        self._skip_pnl = False
+
+        if not skip_run:
+            self.run_indv(suffix=None, st_archive=True)
+            self._run_generate_gdds(case_gddgen)
+
+        # -------------------------------------------------------------------
+        # (3) Set up and perform Prescribed Calendars run
+        # -------------------------------------------------------------------
+        os.chdir(caseroot)
+        self._set_active_case(case_rxboth)
+
+        # Set up stuff that applies to both tests
+        self._setup_all()
+
+        # Add stuff specific to Prescribed Calendars run
+        logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
+        self._append_to_user_nl_clm(
+            [
+                "generate_crop_gdds = .false.",
+                f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'",
+            ]
+        )
+
+        if not skip_run:
+            self.run_indv()
+
+        # -------------------------------------------------------------------
+        # (4) Check Prescribed Calendars run
+        # -------------------------------------------------------------------
+        logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
+        if not skip_run:
+            self._run_check_rxboth_run()
+
+    # Get sowing and harvest dates for this resolution.
+    def _get_rx_dates(self):
+        # Eventually, I want to remove these hard-coded resolutions so that this test can generate
+        # its own sowing and harvest date files at whatever resolution is requested.
+        lnd_grid = self._case.get_value("LND_GRID")
+        input_data_root = self._case.get_value("DIN_LOC_ROOT")
+        processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed"
+        if lnd_grid == "10x15":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
+            )
+        elif lnd_grid == "1.9x2.5":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
+            )
+        elif lnd_grid == "0.9x1.25":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc",
+            )
+        else:
+            error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Ensure files exist
+        error_message = None
+        if not os.path.exists(self._sdatefile):
+            error_message = f"ERROR: Sowing date file not found: {self._sdatefile}"
+        elif not os.path.exists(self._hdatefile):
+            error_message = f"ERROR: Harvest date file not found: {self._sdatefile}"
+        if error_message is not None:
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+    def _setup_all(self):
+        logger.info("RXCROPMATURITY log:  _setup_all start")
+
+        # Get some info
+        self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND")
+        run_startdate = self._case.get_value("RUN_STARTDATE")
+        self._run_startyear = int(run_startdate.split("-")[0])
+
+        # Set sowing dates file (and other crop calendar settings) for all runs
+        logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
+        self._modify_user_nl_allruns()
+        logger.info("RXCROPMATURITY log:  _setup_all done")
+
+    # Make a surface dataset that has every crop in every gridcell
+    def _run_fsurdat_modifier(self):
+
+        # fsurdat should be defined. Where is it?
+        self._fsurdat_in = None
+        with open(self._lnd_in_path, "r") as lnd_in:
+            for line in lnd_in:
+                fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line)
+                if fsurdat_in:
+                    self._fsurdat_in = fsurdat_in.group(1)
+                    break
+        if self._fsurdat_in is None:
+            error_message = "fsurdat not defined"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Where we will save the fsurdat version for this test
+        path, ext = os.path.splitext(self._fsurdat_in)
+        dir_in, filename_in_noext = os.path.split(path)
+        self._fsurdat_out = os.path.join(
+            self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}"
+        )
+
+        # Make fsurdat for this test, if not already done
+        if not os.path.exists(self._fsurdat_out):
+            tool_path = os.path.join(
+                self._ctsm_root,
+                "tools",
+                "modify_input_files",
+                "fsurdat_modifier",
+            )
+
+            # Create configuration file for fsurdat_modifier
+            self._cfg_path = os.path.join(
+                self._path_gddgen,
+                "modify_fsurdat_allcropseverywhere.cfg",
+            )
+            self._create_config_file_evenlysplitcrop()
+
+            command = f"python3 {tool_path} {self._cfg_path} "
+            stu.run_python_script(
+                self._get_caseroot(),
+                self._this_conda_env,
+                command,
+                tool_path,
+            )
+
+        # Modify namelist
+        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
+        self._append_to_user_nl_clm(
+            [
+                "fsurdat = '{}'".format(self._fsurdat_out),
+                "do_transient_crops = .false.",
+                "flanduse_timeseries = ''",
+                "use_init_interp = .true.",
+            ]
+        )
+
+    def _create_config_file_evenlysplitcrop(self):
+        """
+        Open the new and the template .cfg files
+        Loop line by line through the template .cfg file
+        When string matches, replace that line's content
+        """
+        cfg_template_path = os.path.join(
+            self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg"
+        )
+
+        with open(self._cfg_path, "w", encoding="utf-8") as cfg_out:
+            # Copy template, replacing some lines
+            with open(cfg_template_path, "r", encoding="utf-8") as cfg_in:
+                for line in cfg_in:
+                    if re.match(r" *evenly_split_cropland *=", line):
+                        line = f"evenly_split_cropland = True"
+                    elif re.match(r" *fsurdat_in *=", line):
+                        line = f"fsurdat_in = {self._fsurdat_in}"
+                    elif re.match(r" *fsurdat_out *=", line):
+                        line = f"fsurdat_out = {self._fsurdat_out}"
+                    elif re.match(r" *process_subgrid_section *=", line):
+                        line = f"process_subgrid_section = True"
+                    cfg_out.write(line)
+
+            # Add new lines
+            cfg_out.write("\n")
+            cfg_out.write("[modify_fsurdat_subgrid_fractions]\n")
+            cfg_out.write("PCT_CROP    = 100.0\n")
+            cfg_out.write("PCT_NATVEG  = 0.0\n")
+            cfg_out.write("PCT_GLACIER = 0.0\n")
+            cfg_out.write("PCT_WETLAND = 0.0\n")
+            cfg_out.write("PCT_LAKE    = 0.0\n")
+            cfg_out.write("PCT_OCEAN   = 0.0\n")
+            cfg_out.write("PCT_URBAN   = 0.0 0.0 0.0\n")
+
+    def _run_check_rxboth_run(self):
+
+        output_dir = os.path.join(self._get_caseroot(), "run")
+        first_usable_year = self._run_startyear + 2
+        last_usable_year = self._run_startyear + self._run_Nyears - 2
+
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py"
+        )
+        command = (
+            f"python3 {tool_path} "
+            + f"--directory {output_dir} "
+            + f"-y1 {first_usable_year} "
+            + f"-yN {last_usable_year} "
+            + f"--rx-sdates-file {self._sdatefile} "
+            + f"--rx-gdds-file {self._gdds_file} "
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
+    def _modify_user_nl_allruns(self):
+        nl_additions = [
+            "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
+            "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
+            "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
+            "stream_year_first_cropcal = 2000",
+            "stream_year_last_cropcal = 2000",
+            "model_year_align_cropcal = 2000",
+            " ",
+            "! (h1) Annual outputs on sowing or harvest axis",
+            "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'",
+            "hist_nhtfrq(2) = 17520",
+            "hist_mfilt(2) = 999",
+            "hist_type1d_pertape(2) = 'PFTS'",
+            "hist_dov2xy(2) = .false.",
+        ]
+        self._append_to_user_nl_clm(nl_additions)
+
+    def _run_generate_gdds(self, case_gddgen):
+        self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out")
+        os.makedirs(self._generate_gdds_dir)
+
+        # Get arguments to generate_gdds.py
+        dout_sr = case_gddgen.get_value("DOUT_S_ROOT")
+        input_dir = os.path.join(dout_sr, "lnd", "hist")
+        first_season = self._run_startyear + 2
+        last_season = self._run_startyear + self._run_Nyears - 2
+        sdates_file = self._sdatefile
+        hdates_file = self._hdatefile
+
+        # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds.
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py"
+        )
+        command = " ".join(
+            [
+                f"python3 {tool_path}",
+                f"--input-dir {input_dir}",
+                f"--first-season {first_season}",
+                f"--last-season {last_season}",
+                f"--sdates-file {sdates_file}",
+                f"--hdates-file {hdates_file}",
+                f"--output-dir generate_gdds_out",
+                f"--skip-crops miscanthus,irrigated_miscanthus",
+            ]
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
+        # Where were the prescribed maturity requirements saved?
+        generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc"))
+        if len(generated_gdd_files) != 1:
+            error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+        self._gdds_file = generated_gdd_files[0]
+
+    def _get_conda_env(self):
+        conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot())
+
+        # If npl conda environment is available, use that (It has dask, which
+        # enables chunking, which makes reading daily 1-degree netCDF files
+        # much more efficient.
+        if "npl " in os.popen(conda_setup_commands + "conda env list").read():
+            self._this_conda_env = "npl"
+        else:
+            self._this_conda_env = "ctsm_pylib"
+
+    def _append_to_user_nl_clm(self, additions):
+        caseroot = self._get_caseroot()
+        append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions)
+
+    # Is flanduse_timeseries defined? If so, where is it?
+    def _get_flanduse_timeseries_in(self, case):
+        case.create_namelists(component="lnd")
+        self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in")
+        self._flanduse_timeseries_in = None
+        with open(self._lnd_in_path, "r") as lnd_in:
+            for line in lnd_in:
+                flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line)
+                if flanduse_timeseries_in:
+                    self._flanduse_timeseries_in = flanduse_timeseries_in.group(1)
+                    break
diff --git a/cime_config/SystemTests/rxcropmaturityskipbuild.py b/cime_config/SystemTests/rxcropmaturityskipbuild.py
new file mode 100644
index 0000000000..0e16c757fc
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityskipbuild.py
@@ -0,0 +1,9 @@
+from rxcropmaturityshared import RXCROPMATURITYSHARED
+
+
+class RXCROPMATURITYSKIPBUILD(RXCROPMATURITYSHARED):
+    def build_indv(self, sharedlib_only=False, model_only=False):
+        self._case.set_value("BUILD_COMPLETE", "TRUE")
+
+    def run_phase(self):
+        self._run_phase(skip_run=False)
diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py
new file mode 100644
index 0000000000..24fc288373
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityskiprun.py
@@ -0,0 +1,9 @@
+from rxcropmaturityshared import RXCROPMATURITYSHARED
+
+
+class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED):
+    def build_indv(self, sharedlib_only=False, model_only=False):
+        self._case.set_value("BUILD_COMPLETE", "TRUE")
+
+    def run_phase(self):
+        self._run_phase(skip_run=True)
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index c0b6afed9d..115f4c0e89 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -133,6 +133,26 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="RXCROPMATURITYSKIPRUN">
+    <DESC>As RXCROPMATURITY but don't actually run or postprocess; just setup</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
+  <test NAME="RXCROPMATURITYSKIPBUILD">
+    <DESC>As RXCROPMATURITY but don't actually build; just setup and then start "run." Will fail when run start is requested, but should successfully test preprocessing.</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

From 5b3b8afc4f1aa8d8b1a0d13f7bfe822eced2a2df Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 12 Jun 2024 10:47:09 -0600
Subject: [PATCH 0500/1248] RXCROPMATURITY: copy .env_mach_specific.sh to
 gddgen dir.

---
 cime_config/SystemTests/rxcropmaturityshared.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
index 6b3a3191de..0fc8a91cc2 100644
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -137,6 +137,12 @@ def _run_phase(self, skip_run=False):
             # Download files from the server, if needed
             case_gddgen.check_all_input_data()
 
+            # Copy needed file from original to gddgen directory
+            shutil.copyfile(
+                os.path.join(caseroot, ".env_mach_specific.sh"),
+                os.path.join(self._path_gddgen, ".env_mach_specific.sh"),
+            )
+
             # Make custom version of surface file
             logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
             self._run_fsurdat_modifier()

From a2c792f7b285b9d713ca6b16cce3cdf59fa4d37d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 10:39:01 -0600
Subject: [PATCH 0501/1248] Add interpolate_gdds.py.

---
 .../ctsm/crop_calendars/interpolate_gdds.py   | 150 ++++++++++++++++++
 1 file changed, 150 insertions(+)
 create mode 100755 python/ctsm/crop_calendars/interpolate_gdds.py

diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py
new file mode 100755
index 0000000000..b740766d3b
--- /dev/null
+++ b/python/ctsm/crop_calendars/interpolate_gdds.py
@@ -0,0 +1,150 @@
+"""
+Interpolate a maturity requirement (GDD) file
+"""
+
+import os
+import sys
+import argparse
+import logging
+import xarray as xr
+
+# -- add python/ctsm  to path (needed if we want to run this stand-alone)
+_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir)
+sys.path.insert(1, _CTSM_PYTHON)
+
+from ctsm import ctsm_logging  # pylint: disable=wrong-import-position
+
+logger = logging.getLogger(__name__)
+
+OUTPUT_FORMAT = "NETCDF3_CLASSIC"
+
+
+def _file_missing(filepath, descriptor):
+    if not os.path.exists(filepath) and not os.path.exists(os.path.realpath(filepath)):
+        raise FileNotFoundError(f"{descriptor} not found: {filepath}")
+    return os.path.realpath(filepath)
+
+
+def _setup_process_args():
+    """Process input arguments
+
+    Returns:
+        argparse.ArgumentParser: Arguments/options
+    """
+
+    # set up logging allowing user control
+    ctsm_logging.setup_logging_pre_config()
+
+    parser = argparse.ArgumentParser(
+        description=("Interpolate a maturity requirement (GDD) file."),
+    )
+
+    # Define arguments
+    parser.add_argument(
+        "-i",
+        "--input-file",
+        help="Maturity requirement file to interpolate",
+        type=lambda x: _file_missing(x, "Input file"),
+        required=True,
+    )
+    parser.add_argument(
+        "-t",
+        "--target-file",
+        help="File to whose coordinates the interpolation should take place",
+        type=lambda x: _file_missing(x, "Target file"),
+        required=True,
+    )
+    parser.add_argument(
+        "-o",
+        "--output-file",
+        help="Where to save interpolated result",
+        type=str,
+        required=True,
+    )
+    parser.add_argument(
+        "--overwrite",
+        help="If output file exists, overwrite it.",
+        action="store_true",
+        required=False,
+    )
+    parser.add_argument(
+        "--dry-run",
+        help="Check arguments but do not run.",
+        action="store_true",
+        required=False,
+    )
+    ctsm_logging.add_logging_args(parser)
+
+    # Get arguments
+    args = parser.parse_args(sys.argv[1:])
+    ctsm_logging.process_logging_args(args)
+
+    # Process arguments
+    if os.path.exists(os.path.realpath(args.output_file)) and not args.overwrite:
+        raise FileExistsError(f"Output file exists but --overwrite not given: {args.output_file}")
+    args.output_file = os.path.realpath(args.output_file)
+
+    # Make directory for output file, if needed
+    if not args.dry_run:
+        parent_dir = os.path.dirname(args.output_file)
+        if not os.path.exists(parent_dir):
+            os.makedirs(parent_dir)
+
+    return args
+
+
+def interpolate_gdds(args):
+    """
+    Do the interpolation and save
+    """
+
+    # Open inputs
+    ds_in = xr.open_dataset(args.input_file)
+    ds_target = xr.open_dataset(args.target_file)
+
+    # Interpolate
+    ds_out = xr.Dataset()
+    for var in ds_in:
+
+        # Check variable
+        if "gdd1_" not in var:
+            raise RuntimeError(f"Unexpected variable {var} on input file")
+        if args.dry_run:
+            continue
+
+        # Interpolate
+        da_in = ds_in[var]
+        da_out = ds_in[var].interp_like(ds_target)
+
+        # Ensure minimum GDD is respected
+        min_allowed = min(0, da_in.min())
+        da_out = da_out.where(da_out >= min_allowed)
+        da_out = da_out.fillna(min_allowed)
+
+        # Add to dataset
+        ds_out[var] = da_out
+
+    # Finish up
+    ds_out.attrs["original"] = args.input_file
+    ds_out.attrs["interpolation_target"] = args.target_file
+    ds_out.attrs["interpolation_script"] = os.path.basename(__file__)
+    if not args.dry_run:
+        ds_out.to_netcdf(args.output_file, format=OUTPUT_FORMAT)
+    else:
+        print("Dry run looks good!")
+
+
+def main():
+    """
+    Description
+    -----------
+    Calls function that interpolates a maturity requirement (GDD) file.
+    """
+
+    args = _setup_process_args()
+
+    interpolate_gdds(args)
+
+
+if __name__ == "__main__":
+    main()

From 39798ea2b05d0d1d970b35dee0ff95f61c6e55df Mon Sep 17 00:00:00 2001
From: Sean Swenson <swensosc@ucar.edu>
Date: Fri, 14 Jun 2024 11:26:31 -0600
Subject: [PATCH 0502/1248] add hillslope_fsat_equals_zero

---
 bld/CLMBuildNamelist.pm                         |  1 +
 bld/namelist_files/namelist_defaults_ctsm.xml   |  1 +
 bld/namelist_files/namelist_definition_ctsm.xml |  5 +++++
 src/biogeophys/SaturatedExcessRunoffMod.F90     | 17 +++++++++++++++--
 src/main/clm_varctl.F90                         |  2 ++
 src/main/controlMod.F90                         |  7 ++++++-
 6 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index f65414e4af..fbf7b9a8bc 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -3525,6 +3525,7 @@ sub setup_logic_hillslope {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_pft_distribution_method' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_soil_profile_method' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope_routing', 'use_hillslope'=>$nl_flags->{'use_hillslope'} );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_fsat_equals_zero', 'use_hillslope'=>$nl_flags->{'use_hillslope'} );
   my $use_hillslope = $nl->get_value('use_hillslope');
   my $use_hillslope_routing = $nl->get_value('use_hillslope_routing');
   if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 655e97c47c..e04db59cae 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -596,6 +596,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <hillslope_pft_distribution_method           >Standard</hillslope_pft_distribution_method>
 <hillslope_soil_profile_method               >Uniform</hillslope_soil_profile_method>
 <downscale_hillslope_meteorology             >.true.</downscale_hillslope_meteorology>
+<hillslope_fsat_equals_zero                  >.true.</hillslope_fsat_equals_zero>
 
 <!-- Plant hydraulic stress -->
 <use_hydrstress                                                       >.false.</use_hydrstress>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 37c457141c..1a6a5581a8 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -828,6 +828,11 @@ Toggle to turn on meteorological downscaling in hillslope model
 Toggle to turn on surface water routing in the hillslope hydrology model
 </entry>
 
+<entry id="hillslope_fsat_equals_zero" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".true.">
+If true, set fsat to zero for hillslope columns
+</entry>
+
 <entry id="hillslope_head_gradient_method" type="char*256" category="physics"
         group="hillslope_hydrology_inparm" valid_values="Kinematic,Darcy">
 Method for calculating hillslope saturated head gradient
diff --git a/src/biogeophys/SaturatedExcessRunoffMod.F90 b/src/biogeophys/SaturatedExcessRunoffMod.F90
index 5643a95394..9956a7dfb8 100644
--- a/src/biogeophys/SaturatedExcessRunoffMod.F90
+++ b/src/biogeophys/SaturatedExcessRunoffMod.F90
@@ -12,8 +12,8 @@ module SaturatedExcessRunoffMod
   use shr_log_mod  , only : errMsg => shr_log_errMsg
   use decompMod    , only : bounds_type
   use abortutils   , only : endrun
-  use clm_varctl   , only : iulog, use_vichydro, crop_fsat_equals_zero
-  use clm_varcon   , only : spval
+  use clm_varctl   , only : iulog, use_vichydro, crop_fsat_equals_zero, hillslope_fsat_equals_zero
+  use clm_varcon   , only : spval,ispval
   use LandunitType , only : landunit_type
   use landunit_varcon  , only : istcrop
   use ColumnType   , only : column_type
@@ -266,6 +266,19 @@ subroutine SaturatedExcessRunoff (this, bounds, num_hydrologyc, filter_hydrology
        end do
     endif
 
+    ! ------------------------------------------------------------------------
+    ! Set fsat to zero for upland hillslope columns
+    ! ------------------------------------------------------------------------
+    if (hillslope_fsat_equals_zero) then
+       do fc = 1, num_hydrologyc
+          c = filter_hydrologyc(fc)
+          if(col%is_hillslope_column(c) .and. col%active(c)) then
+             ! Set fsat to zero for upland columns
+             if (col%cold(c) /= ispval) fsat(c) = 0._r8
+          endif
+       end do
+    endif
+
     ! ------------------------------------------------------------------------
     ! Compute qflx_sat_excess_surf
     !
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 0daedbbb1f..7423b5ad6a 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -414,6 +414,8 @@ module clm_varctl
   logical, public :: use_hillslope = .false. ! true => use multi-column hillslope hydrology
   logical, public :: downscale_hillslope_meteorology = .false. ! true => downscale meteorological forcing in hillslope model
   logical, public :: use_hillslope_routing = .false. ! true => use surface water routing in hillslope hydrology
+  logical, public :: hillslope_fsat_equals_zero = .false. ! set saturated excess runoff to zero for hillslope columns
+
 
   !----------------------------------------------------------
   ! excess ice physics switch
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 46d9e9958a..cde67aa12a 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -270,6 +270,8 @@ subroutine control_init(dtime)
 
     namelist /clm_inparm/ use_hillslope_routing
 
+    namelist /clm_inparm/ hillslope_fsat_equals_zero
+
     namelist /clm_inparm/ use_hydrstress
 
     namelist /clm_inparm/ use_dynroot
@@ -840,6 +842,8 @@ subroutine control_spmd()
 
     call mpi_bcast (use_hillslope_routing, 1, MPI_LOGICAL, 0, mpicom, ier)
 
+    call mpi_bcast (hillslope_fsat_equals_zero, 1, MPI_LOGICAL, 0, mpicom, ier)
+
     call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier)
 
     call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -1124,8 +1128,9 @@ subroutine control_print ()
 
     write(iulog,*) '   land-ice albedos      (unitless 0-1)   = ', albice
     write(iulog,*) '   hillslope hydrology    = ', use_hillslope
-    write(iulog,*) '   downscale hillslope meteorology    = ', downscale_hillslope_meteorology
+    write(iulog,*) '   downscale hillslope meteorology  = ', downscale_hillslope_meteorology
     write(iulog,*) '   hillslope routing      = ', use_hillslope_routing
+    write(iulog,*) '   hillslope_fsat_equals_zero       = ', hillslope_fsat_equals_zero
     write(iulog,*) '   pre-defined soil layer structure = ', soil_layerstruct_predefined
     write(iulog,*) '   user-defined soil layer structure = ', soil_layerstruct_userdefined
     write(iulog,*) '   user-defined number of soil layers = ', soil_layerstruct_userdefined_nlevsoi

From 46307bca0a850876c67a3041bf786a76441ca853 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 14:19:01 -0600
Subject: [PATCH 0503/1248] generate_gdds: Don't fail if making figures but
 GDDHARV alll NaN.

---
 .../crop_calendars/generate_gdds_functions.py | 32 +++++++++++++------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index 8af2fdc049..38c5d44384 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -575,6 +575,7 @@ def import_and_process_1yr(
         this_crop_gddaccum_da = this_crop_ds[clm_gdd_var]
         if save_figs:
             this_crop_gddharv_da = this_crop_ds["GDDHARV"]
+            check_gddharv = True
         if not this_crop_gddaccum_da.size:
             continue
         log(logger, f"      {vegtype_str}...")
@@ -625,11 +626,18 @@ def import_and_process_1yr(
                 + "NaN after extracting GDDs accumulated at harvest",
             )
         if save_figs and np.any(np.isnan(gddharv_atharv_p)):
-            log(
-                logger,
-                f"         ❗ {np.sum(np.isnan(gddharv_atharv_p))}/{len(gddharv_atharv_p)} "
-                + "NaN after extracting GDDHARV",
-            )
+            if np.all(np.isnan(gddharv_atharv_p)):
+                log(
+                    logger,
+                    "         ❗ All GDDHARV are NaN; should only affect figure"
+                )
+                check_gddharv = False
+            else:
+                log(
+                    logger,
+                    f"         ❗ {np.sum(np.isnan(gddharv_atharv_p))}/{len(gddharv_atharv_p)} "
+                    + "NaN after extracting GDDHARV",
+                )
 
         # Assign these to growing seasons based on whether gs crossed new year
         this_year_active_patch_indices = [
@@ -712,7 +720,7 @@ def import_and_process_1yr(
                     )
                 else:
                     error(logger, "Unexpected NaN for last season's GDD accumulation.")
-            if save_figs and np.any(
+            if save_figs and check_gddharv and np.any(
                 np.isnan(
                     gddharv_yp_list[var][year_index - 1, active_this_year_where_gs_lastyr_indices]
                 )
@@ -1160,9 +1168,13 @@ def make_figures(
             else:
                 error(logger, f"layout {layout} not recognized")
 
-            this_min = int(np.round(np.nanmin(gddharv_map_yx)))
-            this_max = int(np.round(np.nanmax(gddharv_map_yx)))
-            this_title = f"{run1_name} (range {this_min}–{this_max})"
+            gddharv_all_nan = np.all(np.isnan(gddharv_map_yx.values))
+            if gddharv_all_nan:
+                this_title = f"{run1_name} (GDDHARV all NaN?)"
+            else:
+                this_min = int(np.round(np.nanmin(gddharv_map_yx)))
+                this_max = int(np.round(np.nanmax(gddharv_map_yx)))
+                this_title = f"{run1_name} (range {this_min}–{this_max})"
             make_gengdd_map(
                 this_axis,
                 gddharv_map_yx,
@@ -1195,7 +1207,7 @@ def make_figures(
             )
 
             # Difference
-            if layout == "3x2":
+            if not gddharv_all_nan and layout == "3x2":
                 this_axis = fig.add_subplot(spec[2, 0], projection=ccrs.PlateCarree())
                 this_min = int(np.round(np.nanmin(gdd_map_yx)))
                 this_max = int(np.round(np.nanmax(gdd_map_yx)))

From faa536eb00c0afb70cacce239423a5af82ccaf5a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 14:47:19 -0600
Subject: [PATCH 0504/1248] Revert "PlantCrop: GDD-gen runs get gddmaturity
 1e36."

GDD-generating runs should get the CLM default gddmaturity values.

This reverts commit f2518b611408c12ae262c1b71b9b0a128196c934.
---
 src/biogeochem/CNPhenologyMod.F90 | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 41d4107f3f..b346cb119f 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2694,10 +2694,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
 
       ! set GDD target
       did_rx_gdds = .false.
-      if (generate_crop_gdds) then
-         ! Value mostly doesn't matter; it just needs to be large enough to avoid divide-by-zero errors.
-         gddmaturity(p) = 1.e36_r8
-      else if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
+      if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then
          gddmaturity(p) = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p))
          did_rx_gdds = .true.
          if (adapt_cropcal_rx_cultivar_gdds .and. crop_inst%gdd20_baseline_patch(p) > min_gdd20_baseline) then

From bbd63275549c1ad6cfa51bccacccb01e169772d4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 11:09:53 -0600
Subject: [PATCH 0505/1248] Add RXCROPMATURITYSKIPGEN test.

---
 .../SystemTests/rxcropmaturityshared.py       | 71 +++++++++++++++++--
 .../SystemTests/rxcropmaturityskipgen.py      |  7 ++
 cime_config/config_tests.xml                  | 10 +++
 3 files changed, 81 insertions(+), 7 deletions(-)
 create mode 100644 cime_config/SystemTests/rxcropmaturityskipgen.py

diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
index 0fc8a91cc2..991fe687b5 100644
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ b/cime_config/SystemTests/rxcropmaturityshared.py
@@ -24,6 +24,7 @@
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
+from CIME.case import Case
 import shutil, glob
 
 logger = logging.getLogger(__name__)
@@ -34,6 +35,11 @@ def __init__(self, case):
         # initialize an object interface to the SMS system test
         SystemTestsCommon.__init__(self, case)
 
+        # Is this a real RXCROPMATURITY test or not?
+        casebaseid = self._case.get_value("CASEBASEID")
+        full_test = "RXCROPMATURITY_" in casebaseid
+        skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid
+
         # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
         stop_n = self._case.get_value("STOP_N")
         stop_option = self._case.get_value("STOP_OPTION")
@@ -60,11 +66,17 @@ def __init__(self, case):
                 f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), "
                 + "nhour(s), nday(s), nmonth(s), or nyear(s)"
             )
-        elif stop_n < 5:
+        elif full_test and stop_n < 5:
             error_message = (
                 "RXCROPMATURITY must be run for at least 5 years; you requested "
                 + f"{stop_n_orig} {stop_option_orig[1:]}"
             )
+        elif skipgen_test and stop_n < 3:
+            # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish.
+            error_message = (
+                "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested "
+                + f"{stop_n_orig} {stop_option_orig[1:]}"
+            )
         if error_message is not None:
             logger.error(error_message)
             raise RuntimeError(error_message)
@@ -73,7 +85,6 @@ def __init__(self, case):
         self._run_Nyears = int(stop_n)
 
         # Only allow RXCROPMATURITY to be called with test cropMonthOutput
-        casebaseid = self._case.get_value("CASEBASEID")
         if casebaseid.split("-")[-1] != "cropMonthOutput":
             error_message = (
                 "Only call RXCROPMATURITY with test cropMonthOutput "
@@ -85,10 +96,17 @@ def __init__(self, case):
         # Get files with prescribed sowing and harvest dates
         self._get_rx_dates()
 
+        # Get cultivar maturity requirement file to fall back on if not generating it here
+        self._gdds_file = None
+        self._fallback_gdds_file = os.path.join(
+            os.path.dirname(self._sdatefile),
+            "gdds_20230829_161011.nc"
+        )
+
         # Which conda environment should we use?
         self._get_conda_env()
 
-    def _run_phase(self, skip_run=False):
+    def _run_phase(self, skip_run=False, skip_gen=False):
         # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
         # want to be saved as baseline.
 
@@ -157,8 +175,18 @@ def _run_phase(self, skip_run=False):
         # We *do* expect history files here, but anyway. This works.
         self._skip_pnl = False
 
+        # If not generating GDDs, only run a few days of this.
+        if skip_gen:
+            with Case(self._path_gddgen, read_only=False) as case:
+                case.set_value("STOP_N", 5)
+                case.set_value("STOP_OPTION", "ndays")
+
         if not skip_run:
             self.run_indv(suffix=None, st_archive=True)
+        if skip_gen:
+            # Interpolate an existing GDD file. Needed to check obedience to GDD inputs.
+            self._run_interpolate_gdds()
+        else:
             self._run_generate_gdds(case_gddgen)
 
         # -------------------------------------------------------------------
@@ -187,7 +215,7 @@ def _run_phase(self, skip_run=False):
         # -------------------------------------------------------------------
         logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
         if not skip_run:
-            self._run_check_rxboth_run()
+            self._run_check_rxboth_run(skip_gen)
 
     # Get sowing and harvest dates for this resolution.
     def _get_rx_dates(self):
@@ -344,11 +372,16 @@ def _create_config_file_evenlysplitcrop(self):
             cfg_out.write("PCT_OCEAN   = 0.0\n")
             cfg_out.write("PCT_URBAN   = 0.0 0.0 0.0\n")
 
-    def _run_check_rxboth_run(self):
+    def _run_check_rxboth_run(self, skip_gen):
 
         output_dir = os.path.join(self._get_caseroot(), "run")
-        first_usable_year = self._run_startyear + 2
-        last_usable_year = self._run_startyear + self._run_Nyears - 2
+
+        if skip_gen:
+            first_usable_year = self._run_startyear + 1
+            last_usable_year = first_usable_year
+        else:
+            first_usable_year = self._run_startyear + 2
+            last_usable_year = self._run_startyear + self._run_Nyears - 2
 
         tool_path = os.path.join(
             self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py"
@@ -429,6 +462,30 @@ def _run_generate_gdds(self, case_gddgen):
             raise RuntimeError(error_message)
         self._gdds_file = generated_gdd_files[0]
 
+    def _run_interpolate_gdds(self):
+        # Save where?
+        self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc")
+
+        # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds.
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py"
+        )
+        command = " ".join(
+            [
+                f"python3 {tool_path}",
+                f"--input-file {self._fallback_gdds_file}",
+                f"--target-file {self._sdatefile}",
+                f"--output-file {self._gdds_file}",
+                "--overwrite",
+            ]
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
     def _get_conda_env(self):
         conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot())
 
diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py
new file mode 100644
index 0000000000..4fb5257967
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityskipgen.py
@@ -0,0 +1,7 @@
+from rxcropmaturityshared import RXCROPMATURITYSHARED
+
+
+class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED):
+
+    def run_phase(self):
+        self._run_phase(skip_run=False, skip_gen=True)
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index 115f4c0e89..cbddc31b8d 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -133,6 +133,16 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="RXCROPMATURITYSKIPGEN">
+    <DESC>As RXCROPMATURITY but don't actually generate GDDs. Allows short testing with existing GDD inputs.</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
   <test NAME="RXCROPMATURITYSKIPRUN">
     <DESC>As RXCROPMATURITY but don't actually run or postprocess; just setup</DESC>
     <INFO_DBUG>1</INFO_DBUG>

From 6bf99769d28391828b3cf72729ec8b120f0b839f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 15:33:24 -0600
Subject: [PATCH 0506/1248] interpolate_gdds: nearest-neighbor for safety.

---
 python/ctsm/crop_calendars/cropcal_module.py   | 17 +++++++++++++----
 python/ctsm/crop_calendars/interpolate_gdds.py | 18 +++++++++++-------
 2 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index 3fe6942f94..d25e16397e 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -13,6 +13,8 @@
 from ctsm.crop_calendars.cropcal_constants import DEFAULT_GDD_MIN
 from ctsm.crop_calendars.import_ds import import_ds
 
+MISSING_RX_GDD_VAL = -1
+
 
 def check_and_trim_years(year_1, year_n, ds_in):
     """
@@ -231,6 +233,13 @@ def import_max_gs_length(paramfile_dir, my_clm_ver, my_clm_subver):
     return mxmat_dict
 
 
+def unexpected_negative_rx_gdd(data_array):
+    """
+    Return True if there's a negative value not matching the designated missing value
+    """
+    return np.any((data_array.values < 0) & (data_array.values != MISSING_RX_GDD_VAL))
+
+
 def import_rx_dates(var_prefix, date_infile, dates_ds, set_neg1_to_nan=True):
     """
     Import prescribed sowing/harvest dates
@@ -260,19 +269,19 @@ def import_rx_dates(var_prefix, date_infile, dates_ds, set_neg1_to_nan=True):
         v_new = var.replace(var_prefix, "gs")
         this_ds = this_ds.rename({var: v_new})
 
-        # Set -1 prescribed GDD values to NaN. Only warn the first time.
+        # Set GDD values matching MISSING_RX_GDD_VAL to NaN. Only warn the first time.
         if (
             set_neg1_to_nan
             and var_prefix == "gdd"
             and v_new != var
             and np.any(this_ds[v_new].values < 0)
         ):
-            if np.any((this_ds[v_new].values < 0) & (this_ds[v_new].values != -1)):
+            if unexpected_negative_rx_gdd(this_ds[v_new]):
                 raise RuntimeError(f"Unexpected negative value in {var}")
             if not did_warn:
-                print("Setting -1 rx GDD values to NaN")
+                print(f"Setting {MISSING_RX_GDD_VAL} rx GDD values to NaN")
                 did_warn = True
-            this_ds[v_new] = this_ds[v_new].where(this_ds[v_new] != -1)
+            this_ds[v_new] = this_ds[v_new].where(this_ds[v_new] != MISSING_RX_GDD_VAL)
 
     return this_ds
 
diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py
index b740766d3b..e9491480e9 100755
--- a/python/ctsm/crop_calendars/interpolate_gdds.py
+++ b/python/ctsm/crop_calendars/interpolate_gdds.py
@@ -13,6 +13,9 @@
 sys.path.insert(1, _CTSM_PYTHON)
 
 from ctsm import ctsm_logging  # pylint: disable=wrong-import-position
+from ctsm.crop_calendars.cropcal_module import ( # pylint: disable=wrong-import-position
+    unexpected_negative_rx_gdd,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -113,13 +116,14 @@ def interpolate_gdds(args):
             continue
 
         # Interpolate
-        da_in = ds_in[var]
-        da_out = ds_in[var].interp_like(ds_target)
-
-        # Ensure minimum GDD is respected
-        min_allowed = min(0, da_in.min())
-        da_out = da_out.where(da_out >= min_allowed)
-        da_out = da_out.fillna(min_allowed)
+        da_out = ds_in[var].interp_like(
+            ds_target,
+            method="nearest",
+            kwargs={"fill_value": "extrapolate"},  # Otherwise you get NaNs at edges
+        )
+
+        if unexpected_negative_rx_gdd(da_out):
+            raise RuntimeError("Unexpected negative value")
 
         # Add to dataset
         ds_out[var] = da_out

From 81177dd169e3c2f15f97a23216eb9793de4d8f3a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 16:10:34 -0600
Subject: [PATCH 0507/1248] Revert all RXCROPMATURITY changes.

---
 cime_config/SystemTests/rxcropmaturity.py     | 445 ++++++++++++++++-
 .../SystemTests/rxcropmaturityshared.py       | 459 ------------------
 .../SystemTests/rxcropmaturityskipbuild.py    |   9 -
 .../SystemTests/rxcropmaturityskiprun.py      |   9 -
 cime_config/config_tests.xml                  |  20 -
 5 files changed, 442 insertions(+), 500 deletions(-)
 delete mode 100644 cime_config/SystemTests/rxcropmaturityshared.py
 delete mode 100644 cime_config/SystemTests/rxcropmaturityskipbuild.py
 delete mode 100644 cime_config/SystemTests/rxcropmaturityskiprun.py

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 206476f051..75fff8a0e0 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -1,5 +1,444 @@
-from rxcropmaturityshared import RXCROPMATURITYSHARED
+"""
+CTSM-specific test that first performs a GDD-generating run, then calls
+Python code to generate the maturity requirement file. This is then used
+in a sowing+maturity forced run, which finally is tested to ensure
+correct behavior.
+
+Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually,
+this test should be able to generate its own files at whatever resolution it's
+called at. Well, really, the ultimate goal would be to give CLM the files
+at the original resolution (for GGCMI phase 3, 0.5°) and have the stream
+code do the interpolation. However, that wouldn't act on harvest dates
+(which are needed for generate_gdds.py). I could have Python interpolate
+those, but this would cause a potential inconsistency.
+"""
+
+import os
+import re
+import systemtest_utils as stu
+import subprocess
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+from CIME.XML.standard_module_setup import *
+from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
+import shutil, glob
+
+logger = logging.getLogger(__name__)
+
+
+class RXCROPMATURITY(SystemTestsCommon):
+    def __init__(self, case):
+        # initialize an object interface to the SMS system test
+        SystemTestsCommon.__init__(self, case)
+
+        # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
+        stop_n = self._case.get_value("STOP_N")
+        stop_option = self._case.get_value("STOP_OPTION")
+        stop_n_orig = stop_n
+        stop_option_orig = stop_option
+        if "nsecond" in stop_option:
+            stop_n /= 60
+            stop_option = "nminutes"
+        if "nminute" in stop_option:
+            stop_n /= 60
+            stop_option = "nhours"
+        if "nhour" in stop_option:
+            stop_n /= 24
+            stop_option = "ndays"
+        if "nday" in stop_option:
+            stop_n /= 365
+            stop_option = "nyears"
+        if "nmonth" in stop_option:
+            stop_n /= 12
+            stop_option = "nyears"
+        error_message = None
+        if "nyear" not in stop_option:
+            error_message = (
+                f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), "
+                + "nhour(s), nday(s), nmonth(s), or nyear(s)"
+            )
+        elif stop_n < 5:
+            error_message = (
+                "RXCROPMATURITY must be run for at least 5 years; you requested "
+                + f"{stop_n_orig} {stop_option_orig[1:]}"
+            )
+        if error_message is not None:
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Get the number of complete years that will be run
+        self._run_Nyears = int(stop_n)
+
+        # Only allow RXCROPMATURITY to be called with test cropMonthOutput
+        casebaseid = self._case.get_value("CASEBASEID")
+        if casebaseid.split("-")[-1] != "cropMonthOutput":
+            error_message = (
+                "Only call RXCROPMATURITY with test cropMonthOutput "
+                + "to avoid potentially huge sets of daily outputs."
+            )
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Get files with prescribed sowing and harvest dates
+        self._get_rx_dates()
+
+        # Which conda environment should we use?
+        self._get_conda_env()
 
-class RXCROPMATURITY(RXCROPMATURITYSHARED):
     def run_phase(self):
-        self._run_phase()
\ No newline at end of file
+        # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
+        # want to be saved as baseline.
+
+        # -------------------------------------------------------------------
+        # (1) Set up GDD-generating run
+        # -------------------------------------------------------------------
+        # Create clone to be GDD-Generating case
+        logger.info("RXCROPMATURITY log:  cloning setup")
+        case_rxboth = self._case
+        caseroot = self._case.get_value("CASEROOT")
+        clone_path = f"{caseroot}.gddgen"
+        self._path_gddgen = clone_path
+        if os.path.exists(self._path_gddgen):
+            shutil.rmtree(self._path_gddgen)
+        logger.info("RXCROPMATURITY log:  cloning")
+        case_gddgen = self._case.create_clone(clone_path, keepexe=True)
+        logger.info("RXCROPMATURITY log:  done cloning")
+
+        os.chdir(self._path_gddgen)
+        self._set_active_case(case_gddgen)
+
+        # Set up stuff that applies to both tests
+        self._setup_all()
+
+        # Add stuff specific to GDD-Generating run
+        logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
+        self._append_to_user_nl_clm(
+            [
+                "generate_crop_gdds = .true.",
+                "use_mxmat = .false.",
+                " ",
+                "! (h2) Daily outputs for GDD generation and figure-making",
+                "hist_fincl3 = 'GDDACCUM', 'GDDHARV'",
+                "hist_nhtfrq(3) = -24",
+                "hist_mfilt(3) = 365",
+                "hist_type1d_pertape(3) = 'PFTS'",
+                "hist_dov2xy(3) = .false.",
+            ]
+        )
+
+        # If flanduse_timeseries is defined, we need to make a static version for this test. This
+        # should have every crop in most of the world.
+        self._get_flanduse_timeseries_in(case_gddgen)
+        if self._flanduse_timeseries_in is not None:
+
+            # Download files from the server, if needed
+            case_gddgen.check_all_input_data()
+
+            # Make custom version of surface file
+            logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
+            self._run_fsurdat_modifier()
+
+        # -------------------------------------------------------------------
+        # (2) Perform GDD-generating run and generate prescribed GDDs file
+        # -------------------------------------------------------------------
+        logger.info("RXCROPMATURITY log:  Start GDD-Generating run")
+
+        # As per SSP test:
+        # "No history files expected, set suffix=None to avoid compare error"
+        # We *do* expect history files here, but anyway. This works.
+        self._skip_pnl = False
+        self.run_indv(suffix=None, st_archive=True)
+
+        self._run_generate_gdds(case_gddgen)
+
+        # -------------------------------------------------------------------
+        # (3) Set up and perform Prescribed Calendars run
+        # -------------------------------------------------------------------
+        os.chdir(caseroot)
+        self._set_active_case(case_rxboth)
+
+        # Set up stuff that applies to both tests
+        self._setup_all()
+
+        # Add stuff specific to Prescribed Calendars run
+        logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
+        self._append_to_user_nl_clm(
+            [
+                "generate_crop_gdds = .false.",
+                f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'",
+            ]
+        )
+
+        self.run_indv()
+
+        # -------------------------------------------------------------------
+        # (4) Check Prescribed Calendars run
+        # -------------------------------------------------------------------
+        logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
+        self._run_check_rxboth_run()
+
+    # Get sowing and harvest dates for this resolution.
+    def _get_rx_dates(self):
+        # Eventually, I want to remove these hard-coded resolutions so that this test can generate
+        # its own sowing and harvest date files at whatever resolution is requested.
+        lnd_grid = self._case.get_value("LND_GRID")
+        input_data_root = self._case.get_value("DIN_LOC_ROOT")
+        processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed"
+        if lnd_grid == "10x15":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
+            )
+        elif lnd_grid == "1.9x2.5":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
+            )
+        elif lnd_grid == "0.9x1.25":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc",
+            )
+        else:
+            error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Ensure files exist
+        error_message = None
+        if not os.path.exists(self._sdatefile):
+            error_message = f"ERROR: Sowing date file not found: {self._sdatefile}"
+        elif not os.path.exists(self._hdatefile):
+            error_message = f"ERROR: Harvest date file not found: {self._sdatefile}"
+        if error_message is not None:
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+    def _setup_all(self):
+        logger.info("RXCROPMATURITY log:  _setup_all start")
+
+        # Get some info
+        self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND")
+        run_startdate = self._case.get_value("RUN_STARTDATE")
+        self._run_startyear = int(run_startdate.split("-")[0])
+
+        # Set sowing dates file (and other crop calendar settings) for all runs
+        logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
+        self._modify_user_nl_allruns()
+        logger.info("RXCROPMATURITY log:  _setup_all done")
+
+    # Make a surface dataset that has every crop in every gridcell
+    def _run_fsurdat_modifier(self):
+
+        # fsurdat should be defined. Where is it?
+        self._fsurdat_in = None
+        with open(self._lnd_in_path, "r") as lnd_in:
+            for line in lnd_in:
+                fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line)
+                if fsurdat_in:
+                    self._fsurdat_in = fsurdat_in.group(1)
+                    break
+        if self._fsurdat_in is None:
+            error_message = "fsurdat not defined"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Where we will save the fsurdat version for this test
+        path, ext = os.path.splitext(self._fsurdat_in)
+        dir_in, filename_in_noext = os.path.split(path)
+        self._fsurdat_out = os.path.join(
+            self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}"
+        )
+
+        # Make fsurdat for this test, if not already done
+        if not os.path.exists(self._fsurdat_out):
+            tool_path = os.path.join(
+                self._ctsm_root,
+                "tools",
+                "modify_input_files",
+                "fsurdat_modifier",
+            )
+
+            # Create configuration file for fsurdat_modifier
+            self._cfg_path = os.path.join(
+                self._path_gddgen,
+                "modify_fsurdat_allcropseverywhere.cfg",
+            )
+            self._create_config_file_evenlysplitcrop()
+
+            command = f"python3 {tool_path} {self._cfg_path} "
+            stu.run_python_script(
+                self._get_caseroot(),
+                self._this_conda_env,
+                command,
+                tool_path,
+            )
+
+        # Modify namelist
+        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
+        self._append_to_user_nl_clm(
+            [
+                "fsurdat = '{}'".format(self._fsurdat_out),
+                "do_transient_crops = .false.",
+                "flanduse_timeseries = ''",
+                "use_init_interp = .true.",
+            ]
+        )
+
+    def _create_config_file_evenlysplitcrop(self):
+        """
+        Open the new and the template .cfg files
+        Loop line by line through the template .cfg file
+        When string matches, replace that line's content
+        """
+        cfg_template_path = os.path.join(
+            self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg"
+        )
+
+        with open(self._cfg_path, "w", encoding="utf-8") as cfg_out:
+            # Copy template, replacing some lines
+            with open(cfg_template_path, "r", encoding="utf-8") as cfg_in:
+                for line in cfg_in:
+                    if re.match(r" *evenly_split_cropland *=", line):
+                        line = f"evenly_split_cropland = True"
+                    elif re.match(r" *fsurdat_in *=", line):
+                        line = f"fsurdat_in = {self._fsurdat_in}"
+                    elif re.match(r" *fsurdat_out *=", line):
+                        line = f"fsurdat_out = {self._fsurdat_out}"
+                    elif re.match(r" *process_subgrid_section *=", line):
+                        line = f"process_subgrid_section = True"
+                    cfg_out.write(line)
+
+            # Add new lines
+            cfg_out.write("\n")
+            cfg_out.write("[modify_fsurdat_subgrid_fractions]\n")
+            cfg_out.write("PCT_CROP    = 100.0\n")
+            cfg_out.write("PCT_NATVEG  = 0.0\n")
+            cfg_out.write("PCT_GLACIER = 0.0\n")
+            cfg_out.write("PCT_WETLAND = 0.0\n")
+            cfg_out.write("PCT_LAKE    = 0.0\n")
+            cfg_out.write("PCT_OCEAN   = 0.0\n")
+            cfg_out.write("PCT_URBAN   = 0.0 0.0 0.0\n")
+
+    def _run_check_rxboth_run(self):
+
+        output_dir = os.path.join(self._get_caseroot(), "run")
+        first_usable_year = self._run_startyear + 2
+        last_usable_year = self._run_startyear + self._run_Nyears - 2
+
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py"
+        )
+        command = (
+            f"python3 {tool_path} "
+            + f"--directory {output_dir} "
+            + f"-y1 {first_usable_year} "
+            + f"-yN {last_usable_year} "
+            + f"--rx-sdates-file {self._sdatefile} "
+            + f"--rx-gdds-file {self._gdds_file} "
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
+    def _modify_user_nl_allruns(self):
+        nl_additions = [
+            "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
+            "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
+            "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
+            "stream_year_first_cropcal_swindows = 2000",
+            "stream_year_last_cropcal_swindows = 2000",
+            "model_year_align_cropcal_swindows = 2000",
+            " ",
+            "! (h1) Annual outputs on sowing or harvest axis",
+            "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'",
+            "hist_nhtfrq(2) = 17520",
+            "hist_mfilt(2) = 999",
+            "hist_type1d_pertape(2) = 'PFTS'",
+            "hist_dov2xy(2) = .false.",
+        ]
+        self._append_to_user_nl_clm(nl_additions)
+
+    def _run_generate_gdds(self, case_gddgen):
+        self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out")
+        os.makedirs(self._generate_gdds_dir)
+
+        # Get arguments to generate_gdds.py
+        dout_sr = case_gddgen.get_value("DOUT_S_ROOT")
+        input_dir = os.path.join(dout_sr, "lnd", "hist")
+        first_season = self._run_startyear + 2
+        last_season = self._run_startyear + self._run_Nyears - 2
+        sdates_file = self._sdatefile
+        hdates_file = self._hdatefile
+
+        # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds.
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py"
+        )
+        command = " ".join(
+            [
+                f"python3 {tool_path}",
+                f"--input-dir {input_dir}",
+                f"--first-season {first_season}",
+                f"--last-season {last_season}",
+                f"--sdates-file {sdates_file}",
+                f"--hdates-file {hdates_file}",
+                f"--output-dir generate_gdds_out",
+                f"--skip-crops miscanthus,irrigated_miscanthus",
+            ]
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
+        # Where were the prescribed maturity requirements saved?
+        generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc"))
+        if len(generated_gdd_files) != 1:
+            error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+        self._gdds_file = generated_gdd_files[0]
+
+    def _get_conda_env(self):
+        conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot())
+
+        # If npl conda environment is available, use that (It has dask, which
+        # enables chunking, which makes reading daily 1-degree netCDF files
+        # much more efficient.
+        if "npl " in os.popen(conda_setup_commands + "conda env list").read():
+            self._this_conda_env = "npl"
+        else:
+            self._this_conda_env = "ctsm_pylib"
+
+    def _append_to_user_nl_clm(self, additions):
+        caseroot = self._get_caseroot()
+        append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions)
+
+    # Is flanduse_timeseries defined? If so, where is it?
+    def _get_flanduse_timeseries_in(self, case):
+        case.create_namelists(component="lnd")
+        self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in")
+        self._flanduse_timeseries_in = None
+        with open(self._lnd_in_path, "r") as lnd_in:
+            for line in lnd_in:
+                flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line)
+                if flanduse_timeseries_in:
+                    self._flanduse_timeseries_in = flanduse_timeseries_in.group(1)
+                    break
diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
deleted file mode 100644
index 8a944efdf9..0000000000
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ /dev/null
@@ -1,459 +0,0 @@
-"""
-CTSM-specific test that first performs a GDD-generating run, then calls
-Python code to generate the maturity requirement file. This is then used
-in a sowing+maturity forced run, which finally is tested to ensure
-correct behavior.
-
-Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually,
-this test should be able to generate its own files at whatever resolution it's
-called at. Well, really, the ultimate goal would be to give CLM the files
-at the original resolution (for GGCMI phase 3, 0.5°) and have the stream
-code do the interpolation. However, that wouldn't act on harvest dates
-(which are needed for generate_gdds.py). I could have Python interpolate
-those, but this would cause a potential inconsistency.
-
-Note that this is just a parent class. The actual tests are RXCROPMATURITY and
-RXCROPMATURITY_SKIPRUN, the latter of which does everything except perform and 
-check the CTSM runs.
-"""
-
-import os
-import re
-import systemtest_utils as stu
-import subprocess
-from CIME.SystemTests.system_tests_common import SystemTestsCommon
-from CIME.XML.standard_module_setup import *
-from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
-import shutil, glob
-
-logger = logging.getLogger(__name__)
-
-
-class RXCROPMATURITYSHARED(SystemTestsCommon):
-    def __init__(self, case):
-        # initialize an object interface to the SMS system test
-        SystemTestsCommon.__init__(self, case)
-
-        # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
-        stop_n = self._case.get_value("STOP_N")
-        stop_option = self._case.get_value("STOP_OPTION")
-        stop_n_orig = stop_n
-        stop_option_orig = stop_option
-        if "nsecond" in stop_option:
-            stop_n /= 60
-            stop_option = "nminutes"
-        if "nminute" in stop_option:
-            stop_n /= 60
-            stop_option = "nhours"
-        if "nhour" in stop_option:
-            stop_n /= 24
-            stop_option = "ndays"
-        if "nday" in stop_option:
-            stop_n /= 365
-            stop_option = "nyears"
-        if "nmonth" in stop_option:
-            stop_n /= 12
-            stop_option = "nyears"
-        error_message = None
-        if "nyear" not in stop_option:
-            error_message = (
-                f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), "
-                + "nhour(s), nday(s), nmonth(s), or nyear(s)"
-            )
-        elif stop_n < 5:
-            error_message = (
-                "RXCROPMATURITY must be run for at least 5 years; you requested "
-                + f"{stop_n_orig} {stop_option_orig[1:]}"
-            )
-        if error_message is not None:
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Get the number of complete years that will be run
-        self._run_Nyears = int(stop_n)
-
-        # Only allow RXCROPMATURITY to be called with test cropMonthOutput
-        casebaseid = self._case.get_value("CASEBASEID")
-        if casebaseid.split("-")[-1] != "cropMonthOutput":
-            error_message = (
-                "Only call RXCROPMATURITY with test cropMonthOutput "
-                + "to avoid potentially huge sets of daily outputs."
-            )
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Get files with prescribed sowing and harvest dates
-        self._get_rx_dates()
-
-        # Which conda environment should we use?
-        self._get_conda_env()
-
-    def _run_phase(self, skip_run=False):
-        # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
-        # want to be saved as baseline.
-
-        # -------------------------------------------------------------------
-        # (1) Set up GDD-generating run
-        # -------------------------------------------------------------------
-        # Create clone to be GDD-Generating case
-        logger.info("RXCROPMATURITY log:  cloning setup")
-        case_rxboth = self._case
-        caseroot = self._case.get_value("CASEROOT")
-        clone_path = f"{caseroot}.gddgen"
-        self._path_gddgen = clone_path
-        if os.path.exists(self._path_gddgen):
-            shutil.rmtree(self._path_gddgen)
-        logger.info("RXCROPMATURITY log:  cloning")
-        case_gddgen = self._case.create_clone(clone_path, keepexe=True)
-        logger.info("RXCROPMATURITY log:  done cloning")
-
-        os.chdir(self._path_gddgen)
-        self._set_active_case(case_gddgen)
-
-        # Set up stuff that applies to both tests
-        self._setup_all()
-
-        # Add stuff specific to GDD-Generating run
-        logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
-        self._append_to_user_nl_clm(
-            [
-                "generate_crop_gdds = .true.",
-                "stream_fldFileName_cultivar_gdds = ''",
-                "use_mxmat = .false.",
-                " ",
-                "! (h2) Daily outputs for GDD generation and figure-making",
-                "hist_fincl3 = 'GDDACCUM', 'GDDHARV'",
-                "hist_nhtfrq(3) = -24",
-                "hist_mfilt(3) = 365",
-                "hist_type1d_pertape(3) = 'PFTS'",
-                "hist_dov2xy(3) = .false.",
-            ]
-        )
-
-        # If flanduse_timeseries is defined, we need to make a static version for this test. This
-        # should have every crop in most of the world.
-        self._get_flanduse_timeseries_in(case_gddgen)
-        if self._flanduse_timeseries_in is not None:
-
-            # Download files from the server, if needed
-            case_gddgen.check_all_input_data()
-
-            # Copy needed file from original to gddgen directory
-            shutil.copyfile(
-                os.path.join(caseroot, ".env_mach_specific.sh"),
-                os.path.join(self._path_gddgen, ".env_mach_specific.sh"),
-            )
-
-            # Make custom version of surface file
-            logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
-            self._run_fsurdat_modifier()
-
-        # -------------------------------------------------------------------
-        # (2) Perform GDD-generating run and generate prescribed GDDs file
-        # -------------------------------------------------------------------
-        logger.info("RXCROPMATURITY log:  Start GDD-Generating run")
-
-        # As per SSP test:
-        # "No history files expected, set suffix=None to avoid compare error"
-        # We *do* expect history files here, but anyway. This works.
-        self._skip_pnl = False
-
-        if not skip_run:
-            self.run_indv(suffix=None, st_archive=True)
-            self._run_generate_gdds(case_gddgen)
-
-        # -------------------------------------------------------------------
-        # (3) Set up and perform Prescribed Calendars run
-        # -------------------------------------------------------------------
-        os.chdir(caseroot)
-        self._set_active_case(case_rxboth)
-
-        # Set up stuff that applies to both tests
-        self._setup_all()
-
-        # Add stuff specific to Prescribed Calendars run
-        logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
-        self._append_to_user_nl_clm(
-            [
-                "generate_crop_gdds = .false.",
-                f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'",
-            ]
-        )
-
-        if not skip_run:
-            self.run_indv()
-
-        # -------------------------------------------------------------------
-        # (4) Check Prescribed Calendars run
-        # -------------------------------------------------------------------
-        logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
-        if not skip_run:
-            self._run_check_rxboth_run()
-
-    # Get sowing and harvest dates for this resolution.
-    def _get_rx_dates(self):
-        # Eventually, I want to remove these hard-coded resolutions so that this test can generate
-        # its own sowing and harvest date files at whatever resolution is requested.
-        lnd_grid = self._case.get_value("LND_GRID")
-        input_data_root = self._case.get_value("DIN_LOC_ROOT")
-        processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed"
-        if lnd_grid == "10x15":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
-            )
-        elif lnd_grid == "1.9x2.5":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
-            )
-        elif lnd_grid == "0.9x1.25":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc",
-            )
-        else:
-            error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Ensure files exist
-        error_message = None
-        if not os.path.exists(self._sdatefile):
-            error_message = f"ERROR: Sowing date file not found: {self._sdatefile}"
-        elif not os.path.exists(self._hdatefile):
-            error_message = f"ERROR: Harvest date file not found: {self._sdatefile}"
-        if error_message is not None:
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-    def _setup_all(self):
-        logger.info("RXCROPMATURITY log:  _setup_all start")
-
-        # Get some info
-        self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND")
-        run_startdate = self._case.get_value("RUN_STARTDATE")
-        self._run_startyear = int(run_startdate.split("-")[0])
-
-        # Set sowing dates file (and other crop calendar settings) for all runs
-        logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
-        self._modify_user_nl_allruns()
-        logger.info("RXCROPMATURITY log:  _setup_all done")
-
-    # Make a surface dataset that has every crop in every gridcell
-    def _run_fsurdat_modifier(self):
-
-        # fsurdat should be defined. Where is it?
-        self._fsurdat_in = None
-        with open(self._lnd_in_path, "r") as lnd_in:
-            for line in lnd_in:
-                fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line)
-                if fsurdat_in:
-                    self._fsurdat_in = fsurdat_in.group(1)
-                    break
-        if self._fsurdat_in is None:
-            error_message = "fsurdat not defined"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Where we will save the fsurdat version for this test
-        path, ext = os.path.splitext(self._fsurdat_in)
-        dir_in, filename_in_noext = os.path.split(path)
-        self._fsurdat_out = os.path.join(
-            self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}"
-        )
-
-        # Make fsurdat for this test, if not already done
-        if not os.path.exists(self._fsurdat_out):
-            tool_path = os.path.join(
-                self._ctsm_root,
-                "tools",
-                "modify_input_files",
-                "fsurdat_modifier",
-            )
-
-            # Create configuration file for fsurdat_modifier
-            self._cfg_path = os.path.join(
-                self._path_gddgen,
-                "modify_fsurdat_allcropseverywhere.cfg",
-            )
-            self._create_config_file_evenlysplitcrop()
-
-            command = f"python3 {tool_path} {self._cfg_path} "
-            stu.run_python_script(
-                self._get_caseroot(),
-                self._this_conda_env,
-                command,
-                tool_path,
-            )
-
-        # Modify namelist
-        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
-        self._append_to_user_nl_clm(
-            [
-                "fsurdat = '{}'".format(self._fsurdat_out),
-                "do_transient_crops = .false.",
-                "flanduse_timeseries = ''",
-                "use_init_interp = .true.",
-            ]
-        )
-
-    def _create_config_file_evenlysplitcrop(self):
-        """
-        Open the new and the template .cfg files
-        Loop line by line through the template .cfg file
-        When string matches, replace that line's content
-        """
-        cfg_template_path = os.path.join(
-            self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg"
-        )
-
-        with open(self._cfg_path, "w", encoding="utf-8") as cfg_out:
-            # Copy template, replacing some lines
-            with open(cfg_template_path, "r", encoding="utf-8") as cfg_in:
-                for line in cfg_in:
-                    if re.match(r" *evenly_split_cropland *=", line):
-                        line = f"evenly_split_cropland = True"
-                    elif re.match(r" *fsurdat_in *=", line):
-                        line = f"fsurdat_in = {self._fsurdat_in}"
-                    elif re.match(r" *fsurdat_out *=", line):
-                        line = f"fsurdat_out = {self._fsurdat_out}"
-                    elif re.match(r" *process_subgrid_section *=", line):
-                        line = f"process_subgrid_section = True"
-                    cfg_out.write(line)
-
-            # Add new lines
-            cfg_out.write("\n")
-            cfg_out.write("[modify_fsurdat_subgrid_fractions]\n")
-            cfg_out.write("PCT_CROP    = 100.0\n")
-            cfg_out.write("PCT_NATVEG  = 0.0\n")
-            cfg_out.write("PCT_GLACIER = 0.0\n")
-            cfg_out.write("PCT_WETLAND = 0.0\n")
-            cfg_out.write("PCT_LAKE    = 0.0\n")
-            cfg_out.write("PCT_OCEAN   = 0.0\n")
-            cfg_out.write("PCT_URBAN   = 0.0 0.0 0.0\n")
-
-    def _run_check_rxboth_run(self):
-
-        output_dir = os.path.join(self._get_caseroot(), "run")
-        first_usable_year = self._run_startyear + 2
-        last_usable_year = self._run_startyear + self._run_Nyears - 2
-
-        tool_path = os.path.join(
-            self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py"
-        )
-        command = (
-            f"python3 {tool_path} "
-            + f"--directory {output_dir} "
-            + f"-y1 {first_usable_year} "
-            + f"-yN {last_usable_year} "
-            + f"--rx-sdates-file {self._sdatefile} "
-            + f"--rx-gdds-file {self._gdds_file} "
-        )
-        stu.run_python_script(
-            self._get_caseroot(),
-            self._this_conda_env,
-            command,
-            tool_path,
-        )
-
-    def _modify_user_nl_allruns(self):
-        nl_additions = [
-            "cropcals_rx = .true.",
-            "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
-            "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
-            "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
-            "stream_year_first_cropcal_swindows = 2000",
-            "stream_year_last_cropcal_swindows = 2000",
-            "model_year_align_cropcal_swindows = 2000",
-            " ",
-            "! (h1) Annual outputs on sowing or harvest axis",
-            "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'",
-            "hist_nhtfrq(2) = 17520",
-            "hist_mfilt(2) = 999",
-            "hist_type1d_pertape(2) = 'PFTS'",
-            "hist_dov2xy(2) = .false.",
-        ]
-        self._append_to_user_nl_clm(nl_additions)
-
-    def _run_generate_gdds(self, case_gddgen):
-        self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out")
-        os.makedirs(self._generate_gdds_dir)
-
-        # Get arguments to generate_gdds.py
-        dout_sr = case_gddgen.get_value("DOUT_S_ROOT")
-        input_dir = os.path.join(dout_sr, "lnd", "hist")
-        first_season = self._run_startyear + 2
-        last_season = self._run_startyear + self._run_Nyears - 2
-        sdates_file = self._sdatefile
-        hdates_file = self._hdatefile
-
-        # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds.
-        tool_path = os.path.join(
-            self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py"
-        )
-        command = " ".join(
-            [
-                f"python3 {tool_path}",
-                f"--input-dir {input_dir}",
-                f"--first-season {first_season}",
-                f"--last-season {last_season}",
-                f"--sdates-file {sdates_file}",
-                f"--hdates-file {hdates_file}",
-                f"--output-dir generate_gdds_out",
-                f"--skip-crops miscanthus,irrigated_miscanthus",
-            ]
-        )
-        stu.run_python_script(
-            self._get_caseroot(),
-            self._this_conda_env,
-            command,
-            tool_path,
-        )
-
-        # Where were the prescribed maturity requirements saved?
-        generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc"))
-        if len(generated_gdd_files) != 1:
-            error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-        self._gdds_file = generated_gdd_files[0]
-
-    def _get_conda_env(self):
-        conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot())
-
-        # If npl conda environment is available, use that (It has dask, which
-        # enables chunking, which makes reading daily 1-degree netCDF files
-        # much more efficient.
-        if "npl " in os.popen(conda_setup_commands + "conda env list").read():
-            self._this_conda_env = "npl"
-        else:
-            self._this_conda_env = "ctsm_pylib"
-
-    def _append_to_user_nl_clm(self, additions):
-        caseroot = self._get_caseroot()
-        append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions)
-
-    # Is flanduse_timeseries defined? If so, where is it?
-    def _get_flanduse_timeseries_in(self, case):
-        case.create_namelists(component="lnd")
-        self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in")
-        self._flanduse_timeseries_in = None
-        with open(self._lnd_in_path, "r") as lnd_in:
-            for line in lnd_in:
-                flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line)
-                if flanduse_timeseries_in:
-                    self._flanduse_timeseries_in = flanduse_timeseries_in.group(1)
-                    break
diff --git a/cime_config/SystemTests/rxcropmaturityskipbuild.py b/cime_config/SystemTests/rxcropmaturityskipbuild.py
deleted file mode 100644
index 4c3a69fb47..0000000000
--- a/cime_config/SystemTests/rxcropmaturityskipbuild.py
+++ /dev/null
@@ -1,9 +0,0 @@
-from rxcropmaturityshared import RXCROPMATURITYSHARED
-
-class RXCROPMATURITYSKIPBUILD(RXCROPMATURITYSHARED):
-    def build_indv(self, sharedlib_only=False, model_only=False):
-        self._case.set_value("BUILD_COMPLETE", "TRUE")
-
-
-    def run_phase(self):
-        self._run_phase(skip_run=False)
\ No newline at end of file
diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py
deleted file mode 100644
index 7fd217c4ff..0000000000
--- a/cime_config/SystemTests/rxcropmaturityskiprun.py
+++ /dev/null
@@ -1,9 +0,0 @@
-from rxcropmaturityshared import RXCROPMATURITYSHARED
-
-class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED):
-    def build_indv(self, sharedlib_only=False, model_only=False):
-        self._case.set_value("BUILD_COMPLETE", "TRUE")
-
-
-    def run_phase(self):
-        self._run_phase(skip_run=True)
\ No newline at end of file
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index 115f4c0e89..c0b6afed9d 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -133,26 +133,6 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
-  <test NAME="RXCROPMATURITYSKIPRUN">
-    <DESC>As RXCROPMATURITY but don't actually run or postprocess; just setup</DESC>
-    <INFO_DBUG>1</INFO_DBUG>
-    <DOUT_S>FALSE</DOUT_S>
-    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
-    <REST_OPTION>never</REST_OPTION>
-    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
-    <HIST_N>$STOP_N</HIST_N>
-  </test>
-
-  <test NAME="RXCROPMATURITYSKIPBUILD">
-    <DESC>As RXCROPMATURITY but don't actually build; just setup and then start "run." Will fail when run start is requested, but should successfully test preprocessing.</DESC>
-    <INFO_DBUG>1</INFO_DBUG>
-    <DOUT_S>FALSE</DOUT_S>
-    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
-    <REST_OPTION>never</REST_OPTION>
-    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
-    <HIST_N>$STOP_N</HIST_N>
-  </test>
-
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

From 17761a99dd3ec17371bd63b0a9685977233568a3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 16:22:13 -0600
Subject: [PATCH 0508/1248] Leave gdd20_season_(start,end)_patch as real.

---
 src/biogeochem/CropType.F90             | 11 ++---------
 src/biogeophys/TemperatureType.F90      |  1 -
 src/cpl/share_esmf/cropcalStreamMod.F90 |  5 -----
 3 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index a091dfd52d..b1e0e4571d 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -53,11 +53,8 @@ module CropType
      integer , pointer :: rx_swindow_ends_thisyr_patch  (:,:) ! all prescribed sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings]
      real(r8), pointer :: gdd20_baseline_patch          (:)   ! GDD20 baseline for this patch (ddays) [patch]
-
-     ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
-     real(r8), pointer :: gdd20_season_start_patch(:) ! gdd20 season start date for this patch (day of year) [patch]
-     real(r8), pointer :: gdd20_season_end_patch  (:) ! gdd20 season end   date for this patch (day of year) [patch]
-
+     real(r8), pointer :: gdd20_season_start_patch(:) ! gdd20 season start date for this patch (day of year) [patch]. Real to enable history field.
+     real(r8), pointer :: gdd20_season_end_patch  (:) ! gdd20 season end   date for this patch (day of year) [patch]/ Real to enable history field.
      real(r8), pointer :: sdates_thisyr_patch     (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_starts_thisyr_patch(:,:) ! all sowing window start dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_ends_thisyr_patch  (:,:) ! all sowing window end   dates for this patch this year (day of year) [patch, mxsowings]
@@ -242,11 +239,8 @@ subroutine InitAllocate(this, bounds)
     allocate(this%rx_swindow_ends_thisyr_patch(begp:endp,1:mxsowings))  ; this%rx_swindow_ends_thisyr_patch  (:,:) = -1
     allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval
     allocate(this%gdd20_baseline_patch(begp:endp)) ; this%gdd20_baseline_patch(:) = spval
-
-    ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
     allocate(this%gdd20_season_start_patch(begp:endp)); this%gdd20_season_start_patch(:) = spval
     allocate(this%gdd20_season_end_patch(begp:endp))  ; this%gdd20_season_end_patch  (:) = spval
-
     allocate(this%sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%sdates_thisyr_patch(:,:) = spval
     allocate(this%swindow_starts_thisyr_patch(begp:endp,1:mxsowings)) ; this%swindow_starts_thisyr_patch(:,:) = spval
     allocate(this%swindow_ends_thisyr_patch  (begp:endp,1:mxsowings)) ; this%swindow_ends_thisyr_patch  (:,:) = spval
@@ -370,7 +364,6 @@ subroutine InitHistory(this, bounds)
          avgflag='I', long_name='Reason for each crop harvest; should only be output annually', &
          ptr_patch=this%harvest_reason_thisyr_patch, default='inactive')
 
-    ! DEVELOPMENT ONLY; DELETE BEFORE MERGE
     this%gdd20_baseline_patch(begp:endp) = spval
     call hist_addfld1d (fname='GDD20_BASELINE', units='ddays', &
          avgflag='A', long_name='Baseline mean growing-degree days accumulated during accumulation period (from input)', &
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 23fda977dd..afe0948e6d 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1471,7 +1471,6 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
        ! Replace with read-in gdd20 accumulation season, if needed and valid
        ! (If these aren't being read in or they're invalid, they'll be -1)
        if (stream_gdd20_seasons) then
-          ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
           gdd20_season_start = int(gdd20_season_starts(p))
           gdd20_season_end = int(gdd20_season_ends(p))
           if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index e48fa2b6aa..ef406a7e60 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -783,7 +783,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
            ! vegetated pft
            ig = g_to_ig(patch%gridcell(p))
 
-           ! REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
            gdd20_season_starts(p) = real(dataptr2d_gdd20_season_start(ig,n), r8)
            gdd20_season_ends(p)   = real(dataptr2d_gdd20_season_end  (ig,n), r8)
        else
@@ -793,17 +792,14 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
      end do
 
      ! Handle invalid gdd20 season values
-     ! gdd20_season_starts and gdd20_season_ends REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
      if (any(gdd20_season_starts(begp:endp) < 1._r8 .or. gdd20_season_ends(begp:endp) < 1._r8)) then
          ! Fail if not allowing fallback to paramfile sowing windows
-         ! gdd20_season_starts REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
          if ((.not. allow_invalid_gdd20_season_inputs) .and. any(gdd20_season_starts(begp:endp) < 1._r8 .and. patch%wtgcell(begp:endp) > 0._r8 .and. patch%itype(begp:endp) >= npcropmin)) then
              write(iulog, *) 'At least one crop in one gridcell has invalid gdd20 season start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_gdd20_season_inputs to .true.'
              write(iulog, *) 'Affected crops:'
              do ivt = npcropmin, mxpft
                  do fp = 1, num_pcropp
                      p = filter_pcropp(fp)
-                     ! gdd20_season_starts REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
                      if (ivt == patch%itype(p) .and. patch%wtgcell(p) > 0._r8 .and. gdd20_season_starts(p) < 1._r8) then
                          write(iulog, *) '    ',pftname(ivt),'  (',ivt,')'
                          exit  ! Stop looking for patches of this type
@@ -813,7 +809,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
              call ESMF_Finalize(endflag=ESMF_END_ABORT)
 
          ! Fail if a gdd20 season start date is given without an end date (or vice versa)
-         ! gdd20_season_starts and gdd20_season_ends REAL FOR DEVELOPMENT ONLY; REVERT TO INTEGER BEFORE MERGE
          else if (any((gdd20_season_starts(begp:endp) >= 1._r8 .and. gdd20_season_ends(begp:endp) < 1._r8) .or. (gdd20_season_starts(begp:endp) < 1._r8 .and. gdd20_season_ends(begp:endp) >= 1._r8))) then
              write(iulog, *) 'Every gdd20 season start date must have a corresponding end date.'
              call ESMF_Finalize(endflag=ESMF_END_ABORT)

From e286f37c3ac736ad4c9b48967f705975c8ecf8fa Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 15:39:44 -0600
Subject: [PATCH 0509/1248] Add RXCROPMATURITYSKIPGEN test to aux_clm.

Also adds rxcropmaturity test suite with that and a coarse version of the existing RXCROPMATURITY test. So:
* RXCROPMATURITY_Lm61.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput
* RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput
---
 cime_config/testdefs/testlist_clm.xml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index c2a90507ba..432f8e3e9a 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3636,6 +3636,27 @@
     </options>
   </test>
 
+  <test name="RXCROPMATURITY_Lm61" grid="f10_f10_mg37" compset="IHistClm50BgcCrop"  testmods="clm/cropMonthOutput">
+    <machines>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+    </machines>
+    <options>
+      <option name="wallclock">6:00:00</option>
+      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. It first performs a GDD-generating run, then calls Python code to generate the maturity requirement file. This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
+    </options>
+  </test>
+
+  <test name="RXCROPMATURITYSKIPGEN_Ld1097" grid="f10_f10_mg37" compset="IHistClm50BgcCrop"  testmods="clm/cropMonthOutput">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:45:00</option>
+      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. Unlike the RXCROPMATURITY test, however, it does not generate its own maturity requirements, instead interpolating a pre-existing maturity requirement file. (This allows the "GDD-generating" run to be mostly skipped.) This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
+    </options>
+  </test>
+
   <test name="ERP_D_P64x2_Ld10" grid="f10_f10_mg37" compset="I2000Clm60Bgc" testmods="clm/Hillslope">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

From 6f59eab9d04c93b0e67d5b2837ca3b71fd148ba3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 15:45:26 -0600
Subject: [PATCH 0510/1248] Remove RXCROPMATURITY SKIPRUN and SKIPBUILD tests.

---
 .../SystemTests/rxcropmaturityskipbuild.py    |  9 ---------
 .../SystemTests/rxcropmaturityskiprun.py      |  9 ---------
 cime_config/config_tests.xml                  | 20 -------------------
 3 files changed, 38 deletions(-)
 delete mode 100644 cime_config/SystemTests/rxcropmaturityskipbuild.py
 delete mode 100644 cime_config/SystemTests/rxcropmaturityskiprun.py

diff --git a/cime_config/SystemTests/rxcropmaturityskipbuild.py b/cime_config/SystemTests/rxcropmaturityskipbuild.py
deleted file mode 100644
index 0e16c757fc..0000000000
--- a/cime_config/SystemTests/rxcropmaturityskipbuild.py
+++ /dev/null
@@ -1,9 +0,0 @@
-from rxcropmaturityshared import RXCROPMATURITYSHARED
-
-
-class RXCROPMATURITYSKIPBUILD(RXCROPMATURITYSHARED):
-    def build_indv(self, sharedlib_only=False, model_only=False):
-        self._case.set_value("BUILD_COMPLETE", "TRUE")
-
-    def run_phase(self):
-        self._run_phase(skip_run=False)
diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py
deleted file mode 100644
index 24fc288373..0000000000
--- a/cime_config/SystemTests/rxcropmaturityskiprun.py
+++ /dev/null
@@ -1,9 +0,0 @@
-from rxcropmaturityshared import RXCROPMATURITYSHARED
-
-
-class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED):
-    def build_indv(self, sharedlib_only=False, model_only=False):
-        self._case.set_value("BUILD_COMPLETE", "TRUE")
-
-    def run_phase(self):
-        self._run_phase(skip_run=True)
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index cbddc31b8d..5c5bdc2892 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -143,26 +143,6 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
-  <test NAME="RXCROPMATURITYSKIPRUN">
-    <DESC>As RXCROPMATURITY but don't actually run or postprocess; just setup</DESC>
-    <INFO_DBUG>1</INFO_DBUG>
-    <DOUT_S>FALSE</DOUT_S>
-    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
-    <REST_OPTION>never</REST_OPTION>
-    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
-    <HIST_N>$STOP_N</HIST_N>
-  </test>
-
-  <test NAME="RXCROPMATURITYSKIPBUILD">
-    <DESC>As RXCROPMATURITY but don't actually build; just setup and then start "run." Will fail when run start is requested, but should successfully test preprocessing.</DESC>
-    <INFO_DBUG>1</INFO_DBUG>
-    <DOUT_S>FALSE</DOUT_S>
-    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
-    <REST_OPTION>never</REST_OPTION>
-    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
-    <HIST_N>$STOP_N</HIST_N>
-  </test>
-
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

From 104a2be7a108fea4ee232ee656af128b1e315cc5 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 15:47:56 -0600
Subject: [PATCH 0511/1248] Remove RXCROPMATURITY test from expected failure
 list.

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 3365565a5e..9992f7fcb9 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -29,13 +29,6 @@
 
 
   <!-- ctsm_sci test suite failures -->
-  <test name="RXCROPMATURITY_Lm61.f09_g17.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput">
-    <phase name="RUN">
-      <status>PEND</status>
-      <issue>#2460</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Ld12_Mmpi-serial.1x1_urbanc_alpha.I1PtClm60SpRs.derecho_intel.clm-output_sp_highfreq">
     <phase name="RUN">
       <status>FAIL</status>

From dd6e0cb0b8f722c74a6819b48ff4ec534fbc7a87 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 15:50:47 -0600
Subject: [PATCH 0512/1248] Move RXCROPMATURITYSHARED into rxcropmaturity.py.

---
 cime_config/SystemTests/rxcropmaturity.py     | 511 ++++++++++++++++-
 .../SystemTests/rxcropmaturityshared.py       | 514 ------------------
 .../SystemTests/rxcropmaturityskipgen.py      |   2 +-
 3 files changed, 511 insertions(+), 516 deletions(-)
 delete mode 100644 cime_config/SystemTests/rxcropmaturityshared.py

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 12ec608898..e0f6f4df21 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -1,4 +1,513 @@
-from rxcropmaturityshared import RXCROPMATURITYSHARED
+"""
+CTSM-specific test that first performs a GDD-generating run, then calls
+Python code to generate the maturity requirement file. This is then used
+in a sowing+maturity forced run, which finally is tested to ensure
+correct behavior.
+
+Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually,
+this test should be able to generate its own files at whatever resolution it's
+called at. Well, really, the ultimate goal would be to give CLM the files
+at the original resolution (for GGCMI phase 3, 0.5°) and have the stream
+code do the interpolation. However, that wouldn't act on harvest dates
+(which are needed for generate_gdds.py). I could have Python interpolate
+those, but this would cause a potential inconsistency.
+"""
+
+import os
+import re
+import systemtest_utils as stu
+import subprocess
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+from CIME.XML.standard_module_setup import *
+from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
+from CIME.case import Case
+import shutil, glob
+
+logger = logging.getLogger(__name__)
+
+
+class RXCROPMATURITYSHARED(SystemTestsCommon):
+    def __init__(self, case):
+        # initialize an object interface to the SMS system test
+        SystemTestsCommon.__init__(self, case)
+
+        # Is this a real RXCROPMATURITY test or not?
+        casebaseid = self._case.get_value("CASEBASEID")
+        full_test = "RXCROPMATURITY_" in casebaseid
+        skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid
+
+        # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
+        stop_n = self._case.get_value("STOP_N")
+        stop_option = self._case.get_value("STOP_OPTION")
+        stop_n_orig = stop_n
+        stop_option_orig = stop_option
+        if "nsecond" in stop_option:
+            stop_n /= 60
+            stop_option = "nminutes"
+        if "nminute" in stop_option:
+            stop_n /= 60
+            stop_option = "nhours"
+        if "nhour" in stop_option:
+            stop_n /= 24
+            stop_option = "ndays"
+        if "nday" in stop_option:
+            stop_n /= 365
+            stop_option = "nyears"
+        if "nmonth" in stop_option:
+            stop_n /= 12
+            stop_option = "nyears"
+        error_message = None
+        if "nyear" not in stop_option:
+            error_message = (
+                f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), "
+                + "nhour(s), nday(s), nmonth(s), or nyear(s)"
+            )
+        elif full_test and stop_n < 5:
+            error_message = (
+                "RXCROPMATURITY must be run for at least 5 years; you requested "
+                + f"{stop_n_orig} {stop_option_orig[1:]}"
+            )
+        elif skipgen_test and stop_n < 3:
+            # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish.
+            error_message = (
+                "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested "
+                + f"{stop_n_orig} {stop_option_orig[1:]}"
+            )
+        if error_message is not None:
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Get the number of complete years that will be run
+        self._run_Nyears = int(stop_n)
+
+        # Only allow RXCROPMATURITY to be called with test cropMonthOutput
+        if casebaseid.split("-")[-1] != "cropMonthOutput":
+            error_message = (
+                "Only call RXCROPMATURITY with test cropMonthOutput "
+                + "to avoid potentially huge sets of daily outputs."
+            )
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Get files with prescribed sowing and harvest dates
+        self._get_rx_dates()
+
+        # Get cultivar maturity requirement file to fall back on if not generating it here
+        self._gdds_file = None
+        self._fallback_gdds_file = os.path.join(
+            os.path.dirname(self._sdatefile),
+            "gdds_20230829_161011.nc"
+        )
+
+        # Which conda environment should we use?
+        self._get_conda_env()
+
+    def _run_phase(self, skip_run=False, skip_gen=False):
+        # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
+        # want to be saved as baseline.
+
+        # -------------------------------------------------------------------
+        # (1) Set up GDD-generating run
+        # -------------------------------------------------------------------
+        # Create clone to be GDD-Generating case
+        logger.info("RXCROPMATURITY log:  cloning setup")
+        case_rxboth = self._case
+        caseroot = self._case.get_value("CASEROOT")
+        clone_path = f"{caseroot}.gddgen"
+        self._path_gddgen = clone_path
+        if os.path.exists(self._path_gddgen):
+            shutil.rmtree(self._path_gddgen)
+        logger.info("RXCROPMATURITY log:  cloning")
+        case_gddgen = self._case.create_clone(clone_path, keepexe=True)
+        logger.info("RXCROPMATURITY log:  done cloning")
+
+        os.chdir(self._path_gddgen)
+        self._set_active_case(case_gddgen)
+
+        # Set up stuff that applies to both tests
+        self._setup_all()
+
+        # Add stuff specific to GDD-Generating run
+        logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
+        self._append_to_user_nl_clm(
+            [
+                "generate_crop_gdds = .true.",
+                "use_mxmat = .false.",
+                " ",
+                "! (h2) Daily outputs for GDD generation and figure-making",
+                "hist_fincl3 = 'GDDACCUM', 'GDDHARV'",
+                "hist_nhtfrq(3) = -24",
+                "hist_mfilt(3) = 365",
+                "hist_type1d_pertape(3) = 'PFTS'",
+                "hist_dov2xy(3) = .false.",
+            ]
+        )
+
+        # If flanduse_timeseries is defined, we need to make a static version for this test. This
+        # should have every crop in most of the world.
+        self._get_flanduse_timeseries_in(case_gddgen)
+        if self._flanduse_timeseries_in is not None:
+
+            # Download files from the server, if needed
+            case_gddgen.check_all_input_data()
+
+            # Copy needed file from original to gddgen directory
+            shutil.copyfile(
+                os.path.join(caseroot, ".env_mach_specific.sh"),
+                os.path.join(self._path_gddgen, ".env_mach_specific.sh"),
+            )
+
+            # Make custom version of surface file
+            logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
+            self._run_fsurdat_modifier()
+
+        # -------------------------------------------------------------------
+        # (2) Perform GDD-generating run and generate prescribed GDDs file
+        # -------------------------------------------------------------------
+        logger.info("RXCROPMATURITY log:  Start GDD-Generating run")
+
+        # As per SSP test:
+        # "No history files expected, set suffix=None to avoid compare error"
+        # We *do* expect history files here, but anyway. This works.
+        self._skip_pnl = False
+
+        # If not generating GDDs, only run a few days of this.
+        if skip_gen:
+            with Case(self._path_gddgen, read_only=False) as case:
+                case.set_value("STOP_N", 5)
+                case.set_value("STOP_OPTION", "ndays")
+
+        if not skip_run:
+            self.run_indv(suffix=None, st_archive=True)
+        if skip_gen:
+            # Interpolate an existing GDD file. Needed to check obedience to GDD inputs.
+            self._run_interpolate_gdds()
+        else:
+            self._run_generate_gdds(case_gddgen)
+
+        # -------------------------------------------------------------------
+        # (3) Set up and perform Prescribed Calendars run
+        # -------------------------------------------------------------------
+        os.chdir(caseroot)
+        self._set_active_case(case_rxboth)
+
+        # Set up stuff that applies to both tests
+        self._setup_all()
+
+        # Add stuff specific to Prescribed Calendars run
+        logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
+        self._append_to_user_nl_clm(
+            [
+                "generate_crop_gdds = .false.",
+                f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'",
+            ]
+        )
+
+        if not skip_run:
+            self.run_indv()
+
+        # -------------------------------------------------------------------
+        # (4) Check Prescribed Calendars run
+        # -------------------------------------------------------------------
+        logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
+        if not skip_run:
+            self._run_check_rxboth_run(skip_gen)
+
+    # Get sowing and harvest dates for this resolution.
+    def _get_rx_dates(self):
+        # Eventually, I want to remove these hard-coded resolutions so that this test can generate
+        # its own sowing and harvest date files at whatever resolution is requested.
+        lnd_grid = self._case.get_value("LND_GRID")
+        input_data_root = self._case.get_value("DIN_LOC_ROOT")
+        processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed"
+        if lnd_grid == "10x15":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
+            )
+        elif lnd_grid == "1.9x2.5":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
+            )
+        elif lnd_grid == "0.9x1.25":
+            self._sdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc",
+            )
+            self._hdatefile = os.path.join(
+                processed_crop_dates_dir,
+                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc",
+            )
+        else:
+            error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Ensure files exist
+        error_message = None
+        if not os.path.exists(self._sdatefile):
+            error_message = f"ERROR: Sowing date file not found: {self._sdatefile}"
+        elif not os.path.exists(self._hdatefile):
+            error_message = f"ERROR: Harvest date file not found: {self._sdatefile}"
+        if error_message is not None:
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+    def _setup_all(self):
+        logger.info("RXCROPMATURITY log:  _setup_all start")
+
+        # Get some info
+        self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND")
+        run_startdate = self._case.get_value("RUN_STARTDATE")
+        self._run_startyear = int(run_startdate.split("-")[0])
+
+        # Set sowing dates file (and other crop calendar settings) for all runs
+        logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
+        self._modify_user_nl_allruns()
+        logger.info("RXCROPMATURITY log:  _setup_all done")
+
+    # Make a surface dataset that has every crop in every gridcell
+    def _run_fsurdat_modifier(self):
+
+        # fsurdat should be defined. Where is it?
+        self._fsurdat_in = None
+        with open(self._lnd_in_path, "r") as lnd_in:
+            for line in lnd_in:
+                fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line)
+                if fsurdat_in:
+                    self._fsurdat_in = fsurdat_in.group(1)
+                    break
+        if self._fsurdat_in is None:
+            error_message = "fsurdat not defined"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Where we will save the fsurdat version for this test
+        path, ext = os.path.splitext(self._fsurdat_in)
+        dir_in, filename_in_noext = os.path.split(path)
+        self._fsurdat_out = os.path.join(
+            self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}"
+        )
+
+        # Make fsurdat for this test, if not already done
+        if not os.path.exists(self._fsurdat_out):
+            tool_path = os.path.join(
+                self._ctsm_root,
+                "tools",
+                "modify_input_files",
+                "fsurdat_modifier",
+            )
+
+            # Create configuration file for fsurdat_modifier
+            self._cfg_path = os.path.join(
+                self._path_gddgen,
+                "modify_fsurdat_allcropseverywhere.cfg",
+            )
+            self._create_config_file_evenlysplitcrop()
+
+            command = f"python3 {tool_path} {self._cfg_path} "
+            stu.run_python_script(
+                self._get_caseroot(),
+                self._this_conda_env,
+                command,
+                tool_path,
+            )
+
+        # Modify namelist
+        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
+        self._append_to_user_nl_clm(
+            [
+                "fsurdat = '{}'".format(self._fsurdat_out),
+                "do_transient_crops = .false.",
+                "flanduse_timeseries = ''",
+                "use_init_interp = .true.",
+            ]
+        )
+
+    def _create_config_file_evenlysplitcrop(self):
+        """
+        Open the new and the template .cfg files
+        Loop line by line through the template .cfg file
+        When string matches, replace that line's content
+        """
+        cfg_template_path = os.path.join(
+            self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg"
+        )
+
+        with open(self._cfg_path, "w", encoding="utf-8") as cfg_out:
+            # Copy template, replacing some lines
+            with open(cfg_template_path, "r", encoding="utf-8") as cfg_in:
+                for line in cfg_in:
+                    if re.match(r" *evenly_split_cropland *=", line):
+                        line = f"evenly_split_cropland = True"
+                    elif re.match(r" *fsurdat_in *=", line):
+                        line = f"fsurdat_in = {self._fsurdat_in}"
+                    elif re.match(r" *fsurdat_out *=", line):
+                        line = f"fsurdat_out = {self._fsurdat_out}"
+                    elif re.match(r" *process_subgrid_section *=", line):
+                        line = f"process_subgrid_section = True"
+                    cfg_out.write(line)
+
+            # Add new lines
+            cfg_out.write("\n")
+            cfg_out.write("[modify_fsurdat_subgrid_fractions]\n")
+            cfg_out.write("PCT_CROP    = 100.0\n")
+            cfg_out.write("PCT_NATVEG  = 0.0\n")
+            cfg_out.write("PCT_GLACIER = 0.0\n")
+            cfg_out.write("PCT_WETLAND = 0.0\n")
+            cfg_out.write("PCT_LAKE    = 0.0\n")
+            cfg_out.write("PCT_OCEAN   = 0.0\n")
+            cfg_out.write("PCT_URBAN   = 0.0 0.0 0.0\n")
+
+    def _run_check_rxboth_run(self, skip_gen):
+
+        output_dir = os.path.join(self._get_caseroot(), "run")
+
+        if skip_gen:
+            first_usable_year = self._run_startyear + 1
+            last_usable_year = first_usable_year
+        else:
+            first_usable_year = self._run_startyear + 2
+            last_usable_year = self._run_startyear + self._run_Nyears - 2
+
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py"
+        )
+        command = (
+            f"python3 {tool_path} "
+            + f"--directory {output_dir} "
+            + f"-y1 {first_usable_year} "
+            + f"-yN {last_usable_year} "
+            + f"--rx-sdates-file {self._sdatefile} "
+            + f"--rx-gdds-file {self._gdds_file} "
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
+    def _modify_user_nl_allruns(self):
+        nl_additions = [
+            "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
+            "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
+            "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
+            "stream_year_first_cropcal = 2000",
+            "stream_year_last_cropcal = 2000",
+            "model_year_align_cropcal = 2000",
+            " ",
+            "! (h1) Annual outputs on sowing or harvest axis",
+            "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'",
+            "hist_nhtfrq(2) = 17520",
+            "hist_mfilt(2) = 999",
+            "hist_type1d_pertape(2) = 'PFTS'",
+            "hist_dov2xy(2) = .false.",
+        ]
+        self._append_to_user_nl_clm(nl_additions)
+
+    def _run_generate_gdds(self, case_gddgen):
+        self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out")
+        os.makedirs(self._generate_gdds_dir)
+
+        # Get arguments to generate_gdds.py
+        dout_sr = case_gddgen.get_value("DOUT_S_ROOT")
+        input_dir = os.path.join(dout_sr, "lnd", "hist")
+        first_season = self._run_startyear + 2
+        last_season = self._run_startyear + self._run_Nyears - 2
+        sdates_file = self._sdatefile
+        hdates_file = self._hdatefile
+
+        # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds.
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py"
+        )
+        command = " ".join(
+            [
+                f"python3 {tool_path}",
+                f"--input-dir {input_dir}",
+                f"--first-season {first_season}",
+                f"--last-season {last_season}",
+                f"--sdates-file {sdates_file}",
+                f"--hdates-file {hdates_file}",
+                f"--output-dir generate_gdds_out",
+                f"--skip-crops miscanthus,irrigated_miscanthus",
+            ]
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
+        # Where were the prescribed maturity requirements saved?
+        generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc"))
+        if len(generated_gdd_files) != 1:
+            error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}"
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+        self._gdds_file = generated_gdd_files[0]
+
+    def _run_interpolate_gdds(self):
+        # Save where?
+        self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc")
+
+        # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds.
+        tool_path = os.path.join(
+            self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py"
+        )
+        command = " ".join(
+            [
+                f"python3 {tool_path}",
+                f"--input-file {self._fallback_gdds_file}",
+                f"--target-file {self._sdatefile}",
+                f"--output-file {self._gdds_file}",
+                "--overwrite",
+            ]
+        )
+        stu.run_python_script(
+            self._get_caseroot(),
+            self._this_conda_env,
+            command,
+            tool_path,
+        )
+
+    def _get_conda_env(self):
+        conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot())
+
+        # If npl conda environment is available, use that (It has dask, which
+        # enables chunking, which makes reading daily 1-degree netCDF files
+        # much more efficient.
+        if "npl " in os.popen(conda_setup_commands + "conda env list").read():
+            self._this_conda_env = "npl"
+        else:
+            self._this_conda_env = "ctsm_pylib"
+
+    def _append_to_user_nl_clm(self, additions):
+        caseroot = self._get_caseroot()
+        append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions)
+
+    # Is flanduse_timeseries defined? If so, where is it?
+    def _get_flanduse_timeseries_in(self, case):
+        case.create_namelists(component="lnd")
+        self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in")
+        self._flanduse_timeseries_in = None
+        with open(self._lnd_in_path, "r") as lnd_in:
+            for line in lnd_in:
+                flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line)
+                if flanduse_timeseries_in:
+                    self._flanduse_timeseries_in = flanduse_timeseries_in.group(1)
+                    break
 
 
 class RXCROPMATURITY(RXCROPMATURITYSHARED):
diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py
deleted file mode 100644
index 991fe687b5..0000000000
--- a/cime_config/SystemTests/rxcropmaturityshared.py
+++ /dev/null
@@ -1,514 +0,0 @@
-"""
-CTSM-specific test that first performs a GDD-generating run, then calls
-Python code to generate the maturity requirement file. This is then used
-in a sowing+maturity forced run, which finally is tested to ensure
-correct behavior.
-
-Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually,
-this test should be able to generate its own files at whatever resolution it's
-called at. Well, really, the ultimate goal would be to give CLM the files
-at the original resolution (for GGCMI phase 3, 0.5°) and have the stream
-code do the interpolation. However, that wouldn't act on harvest dates
-(which are needed for generate_gdds.py). I could have Python interpolate
-those, but this would cause a potential inconsistency.
-
-Note that this is just a parent class. The actual tests are RXCROPMATURITY and
-RXCROPMATURITY_SKIPRUN, the latter of which does everything except perform and 
-check the CTSM runs.
-"""
-
-import os
-import re
-import systemtest_utils as stu
-import subprocess
-from CIME.SystemTests.system_tests_common import SystemTestsCommon
-from CIME.XML.standard_module_setup import *
-from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
-from CIME.case import Case
-import shutil, glob
-
-logger = logging.getLogger(__name__)
-
-
-class RXCROPMATURITYSHARED(SystemTestsCommon):
-    def __init__(self, case):
-        # initialize an object interface to the SMS system test
-        SystemTestsCommon.__init__(self, case)
-
-        # Is this a real RXCROPMATURITY test or not?
-        casebaseid = self._case.get_value("CASEBASEID")
-        full_test = "RXCROPMATURITY_" in casebaseid
-        skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid
-
-        # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
-        stop_n = self._case.get_value("STOP_N")
-        stop_option = self._case.get_value("STOP_OPTION")
-        stop_n_orig = stop_n
-        stop_option_orig = stop_option
-        if "nsecond" in stop_option:
-            stop_n /= 60
-            stop_option = "nminutes"
-        if "nminute" in stop_option:
-            stop_n /= 60
-            stop_option = "nhours"
-        if "nhour" in stop_option:
-            stop_n /= 24
-            stop_option = "ndays"
-        if "nday" in stop_option:
-            stop_n /= 365
-            stop_option = "nyears"
-        if "nmonth" in stop_option:
-            stop_n /= 12
-            stop_option = "nyears"
-        error_message = None
-        if "nyear" not in stop_option:
-            error_message = (
-                f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), "
-                + "nhour(s), nday(s), nmonth(s), or nyear(s)"
-            )
-        elif full_test and stop_n < 5:
-            error_message = (
-                "RXCROPMATURITY must be run for at least 5 years; you requested "
-                + f"{stop_n_orig} {stop_option_orig[1:]}"
-            )
-        elif skipgen_test and stop_n < 3:
-            # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish.
-            error_message = (
-                "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested "
-                + f"{stop_n_orig} {stop_option_orig[1:]}"
-            )
-        if error_message is not None:
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Get the number of complete years that will be run
-        self._run_Nyears = int(stop_n)
-
-        # Only allow RXCROPMATURITY to be called with test cropMonthOutput
-        if casebaseid.split("-")[-1] != "cropMonthOutput":
-            error_message = (
-                "Only call RXCROPMATURITY with test cropMonthOutput "
-                + "to avoid potentially huge sets of daily outputs."
-            )
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Get files with prescribed sowing and harvest dates
-        self._get_rx_dates()
-
-        # Get cultivar maturity requirement file to fall back on if not generating it here
-        self._gdds_file = None
-        self._fallback_gdds_file = os.path.join(
-            os.path.dirname(self._sdatefile),
-            "gdds_20230829_161011.nc"
-        )
-
-        # Which conda environment should we use?
-        self._get_conda_env()
-
-    def _run_phase(self, skip_run=False, skip_gen=False):
-        # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
-        # want to be saved as baseline.
-
-        # -------------------------------------------------------------------
-        # (1) Set up GDD-generating run
-        # -------------------------------------------------------------------
-        # Create clone to be GDD-Generating case
-        logger.info("RXCROPMATURITY log:  cloning setup")
-        case_rxboth = self._case
-        caseroot = self._case.get_value("CASEROOT")
-        clone_path = f"{caseroot}.gddgen"
-        self._path_gddgen = clone_path
-        if os.path.exists(self._path_gddgen):
-            shutil.rmtree(self._path_gddgen)
-        logger.info("RXCROPMATURITY log:  cloning")
-        case_gddgen = self._case.create_clone(clone_path, keepexe=True)
-        logger.info("RXCROPMATURITY log:  done cloning")
-
-        os.chdir(self._path_gddgen)
-        self._set_active_case(case_gddgen)
-
-        # Set up stuff that applies to both tests
-        self._setup_all()
-
-        # Add stuff specific to GDD-Generating run
-        logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
-        self._append_to_user_nl_clm(
-            [
-                "generate_crop_gdds = .true.",
-                "use_mxmat = .false.",
-                " ",
-                "! (h2) Daily outputs for GDD generation and figure-making",
-                "hist_fincl3 = 'GDDACCUM', 'GDDHARV'",
-                "hist_nhtfrq(3) = -24",
-                "hist_mfilt(3) = 365",
-                "hist_type1d_pertape(3) = 'PFTS'",
-                "hist_dov2xy(3) = .false.",
-            ]
-        )
-
-        # If flanduse_timeseries is defined, we need to make a static version for this test. This
-        # should have every crop in most of the world.
-        self._get_flanduse_timeseries_in(case_gddgen)
-        if self._flanduse_timeseries_in is not None:
-
-            # Download files from the server, if needed
-            case_gddgen.check_all_input_data()
-
-            # Copy needed file from original to gddgen directory
-            shutil.copyfile(
-                os.path.join(caseroot, ".env_mach_specific.sh"),
-                os.path.join(self._path_gddgen, ".env_mach_specific.sh"),
-            )
-
-            # Make custom version of surface file
-            logger.info("RXCROPMATURITY log:  run fsurdat_modifier")
-            self._run_fsurdat_modifier()
-
-        # -------------------------------------------------------------------
-        # (2) Perform GDD-generating run and generate prescribed GDDs file
-        # -------------------------------------------------------------------
-        logger.info("RXCROPMATURITY log:  Start GDD-Generating run")
-
-        # As per SSP test:
-        # "No history files expected, set suffix=None to avoid compare error"
-        # We *do* expect history files here, but anyway. This works.
-        self._skip_pnl = False
-
-        # If not generating GDDs, only run a few days of this.
-        if skip_gen:
-            with Case(self._path_gddgen, read_only=False) as case:
-                case.set_value("STOP_N", 5)
-                case.set_value("STOP_OPTION", "ndays")
-
-        if not skip_run:
-            self.run_indv(suffix=None, st_archive=True)
-        if skip_gen:
-            # Interpolate an existing GDD file. Needed to check obedience to GDD inputs.
-            self._run_interpolate_gdds()
-        else:
-            self._run_generate_gdds(case_gddgen)
-
-        # -------------------------------------------------------------------
-        # (3) Set up and perform Prescribed Calendars run
-        # -------------------------------------------------------------------
-        os.chdir(caseroot)
-        self._set_active_case(case_rxboth)
-
-        # Set up stuff that applies to both tests
-        self._setup_all()
-
-        # Add stuff specific to Prescribed Calendars run
-        logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
-        self._append_to_user_nl_clm(
-            [
-                "generate_crop_gdds = .false.",
-                f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'",
-            ]
-        )
-
-        if not skip_run:
-            self.run_indv()
-
-        # -------------------------------------------------------------------
-        # (4) Check Prescribed Calendars run
-        # -------------------------------------------------------------------
-        logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
-        if not skip_run:
-            self._run_check_rxboth_run(skip_gen)
-
-    # Get sowing and harvest dates for this resolution.
-    def _get_rx_dates(self):
-        # Eventually, I want to remove these hard-coded resolutions so that this test can generate
-        # its own sowing and harvest date files at whatever resolution is requested.
-        lnd_grid = self._case.get_value("LND_GRID")
-        input_data_root = self._case.get_value("DIN_LOC_ROOT")
-        processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed"
-        if lnd_grid == "10x15":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc",
-            )
-        elif lnd_grid == "1.9x2.5":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc",
-            )
-        elif lnd_grid == "0.9x1.25":
-            self._sdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc",
-            )
-            self._hdatefile = os.path.join(
-                processed_crop_dates_dir,
-                "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc",
-            )
-        else:
-            error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Ensure files exist
-        error_message = None
-        if not os.path.exists(self._sdatefile):
-            error_message = f"ERROR: Sowing date file not found: {self._sdatefile}"
-        elif not os.path.exists(self._hdatefile):
-            error_message = f"ERROR: Harvest date file not found: {self._sdatefile}"
-        if error_message is not None:
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-    def _setup_all(self):
-        logger.info("RXCROPMATURITY log:  _setup_all start")
-
-        # Get some info
-        self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND")
-        run_startdate = self._case.get_value("RUN_STARTDATE")
-        self._run_startyear = int(run_startdate.split("-")[0])
-
-        # Set sowing dates file (and other crop calendar settings) for all runs
-        logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
-        self._modify_user_nl_allruns()
-        logger.info("RXCROPMATURITY log:  _setup_all done")
-
-    # Make a surface dataset that has every crop in every gridcell
-    def _run_fsurdat_modifier(self):
-
-        # fsurdat should be defined. Where is it?
-        self._fsurdat_in = None
-        with open(self._lnd_in_path, "r") as lnd_in:
-            for line in lnd_in:
-                fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line)
-                if fsurdat_in:
-                    self._fsurdat_in = fsurdat_in.group(1)
-                    break
-        if self._fsurdat_in is None:
-            error_message = "fsurdat not defined"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-
-        # Where we will save the fsurdat version for this test
-        path, ext = os.path.splitext(self._fsurdat_in)
-        dir_in, filename_in_noext = os.path.split(path)
-        self._fsurdat_out = os.path.join(
-            self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}"
-        )
-
-        # Make fsurdat for this test, if not already done
-        if not os.path.exists(self._fsurdat_out):
-            tool_path = os.path.join(
-                self._ctsm_root,
-                "tools",
-                "modify_input_files",
-                "fsurdat_modifier",
-            )
-
-            # Create configuration file for fsurdat_modifier
-            self._cfg_path = os.path.join(
-                self._path_gddgen,
-                "modify_fsurdat_allcropseverywhere.cfg",
-            )
-            self._create_config_file_evenlysplitcrop()
-
-            command = f"python3 {tool_path} {self._cfg_path} "
-            stu.run_python_script(
-                self._get_caseroot(),
-                self._this_conda_env,
-                command,
-                tool_path,
-            )
-
-        # Modify namelist
-        logger.info("RXCROPMATURITY log:  modify user_nl files: new fsurdat")
-        self._append_to_user_nl_clm(
-            [
-                "fsurdat = '{}'".format(self._fsurdat_out),
-                "do_transient_crops = .false.",
-                "flanduse_timeseries = ''",
-                "use_init_interp = .true.",
-            ]
-        )
-
-    def _create_config_file_evenlysplitcrop(self):
-        """
-        Open the new and the template .cfg files
-        Loop line by line through the template .cfg file
-        When string matches, replace that line's content
-        """
-        cfg_template_path = os.path.join(
-            self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg"
-        )
-
-        with open(self._cfg_path, "w", encoding="utf-8") as cfg_out:
-            # Copy template, replacing some lines
-            with open(cfg_template_path, "r", encoding="utf-8") as cfg_in:
-                for line in cfg_in:
-                    if re.match(r" *evenly_split_cropland *=", line):
-                        line = f"evenly_split_cropland = True"
-                    elif re.match(r" *fsurdat_in *=", line):
-                        line = f"fsurdat_in = {self._fsurdat_in}"
-                    elif re.match(r" *fsurdat_out *=", line):
-                        line = f"fsurdat_out = {self._fsurdat_out}"
-                    elif re.match(r" *process_subgrid_section *=", line):
-                        line = f"process_subgrid_section = True"
-                    cfg_out.write(line)
-
-            # Add new lines
-            cfg_out.write("\n")
-            cfg_out.write("[modify_fsurdat_subgrid_fractions]\n")
-            cfg_out.write("PCT_CROP    = 100.0\n")
-            cfg_out.write("PCT_NATVEG  = 0.0\n")
-            cfg_out.write("PCT_GLACIER = 0.0\n")
-            cfg_out.write("PCT_WETLAND = 0.0\n")
-            cfg_out.write("PCT_LAKE    = 0.0\n")
-            cfg_out.write("PCT_OCEAN   = 0.0\n")
-            cfg_out.write("PCT_URBAN   = 0.0 0.0 0.0\n")
-
-    def _run_check_rxboth_run(self, skip_gen):
-
-        output_dir = os.path.join(self._get_caseroot(), "run")
-
-        if skip_gen:
-            first_usable_year = self._run_startyear + 1
-            last_usable_year = first_usable_year
-        else:
-            first_usable_year = self._run_startyear + 2
-            last_usable_year = self._run_startyear + self._run_Nyears - 2
-
-        tool_path = os.path.join(
-            self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py"
-        )
-        command = (
-            f"python3 {tool_path} "
-            + f"--directory {output_dir} "
-            + f"-y1 {first_usable_year} "
-            + f"-yN {last_usable_year} "
-            + f"--rx-sdates-file {self._sdatefile} "
-            + f"--rx-gdds-file {self._gdds_file} "
-        )
-        stu.run_python_script(
-            self._get_caseroot(),
-            self._this_conda_env,
-            command,
-            tool_path,
-        )
-
-    def _modify_user_nl_allruns(self):
-        nl_additions = [
-            "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
-            "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
-            "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
-            "stream_year_first_cropcal = 2000",
-            "stream_year_last_cropcal = 2000",
-            "model_year_align_cropcal = 2000",
-            " ",
-            "! (h1) Annual outputs on sowing or harvest axis",
-            "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'",
-            "hist_nhtfrq(2) = 17520",
-            "hist_mfilt(2) = 999",
-            "hist_type1d_pertape(2) = 'PFTS'",
-            "hist_dov2xy(2) = .false.",
-        ]
-        self._append_to_user_nl_clm(nl_additions)
-
-    def _run_generate_gdds(self, case_gddgen):
-        self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out")
-        os.makedirs(self._generate_gdds_dir)
-
-        # Get arguments to generate_gdds.py
-        dout_sr = case_gddgen.get_value("DOUT_S_ROOT")
-        input_dir = os.path.join(dout_sr, "lnd", "hist")
-        first_season = self._run_startyear + 2
-        last_season = self._run_startyear + self._run_Nyears - 2
-        sdates_file = self._sdatefile
-        hdates_file = self._hdatefile
-
-        # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds.
-        tool_path = os.path.join(
-            self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py"
-        )
-        command = " ".join(
-            [
-                f"python3 {tool_path}",
-                f"--input-dir {input_dir}",
-                f"--first-season {first_season}",
-                f"--last-season {last_season}",
-                f"--sdates-file {sdates_file}",
-                f"--hdates-file {hdates_file}",
-                f"--output-dir generate_gdds_out",
-                f"--skip-crops miscanthus,irrigated_miscanthus",
-            ]
-        )
-        stu.run_python_script(
-            self._get_caseroot(),
-            self._this_conda_env,
-            command,
-            tool_path,
-        )
-
-        # Where were the prescribed maturity requirements saved?
-        generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc"))
-        if len(generated_gdd_files) != 1:
-            error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}"
-            logger.error(error_message)
-            raise RuntimeError(error_message)
-        self._gdds_file = generated_gdd_files[0]
-
-    def _run_interpolate_gdds(self):
-        # Save where?
-        self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc")
-
-        # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds.
-        tool_path = os.path.join(
-            self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py"
-        )
-        command = " ".join(
-            [
-                f"python3 {tool_path}",
-                f"--input-file {self._fallback_gdds_file}",
-                f"--target-file {self._sdatefile}",
-                f"--output-file {self._gdds_file}",
-                "--overwrite",
-            ]
-        )
-        stu.run_python_script(
-            self._get_caseroot(),
-            self._this_conda_env,
-            command,
-            tool_path,
-        )
-
-    def _get_conda_env(self):
-        conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot())
-
-        # If npl conda environment is available, use that (It has dask, which
-        # enables chunking, which makes reading daily 1-degree netCDF files
-        # much more efficient.
-        if "npl " in os.popen(conda_setup_commands + "conda env list").read():
-            self._this_conda_env = "npl"
-        else:
-            self._this_conda_env = "ctsm_pylib"
-
-    def _append_to_user_nl_clm(self, additions):
-        caseroot = self._get_caseroot()
-        append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions)
-
-    # Is flanduse_timeseries defined? If so, where is it?
-    def _get_flanduse_timeseries_in(self, case):
-        case.create_namelists(component="lnd")
-        self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in")
-        self._flanduse_timeseries_in = None
-        with open(self._lnd_in_path, "r") as lnd_in:
-            for line in lnd_in:
-                flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line)
-                if flanduse_timeseries_in:
-                    self._flanduse_timeseries_in = flanduse_timeseries_in.group(1)
-                    break
diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py
index 4fb5257967..7b836a7b17 100644
--- a/cime_config/SystemTests/rxcropmaturityskipgen.py
+++ b/cime_config/SystemTests/rxcropmaturityskipgen.py
@@ -1,4 +1,4 @@
-from rxcropmaturityshared import RXCROPMATURITYSHARED
+from rxcropmaturity import RXCROPMATURITYSHARED
 
 
 class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED):

From 6c5fdb1d735531f8aaf129420448b2ac1d635a4c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 15:56:50 -0600
Subject: [PATCH 0513/1248] Remove refs to skip_run.

---
 cime_config/SystemTests/rxcropmaturity.py        | 11 ++++-------
 cime_config/SystemTests/rxcropmaturityskipgen.py |  2 +-
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index e0f6f4df21..cffb832e8d 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -102,7 +102,7 @@ def __init__(self, case):
         # Which conda environment should we use?
         self._get_conda_env()
 
-    def _run_phase(self, skip_run=False, skip_gen=False):
+    def _run_phase(self, skip_gen=False):
         # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
         # want to be saved as baseline.
 
@@ -177,8 +177,7 @@ def _run_phase(self, skip_run=False, skip_gen=False):
                 case.set_value("STOP_N", 5)
                 case.set_value("STOP_OPTION", "ndays")
 
-        if not skip_run:
-            self.run_indv(suffix=None, st_archive=True)
+        self.run_indv(suffix=None, st_archive=True)
         if skip_gen:
             # Interpolate an existing GDD file. Needed to check obedience to GDD inputs.
             self._run_interpolate_gdds()
@@ -203,15 +202,13 @@ def _run_phase(self, skip_run=False, skip_gen=False):
             ]
         )
 
-        if not skip_run:
-            self.run_indv()
+        self.run_indv()
 
         # -------------------------------------------------------------------
         # (4) Check Prescribed Calendars run
         # -------------------------------------------------------------------
         logger.info("RXCROPMATURITY log:  output check: Prescribed Calendars")
-        if not skip_run:
-            self._run_check_rxboth_run(skip_gen)
+        self._run_check_rxboth_run(skip_gen)
 
     # Get sowing and harvest dates for this resolution.
     def _get_rx_dates(self):
diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py
index 7b836a7b17..4feb661037 100644
--- a/cime_config/SystemTests/rxcropmaturityskipgen.py
+++ b/cime_config/SystemTests/rxcropmaturityskipgen.py
@@ -4,4 +4,4 @@
 class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED):
 
     def run_phase(self):
-        self._run_phase(skip_run=False, skip_gen=True)
+        self._run_phase(skip_gen=True)

From 3efa49aec741b01d324b2236ca347fa4d4bf349f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 17:02:16 -0600
Subject: [PATCH 0514/1248] Unexpected behavior in rxboth run now errors
 check_rxboth_run.py.

---
 .../crop_calendars/check_constant_vars.py     |  2 +-
 python/ctsm/crop_calendars/check_rx_obeyed.py |  5 +++++
 .../ctsm/crop_calendars/check_rxboth_run.py   | 19 +++++++++++++++----
 python/ctsm/crop_calendars/cropcal_module.py  | 10 ++++++++--
 4 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/python/ctsm/crop_calendars/check_constant_vars.py b/python/ctsm/crop_calendars/check_constant_vars.py
index aa25a412fe..be7718256a 100644
--- a/python/ctsm/crop_calendars/check_constant_vars.py
+++ b/python/ctsm/crop_calendars/check_constant_vars.py
@@ -382,4 +382,4 @@ def check_constant_vars(
         raise RuntimeError("Stopping due to failed check_constant_vars().")
 
     bad_patches = np.unique(bad_patches)
-    return [int(p) for p in bad_patches]
+    return [int(p) for p in bad_patches], any_bad
diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py
index 99b8d80bde..8525f3e890 100644
--- a/python/ctsm/crop_calendars/check_rx_obeyed.py
+++ b/python/ctsm/crop_calendars/check_rx_obeyed.py
@@ -203,9 +203,12 @@ def check_rx_obeyed(
                     else:
                         break
 
+    bad = True
     if all_ok == 2:
+        bad = False
         print(f"✅ {which_ds}: Prescribed {output_var} always obeyed")
     elif all_ok == 1:
+        bad = False
         # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:")
         # for x in diff_str_list: print(x)
         print(
@@ -214,3 +217,5 @@ def check_rx_obeyed(
         )
     elif not verbose:
         print(f"❌ {which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}")
+
+    return bad
diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py
index ae4decde30..8f416e9f8e 100644
--- a/python/ctsm/crop_calendars/check_rxboth_run.py
+++ b/python/ctsm/crop_calendars/check_rxboth_run.py
@@ -75,6 +75,8 @@ def main(argv):
         "HARVEST_REASON_PERHARV",
     ]
 
+    any_bad = False
+
     annual_outfiles = glob.glob(os.path.join(args.directory, "*.clm2.h1.*.nc"))
 
     # These should be constant in a Prescribed Calendars (rxboth) run, as long as the inputs were
@@ -85,13 +87,17 @@ def main(argv):
         "rx_gdds_file": args.rx_gdds_file,
     }
 
-    case["ds"] = cc.import_output(
+    case["ds"], any_bad_import_output = cc.import_output(
         annual_outfiles,
         my_vars=my_vars,
         year_1=args.first_usable_year,
         year_n=args.last_usable_year,
+        throw_errors=False,
     )
-    check_constant_vars(case["ds"], case, ignore_nan=True, verbose=True, throw_error=True)
+    any_bad = any_bad or any_bad_import_output
+
+    _, any_bad_check_const_vars = check_constant_vars(case["ds"], case, ignore_nan=True, verbose=True, throw_error=True)
+    any_bad = any_bad or any_bad_check_const_vars
 
     # Import GGCMI sowing and harvest dates, and check sims
     casename = "Prescribed Calendars"
@@ -128,15 +134,16 @@ def main(argv):
 
         # Check
         if case["rx_sdates_file"]:
-            check_rx_obeyed(
+            sdate_not_obeyed = check_rx_obeyed(
                 case["ds"].vegtype_str.values,
                 case["rx_sdates_ds"].isel(time=0),
                 case["ds"],
                 casename,
                 "SDATES",
             )
+            any_bad = any_bad or sdate_not_obeyed
         if case["rx_gdds_file"]:
-            check_rx_obeyed(
+            gdds_not_obeyed = check_rx_obeyed(
                 case["ds"].vegtype_str.values,
                 case["rx_gdds_ds"].isel(time=0),
                 case["ds"],
@@ -144,6 +151,10 @@ def main(argv):
                 "GDDHARV",
                 gdd_min=gdd_min,
             )
+            any_bad = any_bad or gdds_not_obeyed
+
+    if any_bad:
+        raise RuntimeError("Unexpected behavior in rxboth run")
 
 
 if __name__ == "__main__":
diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index d25e16397e..fa1cc30e7c 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -170,8 +170,10 @@ def check_v0_le_v1(this_ds, var_list, msg_txt=" ", both_nan_ok=False, throw_erro
     if both_nan_ok:
         gdd_lt_hui = gdd_lt_hui | (np.isnan(this_ds[var0]) & np.isnan(this_ds[var1]))
     if np.all(gdd_lt_hui):
+        any_bad = False
         print(f"✅{msg_txt}{var0} always <= {var1}")
     else:
+        any_bad = True
         msg = f"❌{msg_txt}{var0} *not* always <= {var1}"
         gdd_lt_hui_vals = gdd_lt_hui.values
         patch_index = np.where(~gdd_lt_hui_vals)[0][0]
@@ -187,6 +189,7 @@ def check_v0_le_v1(this_ds, var_list, msg_txt=" ", both_nan_ok=False, throw_erro
             print(msg)
         else:
             raise RuntimeError(msg)
+    return any_bad
 
 
 def get_gs_len_da(this_da):
@@ -346,10 +349,13 @@ def import_output(
     sdates_rx_ds=None,
     gdds_rx_ds=None,
     verbose=False,
+    throw_errors=True,
 ):
     """
     Import CLM output
     """
+    any_bad = False
+
     # Import
     this_ds = import_ds(filename, my_vars=my_vars, my_vegtypes=my_vegtypes)
 
@@ -419,7 +425,7 @@ def import_output(
     # Check that e.g., GDDACCUM <= HUI
     for var_list in [["GDDACCUM", "HUI"], ["SYEARS", "HYEARS"]]:
         if all(v in this_ds_gs for v in var_list):
-            check_v0_le_v1(this_ds_gs, var_list, both_nan_ok=True, throw_error=True)
+            any_bad = check_v0_le_v1(this_ds_gs, var_list, both_nan_ok=True, throw_error=throw_errors)
 
     # Check that prescribed calendars were obeyed
     if sdates_rx_ds:
@@ -447,7 +453,7 @@ def import_output(
         raise RuntimeError("How to get NHARVEST_DISCREP for NHARVESTS > 2?")
     this_ds_gs["NHARVEST_DISCREP"] = (this_ds_gs["NHARVESTS"] == 2).astype(int)
 
-    return this_ds_gs
+    return this_ds_gs, any_bad
 
 
 def handle_zombie_crops(this_ds):

From 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 17:08:21 -0600
Subject: [PATCH 0515/1248] Reformat with black.

---
 cime_config/SystemTests/rxcropmaturity.py        | 3 +--
 cime_config/SystemTests/rxcropmaturityskipgen.py | 1 -
 python/ctsm/crop_calendars/check_rxboth_run.py   | 4 +++-
 python/ctsm/crop_calendars/cropcal_module.py     | 4 +++-
 python/ctsm/crop_calendars/interpolate_gdds.py   | 2 +-
 5 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index cffb832e8d..a583432efe 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -95,8 +95,7 @@ def __init__(self, case):
         # Get cultivar maturity requirement file to fall back on if not generating it here
         self._gdds_file = None
         self._fallback_gdds_file = os.path.join(
-            os.path.dirname(self._sdatefile),
-            "gdds_20230829_161011.nc"
+            os.path.dirname(self._sdatefile), "gdds_20230829_161011.nc"
         )
 
         # Which conda environment should we use?
diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py
index 4feb661037..409f2b9847 100644
--- a/cime_config/SystemTests/rxcropmaturityskipgen.py
+++ b/cime_config/SystemTests/rxcropmaturityskipgen.py
@@ -2,6 +2,5 @@
 
 
 class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED):
-
     def run_phase(self):
         self._run_phase(skip_gen=True)
diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py
index 8f416e9f8e..a1014b5e66 100644
--- a/python/ctsm/crop_calendars/check_rxboth_run.py
+++ b/python/ctsm/crop_calendars/check_rxboth_run.py
@@ -96,7 +96,9 @@ def main(argv):
     )
     any_bad = any_bad or any_bad_import_output
 
-    _, any_bad_check_const_vars = check_constant_vars(case["ds"], case, ignore_nan=True, verbose=True, throw_error=True)
+    _, any_bad_check_const_vars = check_constant_vars(
+        case["ds"], case, ignore_nan=True, verbose=True, throw_error=True
+    )
     any_bad = any_bad or any_bad_check_const_vars
 
     # Import GGCMI sowing and harvest dates, and check sims
diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index fa1cc30e7c..b87d26816f 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -425,7 +425,9 @@ def import_output(
     # Check that e.g., GDDACCUM <= HUI
     for var_list in [["GDDACCUM", "HUI"], ["SYEARS", "HYEARS"]]:
         if all(v in this_ds_gs for v in var_list):
-            any_bad = check_v0_le_v1(this_ds_gs, var_list, both_nan_ok=True, throw_error=throw_errors)
+            any_bad = check_v0_le_v1(
+                this_ds_gs, var_list, both_nan_ok=True, throw_error=throw_errors
+            )
 
     # Check that prescribed calendars were obeyed
     if sdates_rx_ds:
diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py
index e9491480e9..2aa0b79997 100755
--- a/python/ctsm/crop_calendars/interpolate_gdds.py
+++ b/python/ctsm/crop_calendars/interpolate_gdds.py
@@ -13,7 +13,7 @@
 sys.path.insert(1, _CTSM_PYTHON)
 
 from ctsm import ctsm_logging  # pylint: disable=wrong-import-position
-from ctsm.crop_calendars.cropcal_module import ( # pylint: disable=wrong-import-position
+from ctsm.crop_calendars.cropcal_module import (  # pylint: disable=wrong-import-position
     unexpected_negative_rx_gdd,
 )
 

From 6af704f3c6d3d55aa9f288f736db2977792ef45a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 17:09:16 -0600
Subject: [PATCH 0516/1248] Add previous commit to .git-blame-ignore-revs.

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index f86a330408..dc56c6b7e2 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -45,3 +45,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 6c6f57e948bfa31e60b383536cc21663fedb8b70
 9660667b1267dcd4150889f5f39db540158be74a
 665cf86102e09b4c4c5a140700676dca23bc55a9
+045d90f1d80f713eb3ae0ac58f6c2352937f1eb0

From 76b7df7d9fb8be59118ac7b260acd46852e196f8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 14 Jun 2024 17:13:10 -0600
Subject: [PATCH 0517/1248] check_rx_obeyed.py: Satisfy pylint.

---
 python/ctsm/crop_calendars/check_rx_obeyed.py | 36 +++++++++++--------
 1 file changed, 22 insertions(+), 14 deletions(-)

diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py
index 8525f3e890..a38b946ec5 100644
--- a/python/ctsm/crop_calendars/check_rx_obeyed.py
+++ b/python/ctsm/crop_calendars/check_rx_obeyed.py
@@ -104,6 +104,27 @@ def get_extreme_info(diff_array, rx_array, mxn, dims, gs_da, patches1d_lon, patc
     return round(themxn, 3), round(this_lon, 3), round(this_lat, 3), this_gs, round(this_rx)
 
 
+def summarize_results(which_ds, output_var, verbose, all_ok, gdd_tolerance, diffs_eg_txt):
+    """
+    Summarize results
+    """
+    bad = True
+    if all_ok == 2:
+        bad = False
+        print(f"✅ {which_ds}: Prescribed {output_var} always obeyed")
+    elif all_ok == 1:
+        bad = False
+        # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:")
+        # for x in diff_str_list: print(x)
+        print(
+            f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable (diffs <= "
+            + f"{gdd_tolerance})"
+        )
+    elif not verbose:
+        print(f"❌ {which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}")
+    return bad
+
+
 def check_rx_obeyed(
     vegtype_list, rx_ds, dates_ds, which_ds, output_var, gdd_min=None, verbose=False
 ):
@@ -203,19 +224,6 @@ def check_rx_obeyed(
                     else:
                         break
 
-    bad = True
-    if all_ok == 2:
-        bad = False
-        print(f"✅ {which_ds}: Prescribed {output_var} always obeyed")
-    elif all_ok == 1:
-        bad = False
-        # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:")
-        # for x in diff_str_list: print(x)
-        print(
-            f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable (diffs <= "
-            + f"{gdd_tolerance})"
-        )
-    elif not verbose:
-        print(f"❌ {which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}")
+    bad = summarize_results(which_ds, output_var, verbose, all_ok, gdd_tolerance, diffs_eg_txt)
 
     return bad

From ba6cc32662ec445f7725ce0221ebacb112f440e3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 14 Jun 2024 20:45:34 -0600
Subject: [PATCH 0518/1248] The gnu compiler on both Derecho and Izumi got
 confused about the InitAllocate methods in the base method as well as the
 Zender extension, I found this out in the debugger, this adds Base to the end
 of the ones in the Base class so they won't be confused with the Zender
 extension

---
 src/biogeochem/DustEmisBase.F90 | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
index ef509add06..c5e4260634 100644
--- a/src/biogeochem/DustEmisBase.F90
+++ b/src/biogeochem/DustEmisBase.F90
@@ -1,4 +1,5 @@
 module DustEmisBase
+#include "shr_assert.h"
 
   !-----------------------------------------------------------------------
   ! !DESCRIPTION:
@@ -68,8 +69,8 @@ module DustEmisBase
      procedure , public   :: GetConstVars    ! Get important constant variables
      procedure , public   :: CleanBase       ! Base object deallocation (allows extension)
      procedure , public   :: Clean => CleanBase ! Deallocation used by callers
-     procedure , private  :: InitAllocate
-     procedure , private  :: InitHistory
+     procedure , private  :: InitAllocateBase
+     procedure , private  :: InitHistoryBase
      procedure , private  :: InitDustVars    ! Initialize variables used in DustEmission method
 
   end type dust_emis_base_type
@@ -130,8 +131,8 @@ subroutine InitBase(this, bounds, NLFilename)
     type(bounds_type), intent(in) :: bounds
     character(len=*),  intent(in) :: NLFilename
 
-    call this%InitAllocate (bounds)
-    call this%InitHistory  (bounds)
+    call this%InitAllocateBase (bounds)
+    call this%InitHistoryBase  (bounds)
     call this%InitDustVars (bounds)
 
   end subroutine InitBase
@@ -162,7 +163,7 @@ subroutine CleanBase(this)
   end subroutine CleanBase
 
   !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
+  subroutine InitAllocateBase(this, bounds)
     !
     ! !ARGUMENTS:
     class (dust_emis_base_type) :: this
@@ -188,10 +189,10 @@ subroutine InitAllocate(this, bounds)
     allocate (this%dmt_vwr(1:ndst))                             ; this%dmt_vwr                   (:)   = nan
     allocate (this%stk_crc(1:ndst))                             ; this%stk_crc                   (:)   = nan
 
-  end subroutine InitAllocate
+  end subroutine InitAllocateBase
 
   !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
+  subroutine InitHistoryBase(this, bounds)
     !
     ! !USES:
     use histFileMod, only : hist_addfld1d
@@ -234,7 +235,7 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='turbulent deposition velocity 4', &
          ptr_patch=this%vlc_trb_4_patch, default='inactive')
 
-  end subroutine InitHistory
+  end subroutine InitHistoryBase
 
   !-----------------------------------------------------------------------
 
@@ -554,6 +555,8 @@ subroutine InitDustVars(this, bounds)
     real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles
     !------------------------------------------------------------------------
 
+      call shr_assert_all((lbound(this%ovr_src_snk_mss) == (/1,1/) ), file=sourcefile, line=__LINE__)
+      call shr_assert_all((ubound(this%ovr_src_snk_mss) == (/dst_src_nbr,ndst/) ), file=sourcefile, line=__LINE__)
       ! allocate local variable
       allocate (dmt_vma_src(dst_src_nbr))
       allocate (gsd_anl_src(dst_src_nbr))

From fda1ae2b57993f84dd96953538bba08b8c5d74fe Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 16 Jun 2024 08:48:17 -0600
Subject: [PATCH 0519/1248] check_rxboth_run: Handle diffs_eg_txt never
 assigned.

---
 python/ctsm/crop_calendars/check_rx_obeyed.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py
index a38b946ec5..383ebbf1e0 100644
--- a/python/ctsm/crop_calendars/check_rx_obeyed.py
+++ b/python/ctsm/crop_calendars/check_rx_obeyed.py
@@ -135,6 +135,7 @@ def check_rx_obeyed(
         dates_ds, which_ds, output_var, verbose
     )
 
+    diffs_eg_txt = None
     for vegtype_str in vegtype_list:
         thisveg_patches = np.where(dates_ds.patches1d_itype_veg_str == vegtype_str)[0]
         if thisveg_patches.size == 0:

From ca15115f512a8dafbf54d1f441dbe2227f96b482 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 16 Jun 2024 08:57:43 -0600
Subject: [PATCH 0520/1248] RXCROPMATURITY: Fix gdd-gen namelist.

---
 cime_config/SystemTests/rxcropmaturity.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 0dbbcad291..0b9c5e8ee0 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -130,6 +130,8 @@ def _run_phase(self, skip_gen=False):
         logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
         self._append_to_user_nl_clm(
             [
+                "cropcals_rx = .true.",
+                "stream_fldFileName_cultivar_gdds = ''",
                 "generate_crop_gdds = .true.",
                 "use_mxmat = .false.",
                 " ",

From 23f6fa295dd6df50770c8737a38297000533d4d9 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 16 Jun 2024 09:17:48 -0600
Subject: [PATCH 0521/1248] PlantCrop: Error if gdd20 <= 0.

---
 src/biogeochem/CNPhenologyMod.F90 | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index b346cb119f..c3eff1538a 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2704,6 +2704,10 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
       else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then
          gddmaturity(p) = hybgdd(ivt(p))
       else
+         if (gdd20 <= 0._r8) then
+            write(iulog, *) 'ERROR: gdd20 ',gdd20,' for ivt ',ivt(p)
+            call endrun(msg="Stopping")
+         end if
          if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. &
                ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean .or. &
                ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
@@ -2716,10 +2720,11 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
                ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
                ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then
             gddmaturity(p) = max(950._r8, min(gdd20*0.85_r8, hybgdd(ivt(p))))
-            if (do_plant_normal) then
+            if (do_plant_normal) then  ! TODO SSR: Add ".and. .not. do_plant_prescribed"?
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
          else
+            ! TODO SSR: Add more descriptive error message
             call endrun(msg="Stopping")
          end if
 

From 682c52651105114c63fd8735a6204a58b94863da Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 12:18:49 -0600
Subject: [PATCH 0522/1248] Be explicit about the things needed from
 unittestSubGridMod, and remove two uneeded setttings

---
 .../test/DustEmis_test/test_DustEmisZender2003.pf         | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 4df64c7da3..a8ac4630da 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -3,7 +3,7 @@ module test_DustEmisZender2003
   ! Tests of DustEmisZender2003
 
   use funit
-  use unittestSubgridMod
+  use unittestSubgridMod, only : bounds, unittest_subgrid_teardown
   use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
   use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
@@ -162,12 +162,6 @@ contains
        this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
     end do
 
-
-    ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager)
-    grc%londeg(:) = 0.0_r8
-
-    grc%area(:) = 10.0_r8
-
   end subroutine setupEnvironment
 
   !-----------------------------------------------------------------------

From 67f4533a5c4fa6e6ab04563e2396532cb1b50dbf Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 12:26:21 -0600
Subject: [PATCH 0523/1248] Move dust emission object creation as last

---
 src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index a8ac4630da..856364e8db 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -81,7 +81,6 @@ contains
     endc = bounds%endc
     allocate( urb_em(begl:endl) )
 
-    allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))
     call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
     atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
                                           glcmec_downscale_longwave = .false., &
@@ -111,6 +110,8 @@ contains
                                is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
     deallocate (snow_depth_col )
     deallocate( urb_em )
+    ! Create the dust emission object last
+    allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))
   end subroutine setUp
 
   !-----------------------------------------------------------------------

From 499c4cfec445299e9e01be4e414372e26238f82a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 12:57:58 -0600
Subject: [PATCH 0524/1248] Remove setting of bedrock, which isn't needed

---
 src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 856364e8db..3d4f4c49c3 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -147,6 +147,7 @@ contains
     real(r8), parameter :: clay = 10.0_r8
 
     !-----------------------------------------------------------------------
+    ! Setting the soil structrure is needed for water_state types
     col%dz(:,1:nlevgrnd) = 1.0_r8
     do j = 1, nlevgrnd
        do c = bounds%begc, bounds%endc
@@ -155,10 +156,6 @@ contains
     end do
 
     do c = bounds%begc, bounds%endc
-       ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are
-       ! considered bedrock
-       col%nbedrock(c) = nlevsoi
-
        this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
        this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
     end do

From 5e43b8f4aa71098b187b7719b3bf18e36aca0527 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 13:18:32 -0600
Subject: [PATCH 0525/1248] Add some comments about the setup, and move atm2lnd
 init more together

---
 .../test/DustEmis_test/test_DustEmisZender2003.pf    | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 3d4f4c49c3..332f808283 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -64,16 +64,19 @@ contains
     integer :: c
     type(atm2lnd_params_type) :: atm2lnd_params
 
+    ! Settings needed for clm_varpar
     soil_layerstruct_predefined = '20SL_8.5m'
     create_crop_landunit = .true.
     use_crop = .false.
     call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
     call clm_varcon_init( is_simple_buildtemp=.true.)
+    ! Water factor initialization
     call this%water_factory%init()
     call this%water_factory%setup_before_subgrid( &
         my_nlevsoi = nlevsoi, &
         nlevgrnd_additional = nlevgrnd - nlevsoi, &
         my_nlevsno = 3)
+    ! Setup the subgrid structure for a single bare-soil patch
     call setup_single_veg_patch( pft_type=0 )
     begl = bounds%begl
     endl = bounds%endl
@@ -81,15 +84,21 @@ contains
     endc = bounds%endc
     allocate( urb_em(begl:endl) )
 
+    ! Create the nolake filter
     call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
+    ! atmospher to land parameter object
     atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
                                           glcmec_downscale_longwave = .false., &
                                           lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
     )
+    call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
+    ! Hydrology and snow (needed for water types)
     allocate (snow_depth_col(begc:endc))
     snow_depth_col(begc:endc) = 0.0_r8
     call SnowHydrologySetControlForTesting()
     call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc))
+    deallocate (snow_depth_col )
+    ! Water and soil state -- after the subgrid setup
     call this%water_factory%setup_after_subgrid(snl = 3)
     call this%soilstate_inst%Init(bounds)
     do c = begc, endc
@@ -97,7 +106,7 @@ contains
     end do
     call this%setupEnvironment( )
     call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
-    call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
+    ! Canopy state, friction velocity, and temperature state ojects
     call this%canopystate_inst%SetNMLForTesting()
     call this%canopystate_inst%Init(bounds)
     call this%frictionvel_inst%InitForTesting(bounds)
@@ -108,7 +117,6 @@ contains
                                em_improad_lun=urb_em(begl:endl), &
                                em_perroad_lun=urb_em(begl:endl), &
                                is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
-    deallocate (snow_depth_col )
     deallocate( urb_em )
     ! Create the dust emission object last
     allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))

From 281fb7b6ba3b4f249a1bb3b5b4da65b3380bf3bd Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 13:35:17 -0600
Subject: [PATCH 0526/1248] Change name of setupEnvironment to setupSoilState
 and move the soil-state initialization together

---
 .../DustEmis_test/test_DustEmisZender2003.pf  | 23 ++++++++++---------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 332f808283..d05dcbaa6f 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -42,7 +42,7 @@ module test_DustEmisZender2003
    contains
      procedure :: setUp
      procedure :: tearDown
-     procedure :: setupEnvironment
+     procedure :: setupSoilState
      procedure :: create_atm2lnd
      procedure :: create_fv
      procedure :: print_values
@@ -70,7 +70,7 @@ contains
     use_crop = .false.
     call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
     call clm_varcon_init( is_simple_buildtemp=.true.)
-    ! Water factor initialization
+    ! Water object initialization -- before subgrid
     call this%water_factory%init()
     call this%water_factory%setup_before_subgrid( &
         my_nlevsoi = nlevsoi, &
@@ -82,11 +82,10 @@ contains
     endl = bounds%endl
     begc = bounds%begc
     endc = bounds%endc
-    allocate( urb_em(begl:endl) )
 
     ! Create the nolake filter
     call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
-    ! atmospher to land parameter object
+    ! atmosphere to land parameter object
     atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
                                           glcmec_downscale_longwave = .false., &
                                           lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
@@ -100,16 +99,13 @@ contains
     deallocate (snow_depth_col )
     ! Water and soil state -- after the subgrid setup
     call this%water_factory%setup_after_subgrid(snl = 3)
-    call this%soilstate_inst%Init(bounds)
-    do c = begc, endc
-       this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1)
-    end do
-    call this%setupEnvironment( )
+    call this%setupSoilState( )   ! This needs to happen before the water_type object creation
     call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
     ! Canopy state, friction velocity, and temperature state ojects
     call this%canopystate_inst%SetNMLForTesting()
     call this%canopystate_inst%Init(bounds)
     call this%frictionvel_inst%InitForTesting(bounds)
+    allocate( urb_em(begl:endl) )
     urb_em(begl:endl) = 0.99_r8
     call this%temperature_inst%Init(bounds,           &
                                em_roof_lun=urb_em(begl:endl), &
@@ -138,7 +134,7 @@ contains
 
   !-----------------------------------------------------------------------
 
-  subroutine setupEnvironment(this)
+  subroutine setupSoilState(this)
     !
     ! !DESCRIPTION:
     ! Sets up the external environment used by Dust emissions - i.e., things accessed via
@@ -163,12 +159,17 @@ contains
        end do
     end do
 
+    call this%soilstate_inst%Init(bounds)
+    do c = bounds%begc, bounds%endc
+       this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1)
+    end do
+    ! These are needed for dust emissions initialization
     do c = bounds%begc, bounds%endc
        this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
        this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
     end do
 
-  end subroutine setupEnvironment
+  end subroutine setupSoilState
 
   !-----------------------------------------------------------------------
 

From 2db3f1c8200598f14cc64172b420b8241f224b43 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 14:00:29 -0600
Subject: [PATCH 0527/1248] Don't actually need clm_varcon here

---
 src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index d05dcbaa6f..90bc00803d 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -7,7 +7,6 @@ module test_DustEmisZender2003
   use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
   use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
-  use clm_varcon, only : clm_varcon_init, clm_varcon_clean
   use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean
   use DustEmisBase
   use DustEmisZender2003
@@ -69,7 +68,6 @@ contains
     create_crop_landunit = .true.
     use_crop = .false.
     call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
-    call clm_varcon_init( is_simple_buildtemp=.true.)
     ! Water object initialization -- before subgrid
     call this%water_factory%init()
     call this%water_factory%setup_before_subgrid( &
@@ -128,7 +126,6 @@ contains
     call SnowHydrologyClean()
     call unittest_subgrid_teardown()
     call this%atm2lnd_inst%Clean()
-    call clm_varcon_clean()
     deallocate( this%filter_nolakep )
   end subroutine tearDown
 

From b173ab575f2976c7b9e4880b2077e107dd905091 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 14:11:11 -0600
Subject: [PATCH 0528/1248] remove snowHydrology parts that weren't needed

---
 .../test/DustEmis_test/test_DustEmisZender2003.pf        | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 90bc00803d..250b7b3a61 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -7,7 +7,6 @@ module test_DustEmisZender2003
   use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
   use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
-  use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean
   use DustEmisBase
   use DustEmisZender2003
   use shr_kind_mod , only : r8 => shr_kind_r8
@@ -57,7 +56,6 @@ contains
     class(TestDustEmisZender2003), intent(inout) :: this
 
     character(len=5) :: NLFilename = 'none'
-    real(r8), allocatable :: snow_depth_col(:)
     real(r8), allocatable :: urb_em(:)
     integer :: begl, endl, begc, endc
     integer :: c
@@ -89,12 +87,6 @@ contains
                                           lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
     )
     call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
-    ! Hydrology and snow (needed for water types)
-    allocate (snow_depth_col(begc:endc))
-    snow_depth_col(begc:endc) = 0.0_r8
-    call SnowHydrologySetControlForTesting()
-    call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc))
-    deallocate (snow_depth_col )
     ! Water and soil state -- after the subgrid setup
     call this%water_factory%setup_after_subgrid(snl = 3)
     call this%setupSoilState( )   ! This needs to happen before the water_type object creation
@@ -123,7 +115,6 @@ contains
 
     call this%dust_emis%Clean()
     call this%water_factory%teardown(this%water_inst)
-    call SnowHydrologyClean()
     call unittest_subgrid_teardown()
     call this%atm2lnd_inst%Clean()
     deallocate( this%filter_nolakep )

From 7ddcbb147acc7e66601e4e1182efbd5683c2c2ef Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 14:21:10 -0600
Subject: [PATCH 0529/1248] More notes, set snl with a parameter so consistent
 between two uses, and remove method not used

---
 .../test/DustEmis_test/test_DustEmisZender2003.pf      | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 250b7b3a61..76bb036339 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -18,7 +18,7 @@ module test_DustEmisZender2003
   use WaterType, only : water_type
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
-  use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay
+  use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, MassFracClay
   use DustEmisFactory, only : create_dust_emissions
 
   implicit none
@@ -54,12 +54,14 @@ contains
   subroutine setUp(this)
     use ColumnType, only : col
     class(TestDustEmisZender2003), intent(inout) :: this
+    ! Allocate and initiatlize the test object for input objects dust-emission needs
 
     character(len=5) :: NLFilename = 'none'
     real(r8), allocatable :: urb_em(:)
     integer :: begl, endl, begc, endc
     integer :: c
     type(atm2lnd_params_type) :: atm2lnd_params
+    integer, parameter :: snl = 3
 
     ! Settings needed for clm_varpar
     soil_layerstruct_predefined = '20SL_8.5m'
@@ -71,7 +73,7 @@ contains
     call this%water_factory%setup_before_subgrid( &
         my_nlevsoi = nlevsoi, &
         nlevgrnd_additional = nlevgrnd - nlevsoi, &
-        my_nlevsno = 3)
+        my_nlevsno = snl)
     ! Setup the subgrid structure for a single bare-soil patch
     call setup_single_veg_patch( pft_type=0 )
     begl = bounds%begl
@@ -88,7 +90,7 @@ contains
     )
     call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
     ! Water and soil state -- after the subgrid setup
-    call this%water_factory%setup_after_subgrid(snl = 3)
+    call this%water_factory%setup_after_subgrid(snl = snl)
     call this%setupSoilState( )   ! This needs to happen before the water_type object creation
     call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
     ! Canopy state, friction velocity, and temperature state ojects
@@ -96,7 +98,7 @@ contains
     call this%canopystate_inst%Init(bounds)
     call this%frictionvel_inst%InitForTesting(bounds)
     allocate( urb_em(begl:endl) )
-    urb_em(begl:endl) = 0.99_r8
+    urb_em(begl:endl) = 0.99_r8  ! Arbitrary won't matter here
     call this%temperature_inst%Init(bounds,           &
                                em_roof_lun=urb_em(begl:endl), &
                                em_wall_lun=urb_em(begl:endl), &

From 1633faac6bb4380f050e108af1220ac297080ea2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 15:56:31 -0600
Subject: [PATCH 0530/1248] Start moving dust emis inputs into it's own module
 to be shared by both Zender and Leung

---
 .../DustEmis_test/test_DustEmisZender2003.pf  | 308 ++++--------------
 src/unit_test_shr/CMakeLists.txt              |   1 +
 src/unit_test_shr/unittestDustEmisInputs.F90  | 249 ++++++++++++++
 3 files changed, 315 insertions(+), 243 deletions(-)
 create mode 100644 src/unit_test_shr/unittestDustEmisInputs.F90

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 76bb036339..a26e2a5a33 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -3,6 +3,7 @@ module test_DustEmisZender2003
   ! Tests of DustEmisZender2003
 
   use funit
+  use unittestDustEmisInputs, only : unittest_dust_emis_input_type
   use unittestSubgridMod, only : bounds, unittest_subgrid_teardown
   use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
   use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
@@ -28,21 +29,10 @@ module test_DustEmisZender2003
   @TestCase
   type, extends(TestCase) :: TestDustEmisZender2003
      class(dust_emis_base_type), allocatable :: dust_emis
-     integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
-     integer :: num_nolakep              ! number of patches in non-lake filter
-     type(atm2lnd_type) :: atm2lnd_inst
-     type(soilstate_type) :: soilstate_inst
-     type(canopystate_type) :: canopystate_inst
-     type(temperature_type) :: temperature_inst
-     type(unittest_water_type_factory_type) :: water_factory
-     type(water_type) :: water_inst
-     type(frictionvel_type) :: frictionvel_inst
+     type(unittest_dust_emis_input_type) :: input
    contains
      procedure :: setUp
      procedure :: tearDown
-     procedure :: setupSoilState
-     procedure :: create_atm2lnd
-     procedure :: create_fv
      procedure :: print_values
      procedure :: validate_patch
   end type TestDustEmisZender2003
@@ -52,60 +42,12 @@ contains
   !-----------------------------------------------------------------------
 
   subroutine setUp(this)
-    use ColumnType, only : col
     class(TestDustEmisZender2003), intent(inout) :: this
-    ! Allocate and initiatlize the test object for input objects dust-emission needs
-
+    ! Allocate and initialize the test object for input objects dust-emission needs
     character(len=5) :: NLFilename = 'none'
-    real(r8), allocatable :: urb_em(:)
-    integer :: begl, endl, begc, endc
-    integer :: c
-    type(atm2lnd_params_type) :: atm2lnd_params
-    integer, parameter :: snl = 3
-
-    ! Settings needed for clm_varpar
-    soil_layerstruct_predefined = '20SL_8.5m'
-    create_crop_landunit = .true.
-    use_crop = .false.
-    call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
-    ! Water object initialization -- before subgrid
-    call this%water_factory%init()
-    call this%water_factory%setup_before_subgrid( &
-        my_nlevsoi = nlevsoi, &
-        nlevgrnd_additional = nlevgrnd - nlevsoi, &
-        my_nlevsno = snl)
-    ! Setup the subgrid structure for a single bare-soil patch
-    call setup_single_veg_patch( pft_type=0 )
-    begl = bounds%begl
-    endl = bounds%endl
-    begc = bounds%begc
-    endc = bounds%endc
-
-    ! Create the nolake filter
-    call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
-    ! atmosphere to land parameter object
-    atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
-                                          glcmec_downscale_longwave = .false., &
-                                          lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
-    )
-    call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
-    ! Water and soil state -- after the subgrid setup
-    call this%water_factory%setup_after_subgrid(snl = snl)
-    call this%setupSoilState( )   ! This needs to happen before the water_type object creation
-    call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
-    ! Canopy state, friction velocity, and temperature state ojects
-    call this%canopystate_inst%SetNMLForTesting()
-    call this%canopystate_inst%Init(bounds)
-    call this%frictionvel_inst%InitForTesting(bounds)
-    allocate( urb_em(begl:endl) )
-    urb_em(begl:endl) = 0.99_r8  ! Arbitrary won't matter here
-    call this%temperature_inst%Init(bounds,           &
-                               em_roof_lun=urb_em(begl:endl), &
-                               em_wall_lun=urb_em(begl:endl), &
-                               em_improad_lun=urb_em(begl:endl), &
-                               em_perroad_lun=urb_em(begl:endl), &
-                               is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
-    deallocate( urb_em )
+
+    call this%input%setUp()
+ 
     ! Create the dust emission object last
     allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))
   end subroutine setUp
@@ -116,153 +58,33 @@ contains
     class(TestDustEmisZender2003), intent(inout) :: this
 
     call this%dust_emis%Clean()
-    call this%water_factory%teardown(this%water_inst)
-    call unittest_subgrid_teardown()
-    call this%atm2lnd_inst%Clean()
-    deallocate( this%filter_nolakep )
+    call this%input%tearDown()
   end subroutine tearDown
 
   !-----------------------------------------------------------------------
 
-  subroutine setupSoilState(this)
-    !
-    ! !DESCRIPTION:
-    ! Sets up the external environment used by Dust emissions - i.e., things accessed via
-    ! 'use' statements.
-    !
-    ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has
-    ! been completed.
-    !
-    use ColumnType, only : col
-    use GridcellType, only : grc
-    class(TestDustEmisZender2003), intent(in) :: this
-    !
-    integer :: c,j
-    real(r8), parameter :: clay = 10.0_r8
-
-    !-----------------------------------------------------------------------
-    ! Setting the soil structrure is needed for water_state types
-    col%dz(:,1:nlevgrnd) = 1.0_r8
-    do j = 1, nlevgrnd
-       do c = bounds%begc, bounds%endc
-          col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j)
-       end do
-    end do
-
-    call this%soilstate_inst%Init(bounds)
-    do c = bounds%begc, bounds%endc
-       this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1)
-    end do
-    ! These are needed for dust emissions initialization
-    do c = bounds%begc, bounds%endc
-       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
-       this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
-    end do
-
-  end subroutine setupSoilState
-
-  !-----------------------------------------------------------------------
-
-  subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho )
-    ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets
-    ! forcing fields based on inputs. Excluded inputs are given a default value
-    class(TestDustEmisZender2003), intent(inout) :: this
-    real(r8), intent(in), optional :: forc_t(:)
-    real(r8), intent(in), optional :: forc_pbot(:)
-    real(r8), intent(in), optional :: forc_rho(:)
-
-    real(r8), parameter :: forc_t_default = 301._r8
-    real(r8), parameter :: forc_pbot_default = 100000._r8
-    real(r8), parameter :: forc_rho_default = 1.1_r8
-    ! ------------------------------------------------------------------------
-
-    if (present(forc_t)) then
-       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:)
-    else
-       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default
-    end if
-
-    if (present(forc_pbot)) then
-       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:)
-    else
-       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default
-    end if
-
-    if (present(forc_rho)) then
-       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:)
-    else
-       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default
-    end if
-
-  end subroutine create_atm2lnd
-
-  !-----------------------------------------------------------------------
-
-  subroutine create_fv(this, fv, u10, ram1)
-    ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
-    ! fields based on inputs. Excluded inputs are given a default value
-    class(TestDustEmisZender2003), intent(inout) :: this
-    real(r8), intent(in), optional :: fv
-    real(r8), intent(in), optional :: u10
-    real(r8), intent(in), optional :: ram1
-
-    real(r8), parameter :: fv_default = 2.0_r8
-    real(r8), parameter :: u10_default = 4._r8
-    real(r8), parameter :: ram1_default = 200._r8
-    ! ------------------------------------------------------------------------
-
-    if (present(fv)) then
-       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv
-    else
-       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default
-    end if
-
-    if (present(u10)) then
-       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10
-    else
-       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default
-    end if
-
-    if (present(ram1)) then
-       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1
-    else
-       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default
-    end if
-
-  end subroutine create_fv
-
   subroutine print_values(this)
-    use LandunitType, only : lun
+    ! For debugging
     use PatchType, only : patch
     class(TestDustEmisZender2003), intent(inout) :: this
     real(r8) :: SaltationFactor
-    integer :: p, c, l
+    integer :: p, c
 
+    call this%input%print_values()
     call this%dust_emis%GetConstVars( SaltationFactor )
-    do l = bounds%begl, bounds%endl
-       print *, 'landunit type= ', lun%itype(l)
-    end do
     do c = bounds%begc, bounds%endc
-       print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1)
-       print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1)
-       print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c)
-       print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c)
-       print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c))
+       print *, 'saltation per rho = ', (SaltationFactor / this%input%atm2lnd_inst%forc_rho_downscaled_col(c))
     end do
     do p = bounds%begp, bounds%endp
-       print *, 'patch type= ', patch%itype(p)
-       print *, 'patch weight= ', patch%wtgcell(p)
-       print *, 'patch active= ', patch%active(p)
-       print *, 'tlai = ', this%canopystate_inst%tlai_patch(p)
-       print *, 'tsai = ', this%canopystate_inst%tsai_patch(p)
        c = patch%column(p)
-       print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) &
-                                     / this%frictionvel_inst%fv_patch(p)
+       print *, 'Wind threshold fraction = ', (SaltationFactor / this%input%atm2lnd_inst%forc_rho_downscaled_col(c)) &
+                                     / this%input%frictionvel_inst%fv_patch(p)
        call this%dust_emis%WritePatchToLog( p )
     end do
   end subroutine print_values
-
+  
   !-----------------------------------------------------------------------
+
   subroutine validate_patch(this, p)
     class(TestDustEmisZender2003), intent(inout) :: this
     integer, intent(in) :: p
@@ -283,12 +105,12 @@ contains
     real(r8) :: vlc_trb_3
     real(r8) :: vlc_trb_4
 
-    call this%create_atm2lnd()
-    call this%create_fv()
-    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+    call this%input%create_atm2lnd()
+    call this%input%create_fv()
+    call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                      this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                      this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+    call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
     do p = bounds%begp, bounds%endp
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
@@ -314,15 +136,15 @@ contains
    real(r8) :: fv
    real(r8) :: SaltationFactor
 
-   call this%create_atm2lnd()
+   call this%input%create_atm2lnd()
    call this%dust_emis%GetConstVars( SaltationFactor )
    ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps))
-   fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15
-   call this%create_fv( fv=fv )
-   call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                     this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                     this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-   call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+   fv = ( SaltationFactor / sqrt( this%input%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15
+   call this%input%create_fv( fv=fv )
+   call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                      this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                      this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+   call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
    call this%print_values()
    do p = bounds%begp, bounds%endp
       call this%validate_patch(p)
@@ -341,13 +163,13 @@ contains
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
 
-   call this%create_atm2lnd()
-   this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8
-   call this%create_fv( )
-   call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                     this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                     this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-   call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+   call this%input%create_atm2lnd()
+   this%input%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8
+   call this%input%create_fv( )
+   call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                      this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                      this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+   call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
    do p = bounds%begp, bounds%endp
       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
       @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
@@ -366,15 +188,15 @@ contains
    integer :: p, l
    real(r8) :: flx_mss_vrt_dst_tot
 
-   call this%create_atm2lnd()
-   call this%create_fv( )
+   call this%input%create_atm2lnd()
+   call this%input%create_fv( )
    ! Set the lanunit type for
    do l = istcrop+1, max_lunit
       lun%itype(bounds%begl:bounds%endl) = l
-      call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                        this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                        this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-      call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+      call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                         this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                         this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+      call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
       do p = bounds%begp, bounds%endp
          call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
          @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
@@ -392,13 +214,13 @@ contains
     real(r8) :: flx_mss_vrt_dst_tot
     character(100) :: expected_msg
  
-    call this%create_atm2lnd()
-    call this%create_fv( )
+    call this%input%create_atm2lnd()
+    call this%input%create_fv( )
     ! Dust should abort with an error on dust mobility when snow fraction greater than 1
-    this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + 1.e-15_r8
-    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                         this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                         this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
+    this%input%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + 1.e-15_r8
+    call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                         this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                         this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
     expected_msg = "ABORTED: Bad value for dust mobilization fraction"
     @assertExceptionRaised(expected_msg)
 
@@ -413,13 +235,13 @@ contains
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
 
-   call this%create_atm2lnd()
-   call this%create_fv( )
-   this%canopystate_inst%tlai_patch(:) = 0.3_r8
-   call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                     this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                     this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-   call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+   call this%input%create_atm2lnd()
+   call this%input%create_fv( )
+   this%input%canopystate_inst%tlai_patch(:) = 0.3_r8
+   call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                     this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                     this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+   call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
    do p = bounds%begp, bounds%endp
       call this%validate_patch(p)
       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
@@ -441,12 +263,12 @@ contains
     real(r8) :: total_dust0, total_dust_higher
 
     ! Run baseline u10
-    call this%create_atm2lnd()
-    call this%create_fv( u10=u10, fv=fv )
-    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+    call this%input%create_atm2lnd()
+    call this%input%create_fv( u10=u10, fv=fv )
+    call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                      this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                      this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+    call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
     do p = bounds%begp, bounds%endp
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
@@ -454,11 +276,11 @@ contains
        @assertEqual( flx_mss_vrt_dst_tot, 2.273879554711299d-5, tolerance=tol )
     end do
     ! Double u10 and show result is higher
-    call this%create_fv( u10=u10*2.0_r8, fv=fv)
-    call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, &
-                      this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, &
-                      this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst)
-    call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst)
+    call this%input%create_fv( u10=u10*2.0_r8, fv=fv)
+    call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                      this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                      this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+    call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
     do p = bounds%begp, bounds%endp
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
diff --git a/src/unit_test_shr/CMakeLists.txt b/src/unit_test_shr/CMakeLists.txt
index 9bf95c728f..f6a204bd72 100644
--- a/src/unit_test_shr/CMakeLists.txt
+++ b/src/unit_test_shr/CMakeLists.txt
@@ -9,6 +9,7 @@ sourcelist_to_parent(clm_genf90_sources)
 list(APPEND clm_sources "${clm_genf90_sources}")
 
 list(APPEND clm_sources
+  unittestDustEmisInputs.F90
   unittestFilterBuilderMod.F90
   unittestGlcMec.F90
   unittestSimpleSubgridSetupsMod.F90
diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90
new file mode 100644
index 0000000000..4cc82fa55e
--- /dev/null
+++ b/src/unit_test_shr/unittestDustEmisInputs.F90
@@ -0,0 +1,249 @@
+module unittestDustEmisInputs
+
+  ! unit testing dust emission inputs
+
+  use unittestSubgridMod, only : bounds, unittest_subgrid_teardown
+  use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
+  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
+  use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
+  use shr_kind_mod , only : r8 => shr_kind_r8
+  use unittestFilterBuilderMod, only : filter_from_range
+  use atm2lndType, only : atm2lnd_type, atm2lnd_params_type
+  use SoilStateType, only : soilstate_type
+  use CanopyStateType, only : canopystate_type
+  use TemperatureType, only : temperature_type
+  use WaterType, only : water_type
+  use FrictionVelocityMod, only : frictionvel_type
+  use unittestWaterTypeFactory, only : unittest_water_type_factory_type
+  use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, MassFracClay
+
+  implicit none
+  private
+
+  type, public :: unittest_dust_emis_input_type
+     integer, allocatable :: filter_nolakep(:)      ! non-lake filter (patches)
+     integer :: num_nolakep              ! number of patches in non-lake filter
+     type(atm2lnd_type) :: atm2lnd_inst
+     type(soilstate_type) :: soilstate_inst
+     type(canopystate_type) :: canopystate_inst
+     type(temperature_type) :: temperature_inst
+     type(unittest_water_type_factory_type) :: water_factory
+     type(water_type) :: water_inst
+     type(frictionvel_type) :: frictionvel_inst
+   contains
+     procedure, public :: setUp
+     procedure, public :: tearDown
+     procedure, private:: setupSoilState
+     procedure, public :: create_atm2lnd
+     procedure, public :: create_fv
+     procedure, public :: print_values
+  end type unittest_dust_emis_input_type
+
+contains
+
+  !-----------------------------------------------------------------------
+
+  subroutine setUp(this)
+    use ColumnType, only : col
+    class(unittest_dust_emis_input_type), intent(inout) :: this
+    ! Allocate and initiatlize the test object for input objects dust-emission needs
+
+    character(len=5) :: NLFilename = 'none'
+    real(r8), allocatable :: urb_em(:)
+    integer :: begl, endl, begc, endc
+    integer :: c
+    type(atm2lnd_params_type) :: atm2lnd_params
+    integer, parameter :: snl = 3
+
+    ! Settings needed for clm_varpar
+    soil_layerstruct_predefined = '20SL_8.5m'
+    create_crop_landunit = .true.
+    use_crop = .false.
+    call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 )
+    ! Water object initialization -- before subgrid
+    call this%water_factory%init()
+    call this%water_factory%setup_before_subgrid( &
+        my_nlevsoi = nlevsoi, &
+        nlevgrnd_additional = nlevgrnd - nlevsoi, &
+        my_nlevsno = snl)
+    ! Setup the subgrid structure for a single bare-soil patch
+    call setup_single_veg_patch( pft_type=0 )
+    begl = bounds%begl
+    endl = bounds%endl
+    begc = bounds%begc
+    endc = bounds%endc
+
+    ! Create the nolake filter
+    call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep)
+    ! atmosphere to land parameter object
+    atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., &
+                                          glcmec_downscale_longwave = .false., &
+                                          lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
+    )
+    call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
+    ! Water and soil state -- after the subgrid setup
+    call this%water_factory%setup_after_subgrid(snl = snl)
+    call this%setupSoilState( )   ! This needs to happen before the water_type object creation
+    call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
+    ! Canopy state, friction velocity, and temperature state ojects
+    call this%canopystate_inst%SetNMLForTesting()
+    call this%canopystate_inst%Init(bounds)
+    call this%frictionvel_inst%InitForTesting(bounds)
+    allocate( urb_em(begl:endl) )
+    urb_em(begl:endl) = 0.99_r8  ! Arbitrary won't matter here
+    call this%temperature_inst%Init(bounds,           &
+                               em_roof_lun=urb_em(begl:endl), &
+                               em_wall_lun=urb_em(begl:endl), &
+                               em_improad_lun=urb_em(begl:endl), &
+                               em_perroad_lun=urb_em(begl:endl), &
+                               is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
+    deallocate( urb_em )
+  end subroutine setUp
+
+  !-----------------------------------------------------------------------
+
+  subroutine tearDown(this)
+    class(unittest_dust_emis_input_type), intent(inout) :: this
+
+    call this%water_factory%teardown(this%water_inst)
+    call unittest_subgrid_teardown()
+    call this%atm2lnd_inst%Clean()
+    deallocate( this%filter_nolakep )
+  end subroutine tearDown
+
+  !-----------------------------------------------------------------------
+
+  subroutine setupSoilState(this)
+    !
+    ! !DESCRIPTION:
+    ! Sets up the external environment used by Dust emissions - i.e., things accessed via
+    ! 'use' statements.
+    !
+    ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has
+    ! been completed.
+    !
+    use ColumnType, only : col
+    use GridcellType, only : grc
+    class(unittest_dust_emis_input_type), intent(in) :: this
+    !
+    integer :: c,j
+    real(r8), parameter :: clay = 10.0_r8
+
+    !-----------------------------------------------------------------------
+    ! Setting the soil structrure is needed for water_state types
+    col%dz(:,1:nlevgrnd) = 1.0_r8
+    do j = 1, nlevgrnd
+       do c = bounds%begc, bounds%endc
+          col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j)
+       end do
+    end do
+
+    call this%soilstate_inst%Init(bounds)
+    do c = bounds%begc, bounds%endc
+       this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1)
+    end do
+    ! These are needed for dust emissions initialization
+    do c = bounds%begc, bounds%endc
+       this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
+       this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
+    end do
+
+  end subroutine setupSoilState
+
+  !-----------------------------------------------------------------------
+
+  subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho )
+    ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets
+    ! forcing fields based on inputs. Excluded inputs are given a default value
+    class(unittest_dust_emis_input_type), intent(inout) :: this
+    real(r8), intent(in), optional :: forc_t(:)
+    real(r8), intent(in), optional :: forc_pbot(:)
+    real(r8), intent(in), optional :: forc_rho(:)
+
+    real(r8), parameter :: forc_t_default = 301._r8
+    real(r8), parameter :: forc_pbot_default = 100000._r8
+    real(r8), parameter :: forc_rho_default = 1.1_r8
+    ! ------------------------------------------------------------------------
+
+    if (present(forc_t)) then
+       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:)
+    else
+       this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default
+    end if
+
+    if (present(forc_pbot)) then
+       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:)
+    else
+       this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default
+    end if
+
+    if (present(forc_rho)) then
+       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:)
+    else
+       this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default
+    end if
+
+  end subroutine create_atm2lnd
+
+  !-----------------------------------------------------------------------
+
+  subroutine create_fv(this, fv, u10, ram1)
+    ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
+    ! fields based on inputs. Excluded inputs are given a default value
+    class(unittest_dust_emis_input_type), intent(inout) :: this
+    real(r8), intent(in), optional :: fv
+    real(r8), intent(in), optional :: u10
+    real(r8), intent(in), optional :: ram1
+
+    real(r8), parameter :: fv_default = 2.0_r8
+    real(r8), parameter :: u10_default = 4._r8
+    real(r8), parameter :: ram1_default = 200._r8
+    ! ------------------------------------------------------------------------
+
+    if (present(fv)) then
+       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv
+    else
+       this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default
+    end if
+
+    if (present(u10)) then
+       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10
+    else
+       this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default
+    end if
+
+    if (present(ram1)) then
+       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1
+    else
+       this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default
+    end if
+
+  end subroutine create_fv
+
+  subroutine print_values(this)
+    use LandunitType, only : lun
+    use PatchType, only : patch
+    class(unittest_dust_emis_input_type), intent(inout) :: this
+    integer :: p, c, l
+
+    do l = bounds%begl, bounds%endl
+       print *, 'landunit type= ', lun%itype(l)
+    end do
+    do c = bounds%begc, bounds%endc
+       print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1)
+       print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1)
+       print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c)
+       print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c)
+    end do
+    do p = bounds%begp, bounds%endp
+       print *, 'patch type= ', patch%itype(p)
+       print *, 'patch weight= ', patch%wtgcell(p)
+       print *, 'patch active= ', patch%active(p)
+       print *, 'tlai = ', this%canopystate_inst%tlai_patch(p)
+       print *, 'tsai = ', this%canopystate_inst%tsai_patch(p)
+    end do
+  end subroutine print_values
+
+  !-----------------------------------------------------------------------
+
+end module unittestDustEmisInputs
\ No newline at end of file

From 65da9cf9c59b19f75e6621e3ca625c9443355dcf Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 16:06:40 -0600
Subject: [PATCH 0531/1248] Remove things not needed

---
 .../test/DustEmis_test/test_DustEmisZender2003.pf  | 14 +-------------
 src/unit_test_shr/unittestDustEmisInputs.F90       |  8 +++++---
 2 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index a26e2a5a33..9bdaa685b0 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -4,22 +4,10 @@ module test_DustEmisZender2003
 
   use funit
   use unittestDustEmisInputs, only : unittest_dust_emis_input_type
-  use unittestSubgridMod, only : bounds, unittest_subgrid_teardown
-  use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
-  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
-  use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
+  use unittestSubgridMod, only : bounds
   use DustEmisBase
   use DustEmisZender2003
   use shr_kind_mod , only : r8 => shr_kind_r8
-  use unittestFilterBuilderMod, only : filter_from_range
-  use atm2lndType, only : atm2lnd_type, atm2lnd_params_type
-  use SoilStateType, only : soilstate_type
-  use CanopyStateType, only : canopystate_type
-  use TemperatureType, only : temperature_type
-  use WaterType, only : water_type
-  use FrictionVelocityMod, only : frictionvel_type
-  use unittestWaterTypeFactory, only : unittest_water_type_factory_type
-  use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, MassFracClay
   use DustEmisFactory, only : create_dust_emissions
 
   implicit none
diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90
index 4cc82fa55e..6b15680ef7 100644
--- a/src/unit_test_shr/unittestDustEmisInputs.F90
+++ b/src/unit_test_shr/unittestDustEmisInputs.F90
@@ -4,7 +4,7 @@ module unittestDustEmisInputs
 
   use unittestSubgridMod, only : bounds, unittest_subgrid_teardown
   use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch
-  use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst
+  use clm_varpar, only : nlevsoi, nlevgrnd, clm_varpar_init
   use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit
   use shr_kind_mod , only : r8 => shr_kind_r8
   use unittestFilterBuilderMod, only : filter_from_range
@@ -26,8 +26,8 @@ module unittestDustEmisInputs
      type(atm2lnd_type) :: atm2lnd_inst
      type(soilstate_type) :: soilstate_inst
      type(canopystate_type) :: canopystate_inst
-     type(temperature_type) :: temperature_inst
-     type(unittest_water_type_factory_type) :: water_factory
+     type(temperature_type), private :: temperature_inst
+     type(unittest_water_type_factory_type), private :: water_factory
      type(water_type) :: water_inst
      type(frictionvel_type) :: frictionvel_inst
    contains
@@ -220,6 +220,8 @@ subroutine create_fv(this, fv, u10, ram1)
 
   end subroutine create_fv
 
+  !-----------------------------------------------------------------------
+
   subroutine print_values(this)
     use LandunitType, only : lun
     use PatchType, only : patch

From eed6886a16996d823a49e0ffa0ae7aef06e56542 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 16:15:32 -0600
Subject: [PATCH 0532/1248] Add note about the call to print_values subroutine
 used for debugging

---
 src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 9bdaa685b0..c8ffb87c32 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -99,6 +99,7 @@ contains
                       this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
                       this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
     call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
+    call this%print_values()   ! Call print subroutine just to make sure it can be used for debugging
     do p = bounds%begp, bounds%endp
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
@@ -133,7 +134,6 @@ contains
                       this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
                       this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
    call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst)
-   call this%print_values()
    do p = bounds%begp, bounds%endp
       call this%validate_patch(p)
       call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )

From 78c5d989e8664d968a156cdac9d2120b17256618 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 17 Jun 2024 16:21:08 -0600
Subject: [PATCH 0533/1248] Handle gdd20 < minimum if generate_crop_gdds.

---
 src/biogeochem/CNPhenologyMod.F90 | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index c3eff1538a..d4f486acb7 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2704,10 +2704,6 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
       else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then
          gddmaturity(p) = hybgdd(ivt(p))
       else
-         if (gdd20 <= 0._r8) then
-            write(iulog, *) 'ERROR: gdd20 ',gdd20,' for ivt ',ivt(p)
-            call endrun(msg="Stopping")
-         end if
          if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. &
                ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean .or. &
                ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. &
@@ -2731,7 +2727,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
       endif
 
       if (gddmaturity(p) < min_gddmaturity) then
-         if (use_cropcal_rx_cultivar_gdds) then
+         if (use_cropcal_rx_cultivar_gdds .or. generate_crop_gdds) then
              if (did_rx_gdds) then
                  write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')'
              end if

From f5407e4c578665fad46438514b480a4738565015 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 17:55:49 -0600
Subject: [PATCH 0534/1248] Add some comments and change comment about
 dust-emis object by things asked for in the code review

---
 src/biogeochem/CNVegStateType.F90  |  2 +-
 src/biogeochem/DustEmisFactory.F90 | 18 ++++++++++++++++--
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90
index 98c1a6ce3a..d63752c5b7 100644
--- a/src/biogeochem/CNVegStateType.F90
+++ b/src/biogeochem/CNVegStateType.F90
@@ -519,7 +519,7 @@ subroutine InitCold(this, bounds)
 
     ! --------------------------------------------------------------------
     ! Initialize terms needed for dust model
-    ! TODO - move these terms to DustEmisZender2003 module variables
+    ! TODO - move these terms to DustEmisBase object variables
     ! --------------------------------------------------------------------
 
     do c = bounds%begc, bounds%endc
diff --git a/src/biogeochem/DustEmisFactory.F90 b/src/biogeochem/DustEmisFactory.F90
index 29787c1855..aee4af0a55 100644
--- a/src/biogeochem/DustEmisFactory.F90
+++ b/src/biogeochem/DustEmisFactory.F90
@@ -1,5 +1,9 @@
 module DustEmisFactory
-
+    !---------------------------------------------------------------------------
+    !
+    ! Factory to figure out whihc dust emission method to instantiate
+    !
+    !---------------------------------------------------------------------------
     use abortutils   , only : endrun
     use shr_log_mod  , only : errMsg => shr_log_errMsg
     use clm_varctl   , only : iulog
@@ -15,16 +19,24 @@ module DustEmisFactory
 
 contains
 
+    !---------------------------------------------------------------------------
+
     function create_dust_emissions(bounds, NLFilename) result(dust_emis)
+        !---------------------------------------------------------------------------
+        ! Create a dust_emission base class objecct
+        ! The method implemented depends on namelist input
+        !---------------------------------------------------------------------------
         use DustEmisBase      , only : dust_emis_base_type
         use DustEmisZender2003, only : dust_emis_zender2003_type
         use clm_varctl        , only : dust_emis_method
         use decompMod         , only : bounds_type
         use shr_kind_mod      , only : CL => shr_kind_cl
         implicit none
+        ! Arguments
         class(dust_emis_base_type), allocatable :: dust_emis
         type(bounds_type), intent(in) :: bounds
         character(len=*),  intent(in) :: NLFilename
+        ! Local variables
         character(len=CL) :: method
 
         method = dust_emis_method
@@ -48,4 +60,6 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis)
 
     end function create_dust_emissions
 
-end module DustEmisFactory
\ No newline at end of file
+    !---------------------------------------------------------------------------
+
+end module DustEmisFactory

From 8e69f12020659b836bec06e7f50a1e2ffe9456fa Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 18:01:16 -0600
Subject: [PATCH 0535/1248] Use dust_emis_method directly as in the review

---
 src/biogeochem/DustEmisFactory.F90 | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/DustEmisFactory.F90 b/src/biogeochem/DustEmisFactory.F90
index aee4af0a55..371e77d6dc 100644
--- a/src/biogeochem/DustEmisFactory.F90
+++ b/src/biogeochem/DustEmisFactory.F90
@@ -37,11 +37,8 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis)
         type(bounds_type), intent(in) :: bounds
         character(len=*),  intent(in) :: NLFilename
         ! Local variables
-        character(len=CL) :: method
 
-        method = dust_emis_method
-
-        select case ( trim(method) )
+        select case ( trim(dust_emis_method) )
 
         case( "Zender_2003" )
            allocate(dust_emis, source=dust_emis_zender2003_type() )
@@ -50,7 +47,7 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis)
         !case( "Leung_2023" )
         !  allocate(dust_emis, source=dust_emis_zender2003_type() )
         case default
-           write(iulog,*) 'ERROR: unknown dust_emis_method: ', method, &
+           write(iulog,*) 'ERROR: unknown dust_emis_method: ', dust_emis_method, &
                            errMsg(sourcefile, __LINE__)
            call endrun( "Unrecognized dust_emis_method"  )
 

From e291534b6b058d6e6ea220432a22e2f8cb2fb97d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 18:08:07 -0600
Subject: [PATCH 0536/1248] Remove the ifs around different dust-emis methods
 for the Zender case as pointed out in the review

---
 src/biogeochem/DustEmisZender2003.F90 | 26 +++++---------------------
 1 file changed, 5 insertions(+), 21 deletions(-)

diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90
index e3c4d4115e..cee704ad47 100644
--- a/src/biogeochem/DustEmisZender2003.F90
+++ b/src/biogeochem/DustEmisZender2003.F90
@@ -31,7 +31,6 @@ module DustEmisZender2003
   use PatchType            , only : patch
   use ZenderSoilErodStreamType,  only : soil_erod_stream_type
   use DustEmisBase         , only : dust_emis_base_type
-  use clm_varctl           , only : dust_emis_method
   !
   ! !PUBLIC TYPES
   implicit none
@@ -160,6 +159,7 @@ end subroutine InitHistory
 
   subroutine InitCold(this, bounds)
     !
+    ! Initialize values from a cold start
     ! !ARGUMENTS:
     class (dust_emis_zender2003_type) :: this
     type(bounds_type), intent(in) :: bounds
@@ -168,27 +168,11 @@ subroutine InitCold(this, bounds)
     integer :: c,l
     !-----------------------------------------------------------------------
 
-    ! Set basin factor to 1 for now
-
-    if (dust_emis_method == 'Leung_2023') then
-       !do c = bounds%begc, bounds%endc
-       !   l = col%landunit(c)
-
-       !   if (.not.lun%lakpoi(l)) then
-       !      this%mbl_bsn_fct_col(c) = 1.0_r8
-       !   end if
-       !end do
-       call endrun( msg="Leung_2023 dust_emis_method is currently not available"//errMsg(sourcefile, __LINE__))
-    else if (dust_emis_method == 'Zender_2003') then
-       if ( this%soil_erod_stream%UseStreams() )then
-          call this%soil_erod_stream%CalcDustSource( bounds, &
-                                   this%mbl_bsn_fct_col(bounds%begc:bounds%endc) )
-       else
-          this%mbl_bsn_fct_col(:) = 1.0_r8
-       end if
+    if ( this%soil_erod_stream%UseStreams() )then
+       call this%soil_erod_stream%CalcDustSource( bounds, &
+                               this%mbl_bsn_fct_col(bounds%begc:bounds%endc) )
     else
-       write(iulog,*) 'dust_emis_method not recognized = ', trim(dust_emis_method)
-       call endrun( msg="dust_emis_method namelist item is not valid "//errMsg(sourcefile, __LINE__))
+       this%mbl_bsn_fct_col(:) = 1.0_r8
     end if
 
   end subroutine InitCold

From 2060a9d77496feeadb106fdb311485f1b9b99c81 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 17 Jun 2024 18:22:57 -0600
Subject: [PATCH 0537/1248] Set the veg patch type explicitly to 1 and add some
 comments regarding it, based on the code review

---
 .../test/DustEmis_test/test_DustEmisZender2003.pf          | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index c8ffb87c32..8641b8cceb 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -218,11 +218,18 @@ contains
 
  @Test
  subroutine dust_zero_when_tlai_high(this)
+   use PatchType, only : patch
    ! Check dust emissions are zero when LAI is high enough
    class(TestDustEmisZender2003), intent(inout) :: this
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
 
+   ! Explicitly set the patch type to a hard-coded 1 (so NOT bare-soil)
+   ! pft indices can't be used without reading them from the parameter file
+   !
+   ! To do this fully the subgrid setup in unittestDustEmisInputs to baresoil
+   ! should really be run again. But, just doing this is likely sufficient for testing
+   patch%itype(bounds%begp:bounds%endp) = 1
    call this%input%create_atm2lnd()
    call this%input%create_fv( )
    this%input%canopystate_inst%tlai_patch(:) = 0.3_r8

From f618893aa8598727e37e6ae8064f317fa3f13182 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 08:46:47 -0600
Subject: [PATCH 0538/1248] Set cropcal_rx true for both parts of
 RXCROPMATURITY*.

---
 cime_config/SystemTests/rxcropmaturity.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 0b9c5e8ee0..46ed8f8be3 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -130,7 +130,6 @@ def _run_phase(self, skip_gen=False):
         logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
         self._append_to_user_nl_clm(
             [
-                "cropcals_rx = .true.",
                 "stream_fldFileName_cultivar_gdds = ''",
                 "generate_crop_gdds = .true.",
                 "use_mxmat = .false.",
@@ -397,6 +396,7 @@ def _run_check_rxboth_run(self, skip_gen):
 
     def _modify_user_nl_allruns(self):
         nl_additions = [
+            "cropcals_rx = .true.",
             "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
             "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
             "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),

From 7578787061226c463828f80fbc6612cdd2388ddc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 10:04:17 -0600
Subject: [PATCH 0539/1248] Add GddGen(OnlyOutputs(Surf)) testmods.

---
 .../testmods_dirs/clm/GddGen/include_user_mods     |  1 +
 .../testdefs/testmods_dirs/clm/GddGen/user_nl_clm  | 11 +++++++++++
 .../clm/GddGenOnlyOutputs/include_user_mods        |  1 +
 .../clm/GddGenOnlyOutputs/user_nl_clm              | 14 ++++++++++++++
 .../clm/GddGenOnlyOutputsSurf/include_user_mods    |  1 +
 .../clm/GddGenOnlyOutputsSurf/user_nl_clm          |  5 +++++
 6 files changed, 33 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
new file mode 100644
index 0000000000..6cc92bc8b3
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
@@ -0,0 +1 @@
+../GddGenOnlyOutputsSurf
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
new file mode 100644
index 0000000000..f36ffd26b9
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
@@ -0,0 +1,11 @@
+cropcals_rx = .true.
+stream_meshfile_cropcal = '/glade/campaign/cesm/cesmdata/inputdata/share/meshes/10x15_nomask_c110308_ESMFmesh.nc'
+stream_fldFileName_swindow_start = '/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc'
+stream_fldFileName_swindow_end   = '/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc'
+stream_year_first_cropcal_swindows = 2000
+stream_year_last_cropcal_swindows = 2000
+model_year_align_cropcal_swindows = 2000
+
+stream_fldFileName_cultivar_gdds = ''
+generate_crop_gdds = .true.
+use_mxmat = .false.
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods
new file mode 100644
index 0000000000..02ec13743f
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods
@@ -0,0 +1 @@
+../cropMonthOutput
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm
new file mode 100644
index 0000000000..8fe842624d
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm
@@ -0,0 +1,14 @@
+! (h1) Annual outputs on sowing or harvest axis
+hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'
+hist_nhtfrq(2) = 17520
+hist_mfilt(2) = 999
+hist_type1d_pertape(2) = 'PFTS'
+hist_dov2xy(2) = .false.
+
+! (h2) Daily outputs for GDD generation and figure-making
+hist_fincl3 = 'GDDACCUM', 'GDDHARV'
+hist_nhtfrq(3) = -24
+hist_mfilt(3) = 365
+hist_type1d_pertape(3) = 'PFTS'
+hist_dov2xy(3) = .false.
+
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods
new file mode 100644
index 0000000000..8c6e50384c
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods
@@ -0,0 +1 @@
+../GddGenOnlyOutputs
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm
new file mode 100644
index 0000000000..184043f013
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm
@@ -0,0 +1,5 @@
+fsurdat = '/glade/derecho/scratch/samrabin/tests_0618-093950de/RXCROPMATURITY_Lm61.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput.0618-093950de.gddgen/surfdata_10x15_hist_1850_78pfts_c240216.all_crops_everywhere.nc'
+do_transient_crops = .false.
+flanduse_timeseries = ''
+use_init_interp = .true.
+

From 787c2f2600212685ee4df732fe2bf33797084fb6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 18 Jun 2024 15:37:04 -0600
Subject: [PATCH 0540/1248] Improve a comment.

---
 cime_config/SystemTests/rxcropmaturity.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index a583432efe..7a179cdf56 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -455,7 +455,7 @@ def _run_generate_gdds(self, case_gddgen):
         self._gdds_file = generated_gdd_files[0]
 
     def _run_interpolate_gdds(self):
-        # Save where?
+        # File where interpolated GDDs should be saved
         self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc")
 
         # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds.

From 752ba73b9df6cf4997685789f2dc2fa1962768e8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 18 Jun 2024 15:38:39 -0600
Subject: [PATCH 0541/1248] Describe rxcropmaturity suite in testlist_clm.xml.

---
 cime_config/testdefs/testlist_clm.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 432f8e3e9a..5443acf2d7 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -10,6 +10,7 @@
         prebeta: Run before CESM beta tags (more extensive, but should have tests outside of prealpha) (subset of aux_clm tests)
         aux_cime_baselines: CESM cime baselines (subset of aux_clm tests)
         hillslope: Experimental test list used for the hillslope option of the model
+        rxcropmaturity: Short tests to be run during development related to prescribed crop calendars
 -->
 <testlist version="2.0">
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/default">

From 6fdcf4cd198cd53733437136a8e90d59e4935369 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 15:50:59 -0600
Subject: [PATCH 0542/1248] UpdateAccVars_CropGDDs: Remove check that patch is
 a crop.

---
 src/biogeophys/TemperatureType.F90 | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index afe0948e6d..79bdce64ef 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1400,7 +1400,6 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use accumulMod       , only : update_accum_field, extract_accum_field, markreset_accum_field
     use clm_time_manager , only : is_doy_in_interval, get_curr_calday
-    use pftconMod        , only : npcropmin
     use CropType, only : crop_type
     !
     ! !ARGUMENTS
@@ -1418,7 +1417,6 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     character(8) :: field_name   ! E.g., GDD0
     character(32) :: format_string
     integer :: p
-    integer :: ivt  ! vegetation type
     logical :: in_accumulation_season
     real(r8) :: lat  ! latitude
     integer :: gdd20_season_start, gdd20_season_end
@@ -1456,9 +1454,8 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
 
     do p = begp,endp
 
-       ! Avoid unnecessary calculations over inactive points and non-crops
-       ivt = patch%itype(p)
-       if (ivt < npcropmin .or. .not. patch%active(p)) then
+       ! Avoid unnecessary calculations over inactive points
+       if (.not. patch%active(p)) then
           cycle
        end if
 

From c6ae96bd6dd557b6baf734431799b78351fd1910 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 16:05:11 -0600
Subject: [PATCH 0543/1248] Add StreamGdd20Seasons testmod.

---
 .../testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm   | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
new file mode 100644
index 0000000000..dd6cd3451d
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
@@ -0,0 +1,2 @@
+stream_gdd20_seasons = .true.
+

From 9c5b2792c38a572e8b297701ebfcf1234e13043d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 16:22:24 -0600
Subject: [PATCH 0544/1248] StreamGdd20Seasons: Set
 allow_invalid_gdd20_season_inputs .true.

---
 .../testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
index dd6cd3451d..86cdffe96a 100644
--- a/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
@@ -1,2 +1,3 @@
 stream_gdd20_seasons = .true.
+allow_invalid_gdd20_season_inputs = .true.
 

From 70b8fe32f6f437d3458013b99b2ae5bb136a6255 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 16:38:16 -0600
Subject: [PATCH 0545/1248] Don't check gdd20_season_starts/ends if not crop.

---
 src/biogeophys/TemperatureType.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 79bdce64ef..4212bcdd0f 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1400,6 +1400,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
     use accumulMod       , only : update_accum_field, extract_accum_field, markreset_accum_field
     use clm_time_manager , only : is_doy_in_interval, get_curr_calday
+    use pftconMod        , only : npcropmin
     use CropType, only : crop_type
     !
     ! !ARGUMENTS
@@ -1467,7 +1468,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
           ((month > 9 .or.  month < 4)  .and. lat <  0._r8)
        ! Replace with read-in gdd20 accumulation season, if needed and valid
        ! (If these aren't being read in or they're invalid, they'll be -1)
-       if (stream_gdd20_seasons) then
+       if (stream_gdd20_seasons .and. patch%itype(p) >= npcropmin) then
           gdd20_season_start = int(gdd20_season_starts(p))
           gdd20_season_end = int(gdd20_season_ends(p))
           if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then

From 41e30bd412045e74d33bb53137a4aa08bb401739 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 16:58:33 -0600
Subject: [PATCH 0546/1248] Correct comment in crop testmod user_nl_clm.

---
 cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
index 67042ea01a..c9598772a2 100644
--- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
@@ -9,7 +9,7 @@
 hist_fincl2  += 'DYN_COL_SOIL_ADJUSTMENTS_C'
 
 
-! Annual crop variables on per-sowing/per-harvest axes, per PFT.
+! Annual crop variables (including per-sowing/per-harvest axes), per PFT.
 hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS'
 hist_nhtfrq(3) = 17520
 hist_mfilt(3) = 1

From 30597ce4b917d88d3f31d850eee7615bfd06d830 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 17:10:47 -0600
Subject: [PATCH 0547/1248] Add four tests to crop_calendars suite:

* SMS_Ld65.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-GddGen.0618-170953de_int
* SMS_Ld65.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-GddGen--clm-StreamGdd20Seasons
* SMS_Ld65.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-GddGen
* SMS_Ld65.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-GddGen--clm-StreamGdd20Seasons
---
 cime_config/testdefs/testlist_clm.xml         | 36 +++++++++++++++++++
 .../clm/StreamGdd20Seasons/user_nl_clm        |  2 ++
 2 files changed, 38 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 254d60c74b..a51e1f92ac 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3767,5 +3767,41 @@
     </options>
   </test>
 
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/GddGen">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">20:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/GddGen--clm/StreamGdd20Seasons">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">20:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">20:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/StreamGdd20Seasons">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">20:00</option>
+    </options>
+  </test>
+
 
 </testlist>
diff --git a/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
index 86cdffe96a..7f140eb719 100644
--- a/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
@@ -1,3 +1,5 @@
 stream_gdd20_seasons = .true.
 allow_invalid_gdd20_season_inputs = .true.
 
+! Annual crop variables (including per-sowing/per-harvest axes), per PFT.
+hist_fincl3 += 'GDD20_BASELINE', 'GDD20_SEASON_START', 'GDD20_SEASON_END'
\ No newline at end of file

From 2573c34721f9dd74f4b82fbbb062edd9b1b48c70 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 18 Jun 2024 18:46:57 -0600
Subject: [PATCH 0548/1248] Fix walltime for GddGen tests.

---
 cime_config/testdefs/testlist_clm.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index a51e1f92ac..c5aa12387c 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3772,7 +3772,7 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
-      <option name="wallclock">20:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
 
@@ -3781,7 +3781,7 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
-      <option name="wallclock">20:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
 
@@ -3790,7 +3790,7 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
-      <option name="wallclock">20:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
 
@@ -3799,7 +3799,7 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
-      <option name="wallclock">20:00</option>
+      <option name="wallclock">00:20:00</option>
     </options>
   </test>
 

From 400c4590ba07db052c6903bf48ee5cc54856497e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 19 Jun 2024 11:03:23 -0600
Subject: [PATCH 0549/1248] Remove some commented-out code from
 check_rx_obeyed.

---
 python/ctsm/crop_calendars/check_rx_obeyed.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py
index 383ebbf1e0..4d8ccd1788 100644
--- a/python/ctsm/crop_calendars/check_rx_obeyed.py
+++ b/python/ctsm/crop_calendars/check_rx_obeyed.py
@@ -114,8 +114,6 @@ def summarize_results(which_ds, output_var, verbose, all_ok, gdd_tolerance, diff
         print(f"✅ {which_ds}: Prescribed {output_var} always obeyed")
     elif all_ok == 1:
         bad = False
-        # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:")
-        # for x in diff_str_list: print(x)
         print(
             f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable (diffs <= "
             + f"{gdd_tolerance})"

From d01520b9000b32de107dcbef35b483ec966c9dc8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 19 Jun 2024 11:11:09 -0600
Subject: [PATCH 0550/1248] Add reference to issue ESCOMP/CTSM#2603.

https://github.com/ESCOMP/CTSM/issues/2603
---
 cime_config/SystemTests/rxcropmaturity.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 7a179cdf56..31deb1442b 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -424,6 +424,7 @@ def _run_generate_gdds(self, case_gddgen):
         hdates_file = self._hdatefile
 
         # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds.
+        # See https://github.com/ESCOMP/CTSM/issues/2603
         tool_path = os.path.join(
             self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py"
         )
@@ -459,6 +460,7 @@ def _run_interpolate_gdds(self):
         self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc")
 
         # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds.
+        # See https://github.com/ESCOMP/CTSM/issues/2603
         tool_path = os.path.join(
             self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py"
         )

From 98e3689e04a2ad2ef2de4c893cab2cf91007aebb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 19 Jun 2024 11:29:05 -0600
Subject: [PATCH 0551/1248] rxcropmaturity: Wrap two long comments.

---
 cime_config/SystemTests/rxcropmaturity.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 31deb1442b..d25bd015ca 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -36,7 +36,9 @@ def __init__(self, case):
         full_test = "RXCROPMATURITY_" in casebaseid
         skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid
 
-        # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency.
+        # Ensure run length is at least 5 years. Minimum to produce one complete growing season
+        # (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season
+        # usable for GDD generation, so you can't check for season-to-season consistency.
         stop_n = self._case.get_value("STOP_N")
         stop_option = self._case.get_value("STOP_OPTION")
         stop_n_orig = stop_n
@@ -68,7 +70,10 @@ def __init__(self, case):
                 + f"{stop_n_orig} {stop_option_orig[1:]}"
             )
         elif skipgen_test and stop_n < 3:
-            # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish.
+            # First year is discarded because crops are already in the ground at restart, and those
+            # aren't affected by the new crop calendar inputs. The second year is useable, but we
+            # need a third year so that all crops planted in the second year have a chance to
+            # finish.
             error_message = (
                 "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested "
                 + f"{stop_n_orig} {stop_option_orig[1:]}"

From 418f6bed1d757d8aada4a0ce932dc501c37d47df Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 19 Jun 2024 11:53:55 -0600
Subject: [PATCH 0552/1248] GDD20_BASELINE and GDD20_SEASON_START/END now
 instantaneous.

---
 src/biogeochem/CropType.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index b1e0e4571d..77da895135 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -366,15 +366,15 @@ subroutine InitHistory(this, bounds)
 
     this%gdd20_baseline_patch(begp:endp) = spval
     call hist_addfld1d (fname='GDD20_BASELINE', units='ddays', &
-         avgflag='A', long_name='Baseline mean growing-degree days accumulated during accumulation period (from input)', &
+         avgflag='I', long_name='Baseline mean growing-degree days accumulated during accumulation period (from input)', &
          ptr_patch=this%gdd20_baseline_patch, default='inactive')
     this%gdd20_season_start_patch(begp:endp) = spval
     call hist_addfld1d (fname='GDD20_SEASON_START', units='day of year', &
-         avgflag='A', long_name='Start of the GDD20 accumulation season (from input)', &
+         avgflag='I', long_name='Start of the GDD20 accumulation season (from input)', &
          ptr_patch=this%gdd20_season_start_patch, default='inactive')
     this%gdd20_season_end_patch(begp:endp) = spval
     call hist_addfld1d (fname='GDD20_SEASON_END', units='day of year', &
-         avgflag='A', long_name='End of the GDD20 accumulation season (from input)', &
+         avgflag='I', long_name='End of the GDD20 accumulation season (from input)', &
          ptr_patch=this%gdd20_season_end_patch, default='inactive')
 
   end subroutine InitHistory

From e3a00f84b3b3b276659673ac766b0d24bfc0d881 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 19 Jun 2024 11:55:57 -0600
Subject: [PATCH 0553/1248] Save GDD20_BASELINE and GDD20_SEASON_START/END in
 crop testmod.

---
 cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
index c9598772a2..a368e97593 100644
--- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
@@ -9,8 +9,8 @@
 hist_fincl2  += 'DYN_COL_SOIL_ADJUSTMENTS_C'
 
 
-! Annual crop variables (including per-sowing/per-harvest axes), per PFT.
-hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS'
+! Annual instantaneous crop variables (including per-sowing/per-harvest axes), per PFT.
+hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS', 'GDD20_BASELINE', 'GDD20_SEASON_START', 'GDD20_SEASON_END'
 hist_nhtfrq(3) = 17520
 hist_mfilt(3) = 1
 hist_type1d_pertape(3) = 'PFTS'

From 3b915fdd953bfcf24fd7a0e3c29722041ca119c1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 19 Jun 2024 12:10:14 -0600
Subject: [PATCH 0554/1248] Simplify crop calendar tests.

---
 cime_config/testdefs/testlist_clm.xml         | 22 ++-----------------
 .../testdefs/testmods_dirs/clm/GddGen/README  |  5 +++++
 .../clm/GddGen/include_user_mods              |  2 +-
 .../testmods_dirs/clm/GddGen/user_nl_clm      | 14 ++++++------
 .../clm/GddGenOnlyOutputs/include_user_mods   |  1 -
 .../clm/GddGenOnlyOutputs/user_nl_clm         | 14 ------------
 .../GddGenOnlyOutputsSurf/include_user_mods   |  1 -
 .../clm/GddGenOnlyOutputsSurf/user_nl_clm     |  5 -----
 .../clm/StreamGdd20Seasons/user_nl_clm        |  3 ---
 .../clm/cropAnnOutputMonthly/user_nl_clm      |  3 +++
 10 files changed, 18 insertions(+), 52 deletions(-)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGen/README
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index c5aa12387c..1a09ce4e80 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3767,7 +3767,7 @@
     </options>
   </test>
 
-  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/GddGen">
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/cropAnnOutputMonthly">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
@@ -3776,25 +3776,7 @@
     </options>
   </test>
 
-  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/GddGen--clm/StreamGdd20Seasons">
-    <machines>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
-
-  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen">
-    <machines>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
-
-  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/StreamGdd20Seasons">
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/cropAnnOutputMonthly--clm/StreamGdd20Seasons">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGen/README b/cime_config/testdefs/testmods_dirs/clm/GddGen/README
new file mode 100644
index 0000000000..3236ca609a
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGen/README
@@ -0,0 +1,5 @@
+The GddGen test is set up just like a GDD-Generating run, with two differences:
+1) It doesn't include an all-crops-everywhere surface dataset,
+2) it doesn't actually run the GDD-generating script,
+and
+3) it includes some extra outputs.
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
index 6cc92bc8b3..02ec13743f 100644
--- a/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
@@ -1 +1 @@
-../GddGenOnlyOutputsSurf
+../cropMonthOutput
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
index f36ffd26b9..87cdd5d5b5 100644
--- a/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
@@ -1,11 +1,11 @@
 cropcals_rx = .true.
-stream_meshfile_cropcal = '/glade/campaign/cesm/cesmdata/inputdata/share/meshes/10x15_nomask_c110308_ESMFmesh.nc'
-stream_fldFileName_swindow_start = '/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc'
-stream_fldFileName_swindow_end   = '/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc'
-stream_year_first_cropcal_swindows = 2000
-stream_year_last_cropcal_swindows = 2000
-model_year_align_cropcal_swindows = 2000
-
 stream_fldFileName_cultivar_gdds = ''
 generate_crop_gdds = .true.
 use_mxmat = .false.
+
+! (h3) Daily outputs for GDD generation and figure-making
+hist_fincl4 = 'GDDACCUM', 'GDDHARV'
+hist_nhtfrq(4) = -24
+hist_mfilt(4) = 365
+hist_type1d_pertape(4) = 'PFTS'
+hist_dov2xy(4) = .false.
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods
deleted file mode 100644
index 02ec13743f..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../cropMonthOutput
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm
deleted file mode 100644
index 8fe842624d..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputs/user_nl_clm
+++ /dev/null
@@ -1,14 +0,0 @@
-! (h1) Annual outputs on sowing or harvest axis
-hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'
-hist_nhtfrq(2) = 17520
-hist_mfilt(2) = 999
-hist_type1d_pertape(2) = 'PFTS'
-hist_dov2xy(2) = .false.
-
-! (h2) Daily outputs for GDD generation and figure-making
-hist_fincl3 = 'GDDACCUM', 'GDDHARV'
-hist_nhtfrq(3) = -24
-hist_mfilt(3) = 365
-hist_type1d_pertape(3) = 'PFTS'
-hist_dov2xy(3) = .false.
-
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods
deleted file mode 100644
index 8c6e50384c..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../GddGenOnlyOutputs
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm
deleted file mode 100644
index 184043f013..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/GddGenOnlyOutputsSurf/user_nl_clm
+++ /dev/null
@@ -1,5 +0,0 @@
-fsurdat = '/glade/derecho/scratch/samrabin/tests_0618-093950de/RXCROPMATURITY_Lm61.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput.0618-093950de.gddgen/surfdata_10x15_hist_1850_78pfts_c240216.all_crops_everywhere.nc'
-do_transient_crops = .false.
-flanduse_timeseries = ''
-use_init_interp = .true.
-
diff --git a/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
index 7f140eb719..8b040d9d43 100644
--- a/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/StreamGdd20Seasons/user_nl_clm
@@ -1,5 +1,2 @@
 stream_gdd20_seasons = .true.
 allow_invalid_gdd20_season_inputs = .true.
-
-! Annual crop variables (including per-sowing/per-harvest axes), per PFT.
-hist_fincl3 += 'GDD20_BASELINE', 'GDD20_SEASON_START', 'GDD20_SEASON_END'
\ No newline at end of file
diff --git a/cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm
new file mode 100644
index 0000000000..1c47a2ebd1
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm
@@ -0,0 +1,3 @@
+! These variables SHOULD only be saved annually in real runs, but for testing purposes it's fine to have them monthly.
+! Modifies h2 history file defined in crop testmod.
+hist_nhtfrq(3) = 0

From 501ba25c34e9f727442d77c0d3d43d7f2f7c9133 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 19 Jun 2024 13:19:18 -0600
Subject: [PATCH 0555/1248] Add tricky ERP test of RxCropCalsAdaptGGCMI.

---
 cime_config/testdefs/testlist_clm.xml                  | 10 ++++++++++
 .../testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm |  1 +
 .../testmods_dirs/clm/midDecStart/include_user_mods    |  1 +
 .../testmods_dirs/clm/midDecStart/shell_commands       |  2 ++
 4 files changed, 14 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods
 create mode 100755 cime_config/testdefs/testmods_dirs/clm/midDecStart/shell_commands

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 1a09ce4e80..40f351ab4a 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3767,6 +3767,16 @@
     </options>
   </test>
 
+  <test name="ERP_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:00:00</option>
+    </options>
+  </test>
+
   <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/cropAnnOutputMonthly">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
index 42e57a675c..dd4ac3117c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
@@ -1,4 +1,5 @@
 
 stream_gdd20_seasons = .true.
+flush_gdd20 = .true.
 !TODO SSR: Try without this once you have half-degree inputs
 allow_invalid_gdd20_season_inputs = .true.
diff --git a/cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/midDecStart/shell_commands b/cime_config/testdefs/testmods_dirs/clm/midDecStart/shell_commands
new file mode 100755
index 0000000000..d044ab8c3b
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/midDecStart/shell_commands
@@ -0,0 +1,2 @@
+./xmlchange RUN_STARTDATE=2001-12-15
+./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append

From 8d754533f0bf796fd5ee365d4fd1eedaee53ab20 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 20 Jun 2024 13:03:36 -0600
Subject: [PATCH 0556/1248] TemperatureType: Save flush_gdd20 regardless of
 stream_gdd20_seasons.

---
 src/biogeophys/TemperatureType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 4212bcdd0f..bb579b8031 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1136,7 +1136,7 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
        end if
     end if
 
-    if (use_crop .and. stream_gdd20_seasons) then
+    if (use_crop) then
        if (flag == 'write') then
           if (this%flush_gdd20) then
              idata = 1

From 6810090b7258c2d4648204e3fe12d2c999cb55f7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 20 Jun 2024 13:27:05 -0600
Subject: [PATCH 0557/1248] cropcal_interp: Ignore init when considering
 stream_gdd20_seasons.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index ef406a7e60..4034f550d4 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -741,7 +741,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
   dataptr2d_gdd20_season_start(:,:) = -1._r8
   allocate(dataptr2d_gdd20_season_end  (lsize, ncft))
   dataptr2d_gdd20_season_end(:,:) = -1._r8
-  if (stream_gdd20_seasons .and. init) then
+  if (stream_gdd20_seasons) then
      ! Starting with npcropmin will skip generic crops
      do n = 1, ncft
         call dshr_fldbun_getFldPtr(sdat_cropcal_gdd20_season_start%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), &
@@ -815,7 +815,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
          end if
      end if
 
-  end if ! stream_gdd20_seasons and init
+  end if ! stream_gdd20_seasons
   deallocate(dataptr2d_gdd20_season_start)
   deallocate(dataptr2d_gdd20_season_end)
 

From 7f2a5c0192aa8f8b842e06259d46f8c095f2ee2b Mon Sep 17 00:00:00 2001
From: wwieder <wwieder@ucar.edu>
Date: Thu, 20 Jun 2024 14:25:27 -0600
Subject: [PATCH 0558/1248] addresses #2563

---
 py_env_create | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py_env_create b/py_env_create
index 9a9b8d940c..ac705edb3c 100755
--- a/py_env_create
+++ b/py_env_create
@@ -122,7 +122,7 @@ if [ "$verbose" == "Yes" ]; then
   verbosity="--verbose"
   loglevel="INFO"
 fi
-cmd="conda install --yes $verbosity --channel conda-forge --name $ctsm_python $condadir/$condafile $option"
+cmd="conda install --yes $verbosity --channel conda-forge --name $ctsm_python --file $condadir/$condafile $option"
 echo "$cmd"
 $cmd
 if [ $? != 0 ]; then

From 23b62613040d3c926a134e7068406289a2edfeae Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 20 Jun 2024 15:36:43 -0600
Subject: [PATCH 0559/1248] Draft ChangeLog/ChangeSum

---
 doc/ChangeLog | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 81 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8b6bb8f0d2..e83b64c564 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,84 @@
 ===============================================================
+Tag name: tmp-240620.n01.ctsm5.2.007
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 20 Jun 2024 03:00:43 PM MDT
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+ Fix long names #2512
+ Dust emissions moved to Object Oriented design #2552
+ Fix RXCROPMATURITY test #2599
+
+ NB: This is the first temporary tag (n01, see full tag name above) in
+ a series of temporary tags while we wait for the completion of the
+ beta01 cesm tag.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2512
+ Fixes #2552
+ Fixes #2599
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ Fix RXCROPMATURITY test #2599
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- IN PROG
+    izumi ------- IN PROG
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ----
+
+Answer changes
+--------------
+Changes answers relative to baseline: No
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2604
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.007
 Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD)
 Date: Fri 31 May 2024 13:49:29 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index b3f1632571..ace44b8037 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+tmp-240620.n01.cts   slevis 06/20/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007)
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems

From d3e68143a2ca5e52568965a666cd6c53be7d0434 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 20 Jun 2024 17:30:14 -0600
Subject: [PATCH 0560/1248] Temporary .gitmodules points to the branches of the
 modules that changed

---
 .gitmodules       | 20 ++++++++++----------
 ccs_config        |  2 +-
 components/cism   |  2 +-
 components/cmeps  |  2 +-
 components/mosart |  2 +-
 components/rtm    |  2 +-
 6 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 699ad22969..e1df4e650c 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,22 +7,22 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release
 
 [submodule "cism"]
 path = components/cism
-url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_001
+url = https://github.com/mvertens/CISM-wrapper
+fxtag = 34339777afa7b810fd4822fce1039826668b33e4
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 
 [submodule "rtm"]
 path = components/rtm
-url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_79
+url = https://github.com/swensosc/RTM
+fxtag = 420c5979d8abf05184992fdfba5ac41c41c91c2e
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
-url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1_0_49
+url = https://github.com/mvertens/MOSART
+fxtag = 01f40dcf589d4e6c5932c76128e3d42faea91e9f
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
@@ -35,8 +35,8 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
         
 [submodule "ccs_config"]
 path = ccs_config
-url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm0.0.106
+url = https://github.com/mvertens/ccs_config_cesm.git
+fxtag = dbb02c0ccd1492fe278885f8a07a71fa80064319
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
@@ -49,8 +49,8 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
-url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps0.14.63
+url = https://github.com/mvertens/CMEPS.git
+fxtag = 4dca7c602e54189b74b1d0195c433d1b83475553
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
diff --git a/ccs_config b/ccs_config
index 2ff978f92a..dbb02c0ccd 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit 2ff978f92a5ac9a6ab243e5c14d06a7e2d2f5799
+Subproject commit dbb02c0ccd1492fe278885f8a07a71fa80064319
diff --git a/components/cism b/components/cism
index c05dd5c4fc..34339777af 160000
--- a/components/cism
+++ b/components/cism
@@ -1 +1 @@
-Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928
+Subproject commit 34339777afa7b810fd4822fce1039826668b33e4
diff --git a/components/cmeps b/components/cmeps
index 6384ff4e4a..4dca7c602e 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 6384ff4e4a6bc82a678f9419a43ffbd5d53ac209
+Subproject commit 4dca7c602e54189b74b1d0195c433d1b83475553
diff --git a/components/mosart b/components/mosart
index 8c682b1b7f..01f40dcf58 160000
--- a/components/mosart
+++ b/components/mosart
@@ -1 +1 @@
-Subproject commit 8c682b1b7f15d146816de302e0d359da3e957056
+Subproject commit 01f40dcf589d4e6c5932c76128e3d42faea91e9f
diff --git a/components/rtm b/components/rtm
index 88503adbc2..420c5979d8 160000
--- a/components/rtm
+++ b/components/rtm
@@ -1 +1 @@
-Subproject commit 88503adbc275fb2ccbb6b598e460deaeb140e515
+Subproject commit 420c5979d8abf05184992fdfba5ac41c41c91c2e

From 24845d2ad8e5f235053bebdcfb845fa0513d42c7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 21 Jun 2024 08:59:56 -0600
Subject: [PATCH 0561/1248] cropcal_interp: Ignore init when considering
 adapt_cropcal_rx_cultivar_gdds.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 4034f550d4..ef3bab03c5 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -685,7 +685,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
    deallocate(dataptr2d_cultivar_gdds)
 
    allocate(dataptr2d_gdd20_baseline(lsize, ncft))
-   if (adapt_cropcal_rx_cultivar_gdds .and. init) then
+   if (adapt_cropcal_rx_cultivar_gdds) then
       ! Read GDD20 baselines from input files
       ! Starting with npcropmin will skip generic crops
       do n = 1, ncft

From a8f1daa14affaca9ddb21b51fe4cd49f6f1e8771 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 21 Jun 2024 09:20:45 -0600
Subject: [PATCH 0562/1248] Add header with notes on variables (copied from the
 CESM header)

---
 .gitmodules | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/.gitmodules b/.gitmodules
index 699ad22969..8a173f0ddd 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,30 @@
+# This is a git submodule file with additional support for
+# git-fleximod (https://github.com/ESMCI/git-fleximod)
+#
+# The additional flags supported by git-fleximod are
+# fxtag - the tag associated with the submodule, this tag can be tested for
+#         consistancy with the submodule hash using git-fleximod status
+#         the hash can be updated to the tag using git-fleximod update
+#
+# fxrequired - indicates if a given submodule should be checked out on install
+#              submoudules can be toplevel or internal and required or optional
+#              toplevel means that the submodule should only be checked out if the
+#              module is the toplevel of the git repo (is not a submodule itself)
+#              internal means that the submodule is needed by the component whether
+#              the component is toplevel or the submodule of another repo
+#              required means that the submodule should always be checked out
+#              optional means that the submodule should only be checked out if the
+#              optional flag is provided to git-fleximod or the submodule name is
+#              explicitly listed on the git-fleximod command line.
+#
+# fxsparse -   this is a path to a git sparse checkout file indicating that the
+#              submodule should be checked out in sparse mode
+#
+# fxDONOTUSEurl    -   this field is used by git-fleximod test to insure that the url is pointing
+#              to the official url of the repo and not to an unofficial fork.
+#              It is intended for use of github workflows to test commits to protected
+#              repository branches.
+#
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates

From 5b49d91ace8161c2a2c14b85b73dac994b1b6413 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 21 Jun 2024 09:41:46 -0600
Subject: [PATCH 0563/1248] Forgot to commit RxCropCalsAdaptFlush testmod.

---
 .../testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods    | 1 +
 .../testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm | 2 ++
 2 files changed, 3 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods
new file mode 100644
index 0000000000..af5fe8591e
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods
@@ -0,0 +1 @@
+../RxCropCalsAdapt
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm
new file mode 100644
index 0000000000..4c6af0f6d2
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm
@@ -0,0 +1,2 @@
+
+flush_gdd20 = .true.

From f7b9b29d686d88abef3e3b29a561598ae9a80da7 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 21 Jun 2024 09:46:49 -0600
Subject: [PATCH 0564/1248] Update ChangeLog/ChangeSum

---
 doc/ChangeLog | 6 +++---
 doc/ChangeSum | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e83b64c564..e6e9215397 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: tmp-240620.n01.ctsm5.2.007
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
-Date: Thu 20 Jun 2024 03:00:43 PM MDT
+Date: Fri 21 Jun 2024 09:42:26 AM MDT
 One-line Summary: Merge b4b-dev
 
 Purpose and description of changes
@@ -60,8 +60,8 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho ----- IN PROG
-    izumi ------- IN PROG
+    derecho ----- OK
+    izumi ------- OK
 
   any other testing (give details below):
 
diff --git a/doc/ChangeSum b/doc/ChangeSum
index ace44b8037..a612b7d2d1 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-tmp-240620.n01.cts   slevis 06/20/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007)
+tmp-240620.n01.cts   slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007)
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems

From 64f1229cebd936536967a9522af703079379d7e3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 21 Jun 2024 13:56:04 -0600
Subject: [PATCH 0565/1248] Add note about each fxDONOTUSEurl line

---
 .gitmodules | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.gitmodules b/.gitmodules
index 8a173f0ddd..e437f56d61 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -30,6 +30,7 @@ path = src/fates
 url = https://github.com/NGEET/fates
 fxtag = sci.1.73.0_api.35.0.0
 fxrequired = AlwaysRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
 
 [submodule "cism"]
@@ -37,6 +38,7 @@ path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
 fxtag = cismwrap_2_2_001
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 
 [submodule "rtm"]
@@ -44,6 +46,7 @@ path = components/rtm
 url = https://github.com/ESCOMP/RTM
 fxtag = rtm1_0_79
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
@@ -51,6 +54,7 @@ path = components/mosart
 url = https://github.com/ESCOMP/MOSART
 fxtag = mosart1_0_49
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
@@ -58,6 +62,7 @@ path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
 fxtag = cesm-coupling.n02_v2.1.2
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
         
 [submodule "ccs_config"]
@@ -65,6 +70,7 @@ path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
 fxtag = ccs_config_cesm0.0.106
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
@@ -72,6 +78,7 @@ path = cime
 url = https://github.com/ESMCI/cime
 fxtag = cime6.0.246
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
@@ -79,6 +86,7 @@ path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
 fxtag = cmeps0.14.63
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
@@ -86,6 +94,7 @@ path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
 fxtag = cdeps1.0.34
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
@@ -93,6 +102,7 @@ path = share
 url = https://github.com/ESCOMP/CESM_share
 fxtag = share1.0.19
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
 [submodule "mct"]
@@ -100,6 +110,7 @@ path = libraries/mct
 url = https://github.com/MCSclimate/MCT
 fxtag = MCT_2.11.0
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/MCSclimate/MCT
 
 [submodule "parallelio"]
@@ -107,6 +118,7 @@ path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
 fxtag = pio2_6_2
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
 [submodule "doc-builder"]
@@ -114,4 +126,5 @@ path = doc/doc-builder
 url = https://github.com/ESMCI/doc-builder
 fxtag = v1.0.8
 fxrequired = ToplevelOptional
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/doc-builder

From 540d87fcc791c68ecac02eb786ca58a2e6874b9c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 21 Jun 2024 16:34:58 -0600
Subject: [PATCH 0566/1248] Update .gitmodules with latest mosart commit

---
 .gitmodules       | 2 +-
 components/mosart | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index e1df4e650c..3d3cb88e80 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -22,7 +22,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/mvertens/MOSART
-fxtag = 01f40dcf589d4e6c5932c76128e3d42faea91e9f
+fxtag = ca0acc0336365456bec653c4c233abb57d9bc62d
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
diff --git a/components/mosart b/components/mosart
index 01f40dcf58..ca0acc0336 160000
--- a/components/mosart
+++ b/components/mosart
@@ -1 +1 @@
-Subproject commit 01f40dcf589d4e6c5932c76128e3d42faea91e9f
+Subproject commit ca0acc0336365456bec653c4c233abb57d9bc62d

From 596dc135a49918c225ce726122874ed55611ad87 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 21 Jun 2024 17:52:16 -0600
Subject: [PATCH 0567/1248] Update .gitmodules with new mosart and rtm tags

---
 .gitmodules       | 8 ++++----
 components/mosart | 2 +-
 components/rtm    | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 3d3cb88e80..6d4298befc 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -14,15 +14,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 
 [submodule "rtm"]
 path = components/rtm
-url = https://github.com/swensosc/RTM
-fxtag = 420c5979d8abf05184992fdfba5ac41c41c91c2e
+url = https://github.com/ESCOMP/RTM
+fxtag = rtm1_0_80
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
-url = https://github.com/mvertens/MOSART
-fxtag = ca0acc0336365456bec653c4c233abb57d9bc62d
+url = https://github.com/ESCOMP/MOSART
+fxtag = mosart1.1.02
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
diff --git a/components/mosart b/components/mosart
index ca0acc0336..e2ffe00004 160000
--- a/components/mosart
+++ b/components/mosart
@@ -1 +1 @@
-Subproject commit ca0acc0336365456bec653c4c233abb57d9bc62d
+Subproject commit e2ffe00004cc416cfc8bcfae2a949474075c1d1f
diff --git a/components/rtm b/components/rtm
index 420c5979d8..b3dfcfbba5 160000
--- a/components/rtm
+++ b/components/rtm
@@ -1 +1 @@
-Subproject commit 420c5979d8abf05184992fdfba5ac41c41c91c2e
+Subproject commit b3dfcfbba58c151ac5a6ab513b3515ef3deff798

From c2e471833dfbbb95bac1e3bf31ddf5de8d16e5f1 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 21 Jun 2024 22:23:47 -0600
Subject: [PATCH 0568/1248] Update change files

---
 doc/ChangeLog | 4 +---
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 4da6b9379f..c4e7ca469e 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: tmp-240620.n02.ctsm5.2.007
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
-Date: Thu 13 Jun 2024 01:13:24 PM MDT
+Date: Fri 21 Jun 2024 10:21:01 PM MDT
 One-line Summary: Another update of git-fleximod
 
 Purpose and description of changes
@@ -47,8 +47,6 @@ Changes to documentation:
 
 Notes of particular relevance for developers:
 ---------------------------------------------
-NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
-[Remove any lines that don't apply. Remove entire section if nothing applies.]
 
 
 Testing summary: regular
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 029f88fe7e..0bffb18cf4 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-tmp-240620.n02.ctsm5.2.007     erik 06/13/2024 Another update of git-fleximod
+tmp-240620.n02.ctsm5.2.007     erik 06/21/2024 Another update of git-fleximod
 tmp-240620.n01.ctsm5.2.007   slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007)
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools

From 5f5c10a30cb78b6d5b8a8c80d545ca5c980303de Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Mon, 24 Jun 2024 10:35:14 -0600
Subject: [PATCH 0569/1248] Turn off explicit ac for clm6_0 and clm5_1

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 4b8b7d3571..d0a45c5727 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -147,8 +147,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <calc_human_stress_indices phys="clm4_5" >NONE</calc_human_stress_indices>
 
 <!-- Explicit, time-varying urban air conditioning adoption rate scheme -->
-<urban_explicit_ac phys="clm6_0" >.true.</urban_explicit_ac>
-<urban_explicit_ac phys="clm5_1" >.true.</urban_explicit_ac>
+<urban_explicit_ac phys="clm6_0" >.false.</urban_explicit_ac>
+<urban_explicit_ac phys="clm5_1" >.false.</urban_explicit_ac>
 <urban_explicit_ac phys="clm5_0" >.false.</urban_explicit_ac>
 <urban_explicit_ac phys="clm4_5" >.false.</urban_explicit_ac>
 

From 917baf78154a9c3116bb3b93b8ca0399d5049734 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 24 Jun 2024 15:54:14 -0600
Subject: [PATCH 0570/1248] Add OBU to the restart file since it's needed by
 Leung-2024 dust emissions

---
 src/biogeophys/FrictionVelocityMod.F90 | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90
index 92d960a7b3..584c490f4a 100644
--- a/src/biogeophys/FrictionVelocityMod.F90
+++ b/src/biogeophys/FrictionVelocityMod.F90
@@ -437,6 +437,11 @@ subroutine Restart(this, bounds, ncid, flag)
          long_name='ground momentum roughness length', units='m', &
          interpinic_flag='interp', readvar=readvar, data=this%z0mg_col)
 
+    call restartvar(ncid=ncid, flag=flag, varname='OBU', xtype=ncd_double,  &
+         dim1name='pft', &
+         long_name='Monin-Obukhov length', units='m', &
+         interpinic_flag='interp', readvar=readvar, data=this%obu_patch)
+
     if(use_luna)then
        call restartvar(ncid=ncid, flag=flag, varname='rb10', xtype=ncd_double,  &
             dim1name='pft', long_name='10-day mean boundary layer resistance at the pacth', units='s/m', &

From 463fac1241827d975948a418dc6a9c90ee34fbc0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 24 Jun 2024 17:32:47 -0600
Subject: [PATCH 0571/1248] Minor comment updates

---
 bld/CLMBuildNamelist.pm                 | 4 ++--
 bld/unit_testers/build-namelist_test.pl | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 44aa07ee28..d0d9328218 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4678,14 +4678,14 @@ sub setup_logic_cnmatrix {
       if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_repr_structure_pool"}) ) {
          $log->fatal_error("for_testing_use_repr_structure_pool can NOT be on when use_matrixcn is on" );
       }
-      # If both matrixcn and soil_matrix are off outmatrix can't be on
+      # If both matrixcn and soil_matrix are off hist_wrt_matrixcn_diag can't be on
       if ( ! &value_is_true($nl->get_value("use_matrixcn")) && ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) {
          my $var = "hist_wrt_matrixcn_diag";
          if ( &value_is_true($nl->get_value($var)) ) {
             $log->fatal_error("$var can NOT be on when both use_matrixcn and use_soil_matrixcn are off" );
          }
       }
-      # If soil_matrix is off ispspinup can't be on
+      # If soil_matrix is off spinup_matrixcn can't be on
       if ( ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) {
          my $var = "spinup_matrixcn";
          if ( &value_is_true($nl->get_value($var)) ) {
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 28a2392736..9b83f9e7ec 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -942,12 +942,12 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
-     "outmatrixWOmatrix"         =>{ options=>"-envxml_dir . -bgc bgc",
+     "matrixcn_diagWOmatrix"     =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"use_soil_matrixcn=.false.,use_matrixcn=F,hist_wrt_matrixcn_diag=T",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",
                                    },
-     "spinupWOsoilmatrix"         =>{ options=>"-envxml_dir . -bgc bgc",
+     "spinupWOsoilmatrix"        =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"use_soil_matrixcn=F,use_matrixcn=T,spinup_matrixcn=T",
                                      GLC_TWO_WAY_COUPLING=>"TRUE",
                                      phys=>"clm5_0",

From 47234a9d429e29612599bcf0590e647b895c28d2 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 24 Jun 2024 18:06:30 -0600
Subject: [PATCH 0572/1248] Add overridable warning that cnmatrix may fail in
 transient mode

---
 bld/CLMBuildNamelist.pm | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index d0d9328218..ffe1c4e522 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4650,6 +4650,16 @@ sub setup_logic_cnmatrix {
                 , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
     }
     @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" );
+    # Matrix items can't be on for transient
+    $nl_flags->{'flanduse_timeseries'} = "null";
+    my $flanduse_timeseries = $nl->get_value('flanduse_timeseries');
+    if ( $flanduse_timeseries ne "null" ) {
+       foreach my $var ( @matrixlist ) {
+          if ( &value_is_true($nl->get_value($var)) ) {
+             $log->warning("$var may FAIL with balance error in transient mode" );
+          }
+       }
+    }
     # Matrix items can't be on for SP mode
     if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
        foreach my $var ( @matrixlist ) {

From 4f702c33657ace2b931a0f33559a2ab676fd4bd4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 25 Jun 2024 11:51:39 -0600
Subject: [PATCH 0573/1248] Add ERP test of RxCropCalsAdaptGGCMI to expected
 failure list.

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 03eb6a157d..0fac518374 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -170,6 +170,13 @@
     </phase>
   </test>
 
+  <test name="ERP_D_P128x1_Ld26.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-midDecStart--clm-RxCropCalsAdaptGGCMI">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2593</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="SMS_D_Ld3.f09_g17.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen_prescribed">

From 18e63e354e604d43c6dd0bca4a43abef3f4480ee Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 25 Jun 2024 12:02:01 -0600
Subject: [PATCH 0574/1248] Abort if matrixcn is .true. and nrepr is not 1

---
 src/biogeochem/CropReprPoolsMod.F90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/biogeochem/CropReprPoolsMod.F90 b/src/biogeochem/CropReprPoolsMod.F90
index dcbb4e4fd9..695af9f00e 100644
--- a/src/biogeochem/CropReprPoolsMod.F90
+++ b/src/biogeochem/CropReprPoolsMod.F90
@@ -98,6 +98,10 @@ subroutine crop_repr_pools_init()
     end if
 
     nrepr = nrepr_grain + nrepr_structure
+    ! matrixcn works with nrepr = 1 only
+    if (use_matrixcn .and. nrepr != 1) then
+       call endrun(msg="ERROR: nrepr should be 1 when use_matrixcn = .true."//errMsg(sourcefile, __LINE__))
+    end if
     allocate(repr_hist_fnames(nrepr))
     allocate(repr_rest_fnames(nrepr))
     allocate(repr_longnames(nrepr))

From d13508bef6c0b31e8569daa758c44c379f9309b8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 25 Jun 2024 12:05:45 -0600
Subject: [PATCH 0575/1248] run_sys_tests: Check Python env for RXCROPMATURITY.

---
 python/ctsm/run_sys_tests.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py
index de93081504..9961fd325d 100644
--- a/python/ctsm/run_sys_tests.py
+++ b/python/ctsm/run_sys_tests.py
@@ -736,13 +736,29 @@ def _check_py_env(test_attributes):
     # whether import is possible.
     # pylint: disable=import-error disable
 
-    # Check requirements for FSURDATMODIFYCTSM, if needed
-    if any("FSURDATMODIFYCTSM" in t for t in test_attributes):
+    # Check requirements for using modify_fsurdat, if needed
+    modify_fsurdat_users = ["FSURDATMODIFYCTSM", "RXCROPMATURITY"]
+    if any(any(u in t for u in modify_fsurdat_users) for t in test_attributes):
         try:
             import ctsm.modify_input_files.modify_fsurdat
         except ModuleNotFoundError as err:
             raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err
 
+    # Check requirements for RXCROPMATURITY, if needed
+    if any("RXCROPMATURITY" in t for t in test_attributes):
+        try:
+            import ctsm.crop_calendars.check_rxboth_run
+        except ModuleNotFoundError as err:
+            raise ModuleNotFoundError("check_rxboth_run" + err_msg) from err
+        try:
+            import ctsm.crop_calendars.generate_gdds
+        except ModuleNotFoundError as err:
+            raise ModuleNotFoundError("generate_gdds" + err_msg) from err
+        try:
+            import ctsm.crop_calendars.interpolate_gdds
+        except ModuleNotFoundError as err:
+            raise ModuleNotFoundError("interpolate_gdds" + err_msg) from err
+
     # Check that list for any testmods that use modify_fates_paramfile.py
     testmods_to_check = ["clm-FatesColdTwoStream", "clm-FatesColdTwoStreamNoCompFixedBioGeo"]
     testmods = _get_testmod_list(test_attributes)

From 422f06f7389094b32baa763628865a53467d0830 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 25 Jun 2024 13:33:42 -0700
Subject: [PATCH 0576/1248] add fates potential vegetation spin up to transient
 test mod

---
 cime_config/testdefs/testlist_clm.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 85824a4404..0706a1ef53 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2615,6 +2615,15 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
+  <test name="PVT_Lm3" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesLUPFT">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
+      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld3" grid="f19_g17" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>

From f9d8349021458c56912edf626a0c8e229e4f58da Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 25 Jun 2024 13:53:01 -0700
Subject: [PATCH 0577/1248] rename fates luh2 harvest modes

---
 .../include_user_mods                                             | 0
 .../{FatesColdLUH2Mode3 => FatesColdLUH2HarvestArea}/user_nl_clm  | 0
 .../include_user_mods                                             | 0
 .../{FatesColdLUH2Mode1 => FatesColdLUH2HarvestEvent}/user_nl_clm | 0
 .../include_user_mods                                             | 0
 .../{FatesColdLUH2Mode4 => FatesColdLUH2HarvestMass}/user_nl_clm  | 0
 .../include_user_mods                                             | 0
 .../{FatesColdLUH2Mode2 => FatesColdLUH2HarvestSurf}/user_nl_clm  | 0
 .../include_user_mods                                             | 0
 .../{FatesColdLUH2Mode0 => FatesColdLUH2NoHarvest}/user_nl_clm    | 0
 10 files changed, 0 insertions(+), 0 deletions(-)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode0 => FatesColdLUH2HarvestArea}/include_user_mods (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode3 => FatesColdLUH2HarvestArea}/user_nl_clm (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode1 => FatesColdLUH2HarvestEvent}/include_user_mods (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode1 => FatesColdLUH2HarvestEvent}/user_nl_clm (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode2 => FatesColdLUH2HarvestMass}/include_user_mods (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode4 => FatesColdLUH2HarvestMass}/user_nl_clm (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode3 => FatesColdLUH2HarvestSurf}/include_user_mods (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode2 => FatesColdLUH2HarvestSurf}/user_nl_clm (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode4 => FatesColdLUH2NoHarvest}/include_user_mods (100%)
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode0 => FatesColdLUH2NoHarvest}/user_nl_clm (100%)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm

From f8330c9a7fba12652562efbc87a56f0de358b669 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 25 Jun 2024 17:16:45 -0600
Subject: [PATCH 0578/1248] Correct earlier commit 47234a9: warning about
 cnmatrix and transient

---
 bld/CLMBuildNamelist.pm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index ffe1c4e522..329030d985 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4651,9 +4651,7 @@ sub setup_logic_cnmatrix {
     }
     @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" );
     # Matrix items can't be on for transient
-    $nl_flags->{'flanduse_timeseries'} = "null";
-    my $flanduse_timeseries = $nl->get_value('flanduse_timeseries');
-    if ( $flanduse_timeseries ne "null" ) {
+    if (not string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
        foreach my $var ( @matrixlist ) {
           if ( &value_is_true($nl->get_value($var)) ) {
              $log->warning("$var may FAIL with balance error in transient mode" );

From 17143eea0e9c447eca85bde97b7f1dda7c2b1ffe Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 25 Jun 2024 17:24:15 -0600
Subject: [PATCH 0579/1248] Correct earlier commit 18e63e3: abort if matrixcn
 and nrepr not 1

---
 src/biogeochem/CropReprPoolsMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CropReprPoolsMod.F90 b/src/biogeochem/CropReprPoolsMod.F90
index 695af9f00e..cbc2f3e2a2 100644
--- a/src/biogeochem/CropReprPoolsMod.F90
+++ b/src/biogeochem/CropReprPoolsMod.F90
@@ -99,7 +99,7 @@ subroutine crop_repr_pools_init()
 
     nrepr = nrepr_grain + nrepr_structure
     ! matrixcn works with nrepr = 1 only
-    if (use_matrixcn .and. nrepr != 1) then
+    if (use_matrixcn .and. nrepr /= 1) then
        call endrun(msg="ERROR: nrepr should be 1 when use_matrixcn = .true."//errMsg(sourcefile, __LINE__))
     end if
     allocate(repr_hist_fnames(nrepr))

From 4b18e79ae14e8c56c51b718aad722ce679b37972 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 25 Jun 2024 17:29:56 -0600
Subject: [PATCH 0580/1248] Replace clm45_monthly_matrixcn_soilCN30 testmod and
 test with clm60

---
 .../clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm           | 2 --
 .../include_user_mods                                         | 0
 .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm           | 4 ++++
 3 files changed, 4 insertions(+), 2 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm
 rename cime_config/testdefs/testmods_dirs/clm/{clm45_monthly_matrixcn_soilCN30 => clm60_monthly_matrixcn_soilCN30}/include_user_mods (100%)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm
deleted file mode 100644
index c7436f5acb..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm
+++ /dev/null
@@ -1,2 +0,0 @@
- use_soil_matrixcn = .true.
- paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm45_params.soilCN30.c220321.nc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
new file mode 100644
index 0000000000..d22154bef6
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -0,0 +1,4 @@
+use_soil_matrixcn = .true.
+paramfile = '/glade/u/home/slevis/paramfiles/ctsm60_params_cn30.c240625.nc'
+! If we keep this paramfile, it should move to the repository
+! paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240625.nc'

From 1761a7becb50cad2849db794243b1f2d37e602c3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 25 Jun 2024 17:34:50 -0600
Subject: [PATCH 0581/1248] Move new param file to inputdata and rimport

---
 .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm           | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
index d22154bef6..df20ced9e8 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -1,4 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '/glade/u/home/slevis/paramfiles/ctsm60_params_cn30.c240625.nc'
-! If we keep this paramfile, it should move to the repository
-! paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240625.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240625.nc'

From 1e97001d0dc5e7359d8fb3b11c37118e3e429fe3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 25 Jun 2024 17:59:00 -0600
Subject: [PATCH 0582/1248] Change use_matrixcn, use_soil_matrixcn to default
 .false. before merge

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 90e397d544..933b504606 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -618,19 +618,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <!-- CN Matrix options -->
+<use_matrixcn>.false.</use_matrixcn>
 <use_matrixcn clm_accelerated_spinup="sasu" use_fates=".false." bgc_mode="bgc" >.true.</use_matrixcn>
 
-<use_matrixcn               use_fates=".false." bgc_mode="bgc"   >.true.</use_matrixcn>
-<use_matrixcn phys="clm4_5" use_fates=".false." bgc_mode="bgc"   >.false.</use_matrixcn>
-<use_matrixcn                                   bgc_mode="sp"    >.false.</use_matrixcn>
-<use_matrixcn                                   bgc_mode="fates" >.false.</use_matrixcn>
-
+<use_soil_matrixcn>.false.</use_soil_matrixcn>
 <use_soil_matrixcn clm_accelerated_spinup="sasu" use_fates=".false." soil_decomp_method="CENTURYKoven2013" >.true.</use_soil_matrixcn>
-<use_soil_matrixcn               use_fates=".false." soil_decomp_method="CENTURYKoven2013" >.true.</use_soil_matrixcn>
-<use_soil_matrixcn phys="clm4_5" use_fates=".false." soil_decomp_method="CENTURYKoven2013" >.false.</use_soil_matrixcn>
-<use_soil_matrixcn               bgc_mode="sp"    >.false.</use_soil_matrixcn>
-<use_soil_matrixcn               bgc_mode="fates" >.false.</use_soil_matrixcn>
-<use_soil_matrixcn                                >.false.</use_soil_matrixcn>
 
 <hist_wrt_matrixcn_diag clm_accelerated_spinup="on"                             >.false.</hist_wrt_matrixcn_diag>
 <hist_wrt_matrixcn_diag clm_accelerated_spinup="sasu"                           >.false.</hist_wrt_matrixcn_diag>

From 7feb6572d51e5d3ba2596ae9a1b4ededd045928d Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 25 Jun 2024 18:04:46 -0600
Subject: [PATCH 0583/1248] Rm redunant LG* and LR* tests and corresponding
 expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 13 -------------
 cime_config/testdefs/testlist_clm.xml      | 20 --------------------
 2 files changed, 33 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 5968e73760..664b1c8e35 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -58,19 +58,6 @@
     </phase>
   </test>
 
-  <test name="LGRAIN2_Ly1_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
-    </phase>
-  </test>
-  <test name="LREPRSTRUCT_Ly1_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#640, same test with clm-ciso_soil_matrixcn_only works</issue>
-    </phase>
-  </test>
-
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 9a2390bd58..625a9f3504 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3386,26 +3386,6 @@
     </options>
   </test>
 
-  <test name="LGRAIN2_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
-    <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a second grain pool, and that we can get bit-for-bit identical answers with a standard run with just one grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code). This and other tests with the ciso_soil_matrixcn_only testmods become redundant when default use_matrixcn = .false.. There are 2 more LGRAIN and two more LREPR tests with the same names but ciso testmods for when default use_matrixcn = .true..</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
-  <test name="LREPRSTRUCT_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_soil_matrixcn_only--clm/cropMonthOutput">
-    <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm">
-        <options>
-          <option name="wallclock">02:00:00</option>
-          <option name="comment">Ensure that it works to have a crop reproductive structure pool, and that we can get bit-for-bit identical answers when using that pool compared to a run with a single reproductive grain pool. This tests infrastructure that will be needed when incorporating AgSys. This test can be dropped once we have some tests exercising AgSys (which will exercise this code).</option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="LGRAIN2_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>

From bb1bd9ca8ed2cfe2e8b8d6ae756925af3100bee3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 25 Jun 2024 22:21:10 -0600
Subject: [PATCH 0584/1248] Make Leung_2023 the default, remove error checking
 about using it

---
 bld/CLMBuildNamelist.pm                       | 3 ---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 bld/unit_testers/build-namelist_test.pl       | 7 +------
 3 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 6a24e6c899..549622a765 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4008,9 +4008,6 @@ sub setup_logic_dust_emis {
                             "$option is being set, need to change one or the other" );
         }
      }
-     if ( $dust_emis_method eq "Leung_2023" ) {
-        $log->warning("dust_emis_method is Leung_2023 and that option has NOT been brought into CTSM yet");
-     }
   }
 }
 
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 7fe7fb18c1..753a08b081 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2780,7 +2780,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <!-- Defaults for Zender's soil erodibility data  -->
 <!-- ===========================================  -->
 
-<dust_emis_method>Zender_2003</dust_emis_method>
+<dust_emis_method>Leung_2023</dust_emis_method>
 <zender_soil_erod_source dust_emis_method="Zender_2003">atm</zender_soil_erod_source>
 <zendersoilerod_mapalgo>bilinear</zendersoilerod_mapalgo>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index b6600983ed..50e131e824 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1612;
+my $ntests = 1611;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 945;
@@ -1273,11 +1273,6 @@ sub cat_and_create_namelistinfile {
 
 my %warntest = (
      # Warnings without the -ignore_warnings option given
-     "dustemisLeung"             =>{ options=>"-envxml_dir .",
-                                     namelst=>"dust_emis_method = 'Leung_2023'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
-                                   },
      "coldwfinidat"              =>{ options=>"-envxml_dir . -clm_start_type cold",
                                      namelst=>"finidat = 'testfile.nc'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

From 5a46b9382ee15fea803cb5e7091ed6915c2169a1 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 26 Jun 2024 10:53:02 -0700
Subject: [PATCH 0585/1248] remove fates land use no harvest due to overlap

---
 .../testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods   | 1 -
 .../testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm         | 1 -
 2 files changed, 2 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods
deleted file mode 100644
index 7eb8bb1579..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm
deleted file mode 100644
index b3b338e232..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm
+++ /dev/null
@@ -1 +0,0 @@
-fates_harvest_mode = no_harvest

From 3318d3b46df34013afcb5fadc4ad9f4184779f28 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 26 Jun 2024 11:03:10 -0700
Subject: [PATCH 0586/1248] update fates landuse harvest test mod names

---
 cime_config/testdefs/testlist_clm.xml | 19 +++++--------------
 1 file changed, 5 insertions(+), 14 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 0706a1ef53..ed0627f242 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2570,7 +2570,7 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode0">
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestArea">
     <machines>
       <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
       <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
@@ -2579,7 +2579,7 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode1">
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestEvent">
     <machines>
       <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
       <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
@@ -2588,7 +2588,7 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode2">
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestMass">
     <machines>
       <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
       <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
@@ -2597,16 +2597,7 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode3">
-    <machines>
-      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
-      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-    </options>
-  </test>
-  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2Mode4">
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestSurf">
     <machines>
       <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
       <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
@@ -2621,7 +2612,7 @@
       <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:60:00</option>
     </options>
   </test>
   <test name="ERS_D_Ld3" grid="f19_g17" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">

From f15eadec091721e236f0c83af26cc99ad2b1754e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 26 Jun 2024 12:10:24 -0600
Subject: [PATCH 0587/1248] Repl. NIWO with HARV in a test and update expected
 fails for two tests

---
 cime_config/testdefs/ExpectedTestFails.xml | 17 +----------------
 cime_config/testdefs/testlist_clm.xml      |  2 +-
 2 files changed, 2 insertions(+), 17 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 156bee9f80..cf348c0f8d 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -58,15 +58,11 @@
     </phase>
   </test>
 
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-default--clm-NEON-NIWO">
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-default--clm-NEON-HARV">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
       <issue>#2310</issue>
     </phase>
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
   </test>
   
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-NEON-MOAB--clm-PRISM">
@@ -80,17 +76,6 @@
     </phase>
   </test>
   
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
-    <phase name="SHAREDLIB_BUILD">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
-  </test>
-  
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 049d9cf873..fee8e1a429 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1873,7 +1873,7 @@
       <option name="comment">Want to keep a little single-point testing on HPC machines</option>
     </options>
   </test>
-  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/NIWO">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/HARV">
     <machines>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>

From 00e3d62d1f4c38a651178a77fd075b21b3572f3c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 26 Jun 2024 12:26:05 -0600
Subject: [PATCH 0588/1248] Remove abort on Leung dust method

Add some log statements around this.
---
 src/biogeochem/DUSTMod.F90 | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index c6a48b8145..4af9fe0acd 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -330,14 +330,7 @@ subroutine InitCold(this, bounds)
     ! Set basin factor to 1 for now
 
     if (dust_emis_method == 'Leung_2023') then
-       !do c = bounds%begc, bounds%endc
-       !   l = col%landunit(c)
-
-       !   if (.not.lun%lakpoi(l)) then
-       !      this%mbl_bsn_fct_col(c) = 1.0_r8
-       !   end if
-       !end do
-       call endrun( msg="Leung_2023 dust_emis_method is currently not available"//errMsg(sourcefile, __LINE__))
+       write(iulog,*) 'Using the new Leung_2023 dust emission scheme'
     else if (dust_emis_method == 'Zender_2003') then
        if ( this%soil_erod_stream%UseStreams() )then
           call this%soil_erod_stream%CalcDustSource( bounds, &
@@ -345,6 +338,7 @@ subroutine InitCold(this, bounds)
        else
           this%mbl_bsn_fct_col(:) = 1.0_r8
        end if
+       write(iulog,*) 'WARNING: Asked to use the old Zender_2003 dust emission scheme, which is not currently setup completely'
     else
        write(iulog,*) 'dust_emis_method not recognized = ', trim(dust_emis_method)
        call endrun( msg="dust_emis_method namelist item is not valid "//errMsg(sourcefile, __LINE__))

From a5da93ec5d016aabc11452870d8c3fab1677ef25 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 26 Jun 2024 12:31:05 -0600
Subject: [PATCH 0589/1248] generate_gdd20_baseline: Add optional -y1 and -yN
 args.

---
 .../crop_calendars/generate_gdd20_baseline.py | 39 +++++++++++++++++--
 1 file changed, 35 insertions(+), 4 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 89a38a0a08..4357bd6dd1 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -70,6 +70,24 @@ def _parse_args():
         help="Overwrite existing output file, if any",
         action="store_true",
     )
+    parser.add_argument(
+        "-y1",
+        "--first-year",
+        help=(
+            "First calendar year to include"
+        ),
+        type=int,
+        required=False,
+    )
+    parser.add_argument(
+        "-yN",
+        "--last-year",
+        help=(
+            "Last calendar year to include"
+        ),
+        type=int,
+        required=False,
+    )
 
     # Get arguments
     args = parser.parse_args(sys.argv[1:])
@@ -78,7 +96,19 @@ def _parse_args():
     if os.path.exists(args.output_file) and not args.overwrite:
         raise FileExistsError("Output file exists but --overwrite is not specified")
 
-    return args
+    # Process time slice
+    # Assumes CESM behavior where data for e.g. 1987 is saved as 1988-01-01
+    if args.first_year is not None:
+        date_1 = f"{args.first_year+1}-01-01"
+    else:
+        date_1 = "0000-01-01"
+    if args.last_year is not None:
+        date_n = f"{args.last_year+1}-01-01"
+    else:
+        date_n = "9999-12-31"
+    time_slice = slice(date_1, date_n)
+
+    return args, time_slice
 
 
 def _get_cft_list(crop_list):
@@ -161,7 +191,7 @@ def _add_time_axis(da_in):
     return da_out
 
 
-def generate_gdd20_baseline(input_files, output_file, author):
+def generate_gdd20_baseline(input_files, output_file, author, time_slice):
     """
     Generate stream_fldFileName_gdd20_baseline file from CTSM outputs
     """
@@ -173,7 +203,7 @@ def generate_gdd20_baseline(input_files, output_file, author):
     input_files.sort()
 
     # Import history files and ensure they have lat/lon dims
-    ds_in = import_ds(input_files, VAR_LIST_IN + GRIDDING_VAR_LIST)
+    ds_in = import_ds(input_files, VAR_LIST_IN + GRIDDING_VAR_LIST, time_slice=time_slice)
     if not all(x in ds_in.dims for x in ["lat", "lon"]):
         raise RuntimeError("Input files must have lat and lon dimensions")
 
@@ -247,9 +277,10 @@ def main():
     """
     main() function for calling generate_gdd20_baseline.py from command line.
     """
-    args = _parse_args()
+    args, time_slice = _parse_args()
     generate_gdd20_baseline(
         args.input_files,
         args.output_file,
         args.author,
+        time_slice
     )

From ddef21bdde3fdbe0990a45b6997393faaa70ccde Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 26 Jun 2024 12:35:58 -0600
Subject: [PATCH 0590/1248] Correction to the expected-fails update for one of
 the tests

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index cf348c0f8d..c5d8a85724 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -76,6 +76,13 @@
     </phase>
   </test>
   
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2310</issue>
+    </phase>
+  </test>
+
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>

From 5427891e02b3d6e4292e30ac3a1f827394a294d5 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 26 Jun 2024 12:50:25 -0600
Subject: [PATCH 0591/1248] Revert last correction (it was fine to begin with)

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index c5d8a85724..cf348c0f8d 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -76,13 +76,6 @@
     </phase>
   </test>
   
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
-    <phase name="SHAREDLIB_BUILD">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>

From b0c79e1c2ccde049102caf390656b123503a648a Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 26 Jun 2024 12:54:34 -0600
Subject: [PATCH 0592/1248] Make one more update to expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index cf348c0f8d..a62a25151a 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -244,10 +244,6 @@
       <status>FAIL</status>
       <issue>#2310</issue>
     </phase>
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2310</issue>
-    </phase>
   </test>
 
   <!-- Other external test list failures (MOSART, RTM, etc. -->

From 4edaa461a4cbd56bf98c5014aa85b9cd84e7fe3c Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 26 Jun 2024 14:21:18 -0600
Subject: [PATCH 0593/1248] move from depricated shr_file to shr_log

---
 src/cpl/nuopc/lnd_comp_nuopc.F90 | 37 ++++++++++++++++----------------
 1 file changed, 18 insertions(+), 19 deletions(-)

diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90
index 3852a1bf1b..7fe93454ac 100644
--- a/src/cpl/nuopc/lnd_comp_nuopc.F90
+++ b/src/cpl/nuopc/lnd_comp_nuopc.F90
@@ -29,7 +29,7 @@ module lnd_comp_nuopc
   use NUOPC_Model            , only : NUOPC_ModelGet
   use shr_kind_mod           , only : r8 => shr_kind_r8, cl=>shr_kind_cl
   use shr_sys_mod            , only : shr_sys_abort
-  use shr_file_mod           , only : shr_file_getlogunit, shr_file_setlogunit
+  use shr_log_mod            , only : shr_log_setLogUnit, shr_log_getLogUnit
   use shr_orb_mod            , only : shr_orb_decl, shr_orb_params, SHR_ORB_UNDEF_REAL, SHR_ORB_UNDEF_INT
   use shr_cal_mod            , only : shr_cal_noleap, shr_cal_gregorian, shr_cal_ymd2date
   use spmdMod                , only : masterproc, mpicom, spmd_init
@@ -66,7 +66,7 @@ module lnd_comp_nuopc
   private :: clm_orbital_init    ! Initialize the orbital information
   private :: clm_orbital_update  ! Update the orbital information
   private :: CheckImport
-  
+
   !--------------------------------------------------------------------------
   ! Private module data
   !--------------------------------------------------------------------------
@@ -333,8 +333,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
     !----------------------------------------------------------------------------
     ! reset shr logging to original values
     !----------------------------------------------------------------------------
-
-    call shr_file_setLogUnit (shrlogunit)
+    call shr_log_setLogUnit(shrlogunit)
     call ESMF_LogWrite(subname//' done', ESMF_LOGMSG_INFO)
 
   end subroutine InitializeAdvertise
@@ -497,8 +496,8 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     ! Reset shr logging to my log file
     !----------------------------------------------------------------------------
 
-    call shr_file_getLogUnit (shrlogunit)
-    call shr_file_setLogUnit (iulog)
+    call shr_log_getLogUnit (shrlogunit)
+    call shr_log_setLogUnit (iulog)
 #if (defined _MEMTRACE)
     if (masterproc) then
        lbnum=1
@@ -683,7 +682,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
     endif
 
-    call shr_file_setLogUnit (shrlogunit)
+    call shr_log_setLogUnit (shrlogunit)
 
 #if (defined _MEMTRACE)
     if(masterproc) then
@@ -774,8 +773,8 @@ subroutine ModelAdvance(gcomp, rc)
     ! Reset share log units
     !--------------------------------
 
-    call shr_file_getLogUnit (shrlogunit)
-    call shr_file_setLogUnit (iulog)
+    call shr_log_getLogUnit (shrlogunit)
+    call shr_log_setLogUnit (iulog)
 
 #if (defined _MEMTRACE)
     if(masterproc) then
@@ -864,7 +863,7 @@ subroutine ModelAdvance(gcomp, rc)
        rstwr = .false.
        if (nlend .and. write_restart_at_endofrun) then
           rstwr = .true.
-       else 
+       else
           call ESMF_ClockGetAlarm(clock, alarmname='alarm_restart', alarm=alarm, rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           if (ESMF_AlarmIsCreated(alarm, rc=rc)) then
@@ -964,7 +963,7 @@ subroutine ModelAdvance(gcomp, rc)
     ! Reset shr logging to my original values
     !--------------------------------
 
-    call shr_file_setLogUnit (shrlogunit)
+    call shr_log_setLogUnit (shrlogunit)
 
     call ESMF_LogWrite(subname//' done', ESMF_LOGMSG_INFO)
 
@@ -1289,14 +1288,14 @@ subroutine CheckImport(gcomp, rc)
     type(ESMF_GridComp) :: gcomp
     integer, intent(out) :: rc
     character(len=*) , parameter :: subname = "("//__FILE__//":CheckImport)"
-    
+
     ! This is the routine that enforces the explicit time dependence on the
     ! import fields. This simply means that the timestamps on the Fields in the
-    ! importState are checked against the currentTime on the Component's 
+    ! importState are checked against the currentTime on the Component's
     ! internalClock. Consequenty, this model starts out with forcing fields
-    ! at the current time as it does its forward step from currentTime to 
+    ! at the current time as it does its forward step from currentTime to
     ! currentTime + timeStep.
-    
+
     ! local variables
     type(ESMF_Clock)              :: clock
     type(ESMF_Time)               :: time
@@ -1320,7 +1319,7 @@ subroutine CheckImport(gcomp, rc)
     ! query the component for info
     call NUOPC_CompGet(gcomp, name=name, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
-    
+
     ! query the Component for its clock and importState
     call ESMF_GridCompGet(gcomp, clock=clock, importState=importState, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
@@ -1328,11 +1327,11 @@ subroutine CheckImport(gcomp, rc)
     ! get the current time out of the clock
     call ESMF_ClockGet(clock, currTime=time, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
-    
+
     ! check that Fields in the importState show correct timestamp
     allCurrent = NUOPC_IsAtTime(importState, time, fieldList=fieldList, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
-      
+
     if (.not.allCurrent) then
       !TODO: introduce and use INCOMPATIBILITY return codes!!!!
       do i=1, size(fieldList)
@@ -1354,6 +1353,6 @@ subroutine CheckImport(gcomp, rc)
         rcToReturn=rc)
       return  ! bail out
     endif
-    
+
   end subroutine CheckImport
 end module lnd_comp_nuopc

From 23c8743ae67e8b550ee3ba89c10f2a2d17a51c3b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 26 Jun 2024 14:27:22 -0600
Subject: [PATCH 0594/1248] generate_gdds: Map sdate in/out diffs.

---
 .../crop_calendars/generate_gdd20_baseline.py |  5 +++-
 python/ctsm/crop_calendars/generate_gdds.py   |  1 +
 .../crop_calendars/generate_gdds_functions.py | 28 +++++++++++++++++--
 3 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 4357bd6dd1..476717b887 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -97,7 +97,10 @@ def _parse_args():
         raise FileExistsError("Output file exists but --overwrite is not specified")
 
     # Process time slice
-    # Assumes CESM behavior where data for e.g. 1987 is saved as 1988-01-01
+    # Assumes CESM behavior where data for e.g. 1987 is saved as 1988-01-01.
+    # It would be more robust, accounting for upcoming behavior (where timestamp for a year is the
+    # middle of that year), to do slice("YEAR1-01-03", "YEARN-01-02"), but that's not compatible
+    # with ctsm_pylib as of the version using python 3.7.9. See safer_timeslice() in cropcal_utils.
     if args.first_year is not None:
         date_1 = f"{args.first_year+1}-01-01"
     else:
diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py
index 156ebfb20e..49226e6f75 100644
--- a/python/ctsm/crop_calendars/generate_gdds.py
+++ b/python/ctsm/crop_calendars/generate_gdds.py
@@ -178,6 +178,7 @@ def main(
                 mxmats,
                 cc.get_gs_len_da,
                 skip_crops,
+                outdir_figs,
                 logger,
             )
 
diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index 38c5d44384..2658e1de87 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -22,6 +22,7 @@
     # pylint: disable=import-error
     from ctsm.crop_calendars.cropcal_figs_module import *
     from matplotlib.transforms import Bbox
+    import matplotlib.pyplot as plt
 
     warnings.filterwarnings(
         "ignore",
@@ -63,7 +64,7 @@ def error(logger, string):
     raise RuntimeError(string)
 
 
-def check_sdates(dates_ds, sdates_rx, logger, verbose=False):
+def check_sdates(dates_ds, sdates_rx, outdir_figs, logger, verbose=False):
     """
     Checking that input and output sdates match
     """
@@ -106,8 +107,28 @@ def check_sdates(dates_ds, sdates_rx, logger, verbose=False):
             log(logger, out_map_notnan[here][0:4])
             log(logger, "diff:")
             log(logger, diff_map_notnan[here][0:4])
+            first_diff = all_ok
             all_ok = False
 
+            if CAN_PLOT:
+                sdate_diffs_dir = os.path.join(outdir_figs, "sdate_diffs")
+                if first_diff:
+                    log(logger, f"Saving sdate difference figures to {sdate_diffs_dir}")
+                if not os.path.exists(sdate_diffs_dir):
+                    os.makedirs(sdate_diffs_dir)
+                in_map.where(~np.isnan(out_map)).plot()
+                plt.title(f"{vegtype_str} sdates in (masked)")
+                plt.savefig(os.path.join(sdate_diffs_dir, f"{vegtype_str}.in.png"))
+                plt.close()
+                out_map.plot()
+                plt.title(f"{vegtype_str} sdates out")
+                plt.savefig(os.path.join(sdate_diffs_dir, f"{vegtype_str}.out.png"))
+                plt.close()
+                diff_map.plot()
+                plt.title(f"{vegtype_str} sdates diff (out - in)")
+                plt.savefig(os.path.join(sdate_diffs_dir, f"{vegtype_str}.diff.png"))
+                plt.close()
+
     if not any_found:
         error(logger, "No matching variables found in sdates_rx!")
 
@@ -234,6 +255,7 @@ def import_and_process_1yr(
     mxmats,
     get_gs_len_da,
     skip_crops,
+    outdir_figs,
     logger,
 ):
     """
@@ -272,6 +294,8 @@ def import_and_process_1yr(
         time_slice=slice(f"{this_year}-01-01", f"{this_year}-12-31"),
         chunks=chunks,
     )
+    for timestep in dates_ds["time"].values:
+        print(timestep)
 
     if dates_ds.dims["time"] > 1:
         if dates_ds.dims["time"] == 365:
@@ -466,7 +490,7 @@ def import_and_process_1yr(
     # Import expected sowing dates. This will also be used as our template output file.
     imported_sdates = isinstance(sdates_rx, str)
     sdates_rx = import_rx_dates("s", sdates_rx, incl_patches1d_itype_veg, mxsowings, logger)
-    check_sdates(dates_incl_ds, sdates_rx, logger)
+    check_sdates(dates_incl_ds, sdates_rx, outdir_figs, logger)
 
     # Import hdates, if needed
     imported_hdates = isinstance(hdates_rx, str)

From 19f793f2ff0764f7a5877440f765cdd8a5d9f8b3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 26 Jun 2024 17:53:03 -0600
Subject: [PATCH 0595/1248] Update cam and cice6 tags to that in cesm2_3_beta17

---
 Externals.cfg | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 5ae9973d32..58639eafb3 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -41,15 +41,15 @@ local_path = components/cice5
 required = True
 
 [cice6]
-tag = cesm_cice6_4_1_10
+tag = cesm_cice6_5_0_7
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CICE
 local_path = components/cice
 externals = Externals.cfg
 required = True
 
-[cam6]
-tag = cam6_3_135
+[cam]
+tag = cam6_3_160
 protocol = git
 repo_url = https://github.com/ESCOMP/CAM
 local_path = components/cam

From 34c4db0b185b4cb62fc6fa22de96b23c949c0dfd Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 26 Jun 2024 23:47:14 -0700
Subject: [PATCH 0596/1248] Revert "Apply relevant changes from
 rgknox/fates-auto-params."

This reverts commit 7216006b1c2400d1ca2932899671f9bcec85b6af.
---
 .../testdefs/testmods_dirs/clm/Fates/shell_commands   |  5 -----
 .../testdefs/testmods_dirs/clm/Fates/user_nl_clm      |  1 -
 .../testdefs/testmods_dirs/clm/_scripts/README        |  2 --
 .../clm/_scripts/get_fates_shell_commands_vars.sh     | 11 -----------
 4 files changed, 19 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/_scripts/README
 delete mode 100755 cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh

diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands
index 3443bacef0..41a2342a51 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands
@@ -1,7 +1,2 @@
 ./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
 ./xmlchange BFBFLAG="TRUE"
-
-SRCROOT=`./xmlquery SRCROOT --value`
-. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
-
-ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
index 57adea1ff6..91df3e2e61 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -4,7 +4,6 @@ hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 hist_ndens = 1
 fates_spitfire_mode = 1
-fates_paramfile='${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc'
 hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD',
 'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON',
diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/README b/cime_config/testdefs/testmods_dirs/clm/_scripts/README
deleted file mode 100644
index 66eb22a375..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/_scripts/README
+++ /dev/null
@@ -1,2 +0,0 @@
-This directory contains scripts that can be called in
-shell_commands of multiple testmods.
diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh b/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
deleted file mode 100755
index 382fb4e53e..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-# This script should be called in shell_commands with
-#    . "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
-# where the leading period ensures it's run in the same shell.
-
-CASE=`./xmlquery CASE --value`
-FATESDIR="${SRCROOT}/src/fates"
-FATESPARAMDIR="${SRCROOT}/src/fates/parameter_files/binaries"
-mkdir -p "${FATESPARAMDIR}"
-FATESPARAMFILE="${FATESPARAMDIR}/${CASE}-params.nc"
-
-# No exit status because it should be called in the same shell.

From 0c9b5489e5bc81b75478499461c19ec33ecd0775 Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Thu, 27 Jun 2024 12:22:42 -0400
Subject: [PATCH 0597/1248] changing prescribed N and P uptake to 1 in the PRT2
 test

---
 .../testmods_dirs/clm/FatesColdPRT2/shell_commands    | 11 +++++++++++
 .../testmods_dirs/clm/FatesColdPRT2/user_nl_clm       |  1 +
 2 files changed, 12 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/shell_commands

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/shell_commands
new file mode 100644
index 0000000000..632b61bf15
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/shell_commands
@@ -0,0 +1,11 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates/
+FATESPARAMFILE=$CASEDIR/fates_params_prt2_prescribed_np.nc
+
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
+
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_cnp_prescribed_nuptake --val 1.0 --allpfts
+
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_cnp_prescribed_puptake --val 1.0 --allpfts
+
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm
index 679f025b60..196d559cb7 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm
@@ -1,3 +1,4 @@
+fates_paramfile = '$CASEROOT/fates_params_prt2_prescribed_np.nc'
 fates_parteh_mode = 2
 hist_fincl1       = 'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF',
 'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF',

From 6f3a068cc301039ce7eb6ce98fc062f4a1257bb0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 27 Jun 2024 14:22:32 -0600
Subject: [PATCH 0598/1248] Finish fsat_hillslope merge (update ChangeLog/Sum).

---
 doc/ChangeLog | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 60 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index c4e7ca469e..05b43c20ab 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,63 @@
 ===============================================================
+Tag name: tmp-240620.n03.ctsm5.2.007
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Thu Jun 27 14:17:02 MDT 2024
+One-line Summary: Set upland hillslope column fsat values to zero
+
+Purpose and description of changes
+----------------------------------
+
+The topmodel-based fsat surface runoff scheme is not appropriate for upland hillslope columns, so set upland hillslope column fsat values to zero. User can revert this behavior by setting hillslope_fsat_equals_zero to false.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+- Added parameter hillslope_fsat_equals_zero (default true). Set to false for previous behavior.
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- DIFF
+    izumi ------- DIFF
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, but only for hillslope tests.
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2600 (https://github.com/ESCOMP/CTSM/pull/2600)
+
+===============================================================
+===============================================================
 Tag name: tmp-240620.n02.ctsm5.2.007
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri 21 Jun 2024 10:21:01 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 0bffb18cf4..7dd063df45 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+tmp-240620.n03.ctsm5.2.007 samrabin 06/27/2024 Set upland hillslope column fsat values to zero
 tmp-240620.n02.ctsm5.2.007     erik 06/21/2024 Another update of git-fleximod
 tmp-240620.n01.ctsm5.2.007   slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007)
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly

From 99d0f2bb4c93c739e5875781070a3d66c6bb8cbd Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 27 Jun 2024 16:56:21 -0700
Subject: [PATCH 0599/1248] move fates landuse test mods to fates suite

---
 cime_config/testdefs/testlist_clm.xml | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index ef4358f763..347fd33e8e 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2573,8 +2573,7 @@
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestArea">
     <machines>
-      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
-      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+      <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2582,8 +2581,7 @@
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestEvent">
     <machines>
-      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
-      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+      <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2591,8 +2589,7 @@
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestMass">
     <machines>
-      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
-      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+      <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2600,8 +2597,7 @@
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestSurf">
     <machines>
-      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
-      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+      <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2609,8 +2605,7 @@
   </test>
   <test name="PVT_Lm3" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesLUPFT">
     <machines>
-      <machine name="derecho" compiler="intel" category="fates_landuse_v2"/>
-      <machine name="izumi" compiler="nag" category="fates_landuse_v2"/>
+      <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>

From 535033b959f6eab9c5d39d7edff410c47dfacb80 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 27 Jun 2024 17:11:47 -0700
Subject: [PATCH 0600/1248] remove flandusepft and fluh_times pointers for
 testmod

Use default currently.
---
 .../testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm        | 2 --
 1 file changed, 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
index 970e7df7cd..e25490ffbb 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
@@ -2,10 +2,8 @@
 ! Run a transient case, with vegetation starting from bare ground, but land use starting from LUH state vector on starting date, in a nocomp configuration.
 ! From Charlie's list of valid FATES configurations:
 ! https://docs.google.com/spreadsheets/d/1eE3sRMYxfocZKbT8uIQhXpjjtfM2feXPRSWXJNoo4jM/edit#gid=0
-flandusepftdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc'
 use_fates_luh = .true.
 use_fates_nocomp = .true.
 use_fates_fixed_biogeog = .true.
 use_fates_sp = .false.
 use_fates_potentialveg = .false.
-fluh_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc'

From 8793f477483bf0332bf423e3c7b3bb66b31f88aa Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 27 Jun 2024 17:15:29 -0700
Subject: [PATCH 0601/1248] add readme noting grid resolution limitation

---
 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README
new file mode 100644
index 0000000000..79d6511d17
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README
@@ -0,0 +1,2 @@
+Currently the FATES LUH2 category of test mods currently only supports 
+4x5 grid resolutions.

From 35d5a5081c6b95690276f43d78e965792d7b3dd6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 28 Jun 2024 12:26:54 -0600
Subject: [PATCH 0602/1248] Update Change files

---
 doc/ChangeLog | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  7 +++---
 2 files changed, 72 insertions(+), 3 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 05b43c20ab..2ab7676ddc 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,72 @@
 ===============================================================
+Tag name: ctsm5.2.008
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Fri 28 Jun 2024 12:22:46 PM MDT
+One-line Summary: Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
+
+Purpose and description of changes
+----------------------------------
+
+Bring in changes that came in on the tmp-240620 branch to master now that cesm3_0_beta01 has
+been made. The changes are documented in below but include the following tags:
+
+  tmp-240620.n03.ctsm5.2.007 samrabin -- upland hillslope column fsat values to zero
+  tmp-240620.n02.ctsm5.2.007 erik ------ Another update of git-fleximod
+  tmp-240620.n01.ctsm5.2.007 slevis ---- Merge b4b-dev
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+Notes of particular relevance for users
+---------------------------------------
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Testing summary:  
+----------------
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit with branch_tags/tmp-240620.n03.ctsm5.2.007
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+===============================================================
+===============================================================
 Tag name: tmp-240620.n03.ctsm5.2.007
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Thu Jun 27 14:17:02 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 7dd063df45..ea9417fe41 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,8 +1,9 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-tmp-240620.n03.ctsm5.2.007 samrabin 06/27/2024 Set upland hillslope column fsat values to zero
-tmp-240620.n02.ctsm5.2.007     erik 06/21/2024 Another update of git-fleximod
-tmp-240620.n01.ctsm5.2.007   slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007)
+       ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
+tmp-240620.n03.ctsm5.2.007  06/27/2024 Set upland hillslope column fsat values to zero (samrabin)
+tmp-240620.n02.ctsm5.2.007  06/21/2024 Another update of git-fleximod (erik)
+tmp-240620.n01.ctsm5.2.007  06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) (slevis)
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems

From 95bf3f82fb09d4022ac1af285569e9c1fd1aefa0 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 13:52:40 -0700
Subject: [PATCH 0603/1248] add fates harvest event expected failure

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 cime_config/testdefs/testlist_clm.xml      | 3 ++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 65419a5903..de864aeee6 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -165,6 +165,13 @@
 
   <!-- fates test suite failures -->
 
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLUH2HarvestEvent">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>FATES#1216</issue>
+    </phase>
+  </test>
+
   <test name="SMS_D_Ld3.f09_g17.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen_prescribed">
     <phase name="RUN">
       <status>FAIL</status>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 347fd33e8e..16359b88be 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2579,7 +2579,7 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestEvent">
+  <test name="ERS_D_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestEvent">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
     </machines>
@@ -2609,6 +2609,7 @@
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
+      <option name="comment">FATES land use potential vegetation spin-up to transient run mode test</option>
     </options>
   </test>
   <test name="ERS_D_Ld3" grid="f19_g17" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">

From 889cc97d4172e85edc7f6c53f4a71ec89048a4d5 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 27 Jun 2024 17:51:13 -0600
Subject: [PATCH 0604/1248] update seed dispersal test mod to put on-the-fly
 generated paramfile in the case directory

---
 .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands | 2 +-
 .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
index 94a832af25..db5a1f8672 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
@@ -1,7 +1,7 @@
 SRCDIR=`./xmlquery SRCROOT --value`
 CASEDIR=`./xmlquery CASEROOT --value`
 FATESDIR=$SRCDIR/src/fates/
-FATESPARAMFILE=$SRCDIR/fates_params_seeddisp_4x5.nc
+FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc
 
 ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
 
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
index e8d24253c1..ecd1dc8b57 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
@@ -1,3 +1,3 @@
-fates_paramfile = '$SRCROOT/fates_params_seeddisp_4x5.nc'
+fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc'
 fates_seeddisp_cadence = 1
 hist_fincl1       = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF'

From f58cd7ee463f5ad7d8838a618f6e51bc7c37fb07 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 27 Jun 2024 23:43:20 -0600
Subject: [PATCH 0605/1248] reinstate fates-landuse as a second, shorter test
 list

---
 cime_config/testdefs/testlist_clm.xml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 16359b88be..68862c0dce 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2565,6 +2565,7 @@
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates-landuse"/>
       <machine name="izumi" compiler="nag" category="fates"/>
     </machines>
     <options>
@@ -2574,6 +2575,7 @@
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestArea">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates-landuse"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2582,6 +2584,7 @@
   <test name="ERS_D_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestEvent">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates-landuse"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2590,6 +2593,7 @@
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestMass">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates-landuse"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2598,6 +2602,7 @@
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestSurf">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates-landuse"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2606,6 +2611,7 @@
   <test name="PVT_Lm3" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesLUPFT">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates-landuse"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>

From 9465da6202b0fd2ca8cbd9d39b6ffb5cc2e9f1e0 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 27 Jun 2024 23:44:49 -0600
Subject: [PATCH 0606/1248] fix luh2 harvest testmod

---
 .../testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm      | 2 +-
 .../testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm
index d760105e68..426b41b49e 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = luhdata_area
+fates_harvest_mode = 'luhdata_area'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm
index bb5f30f75d..7b6bc24f5a 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = luhdata_mass
+fates_harvest_mode = 'luhdata_mass'

From c2deb25a278e7b177c47b5ae189f1c8697cd8d58 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 27 Jun 2024 23:48:18 -0600
Subject: [PATCH 0607/1248] rename fates landuse to luh2harvestevent

---
 .../testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm     | 3 ++-
 .../testmods_dirs/clm/FatesColdLandUse/include_user_mods       | 1 -
 .../testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm    | 2 --
 3 files changed, 2 insertions(+), 4 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
index 61e1daaa93..a23336f36c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
@@ -1 +1,2 @@
-fates_harvest_mode = surfdata_file
+flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_hist_16_CMIP6_1850-2015_c230620.nc'
+fates_harvest_mode = 'surfdata_file'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods
deleted file mode 100644
index 14f7591b72..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../FatesCold
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm
deleted file mode 100644
index 668f9c861d..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm
+++ /dev/null
@@ -1,2 +0,0 @@
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_hist_16_CMIP6_1850-2015_c230620.nc'
-do_harvest = .true.

From 4d0b49a81fa68653ba92ca59cfdd791cc053378a Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 12:32:36 -0600
Subject: [PATCH 0608/1248] fix fates harvest event code testmod

---
 .../testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm
index c0e1c476be..d2079d9e43 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm
@@ -1 +1 @@
-fates_harvest_mode = event_code
+fates_harvest_mode = 'event_code'

From 387ac5ed9163f77bd037ff8f935e56e73a832702 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:49:55 -0600
Subject: [PATCH 0609/1248] add description to flandusepftdat definition

---
 bld/namelist_files/namelist_definition_ctsm.xml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index c12cb75ab6..fd3020f320 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -826,7 +826,13 @@ types to vary over time.
 
 <entry id="flandusepftdat" type="char*256" category="datasets"
        input_pathname="abs" group="clm_inparm" valid_values="" >
-Full pathname of fates landuse x pft static data map.
+Full pathname of fates landuse x pft association static data map.  
+The file associates land use types with pfts across a static global map.
+This file is necessary for running FATES with use_fates_luh, 
+use_fates_nocomp, and use_fates_fixedbiogeo engaged.  The file is output
+by the FATES land use data tool (https://github.com/NGEET/tools-fates-landusedata)
+which processes the raw land use data from the THEMIS tool data sets
+(https://doi.org/10.5065/29s7-7b41)
 </entry>
 
 <entry id="use_luna" type="logical" category="physics"

From 16a922310c009ecb9b8193b0a3988e6a6a68d91b Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:04:09 -0700
Subject: [PATCH 0610/1248] update flandusepftdat description with note about
 use_fates_lupft

---
 bld/namelist_files/namelist_definition_ctsm.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index fd3020f320..fb4f5d07a9 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -829,7 +829,8 @@ types to vary over time.
 Full pathname of fates landuse x pft association static data map.  
 The file associates land use types with pfts across a static global map.
 This file is necessary for running FATES with use_fates_luh, 
-use_fates_nocomp, and use_fates_fixedbiogeo engaged.  The file is output
+use_fates_nocomp, and use_fates_fixedbiogeo engaged (note that use_fates_lupft
+is provided as a namelist option to engage all necessary options).  The file is output
 by the FATES land use data tool (https://github.com/NGEET/tools-fates-landusedata)
 which processes the raw land use data from the THEMIS tool data sets
 (https://doi.org/10.5065/29s7-7b41)

From f985fbafafd5710e944d7715522966e042743361 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:23:29 -0700
Subject: [PATCH 0611/1248] rename misleading surfdata_file option name to the
 landuse_timeseries

---
 bld/CLMBuildNamelist.pm                                    | 4 ++--
 bld/namelist_files/namelist_definition_ctsm.xml            | 7 ++++---
 .../testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm | 2 +-
 src/dyn_subgrid/dynFATESLandUseChangeMod.F90               | 2 +-
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index c336d41ca9..0fb7963c67 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4652,7 +4652,7 @@ sub setup_logic_fates {
               if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
                 $log->fatal_error("use_fates_luh is required to be true when $var is luhdata_mass or luhdata_area" );
               }
-           } elsif ( $mode  eq 'surfdata_file' ) {
+           } elsif ( $mode  eq 'landuse_timeseries' ) {
               # Check to make sure that the user set the flanduse_timeseries file
               # Since the flanduse_timeseries logic checking is upstream of the fates logic,
               # don't add the default here.  The onus is on the user to match the correct timeseries
@@ -4660,7 +4660,7 @@ sub setup_logic_fates {
               my $var = "flanduse_timeseries";
               my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
               if ( ! defined($nl->get_value($var))  ) {
-                $log->fatal_error("$var is required when fates_harvest_mode is surfdata_file" );
+                $log->fatal_error("$var is required when fates_harvest_mode is landuse_timeseries" );
               } elsif ( ! -f "$fname" ) {
                 $log->fatal_error("$var does NOT point to a valid filename" );
               }
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index fb4f5d07a9..046de32c11 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -734,15 +734,16 @@ Toggle to turn on no competition mode (only relevant if FATES is being used).
 Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used).                        
 </entry>
 
-<entry id="fates_harvest_mode" type="char*13" category="physics"
-        group="clm_inparm" valid_values="no_harvest,event_code,surfdata_file,luhdata_area,luhdata_mass">
+<entry id="fates_harvest_mode" type="char*18" category="physics"
+        group="clm_inparm" valid_values="no_harvest,event_code,landuse_timeseries,luhdata_area,luhdata_mass">
 Set FATES harvesting mode by setting fates_harvest_mode to a valid string option.
 Allowed values are:
  no_harvest: no fates harvesting of any kind
  event_code: fates logging via fates logging event codes (see fates parameter file) only
- surfdata_file: fates harvest driven by CLM landuse timeseries data (dynHarvestMod)
+ landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod)
  luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
  luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
+Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file.
 </entry>
 
 <entry id="use_fates_planthydro" type="logical" category="physics"
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
index a23336f36c..b27a74031c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
@@ -1,2 +1,2 @@
 flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_hist_16_CMIP6_1850-2015_c230620.nc'
-fates_harvest_mode = 'surfdata_file'
+fates_harvest_mode = 'landuse_timeseries'
diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
index d7c1063494..b440b55dc9 100644
--- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
+++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
@@ -37,7 +37,7 @@ module dynFATESLandUseChangeMod
   ! Define the fates landuse namelist mode switch values
   character(len=13), public, parameter    :: fates_harvest_no_logging   = 'no_harvest'
   character(len=13), public, parameter    :: fates_harvest_logging_only = 'event_code'
-  character(len=13), public, parameter    :: fates_harvest_clmlanduse   = 'surfdata_file'
+  character(len=13), public, parameter    :: fates_harvest_clmlanduse   = 'landuse_timeseries'
   character(len=13), public, parameter    :: fates_harvest_luh_area     = 'luhdata_area'
   character(len=13), public, parameter    :: fates_harvest_luh_mass     = 'luhdata_mass'
 

From 31803d9fbc743ccd4350af112b4266cffe36bcb1 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:25:37 -0700
Subject: [PATCH 0612/1248] add language about age and possible future
 deprication of landuse_timeseries option

---
 bld/namelist_files/namelist_definition_ctsm.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 046de32c11..9b495ccda4 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -744,6 +744,7 @@ Allowed values are:
  luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
  luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
 Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file.
+This option is older than the luhdata options and may be depricated at some point in the future.
 </entry>
 
 <entry id="use_fates_planthydro" type="logical" category="physics"

From 3ff5f4a533daff344b32c26e015338b0ebf565ed Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:29:38 -0700
Subject: [PATCH 0613/1248] fix copy/paste typo

---
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 9b495ccda4..b80bbda2d6 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -806,7 +806,7 @@ This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harv
 </entry>
 
 <entry id="use_fates_lupft" type="logical" category="physics"
-       group="elm_inparm" valid_values="" value=".false.">
+       group="clm_inparm" valid_values="" value=".false.">
 If TRUE, enable use of fates land use x pft mapping data file.
 (Only valid for use_fates = true and is incompatible with transient runs currently.)
 </entry>

From 32b2554189d6cbdb11361ed376eb53c4bb8d2857 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:32:39 -0700
Subject: [PATCH 0614/1248] add clarifying language for use_fates_potentialveg

---
 bld/namelist_files/namelist_definition_ctsm.xml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index b80bbda2d6..bbc860df6c 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -814,7 +814,9 @@ If TRUE, enable use of fates land use x pft mapping data file.
 <entry id="use_fates_potentialveg" type="logical" category="physics"
        group="clm_inparm" valid_values="" >
 If TRUE, ignore the land-use state vector and transitions, and assert that all lands
-are primary, and that there is no harvest.
+are primary, and that there is no harvest.  This mode is only relevant for FATES
+spin-up workflows that are intending to use the spin-up restart output to start a
+FATES land use transient case using the use_fates_lupft namelist option.
 </entry>
 
 <!-- This could eventually be included in the "dynamic_subgrid" -->

From aaaff224b18585a4f93c4b83595b2017ee96f607 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:40:32 -0700
Subject: [PATCH 0615/1248] add clearer instructions about when to
 use_fates_potentialveg

---
 bld/namelist_files/namelist_definition_ctsm.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index bbc860df6c..252d83aa21 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -816,7 +816,8 @@ If TRUE, enable use of fates land use x pft mapping data file.
 If TRUE, ignore the land-use state vector and transitions, and assert that all lands
 are primary, and that there is no harvest.  This mode is only relevant for FATES
 spin-up workflows that are intending to use the spin-up restart output to start a
-FATES land use transient case using the use_fates_lupft namelist option.
+FATES land use transient case using the use_fates_lupft namelist option.  The option
+should be set to true for the spin-up case and false for the transient case.
 </entry>
 
 <!-- This could eventually be included in the "dynamic_subgrid" -->

From f6f7b2d135253f5a13dbd6e5ae66328a01c97d76 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:45:13 -0700
Subject: [PATCH 0616/1248] add language explaining what use_fates_lupft does

---
 bld/namelist_files/namelist_definition_ctsm.xml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 252d83aa21..5a478f0bfa 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -807,7 +807,9 @@ This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harv
 
 <entry id="use_fates_lupft" type="logical" category="physics"
        group="clm_inparm" valid_values="" value=".false.">
-If TRUE, enable use of fates land use x pft mapping data file.
+If TRUE, enable use of FATES land use with no competition and fixed biogeography.  This mode
+requires the use of the land use x pft association static data map file.  See the
+flandusepftdat definition entry in this file for more information.
 (Only valid for use_fates = true and is incompatible with transient runs currently.)
 </entry>
 

From 2539cea91b481f4680e2696c6c517df3d952befa Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 28 Jun 2024 16:31:36 -0700
Subject: [PATCH 0617/1248] add readme to FatesLUPFT test mod

---
 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README
new file mode 100644
index 0000000000..88f5c2c8fb
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README
@@ -0,0 +1,9 @@
+This test mod does not use cold start and is intended to 
+be used in conjunction with a test workflow that provides
+an initialization file.  Currently this is accomplished
+by using the test mod in conjunction with the PVT
+system test.  The PVT system test runs a FATES spin-up 
+case using the use_fates_potentialveg mode and then
+references the restart output to run a use_fates_lupft
+transient mode case.
+

From bf46d33d289f85077082dc01ec79c1945c42c3f4 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sun, 30 Jun 2024 23:04:07 -0700
Subject: [PATCH 0618/1248] update fates logging test with new harvest event
 code

Remove duplicate and misnamed FatesColdLUH2HarvestEvent
---
 .../clm/FatesColdLUH2HarvestEvent/include_user_mods            | 1 -
 .../testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm    | 1 -
 .../testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm    | 3 +--
 3 files changed, 1 insertion(+), 4 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods
deleted file mode 100644
index 7eb8bb1579..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm
deleted file mode 100644
index d2079d9e43..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm
+++ /dev/null
@@ -1 +0,0 @@
-fates_harvest_mode = 'event_code'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm
index 5f457f3f1c..d2079d9e43 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm
@@ -1,2 +1 @@
-! TODO SSR: Replace this with fates_harvest_mode
-use_fates_logging= .true.
+fates_harvest_mode = 'event_code'

From 96d1a78b3c28c9f1bc8185e646f6a4f975236a42 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sun, 30 Jun 2024 23:07:59 -0700
Subject: [PATCH 0619/1248] reinstate FatesColdLandUse

This will provide continuity to the previous test and fixes the
incorrect use of FatesColdLUH2 as the test to inherit from
---
 .../testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods | 1 -
 .../testmods_dirs/clm/FatesColdLandUse/include_user_mods         | 1 +
 .../{FatesColdLUH2HarvestSurf => FatesColdLandUse}/user_nl_clm   | 0
 3 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods
 rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2HarvestSurf => FatesColdLandUse}/user_nl_clm (100%)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods
deleted file mode 100644
index 7eb8bb1579..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../FatesColdLUH2
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods
new file mode 100644
index 0000000000..14f7591b72
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods
@@ -0,0 +1 @@
+../FatesCold
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm
rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm

From f47e2bfe035571268743f5bed11b2b97169d31e0 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sun, 30 Jun 2024 23:10:43 -0700
Subject: [PATCH 0620/1248] remove duplicate tests

---
 cime_config/testdefs/testlist_clm.xml | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 68862c0dce..272d4093d8 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2581,15 +2581,6 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestEvent">
-    <machines>
-      <machine name="derecho" compiler="intel" category="fates"/>
-      <machine name="derecho" compiler="intel" category="fates-landuse"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-    </options>
-  </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestMass">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
@@ -2599,15 +2590,6 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2HarvestSurf">
-    <machines>
-      <machine name="derecho" compiler="intel" category="fates"/>
-      <machine name="derecho" compiler="intel" category="fates-landuse"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-    </options>
-  </test>
   <test name="PVT_Lm3" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesLUPFT">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>

From 6dd55eeef55c093e53f500867d516df1beb16f39 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 1 Jul 2024 11:31:06 -0600
Subject: [PATCH 0621/1248] Update .gitmodules with new cismwrapper, cmeps, and
 ccs_config tags

---
 .gitmodules      | 12 ++++++------
 ccs_config       |  2 +-
 components/cism  |  2 +-
 components/cmeps |  2 +-
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 6d4298befc..eb2a0980f4 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,8 +7,8 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release
 
 [submodule "cism"]
 path = components/cism
-url = https://github.com/mvertens/CISM-wrapper
-fxtag = 34339777afa7b810fd4822fce1039826668b33e4
+url = https://github.com/ESCOMP/CISM-wrapper
+fxtag = cismwrap_2_2_001
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 
@@ -35,8 +35,8 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
         
 [submodule "ccs_config"]
 path = ccs_config
-url = https://github.com/mvertens/ccs_config_cesm.git
-fxtag = dbb02c0ccd1492fe278885f8a07a71fa80064319
+url = https://github.com/ESMCI/ccs_config_cesm.git
+fxtag = ccs_config_cesm0.0.110
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
@@ -49,8 +49,8 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
-url = https://github.com/mvertens/CMEPS.git
-fxtag = 4dca7c602e54189b74b1d0195c433d1b83475553
+url = https://github.com/ESCOMP/CMEPS.git
+fxtag = cmeps0.14.67
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
diff --git a/ccs_config b/ccs_config
index dbb02c0ccd..c30a283155 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit dbb02c0ccd1492fe278885f8a07a71fa80064319
+Subproject commit c30a2831556f269675971b11c5c156ea92599878
diff --git a/components/cism b/components/cism
index 34339777af..c05dd5c4fc 160000
--- a/components/cism
+++ b/components/cism
@@ -1 +1 @@
-Subproject commit 34339777afa7b810fd4822fce1039826668b33e4
+Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928
diff --git a/components/cmeps b/components/cmeps
index 4dca7c602e..90f815ba9e 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 4dca7c602e54189b74b1d0195c433d1b83475553
+Subproject commit 90f815ba9e7493d71043b5d8e627a3f20bd5dc78

From fb9529577c1e1f294cce17c0a0285f78b98554ce Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 1 Jul 2024 12:59:23 -0600
Subject: [PATCH 0622/1248] Update cismwrapper tag to the correct new one

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index eb2a0980f4..615de28b6f 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -8,7 +8,7 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_001
+fxtag = cismwrap_2_2_002
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 

From de1b44ca4c9ef7c9116b41f1969a7998bcf21a84 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 1 Jul 2024 13:01:37 -0600
Subject: [PATCH 0623/1248] Ran ./bin/git-fleximod update, so now update the
 cism module itself

---
 components/cism | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/cism b/components/cism
index c05dd5c4fc..c84cc9f5b3 160000
--- a/components/cism
+++ b/components/cism
@@ -1 +1 @@
-Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928
+Subproject commit c84cc9f5b3103766a35d0a7ddd5e9dbd7deae762

From e1b2bdabb4b2c74a27bbf12d4cca677452396de7 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Tue, 2 Jul 2024 17:03:19 -0600
Subject: [PATCH 0624/1248] Correct the tags that I used for ccs_config and
 cmeps

---
 .gitmodules      | 4 ++--
 ccs_config       | 2 +-
 components/cmeps | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 615de28b6f..897824e9cc 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm0.0.110
+fxtag = ccs_config_cesm1.0.0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
@@ -50,7 +50,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps0.14.67
+fxtag = cmeps0.14.77
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
diff --git a/ccs_config b/ccs_config
index c30a283155..69a958581e 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit c30a2831556f269675971b11c5c156ea92599878
+Subproject commit 69a958581ecd2d32ee9cb1c38bcd3847b8b920bf
diff --git a/components/cmeps b/components/cmeps
index 90f815ba9e..47fb4e633a 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 90f815ba9e7493d71043b5d8e627a3f20bd5dc78
+Subproject commit 47fb4e633a76ec6d60969b1af751f90790387246

From 0e6eed5f399eb85744410ecf1962c0416c7846ba Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 5 Jul 2024 10:57:34 -0700
Subject: [PATCH 0625/1248] Revert "update seed dispersal test mod to put
 on-the-fly generated paramfile in the case directory"

This reverts commit 889cc97d4172e85edc7f6c53f4a71ec89048a4d5.
I forgot that #2322 prevents this from working.
---
 .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands | 2 +-
 .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
index db5a1f8672..94a832af25 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
@@ -1,7 +1,7 @@
 SRCDIR=`./xmlquery SRCROOT --value`
 CASEDIR=`./xmlquery CASEROOT --value`
 FATESDIR=$SRCDIR/src/fates/
-FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc
+FATESPARAMFILE=$SRCDIR/fates_params_seeddisp_4x5.nc
 
 ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
 
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
index ecd1dc8b57..e8d24253c1 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
@@ -1,3 +1,3 @@
-fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc'
+fates_paramfile = '$SRCROOT/fates_params_seeddisp_4x5.nc'
 fates_seeddisp_cadence = 1
 hist_fincl1       = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF'

From 8ae9c3329165f8f5f63cd35a415e3ba9478d52f8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 5 Jul 2024 13:53:49 -0600
Subject: [PATCH 0626/1248] Add cam7 lnd_tuning moode options and settings

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 468 ++++++++++++++++++
 .../namelist_definition_ctsm.xml              |   4 +-
 bld/unit_testers/build-namelist_test.pl       |   4 +-
 3 files changed, 472 insertions(+), 4 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e04db59cae..8656389103 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -243,18 +243,24 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >30.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_CRUv7"
 >30.0d00</rh_low>
+<rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam7.0"
+>20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam6.0"
 >20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam5.0"
 >20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam4.0"
 >20.0d00</rh_low>
+<rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam7.0"
+>20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam6.0"
 >20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam5.0"
 >20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam4.0"
 >20.0d00</rh_low>
+<rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm6_0_cam7.0"
+>20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm6_0_cam6.0"
 >20.0d00</rh_low>
 <rh_low                   fire_method="li2016crufrc" lnd_tuning_mode="clm6_0_cam5.0"
@@ -274,18 +280,24 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >0.010d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_CRUv7"
 >0.010d00</pot_hmn_ign_counts_alpha>
+<pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam7.0"
+>0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam6.0"
 >0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam5.0"
 >0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_0_cam4.0"
 >0.008d00</pot_hmn_ign_counts_alpha>
+<pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam7.0"
+>0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam6.0"
 >0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam5.0"
 >0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm5_1_cam4.0"
 >0.008d00</pot_hmn_ign_counts_alpha>
+<pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm6_0_cam7.0"
+>0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm6_0_cam6.0"
 >0.008d00</pot_hmn_ign_counts_alpha>
 <pot_hmn_ign_counts_alpha fire_method="li2016crufrc" lnd_tuning_mode="clm6_0_cam5.0"
@@ -634,6 +646,65 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- ==================================
      For an exact match for these grids
 ======================================== -->
+<!--
+     clm5_0 physics with CAM7.0 grids...
+-->
+<!-- These first five are for SP mode and CLM5.0 only -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="0.9x1.25"            >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"             >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTICGRIS.ne30x8">.true.</use_init_interp>
+<!-- 2003 -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2003" lnd_tuning_mode="clm5_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"                 >.true.</use_init_interp>
+
+<!-- 2013 -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm5_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4CONUS.ne30x8"      >.true.</use_init_interp>
+<!--
+     clm5_1 physics with CAM7.0 grids...
+-->
+<!-- These first five are for SP mode and CLM5.1 only -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="0.9x1.25"            >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"             >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTICGRIS.ne30x8">.true.</use_init_interp>
+<!-- 2003 -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2003" lnd_tuning_mode="clm5_1_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"                 >.true.</use_init_interp>
+
+<!-- 2013 -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm5_1_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4CONUS.ne30x8"      >.true.</use_init_interp>
+
+<!--
+     clm6_0 physics with CAM7.0 grids...
+-->
+<!-- These first five are for SP mode and CLM6.0 only -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="0.9x1.25"            >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"             >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTICGRIS.ne30x8">.true.</use_init_interp>
+<!-- 2003 -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2003" lnd_tuning_mode="clm6_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"                 >.true.</use_init_interp>
+
+<!-- 2013 -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm6_0_cam7.0"
+                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4CONUS.ne30x8"      >.true.</use_init_interp>
+
 <!--
      clm5_0 physics with CAM6.0 grids...
 -->
@@ -701,6 +772,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- For an inexact match use either low resolution or high resolution match for SP or BGC mode CLM4.5 -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2000"  lnd_tuning_mode="clm4_5_GSWP3v1"  >.true.</use_init_interp>
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2000"  lnd_tuning_mode="clm4_5_CRUv7"    >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979"  lnd_tuning_mode="clm4_5_cam7.0"   >.true.</use_init_interp>
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979"  lnd_tuning_mode="clm4_5_cam6.0"   >.true.</use_init_interp>
 <!-- Let CAM4 and CAM5 lnd_tuning mode be FALSE (so do a coldstart) -->
 <!-- Yes, the phys setting is essentially duplicated here but it is needed to ensure this is used and isn't matched above -->
@@ -734,6 +806,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam7.0"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam6.0"
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
@@ -755,6 +831,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
@@ -777,6 +857,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam7.0"
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam6.0"
 >hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
@@ -800,6 +884,150 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 <!-- specific low resolution grids should use the 1-degree file for just CLM5.0 -->
+<!-- matches for clm5_0 physics with CAM7.0 -->
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+                        hgrid="0.9x1.25"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+                        hgrid="4x5"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+                        hgrid="10x15"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="1.9x2.5"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="ne3np4.pg3"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="ne5np4.pg3"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="ne16np4"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="ne16np4.pg3"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="ne30np4"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="C24"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="C48"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="C96"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<!-- clm5_1 physics -->
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_cam7.0"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<!-- clm6_0 physics -->
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<!-- MPAS -->
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="mpasa480"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="mpasa240"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="mpasa120"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+			hgrid="mpasa60"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+            hgrid="mpasa30"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+            hgrid="mpasa15"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+
+<!-- Anything else should use the high resolution file, but just for CLM5.0 -->
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+>hgrid=ne120np4.pg3 maxpft=79 mask=tx0.1v3 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+
+<!-- If an exact match for these grids and start years -->
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+                        hgrid="0.9x1.25" use_cn=".false." maxpft="17"
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+                        hgrid="1.9x2.5" use_cn=".false." maxpft="17"
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+                        hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
+>hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+                        hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
+>hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<!-- 2003 -->
+<init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
+                        hgrid="1.9x2.5" use_cn=".false." maxpft="17"
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<!-- 2013 IC's - exact match for CONUS grid ... -->
+<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
+>hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+
+
 <!-- matches for clm5_0 physics with CAM6.0 -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="0.9x1.25"
@@ -961,6 +1189,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.I1850Clm45BgcCruGs.1101-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
+<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+         lnd_tuning_mode="clm4_5_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.B1850Clm45BgcGs.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
+</finidat>
+
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
@@ -992,6 +1227,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCropCru-ciso.1526-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
 </finidat>
 
+<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
+</finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
@@ -1066,6 +1307,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 
+<!-- Present day no crop spinup f09/f19 grid with irrigation on -->
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm4_5_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+</finidat>
+
 <!-- Present day no crop spinup f09/f19 grid with irrigation on -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
@@ -1074,6 +1323,213 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
+<!--
+     finidat files for CAM resolutions for being coupled to CAM
+-->
+<!-- clm5_0 -->
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+</finidat>
+
+<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day no crop spinup ARCTIC grid with irrigation on -->
+<finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
+<finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
+<finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
+</finidat>
+
+<!-- Present day for coupled cases at low resolution -->
+<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+</finidat>
+
+<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+</finidat>
+
+<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+</finidat>
+
+<!-- 2003 -->
+<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
+</finidat>
+
+
+<!-- 2013 -->
+<finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
+</finidat>
+<!-- Repeat above for clm5_1 -->
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+</finidat>
+
+<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day no crop spinup ARCTIC grid with irrigation on -->
+<finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
+<finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
+<finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
+</finidat>
+
+<!-- Present day for coupled cases at low resolution -->
+<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+</finidat>
+
+<!-- 2003 -->
+<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
+</finidat>
+
+
+<!-- 2013 -->
+<finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
+</finidat>
+<!-- Repeat above for clm6_0 -->
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+</finidat>
+
+<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day no crop spinup ARCTIC grid with irrigation on -->
+<finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
+<finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
+</finidat>
+
+<!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
+<finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
+</finidat>
+
+<!-- Present day for coupled cases at low resolution -->
+<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+</finidat>
+
+<!-- 2003 -->
+<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
+</finidat>
+
+
+<!-- 2013 -->
+<finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
+</finidat>
+
 <!--
      finidat files for CAM resolutions for being coupled to CAM
 -->
@@ -1951,6 +2407,12 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <dust_emis_method>Zender_2003</dust_emis_method>
 <zender_soil_erod_source dust_emis_method="Zender_2003">atm</zender_soil_erod_source>
 <zendersoilerod_mapalgo>bilinear</zendersoilerod_mapalgo>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam6.0"
@@ -1975,6 +2437,12 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam4.0" hgrid="0.9x1.25"
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam6.0"
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 1a6a5581a8..02b7356b52 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -2040,10 +2040,10 @@ hist means do NOT use a future scenario, just use historical data.
 Land mask description
 </entry> 
 
-<!-- lnd_tuning_mode, there needs to be a setting for: CRUv7, GSWP3v1, and cam6.0 for each valid physics option -->
+<!-- lnd_tuning_mode, there needs to be a setting for: CRUv7, GSWP3v1, cam6.0, and cam7.0 for each valid physics option -->
 <entry id="lnd_tuning_mode" type="char*20" category="default_settings"
        group="default_settings"
-       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm4_5_cam5.0,clm4_5_cam4.0,clm5_0_cam6.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_CRUv7,clm5_1_cam6.0,clm5_1_cam5.0,clm5_1_cam4.0,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam5.0,clm6_0_cam4.0">
+       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam7.0,clm4_5_cam6.0,clm4_5_cam5.0,clm4_5_cam4_0,clm5_0_cam7.0,clm5_0_cam6.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_CRUv7,clm5_1_cam7.0,clm5_1_cam6.0,clm5_1_cam5.0,clm5_1_cam4.0,clm6_0_GSWP3v1,clm6_0_cam7.0,clm6_0_cam6.0,clm6_0_cam5.0,clm6_0_cam4.0">
 General configuration of model version and atmospheric forcing to tune the model to run under.
 This sets the model to run with constants and initial conditions that were set to run well under 
 the configuration of model version and atmospheric forcing. To run well constants would need to be changed
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 53c71ae0e9..2147fdea31 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3254;
+my $ntests = 3278;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2001;
@@ -1802,7 +1802,7 @@ sub cat_and_create_namelistinfile {
   my $mode = "-phys $phys";
   &make_config_cache($phys);
   my @forclist = ();
-  @forclist = ( "CRUv7", "GSWP3v1", "cam6.0", "cam5.0", "cam4.0" );
+  @forclist = ( "CRUv7", "GSWP3v1", "cam7.0", "cam6.0", "cam5.0", "cam4.0" );
   foreach my $forc ( @forclist ) {
      foreach my $bgc ( "sp", "bgc" ) {
         my $lndtuningmode = "${phys}_${forc}";

From f303264ff62cfc0f9752573a0bc404573287c787 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 5 Jul 2024 15:11:58 -0600
Subject: [PATCH 0627/1248] Fix cam4.0 clm4_5 lnd_tuning_mode name

---
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 02b7356b52..5e65a3a603 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -2043,7 +2043,7 @@ Land mask description
 <!-- lnd_tuning_mode, there needs to be a setting for: CRUv7, GSWP3v1, cam6.0, and cam7.0 for each valid physics option -->
 <entry id="lnd_tuning_mode" type="char*20" category="default_settings"
        group="default_settings"
-       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam7.0,clm4_5_cam6.0,clm4_5_cam5.0,clm4_5_cam4_0,clm5_0_cam7.0,clm5_0_cam6.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_CRUv7,clm5_1_cam7.0,clm5_1_cam6.0,clm5_1_cam5.0,clm5_1_cam4.0,clm6_0_GSWP3v1,clm6_0_cam7.0,clm6_0_cam6.0,clm6_0_cam5.0,clm6_0_cam4.0">
+       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam7.0,clm4_5_cam6.0,clm4_5_cam5.0,clm4_5_cam4.0,clm5_0_cam7.0,clm5_0_cam6.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_CRUv7,clm5_1_cam7.0,clm5_1_cam6.0,clm5_1_cam5.0,clm5_1_cam4.0,clm6_0_GSWP3v1,clm6_0_cam7.0,clm6_0_cam6.0,clm6_0_cam5.0,clm6_0_cam4.0">
 General configuration of model version and atmospheric forcing to tune the model to run under.
 This sets the model to run with constants and initial conditions that were set to run well under 
 the configuration of model version and atmospheric forcing. To run well constants would need to be changed

From 4670b6e2c3df9af6d03eb900cd0eed4877eaab59 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 5 Jul 2024 15:57:35 -0600
Subject: [PATCH 0628/1248] Allow a C or E to follow the period, which is
 needed by cesm3 all active compsets

---
 cime_config/config_component.xml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index d69bdbc302..859883db8e 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -199,22 +199,22 @@
     <default_value>UNSET</default_value>
     <values>
       <!-- Use SSP5-8.5 for PI to PDAY so will have data up to the current year available (for WACCM compsets that use PDAY) -->
-      <value compset="^2010_"                       >2010_control</value>
-      <value compset="^2000_"                	    >2000_control</value>
-      <value compset="^1850_"		            >1850_control</value>
+      <value compset="^2010[CE]+_"                  >2010_control</value>
+      <value compset="^2000[CE]+_"                  >2000_control</value>
+      <value compset="^1850[CE]+_"		    >1850_control</value>
       <value compset="^1850_.*_CLM60%[^_]*NOANTHRO" >1850_noanthro_control</value>
       <value compset="^1850_.*_CLM50%[^_]*NOANTHRO" >1850_noanthro_control</value>
-      <value compset="^HIST_"                       >20thC_transient</value>
-      <value compset="^SSP585_"	                    >1850-2100_SSP5-8.5_transient</value>
-      <value compset="^SSP126_"	                    >1850-2100_SSP1-2.6_transient</value>
-      <value compset="^SSP370_"	                    >1850-2100_SSP3-7.0_transient</value>
-      <value compset="^SSP534_"	                    >1850-2100_SSP5-3.4_transient</value>
-      <value compset="^SSP245_"	                    >1850-2100_SSP2-4.5_transient</value>
+      <value compset="^HIST[CE]+_"                  >20thC_transient</value>
+      <value compset="^SSP585[CE]+_"	            >1850-2100_SSP5-8.5_transient</value>
+      <value compset="^SSP126[CE]+_"	            >1850-2100_SSP1-2.6_transient</value>
+      <value compset="^SSP370[CE]+_"	            >1850-2100_SSP3-7.0_transient</value>
+      <value compset="^SSP534[CE]+_"	            >1850-2100_SSP5-3.4_transient</value>
+      <value compset="^SSP245[CE]+_"	            >1850-2100_SSP2-4.5_transient</value>
       <value compset="^HIST" grid="ne0np4"          >1850-2100_SSP2-4.5_transient</value>
-      <value compset="^SSP119_"	                    >1850-2100_SSP1-1.9_transient</value>
-      <value compset="^SSP434_"	                    >1850-2100_SSP4-3.4_transient</value>
-      <value compset="^SSP460_"	                    >1850-2100_SSP4-6.0_transient</value>
-      <value compset="^SSP585_"	                    >1850-2100_SSP5-8.5_transient</value>
+      <value compset="^SSP119[CE]+_"	            >1850-2100_SSP1-1.9_transient</value>
+      <value compset="^SSP434[CE]+_"	            >1850-2100_SSP4-3.4_transient</value>
+      <value compset="^SSP460[CE]+_"	            >1850-2100_SSP4-6.0_transient</value>
+      <value compset="^SSP585[CE]+_"	            >1850-2100_SSP5-8.5_transient</value>
       <value compset="^AMIP_"	                    >20thC_transient</value>
       <value compset="^PIPD_"                       >1850-2100_SSP5-8.5_transient</value>
     </values>

From 03fb25a2a6d94753d7abbb4300fa32b917883969 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 5 Jul 2024 16:18:47 -0600
Subject: [PATCH 0629/1248] Two new tests in testlist_clm and two new tests in
 expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 15 +++++++++++++++
 cime_config/testdefs/testlist_clm.xml      | 20 ++++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 664b1c8e35..59802d9109 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -44,6 +44,21 @@
   </test>
 
   <!-- aux_clm test suite failures -->
+  <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn">
+    <phase name="BASELINE">
+      <status>FAIL</status>
+      <issue>#2619</issue>
+      <comment>This failure relates to the following REP failure.</comment>
+    </phase>
+  </test>
+  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn">
+    <phase name="COMPARE_base_rep2">
+      <status>FAIL</status>
+      <issue>#2619</issue>
+      <comment>This failure relates to the preceding ERP failure.</comment>
+    </phase>
+  </test>
+
   <test name="SMS_D_Ld10.f10_f10_mg37.I2000Clm50BgcCrop.izumi_intel.clm-tracer_consistency">
     <phase name="RUN">
       <status>FAIL</status>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 625a9f3504..23cc5ebcc5 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1445,6 +1445,26 @@
       <option name="comment"  >Repeat ERP_P64x2_Lm13...monthly test with matrixcnOn</option>
     </options>
   </test>
+  <test name="REP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">02:00:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment">Repeat ERP_P64x2_Lm13...monthly test with matrixcnOn as REP test because both tests fail as reported in #2619</option>
+    </options>
+  </test>
+  <test name="REP_P64x2_Ld13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">02:00:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment">Repeat REP_P64x2_Lm13...monthly test with matrixcnOn as shorter REP_P64x2_Ld13 because the longer one fails as reported in issue #2619</option>
+    </options>
+  </test>
   <test name="ERP_P64x2_D" grid="f10_f10_mg37" compset="I2000Clm50SpRtmFl" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

From 0efd37fe16814134389b9c49a30c7c033828c462 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 5 Jul 2024 17:55:44 -0600
Subject: [PATCH 0630/1248] New testmods /matrixcnOn_Hist to use
 -ignore_warnings in IHist compsets

---
 cime_config/testdefs/ExpectedTestFails.xml    |  4 +--
 cime_config/testdefs/testlist_clm.xml         | 28 +++++++++----------
 .../clm/matrixcnOn_Hist/include_user_mods     |  1 +
 .../clm/matrixcnOn_Hist/shell_commands        |  3 ++
 4 files changed, 20 insertions(+), 16 deletions(-)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 59802d9109..1243c125c0 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -44,14 +44,14 @@
   </test>
 
   <!-- aux_clm test suite failures -->
-  <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn">
+  <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_Hist">
     <phase name="BASELINE">
       <status>FAIL</status>
       <issue>#2619</issue>
       <comment>This failure relates to the following REP failure.</comment>
     </phase>
   </test>
-  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn">
+  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_Hist">
     <phase name="COMPARE_base_rep2">
       <status>FAIL</status>
       <issue>#2619</issue>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 23cc5ebcc5..1fe5ed770d 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -548,7 +548,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn">
+  <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -794,7 +794,7 @@
       <option name="comment">Use a transient compset so we allocate and run all PFTs (non-transient cases only allocate memory for non-zero-weight PFTs)</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive--clm/matrixcnOn">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1002,7 +1002,7 @@
       <option name="comment"  >Transient case with isotopes with a December start</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart--clm/matrixcnOn">
+  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1020,7 +1020,7 @@
       <option name="comment"  >Transient case with isotopes with a December start, without Meier roughness</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1038,7 +1038,7 @@
       <option name="comment"  >Transient case with a December 1990 start, and Gross Unrepresented Land Use and Land Cover change on, with f09 datasets with non-zero GU_LULCC values</option>
     </options>
   </test>
-  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn">
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1234,7 +1234,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P48x1" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn">
+  <test name="ERP_D_P48x1" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn_Hist">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
       <machine name="izumi" compiler="nag" category="prealpha"/>
@@ -1354,7 +1354,7 @@
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
     </options>
   </test>
-  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn">
+  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1435,7 +1435,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn">
+  <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1445,7 +1445,7 @@
       <option name="comment"  >Repeat ERP_P64x2_Lm13...monthly test with matrixcnOn</option>
     </options>
   </test>
-  <test name="REP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn">
+  <test name="REP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1455,7 +1455,7 @@
       <option name="comment">Repeat ERP_P64x2_Lm13...monthly test with matrixcnOn as REP test because both tests fail as reported in #2619</option>
     </options>
   </test>
-  <test name="REP_P64x2_Ld13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn">
+  <test name="REP_P64x2_Ld13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1793,7 +1793,7 @@
       <option name="comment"  >Want a multi-year global test of transient crops; also want a multi-year transient restart test.  Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test</option>
     </options>
   </test>
-  <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn">
+  <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1849,7 +1849,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn">
+  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn_Hist">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1925,7 +1925,7 @@
       <option name="comment"  >Make sure Carbon isotopes on and off with land-use change, does NOT change answers. To verify for landuse change must go beyond a year boundary, because of #404 we can't use a December start, so need to run for beyond the year boundary.</option>
     </options>
   </test>
-  <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn">
+  <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
@@ -2369,7 +2369,7 @@
       <option name="comment"  >Want a test of the c13 and c14 timeseries that crosses the year boundary. Ideally this test would include crops (in order to cover as much code as possible combined with the c13/c14 timeseries, even though there are no direct interactions between these timeseries and crops), but crop DecStart tests currently fail because of https://github.com/ESCOMP/ctsm/issues/404 and I didn't want to add another long test just to test these options, so for now using a compset without crops. Using a compset with SGLC to avoid problems with CISM in DecStart tests; the only IHistClm50Bgc compset we have with SGLC is this Qian compset, so I'm using this one.</option>
     </options>
   </test>
-  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn">
+  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn_Hist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods
new file mode 100644
index 0000000000..a3c70cba11
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods
@@ -0,0 +1 @@
+../matrixcnOn
diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands
new file mode 100644
index 0000000000..f0547f3f26
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./xmlchange CLM_BLDNML_OPTS="-ignore_warnings" --append

From a486e86065223a882790a6078647a82c592ffdaf Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 5 Jul 2024 17:15:08 -0700
Subject: [PATCH 0631/1248] update harvest parameter variables lengths

Updating all lengths to account for the update to the clmlanduse name
option change
---
 src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
index b440b55dc9..681d39f38c 100644
--- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
+++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
@@ -35,11 +35,11 @@ module dynFATESLandUseChangeMod
   integer, public, parameter    :: num_landuse_harvest_vars = 5
 
   ! Define the fates landuse namelist mode switch values
-  character(len=13), public, parameter    :: fates_harvest_no_logging   = 'no_harvest'
-  character(len=13), public, parameter    :: fates_harvest_logging_only = 'event_code'
-  character(len=13), public, parameter    :: fates_harvest_clmlanduse   = 'landuse_timeseries'
-  character(len=13), public, parameter    :: fates_harvest_luh_area     = 'luhdata_area'
-  character(len=13), public, parameter    :: fates_harvest_luh_mass     = 'luhdata_mass'
+  character(len=18), public, parameter    :: fates_harvest_no_logging   = 'no_harvest'
+  character(len=18), public, parameter    :: fates_harvest_logging_only = 'event_code'
+  character(len=18), public, parameter    :: fates_harvest_clmlanduse   = 'landuse_timeseries'
+  character(len=18), public, parameter    :: fates_harvest_luh_area     = 'luhdata_area'
+  character(len=18), public, parameter    :: fates_harvest_luh_mass     = 'luhdata_mass'
 
   ! Define landuse harvest unit integer representation
   integer, public, parameter    :: landuse_harvest_area_units = 1

From d940ee014cb52f92cdc0da415084f349ab45abae Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Sat, 6 Jul 2024 13:00:34 -0600
Subject: [PATCH 0632/1248] Add ._r8 to hardwired constants

---
 src/biogeochem/VOCEmissionMod.F90 | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
index 9833fe3de9..7ba90fd457 100644
--- a/src/biogeochem/VOCEmissionMod.F90
+++ b/src/biogeochem/VOCEmissionMod.F90
@@ -835,13 +835,13 @@ function get_gamma_SM(btran_in)
     real(r8),intent(in) :: btran_in
     
     !!!------- the drought algorithm--------
-    real(r8), parameter :: a1 = -7.4463      
-    real(r8), parameter :: b1 = 3.2552       
+    real(r8), parameter :: a1 = -7.4463_r8
+    real(r8), parameter :: b1 = 3.2552_r8
     real(r8)            :: get_gamma_SM
-             if (btran_in >= 1.) then
+             if (btran_in >= 1._r8) then
                 get_gamma_SM = 1
              else
-                get_gamma_SM = 1/(1+b1*exp(a1*(btran_in-0.2)))
+                get_gamma_SM = 1._r8 / (1._r8 + b1 * exp(a1 * (btran_in - 0.2_r8)))
              endif 
   end function get_gamma_SM
  
@@ -968,9 +968,9 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
        topt = co1 + (co2 * (t_veg240_in-tstd0))
        if ( (ivt_in == nbrdlf_dcd_brl_shrub) ) then  ! boreal-deciduous-shrub
        ! coming from BEAR-oNS campaign willows results
-             Eopt = 7.9 * exp (0.217_r8 * (t_veg24_in-273.15_r8-24.0_r8))
+             Eopt = 7.9_r8 * exp (0.217_r8 * (t_veg24_in - 273.15_r8 - 24.0_r8))
        else if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-             Eopt = exp(0.12*(t_veg240_in-288.15_r8))
+             Eopt = exp(0.12_r8 * (t_veg240_in - 288.15_r8))
        else
              Eopt = Ceo_in * exp (co4 * (t_veg24_in-tstd0)) * exp(co4 * (t_veg240_in -tstd0))
        endif
@@ -982,13 +982,13 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     x = ( (1._r8/topt) - (1._r8/(t_veg_in)) ) / ct3
     ! for the boreal grass from BEAR-oNS campaign
     if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-        bet_arc_c3  = 95+9.49*exp(0.53*(288.15_r8-t_veg240_in))
-        if (bet_arc_c3 .gt. 300) then
-            bet_arc_c3 = 300
+        bet_arc_c3 = 95._r8 + 9.49_r8 * exp(0.53_r8 * (288.15_r8 - t_veg240_in))
+        if (bet_arc_c3 > 300._r8) then
+            bet_arc_c3 = 300._r8
         endif
-        gamma_t_LDF = Eopt * exp(bet_arc_c3*((1/303.15_r8 - 1.0_r8/(t_veg_in))/ct3))
+        gamma_t_LDF = Eopt * exp(bet_arc_c3 * ((1._r8 / 303.15_r8 - 1.0_r8 / t_veg_in) / ct3))
     else
-        gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x)/(ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
+        gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x) / (ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
     endif
     
     

From de689e418343c903193bbb4e0f7075a91a94dc1b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <ekluzek@users.noreply.github.com>
Date: Mon, 8 Jul 2024 11:23:22 -0600
Subject: [PATCH 0633/1248] Update
 bld/namelist_files/namelist_defaults_ctsm.xml

Co-authored-by: Samuel Levis <slevis@ucar.edu>
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 8656389103..e81cd6dab9 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2407,11 +2407,11 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <dust_emis_method>Zender_2003</dust_emis_method>
 <zender_soil_erod_source dust_emis_method="Zender_2003">atm</zender_soil_erod_source>
 <zendersoilerod_mapalgo>bilinear</zendersoilerod_mapalgo>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam7.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam7.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam7.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>

From f745c21641baa3cbabd0e2dbe5e734a237a31e22 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 8 Jul 2024 13:33:10 -0600
Subject: [PATCH 0634/1248] Consistency in RE and don't require a C or E

Make the Regular Expressions more consistent. Don't allow the use of
CLM51 for all options. Make CPLHIST CAM version depend on which
CLM version is used. Make sure explicit matches for CAM60 are there.
---
 cime_config/config_component.xml | 68 +++++++++++++++++---------------
 1 file changed, 36 insertions(+), 32 deletions(-)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 859883db8e..04306c0e40 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -87,10 +87,11 @@
       <value compset="DATM%CRU_CLM45"    >clm4_5_CRUv7</value>
       <value compset="DATM%GSWP3v1_CLM45">clm4_5_GSWP3v1</value>
       <value compset="CAM[^_]+_CLM45"    >clm4_5_cam6.0</value>
-      <value compset="CAM40.*_CLM45"     >clm4_5_cam4.0</value>
-      <value compset="CAM50.*_CLM45"     >clm4_5_cam5.0</value>
-      <value compset="CAM7[^_]+_CLM45"   >clm4_5_cam7.0</value>
-      <value compset="DATM%CPLHIST_CLM45">clm4_5_cam6.0</value>
+      <value compset="CAM40[^_]*_CLM45"  >clm4_5_cam4.0</value>
+      <value compset="CAM50[^_]*_CLM45"  >clm4_5_cam5.0</value>
+      <value compset="CAM60[^_]*_CLM45"  >clm4_5_cam6.0</value>
+      <value compset="CAM70[^_]*_CLM45"  >clm4_5_cam7.0</value>
+      <value compset="DATM%CPLHIST_CLM45">clm4_5_cam5.0</value>
       <value compset="DATM%QIA_CLM45"    >clm4_5_QIAN</value>
       <value compset="DATM%WISOQIA_CLM45">clm4_5_QIAN</value>
       <value compset="DATM%1PT_CLM45"    >clm4_5_1PT</value>
@@ -102,9 +103,10 @@
       <value compset="SATM_CLM50"        >clm5_0_GSWP3v1</value>
       <value compset="DATM%GSWP3v1_CLM50">clm5_0_GSWP3v1</value>
       <value compset="CAM[^_]+_CLM50"    >clm5_0_cam6.0</value>
-      <value compset="CAM40.*_CLM50"     >clm5_0_cam4.0</value>
-      <value compset="CAM50.*_CLM50"     >clm5_0_cam5.0</value>
-      <value compset="CAM7[^_]+_CLM50"   >clm5_0_cam7.0</value>
+      <value compset="CAM40[^_]*_CLM50"  >clm5_0_cam4.0</value>
+      <value compset="CAM50[^_]*_CLM50"  >clm5_0_cam5.0</value>
+      <value compset="CAM60[^_]*_CLM50"  >clm5_0_cam6.0</value>
+      <value compset="CAM70[^_]*_CLM50"  >clm5_0_cam7.0</value>
       <value compset="DATM%CPLHIST_CLM50">clm5_0_cam6.0</value>
       <value compset="DATM%QIA_CLM50"    >clm5_0_QIAN</value>
       <value compset="DATM%WISOQIA_CLM50">clm5_0_QIAN</value>
@@ -112,22 +114,24 @@
       <value compset="DATM%NLDAS2_CLM50" >clm5_0_NLDAS2</value>
       <value compset="DATM%ERA5_CLM50"   >clm5_0_ERA5</value>
       <!-- All the clm5_1 physics options -->
-      <value compset="SATM_CLM51"        >clm5_1_GSWP3v1</value>
       <value compset="DATM%GSWP3v1_CLM51">clm5_1_GSWP3v1</value>
-      <value compset="CAM[^_]+_CLM51"    >clm5_1_cam6.0</value>
-      <value compset="CAM40.*_CLM51"     >clm5_1_cam4.0</value>
-      <value compset="CAM50.*_CLM51"     >clm5_1_cam5.0</value>
-      <value compset="DATM%CPLHIST_CLM51">clm5_1_cam6.0</value>
+      <value compset="CAM[^_]*_CLM51"    >INVALID_USE_CLM60_NOT_CLM51</value>
+      <value compset="CAM40[^_]*_CLM51"  >clm5_1_cam4.0</value>
+      <value compset="CAM50[^_]*_CLM51"  >clm5_1_cam5.0</value>
+      <value compset="CAM60[^_]*_CLM51"  >clm5_1_cam6.0</value>
+      <value compset="CAM70[^_]*_CLM51"  >INVALID_USE_CLM60_NOT_CLM51_FOR_CAM70</value>
+      <value compset="DATM%CPLHIST_CLM51">INVALID_USE_CLM60_NOT_CLM51_FOR_CPLHIST</value>
       <!-- All the clm6_0 physics options -->
       <value compset="DATM%CRUv7_CLM60"  >clm6_0_CRUv7</value>
       <value compset="DATM%CRU_CLM60"    >clm6_0_CRUv7</value>
       <value compset="SATM_CLM60"        >clm6_0_GSWP3v1</value>
       <value compset="DATM%GSWP3v1_CLM60">clm6_0_GSWP3v1</value>
       <value compset="CAM[^_]+_CLM60"    >clm6_0_cam6.0</value>
-      <value compset="CAM40.*_CLM60"     >clm6_0_cam4.0</value>
-      <value compset="CAM50.*_CLM60"     >clm6_0_cam5.0</value>
-      <value compset="CAM7[^_]+_CLM60"   >clm6_0_cam7.0</value>
-      <value compset="DATM%CPLHIST_CLM60">clm6_0_cam6.0</value>
+      <value compset="CAM40[^_]*_CLM60"  >clm6_0_cam4.0</value>
+      <value compset="CAM50[^_]*_CLM60"  >clm6_0_cam5.0</value>
+      <value compset="CAM60[^_]*_CLM60"  >clm6_0_cam6.0</value>
+      <value compset="CAM70[^_]*_CLM60"  >clm6_0_cam7.0</value>
+      <value compset="DATM%CPLHIST_CLM60">clm6_0_cam7.0</value>
       <value compset="DATM%QIA_CLM60"    >clm6_0_QIAN</value>
       <value compset="DATM%WISOQIA_CLM60">clm6_0_QIAN</value>
       <value compset="DATM%1PT_CLM60"    >clm6_0_1PT</value>
@@ -199,24 +203,24 @@
     <default_value>UNSET</default_value>
     <values>
       <!-- Use SSP5-8.5 for PI to PDAY so will have data up to the current year available (for WACCM compsets that use PDAY) -->
-      <value compset="^2010[CE]+_"                  >2010_control</value>
-      <value compset="^2000[CE]+_"                  >2000_control</value>
-      <value compset="^1850[CE]+_"		    >1850_control</value>
+      <value compset="^2010[CE]?_" >2010_control</value>
+      <value compset="^2000[CE]?_" >2000_control</value>
+      <value compset="^1850[CE]?_" >1850_control</value>
       <value compset="^1850_.*_CLM60%[^_]*NOANTHRO" >1850_noanthro_control</value>
       <value compset="^1850_.*_CLM50%[^_]*NOANTHRO" >1850_noanthro_control</value>
-      <value compset="^HIST[CE]+_"                  >20thC_transient</value>
-      <value compset="^SSP585[CE]+_"	            >1850-2100_SSP5-8.5_transient</value>
-      <value compset="^SSP126[CE]+_"	            >1850-2100_SSP1-2.6_transient</value>
-      <value compset="^SSP370[CE]+_"	            >1850-2100_SSP3-7.0_transient</value>
-      <value compset="^SSP534[CE]+_"	            >1850-2100_SSP5-3.4_transient</value>
-      <value compset="^SSP245[CE]+_"	            >1850-2100_SSP2-4.5_transient</value>
-      <value compset="^HIST" grid="ne0np4"          >1850-2100_SSP2-4.5_transient</value>
-      <value compset="^SSP119[CE]+_"	            >1850-2100_SSP1-1.9_transient</value>
-      <value compset="^SSP434[CE]+_"	            >1850-2100_SSP4-3.4_transient</value>
-      <value compset="^SSP460[CE]+_"	            >1850-2100_SSP4-6.0_transient</value>
-      <value compset="^SSP585[CE]+_"	            >1850-2100_SSP5-8.5_transient</value>
-      <value compset="^AMIP_"	                    >20thC_transient</value>
-      <value compset="^PIPD_"                       >1850-2100_SSP5-8.5_transient</value>
+      <value compset="^HIST[CE]?_" >20thC_transient</value>
+      <value compset="^SSP585[CE]?_" >1850-2100_SSP5-8.5_transient</value>
+      <value compset="^SSP126[CE]?_" >1850-2100_SSP1-2.6_transient</value>
+      <value compset="^SSP370[CE]?_" >1850-2100_SSP3-7.0_transient</value>
+      <value compset="^SSP534[CE]?_" >1850-2100_SSP5-3.4_transient</value>
+      <value compset="^SSP245[CE]?_" >1850-2100_SSP2-4.5_transient</value>
+      <value compset="^HIST" grid="ne0np4" >1850-2100_SSP2-4.5_transient</value>
+      <value compset="^SSP119[CE]?_" >1850-2100_SSP1-1.9_transient</value>
+      <value compset="^SSP434[CE]?_" >1850-2100_SSP4-3.4_transient</value>
+      <value compset="^SSP460[CE]?_" >1850-2100_SSP4-6.0_transient</value>
+      <value compset="^SSP585[CE]?_" >1850-2100_SSP5-8.5_transient</value>
+      <value compset="^AMIP_" >20thC_transient</value>
+      <value compset="^PIPD_" >1850-2100_SSP5-8.5_transient</value>
     </values>
     <group>run_component_ctsm</group>
     <file>env_run.xml</file>

From bf02a881a6e18c137e5e7917754d381d62c2b94b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 8 Jul 2024 13:51:42 -0600
Subject: [PATCH 0635/1248] Change some comments to respond to @slevis-lmwg
 review

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e81cd6dab9..eb25cbf486 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -706,7 +706,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4CONUS.ne30x8"      >.true.</use_init_interp>
 
 <!--
-     clm5_0 physics with CAM6.0 grids...
+     clm5_0 physics with CAM6.0 grids (Duplicates the above CAM7.0 section)...
 -->
 <!-- These first five are for SP mode and CLM5.0 only -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_0_cam6.0"
@@ -725,7 +725,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm5_0_cam6.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4CONUS.ne30x8"      >.true.</use_init_interp>
 <!--
-     clm5_1 physics with CAM6.0 grids...
+     clm5_1 physics with CAM6.0 grids (duplicates above)
 -->
 <!-- These first five are for SP mode and CLM5.1 only -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam6.0"
@@ -1365,7 +1365,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
-<!-- Present day for coupled cases at low resolution -->
+<!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1442,7 +1442,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
-<!-- Present day for coupled cases at low resolution -->
+<!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1505,7 +1505,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
-<!-- Present day for coupled cases at low resolution -->
+<!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1572,7 +1572,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
-<!-- Present day for coupled cases at low resolution -->
+<!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1649,7 +1649,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
-<!-- Present day for coupled cases at low resolution -->
+<!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1712,7 +1712,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
 </finidat>
 
-<!-- Present day for coupled cases at low resolution -->
+<!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."

From 37818ef174604a77522772f75099b3cbe950c3f3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 8 Jul 2024 14:07:35 -0600
Subject: [PATCH 0636/1248] More lines to describe the finidat sections

Add some comments to talk about what kind of land
tuning mode is being done for a section of finidat files.
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index eb25cbf486..c6430bfff2 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1326,7 +1326,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!--
      finidat files for CAM resolutions for being coupled to CAM
 -->
-<!-- clm5_0 -->
+<!-- clm5_0 and cam7.0 -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
@@ -1373,6 +1373,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
+
+<!-- clm5_1 and cam7.0 -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1380,6 +1382,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
+<!-- clm6_0 and cam7.0 -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1387,6 +1390,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
+<!-- clm5_0 and cam7.0 -->
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
@@ -1533,7 +1537,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!--
      finidat files for CAM resolutions for being coupled to CAM
 -->
-<!-- clm5_0 -->
+<!-- clm5_0 and cam6.0-->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
@@ -1611,6 +1615,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm5_1 -->
+<!-- clm5_1 and cam6.0-->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
@@ -1674,6 +1679,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm6_0 -->
+<!-- clm6_0 and cam6.0-->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."

From 06759a0734445a2a934d7f088740ee6d2b81c210 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 8 Jul 2024 14:30:22 -0600
Subject: [PATCH 0637/1248] Update test number

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 2147fdea31..3464dfadef 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -166,7 +166,7 @@ sub cat_and_create_namelistinfile {
 my $ntests = 3278;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2001;
+   $ntests += 1981;
 }
 plan( tests=>$ntests );
 

From fafc8137baeb39c07c65e697def4488b86aab612 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 8 Jul 2024 14:53:52 -0700
Subject: [PATCH 0638/1248] update fates submodule to api 36

---
 .gitmodules | 4 ++--
 src/fates   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 049c62ade8..9ed4402c7e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -27,8 +27,8 @@
 #
 [submodule "fates"]
 path = src/fates
-url = https://github.com/ckoven/fates
-fxtag = 4b018eade498d063b21dddf26f77c9658ff80261
+url = https://github.com/NGEET/fates
+fxtag = sci.1.77.0_api.36.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
diff --git a/src/fates b/src/fates
index 4b018eade4..fd7f3438c2 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit 4b018eade498d063b21dddf26f77c9658ff80261
+Subproject commit fd7f3438c2ff821672b703050e7011f293649ee9

From 7fac3e9c5c205391b0e359a4838bc48447b58240 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 8 Jul 2024 16:46:10 -0600
Subject: [PATCH 0639/1248] Change cam6 lnd_tuning_mode to cam7, and remove the
 cam7 Zender Dust tests (as Zender won't be the option for cam7)

---
 cime_config/testdefs/testlist_clm.xml         | 79 ++++++++++---------
 .../include_user_mods                         |  1 -
 .../clm60cam6LndTuningModeCiso/user_nl_clm    |  5 --
 .../include_user_mods                         |  1 -
 .../user_nl_clm                               |  3 -
 .../include_user_mods                         |  1 -
 .../include_user_mods                         |  1 -
 .../include_user_mods                         |  1 +
 .../shell_commands                            |  0
 .../include_user_mods                         |  1 +
 .../shell_commands                            |  0
 11 files changed, 42 insertions(+), 51 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/user_nl_clm
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/user_nl_clm
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_1979Start/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_2013Start/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_1979Start/include_user_mods
 rename cime_config/testdefs/testmods_dirs/clm/{clm60cam6LndTuningMode_1979Start => clm60cam7LndTuningMode_1979Start}/shell_commands (100%)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_2013Start/include_user_mods
 rename cime_config/testdefs/testmods_dirs/clm/{clm60cam6LndTuningMode_2013Start => clm60cam7LndTuningMode_2013Start}/shell_commands (100%)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 707a310f89..4b6f1dc46f 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -63,6 +63,7 @@
   </test>
   <test name="SMS_Ln9" grid="f09_f09_mg17" compset="I1850Clm45Bgc" testmods="clm/clm45cam4LndTuningModeZDustSoilErod">
     <machines>
+
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -80,22 +81,22 @@
       <option name="comment">Simple test use soil eroditability in CTSM for CAM5 tuning</option>
     </options>
   </test>
-  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningModeZDustSoilErod">
+  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution, use soil eroditability in CTSM</option>
+      <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution</option>
     </options>
   </test>
-    <test name="ERP_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningModeZDustSoilErod">
+    <test name="ERP_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment">CESM3 development Exact restart test with change in the processor count at f10, for izumi nag, use soil eroditability in CTSM</option>
+      <option name="comment">CESM3 development Exact restart test with change in the processor count at f10, for izumi nag</option>
     </options>
   </test>
   <!-- this will be removed when CESM no longer needs it-->
@@ -109,7 +110,7 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="IHistClm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
+  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="IHistClm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -118,7 +119,7 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution for transient</option>
     </options>
   </test>
-  <test name="PEM_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
+  <test name="PEM_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -127,7 +128,7 @@
       <option name="comment">CESM3 development test with change in the processor count at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERS_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
+  <test name="ERS_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -136,7 +137,7 @@
       <option name="comment">CESM3 development simple exact restart test at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERI_D" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
+  <test name="ERI_D" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -145,7 +146,7 @@
       <option name="comment">CESM3 development Exact restart test for all startup types at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="SMS_Lm1" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Lm1" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
@@ -155,7 +156,7 @@
       <option name="comment">CESM3 development test at the standard coupled resolution for a month</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg3_t232" compset="I2000Clm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne30pg3_t232" compset="I2000Clm60BgcCrop" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -182,7 +183,7 @@
       <option name="comment"  >CTSM science test list for the half degree grid with latest CLM version for historical</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -191,7 +192,7 @@
       <option name="comment">We have one C96 test in aux_clm; this is another that uses a different compset. No needn't run this additional C96 test with every tag, but include it in the less frequent ctsm_sci testing.</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I1850Clm60SpRs" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I1850Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -200,7 +201,7 @@
       <option name="comment">mpasa low resolution grid, tested in CAM, so do both 1850 and 2000 with latest CLM version and include in the CTSM science test list</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I2000Clm60SpRs" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -209,7 +210,7 @@
       <option name="comment">mpasa low resolution grid, tested in CAM, so do both 1850 and 2000 with latest CLM version and include in the CTSM science test list</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -218,7 +219,7 @@
       <option name="comment">Test that the workhorse mpasa resolution functions for CAM, for both Hist and 2000 with latest CLM version. No need to run this test with every tag, but include it in the less frequent ctsm_sci testing.</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -227,7 +228,7 @@
       <option name="comment">Test that the workhorse mpasa resolution functions for CAM, for both Hist and 2000 with latest CLM version. No need to run this test with every tag, but include it in the less frequent ctsm_sci testing.</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -236,7 +237,7 @@
       <option name="comment">Higher resolution mpasa grid for CAM with latest CLM version. Include it in the less frequent ctsm_sci testing.</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa15_mpasa15" compset="I2000Clm60SpRs" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa15_mpasa15" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -246,7 +247,7 @@
     </options>
   </test>
 <!--
-  <test name="SMS_P36x128_Ln9" grid="mpasa15-3-conus_mpasa15-3-conus" compset="I2000Clm60SpRs" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_P36x128_Ln9" grid="mpasa15-3-conus_mpasa15-3-conus" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -329,22 +330,22 @@
       <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f09 with CAM6</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f09 with CAM7</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19 with CAM6</option>
+      <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19 with CAM7</option>
     </options>
   </test>
   <test name="ERP_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50Sp" testmods="clm/prescribed">
@@ -576,7 +577,7 @@
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="IHistClm60SpRs" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="IHistClm60SpRs" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -585,7 +586,7 @@
       <option name="comment">Low resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm60SpRs" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -594,7 +595,7 @@
       <option name="comment">Low resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -603,7 +604,7 @@
       <option name="comment">Medium resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, test both 1850 and 2000</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -612,7 +613,7 @@
       <option name="comment">Medium resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, test both 1850 and 2000</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -621,7 +622,7 @@
       <option name="comment">Medium resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, test IHist</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30_g17" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne30_g17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -630,7 +631,7 @@
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -639,7 +640,7 @@
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -648,7 +649,7 @@
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-   <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode">
+   <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -657,7 +658,7 @@
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -666,7 +667,7 @@
       <option name="comment">Workhorse SE grid for running with CAM and with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -675,7 +676,7 @@
       <option name="comment">High resolution SE grid for running with CAM and with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -1289,7 +1290,7 @@
       <option name="comment"  >Test transient PFTs (via HIST) in conjunction with changing glacier area. This test also covers the reset_dynbal_baselines option. CISM is not answer preserving across processor changes, but short test length should be OK.</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="C96_C96_mg17" compset="IHistClm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="C96_C96_mg17" compset="IHistClm60BgcCrop" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -1646,7 +1647,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode_1979Start">
+  <test name="SMS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_1979Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -1655,7 +1656,7 @@
       <option name="comment"  >Run ARCTIC for transient case starting in 1979 as for AMIP CAM cases (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode_1979Start">
+  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_1979Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -1664,7 +1665,7 @@
       <option name="comment"  >Run ARCTICGRIS for transient case starting in 1979 as for AMIP CAM cases (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -1673,7 +1674,7 @@
       <option name="comment"  >Run ARCTICGRIS for 1850 case (do not run this expensive test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam6LndTuningMode_2013Start">
+  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_2013Start">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/include_user_mods
deleted file mode 100644
index 3dabdc9aeb..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../clm60cam6LndTuningMode
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/user_nl_clm
deleted file mode 100644
index e7627dea50..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/user_nl_clm
+++ /dev/null
@@ -1,5 +0,0 @@
-! Turn on Carbon isotopes
-use_c13 = .true.
-use_c14 = .true.
-use_c13_timeseries = .true.
-use_c14_bombspike = .true.
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/include_user_mods
deleted file mode 100644
index 3dabdc9aeb..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../clm60cam6LndTuningMode
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/user_nl_clm
deleted file mode 100644
index 93b7ee2e48..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/user_nl_clm
+++ /dev/null
@@ -1,3 +0,0 @@
-! Turn on using the soil eroditability file in CTSM
-dust_emis_method = 'Zender_2003'
-zender_soil_erod_source = 'lnd'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_1979Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_1979Start/include_user_mods
deleted file mode 100644
index 3dabdc9aeb..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_1979Start/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../clm60cam6LndTuningMode
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_2013Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_2013Start/include_user_mods
deleted file mode 100644
index 3dabdc9aeb..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_2013Start/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../clm60cam6LndTuningMode
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_1979Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_1979Start/include_user_mods
new file mode 100644
index 0000000000..ef8619d930
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_1979Start/include_user_mods
@@ -0,0 +1 @@
+../clm60cam7LndTuningMode
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_1979Start/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_1979Start/shell_commands
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_1979Start/shell_commands
rename to cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_1979Start/shell_commands
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_2013Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_2013Start/include_user_mods
new file mode 100644
index 0000000000..ef8619d930
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_2013Start/include_user_mods
@@ -0,0 +1 @@
+../clm60cam7LndTuningMode
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_2013Start/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_2013Start/shell_commands
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_2013Start/shell_commands
rename to cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_2013Start/shell_commands

From 1356d0ba0aa4582f1b7b83ae416c5d908f4cb02a Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 8 Jul 2024 17:04:15 -0600
Subject: [PATCH 0640/1248] dmleung add a little tuning to reduce the
 sensitivity of dust emission to clay fraction. dmleung also corrected the
 output of soil surface friction velocity (wnd_frc_slt). Coded on 5 Jul 2024
 and committed on 8 Jul 2024

---
 src/biogeochem/DUSTMod.F90                   |  6 +++++-
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 15 ++++++++++++++-
 2 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index b23a26b429..197ede35fd 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -693,8 +693,9 @@ subroutine DustEmission (bounds, &
             frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor
 
          else    ! for lnd_frc_mbl=0, do not change friction velocity and assume drag partition factor = 0
-            wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
+            !wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
             frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > 1, the drag partition effect is zero. dmleung 16 Feb 2024.
+            wnd_frc_slt = fv(p) * frc_thr_rghn_fct(p) ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission. dmleung added 5 Jul 2024
          end if
 
          !########## end of drag partition effect #######################################################
@@ -727,7 +728,10 @@ subroutine DustEmission (bounds, &
                !################ uncomment the below block if want to use Leung's scheme ###################
 
                !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
+
+               ! dmleung: instead of using mss_frc_cly_vld(c) with a range of [0,0.2] , which makes dust too sensitive to input clay surface dataset), for now use 0.1 + mss_frc_cly_vld(c) * 0.1 / 0.20 with a range of [0.1,0.2]. So, instead of scaling dust emission to 1/20 times for El Djouf (western Sahara) because of its 1 % clay fraction, scale its emission to 1/2 times. This reduces the sensitivity of dust emission to the clay input dataset. In particular, because dust emission is a small-scale process and the grid-averaged clay from the new WISE surface dataset over El Djouf is 1 %, much lower than the former FAO estimation of 5 %, dmleung is not sure if the clay value of 1 % suppresses too much of El Djouf's small-scale dust emission process. Similar to Charlie Zender's feeling suspicious about the soil texture datasets (or the dust emission schemes' sandblasting process), dmleung feels the same and for now decides to still allow dust emission  to weakly scale with clay fraction, however limiting the scaling factor to 0.1-0.2. See modification in SoilStateInitTimeConst.F90. dmleung 5 Jul 2024
                flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
+               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * ( 0.1_r8 + mss_frc_cly_vld(c) * 0.1_r8 / 0.20_r8 ) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt 
 
                ! account for bare soil fraction, frozen soil fraction, and apply global tuning parameter (Kok et al. 2014)
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * lnd_frc_mbl(p) * C_tune * liqfrac
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 3c8945e9d2..d0315e76ff 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -697,7 +697,16 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     end do
 
     ! --------------------------------------------------------------------
-    ! Initialize threshold soil moisture and mass fracion of clay limited to 0.20
+    ! Initialize threshold soil moisture, and mass fraction of clay as 
+    ! scaling coefficient of dust emission flux (kg/m2/s) in DUSTMod.F90
+    ! dmleung modified 5 Jul 2024, reducing sensitivity of dust emission 
+    ! flux to clay fraction.
+    ! Also, for threshold soil moisture, dmleung followed Zender (2003)
+    ! DEAD scheme to again avoid dust flux being too sensitive to the choice
+    ! of clay dataset. This is different from what Leung et al. (2023)
+    ! intended to do.
+    ! Both decisions are based on tuning preference and could subject to
+    ! future changes. dmleung 5 Jul 2024
     ! --------------------------------------------------------------------
 
     do c = begc,endc
@@ -709,7 +718,11 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
        ! There are different options: E.g., a = 1 gives the first line below. E.g., Kok et al. (2014a, b) chose to use a = 1. A second choice is proposed by Charlie Zender (2003a):  a = 1/clay3d, which gives the second line below. 
        !soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Jasper Kok et al. (2014) modified the equation of soil moisture effect for dust emissions using a tuning factor of a = 1. 0.01 is to convert the threshold gravimetric soil moisture from % to fraction. Danny M. Leung et al. (2023) followed K14 and used this equation for offline dust emission calculations using MERRA-2 met fields. Later, Leung et al. (2024) changed to a = 2 for CESM2 simulations. However, Danny Leung later (Dec 2023) decided to revert to Zender's choice and use a = 1 / (clay3d), which overall encourages more dust emissions from seriamid and more marginal dust sources. This note should probably be on the CLM tech note since dmleung has made a different decision for CESM than his own paper. dmleung added this detailed comment on 19 Feb 2024; edited 24 May 2024.
        soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with a = 1 / (%clay) being the tuning factor for soil moisture effect in Zender's dust emission scheme. Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) dust emission scheme in the CESM will use Zender's tuning of a = 1 / (%clay), which overall encourages more dust emissions from seriamid and more marginal dust sources. Another advantage of using this tuning factor instead of a = 1 is that the dust emission threshold is linearly dependent on the clay fraction instead of parabolically dependent on clay fraction as in the above line. This means that dust emission becomes a little less sensitive to clay content (soil texture). 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to convert surface clay fraction from percentage to fraction. dmleung added this detailed comment on 19 Feb 2024.
+
+       ! dust emission scaling factor dependent on clay fraction
        soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
+       soilstate_inst%mss_frc_cly_vld_col(c) = 0.1_r8 + soilstate_inst%mss_frc_cly_vld_col(c) * 0.1_r8 / 0.20_r8   ! dmleung added this line to reduce the sensitivity of dust emission flux to clay fraction in DUSTMod. 5 Jul 2024
+
     end do
 
     ! --------------------------------------------------------------------

From cb7376eb55987f0785dd9a857c2fd24a720e6017 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 9 Jul 2024 01:25:57 -0600
Subject: [PATCH 0641/1248] Remove whitespace at end of lines

---
 src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
index 467d00de59..c811cab5f5 100644
--- a/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
+++ b/src/drv_test/shr_dust_emis_test/test_shr_dust_emis.pf
@@ -59,7 +59,7 @@ contains
     @assertFalse(not_init)
 
   end subroutine check_when_initialized_runs
- 
+
    @Test
   subroutine check_dust_emis(this)
     ! Test that the dust_emis logical functions work as expected
@@ -75,7 +75,6 @@ contains
 
   end subroutine check_dust_emis
 
-   
   @Test
   subroutine check_zender_soil(this)
     ! Test that the dust_emis_Zender logical functions work as expected
@@ -91,7 +90,6 @@ contains
 
   end subroutine check_zender_soil
 
-     
   @Test
   subroutine check_options(this)
     ! Test that the check_options subroutine catches errors that should die
@@ -110,5 +108,5 @@ contains
     @assertExceptionRaised(endrun_msg('(check_options_finish_init) ERROR: zender_soil_erod_source can only be lnd or atm'))
 
   end subroutine check_options
- 
+
 end module test_shr_dust_emis

From e49c11dafe49ec306848a31cabfbf6b87d0d62da Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 9 Jul 2024 10:25:04 -0700
Subject: [PATCH 0642/1248] update ChangeLog and ChangeSum

---
 doc/ChangeLog | 117 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 118 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 2ab7676ddc..26deed83db 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,121 @@
 ===============================================================
+Tag name: ctsm5.2.009
+Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Tue 9 Jul 2024 10:50:00 AM MDT
+One-line Summary: FATES Land Use V2
+
+Purpose and description of changes
+----------------------------------
+
+This tag enables FATES to utilize its land use mode with fixed
+biogeography and no competition mode engaged.  To facilitate
+this update, the host land model reads in a new static map data
+set that associates land use with FATES plant functional types.
+This tag also updates the pre-existing FATES dynamic land use
+module to provide access to the raw LUH2 harvest data from the
+FATES LUH2 timeseries data set (added in ctsm5.1.dev160).
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+   FATES satellite phenology mode and land use mode are currently incompatible
+   and trying to engage both will result in a graceful build failure message
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   New FATES namelist option: fates_harvest_mode
+      - This new option provides five harvest modes
+      - The 'event_code' mode takes over the now defunct use_fates_logging option
+
+   New FATES namelist option: use_fates_lupft
+      - This option enables the necessary namelist options and data sets to run
+	FATES with land use, no competition, and fixed biogeography modes.
+
+   New FATES namelist option: flandusepftdat
+      - This data set is necessary for running with use_fates_lupft.
+
+   New FATES namelist option: use_potential_veg
+      - This option is only necessary for use with FATES spin-up to transient
+	workflows that will engage the use_fates_lupft mode for the transient case
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   The default FATES parameter file has been updated to account for the new
+   parameters necessary for land use v2.
+
+   A new default data set has been provided for flandusepftdat.  Only a 4x5 grid
+   resolution is currently provided.
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+   The FATES land use timeseries data set, fluh_timeseries, has been updated to
+   provide a wider timeseries range, from 0850-2015.
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+   New FATES testmods have been added to account for the additional harvest mode
+   and use_fates_lupft namelist options.  Additoinally a new system text prefix,
+   PVT, has been added to test the use_fates_potentialveg spin-up to use_fates_lupft
+   transient workflow.  These have been added to the fates test suite.
+
+
+Testing summary:
+----------------
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- TBD
+    izumi ------- TBD
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+   fates tested against fates-sci.1.76.4_api.35.1.0-ctsm5.2.008
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Only for FATES test mods, otherwise B4B
+
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   FATES: sci.1.73.0_api.35.0.0 -> sci.1.77.0_api.36.0.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+#2507 -- FATES land use v2 API update (CTSM-side)
+NGEET#1116 -- V2 Land Use Change
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.008
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri 28 Jun 2024 12:22:46 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index ea9417fe41..209c7e9a51 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.009 glemieux 07/09/2024 FATES Land Use V2
        ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
 tmp-240620.n03.ctsm5.2.007  06/27/2024 Set upland hillslope column fsat values to zero (samrabin)
 tmp-240620.n02.ctsm5.2.007  06/21/2024 Another update of git-fleximod (erik)

From da50efd1477e53db42abc11db90b97648daabadf Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 9 Jul 2024 10:27:48 -0700
Subject: [PATCH 0643/1248] add clarifying language for user about FATES and
 do_harvest

---
 doc/ChangeLog | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 26deed83db..7b40fe908a 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -45,6 +45,8 @@ Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
    New FATES namelist option: fates_harvest_mode
       - This new option provides five harvest modes
       - The 'event_code' mode takes over the now defunct use_fates_logging option
+      - The 'landuse_timeseries' option supersedes the use of do_harvest option
+	with FATES.  Using do_harvest is no longer compatible with FATES.
 
    New FATES namelist option: use_fates_lupft
       - This option enables the necessary namelist options and data sets to run

From 2b50ebb8dfcfaa609a13b50d04270ed3169fcce8 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 9 Jul 2024 10:29:14 -0700
Subject: [PATCH 0644/1248] correct fluh_timeseries file name

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 754510289f..97424eb13a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1558,7 +1558,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- This one is just for testing until Issue #2304 is resolved -->
 <fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."
- >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1650-2015_c240216.nc</fluh_timeseries>
+ >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr0850-2015_c240216.nc</fluh_timeseries>
 
 <!-- Fixation and Uptake of Nitrogen Model (FUN2.0) -->
 <use_fun                                                            >.false.</use_fun>

From 03ab3bdefa98b776263c057b50cf4b803f6c4fd7 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 9 Jul 2024 10:41:40 -0700
Subject: [PATCH 0645/1248] remove out-dated-comment

Checking the landuse x pft data is handled on the fates-side
---
 src/utils/clmfates_interfaceMod.F90 | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 43a574d6e3..d15288d3a3 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -3915,8 +3915,6 @@ subroutine GetLandusePFTData(bounds, landuse_pft_file, landuse_pft_map, landuse_
    deallocate(arraylocal_bareground)
    call ncd_pio_closefile(ncid)
 
-   ! Check that sums equal to unity
-
  end subroutine GetLandusePFTData
 
 

From 272f99f405e95adec9774519323a34c0f2f9c874 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 9 Jul 2024 13:41:55 -0700
Subject: [PATCH 0646/1248] remove unused land use mod subroutine

---
 src/utils/clmfates_interfaceMod.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index d15288d3a3..e3e7644b90 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -182,7 +182,6 @@ module CLMFatesInterfaceMod
    use dynFATESLandUseChangeMod, only : num_landuse_transition_vars, num_landuse_state_vars
    use dynFATESLandUseChangeMod, only : landuse_transitions, landuse_states
    use dynFATESLandUseChangeMod, only : landuse_transition_varnames, landuse_state_varnames
-   use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp
    use dynFATESLandUseChangeMod, only : num_landuse_harvest_vars
    use dynFATESLandUseChangeMod, only : fates_harvest_no_logging
    use dynFATESLandUseChangeMod, only : fates_harvest_clmlanduse

From 72ab1cbf97522984acaceda494b5279fb4ea3621 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 9 Jul 2024 15:48:06 -0600
Subject: [PATCH 0647/1248] Remove use_dynroot and corresponding code and
 testing

---
 bld/CLMBuildNamelist.pm                       |  20 --
 bld/namelist_files/namelist_defaults_ctsm.xml |   3 -
 .../namelist_definition_ctsm.xml              |   5 -
 bld/unit_testers/build-namelist_test.pl       |   5 -
 cime_config/testdefs/testlist_clm.xml         |  17 --
 .../clm/clm50dynroots/include_user_mods       |   1 -
 .../clm/clm50dynroots/user_nl_clm             |   2 -
 src/biogeochem/CNDriverMod.F90                |  17 +-
 src/biogeochem/CNRootDynMod.F90               | 271 ------------------
 src/biogeophys/IrrigationMod.F90              |   5 +-
 src/biogeophys/SoilStateType.F90              |  26 +-
 src/main/clm_varctl.F90                       |   6 -
 src/main/controlMod.F90                       |  10 -
 src/main/pftconMod.F90                        |  14 +-
 14 files changed, 7 insertions(+), 395 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm
 delete mode 100644 src/biogeochem/CNRootDynMod.F90

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index f65414e4af..146cf5bd32 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1582,7 +1582,6 @@ sub process_namelist_inline_logic {
   setup_logic_hillslope($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_o3_veg_stress_method($opts, $nl_flags, $definition, $defaults, $nl,$physv);
   setup_logic_hydrstress($opts,  $nl_flags, $definition, $defaults, $nl);
-  setup_logic_dynamic_roots($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_params_file($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_create_crop_landunit($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_subgrid($opts,  $nl_flags, $definition, $defaults, $nl);
@@ -3581,25 +3580,6 @@ sub setup_logic_grainproduct {
 
 #-------------------------------------------------------------------------------
 
-sub setup_logic_dynamic_roots {
-  #
-  # dynamic root model
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_dynroot', 'phys'=>$physv->as_string(), 'bgc_mode'=>$nl_flags->{'bgc_mode'});
-  my $use_dynroot = $nl->get_value('use_dynroot');
-  if ( &value_is_true($use_dynroot) && ($nl_flags->{'bgc_mode'} eq "sp") ) {
-     $log->fatal_error("Cannot turn dynroot mode on mode bgc=sp\n" .
-                       "Set the bgc mode to 'bgc'.");
-  }
-  if ( &value_is_true( $use_dynroot ) && &value_is_true( $nl_flags->{'use_hydrstress'} ) ) {
-     $log->fatal_error("Cannot turn use_dynroot on when use_hydrstress is on" );
-  }
-}
-
-#-------------------------------------------------------------------------------
-
 sub setup_logic_c_isotope {
   #
   # Error checking for C-isotope options
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 655e97c47c..794c9278ca 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -568,9 +568,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Whether to use subgrid fluxes for snow -->
 <use_subgrid_fluxes>.true.</use_subgrid_fluxes>
 
-<!-- dynamic roots -->
-<use_dynroot >.false.</use_dynroot>
-
 <!-- Guardrail for ensuring leaf-Nitrogen doesn't go too small or negative on updates -->
 <use_nguardrail                use_cn=".false.">.false.</use_nguardrail>
 <use_nguardrail                use_cn=".true." >.true.</use_nguardrail>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 37c457141c..e13d8f867a 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1364,11 +1364,6 @@ Percentage threshold above which the model keeps the urban landunits. Selecting
 <default>Default: 0</default>
 </entry>
 
-<entry id="use_dynroot" type="logical" category="physics"
-       group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the dynamic root model
-</entry>
-
 <entry id="use_SSRE" type="logical" category="physics"
        group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on on diagnostic Snow Radiative Effect
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 53c71ae0e9..e754883785 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1062,11 +1062,6 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
-     "useHYDSTwithdynroot"       =>{ options=>"-bgc bgc -envxml_dir . -megan",
-                                     namelst=>"use_hydrstress=.true., use_dynroot=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_0",
-                                   },
      "specWOfireemis"            =>{ options=>"-envxml_dir . -no-fire_emis",
                                      namelst=>"fire_emis_specifier='bc_a1 = BC'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index fee8e1a429..e3c0053698 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1345,15 +1345,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/clm50dynroots">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-      <machine name="izumi"  compiler="intel" category="prebeta"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/deepsoil_bedrock">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -2134,14 +2125,6 @@
       <option name="comment"  >Long enough test for SMB to be generated in bare land areas; add a month beyond the 3rd year to allow time for CLM to respond to CISM forcing from the 3rd year. (Note: if we had spun-up initial conditions for an IG compset, we could test this with much shorter test, if it also used the glc override options - much of the need for this long test is to allow the snow pack to spin up.)</option>
     </options>
   </test>
-  <test name="SMS_Ly3_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/clm50dynroots">
-    <machines>
-      <machine name="izumi" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:40:00</option>
-    </options>
-  </test>
   <test name="SMS_Ly3_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm60BgcCropQianRs" testmods="clm/monthly">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods
deleted file mode 100644
index fe0e18cf88..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm
deleted file mode 100644
index e493c3e8e7..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm
+++ /dev/null
@@ -1,2 +0,0 @@
-use_dynroot = .true.
-use_hydrstress = .false.
diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90
index b23019eb23..0381711258 100644
--- a/src/biogeochem/CNDriverMod.F90
+++ b/src/biogeochem/CNDriverMod.F90
@@ -6,7 +6,7 @@ module CNDriverMod
   !
   ! !USES:
   use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use clm_varctl                      , only : use_c13, use_c14, use_fates,  use_fates_bgc, use_dynroot
+  use clm_varctl                      , only : use_c13, use_c14, use_fates, use_fates_bgc
   use dynSubgridControlMod            , only : get_do_harvest, get_do_grossunrep
   use decompMod                       , only : bounds_type
   use perf_mod                        , only : t_startf, t_stopf
@@ -147,7 +147,6 @@ subroutine CNDriverNoLeaching(bounds,
     use SoilBiogeochemNitrifDenitrifMod   , only: SoilBiogeochemNitrifDenitrif
     use SoilBiogeochemNStateUpdate1Mod    , only: SoilBiogeochemNStateUpdate1
     use NutrientCompetitionMethodMod      , only: nutrient_competition_method_type
-    use CNRootDynMod                      , only: CNRootDyn
     use CNPrecisionControlMod             , only: CNPrecisionControl
     !
     ! !ARGUMENTS:
@@ -564,20 +563,6 @@ subroutine CNDriverNoLeaching(bounds,
          
     call t_stopf('CNGResp')
 
-    !--------------------------------------------
-    ! Dynamic Roots
-    !--------------------------------------------
-
-    if( use_dynroot ) then
-        call t_startf('CNRootDyn')
-
-        call CNRootDyn(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, &
-             cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst,  &
-             cnveg_state_inst, crop_inst,  soilstate_inst, soilbiogeochem_nitrogenstate_inst)
-
-        call t_stopf('CNRootDyn')
-     end if
-
     !--------------------------------------------------------------------------
     ! CNUpdate0
     ! The state updates are still called for the matrix solution (use_matrixn
diff --git a/src/biogeochem/CNRootDynMod.F90 b/src/biogeochem/CNRootDynMod.F90
deleted file mode 100644
index 3f43424cfa..0000000000
--- a/src/biogeochem/CNRootDynMod.F90
+++ /dev/null
@@ -1,271 +0,0 @@
-module CNRootDynMod
-
-!-----------------------------------------------------------------------
-! !DESCRIPTION:
-! Module holding routines used for determining fine root distribution for all pfts.
-! Includes dynamic root depth for crops
-!
-! !USES:
-   use shr_kind_mod                    , only : r8 => shr_kind_r8
-   use clm_time_manager                , only : get_step_size_real
-   use abortutils                      , only : endrun
-   use clm_varpar                      , only : nlevsoi, nlevgrnd
-   use clm_varctl                      , only : use_bedrock
-   use decompMod                       , only : bounds_type
-   use pftconMod                       , only : noveg, npcropmin, pftcon 
-   use ColumnType                      , only : col
-   use PatchType                       , only : patch
-   use CNVegStateType                  , only : cnveg_state_type
-   use CNVegCarbonStateType            , only : cnveg_carbonstate_type
-   use CNVegCarbonFluxType             , only : cnveg_carbonflux_type
-   use CNVegnitrogenstateType          , only : cnveg_nitrogenstate_type
-   use SoilStateType                   , only : soilstate_type
-   use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
-   use CropType                        , only : crop_type
-
-! !PUBLIC TYPES:
-  implicit none
-  save
-  private
-  public :: CNRootDyn
-!-----------------------------------------------------------------------
-
-contains
-
-!-----------------------------------------------------------------------
-!
-subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-           cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst,   &
-           cnveg_state_inst, crop_inst,  soilstate_inst, soilbiogeochem_nitrogenstate_inst)
-!
-! !DESCRIPTION:
-! This routine determine the fine root distribution
-! Needs to be called after the photosynthesis calculation
-! May need to update other subroutines that use the fixed root profile for calculations
-! i.e. CNVerticalProfileMod
-!
-! !USES:
-
-
-! !ARGUMENTS:
-   type(bounds_type), intent(in) :: bounds  ! bounds
-   integer, intent(in) :: num_soilc
-   integer, intent(in) :: filter_soilc(:)
-   integer, intent(in) :: num_soilp              ! number of soil pfts in filter
-   integer, intent(in) :: filter_soilp(:)        ! filter for soil pfts
-   type(cnveg_state_type)                  , intent(in)    :: cnveg_state_inst
-   type(cnveg_carbonstate_type)            , intent(in)    :: cnveg_carbonstate_inst
-   type(cnveg_carbonflux_type)             , intent(in)    :: cnveg_carbonflux_inst
-   type(cnveg_nitrogenstate_type)          , intent(in)    :: cnveg_nitrogenstate_inst
-   type(crop_type)                         , intent(in)    :: crop_inst
-   type(soilbiogeochem_nitrogenstate_type) , intent(in)    :: soilbiogeochem_nitrogenstate_inst
-   type(soilstate_type)                    , intent(inout) :: soilstate_inst
-
-!
-! !LOCAL VARIABLES:
-       
-   integer :: f,c,p,lev,j                        ! indices
-   real(r8):: dt                                 ! radiation time step delta t (seconds)
-   real(r8), allocatable :: w_limit(:)
-   real(r8), allocatable :: rswa(:,:)            ! soil water availability in each soil layer 
-   real(r8), allocatable :: rsmn(:,:)            ! soil nitrogen availability in each soil layer 
-   real(r8), allocatable :: sumrswa(:)           ! scaling soil water availability in each soil layer 
-   real(r8), allocatable :: sumrsmn(:)           ! scaling  soil mineral N availability in each soil layer
-   real(r8) :: frootc_dz(bounds%begp:bounds%endp, 1:nlevgrnd)
-   real(r8), allocatable :: sumfrootc(:)         ! fine root carbon total before turnover in each step
-   real(r8):: minpsi                             ! minimum soil moisture potential
-   real(r8):: psi
-   real(r8):: maxpsi
-   real(r8):: new_growth
-
-!-----------------------------------------------------------------------
-   ! Assign local pointers to derived type arrays (in)
-    associate(&
-    ivt                    => patch%itype                                       , & ! Input:  [integer (:)]  pft vegetation type
-    pcolumn                => patch%column                                      , & ! Input:  [integer (:)]  pft's column index
-    roota_par              => pftcon%roota_par                                  , & ! Input:  [real(r8) (:)] pft's roota index
-    rootb_par              => pftcon%rootb_par                                  , & ! Input:  [real(r8) (:)] pft's rootb index
-    root_dmx               => pftcon%root_dmx                                   , & ! Input:  [real(r8) (:)] crop maximum root depth
-    cpool_to_frootc        => cnveg_carbonflux_inst%cpool_to_frootc_patch       , & ! Input:  [real(r8) (:)] allocation to fine root C (gC/m2/s)
-    frootc_xfer_to_frootc  => cnveg_carbonflux_inst%frootc_xfer_to_frootc_patch , & ! Input:  [real(r8) (:)] fine root C growth from storage (gC/m2/s)
-    dormant_flag           => cnveg_state_inst%dormant_flag_patch               , & ! Input:  [real(r8) (:)]  dormancy flag
-    root_depth             => soilstate_inst%root_depth_patch                   , & ! InOut:  [real(r8) (:)] current root depth
-    dz                     => col%dz                                            , & ! Input:  layer thickness (m)  (-nlevsno+1:nlevgrnd)
-    zi                     => col%zi                                            , & ! Input:  interface level below a "z" level (m) (-nlevsno+0:nlevgrnd)
-    rootfr                 => soilstate_inst%rootfr_patch                       , & ! Output: [real(r8) (:,:)]  fraction of roots in each soil layer
-    sucsat                 => soilstate_inst%sucsat_col                         , & ! Input:  minimum soil suction (mm)
-    soilpsi                => soilstate_inst%soilpsi_col                        , & ! Input:  soil water potential in each soil layer (MPa)
-    sminn_vr               => soilbiogeochem_nitrogenstate_inst%sminn_vr_col    , & ! Iniput:  [real(r8) (:,:)]  (gN/m3) soil mineral N
-    frootc                 => cnveg_carbonstate_inst%frootc_patch               , & ! Input:  [real(r8) (:)]  (gC/m2) fine root C
-    hui                    => crop_inst%hui_patch                               , & ! Input:  [real(r8) (:)]  crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest
-    croplive               => crop_inst%croplive_patch                          , & ! Input:  [logical (:)]  flag, true if planted, not harvested
-    huigrain               => cnveg_state_inst%huigrain_patch                     & ! Input: [real(r8) (:)]  same to reach vegetative maturity
-    )
-   
-! set time steps
-   dt = get_step_size_real()
-
-! set minpsi to permanent wilting point
-   minpsi = -1.5_r8
- 
-   allocate(sumrswa(bounds%begp:bounds%endp)) 
-   allocate(sumrsmn(bounds%begp:bounds%endp))
-   allocate(sumfrootc(bounds%begp:bounds%endp))
-   allocate(rswa(bounds%begp:bounds%endp,nlevgrnd))
-   allocate(rsmn(bounds%begp:bounds%endp,nlevgrnd))
-   allocate(w_limit(bounds%begp:bounds%endp))
-
-!initialize to 0
-   w_limit(bounds%begp:bounds%endp)   = 0._r8
-   sumrswa(bounds%begp:bounds%endp)   = 0._r8 
-   sumrsmn(bounds%begp:bounds%endp)   = 0._r8 
-   sumfrootc(bounds%begp:bounds%endp) = 0._r8
-   rswa(bounds%begp:bounds%endp,:) = 0._r8
-   rsmn(bounds%begp:bounds%endp,:) = 0._r8
-    
-   frootc_dz(bounds%begp:bounds%endp,1:nlevgrnd) = 0._r8
-
-
-!---------------------------------------------------------------
-! Set root depth, dynamic for crops, fixed for other vegetation
-!---------------------------------------------------------------
-
-         do f = 1, num_soilp
-            p = filter_soilp(f)
-            c = pcolumn(p)
-            if (ivt(p) /= noveg) then
-                if((ivt(p)) >= npcropmin)then !skip generic crop types
-                    if (.not. croplive(p)) then
-                        root_depth(p) = 0._r8
-                    else if(huigrain(p) > 0._r8)then
-                        root_depth(p) = max(zi(c,2), min(hui(p)/huigrain(p)* root_dmx(ivt(p)), root_dmx(ivt(p))))
-                    end if
-                else
-                ! this can be changed to any depth (i.e. the maximum soil depth)
-                    root_depth(p) = zi(c,nlevsoi) 
-                end if
-                if (use_bedrock) then
-                   root_depth(p) = min(root_depth(p),zi(c,col%nbedrock(c)))
-                end if
-            else
-                root_depth(p) = 0._r8
-            end if
-         end do
-
-!----------------------------------------------------------------
-!  ! calculate a weighting function by soil depth that depends on the
-   ! fine root distribution per pft and depth and the pft weight on the column.
-   ! This will be used to weight the temperature and water potential scalars
-   ! for decomposition control.  
-
-   ! calculate the rate constant scalar for soil water content.
-   ! Uses the log relationship with water potential given in
-   ! Andren, O., and K. Paustian, 1987. Barley straw decomposition in the field:
-   ! a comparison of models. Ecology, 68(5):1190-1200.
-   ! and supported by data in
-   ! Orchard, V.A., and F.J. Cook, 1983. Relationship between soil respiration
-   ! and soil moisture. Soil Biol. Biochem., 15(4):447-453.
-
-   do j = 1,nlevsoi
-      do f = 1,num_soilp
-         p = filter_soilp(f)
-         c = pcolumn(p)
-         maxpsi = sucsat(c,j) * (-9.8e-6_r8)
-         psi = min(soilpsi(c,j),maxpsi)
-         if (psi > minpsi) then
-! First calculate water in the root zone
-            if(root_depth(p) >  0.15_r8 .and. (zi(c,j) <= root_depth(p) .or. &
-              (zi(c,j-1) < root_depth(p) .and. zi(c,j) > root_depth(p)))) then
-                 w_limit(p) = w_limit(p) + max(0._r8,log(minpsi/psi)/log(minpsi/maxpsi))*rootfr(p,j)
-             end if
-! Calculate the water in each soil layer
-             if (root_depth(p) >= zi(c,j) .or. &
-               (zi(c,j-1) < root_depth(p) .and. zi(c,j) > root_depth(p))) then
-                 rswa(p,j) = max(0._r8, (log(minpsi/psi)/log(minpsi/maxpsi)))
-             end if
-         end if
-         sumrswa(p) = sumrswa(p) + rswa(p,j)
-
-! Calculate the nitrogen profile in each layer
-! For now, the profile for each PFT is equivilent to the
-! column profile, in the future, this could be changed to a weighted profile
-         rsmn(p,j) = sminn_vr(c,j) 
-         if (root_depth(p) >= zi(c,j).or. &
-               (zi(c,j-1) < root_depth(p) .and. zi(c,j) > root_depth(p))) then
-            sumrsmn(p) = sumrsmn(p) + rsmn(p,j)      
-         end if
-      end do
-   end do
-
-
-!--------------------------------------------------------------------
-! Now calculate the density of roots in each soil layer for each pft
-! based on this timesteps growth
-!--------------------------------------------------------------------
-    do lev = 1, nlevgrnd
-    
-         do f = 1, num_soilp
-            p = filter_soilp(f) 
-            c = pcolumn(p)
-
-            new_growth = (cpool_to_frootc(p) + frootc_xfer_to_frootc(p))*dt
-            if(zi(c,lev) <= root_depth(p) .or. &
-               (zi(c,lev-1) < root_depth(p) .and. zi(c,lev) > root_depth(p))) then 
-               if(sumrswa(p) <= 0._r8 .or. sumrsmn(p) <= 0._r8) then
-!                   when sumrswa or sumrsmn are less than or equal to 0 rootfr will not be updated
-               else
-                   frootc_dz(p,lev) = (frootc(p))*rootfr(p,lev) & 
-                                 + new_growth * ((1._r8 - w_limit(p)) * rswa(p,lev) / sumrswa(p) &
-                                 + w_limit(p) * rsmn(p,lev) / sumrsmn(p))
-               end if
-            else
-               frootc_dz(p,lev) = 0._r8
-            end if
-     
-            sumfrootc(p) = sumfrootc(p) + frootc_dz(p,lev)
-       
-         end do
-    end do
-!----------------------------------
-!Calculate root fraction
-!----------------------------------
-
-     do lev = 1, nlevgrnd
-        do f = 1, num_soilp
-           p = filter_soilp(f)
-           c = pcolumn(p)
-             if(sumfrootc(p) > 0._r8)then 
-                rootfr(p,lev) = frootc_dz(p,lev)/sumfrootc(p)
-             end if
-             if(ivt(p) >= npcropmin .and. .not. croplive(p))then
-! CROPS are dormant, there are no roots! 
-! but, need an initial frootr so crops can start root production
-                 if (lev <  2)then
-                    rootfr(p,lev) = .5_r8*( exp(-roota_par(patch%itype(p)) * zi(c,lev-1))  &
-                                   + exp(-rootb_par(patch%itype(p)) * zi(c,lev-1))  &
-                                   - exp(-roota_par(patch%itype(p)) * zi(c,lev  ))  &
-                                   - exp(-rootb_par(patch%itype(p)) * zi(c,lev  )) )
-                 elseif (lev == 2) then
-                     rootfr(p,lev) = .5_r8*( exp(-roota_par(patch%itype(p)) * zi(c,lev-1))  &
-                                    + exp(-rootb_par(patch%itype(p)) * zi(c,lev-1)) )
-                 else
-                     rootfr(p,lev) =  0.0_r8
-                 end if
-      
-             end if
-          end do
-     end do
-
-!**********************
-     deallocate(sumrswa)
-     deallocate(sumrsmn)
-     deallocate(sumfrootc)
-     deallocate(rsmn)
-     deallocate(rswa)
-     deallocate(w_limit)
-
-     end associate
-
- end subroutine CNRootDyn
-
-end module CNRootDynMod
diff --git a/src/biogeophys/IrrigationMod.F90 b/src/biogeophys/IrrigationMod.F90
index 27cf050dd3..11c9132eea 100644
--- a/src/biogeophys/IrrigationMod.F90
+++ b/src/biogeophys/IrrigationMod.F90
@@ -221,9 +221,8 @@ module IrrigationMod
   ! There is no reason to make this a tunable parameter, because the behavior it governs
   ! (the trigger for irrigation) can be tuned via other parameters.
   !
-  ! TODO(wjs, 2016-09-08) It looks like there is other code in CLM that also uses an
-  ! assumed wilting point (CNRootDynMod, maybe others). We should probably make this a
-  ! shared parameter, e.g., in clm_varcon.
+  ! TODO(wjs, 2016-09-08, updated by slevis 2024-07-06) assumed wilting point:
+  ! Make this a shared parameter? E.g., in clm_varcon
   real(r8), parameter, private :: wilting_point_smp = -150000._r8
 
   ! Conversion factors
diff --git a/src/biogeophys/SoilStateType.F90 b/src/biogeophys/SoilStateType.F90
index e301cc27b9..2e7225f962 100644
--- a/src/biogeophys/SoilStateType.F90
+++ b/src/biogeophys/SoilStateType.F90
@@ -9,7 +9,7 @@ module SoilStateType
   use abortutils      , only : endrun
   use clm_varpar      , only : nlevsoi, nlevgrnd, nlevlak, nlayer, nlevsno, nlevmaxurbgrnd
   use clm_varcon      , only : spval
-  use clm_varctl      , only : use_hydrstress, use_cn, use_lch4, use_dynroot, use_fates
+  use clm_varctl      , only : use_hydrstress, use_cn, use_lch4, use_fates
   use clm_varctl      , only : iulog, hist_wrtch4diag
   use LandunitType    , only : lun                
   use ColumnType      , only : col                
@@ -231,20 +231,6 @@ subroutine InitHistory(this, bounds)
             ptr_col=this%bsw_col, default='inactive')
     end if
 
-    if (use_dynroot) then
-       this%rootfr_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='ROOTFR', units='proportion', type2d='levgrnd', &
-            avgflag='A', long_name='fraction of roots in each soil layer', &
-            ptr_patch=this%rootfr_patch, default='active')
-    end if
-
-    if ( use_dynroot ) then
-       this%root_depth_patch(begp:endp) = spval
-        call hist_addfld1d (fname='ROOT_DEPTH', units="m", &
-             avgflag='A', long_name='rooting depth', &
-             ptr_patch=this%root_depth_patch )
-     end if
-
     if (use_cn) then
        this%rootr_patch(begp:endp,:) = spval
        call hist_addfld2d (fname='ROOTR', units='proportion', type2d='levgrnd', &
@@ -393,15 +379,7 @@ subroutine Restart(this, bounds, ncid, flag)
          scale_by_thickness=.true., &
          interpinic_flag='interp', readvar=readvar, data=this%hk_l_col)
 
-     if( use_dynroot ) then
-         call restartvar(ncid=ncid, flag=flag, varname='rootfr', xtype=ncd_double,  &
-              dim1name='pft', dim2name='levgrnd', switchdim=.true., &
-              long_name='root fraction', units='', &
-              scale_by_thickness=.false., &
-              interpinic_flag='interp', readvar=readrootfr, data=this%rootfr_patch)
-     else
-         readrootfr = .false.
-     end if
+     readrootfr = .false.
      if (flag=='read' .and. .not. readrootfr ) then
             if (masterproc) then
                write(iulog,*) "can't find rootfr in restart (or initial) file..."
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 0daedbbb1f..cbfcbfd8ea 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -426,12 +426,6 @@ module clm_varctl
 
   logical, public :: use_hydrstress = .false. ! true => use plant hydraulic stress calculation
 
-  !----------------------------------------------------------
-  ! dynamic root switch
-  !----------------------------------------------------------
-
-  logical, public :: use_dynroot = .false. ! true => use dynamic root module
-
   !----------------------------------------------------------
   ! glacier_mec control variables: default values (may be overwritten by namelist)
   !----------------------------------------------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 46d9e9958a..4773cc6921 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -272,8 +272,6 @@ subroutine control_init(dtime)
 
     namelist /clm_inparm/ use_hydrstress
 
-    namelist /clm_inparm/ use_dynroot
-
     namelist /clm_inparm/  &
          use_c14_bombspike, atm_c14_filename, use_c13_timeseries, atm_c13_filename
 
@@ -613,11 +611,6 @@ subroutine control_init(dtime)
             errMsg(sourcefile, __LINE__))
     end if
 
-    if ( use_dynroot .and. use_hydrstress ) then
-       call endrun(msg=' ERROR:: dynroot and hydrstress can NOT be on at the same time'//&
-            errMsg(sourcefile, __LINE__))
-    end if
-
     ! Check on run type
     if (nsrest == iundef) then
        call endrun(msg=' ERROR:: must set nsrest'//&
@@ -842,8 +835,6 @@ subroutine control_spmd()
 
     call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier)
 
-    call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier)
-
     if (use_cn .or. use_fates) then
        ! vertical soil mixing variables
        call mpi_bcast (som_adv_flux, 1, MPI_REAL8,  0, mpicom, ier)
@@ -1130,7 +1121,6 @@ subroutine control_print ()
     write(iulog,*) '   user-defined soil layer structure = ', soil_layerstruct_userdefined
     write(iulog,*) '   user-defined number of soil layers = ', soil_layerstruct_userdefined_nlevsoi
     write(iulog,*) '   plant hydraulic stress = ', use_hydrstress
-    write(iulog,*) '   dynamic roots          = ', use_dynroot
     if (nsrest == nsrContinue) then
        write(iulog,*) 'restart warning:'
        write(iulog,*) '   Namelist not checked for agreement with initial run.'
diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90
index e5379100e0..7988b57e75 100644
--- a/src/main/pftconMod.F90
+++ b/src/main/pftconMod.F90
@@ -280,9 +280,6 @@ module pftconMod
      real(r8), allocatable :: FUN_fracfixers(:)   ! Fraction of C that can be used for fixation.    
 
 
-     ! pft parameters for dynamic root code
-     real(r8), allocatable :: root_dmx(:)     !maximum root depth
-
    contains
 
      procedure, public  :: Init
@@ -494,7 +491,6 @@ subroutine InitAllocate (this)
     allocate( this%kn_nonmyc     (0:mxpft) )
     allocate( this%kr_resorb     (0:mxpft) )
     allocate( this%perecm        (0:mxpft) )
-    allocate( this%root_dmx      (0:mxpft) )
     allocate( this%fun_cn_flex_a (0:mxpft) )
     allocate( this%fun_cn_flex_b (0:mxpft) )
     allocate( this%fun_cn_flex_c (0:mxpft) )
@@ -520,7 +516,7 @@ subroutine InitRead(this)
     use fileutils   , only : getfil
     use ncdio_pio   , only : ncd_io, ncd_pio_closefile, ncd_pio_openfile, file_desc_t
     use ncdio_pio   , only : ncd_inqdid, ncd_inqdlen
-    use clm_varctl  , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage, z0param_method
+    use clm_varctl  , only : paramfile, use_fates, use_flexibleCN, use_biomass_heat_storage, z0param_method
     use spmdMod     , only : masterproc
     use CLMFatesParamInterfaceMod, only : FatesReadPFTs
     use SoilBiogeochemDecompCascadeConType, only : mimics_decomp, decomp_method
@@ -1105,13 +1101,8 @@ subroutine InitRead(this)
     end if
 
     !
-    ! Dynamic Root variables for crops
     !
-    if ( use_crop .and. use_dynroot )then
-       call ncd_io('root_dmx', this%root_dmx, 'read', ncid, readvar=readv)
-       if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-    end if
-   
+    !
     call ncd_io('nstem',this%nstem, 'read', ncid, readvar=readv)
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
     call ncd_io('taper',this%taper, 'read', ncid, readvar=readv)
@@ -1583,7 +1574,6 @@ subroutine Clean(this)
     deallocate( this%kn_nonmyc)
     deallocate( this%kr_resorb)
     deallocate( this%perecm)
-    deallocate( this%root_dmx)
     deallocate( this%fun_cn_flex_a)
     deallocate( this%fun_cn_flex_b)
     deallocate( this%fun_cn_flex_c)

From a5b4d34720d81eac9f052ea7e8230af57955dee8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 9 Jul 2024 21:57:55 -0600
Subject: [PATCH 0648/1248] Fix the lnd_tuning_mode for the zendersoil files

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 48 +++++++++----------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index c6430bfff2..c535bc96e4 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2419,53 +2419,53 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam6.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam6.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam5.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam5.0"
 >lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam5.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam5.0"
 >lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam5.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam5.0"
 >lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam4.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam4.0"
 >lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam4.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam4.0"
 >lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam4.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam4.0"
 >lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam4.0" hgrid="0.9x1.25"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam4.0" hgrid="0.9x1.25"
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam4.0" hgrid="0.9x1.25"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam4.0" hgrid="0.9x1.25"
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam4.0" hgrid="0.9x1.25"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam4.0" hgrid="0.9x1.25"
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam7.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam7.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam7.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_cam6.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_cam6.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_cam6.0"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_CRUv7"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_CRUv7"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_CRUv7"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_CRUv7"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_CRUv7"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_CRUv7"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam45_GSWP3v1"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_GSWP3v1"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam50_GSWP3v1"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_GSWP3v1"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
-<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="cam51_GSWP3v1"
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_GSWP3v1"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 
 <stream_meshfile_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd"

From c4e1de68a319dc2effe4e5dc7f28ddadc8b3a775 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 9 Jul 2024 23:54:45 -0600
Subject: [PATCH 0649/1248] Add clm6_0 for Zdust

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index c535bc96e4..a2200cb7fa 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2419,54 +2419,72 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_cam6.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam5.0"
 >lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam5.0"
 >lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam5.0"
 >lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_cam5.0"
+>lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam4.0"
 >lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam4.0"
 >lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam4.0"
 >lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_cam4.0"
+>lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam4.0" hgrid="0.9x1.25"
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam4.0" hgrid="0.9x1.25"
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam4.0" hgrid="0.9x1.25"
 >lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_cam4.0" hgrid="0.9x1.25"
+>lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_cam7.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_cam6.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_cam6.0"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_CRUv7"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_CRUv7"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_CRUv7"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_CRUv7"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_GSWP3v1"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_0_GSWP3v1"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm5_1_GSWP3v1"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_GSWP3v1"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 
 <stream_meshfile_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd"
 >lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c230730.nc</stream_meshfile_zendersoilerod>

From 97b8c552f4df54eff77f05cb1dad078c2fa2908e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 10 Jul 2024 00:07:48 -0600
Subject: [PATCH 0650/1248] Add files for the new clm60cam7 test mod

---
 .../clm/clm60cam7LndTuningMode/include_user_mods             | 1 +
 .../testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands  | 5 +++++
 2 files changed, 6 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands

diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands
new file mode 100644
index 0000000000..7dd25a08bf
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+./xmlchange LND_TUNING_MODE="clm6_0_cam7.0"
+./xmlchange ROF_NCPL='$ATM_NCPL'
+

From 197e8abb184425d1ed46c53435340a2803efdd3a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 10 Jul 2024 00:14:35 -0600
Subject: [PATCH 0651/1248] Update expected fail for new test

---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index dad6acb63d..3c3bde2ff6 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -44,7 +44,7 @@
     </phase>
   </test>
 
-  <test name="PEM_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam6LndTuningMode">
+  <test name="PEM_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningMode">
     <phase name="COMPARE_base_modpes">
       <status>FAIL</status>
       <issue>#2542</issue>

From 334b144b59ce0d649116408be1d67007c0ff6d14 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 10 Jul 2024 01:38:21 -0600
Subject: [PATCH 0652/1248] Fix typo in lnd_tuning_mode for Zender dust
 emission soil eroditability file

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fbf7b9a8bc..b3141f1b42 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4002,7 +4002,7 @@ sub setup_logic_dust_emis {
         foreach my $option ( @zender_files_in_lnd_opts ) {
            add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $option,
                        'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source,
-                       'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} );
+                       'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
         }
      } else {
         foreach my $option ( @zender_files_in_lnd_opts ) {

From 734dbf2e24b7f98d108e3ab9a6605f978cdb5787 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 10 Jul 2024 13:34:29 -0600
Subject: [PATCH 0653/1248] Update change files

---
 doc/ChangeLog | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 95 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 2ab7676ddc..9f62ca5a87 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,98 @@
 ===============================================================
+Tag name: ctsm5.2.009
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Wed 10 Jul 2024 12:21:23 PM MDT
+One-line Summary: Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names
+
+Purpose and description of changes
+----------------------------------
+
+Changes so that CAM7 is allowed for the land-tuning mode. Allow "C" and "E" after period designation in long compset names. Fix an
+issue with Zender dust emission soil eroditability files.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes #2480 -- cam7 lnd_tuning_mode
+   Fixes #2634 -- allow period part of long-compset name to have a "C" or "E"
+   Fixes #2637 -- bad lnd_tuning_mode for Zender soil eroditability file settings
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+   LND_TUNING_MODE will fail with an error for CAM (that's NOT cam4/cam5/cam6), or CPLHIST with CLM51
+   use CLM60 instead
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   Add lnd_tuning_mode options for cam7.0 to namelist defaults
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   lnd_tuning_mode options duplicate a bunch of XML code lines and should be refactored
+
+Changes to tests or testing:
+  Add cam7.0 test mod directories
+  Change tests for clm6_0_cam6.0 lnd_tuning_mode to clm6_0_cam7.0
+
+Testing summary: regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Only the cam4/cam5 lnd_tuning_mode tests
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: lnd_tuning_mode ending with _cam4.0 or _cam5.0 suffix with zender_soil_erod_source='lnd'
+    - what platforms/compilers: All
+    - nature of change: new dust emissions
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+  #2632 -- Handle CAM7
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.008
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri 28 Jun 2024 12:22:46 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index ea9417fe41..22a9b12230 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.009     erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names
        ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
 tmp-240620.n03.ctsm5.2.007  06/27/2024 Set upland hillslope column fsat values to zero (samrabin)
 tmp-240620.n02.ctsm5.2.007  06/21/2024 Another update of git-fleximod (erik)

From 525914480cdbb7aab6963942c284ae80972b37d8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 10 Jul 2024 13:47:58 -0600
Subject: [PATCH 0654/1248] Add cam7 testing and change tests for cam6.0 to
 cam7.0

---
 bld/unit_testers/build-namelist_test.pl | 26 ++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 53c71ae0e9..183a511020 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3254;
+my $ntests = 3278;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2001;
+   $ntests += 1981;
 }
 plan( tests=>$ntests );
 
@@ -414,17 +414,17 @@ sub cat_and_create_namelistinfile {
    $mode = "-phys $phys";
    &make_config_cache($phys);
    foreach my $options (
-                      "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res ne0np4.ARCTICGRIS.ne30x8 -bgc sp -use_case 1850_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res 0.9x1.25 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res 0.9x1.25 -bgc bgc -crop -use_case 20thC_transient -namelist '&a start_ymd=19500101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res ne0np4CONUS.ne30x8 -bgc sp -use_case 2000_control  -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20030101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res 1.9x2.5 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam6.0",
+                      "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res ne0np4.ARCTICGRIS.ne30x8 -bgc sp -use_case 1850_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res 0.9x1.25 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res 0.9x1.25 -bgc bgc -crop -use_case 20thC_transient -namelist '&a start_ymd=19500101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res ne0np4CONUS.ne30x8 -bgc sp -use_case 2000_control  -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20030101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res 1.9x2.5 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam7.0",
                       "-res 1x1_brazil -no-megan -use_case 2000_control -lnd_tuning_mode ${phys}_CRUv7",
-                      "-res C96 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam6.0",
-                      "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam6.0",
+                      "-res C96 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam7.0",
+                      "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam7.0",
                      ) {
       &make_env_run();
       eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
@@ -1802,7 +1802,7 @@ sub cat_and_create_namelistinfile {
   my $mode = "-phys $phys";
   &make_config_cache($phys);
   my @forclist = ();
-  @forclist = ( "CRUv7", "GSWP3v1", "cam6.0", "cam5.0", "cam4.0" );
+  @forclist = ( "CRUv7", "GSWP3v1", "cam7.0", "cam6.0", "cam5.0", "cam4.0" );
   foreach my $forc ( @forclist ) {
      foreach my $bgc ( "sp", "bgc" ) {
         my $lndtuningmode = "${phys}_${forc}";

From 237f84815c06b9ea86eb00f96b29cc35abd044c8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 10 Jul 2024 15:11:49 -0600
Subject: [PATCH 0655/1248] Revert "Add ._r8 to hardwired constants"

This reverts commit d940ee014cb52f92cdc0da415084f349ab45abae
because answers were changing from the baseline in tests
ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream
ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream
---
 src/biogeochem/VOCEmissionMod.F90 | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
index 7ba90fd457..9833fe3de9 100644
--- a/src/biogeochem/VOCEmissionMod.F90
+++ b/src/biogeochem/VOCEmissionMod.F90
@@ -835,13 +835,13 @@ function get_gamma_SM(btran_in)
     real(r8),intent(in) :: btran_in
     
     !!!------- the drought algorithm--------
-    real(r8), parameter :: a1 = -7.4463_r8
-    real(r8), parameter :: b1 = 3.2552_r8
+    real(r8), parameter :: a1 = -7.4463      
+    real(r8), parameter :: b1 = 3.2552       
     real(r8)            :: get_gamma_SM
-             if (btran_in >= 1._r8) then
+             if (btran_in >= 1.) then
                 get_gamma_SM = 1
              else
-                get_gamma_SM = 1._r8 / (1._r8 + b1 * exp(a1 * (btran_in - 0.2_r8)))
+                get_gamma_SM = 1/(1+b1*exp(a1*(btran_in-0.2)))
              endif 
   end function get_gamma_SM
  
@@ -968,9 +968,9 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
        topt = co1 + (co2 * (t_veg240_in-tstd0))
        if ( (ivt_in == nbrdlf_dcd_brl_shrub) ) then  ! boreal-deciduous-shrub
        ! coming from BEAR-oNS campaign willows results
-             Eopt = 7.9_r8 * exp (0.217_r8 * (t_veg24_in - 273.15_r8 - 24.0_r8))
+             Eopt = 7.9 * exp (0.217_r8 * (t_veg24_in-273.15_r8-24.0_r8))
        else if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-             Eopt = exp(0.12_r8 * (t_veg240_in - 288.15_r8))
+             Eopt = exp(0.12*(t_veg240_in-288.15_r8))
        else
              Eopt = Ceo_in * exp (co4 * (t_veg24_in-tstd0)) * exp(co4 * (t_veg240_in -tstd0))
        endif
@@ -982,13 +982,13 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     x = ( (1._r8/topt) - (1._r8/(t_veg_in)) ) / ct3
     ! for the boreal grass from BEAR-oNS campaign
     if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-        bet_arc_c3 = 95._r8 + 9.49_r8 * exp(0.53_r8 * (288.15_r8 - t_veg240_in))
-        if (bet_arc_c3 > 300._r8) then
-            bet_arc_c3 = 300._r8
+        bet_arc_c3  = 95+9.49*exp(0.53*(288.15_r8-t_veg240_in))
+        if (bet_arc_c3 .gt. 300) then
+            bet_arc_c3 = 300
         endif
-        gamma_t_LDF = Eopt * exp(bet_arc_c3 * ((1._r8 / 303.15_r8 - 1.0_r8 / t_veg_in) / ct3))
+        gamma_t_LDF = Eopt * exp(bet_arc_c3*((1/303.15_r8 - 1.0_r8/(t_veg_in))/ct3))
     else
-        gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x) / (ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
+        gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x)/(ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
     endif
     
     

From ee3e6a678ff3c336fdc1bc17c5a61ed8557d92e9 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 10 Jul 2024 17:21:18 -0600
Subject: [PATCH 0656/1248] Update ChangeLog/ChangeSum

---
 doc/ChangeLog | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 78 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 9f62ca5a87..f9fa259a05 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,81 @@
 ===============================================================
+Tag name: ctsm5.2.010
+Originator(s): @cathyxinchangli (Cathy Xinchang Li, U of Illinois - Urbana-Champaign), @Face2sea, @olyson, @fang-bowen, @keerzhang1
+Date: Wed 10 Jul 2024 05:00:24 PM MDT
+One-line Summary: Explicit A/C adoption
+
+Purpose and description of changes
+----------------------------------
+
+ Code changes for adding an explicit air-conditioning (AC) adoption parameterization scheme in CLMU. This includes adding a new time-varying input variable (AC adoption rate, p_ac), changes to building energy calculations, and a toggle (new namelist variable urban_explicit_ac)
+
+ In this tag we keep the change off by default in order to show that answers do not change:
+ - If explicit AC adoption is off, the p_ac_[TBD/HD/MD] variables are set to 1 universally, and the building interior setpoints (tbuildmax_[TBD/HD/MD]) remain unchanged, to ensure the model reproduces previous results.
+ - If explicit AC adoption is on, the p_ac_[TBD/HD/MD] variables take on actual AC adoption rate values (present-day global data were developed together with the code change), and tbuildmax_[TBD/HD/MD] are set to 300K/27°C universally.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2254 Explicitly representing air-conditioning adoption in CESM
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ New namelist variable urban_explicit_ac = .false. by default
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ The default urban time-varying input data file (namelist variable stream_fldfilename_urbantv) now includes p_ac_[TBD/HD/MD] variables, whether or not the explicit-AC-adoption scheme is on and the new file has been rimported to svn: CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc
+
+Changes to documentation:
+
+Substantial timing or memory changes:
+[e.g., check PFS test in the test suite and look at timings, if you
+expect possible significant timing changes]
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- IN PROGRESS
+    izumi -------
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+ No, because we have introduced the changes as default .false. at this time
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2275
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.009
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Wed 10 Jul 2024 12:21:23 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 22a9b12230..be04c9c22e 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.010 multiple 07/10/2024 Explicit A/C adoption
        ctsm5.2.009     erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names
        ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
 tmp-240620.n03.ctsm5.2.007  06/27/2024 Set upland hillslope column fsat values to zero (samrabin)

From 4ca2b6aeeb3388efa9b4026b826d902d8a9f6f95 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 10 Jul 2024 18:17:29 -0600
Subject: [PATCH 0657/1248] Add error: matrixcn not ok with NTHRDS_LND > 1 (the
 check does not work)

---
 bld/CLMBuildNamelist.pm                 | 16 ++++++++++++++--
 bld/unit_testers/build-namelist_test.pl |  2 +-
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 329030d985..7038351688 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1655,7 +1655,7 @@ sub process_namelist_inline_logic {
   if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) {
     setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   }
-  setup_logic_cnmatrix($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_cnmatrix($opts,  $nl_flags, $definition, $defaults, $nl, $envxml_ref);
   setup_logic_spinup($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
@@ -4640,7 +4640,7 @@ sub setup_logic_cnmatrix {
     #
     # Set some default options related to the CN Matrix options
     #
-    my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+    my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;
 
     my @matrixlist = ( "use_matrixcn", "hist_wrt_matrixcn_diag" );
     foreach my $var ( @matrixlist ) {
@@ -4650,6 +4650,18 @@ sub setup_logic_cnmatrix {
                 , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
     }
     @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" );
+    # Matrix items can't be on for NTHRDS_LND > 1
+    my $var_xml = "NTHRDS_LND";
+    my $val_xml = int($envxml_ref->{$var_xml});
+    print "$var_xml = $val_xml";
+    if ( $val_xml > 1) {
+       foreach my $var ( @matrixlist ) {
+          if ( &value_is_true($nl->get_value($var)) ) {
+             $log->warning("$var and $var_xml > 1 causes a clm threading test to FAIL (as of 2024/7/10), so use at your own risk." );
+          }
+       }
+    }
+
     # Matrix items can't be on for transient
     if (not string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
        foreach my $var ( @matrixlist ) {
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 9b83f9e7ec..df159a8870 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -42,7 +42,7 @@ sub make_env_run {
     my %settings = @_;
 
     # Set default settings
-    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" );
+    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NTHRDS_LND=>"1", NEONSITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
        $env_vars{$item} = $settings{$item};

From 17fb3d8ee57c94c757405b8f77afcf97de5b927f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 11 Jul 2024 01:27:49 -0600
Subject: [PATCH 0658/1248] Changes to remove dust_emis namelist items from
 CTSM fortran code and use shr_dust_emis_mod from CMEPS

---
 components/cmeps                               |  2 +-
 src/biogeochem/DustEmisBase.F90                |  1 -
 src/biogeochem/DustEmisFactory.F90             | 14 ++++++--------
 .../DustEmis_test/test_DustEmisZender2003.pf   |  2 ++
 src/cpl/nuopc/lnd_import_export.F90            |  5 +++++
 .../share_esmf/ZenderSoilErodStreamType.F90    | 18 ++++++------------
 src/main/clm_varctl.F90                        |  5 -----
 src/main/controlMod.F90                        |  6 ------
 8 files changed, 20 insertions(+), 33 deletions(-)

diff --git a/components/cmeps b/components/cmeps
index 6384ff4e4a..e1335d32fc 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 6384ff4e4a6bc82a678f9419a43ffbd5d53ac209
+Subproject commit e1335d32fca0e5571a0d5a7edb0d1473266b7923
diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
index c5e4260634..47f2f32688 100644
--- a/src/biogeochem/DustEmisBase.F90
+++ b/src/biogeochem/DustEmisBase.F90
@@ -31,7 +31,6 @@ module DustEmisBase
   use LandunitType         , only : lun
   use ColumnType           , only : col
   use PatchType            , only : patch
-  use clm_varctl           , only : dust_emis_method
   !
   ! !PUBLIC TYPES
   implicit none
diff --git a/src/biogeochem/DustEmisFactory.F90 b/src/biogeochem/DustEmisFactory.F90
index 371e77d6dc..24162fde24 100644
--- a/src/biogeochem/DustEmisFactory.F90
+++ b/src/biogeochem/DustEmisFactory.F90
@@ -28,9 +28,9 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis)
         !---------------------------------------------------------------------------
         use DustEmisBase      , only : dust_emis_base_type
         use DustEmisZender2003, only : dust_emis_zender2003_type
-        use clm_varctl        , only : dust_emis_method
         use decompMod         , only : bounds_type
         use shr_kind_mod      , only : CL => shr_kind_cl
+        use shr_dust_emis_mod , only : is_dust_emis_zender, is_dust_emis_leung
         implicit none
         ! Arguments
         class(dust_emis_base_type), allocatable :: dust_emis
@@ -38,20 +38,18 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis)
         character(len=*),  intent(in) :: NLFilename
         ! Local variables
 
-        select case ( trim(dust_emis_method) )
-
-        case( "Zender_2003" )
+        if ( is_dust_emis_zender() )then
            allocate(dust_emis, source=dust_emis_zender2003_type() )
         
         ! This will be added when the Leung2023 comes in
-        !case( "Leung_2023" )
+        !else if ( is_dust_emis_leung() )
         !  allocate(dust_emis, source=dust_emis_zender2003_type() )
-        case default
-           write(iulog,*) 'ERROR: unknown dust_emis_method: ', dust_emis_method, &
+        else
+           write(iulog,*) 'ERROR: unknown dust_emis_method: ', &
                            errMsg(sourcefile, __LINE__)
            call endrun( "Unrecognized dust_emis_method"  )
 
-        end select
+        end if
 
         call dust_emis%Init(bounds, NLFilename)
 
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 8641b8cceb..0289cadabc 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -9,6 +9,7 @@ module test_DustEmisZender2003
   use DustEmisZender2003
   use shr_kind_mod , only : r8 => shr_kind_r8
   use DustEmisFactory, only : create_dust_emissions
+  use shr_dust_emis_mod, only : dust_emis_set_options
 
   implicit none
 
@@ -37,6 +38,7 @@ contains
     call this%input%setUp()
  
     ! Create the dust emission object last
+    call dust_emis_set_options( 'Zender_2003', 'atm')
     allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))
   end subroutine setUp
 
diff --git a/src/cpl/nuopc/lnd_import_export.F90 b/src/cpl/nuopc/lnd_import_export.F90
index b9966f81e9..624590b9a6 100644
--- a/src/cpl/nuopc/lnd_import_export.F90
+++ b/src/cpl/nuopc/lnd_import_export.F90
@@ -160,9 +160,11 @@ subroutine advertise_fields(gcomp, flds_scalar_name, glc_present, cism_evolve, r
 
     use shr_carma_mod     , only : shr_carma_readnl
     use shr_ndep_mod      , only : shr_ndep_readnl
+    use shr_dust_emis_mod , only : shr_dust_emis_readnl
     use shr_fire_emis_mod , only : shr_fire_emis_readnl
     use clm_varctl        , only : ndep_from_cpl
     use controlMod        , only : NLFilename
+    use spmdMod           , only : mpicom
 
     ! input/output variables
     type(ESMF_GridComp)            :: gcomp
@@ -237,6 +239,9 @@ subroutine advertise_fields(gcomp, flds_scalar_name, glc_present, cism_evolve, r
 
     ! The following namelist reads should always be called regardless of the send_to_atm value
 
+    ! Dust emissions from land to atmosphere
+    call shr_dust_emis_readnl( mpicom, "drv_flds_in")
+
     ! Dry Deposition velocities from land - ALSO initialize drydep here
     call shr_drydep_readnl("drv_flds_in", drydep_nflds)
 
diff --git a/src/cpl/share_esmf/ZenderSoilErodStreamType.F90 b/src/cpl/share_esmf/ZenderSoilErodStreamType.F90
index 194e022132..32e776063b 100644
--- a/src/cpl/share_esmf/ZenderSoilErodStreamType.F90
+++ b/src/cpl/share_esmf/ZenderSoilErodStreamType.F90
@@ -42,7 +42,6 @@ module ZenderSoilErodStreamType
 
   ! ! PRIVATE DATA:
   type, private :: streamcontrol_type
-     character(len=CL)  :: zender_soil_erod_source             ! if calculed in lnd or atm
      character(len=CL)  :: stream_fldFileName_zendersoilerod   ! data Filename
      character(len=CL)  :: stream_meshfile_zendersoilerod      ! mesh Filename
      character(len=CL)  :: zendersoilerod_mapalgo              ! map algo
@@ -179,7 +178,7 @@ logical function UseStreams(this)
     ! file is being used with it
     !
     ! !USES:
-    use clm_varctl, only : dust_emis_method
+    use shr_dust_emis_mod, only : is_dust_emis_zender, is_zender_soil_erod_from_land
     !
     ! !ARGUMENTS:
     implicit none
@@ -189,7 +188,7 @@ logical function UseStreams(this)
     if ( .not. control%namelist_set )then
        call endrun(msg=' ERROR namelist NOT set before being used'//errMsg(sourcefile, __LINE__))
     end if
-    if ( (trim(dust_emis_method) == 'Zender_2003') .and. (control%zender_soil_erod_source == "lnd") )then
+    if ( is_dust_emis_zender() .and. is_zender_soil_erod_from_land() )then
        UseStreams = .true.
     else
        UseStreams = .false.
@@ -289,6 +288,7 @@ subroutine ReadNML(this, bounds, NLFilename)
    use shr_nl_mod       , only : shr_nl_find_group_name
    use shr_log_mod      , only : errMsg => shr_log_errMsg
    use shr_mpi_mod      , only : shr_mpi_bcast
+   use shr_dust_emis_mod, only : is_zender_soil_erod_from_land
    !
    ! arguments
    implicit none
@@ -304,14 +304,13 @@ subroutine ReadNML(this, bounds, NLFilename)
    character(len=CL)  :: stream_meshfile_zendersoilerod = ' '
    character(len=CL)  :: zendersoilerod_mapalgo = ' '
    character(len=CL)  :: tmp_file_array(3)
-   character(len=3)   :: zender_soil_erod_source = 'atm'
    character(len=*), parameter :: namelist_name = 'zendersoilerod'    ! MUST agree with group name in namelist definition to read.
    character(len=*), parameter :: subName = "('zendersoilerod::ReadNML')"
    !-----------------------------------------------------------------------
 
    namelist /zendersoilerod/ &               ! MUST agree with namelist_name above
         zendersoilerod_mapalgo,  stream_fldFileName_zendersoilerod, &
-        stream_meshfile_zendersoilerod, zender_soil_erod_source
+        stream_meshfile_zendersoilerod
 
    ! Default values for namelist
 
@@ -330,12 +329,11 @@ subroutine ReadNML(this, bounds, NLFilename)
       close(nu_nml)
    endif
 
-   call shr_mpi_bcast(zender_soil_erod_source           , mpicom)
    call shr_mpi_bcast(zendersoilerod_mapalgo            , mpicom)
    call shr_mpi_bcast(stream_fldFileName_zendersoilerod , mpicom)
    call shr_mpi_bcast(stream_meshfile_zendersoilerod    , mpicom)
 
-   if (masterproc .and. (zender_soil_erod_source == "lnd") ) then
+   if (masterproc .and. is_zender_soil_erod_from_land() ) then
       write(iulog,*) ' '
       write(iulog,*) namelist_name, ' stream settings:'
       write(iulog,*) '  stream_fldFileName_zendersoilerod = ',stream_fldFileName_zendersoilerod
@@ -343,13 +341,10 @@ subroutine ReadNML(this, bounds, NLFilename)
       write(iulog,*) '  zendersoilerod_mapalgo            = ',zendersoilerod_mapalgo
    endif
 
-   if ( (trim(zender_soil_erod_source) /= 'atm') .and. (trim(zender_soil_erod_source) /= 'lnd')  )then
-      call endrun(msg=' ERROR zender_soil_erod_source must be either lnd or atm and is NOT'//errMsg(sourcefile, __LINE__))
-   end if
    tmp_file_array(1) = stream_fldFileName_zendersoilerod
    tmp_file_array(2) = stream_meshfile_zendersoilerod
    tmp_file_array(3) = zendersoilerod_mapalgo
-   if ( trim(zender_soil_erod_source) == 'lnd' )then
+   if ( is_zender_soil_erod_from_land() ) then
       do i = 1, size(tmp_file_array)
          if ( len_trim(tmp_file_array(i)) == 0 )then
             call endrun(msg=' ERROR '//trim(tmp_file_array(i))//' must be set when Zender_2003 is being used and zender_soil_erod_source is lnd'//errMsg(sourcefile, __LINE__))
@@ -365,7 +360,6 @@ subroutine ReadNML(this, bounds, NLFilename)
    this%stream_fldFileName_zendersoilerod = stream_fldFileName_zendersoilerod
    this%stream_meshfile_zendersoilerod    = stream_meshfile_zendersoilerod
    this%zendersoilerod_mapalgo            = zendersoilerod_mapalgo
-   this%zender_soil_erod_source           = zender_soil_erod_source
 
    this%namelist_set = .true.
 
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index cbfcbfd8ea..97c818af94 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -276,11 +276,6 @@ module clm_varctl
   ! option to activate OC in snow in SNICAR
   logical, public :: do_sno_oc = .false.  ! control to include organic carbon (OC) in snow
 
-  !----------------------------------------------------------
-  ! DUST emission method
-  !----------------------------------------------------------
-  character(len=25), public :: dust_emis_method = 'Zender_2003'  ! Dust emisison method to use: Zender_2003 or Leung_2023
-
   !----------------------------------------------------------
   ! C isotopes
   !----------------------------------------------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 4773cc6921..c92732806c 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -207,12 +207,6 @@ subroutine control_init(dtime)
          for_testing_no_crop_seed_replenishment, &
          z0param_method, use_z0m_snowmelt
 
-    ! NOTE: EBK 02/26/2024: dust_emis_method is here in CTSM temporarily until it's moved to CMEPS
-    ! See: https://github.com/ESCOMP/CMEPS/pull/429
-    ! Normally this should also need error checking and a broadcast, but since
-    ! there is only one hardcoded option right now that is unneeded.
-    namelist /clm_inparm/ dust_emis_method
-
     ! vertical soil mixing variables
     namelist /clm_inparm/  &
          som_adv_flux, max_depth_cryoturb

From 7dd9af0195592c2a2d9c49fc6767f53ea1bff128 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 11 Jul 2024 02:48:19 -0600
Subject: [PATCH 0659/1248] Update test number

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index a24b308620..cf5aedef9b 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3259;
+my $ntests = 3256;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2001;

From 18084b8614d36b6ec24860af95e34df400aa8872 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 11 Jul 2024 11:59:22 -0600
Subject: [PATCH 0660/1248] Final ChangeLog/ChangeSum

---
 doc/ChangeLog | 10 +++-------
 doc/ChangeSum |  2 +-
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index f9fa259a05..beca7fbd7f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.010
 Originator(s): @cathyxinchangli (Cathy Xinchang Li, U of Illinois - Urbana-Champaign), @Face2sea, @olyson, @fang-bowen, @keerzhang1
-Date: Wed 10 Jul 2024 05:00:24 PM MDT
+Date: Thu 11 Jul 2024 11:57:15 AM MDT
 One-line Summary: Explicit A/C adoption
 
 Purpose and description of changes
@@ -48,10 +48,6 @@ Changes to the datasets (e.g., parameter, surface or initial files):
 
 Changes to documentation:
 
-Substantial timing or memory changes:
-[e.g., check PFS test in the test suite and look at timings, if you
-expect possible significant timing changes]
-
 
 Testing summary:
 ----------------
@@ -60,8 +56,8 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho ----- IN PROGRESS
-    izumi -------
+    derecho ----- OK
+    izumi ------- OK
 
 Answer changes
 --------------
diff --git a/doc/ChangeSum b/doc/ChangeSum
index be04c9c22e..5df9aa34cf 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.010 multiple 07/10/2024 Explicit A/C adoption
+       ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption
        ctsm5.2.009     erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names
        ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
 tmp-240620.n03.ctsm5.2.007  06/27/2024 Set upland hillslope column fsat values to zero (samrabin)

From 976347ddcd0e158a54483b72f7a48d8825c96f37 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 11 Jul 2024 13:16:32 -0600
Subject: [PATCH 0661/1248] Update cmeps and ccs_config to versions used in
 #2590 which allows cases to build

---
 .gitmodules | 4 ++--
 ccs_config  | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index b48068c9f6..ee06997ce5 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm0.0.106
+fxtag = ccs_config_cesm1.0.0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
@@ -50,7 +50,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps0.14.73
+fxtag = cmeps0.14.77
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
diff --git a/ccs_config b/ccs_config
index 2ff978f92a..69a958581e 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit 2ff978f92a5ac9a6ab243e5c14d06a7e2d2f5799
+Subproject commit 69a958581ecd2d32ee9cb1c38bcd3847b8b920bf

From 170b3a518701e7fb0494423bcc9ef11d90e87f62 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 11 Jul 2024 13:17:21 -0600
Subject: [PATCH 0662/1248] Update cmeps and ccs_config to versions used in
 #2590 which allows cases to build

---
 components/cmeps | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/cmeps b/components/cmeps
index e1335d32fc..47fb4e633a 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit e1335d32fca0e5571a0d5a7edb0d1473266b7923
+Subproject commit 47fb4e633a76ec6d60969b1af751f90790387246

From ba28bea5ca49e44e48d3739647baae04915d805f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 11 Jul 2024 13:20:10 -0600
Subject: [PATCH 0663/1248] Update number of tests and comment out the whole
 values section as it fails without at least one thing set

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 cime_config/config_component.xml        | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index cf5aedef9b..5abb381c16 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -166,7 +166,7 @@ sub cat_and_create_namelistinfile {
 my $ntests = 3256;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2001;
+   $ntests += 1965;
 }
 plan( tests=>$ntests );
 
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 01990e162f..7500668905 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -166,11 +166,11 @@
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>
     <default_value>TRUE</default_value>
+    <!-- Until CAM sets dust settings in drv_flds_in this should only be TRUE
     <values>
-      <!-- Until CAM sets dust settings in drv_flds_in this should only be TRUE
       <value compset="CAM"  >FALSE</value>
-      -->
     </values>
+    -->
     <group>run_component_cpl</group>
     <file>env_run.xml</file>
     <desc>If CTSM will set the dust settings in drv_flds_in (TRUE), or if ATM (i.e. CAM) will - DO NOT EDIT (set by compset name)</desc>

From d67a354298714a5de2357a0216770b1b74603d09 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 11 Jul 2024 13:46:45 -0600
Subject: [PATCH 0664/1248] Correct number of tests in build-namelist_test and
 update ChangeLog

---
 bld/unit_testers/build-namelist_test.pl |  2 +-
 doc/ChangeLog                           | 78 +++++++++++++++++++++++++
 doc/ChangeSum                           |  3 +-
 3 files changed, 81 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 7c2be32719..02088eecbe 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3278;
+my $ntests = 3277;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 1981;
diff --git a/doc/ChangeLog b/doc/ChangeLog
index beca7fbd7f..3a33553f64 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,82 @@
 ===============================================================
+Tag name: ctsm5.2.011
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 11 Jul 2024 01:14:12 PM MDT
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+#2638 Remove use_dynroot and corresponding code and testing (slevis)
+#2623 Change a NIWO test to HARV and update expected failures (slevis)
+#2607 Fix py env create (wwieder)
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+Fixes #2451 Remove use_dynroot from clm codes and testing
+Fixes #2563 Unable to install ctsm_pylib environment for mksurfdata_esmf in CTSM5.2.005
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+Change a NIWO test to HARV and update expected failures
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - OK
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - OK
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- IN PROG
+    izumi ------- NOT STARTED
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Other details
+-------------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2638
+ https://github.com/ESCOMP/ctsm/pull/2623
+ https://github.com/ESCOMP/ctsm/pull/2607
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.010
 Originator(s): @cathyxinchangli (Cathy Xinchang Li, U of Illinois - Urbana-Champaign), @Face2sea, @olyson, @fang-bowen, @keerzhang1
 Date: Thu 11 Jul 2024 11:57:15 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 5df9aa34cf..892913c52f 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,11 +1,12 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.011   slevis 07/11/2024 Merge b4b-dev
        ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption
        ctsm5.2.009     erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names
        ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
 tmp-240620.n03.ctsm5.2.007  06/27/2024 Set upland hillslope column fsat values to zero (samrabin)
 tmp-240620.n02.ctsm5.2.007  06/21/2024 Another update of git-fleximod (erik)
-tmp-240620.n01.ctsm5.2.007  06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) (slevis)
+tmp-240620.n01.ctsm5.2.007  06/21/2024 Merge b4b-dev (slevis)
        ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly
        ctsm5.2.006   slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools
        ctsm5.2.005     erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems

From 4f436dcc855d00d0daf69c8d351cf8b19f525924 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 11 Jul 2024 15:48:50 -0600
Subject: [PATCH 0665/1248] Draft ChangeLog/ChangeSum files

---
 doc/ChangeLog | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 67 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 2ab7676ddc..4ebd09163a 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,70 @@
 ===============================================================
+Tag name: ctsm5.2.013
+Originator(s): sacks (Bill Sacks, UCAR/NCAR/CGD)
+Date: Thu 11 Jul 2024 03:38:12 PM MDT
+One-line Summary: Relax tolerance for truncating small snocan values in CanopyFluxes
+
+Purpose and description of changes
+----------------------------------
+
+Details in the PR #2457.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+Fixes #2444 Failing water isotope test on the ctsm5.2 branch
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to documentation: None
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+ Yes, roundoff.
+
+    - what code configurations: All
+    - what platforms/compilers: All
+    - nature of change: Changes start roundoff level and grow over time.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2457
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.008
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri 28 Jun 2024 12:22:46 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index ea9417fe41..1af9fcf58e 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.013    sacks 07/??/2024 Relax tolerance for truncating small snocan values in CanopyFluxes
        ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat
 tmp-240620.n03.ctsm5.2.007  06/27/2024 Set upland hillslope column fsat values to zero (samrabin)
 tmp-240620.n02.ctsm5.2.007  06/21/2024 Another update of git-fleximod (erik)

From 7994c82a4427860494c79611fc32fa0efecadeb3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 11 Jul 2024 16:29:12 -0600
Subject: [PATCH 0666/1248] Save crop date variables in testmods more
 frequently.

---
 cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm    | 7 +++++--
 .../testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
index a368e97593..aea8e39e6c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
@@ -9,9 +9,12 @@
 hist_fincl2  += 'DYN_COL_SOIL_ADJUSTMENTS_C'
 
 
-! Annual instantaneous crop variables (including per-sowing/per-harvest axes), per PFT.
+! Instantaneous crop variables (including per-sowing/per-harvest axes), per PFT.
+! Note that, under normal circumstances, these should only be saved annually.
+! That's needed for the mxsowings and mxharvests axes to make sense.
+! However, for testing purposes, it makes sense to save more frequently.
 hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS', 'GDD20_BASELINE', 'GDD20_SEASON_START', 'GDD20_SEASON_END'
-hist_nhtfrq(3) = 17520
+hist_nhtfrq(3) = -24
 hist_mfilt(3) = 1
 hist_type1d_pertape(3) = 'PFTS'
 hist_dov2xy(3) = .false.
diff --git a/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm
index 8f779ed011..18220de5ef 100644
--- a/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm
@@ -1,4 +1,4 @@
- hist_nhtfrq    = 0,-240,17520
+ hist_nhtfrq    = 0,-240,0
  hist_mfilt     = 1,1,1
 
 ! NOTE slevis (2024/2/23) Adding option for tests to pass. In the long term

From 014800df4825a909f3a0297951fcd4f8f05f232b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 11 Jul 2024 16:32:25 -0600
Subject: [PATCH 0667/1248] Add tweak_latlons.py.

---
 python/ctsm/crop_calendars/tweak_latlons.py | 168 ++++++++++++++++++++
 1 file changed, 168 insertions(+)
 create mode 100644 python/ctsm/crop_calendars/tweak_latlons.py

diff --git a/python/ctsm/crop_calendars/tweak_latlons.py b/python/ctsm/crop_calendars/tweak_latlons.py
new file mode 100644
index 0000000000..de35ced0d1
--- /dev/null
+++ b/python/ctsm/crop_calendars/tweak_latlons.py
@@ -0,0 +1,168 @@
+# %%
+import numpy as np
+import xarray as xr
+import os
+import sys
+from netCDF4 import Dataset
+import contextlib
+
+# -- add python/ctsm  to path (needed if we want to run this stand-alone)
+_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir)
+sys.path.insert(1, _CTSM_PYTHON)
+# pylint: disable=wrong-import-position
+from ctsm.mesh_maker import main as mesh_maker
+
+topdir = "/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/cropdata/calendars/processed/"
+file_list_in = [
+    "swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc",
+    "swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc",
+    "gdds_20230829_161011.nc",
+]
+file_mesh_in = (
+    "/glade/campaign/cesm/cesmdata/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc"
+)
+
+file_list_out = []
+coord_list = ["lat", "lon"]
+
+# %%
+
+
+def apply_tweak(ds, coord_str, tweak=1e-6):
+    # Apply tweak
+    da = ds[coord_str]
+    coord2 = da.values
+    coord2 += tweak
+    while np.any(coord2 == da.values):
+        tweak *= 10
+        coord2 = da.values
+        coord2 += tweak
+    coord_tweak = np.full_like(coord2, tweak)
+
+    # Ensure that no value is above maximum in input data. This is needed for mesh_maker to work.
+    max_coord = np.max(da.values)
+    where_toohigh = np.where(coord2 > max_coord)
+    Ntoohigh = len(where_toohigh[0])
+    if Ntoohigh != 1:
+        raise RuntimeError(f"Expected 1 coordinate value too high; got {Ntoohigh}")
+    coord2[where_toohigh] = max_coord
+    coord_tweak[where_toohigh] = max_coord
+
+    # Convert to DataArray
+    new_coords_dict = {coord_str: coord2}
+    da2 = xr.DataArray(
+        data=coord2,
+        coords=new_coords_dict,
+        dims=da.dims,
+        attrs=da.attrs,
+    )
+
+    # Replace coordinate in dataset
+    ds[coord_str] = da2
+
+    # Add a variable with the amount of the tweak
+    tweak_attrs = {}
+    if "standard_name" in da:
+        coord_name = da.attrs["standard_name"]
+    else:
+        coord_name = da.attrs["long_name"].replace("coordinate_", "")
+    tweak_attrs["standard_name"] = coord_name + "_tweak"
+    tweak_attrs[
+        "long_name"
+    ] = f"Amount {coord_name} was shifted to avoid ambiguous nearest neighbors"
+    tweak_attrs["units"] = da.attrs["units"]
+    da_tweak = xr.DataArray(
+        data=coord_tweak,
+        coords=new_coords_dict,
+        dims=da.dims,
+        attrs=tweak_attrs,
+    )
+    tweak_name = coord_str + "_tweak"
+    ds[tweak_name] = da_tweak
+
+    return ds
+
+
+# %% Apply tweak to all files
+
+for filename in file_list_in:
+    file_in = os.path.join(topdir, filename)
+    ds = xr.open_dataset(file_in)
+
+    for coord in coord_list:
+        ds = apply_tweak(ds, coord, tweak=1e-6)
+
+    # Set up for save
+    file_out = file_in.replace(".nc", ".tweaked_latlons.nc")
+    with Dataset(file_in, "r") as netcdf_file:
+        netcdf_format = netcdf_file.data_model
+
+    # Save
+    print(f"Saving {file_out}")
+    ds.to_netcdf(file_out, format=netcdf_format)
+    file_list_out.append(file_out)
+print("Done")
+
+
+# %% Ensure all files got the same tweaks
+
+ds = xr.open_dataset(file_list_out[0])
+
+for filename in file_list_out[1:]:
+    ds2 = xr.open_dataset(filename)
+    for coord in coord_list:
+        # Ensure that coordinates are the same
+        var = coord
+        assert np.array_equal(ds[var].values, ds2[var].values)
+        # Ensure that tweaks were the same
+        var = coord + "_tweak"
+        assert np.array_equal(ds[var].values, ds2[var].values)
+print("All good!")
+
+
+# %% Save new mesh file
+
+outfile_name = os.path.basename(file_mesh_in)
+outfile_name = outfile_name.replace(".nc", ".tweaked_latlons.nc")
+outdir = os.path.dirname(file_list_out[0])
+file_mesh_out = os.path.join(outdir, outfile_name)
+
+@contextlib.contextmanager
+def redirect_argv(arglist):
+    argv_tmp = sys.argv[:]
+    sys.argv=arglist
+    yield
+    sys.argv = argv_tmp
+
+
+mesh_maker_args = [
+    "mesh_maker",
+    "--input",
+    file_list_out[0],
+    "--output",
+    file_mesh_out,
+    "--lat",
+    "lat",
+    "--lon",
+    "lon",
+    "--overwrite",
+]
+print(f"Saving {file_mesh_out}...")
+with redirect_argv(mesh_maker_args):
+    mesh_maker()
+
+# Change format, if needed
+with Dataset(file_mesh_in, "r") as netcdf_file:
+    netcdf_format_in = netcdf_file.data_model
+with Dataset(file_mesh_out, "r") as netcdf_file:
+    netcdf_format_out = netcdf_file.data_model
+if netcdf_format_in != netcdf_format_out:
+    file_mesh_out_tmp = file_mesh_out + ".tmp"
+    os.rename(file_mesh_out, file_mesh_out_tmp)
+    ds = xr.open_dataset(file_mesh_out_tmp)
+    ds.to_netcdf(file_mesh_out, format=netcdf_format_in)
+    os.remove(file_mesh_out_tmp)
+
+
+print("Done")
+# %%

From 4c1d66f88985340b2b95dc909b55587475d75514 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 11 Jul 2024 16:37:20 -0600
Subject: [PATCH 0668/1248] mesh_type.py: Handle a broadcast error.

---
 python/ctsm/site_and_regional/mesh_type.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/site_and_regional/mesh_type.py b/python/ctsm/site_and_regional/mesh_type.py
index be785e745d..0260f1c816 100644
--- a/python/ctsm/site_and_regional/mesh_type.py
+++ b/python/ctsm/site_and_regional/mesh_type.py
@@ -235,8 +235,16 @@ def create_2d_coords(self):
             lons_size = self.center_lons.size
 
             # -- convert center points from 1d to 2d
-            self.center_lat2d = np.broadcast_to(self.center_lats[:], (lons_size, lats_size))
-            self.center_lon2d = np.broadcast_to(self.center_lons[:], (lons_size, lats_size))
+            try:
+                self.center_lat2d = np.broadcast_to(self.center_lats[:], (lons_size, lats_size))
+                self.center_lon2d = np.broadcast_to(self.center_lons[:], (lons_size, lats_size))
+            except ValueError:
+                self.center_lat2d = np.broadcast_to(
+                    np.expand_dims(self.center_lats[:], 0), (lons_size, lats_size)
+                )
+                self.center_lon2d = np.broadcast_to(
+                    np.expand_dims(self.center_lons[:], 1), (lons_size, lats_size)
+                )
         elif self.lat_dims == 2:
             # -- 2D lats and lons
             dims = self.center_lons.shape

From f11003ba4e751e7749ebf2ddfb7a26a73ebb04f7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 11 Jul 2024 16:37:46 -0600
Subject: [PATCH 0669/1248] mesh_type.py: Improve error for lon > 360.

---
 python/ctsm/site_and_regional/mesh_type.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/site_and_regional/mesh_type.py b/python/ctsm/site_and_regional/mesh_type.py
index 0260f1c816..47c0295593 100644
--- a/python/ctsm/site_and_regional/mesh_type.py
+++ b/python/ctsm/site_and_regional/mesh_type.py
@@ -359,7 +359,7 @@ def calculate_corners(self, unit="degrees"):
         )
         # Longitudes should stay within 0 to 360
         if np.any(self.corner_lons > 360.0):
-            abort("Corners have longitudes greater than 360")
+            abort(f"Corners have longitudes greater than 360 (max: {np.max(self.corner_lons)})")
         if np.any(self.corner_lons < 0.0):
             logger.warning(
                 "Corners have longitudes less than zero -- %s %s",

From 231b4ac4372421a714106ec10178416dcb3cb2c6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 11 Jul 2024 16:44:31 -0600
Subject: [PATCH 0670/1248] tweak_latlons.py: Add more files.

---
 python/ctsm/crop_calendars/tweak_latlons.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/python/ctsm/crop_calendars/tweak_latlons.py b/python/ctsm/crop_calendars/tweak_latlons.py
index de35ced0d1..89144a80ae 100644
--- a/python/ctsm/crop_calendars/tweak_latlons.py
+++ b/python/ctsm/crop_calendars/tweak_latlons.py
@@ -17,6 +17,9 @@
     "swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc",
     "swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc",
     "gdds_20230829_161011.nc",
+    "gdd20bl.copied_from.gdds_20230829_161011.v2.nc",
+    "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc",
+    "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc",
 ]
 file_mesh_in = (
     "/glade/campaign/cesm/cesmdata/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc"

From 9f186d489d9ce2d3b982cd367756dd43102262a8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 11 Jul 2024 16:45:50 -0600
Subject: [PATCH 0671/1248] Use tweaked_latlon cropcal inputs.

This avoids different "nearest neighbors" being chosen when using a different number of processors.
See https://github.com/orgs/esmf-org/discussions/261
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 22 +++++++++----------
 .../clm/sowingWindows/user_nl_clm             |  6 ++---
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index ae9f9dee6a..d1f9d8545c 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1704,17 +1704,17 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <model_year_align_cropcal_cultivar_gdds   >2000</model_year_align_cropcal_cultivar_gdds>
 
 <!-- crop calendars: default input files -->
-<stream_fldFileName_swindow_start cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
-<stream_fldFileName_swindow_end cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
-<stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
-<stream_meshfile_cropcal cropcals_rx=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>
-<stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_start>
-<stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc</stream_fldFileName_swindow_end>
-<stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.nc</stream_fldfilename_cultivar_gdds>
-<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.nc</stream_fldFileName_gdd20_baseline>
-<stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_start>
-<stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc</stream_fldFileName_gdd20_season_end>
-<stream_meshfile_cropcal cropcals_rx_adapt=".true.">share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc</stream_meshfile_cropcal>
+<stream_fldFileName_swindow_start cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
+<stream_fldFileName_swindow_end cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
+<stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
+<stream_meshfile_cropcal cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_meshfile_cropcal>
+<stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
+<stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
+<stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_start>
+<stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_end>
+<stream_meshfile_cropcal cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_meshfile_cropcal>
 
 <!-- lightning streams namelist defaults -->
 
diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
index 545e5f6ebd..7024e99b96 100644
--- a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
@@ -1,5 +1,5 @@
-stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
-stream_fldFileName_swindow_end = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
-stream_meshfile_cropcal = '$DIN_LOC_ROOT/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc'
+stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc'
+stream_fldFileName_swindow_end = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc'
+stream_meshfile_cropcal = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc'
 stream_year_first_cropcal_swindows = 2000
 stream_year_last_cropcal_swindows = 2000

From 3ce1bb42c09670d87cd9fdca86cdbd24b19fd1f2 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 11 Jul 2024 17:34:25 -0600
Subject: [PATCH 0672/1248] Code mods to get the error check in the previous
 commit to work

---
 bld/CLMBuildNamelist.pm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 7038351688..caa116e3bc 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4650,14 +4650,13 @@ sub setup_logic_cnmatrix {
                 , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
     }
     @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" );
-    # Matrix items can't be on for NTHRDS_LND > 1
-    my $var_xml = "NTHRDS_LND";
-    my $val_xml = int($envxml_ref->{$var_xml});
-    print "$var_xml = $val_xml";
+    # Matrix items can't be on for OMP_NUM_THREADS (also known as NTHRDS_LND) > 1
+    my $var_xml = "OMP_NUM_THREADS";
+    my $val_xml = $ENV{$var_xml};
     if ( $val_xml > 1) {
        foreach my $var ( @matrixlist ) {
           if ( &value_is_true($nl->get_value($var)) ) {
-             $log->warning("$var and $var_xml > 1 causes a clm threading test to FAIL (as of 2024/7/10), so use at your own risk." );
+             $log->warning("$var and $var_xml > 1 (in this case $val_xml) causes a clm threading test to FAIL (as of 2024/7/10), so use at your own risk." );
           }
        }
     }

From c6fba2250092ac1ad776b0ab2fbff9a09db6ad46 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 12 Jul 2024 09:47:27 -0600
Subject: [PATCH 0673/1248] Final ChangeLog/ChangeSum files

---
 doc/ChangeLog | 6 +++---
 doc/ChangeSum | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 3a33553f64..d12c30e731 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.011
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
-Date: Thu 11 Jul 2024 01:14:12 PM MDT
+Date: Fri 12 Jul 2024 09:45:59 AM MDT
 One-line Summary: Merge b4b-dev
 
 Purpose and description of changes
@@ -56,8 +56,8 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho ----- IN PROG
-    izumi ------- NOT STARTED
+    derecho ----- OK
+    izumi ------- OK
 
 Answer changes
 --------------
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 892913c52f..79ee06377d 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.011   slevis 07/11/2024 Merge b4b-dev
+       ctsm5.2.011   slevis 07/12/2024 Merge b4b-dev
        ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption
        ctsm5.2.009     erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names
        ctsm5.2.008     erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat

From 1377d48022c5db5a7352744b7356aa4cce1e8413 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 12 Jul 2024 10:12:26 -0600
Subject: [PATCH 0674/1248] Fix default stream_meshfile_cropcal.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index d1f9d8545c..3f8bc1f382 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1707,14 +1707,14 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldFileName_swindow_start cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
 <stream_fldFileName_swindow_end cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
-<stream_meshfile_cropcal cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_meshfile_cropcal>
+<stream_meshfile_cropcal cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/360x720_120830_ESMFmesh_c20210507_cdf5.tweaked_latlons.nc</stream_meshfile_cropcal>
 <stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
 <stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
 <stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
 <stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_start>
 <stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_end>
-<stream_meshfile_cropcal cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_meshfile_cropcal>
+<stream_meshfile_cropcal cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/360x720_120830_ESMFmesh_c20210507_cdf5.tweaked_latlons.nc</stream_meshfile_cropcal>
 
 <!-- lightning streams namelist defaults -->
 

From d60dc80d74609096b63c942ca41e0ca38177683b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 12 Jul 2024 10:13:06 -0600
Subject: [PATCH 0675/1248] Fix reset of sowing_reason_perharv_patch.

---
 src/biogeochem/CNPhenologyMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index d4f486acb7..d1d3c85b21 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -1976,7 +1976,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp                     , &
                cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8
                crop_inst%gddaccum_thisyr_patch(p,s) = -1._r8
                crop_inst%hui_thisyr_patch(p,s) = -1._r8
-               crop_inst%sowing_reason_perharv_patch = -1._r8
+               crop_inst%sowing_reason_perharv_patch(p,s) = -1._r8
                crop_inst%harvest_reason_thisyr_patch(p,s) = -1._r8
                do k = repr_grain_min, repr_grain_max
                   cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch(p,s,k) = 0._r8

From 093f5fb615988c4ec3cf9e41997178ca45e4808c Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 09:55:43 -0700
Subject: [PATCH 0676/1248] Update
 bld/namelist_files/namelist_definition_ctsm.xml with note asterisks

---
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index c8118031cc..ce2c1b3c5a 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -740,7 +740,7 @@ Set FATES harvesting mode by setting fates_harvest_mode to a valid string option
 Allowed values are:
  no_harvest: no fates harvesting of any kind
  event_code: fates logging via fates logging event codes (see fates parameter file) only
- landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod)
+ landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod)**
  luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
  luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
 Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file.

From 63c458254274edf650aac6bb0da359630446bfca Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 09:57:09 -0700
Subject: [PATCH 0677/1248] Update
 bld/namelist_files/namelist_definition_ctsm.xml with astericks

Link to note
---
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index ce2c1b3c5a..208c42038e 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -743,7 +743,7 @@ Allowed values are:
  landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod)**
  luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
  luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
-Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file.
+**Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file.
 This option is older than the luhdata options and may be depricated at some point in the future.
 </entry>
 

From 7417640e49d9b83932b0ba608b13987b5e62de2c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 12 Jul 2024 11:07:12 -0600
Subject: [PATCH 0678/1248] Allow tests with threading to proceed with
 -ignore_warnings

---
 cime_config/testdefs/testlist_clm.xml         | 42 +++++++++----------
 .../clm/matrixcnOn_Hist/shell_commands        |  3 --
 .../include_user_mods                         |  0
 .../matrixcnOn_ignore_warnings/shell_commands |  7 ++++
 4 files changed, 28 insertions(+), 24 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands
 rename cime_config/testdefs/testmods_dirs/clm/{matrixcnOn_Hist => matrixcnOn_ignore_warnings}/include_user_mods (100%)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 1fe5ed770d..7ead363a6d 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -548,7 +548,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn_Hist">
+  <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -794,7 +794,7 @@
       <option name="comment">Use a transient compset so we allocate and run all PFTs (non-transient cases only allocate memory for non-zero-weight PFTs)</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive--clm/matrixcnOn_Hist">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1002,7 +1002,7 @@
       <option name="comment"  >Transient case with isotopes with a December start</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart--clm/matrixcnOn_Hist">
+  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1020,7 +1020,7 @@
       <option name="comment"  >Transient case with isotopes with a December start, without Meier roughness</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default--clm/matrixcnOn_Hist">
+  <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1038,7 +1038,7 @@
       <option name="comment"  >Transient case with a December 1990 start, and Gross Unrepresented Land Use and Land Cover change on, with f09 datasets with non-zero GU_LULCC values</option>
     </options>
   </test>
-  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn_Hist">
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1074,7 +1074,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_short"/>
@@ -1092,7 +1092,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/coldStart--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/coldStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1145,7 +1145,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1162,7 +1162,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
+  <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1234,7 +1234,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P48x1" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn_Hist">
+  <test name="ERP_D_P48x1" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
       <machine name="izumi" compiler="nag" category="prealpha"/>
@@ -1354,7 +1354,7 @@
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
     </options>
   </test>
-  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_Hist">
+  <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1390,7 +1390,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso--clm/matrixcnOn">
+  <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1435,7 +1435,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_Hist">
+  <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1445,7 +1445,7 @@
       <option name="comment"  >Repeat ERP_P64x2_Lm13...monthly test with matrixcnOn</option>
     </options>
   </test>
-  <test name="REP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_Hist">
+  <test name="REP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1455,7 +1455,7 @@
       <option name="comment">Repeat ERP_P64x2_Lm13...monthly test with matrixcnOn as REP test because both tests fail as reported in #2619</option>
     </options>
   </test>
-  <test name="REP_P64x2_Ld13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_Hist">
+  <test name="REP_P64x2_Ld13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1793,7 +1793,7 @@
       <option name="comment"  >Want a multi-year global test of transient crops; also want a multi-year transient restart test.  Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test</option>
     </options>
   </test>
-  <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_Hist">
+  <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1849,7 +1849,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn_Hist">
+  <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1897,7 +1897,7 @@
       <option name="comment"  >Exercise the init_interp_method='use_finidat_areas' option. See documentation at the top of the python script implementing this test for more details and rationale. This test requires a compatible finidat file (i.e., a file that can be used without interpolation). If no such file is available out-of-the-box, then the test will need to use a testmod that points to a compatible file.</option>
     </options>
   </test>
-  <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1925,7 +1925,7 @@
       <option name="comment"  >Make sure Carbon isotopes on and off with land-use change, does NOT change answers. To verify for landuse change must go beyond a year boundary, because of #404 we can't use a December start, so need to run for beyond the year boundary.</option>
     </options>
   </test>
-  <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn_Hist">
+  <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
@@ -1982,7 +1982,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
+  <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2369,7 +2369,7 @@
       <option name="comment"  >Want a test of the c13 and c14 timeseries that crosses the year boundary. Ideally this test would include crops (in order to cover as much code as possible combined with the c13/c14 timeseries, even though there are no direct interactions between these timeseries and crops), but crop DecStart tests currently fail because of https://github.com/ESCOMP/ctsm/issues/404 and I didn't want to add another long test just to test these options, so for now using a compset without crops. Using a compset with SGLC to avoid problems with CISM in DecStart tests; the only IHistClm50Bgc compset we have with SGLC is this Qian compset, so I'm using this one.</option>
     </options>
   </test>
-  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn_Hist">
+  <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands
deleted file mode 100644
index f0547f3f26..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./xmlchange CLM_BLDNML_OPTS="-ignore_warnings" --append
diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands
new file mode 100644
index 0000000000..d94ef06a5c
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+./xmlchange CLM_BLDNML_OPTS="-ignore_warnings" --append
+
+# In this testmod directory we are ignoring warnings about running
+# matrixcn in transient simulations AND/OR
+# warnings about running matrixcn with threading NTHRDS_LND > 1.

From 1e9df4973fdfcb9e685026ecaed2b56745b24663 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 10:27:07 -0700
Subject: [PATCH 0679/1248] update comment regarding landuse x pft data set

Pre-generating files is a more likely next step relative to auto-gen
---
 cime_config/SystemTests/pvt.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
index feef6cb04c..2a3dbafdc3 100644
--- a/cime_config/SystemTests/pvt.py
+++ b/cime_config/SystemTests/pvt.py
@@ -30,9 +30,8 @@ def __init__(self,case):
             error_message = (f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected.")
 
         # Only allow to run if resolution is 4x5 for now
-        # Eventually we could set this up to generate the necessary land use x pft mapping
-        # on the fly, although this would also require generating the land use timeseries
-        # regridding on the fly which is a more time consuming endevour currently
+        # Other grid resolutions will be pre-processed and included in the namelist defaults at a future date.
+        # Potentially we could generate these on the fly although doing so would result in increased build time
         lnd_grid = self._case.get_value("LND_GRID")
         if lnd_grid != "4x5":
             error_message = (f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected.")

From 48aeb43c9575c80a1547a85c1b02b529b690ac05 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 10:40:15 -0700
Subject: [PATCH 0680/1248] Update README with suggested clarification

---
 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README
index 79d6511d17..9b782cb2a7 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README
@@ -1,2 +1,4 @@
 Currently the FATES LUH2 category of test mods currently only supports 
-4x5 grid resolutions.
+4x5 grid resolutions.  This is because we only have one LUH2 time series
+dataset for the 4x5 resolution. In the future we will provide more resolutions
+which will be added to the namelist defaults.

From 5c3e71fe608c73c47f8f3e9b8ac6ee4102ce63a5 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 12 Jul 2024 11:46:58 -0600
Subject: [PATCH 0681/1248] Remove midDecStart-RxCropCalsAdaptGGCMI test from
 expected fails.

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 0fac518374..03eb6a157d 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -170,13 +170,6 @@
     </phase>
   </test>
 
-  <test name="ERP_D_P128x1_Ld26.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-midDecStart--clm-RxCropCalsAdaptGGCMI">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>#2593</issue>
-    </phase>
-  </test>
-
   <!-- fates test suite failures -->
 
   <test name="SMS_D_Ld3.f09_g17.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen_prescribed">

From dc488c77a715bba7115c92c43948b668c6c38bc0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 12 Jul 2024 14:46:59 -0600
Subject: [PATCH 0682/1248] Improve interpolate_gdds.py.

---
 python/ctsm/crop_calendars/interpolate_gdds.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py
index 2aa0b79997..809be98826 100755
--- a/python/ctsm/crop_calendars/interpolate_gdds.py
+++ b/python/ctsm/crop_calendars/interpolate_gdds.py
@@ -64,6 +64,14 @@ def _setup_process_args():
         type=str,
         required=True,
     )
+    parser.add_argument(
+        "-p",
+        "--variable-prefix",
+        help="Interpolate variables whose names start with this string",
+        type=str,
+        required=False,
+        default="gdd1_"
+    )
     parser.add_argument(
         "--overwrite",
         help="If output file exists, overwrite it.",
@@ -110,8 +118,12 @@ def interpolate_gdds(args):
     for var in ds_in:
 
         # Check variable
-        if "gdd1_" not in var:
-            raise RuntimeError(f"Unexpected variable {var} on input file")
+        if "lat" not in ds_in[var].dims and "lon" not in ds_in[var].dims:
+            print(f"Skipping variable {var} with dimensions {ds_in[var].dims}")
+            continue
+        elif args.variable_prefix not in var:
+            print(f"Unexpected variable {var} on input file. Skipping.")
+            continue
         if args.dry_run:
             continue
 

From 9ee75610973c32376f6dc407c99a0bc8d55cad83 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 14:09:26 -0700
Subject: [PATCH 0683/1248] fix how harvest mode is passed to add_default for
 use_fates_luh

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 47e0fff402..ac87d6f4ca 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4522,7 +4522,7 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
                     'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
                     'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'),
-                    'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') );
+                    'fates_harvest_mode'=>remove_leading_and_trailing_quotes($nl->get_value('fates_harvest_mode')) );
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'},
                     'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
                     'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );

From 48368ac9a5fd2c36fb57cd21c3be76f773e3744d Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 15:11:48 -0700
Subject: [PATCH 0684/1248] add comment pointing to luh2 data set readme

---
 src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
index 681d39f38c..1bc6ab929e 100644
--- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
+++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90
@@ -50,6 +50,7 @@ module dynFATESLandUseChangeMod
   type(dyn_file_type), target   :: dynFatesLandUse_file
 
   ! LUH2 raw wood harvest area fraction
+  ! LUH2 data set variable names can be found at https://luh.umd.edu/LUH2/LUH2_v2h_README.pdf
   character(len=10), target :: landuse_harvest_area_varnames(num_landuse_harvest_vars) = &
        [character(len=10) :: 'primf_harv', 'primn_harv', 'secmf_harv', 'secyf_harv', 'secnf_harv']
 

From b0e6565a8d802db3c1a4a2ad3322726ed680b09f Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 15:18:54 -0700
Subject: [PATCH 0685/1248] add single quotes around fates_harvest_mode in unit
 tests

---
 bld/unit_testers/build-namelist_test.pl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index b343e3d194..e60a411ccb 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1009,7 +1009,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "useloggingButNOTFATES"     =>{ options=>"-envxml_dir . -no-megan",
-                                     namelst=>"fates_harvest_mode=event_code",
+                                     namelst=>"fates_harvest_mode='event_code'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
@@ -1064,12 +1064,12 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan",
-                                     namelst=>"use_fates_potentialveg=T,fates_harvest_mode=event_code",
+                                     namelst=>"use_fates_potentialveg=T,fates_harvest_mode='event_code'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
      "useFATESHARVEST3WOLUH"     =>{ options=>"-bgc fates -envxml_dir . -no-megan",
-                                     namelst=>"use_fates_luh=F,fates_harvest_mode=luhdata_area",
+                                     namelst=>"use_fates_luh=F,fates_harvest_mode='luhdata_area'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },

From 3db9bf2788141d9eaea0d9f8dd331c96f7d01165 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 12 Jul 2024 15:08:03 -0600
Subject: [PATCH 0686/1248] tweak_latlons: Include gdd20 files.

---
 python/ctsm/crop_calendars/tweak_latlons.py | 105 +++++++++++++++-----
 1 file changed, 80 insertions(+), 25 deletions(-)

diff --git a/python/ctsm/crop_calendars/tweak_latlons.py b/python/ctsm/crop_calendars/tweak_latlons.py
index 89144a80ae..0031d492e0 100644
--- a/python/ctsm/crop_calendars/tweak_latlons.py
+++ b/python/ctsm/crop_calendars/tweak_latlons.py
@@ -20,6 +20,8 @@
     "gdd20bl.copied_from.gdds_20230829_161011.v2.nc",
     "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc",
     "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc",
+    "/glade/work/samrabin/cropCals_testing_20240626/gdds_20240712_114642_10x15_interpd_halfdeg.nc",
+    "/glade/work/samrabin/gdd20_baselines/gswp3.10x15_interpd_halfdeg.1980-2009.nc",
 ]
 file_mesh_in = (
     "/glade/campaign/cesm/cesmdata/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc"
@@ -27,19 +29,43 @@
 
 file_list_out = []
 coord_list = ["lat", "lon"]
+COORD_DATATYPE = np.float64
 
-# %%
-
+# %% Define functions
 
-def apply_tweak(ds, coord_str, tweak=1e-6):
-    # Apply tweak
-    da = ds[coord_str]
-    coord2 = da.values
+def get_ds(topdir, file_in):
+    if not os.path.exists(file_in):
+        file_in = os.path.join(topdir, file_in)
+    ds = xr.open_dataset(file_in)
+    return file_in, ds
+
+def get_tweak(ds_in, coord_str, init_tweak):
+    """
+    Get the tweak that will be applied to all datasets' lat/lon coordinates
+    """
+    da = ds_in[coord_str]
+    coord2_orig = da.values.astype(COORD_DATATYPE)
+    coord2 = coord2_orig
+    tweak = init_tweak
     coord2 += tweak
+
+    # This is necessary if precision is lower than float64
+    max_tweak = 1e-2
     while np.any(coord2 == da.values):
         tweak *= 10
-        coord2 = da.values
+        if tweak > max_tweak:
+            raise RuntimeError(f"Tweaking by +{max_tweak} failed to 'take'")
+        coord2 = coord2_orig
         coord2 += tweak
+    return tweak
+
+def apply_tweak(ds_in, coord_str, tweak):
+    # Apply tweak
+    da = ds_in[coord_str]
+    coord2 = da.values.astype(COORD_DATATYPE)
+    coord2 += tweak
+    if np.any(coord2 == da.values):
+        raise RuntimeError('Tweak didn''t "take"')
     coord_tweak = np.full_like(coord2, tweak)
 
     # Ensure that no value is above maximum in input data. This is needed for mesh_maker to work.
@@ -61,19 +87,22 @@ def apply_tweak(ds, coord_str, tweak=1e-6):
     )
 
     # Replace coordinate in dataset
-    ds[coord_str] = da2
+    ds_in[coord_str] = da2
 
     # Add a variable with the amount of the tweak
     tweak_attrs = {}
-    if "standard_name" in da:
+    if "standard_name" in da.attrs:
         coord_name = da.attrs["standard_name"]
-    else:
+    elif "long_name" in da.attrs:
         coord_name = da.attrs["long_name"].replace("coordinate_", "")
+    else:
+        coord_name = coord_str
     tweak_attrs["standard_name"] = coord_name + "_tweak"
     tweak_attrs[
         "long_name"
     ] = f"Amount {coord_name} was shifted to avoid ambiguous nearest neighbors"
-    tweak_attrs["units"] = da.attrs["units"]
+    if "units" in da.attrs:
+        tweak_attrs["units"] = da.attrs["units"]
     da_tweak = xr.DataArray(
         data=coord_tweak,
         coords=new_coords_dict,
@@ -81,19 +110,48 @@ def apply_tweak(ds, coord_str, tweak=1e-6):
         attrs=tweak_attrs,
     )
     tweak_name = coord_str + "_tweak"
-    ds[tweak_name] = da_tweak
+    ds_in[tweak_name] = da_tweak
+
+    return ds_in
+
+def check(ds, f0_base, ds2, f_base, var):
+    if not np.array_equal(ds[var].values, ds2[var].values):
+        if not np.array_equal(ds[var].shape, ds2[var].shape):
+            msg = f"{var} shapes differ b/w {f0_base} ({ds[var].shape}) and {f_base} ({ds2[var].shape})"
+            raise RuntimeError(msg)
+        max_diff = np.max(np.abs(ds[var].values - ds2[var].values))
+        msg = f"{var}s differ between {f0_base} and {f_base}; max = {max_diff}"
+        type0 = type(ds[var].values[0])
+        type2 = type(ds2[var].values[0])
+        if type0 != type2:
+            msg += f"\nTypes also differ: {type0} vs. {type2}"
+        raise RuntimeError(msg)
 
-    return ds
+# %% Apply tweak to all files
 
+# Set up empty dicts
+tweak_dict = {}
+coord_type_dict = {}
+for coord in coord_list:
+    tweak_dict[coord] = -np.inf
 
-# %% Apply tweak to all files
+# Get tweaks
+for file_in in file_list_in:
+    file_in, ds = get_ds(topdir, file_in)
+    for coord in coord_list:
+        this_tweak = get_tweak(ds, coord, init_tweak=1e-6)
+        if this_tweak > tweak_dict[coord]:
+            tweak_dict[coord] = this_tweak
+for coord in coord_list:
+    print(f"Tweaking {coord} by {tweak_dict[coord]}")
+print(" ")
 
-for filename in file_list_in:
-    file_in = os.path.join(topdir, filename)
-    ds = xr.open_dataset(file_in)
+# Apply tweaks
+for file_in in file_list_in:
+    file_in, ds = get_ds(topdir, file_in)
 
     for coord in coord_list:
-        ds = apply_tweak(ds, coord, tweak=1e-6)
+        ds = apply_tweak(ds, coord, tweak_dict[coord])
 
     # Set up for save
     file_out = file_in.replace(".nc", ".tweaked_latlons.nc")
@@ -110,16 +168,14 @@ def apply_tweak(ds, coord_str, tweak=1e-6):
 # %% Ensure all files got the same tweaks
 
 ds = xr.open_dataset(file_list_out[0])
+f0_base = os.path.basename(file_list_out[0])
 
 for filename in file_list_out[1:]:
     ds2 = xr.open_dataset(filename)
+    f_base = os.path.basename(filename)
     for coord in coord_list:
-        # Ensure that coordinates are the same
-        var = coord
-        assert np.array_equal(ds[var].values, ds2[var].values)
-        # Ensure that tweaks were the same
-        var = coord + "_tweak"
-        assert np.array_equal(ds[var].values, ds2[var].values)
+        check(ds, f0_base, ds2, f_base, coord)
+        check(ds, f0_base, ds2, f_base, coord + "_tweak")
 print("All good!")
 
 
@@ -168,4 +224,3 @@ def redirect_argv(arglist):
 
 
 print("Done")
-# %%

From 8e618bb5384ba72d2b53b45a778aad29be542221 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 12 Jul 2024 16:44:47 -0600
Subject: [PATCH 0687/1248] Add new test to build-namelist_test.pl (currently
 failing)

---
 bld/unit_testers/build-namelist_test.pl | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 005f2c3f96..1810d4434b 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -41,7 +41,7 @@ sub make_env_run {
 #
     my %settings = @_;
 
-    # Set default settings
+    # Set default settings  TODO slevis: NTHRDS_LND fails, OMP_NUM_THREADS fails
     my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NTHRDS_LND=>"1", NEONSITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3306;
+my $ntests = 3309;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2045;
@@ -1320,6 +1320,12 @@ sub cat_and_create_namelistinfile {
 
 my %warntest = (
      # Warnings without the -ignore_warnings option given
+     "matrixcnOn_with_threading" =>{ options=>"-envxml_dir . -bgc bgc",
+                                     namelst=>"use_matrixcn=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"TRUE",
+                                     NTHRDS_LND=>"2",
+                                     phys=>"clm5_0",
+                                   },
      "dustemisLeung"             =>{ options=>"-envxml_dir .",
                                      namelst=>"dust_emis_method = 'Leung_2023'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1376,7 +1382,13 @@ sub cat_and_create_namelistinfile {
    &make_config_cache($warntest{$key}{"phys"});
    my $options  = $warntest{$key}{"options"};
    my $namelist = $warntest{$key}{"namelst"};
-   &make_env_run( GLC_TWO_WAY_COUPLING=>$warntest{$key}{"GLC_TWO_WAY_COUPLING"} );
+   my %settings;
+   foreach my $xmlvar ( "GLC_TWO_WAY_COUPLING", "NTHRDS_LND") {
+      if ( defined($failtest{$key}{$xmlvar}) ) {
+         $settings{$xmlvar} = $failtest{$key}{$xmlvar};
+      }
+   }
+   &make_env_run( %settings );
    eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
    isnt( $?, 0, $key );
    system( "cat $tempfile" );

From 64302ad0c48b2afd7a074659c6509ae3344a4ac3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 12 Jul 2024 16:54:46 -0600
Subject: [PATCH 0688/1248] Additions/tweaks to CLM testlist.

---
 cime_config/testdefs/testlist_clm.xml | 44 +++++++++++++++++++++++++--
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 40f351ab4a..3fde176440 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3663,6 +3663,8 @@
   <test name="RXCROPMATURITY_Lm61" grid="f09_g17" compset="IHistClm50BgcCrop"  testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">12:00:00</option>
@@ -3673,6 +3675,7 @@
   <test name="RXCROPMATURITY_Lm61" grid="f10_f10_mg37" compset="IHistClm50BgcCrop"  testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">6:00:00</option>
@@ -3684,6 +3687,42 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:45:00</option>
+      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. Unlike the RXCROPMATURITY test, however, it does not generate its own maturity requirements, instead interpolating a pre-existing maturity requirement file. (This allows the "GDD-generating" run to be mostly skipped.) This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
+    </options>
+  </test>
+
+    <test name="RXCROPMATURITY_Lm61" grid="f09_g17" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
+    <machines>
+      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">12:00:00</option>
+      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. It first performs a GDD-generating run, then calls Python code to generate the maturity requirement file. This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
+    </options>
+  </test>
+
+  <test name="RXCROPMATURITY_Lm61" grid="f10_f10_mg37" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
+    <machines>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">6:00:00</option>
+      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. It first performs a GDD-generating run, then calls Python code to generate the maturity requirement file. This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
+    </options>
+  </test>
+
+  <test name="RXCROPMATURITYSKIPGEN_Ld1097" grid="f10_f10_mg37" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:45:00</option>
@@ -3754,13 +3793,14 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
-      <option name="wallclock">01:00:00</option>
+      <option name="wallclock">02:00:00</option>
     </options>
   </test>
 
   <test name="SMS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -3773,7 +3813,7 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
-      <option name="wallclock">01:00:00</option>
+      <option name="wallclock">00:30:00</option>
     </options>
   </test>
 

From 12c60f3de477bbdaa2cf7a8afe0d089886d2c960 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:01:12 -0700
Subject: [PATCH 0689/1248] correct POTVEG fail unit test

This needs to have use_fates_luh to avoid the false
negative of failing due to not having this mode with
use_fates_potentialveg
---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index fc1e83f162..741964d8a1 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1063,7 +1063,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan",
-                                     namelst=>"use_fates_potentialveg=T,fates_harvest_mode='event_code'",
+                                     namelst=>"use_fates_potentialveg=T,fates_harvest_mode='event_code',use_fates_luh=T",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },

From 0da6eb5c706217606c1323b2b1a57eb136e32f1a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 14 Jul 2024 12:01:58 -0600
Subject: [PATCH 0690/1248] Remove Clm50 RXCROPMATURITY tests.

---
 cime_config/testdefs/testlist_clm.xml | 37 +--------------------------
 1 file changed, 1 insertion(+), 36 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 3fde176440..86210256ff 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3660,42 +3660,7 @@
     </options>
   </test>
 
-  <test name="RXCROPMATURITY_Lm61" grid="f09_g17" compset="IHistClm50BgcCrop"  testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">12:00:00</option>
-      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. It first performs a GDD-generating run, then calls Python code to generate the maturity requirement file. This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
-    </options>
-  </test>
-
-  <test name="RXCROPMATURITY_Lm61" grid="f10_f10_mg37" compset="IHistClm50BgcCrop"  testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">6:00:00</option>
-      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. It first performs a GDD-generating run, then calls Python code to generate the maturity requirement file. This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
-    </options>
-  </test>
-
-  <test name="RXCROPMATURITYSKIPGEN_Ld1097" grid="f10_f10_mg37" compset="IHistClm50BgcCrop"  testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:45:00</option>
-      <option name="comment">This test is designed to test the ability to prescribe crop sowing dates and maturity requirements. Unlike the RXCROPMATURITY test, however, it does not generate its own maturity requirements, instead interpolating a pre-existing maturity requirement file. (This allows the "GDD-generating" run to be mostly skipped.) This is then used in a sowing+maturity forced run, which finally is tested to ensure correct behavior.</option>
-    </options>
-  </test>
-
-    <test name="RXCROPMATURITY_Lm61" grid="f09_g17" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
+  <test name="RXCROPMATURITY_Lm61" grid="f09_g17" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
       <machine name="derecho" compiler="intel" category="rxcropmaturity"/>

From 87d1fa1a4b2a69c2d01898be9d8f9e661af8d163 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 14 Jul 2024 12:43:31 -0600
Subject: [PATCH 0691/1248] Move tweak_latlons.py to tools/contrib/.

This is hopefully not something that will be needed permanently or even in the medium term, so it's not worth cleaning up and unit-/system-testing.
---
 {python/ctsm/crop_calendars => tools/contrib}/tweak_latlons.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {python/ctsm/crop_calendars => tools/contrib}/tweak_latlons.py (100%)

diff --git a/python/ctsm/crop_calendars/tweak_latlons.py b/tools/contrib/tweak_latlons.py
similarity index 100%
rename from python/ctsm/crop_calendars/tweak_latlons.py
rename to tools/contrib/tweak_latlons.py

From f6ff13409d58a50299d0d62207e99a12b2c426a6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 14 Jul 2024 14:07:51 -0600
Subject: [PATCH 0692/1248] Rework tweak_latlons.py to run from command line.

---
 tools/contrib/tweak_latlons.py | 285 +++++++++++++++++++--------------
 1 file changed, 164 insertions(+), 121 deletions(-)

diff --git a/tools/contrib/tweak_latlons.py b/tools/contrib/tweak_latlons.py
index 0031d492e0..2bae06d229 100644
--- a/tools/contrib/tweak_latlons.py
+++ b/tools/contrib/tweak_latlons.py
@@ -1,44 +1,23 @@
-# %%
-import numpy as np
-import xarray as xr
+"""
+'Tweak' the latitude and longitude coordinates to avoid ambiguous nearest neighbors
+"""
 import os
 import sys
-from netCDF4 import Dataset
 import contextlib
+import argparse
+import numpy as np
+import xarray as xr
+from netCDF4 import Dataset  # pylint: disable=no-name-in-module
 
 # -- add python/ctsm  to path (needed if we want to run this stand-alone)
-_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir)
+_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python")
 sys.path.insert(1, _CTSM_PYTHON)
 # pylint: disable=wrong-import-position
 from ctsm.mesh_maker import main as mesh_maker
 
-topdir = "/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/cropdata/calendars/processed/"
-file_list_in = [
-    "swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc",
-    "swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc",
-    "gdds_20230829_161011.nc",
-    "gdd20bl.copied_from.gdds_20230829_161011.v2.nc",
-    "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc",
-    "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.nc",
-    "/glade/work/samrabin/cropCals_testing_20240626/gdds_20240712_114642_10x15_interpd_halfdeg.nc",
-    "/glade/work/samrabin/gdd20_baselines/gswp3.10x15_interpd_halfdeg.1980-2009.nc",
-]
-file_mesh_in = (
-    "/glade/campaign/cesm/cesmdata/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc"
-)
-
-file_list_out = []
-coord_list = ["lat", "lon"]
+COORD_LIST = ["lat", "lon"]
 COORD_DATATYPE = np.float64
 
-# %% Define functions
-
-def get_ds(topdir, file_in):
-    if not os.path.exists(file_in):
-        file_in = os.path.join(topdir, file_in)
-    ds = xr.open_dataset(file_in)
-    return file_in, ds
-
 def get_tweak(ds_in, coord_str, init_tweak):
     """
     Get the tweak that will be applied to all datasets' lat/lon coordinates
@@ -73,7 +52,9 @@ def apply_tweak(ds_in, coord_str, tweak):
     where_toohigh = np.where(coord2 > max_coord)
     Ntoohigh = len(where_toohigh[0])
     if Ntoohigh != 1:
-        raise RuntimeError(f"Expected 1 coordinate value too high; got {Ntoohigh}")
+        raise RuntimeError(
+            f"Expected 1 coordinate value too high; got {Ntoohigh}"
+        )
     coord2[where_toohigh] = max_coord
     coord_tweak[where_toohigh] = max_coord
 
@@ -127,100 +108,162 @@ def check(ds, f0_base, ds2, f_base, var):
             msg += f"\nTypes also differ: {type0} vs. {type2}"
         raise RuntimeError(msg)
 
-# %% Apply tweak to all files
-
-# Set up empty dicts
-tweak_dict = {}
-coord_type_dict = {}
-for coord in coord_list:
-    tweak_dict[coord] = -np.inf
-
-# Get tweaks
-for file_in in file_list_in:
-    file_in, ds = get_ds(topdir, file_in)
-    for coord in coord_list:
-        this_tweak = get_tweak(ds, coord, init_tweak=1e-6)
-        if this_tweak > tweak_dict[coord]:
-            tweak_dict[coord] = this_tweak
-for coord in coord_list:
-    print(f"Tweaking {coord} by {tweak_dict[coord]}")
-print(" ")
-
-# Apply tweaks
-for file_in in file_list_in:
-    file_in, ds = get_ds(topdir, file_in)
-
-    for coord in coord_list:
-        ds = apply_tweak(ds, coord, tweak_dict[coord])
-
-    # Set up for save
-    file_out = file_in.replace(".nc", ".tweaked_latlons.nc")
-    with Dataset(file_in, "r") as netcdf_file:
-        netcdf_format = netcdf_file.data_model
-
-    # Save
-    print(f"Saving {file_out}")
-    ds.to_netcdf(file_out, format=netcdf_format)
-    file_list_out.append(file_out)
-print("Done")
-
-
-# %% Ensure all files got the same tweaks
-
-ds = xr.open_dataset(file_list_out[0])
-f0_base = os.path.basename(file_list_out[0])
-
-for filename in file_list_out[1:]:
-    ds2 = xr.open_dataset(filename)
-    f_base = os.path.basename(filename)
-    for coord in coord_list:
-        check(ds, f0_base, ds2, f_base, coord)
-        check(ds, f0_base, ds2, f_base, coord + "_tweak")
-print("All good!")
-
-
-# %% Save new mesh file
-
-outfile_name = os.path.basename(file_mesh_in)
-outfile_name = outfile_name.replace(".nc", ".tweaked_latlons.nc")
-outdir = os.path.dirname(file_list_out[0])
-file_mesh_out = os.path.join(outdir, outfile_name)
-
 @contextlib.contextmanager
 def redirect_argv(arglist):
+    """
+    Preserve actual arg list while giving a new one to mesh_maker
+    """
     argv_tmp = sys.argv[:]
-    sys.argv=arglist
+    sys.argv = arglist
     yield
     sys.argv = argv_tmp
 
+def main(input_files, mesh_file_in, output_files):
+    """
+    Apply tweak to all files
+    """
+
+    # Set up
+    tweak_dict = {}
+    for coord in COORD_LIST:
+        tweak_dict[coord] = -np.inf
+    mesh_file_out = output_files[-1]
+    output_files = output_files[:-1]
+
+    # Get tweaks
+    for file_in in input_files:
+        ds = xr.open_dataset(file_in)
+        for coord in COORD_LIST:
+            this_tweak = get_tweak(ds, coord, init_tweak=1e-6)
+            if this_tweak > tweak_dict[coord]:
+                tweak_dict[coord] = this_tweak
+    for coord in COORD_LIST:
+        print(f"Tweaking {coord} by {tweak_dict[coord]}")
+    print(" ")
+
+    # Apply tweaks
+    for i, file_in in enumerate(input_files):
+        ds = xr.open_dataset(file_in)
+
+        for coord in COORD_LIST:
+            ds = apply_tweak(ds, coord, tweak_dict[coord])
+
+        # Set up for save
+        file_out = output_files[i]
+        with Dataset(file_in, "r") as netcdf_file:
+            netcdf_format = netcdf_file.data_model
+
+        # Make output dir, if needed
+        output_dir = os.path.dirname(file_out)
+        if not os.path.exists(output_dir):
+            os.makedirs(output_dir)
+
+        # Save
+        print(f"Saving {file_out}")
+        ds.to_netcdf(file_out, format=netcdf_format)
+    print("Done")
+
+
+    # Ensure all files got the same tweaks
+    ds = xr.open_dataset(output_files[0])
+    f0_base = os.path.basename(output_files[0])
+    for file_out in output_files[1:]:
+        ds2 = xr.open_dataset(file_out)
+        f_base = os.path.basename(file_out)
+        for coord in COORD_LIST:
+            check(ds, f0_base, ds2, f_base, coord)
+            check(ds, f0_base, ds2, f_base, coord + "_tweak")
+
+
+    # Save new mesh file
+    mesh_maker_args = [
+        "mesh_maker",
+        "--input",
+        output_files[0],
+        "--output",
+        mesh_file_out,
+        "--lat",
+        "lat",
+        "--lon",
+        "lon",
+        "--overwrite",
+    ]
+    print(f"Saving {mesh_file_out}...")
+    with redirect_argv(mesh_maker_args):
+        mesh_maker()
+
+    # Change format, if needed
+    with Dataset(mesh_file_in, "r") as netcdf_file:
+        netcdf_format_in = netcdf_file.data_model
+    with Dataset(mesh_file_out, "r") as netcdf_file:
+        netcdf_format_out = netcdf_file.data_model
+    if netcdf_format_in != netcdf_format_out:
+        mesh_file_out_tmp = mesh_file_out + ".tmp"
+        os.rename(mesh_file_out, mesh_file_out_tmp)
+        ds = xr.open_dataset(mesh_file_out_tmp)
+        ds.to_netcdf(mesh_file_out, format=netcdf_format_in)
+        os.remove(mesh_file_out_tmp)
+
+    print("Done")
+
+
+
+
+if __name__ == "__main__":
+    ###############################
+    ### Process input arguments ###
+    ###############################
+    parser = argparse.ArgumentParser(
+        description="'Tweak' the latitude and longitude coordinates to avoid ambiguous nearest neighbors",
+    )
+
+    # Required
+    parser.add_argument(
+        "-i",
+        "--input-files",
+        help="Comma-separated stream files whose coordinates need tweaking",
+        required=True,
+    )
+    parser.add_argument(
+        "-m",
+        "--mesh-file",
+        help="Mesh file associated with input files",
+        required=True,
+    )
+
+    # Optional
+    parser.add_argument(
+        "--overwrite",
+        help="Overwrite any existing output files",
+        action="store_true",
+        default=False,
+    )
+    default_output_dir = os.getcwd()
+    parser.add_argument(
+        "-o",
+        "--output-dir",
+        help=f"Directory where output files should be saved. Default is current working directory: {default_output_dir}",
+        default=default_output_dir,
+    )
 
-mesh_maker_args = [
-    "mesh_maker",
-    "--input",
-    file_list_out[0],
-    "--output",
-    file_mesh_out,
-    "--lat",
-    "lat",
-    "--lon",
-    "lon",
-    "--overwrite",
-]
-print(f"Saving {file_mesh_out}...")
-with redirect_argv(mesh_maker_args):
-    mesh_maker()
-
-# Change format, if needed
-with Dataset(file_mesh_in, "r") as netcdf_file:
-    netcdf_format_in = netcdf_file.data_model
-with Dataset(file_mesh_out, "r") as netcdf_file:
-    netcdf_format_out = netcdf_file.data_model
-if netcdf_format_in != netcdf_format_out:
-    file_mesh_out_tmp = file_mesh_out + ".tmp"
-    os.rename(file_mesh_out, file_mesh_out_tmp)
-    ds = xr.open_dataset(file_mesh_out_tmp)
-    ds.to_netcdf(file_mesh_out, format=netcdf_format_in)
-    os.remove(file_mesh_out_tmp)
-
-
-print("Done")
+    # Get arguments
+    args = parser.parse_args(sys.argv[1:])
+
+    # Check/process input and output files
+    _input_files = args.input_files.split(",")
+    _output_files = []
+    for file in _input_files + [args.mesh_file]:
+        if not os.path.exists(file):
+            raise FileNotFoundError(f"File not found: {file}")
+
+        filename, ext = os.path.splitext(os.path.basename(file))
+        output_file = os.path.join(
+            args.output_dir, filename + ".tweaked_latlons" + ext
+        )
+        if os.path.exists(output_file) and not args.overwrite:
+            raise FileExistsError(
+                f"Output file exists but --overwrite not specified: {output_file}"
+            )
+        _output_files.append(output_file)
+
+    main(_input_files, args.mesh_file, _output_files)

From 227426345fcd0bd552e755b5c4cceb503cea94c6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Sun, 14 Jul 2024 14:28:50 -0600
Subject: [PATCH 0693/1248] Refine RxCropCals* testlist.

---
 cime_config/testdefs/testlist_clm.xml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 86210256ff..c2926a25e7 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3755,7 +3755,7 @@
 
   <test name="ERS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdapt">
     <machines>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="derecho" compiler="gnu" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -3765,7 +3765,8 @@
   <test name="SMS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="crop_calendars"/>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -3782,6 +3783,17 @@
     </options>
   </test>
 
+  <test name="PEM_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+      <option name="comment">This test is potentially duplicative of the equivalent ERP test. However, ambiguous nearest neighbors can result in different pixels being chosen based on number of processors. Because crop calendar inputs are only updated at beginning of year, this can cause PEM test to fail where ERP test passes.</option>
+    </options>
+  </test>
+
   <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/cropAnnOutputMonthly">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>

From f957f21066335c99f10336560e66b1d72cb4e217 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Mon, 15 Jul 2024 11:12:50 -0600
Subject: [PATCH 0694/1248] fix argument passing

---
 src/main/clm_instMod.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index f3cfa9923d..04c4af6611 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -316,7 +316,8 @@ subroutine clm_instInit(bounds)
          em_wall_lun=urbanparams_inst%em_wall(begl:endl),    &
          em_improad_lun=urbanparams_inst%em_improad(begl:endl), &
          em_perroad_lun=urbanparams_inst%em_perroad(begl:endl), &
-         is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp() )
+         is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp(), &
+         exice_init_stream_col=exice_init_stream_col(bounds%begc:bounds%endc) )
 
     call active_layer_inst%Init(bounds)
 

From 5686defdd31c03cdba0bcc247e3d590a0069d9d4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <ekluzek@users.noreply.github.com>
Date: Mon, 15 Jul 2024 11:40:38 -0600
Subject: [PATCH 0695/1248] Update bld/unit_testers/build-namelist_test.pl

Syntax of breaking up into two lines was confusing, so just making a longer line that is more clear.
---
 bld/unit_testers/build-namelist_test.pl | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 5abb381c16..a22cdd4059 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1095,8 +1095,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_1",
                                      },
      "soil_erod_none_w_Zender"  =>{ options=>"--envxml_dir .",
-                                     namelst=>"dust_emis_method='Zender_2003', " .
-                                     "zender_soil_erod_source='none'",
+                                     namelst=>"dust_emis_method='Zender_2003', zender_soil_erod_source='none'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                      },

From af11aaab0644357cbff66aecbbc2f94a25778ab7 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 15 Jul 2024 14:02:15 -0600
Subject: [PATCH 0696/1248] Remove new test from build-namelist_test.pl for now

---
 bld/unit_testers/build-namelist_test.pl | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 1810d4434b..16f6ba2a62 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -41,8 +41,8 @@ sub make_env_run {
 #
     my %settings = @_;
 
-    # Set default settings  TODO slevis: NTHRDS_LND fails, OMP_NUM_THREADS fails
-    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NTHRDS_LND=>"1", NEONSITE=>"" );
+    # Set default settings
+    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
        $env_vars{$item} = $settings{$item};
@@ -1320,12 +1320,6 @@ sub cat_and_create_namelistinfile {
 
 my %warntest = (
      # Warnings without the -ignore_warnings option given
-     "matrixcnOn_with_threading" =>{ options=>"-envxml_dir . -bgc bgc",
-                                     namelst=>"use_matrixcn=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"TRUE",
-                                     NTHRDS_LND=>"2",
-                                     phys=>"clm5_0",
-                                   },
      "dustemisLeung"             =>{ options=>"-envxml_dir .",
                                      namelst=>"dust_emis_method = 'Leung_2023'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1383,7 +1377,7 @@ sub cat_and_create_namelistinfile {
    my $options  = $warntest{$key}{"options"};
    my $namelist = $warntest{$key}{"namelst"};
    my %settings;
-   foreach my $xmlvar ( "GLC_TWO_WAY_COUPLING", "NTHRDS_LND") {
+   foreach my $xmlvar ( "GLC_TWO_WAY_COUPLING" ) {
       if ( defined($failtest{$key}{$xmlvar}) ) {
          $settings{$xmlvar} = $failtest{$key}{$xmlvar};
       }

From 322097f0a2b5cf0c3b6bdd5a3eccb70845cb6990 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 15 Jul 2024 13:05:59 -0700
Subject: [PATCH 0697/1248] change folder name for fates land use x pft files

This matches the corresponding fates tag that also impliments
using this file
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 6f29513e6b..d4167228b9 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2019,7 +2019,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
  >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
 
 <!-- Land Use Harmonization static landuse x pft mapping data sets for FATES land use change -->
-<flandusepftdat hgrid="4x5" use_fates=".true." >lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc</flandusepftdat>
+<flandusepftdat hgrid="4x5" use_fates=".true." >lnd/clm2/surfdata_map/fates-sci.1.77.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc</flandusepftdat>
 
 <!-- This one is just for testing until Issue #2304 is resolved -->
 <fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."

From 7dbc538216ed01ed92dd656b7133238e0bad8ea6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 15 Jul 2024 15:08:44 -0600
Subject: [PATCH 0698/1248] Remove duplicated tests, and new dust tests with
 clm6_0

---
 bld/unit_testers/build-namelist_test.pl | 22 +++++-----------------
 1 file changed, 5 insertions(+), 17 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 5abb381c16..0b26e86476 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1072,39 +1072,27 @@ sub cat_and_create_namelistinfile {
      "soil_erod_wo_Zender"      =>{ options=>"--envxml_dir . --ignore_warnings",
                                      namelst=>"dust_emis_method='Leung_2023', " .
                                      "stream_meshfile_zendersoilerod = '/dev/null'",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                      },
      "soil_erod_wo_lnd_source"  =>{ options=>"--envxml_dir .",
                                      namelst=>"dust_emis_method='Zender_2003', " .
                                      "stream_fldfilename_zendersoilerod = '/dev/null', zender_soil_erod_source='atm'",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                      },
      "soil_erod_none_w_Zender"  =>{ options=>"--envxml_dir .",
                                      namelst=>"dust_emis_method='Zender_2003', " .
                                      "zender_soil_erod_source='none'",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                      },
      "soil_erod_bad_w_Zender"   =>{ options=>"--envxml_dir .",
                                      namelst=>"dust_emis_method='Zender_2003', " .
                                      "zender_soil_erod_source='zztop'",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                      },
      "Set_Dust_When_CAM_Sets"   =>{ options=>"--envxml_dir .",
                                      namelst=>"dust_emis_method='Zender_2003'",
                                      LND_SETS_DUST_EMIS_DRV_FLDS=>"FALSE",
-                                     phys=>"clm5_1",
-                                     },
-     "soil_erod_none_w_Zender"  =>{ options=>"--envxml_dir .",
-                                     namelst=>"dust_emis_method='Zender_2003', " .
-                                     "zender_soil_erod_source='none'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
-                                     },
-     "soil_erod_bad_w_Zender"   =>{ options=>"--envxml_dir .",
-                                     namelst=>"dust_emis_method='Zender_2003', " .
-                                     "zender_soil_erod_source='zztop'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                      },
                );
 foreach my $key ( keys(%failtest) ) {

From 02f9cb325d3884add3ecfb45904c34bb3edb0f62 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 15 Jul 2024 15:25:35 -0600
Subject: [PATCH 0699/1248] Make fail tests lines where the namelst option is
 split up into two lines into one long line, because the way they were
 concatonated look obscure and possibly wrong, the long lines are easier to
 read

---
 bld/unit_testers/build-namelist_test.pl | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 0b26e86476..d72331b1c2 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1070,23 +1070,19 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                      },
      "soil_erod_wo_Zender"      =>{ options=>"--envxml_dir . --ignore_warnings",
-                                     namelst=>"dust_emis_method='Leung_2023', " .
-                                     "stream_meshfile_zendersoilerod = '/dev/null'",
+                                     namelst=>"dust_emis_method='Leung_2023', stream_meshfile_zendersoilerod = '/dev/null'",
                                      phys=>"clm6_0",
                                      },
      "soil_erod_wo_lnd_source"  =>{ options=>"--envxml_dir .",
-                                     namelst=>"dust_emis_method='Zender_2003', " .
-                                     "stream_fldfilename_zendersoilerod = '/dev/null', zender_soil_erod_source='atm'",
+                                     namelst=>"dust_emis_method='Zender_2003', stream_fldfilename_zendersoilerod = '/dev/null', zender_soil_erod_source='atm'",
                                      phys=>"clm6_0",
                                      },
      "soil_erod_none_w_Zender"  =>{ options=>"--envxml_dir .",
-                                     namelst=>"dust_emis_method='Zender_2003', " .
-                                     "zender_soil_erod_source='none'",
+                                     namelst=>"dust_emis_method='Zender_2003', zender_soil_erod_source='none'",
                                      phys=>"clm6_0",
                                      },
      "soil_erod_bad_w_Zender"   =>{ options=>"--envxml_dir .",
-                                     namelst=>"dust_emis_method='Zender_2003', " .
-                                     "zender_soil_erod_source='zztop'",
+                                     namelst=>"dust_emis_method='Zender_2003', zender_soil_erod_source='zztop'",
                                      phys=>"clm6_0",
                                      },
      "Set_Dust_When_CAM_Sets"   =>{ options=>"--envxml_dir .",

From 6e806b5a0d0b1db561f01a403cbae2fc5b450e82 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Tue, 16 Jul 2024 08:50:08 -0600
Subject: [PATCH 0700/1248] update defaults

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 2c6b375140..47f9802aff 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2058,8 +2058,9 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- =========================================  -->
 
 <use_excess_ice>.false.</use_excess_ice>
-
-<excess_ice_coldstart_temp use_excess_ice=".true.">-2.15</excess_ice_coldstart_temp>
+<excess_ice_coldstart_temp>0.0</excess_ice_coldstart_temp>
+<excess_ice_coldstart_depth>1.0</excess_ice_coldstart_depth>
+<excess_ice_coldstart_temp use_excess_ice=".true.">-3.15</excess_ice_coldstart_temp>
 <excess_ice_coldstart_depth use_excess_ice=".true.">0.5</excess_ice_coldstart_depth>
 <stream_fldfilename_exice use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc</stream_fldfilename_exice>
 <stream_meshfile_exice    use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc</stream_meshfile_exice>

From 455ae5ad3a34761dbe55c312ee5fbd7b17f0f756 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 16 Jul 2024 08:58:38 -0600
Subject: [PATCH 0701/1248] Final ChangeLog/ChangeSum

---
 doc/ChangeLog | 2 +-
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index b723b849ae..00c576d0d8 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.012
 Originator(s): sacks (Bill Sacks, UCAR/NCAR/CGD)
-Date: Mon 15 Jul 2024 11:55:45 AM MDT
+Date: Tue 16 Jul 2024 08:57:42 AM MDT
 One-line Summary: Relax tolerance for truncating small snocan values in CanopyFluxes
 
 Purpose and description of changes
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 034c02429c..381b0db858 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.012    sacks 07/15/2024 Relax tolerance for truncating small snocan values in CanopyFluxes
+       ctsm5.2.012    sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes
        ctsm5.2.011   slevis 07/12/2024 Merge b4b-dev
        ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption
        ctsm5.2.009     erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names

From aa923a4d2dc279cd9a85c2f691fd73ab7ab83e56 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 16 Jul 2024 12:12:33 -0600
Subject: [PATCH 0702/1248] Correct two test names in ExpectedTestFails.xml

---
 cime_config/testdefs/ExpectedTestFails.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 6a2186d6d9..7a07a056f7 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -37,14 +37,14 @@
   </test>
 
   <!-- aux_clm test suite failures -->
-  <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_Hist">
+  <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
     <phase name="BASELINE">
       <status>FAIL</status>
       <issue>#2619</issue>
       <comment>This failure relates to the following REP failure.</comment>
     </phase>
   </test>
-  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_Hist">
+  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
     <phase name="COMPARE_base_rep2">
       <status>FAIL</status>
       <issue>#2619</issue>

From ef970e2e8062e0852583216acda18c4ade60cd5e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 16 Jul 2024 12:13:21 -0600
Subject: [PATCH 0703/1248] Make hillslope_fsat_equals_zero .false. unless
 use_hillslope = .true.

---
 bld/namelist_files/namelist_defaults_ctsm.xml   | 3 ++-
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 0777f423ca..e2ba2de74b 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -625,7 +625,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <hillslope_pft_distribution_method           >Standard</hillslope_pft_distribution_method>
 <hillslope_soil_profile_method               >Uniform</hillslope_soil_profile_method>
 <downscale_hillslope_meteorology             >.true.</downscale_hillslope_meteorology>
-<hillslope_fsat_equals_zero                  >.true.</hillslope_fsat_equals_zero>
+<hillslope_fsat_equals_zero>.false.</hillslope_fsat_equals_zero>
+<hillslope_fsat_equals_zero use_hillslope=".true.">.true.</hillslope_fsat_equals_zero>
 
 <!-- Plant hydraulic stress -->
 <use_hydrstress                                                       >.false.</use_hydrstress>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 52f5aee138..bc92dafbf0 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -829,7 +829,7 @@ Toggle to turn on surface water routing in the hillslope hydrology model
 </entry>
 
 <entry id="hillslope_fsat_equals_zero" type="logical" category="physics"
-        group="clm_inparm" valid_values="" value=".true.">
+        group="clm_inparm" valid_values="" value=".false.">
 If true, set fsat to zero for hillslope columns
 </entry>
 

From 8478b730663ee4a6698b70804e95a1f029662aab Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 16 Jul 2024 13:58:00 -0600
Subject: [PATCH 0704/1248] Comments about move to CMEPS

---
 src/drv_test/CMakeLists.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/drv_test/CMakeLists.txt b/src/drv_test/CMakeLists.txt
index adf66b8b92..938e55a598 100644
--- a/src/drv_test/CMakeLists.txt
+++ b/src/drv_test/CMakeLists.txt
@@ -1 +1,3 @@
+# This test should be moved to be under CMEPS
+# See: https://github.com/ESCOMP/CMEPS/issues/458
 add_subdirectory(shr_dust_emis_test)

From 9db4d48623697669e5120830ded96ea2cb7047e0 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 16 Jul 2024 15:38:28 -0700
Subject: [PATCH 0705/1248] add izumi luh2 failure to expected list

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index a4033aa6cd..ee1f188f15 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -150,6 +150,13 @@
 
   <!-- fates test suite failures -->
 
+  <test name="ERS_D_Ld3.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLUH2">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2653</issue>
+    </phase>
+  </test>
+
   <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLUH2HarvestEvent">
     <phase name="RUN">
       <status>FAIL</status>

From 525c78bf49e9c6d71a082cf35f979c48fa6683ab Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 16 Jul 2024 19:12:39 -0600
Subject: [PATCH 0706/1248] Remove leftover conflict header, so can compile

---
 src/biogeochem/DUSTMod.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index 24c4f13069..bf04311cbe 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -743,7 +743,6 @@ subroutine DustEmission (bounds, &
                !################### for Leung et al. (2023) ################################################
                !################ uncomment the below block if want to use Leung's scheme ###################
 
-<<<<<<< HEAD
                !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
 
                ! dmleung: instead of using mss_frc_cly_vld(c) with a range of [0,0.2] , which makes dust too sensitive to input clay surface dataset), for now use 0.1 + mss_frc_cly_vld(c) * 0.1 / 0.20 with a range of [0.1,0.2]. So, instead of scaling dust emission to 1/20 times for El Djouf (western Sahara) because of its 1 % clay fraction, scale its emission to 1/2 times. This reduces the sensitivity of dust emission to the clay input dataset. In particular, because dust emission is a small-scale process and the grid-averaged clay from the new WISE surface dataset over El Djouf is 1 %, much lower than the former FAO estimation of 5 %, dmleung is not sure if the clay value of 1 % suppresses too much of El Djouf's small-scale dust emission process. Similar to Charlie Zender's feeling suspicious about the soil texture datasets (or the dust emission schemes' sandblasting process), dmleung feels the same and for now decides to still allow dust emission  to weakly scale with clay fraction, however limiting the scaling factor to 0.1-0.2. See modification in SoilStateInitTimeConst.F90. dmleung 5 Jul 2024

From 1de58fbb04d862245f69239835a00c15e062dc54 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 17 Jul 2024 12:37:45 -0700
Subject: [PATCH 0707/1248] update fates to sci.1.77.1_api.36.0.0

---
 .gitmodules | 2 +-
 src/fates   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 9ed4402c7e..8127cac482 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.77.0_api.36.0.0
+fxtag = sci.1.77.1_api.36.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
diff --git a/src/fates b/src/fates
index fd7f3438c2..1982b0032c 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit fd7f3438c2ff821672b703050e7011f293649ee9
+Subproject commit 1982b0032c3cab6278892eccb85f643114ffb1af

From 47571d844674d836a7501c3cd98f65ac545f4e39 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 17 Jul 2024 13:23:11 -0700
Subject: [PATCH 0708/1248] formatting fixed for changelog

---
 doc/ChangeLog | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 71b07aa2f2..54e3b4cc4b 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,3 +1,5 @@
+===============================================================
+Tag name: ctsm5.2.013
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 	       glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
 Date: Wed 17 Jul 2024 01:20:00 PM MDT

From e4142b96425712afa44cb6ab440d297a56aeaae1 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 17 Jul 2024 13:26:45 -0700
Subject: [PATCH 0709/1248] fixing bad merge with changelog

---
 doc/ChangeLog | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 54e3b4cc4b..3c6a104725 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -79,7 +79,6 @@ Changes to tests or testing:
    and use_fates_lupft namelist options.  Additoinally a new system text prefix,
    PVT, has been added to test the use_fates_potentialveg spin-up to use_fates_lupft
    transient workflow.  These have been added to the fates test suite.
-=======
 
 Bugs fixed
 ----------
@@ -154,6 +153,19 @@ Does this tag change answers significantly for any of the following physics conf
 
 [ ] clm4_5
 
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+Fixes #2444 Failing water isotope test on the ctsm5.2 branch
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to documentation: None
+
+Testing summary:
+----------------
+
  [PASS means all tests PASS; OK means tests PASS other than expected fails.]
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):

From 75cd2f4c866bd8148dff0e310e1ba0711bef13f3 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 17 Jul 2024 14:07:23 -0700
Subject: [PATCH 0710/1248] reformat new and updated systests with black

---
 cime_config/SystemTests/pvt.py              | 15 +++++++++------
 cime_config/SystemTests/systemtest_utils.py |  7 ++++---
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py
index 2a3dbafdc3..cf923dd334 100644
--- a/cime_config/SystemTests/pvt.py
+++ b/cime_config/SystemTests/pvt.py
@@ -16,9 +16,10 @@
 
 logger = logging.getLogger(__name__)
 
+
 class PVT(SystemTestsCommon):
-    def __init__(self,case):
-        SystemTestsCommon.__init__(self,case)
+    def __init__(self, case):
+        SystemTestsCommon.__init__(self, case)
 
         # Do not allow PVT to be run with certain testmods
         # Should this be targeted to a specific testmod for simplicity for now?
@@ -27,14 +28,16 @@ def __init__(self,case):
         casebaseid = self._case.get_value("CASEBASEID")
         casebaseid = casebaseid.split("-")[-1]
         if casebaseid[0:10] != "FatesLUPFT":
-            error_message = (f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected.")
+            error_message = f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected."
 
         # Only allow to run if resolution is 4x5 for now
         # Other grid resolutions will be pre-processed and included in the namelist defaults at a future date.
         # Potentially we could generate these on the fly although doing so would result in increased build time
         lnd_grid = self._case.get_value("LND_GRID")
         if lnd_grid != "4x5":
-            error_message = (f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected.")
+            error_message = (
+                f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected."
+            )
 
         if error_message is not None:
             logger.error(error_message)
@@ -79,7 +82,7 @@ def run_phase(self):
         # Turn off fates_harvest_mode for the spin up.
 
         logger.info("PVT log:  modify user_nl_clm file for spin up run")
-        added_content = ["use_fates_potentialveg = .true.","fates_harvest_mode = 'no_harvest'"]
+        added_content = ["use_fates_potentialveg = .true.", "fates_harvest_mode = 'no_harvest'"]
         append_to_user_nl_files(clone_path, "clm", added_content)
 
         # Run the spin up case
@@ -100,7 +103,7 @@ def run_phase(self):
         # obtain rpointer files and necessary restart files from short term archiving directory
         rundir = self._case.get_value("RUNDIR")
 
-        refdate = str(refcase_year) + '-01-01-00000'
+        refdate = str(refcase_year) + "-01-01-00000"
         rest_path = os.path.join(dout_sr, "rest", "{}".format(refdate))
 
         for item in glob.glob("{}/*{}*".format(rest_path, refdate)):
diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py
index c39f5171ba..c252f73251 100644
--- a/cime_config/SystemTests/systemtest_utils.py
+++ b/cime_config/SystemTests/systemtest_utils.py
@@ -86,14 +86,15 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path):
         print(f"ERROR trying to run {tool_name}.")
         raise
 
+
 # Read a user_nl file and return the namelist option if found
 def find_user_nl_option(caseroot, component, namelist_option):
-    
+
     # This is a copy of the CIME _get_list_of_user_nl_files
     # which could be used if this moved into the CIME project
     file_pattern = "user_nl_" + component + "*"
     file_list = glob.glob(os.path.join(caseroot, file_pattern))
-    
+
     # Check that there is at least one file
     if len(file_list) == 0:
         raise RuntimeError("No user_nl files found for component " + component)
@@ -103,7 +104,7 @@ def find_user_nl_option(caseroot, component, namelist_option):
     for one_file in file_list:
         with open(one_file, "r") as user_nl_file:
             user_nl_text = user_nl_file.read()
-            reg = fr'{namelist_option}.*?(?=,|\n)'
+            reg = rf"{namelist_option}.*?(?=,|\n)"
             find_out = re.findall(reg, user_nl_text)
             output[one_file] = find_out
     return output

From e14313858df6e9e6f2488951af2551349e349c65 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 10:11:33 -0600
Subject: [PATCH 0711/1248] generate_gdd20_baseline: Clarity rearrangement.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 476717b887..5d4fac3aff 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -246,16 +246,18 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice):
         if gddn is None:
             # Crop not handled yet? Fill it entirely with missing value
             this_da = dummy_da
-            long_name = "Dummy GDD20"
             print("   dummy GDD20")
         else:
             # this_da = ds_in[gddn].fillna(MISSING_FILL)
             this_da = ds_in[gddn]
             this_da = _add_time_axis(this_da)
-            long_name = gddn.replace("X", "20")
             print(f"   {gddn}")
 
-        # Add attributes
+        # Add attributes of output file
+        if gddn is None:
+            long_name = "Dummy GDD20"
+        else:
+            long_name = gddn.replace("X", "20")
         this_da.attrs["long_name"] = long_name + f" baseline for {cft_str}"
         this_da.attrs["units"] = "°C days"
         # this_da.attrs["_FillValue"] = MISSING_FILL

From 699936eef5097066b4faea29de920541be1d36d0 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 18 Jul 2024 10:47:24 -0600
Subject: [PATCH 0712/1248] Move namelist vars, add checks

---
 bld/CLMBuildNamelist.pm                       | 43 +++++++--
 .../namelist_definition_ctsm.xml              |  9 +-
 src/biogeophys/TemperatureType.F90            | 91 ++++++++++++++++++-
 src/main/clm_instMod.F90                      |  4 +-
 src/main/clm_varctl.F90                       |  4 -
 src/main/controlMod.F90                       | 12 +--
 6 files changed, 132 insertions(+), 31 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 45c0a7bdb8..498de96a4d 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1812,10 +1812,15 @@ sub process_namelist_inline_logic {
   #########################################
   setup_logic_initinterp($opts, $nl_flags, $definition, $defaults, $nl);
 
-  ###############################
-  # namelist group: exice_streams   #
-  ###############################
+  #################################
+  # namelist group: exice_streams #
+  #################################
   setup_logic_exice($opts, $nl_flags, $definition, $defaults, $nl);
+
+  ##########################################
+  # namelist group: clm_temperature_inparm #
+  ##########################################
+  setup_logic_coldstart_temp($opts,$nl_flags, $definition, $defaults, $nl);
 }
 
 #-------------------------------------------------------------------------------
@@ -4599,7 +4604,7 @@ sub setup_logic_exice {
      }
   # Otherwise if ice streams are off
   } else {
-     my @list = ( "stream_meshfile_exice", "stream_fldfilename_exice" , "excess_ice_coldstart_temp" , "excess_ice_coldstart_depth");
+     my @list = ( "stream_meshfile_exice", "stream_fldfilename_exice" );
      # fail is excess ice streams files are set
      foreach my $var ( @list ) {
         if ( defined($nl->get_value($var)) ) {
@@ -4618,8 +4623,6 @@ sub setup_logic_exice {
      if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice');
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice');
-       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_temp');
-       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_depth');
        # If excess ice streams on, but NOT the NUOPC driver fail
        if ( not $opts->{'driver'} eq "nuopc" ) {
           $log->fatal_error("nuopc driver is required when use_excess_ice_streams is set to true" );
@@ -4633,6 +4636,33 @@ sub setup_logic_exice {
 
 } # end exice streams
 
+sub setup_logic_coldstart_temp {
+
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+  # set initial temperatures for excess ice gridcells:
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_temp');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_depth');
+
+  my $use_exice = $nl->get_value( 'use_excess_ice' );
+  my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' );
+  my $exice_cs_temp = $nl->get_value( 'excess_ice_coldstart_temp' );
+  my $exice_cs_depth = $nl->get_value( 'excess_ice_coldstart_depth' );
+
+  if (defined($use_exice) && value_is_true($use_exice)) {
+     # Checking this setting only needed IF excess ice streams are on get the stream defaults
+     if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
+      if (defined($exice_cs_depth) && $exice_cs_depth <= 0.0 ) {
+        $log->fatal_error("excess_ice_coldstart_depth is <= 0.0" );
+      }
+      if (defined($exice_cs_temp) && $exice_cs_temp >= 0.0 ) {
+        $log->fatal_error("excess_ice_coldstart_temp is >= 0.0, no excess ice will be present in this run" );
+      }
+     }
+  }
+}
+
 #-------------------------------------------------------------------------------
 
 sub setup_logic_z0param {
@@ -4728,6 +4758,7 @@ sub write_output_files {
   push @groups, "lifire_inparm";
   push @groups, "ch4finundated";
   push @groups, "exice_streams";
+  push @groups, "clm_temperature_inparm";
   push @groups, "soilbgc_decomp";
   push @groups, "clm_canopy_inparm";
   push @groups, "zendersoilerod";
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 2eb8a67e8c..575d72856f 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -2825,13 +2825,14 @@ If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020)
 </entry>
 
 <entry id="excess_ice_coldstart_temp" type="real" category="clm_physics"
-       group="clm_inparm" >
-Initial soil temperature to use for gridcells with excess ice present during a run starting with coldstart (deg C)
+       group="clm_temperature_inparm" >
+Initial soil temperature to use for gridcells with excess ice present during a run starting with coldstart (deg C). Value is only apply if use_excess_ice is true.
 </entry>
 
 <entry id="excess_ice_coldstart_depth" type="real" category="clm_physics"
-       group="clm_inparm" >
-Soil depth below which initial excess ice concentration will be applied during a run starting with coldstart (m)
+       group="clm_temperature_inparm" >
+Soil depth below which initial excess ice concentration will be applied during a run starting with coldstart (m). Value is only apply if use_excess_ice is true. 
+If this is set below depth of the soil depth, only the last soil layer will get excess ice.
 </entry>
 
 
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 0a31bba6e6..6084c7ee2c 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -118,6 +118,10 @@ module TemperatureType
      real(r8), pointer    :: xmf_h2osfc_col        (:)   ! latent heat of phase change of surface water
      real(r8), pointer    :: fact_col              (:,:) ! used in computing tridiagonal matrix
      real(r8), pointer    :: c_h2osfc_col          (:)   ! heat capacity of surface water
+
+     ! Namelist parameters for initialization
+     real(r8), private    :: excess_ice_coldstart_depth  ! depth below which excess ice will be present
+     real(r8), private    :: excess_ice_coldstart_temp   ! coldstart temperature of layers with excess ice present
      
    contains
 
@@ -130,6 +134,8 @@ module TemperatureType
      procedure, public  :: InitAccVars
      procedure, public  :: UpdateAccVars
 
+     procedure, private :: ReadNL
+
   end type temperature_type
 
   character(len=*), parameter, private :: sourcefile = &
@@ -141,7 +147,7 @@ module TemperatureType
   !------------------------------------------------------------------------
   subroutine Init(this, bounds, &
        em_roof_lun,  em_wall_lun, em_improad_lun, em_perroad_lun, &
-       is_simple_buildtemp, is_prog_buildtemp, exice_init_stream_col)
+       is_simple_buildtemp, is_prog_buildtemp, exice_init_stream_col, NLFileName)
     !
     ! !DESCRIPTION:
     !
@@ -157,7 +163,10 @@ subroutine Init(this, bounds, &
     logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
     logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
     real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:)  ! initial excess ice concentration from the stream file
+    character(len=*)  , intent(in) :: NLFilename ! Namelist filename
 
+
+    call this%ReadNL(NLFilename)
     call this%InitAllocate ( bounds )
     call this%InitHistory ( bounds, is_simple_buildtemp, is_prog_buildtemp )
     call this%InitCold ( bounds,                  &
@@ -654,7 +663,7 @@ subroutine InitCold(this, bounds, &
     use column_varcon  , only : icol_road_imperv, icol_roof, icol_sunwall
     use column_varcon  , only : icol_shadewall, icol_road_perv
     use clm_varctl     , only : iulog, use_vancouver, use_mexicocity
-    use clm_varctl     , only : use_excess_ice, excess_ice_coldstart_depth, excess_ice_coldstart_temp
+    use clm_varctl     , only : use_excess_ice
     use initVerticalMod , only : find_soil_layer_containing_depth
     !
     ! !ARGUMENTS:
@@ -750,12 +759,21 @@ subroutine InitCold(this, bounds, &
                this%t_soisno_col(c,1:nlevgrnd) = 272._r8
                if (use_excess_ice .and. exice_init_stream_col(c) > 0.0_r8) then
                   nexice_start = nlevsoi - 1
-                  if (zisoi(nlevsoi) >= excess_ice_coldstart_depth) then
-                     call find_soil_layer_containing_depth(0.5_r8,nexice_start)
+                  if (this%excess_ice_coldstart_depth <= 0.0_r8) then
+                     ! we double check this here, and when building namelists
+                      call endrun(msg="ERROR excess_ice_coldstart_depth <= 0.0. Set a positive value in the namelist"//errmsg(sourcefile, __LINE__))
+                  endif
+                  if (zisoi(nlevsoi) >= this%excess_ice_coldstart_depth) then
+                     call find_soil_layer_containing_depth(this%excess_ice_coldstart_depth,nexice_start)
                   else
                        nexice_start=nlevsoi-1
                   endif
-                  this%t_soisno_col(c,nexice_start:nlevgrnd) = SHR_CONST_TKFRZ + excess_ice_coldstart_temp !needs to be below freezing to properly initiate excess ice
+                  if (this%excess_ice_coldstart_temp >= 0.0_r8) then
+                     ! this is here, since we care about excess_ice_coldstart_temp only when there is excess ice in the gridcell
+                     ! which happens only when the streams are read.
+                     call endrun(msg="ERROR excess_ice_coldstart_temp is not below freezing point"//errmsg(sourcefile, __LINE__))
+                  endif
+                  this%t_soisno_col(c,nexice_start:nlevgrnd) = SHR_CONST_TKFRZ + this%excess_ice_coldstart_temp
                end if
             endif
          endif
@@ -1646,4 +1664,67 @@ subroutine Clean(this)
   
    end subroutine Clean
 
+   !-----------------------------------------------------------------------
+   subroutine ReadNL( this, NLFilename )
+     !
+     ! !DESCRIPTION:
+     ! Read namelist for Temperature type
+     ! right now (17.07.2024) it only reads variables related to excess ice coldstart initialization
+     ! but can be extended to replace hardocded values in InitCold by namelist variables
+     !
+     ! !USES:
+     use shr_mpi_mod    , only : shr_mpi_bcast
+     use shr_log_mod    , only : errMsg => shr_log_errMsg
+     use spmdMod        , only : masterproc, mpicom
+     use fileutils      , only : getavu, relavu, opnfil
+     use clm_nlUtilsMod , only : find_nlgroup_name
+     use clm_varctl     , only : iulog 
+     use abortutils     , only : endrun
+     !
+     ! !ARGUMENTS:
+     class(temperature_type) :: this
+     character(len=*), intent(in) :: NLFilename ! Namelist filename
+     !
+     ! !LOCAL VARIABLES:
+     integer  :: ierr                          ! error code
+     integer  :: unitn                         ! unit for namelist file
+     real(r8) :: excess_ice_coldstart_temp = spval ! coldstart temperature of layers with excess ice present (deg C)
+     real(r8) :: excess_ice_coldstart_depth = spval        ! depth below which excess ice will be present (m)
+     character(len=32) :: subname = 'Temperature_readnl'  ! subroutine name
+     !-----------------------------------------------------------------------
+
+     namelist / clm_temperature_inparm / excess_ice_coldstart_depth, excess_ice_coldstart_temp
+
+     if ( masterproc )then
+
+        unitn = getavu()
+        write(iulog,*) 'Read in clm_temperature_inparm  namelist'
+        call opnfil (NLFilename, unitn, 'F')
+        call find_nlgroup_name(unitn, 'clm_temperature_inparm', status=ierr)
+        if (ierr == 0) then
+           read(unitn, nml=clm_temperature_inparm, iostat=ierr)
+           if (ierr /= 0) then
+              call endrun(msg="ERROR reading clm_temperature_inparm namelist"//errmsg(sourcefile, __LINE__))
+           end if
+        else
+           call endrun(msg="ERROR finding clm_temperature_inparm namelist"//errmsg(sourcefile, __LINE__))
+        end if
+        call relavu( unitn )
+        ! namelist might be read but the values not properly set
+       if ( excess_ice_coldstart_depth == spval ) then
+          call endrun(msg="ERROR exice_coldstart_depth namelist value is not properly set"//errmsg(sourcefile, __LINE__))
+       endif
+       if ( excess_ice_coldstart_temp == spval ) then
+          call endrun(msg="ERROR exice_coldstart_temp namelist value is not properly set"//errmsg(sourcefile, __LINE__))
+       endif
+     end if
+
+     call shr_mpi_bcast(excess_ice_coldstart_depth, mpicom)
+     call shr_mpi_bcast(excess_ice_coldstart_temp, mpicom)
+
+     this%excess_ice_coldstart_depth = excess_ice_coldstart_depth
+     this%excess_ice_coldstart_temp = excess_ice_coldstart_temp
+
+   end subroutine ReadNL
+
 end module TemperatureType
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index 04c4af6611..242df92c43 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -222,7 +222,7 @@ subroutine clm_instInit(bounds)
     type(file_desc_t)     :: params_ncid  ! pio netCDF file id for parameter file
     real(r8), allocatable :: h2osno_col(:)
     real(r8), allocatable :: snow_depth_col(:)
-    real(r8), allocatable :: exice_init_stream_col(:)
+    real(r8), allocatable :: exice_init_stream_col(:) ! initial concentration of excess ice in the soil (-)
     type(excessicestream_type)  :: exice_stream
 
     integer :: dummy_to_make_pgi_happy
@@ -317,7 +317,7 @@ subroutine clm_instInit(bounds)
          em_improad_lun=urbanparams_inst%em_improad(begl:endl), &
          em_perroad_lun=urbanparams_inst%em_perroad(begl:endl), &
          is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp(), &
-         exice_init_stream_col=exice_init_stream_col(bounds%begc:bounds%endc) )
+         exice_init_stream_col=exice_init_stream_col(bounds%begc:bounds%endc) , NLFileName=NLFilename)
 
     call active_layer_inst%Init(bounds)
 
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index eff05511cd..8804ad2c01 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -422,10 +422,6 @@ module clm_varctl
   !----------------------------------------------------------
   logical, public :: use_excess_ice = .false. ! true. => use excess ice physics
 
-  real(r8), public :: excess_ice_coldstart_temp = rundef ! initial coldstart soil temperature for gridcells where excess ice is present
-
-  real(r8), public :: excess_ice_coldstart_depth = rundef ! initial coldstart depth at which excess ice might be present and excess_ice_coldstart_temp will be applied
-
   !----------------------------------------------------------
   ! plant hydraulic stress switch
   !----------------------------------------------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index a5321e0797..47ce6dce7c 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -256,8 +256,8 @@ subroutine control_init(dtime)
 
     namelist /clm_inparm/ use_soil_moisture_streams
 
-    ! excess ice flag and parameters
-    namelist /clm_inparm/ use_excess_ice , excess_ice_coldstart_depth, excess_ice_coldstart_temp
+    ! excess ice flag
+    namelist /clm_inparm/ use_excess_ice 
 
     namelist /clm_inparm/ use_lai_streams
 
@@ -829,10 +829,6 @@ subroutine control_spmd()
 
     call mpi_bcast (use_excess_ice, 1, MPI_LOGICAL, 0, mpicom,ier)
 
-    call mpi_bcast (excess_ice_coldstart_depth, 1, MPI_REAL8, 0, mpicom, ier)
-
-    call mpi_bcast (excess_ice_coldstart_temp, 1, MPI_REAL8, 0, mpicom, ier)
-
     call mpi_bcast (use_lai_streams, 1, MPI_LOGICAL, 0, mpicom, ier)
 
     call mpi_bcast (use_cropcal_streams, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -989,10 +985,6 @@ subroutine control_print ()
     write(iulog,*) '    use_extralakelayers = ', use_extralakelayers
     write(iulog,*) '    use_vichydro = ', use_vichydro
     write(iulog,*) '    use_excess_ice = ', use_excess_ice
-    if (use_excess_ice) then
-       write(iulog,*) '    excess_ice_coldstart_depth = ', excess_ice_coldstart_depth
-       write(iulog,*) '    excess_ice_coldstart_temp = ', excess_ice_coldstart_temp
-    endif
     write(iulog,*) '    use_cn = ', use_cn
     write(iulog,*) '    use_cndv = ', use_cndv
     write(iulog,*) '    use_crop = ', use_crop

From 3416574a862e2f1df62d29abb82efe76686084dd Mon Sep 17 00:00:00 2001
From: adrifoster <adrifost@ucar.edu>
Date: Thu, 18 Jul 2024 10:51:28 -0600
Subject: [PATCH 0713/1248] update date

---
 doc/ChangeLog | 2 +-
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 3c6a104725..8cc3198fae 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -2,7 +2,7 @@
 Tag name: ctsm5.2.013
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 	       glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
-Date: Wed 17 Jul 2024 01:20:00 PM MDT
+Date: Thu Jul 18 10:51:11 MDT 2024
 One-line Summary: FATES Land Use V2
 
 Purpose and description of changes
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 92ca8281cf..df8e6dcf6a 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.013 glemieux 07/17/2024 FATES Land Use V2
+       ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2
        ctsm5.2.012    sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes
        ctsm5.2.011   slevis 07/12/2024 Merge b4b-dev
        ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption

From 647fc52df1eb32b10646eb54ed4240d4cc9cfc00 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 11:07:00 -0600
Subject: [PATCH 0714/1248] import_ds: Workaround to import multiple files
 without dask.

---
 python/ctsm/crop_calendars/import_ds.py | 53 +++++++++++++++++--------
 1 file changed, 37 insertions(+), 16 deletions(-)

diff --git a/python/ctsm/crop_calendars/import_ds.py b/python/ctsm/crop_calendars/import_ds.py
index 77a22b626b..0526d3c720 100644
--- a/python/ctsm/crop_calendars/import_ds.py
+++ b/python/ctsm/crop_calendars/import_ds.py
@@ -41,6 +41,29 @@ def compute_derived_vars(ds_in, var):
     return ds_in
 
 
+def manual_mfdataset(filelist, my_vars, my_vegtypes, time_slice):
+    """
+    Opening a list of files with Xarray's open_mfdataset requires dask. This function is a
+    workaround for Python environments that don't have dask.
+    """
+    ds_out = None
+    for filename in filelist:
+        ds_in = xr.open_dataset(filename)
+        ds_in = mfdataset_preproc(ds_in, my_vars, my_vegtypes, time_slice)
+        if ds_out is None:
+            ds_out = ds_in
+        else:
+            ds_out = xr.concat(
+                [ds_out, ds_in],
+                data_vars="minimal",
+                compat="override",
+                coords="all",
+                dim="time",
+                # combine="nested",
+            )
+    return ds_out
+
+
 def mfdataset_preproc(ds_in, vars_to_import, vegtypes_to_import, time_slice):
     """
     Function to drop unwanted variables in preprocessing of open_mfdataset().
@@ -221,22 +244,20 @@ def import_ds(
     if isinstance(filelist, list):
         with warnings.catch_warnings():
             warnings.filterwarnings(action="ignore", category=DeprecationWarning)
-            if find_spec("dask") is None:
-                raise ModuleNotFoundError(
-                    "You have asked xarray to import a list of files as a single Dataset using"
-                    " open_mfdataset(), but this requires dask, which is not available.\nFile"
-                    f" list: {filelist}"
-                )
-        this_ds = xr.open_mfdataset(
-            sorted(filelist),
-            data_vars="minimal",
-            preprocess=mfdataset_preproc_closure,
-            compat="override",
-            coords="all",
-            concat_dim="time",
-            combine="nested",
-            chunks=chunks,
-        )
+            dask_unavailable = find_spec("dask") is None
+        if dask_unavailable:
+            this_ds = manual_mfdataset(filelist, my_vars, my_vegtypes, time_slice)
+        else:
+            this_ds = xr.open_mfdataset(
+                sorted(filelist),
+                data_vars="minimal",
+                preprocess=mfdataset_preproc_closure,
+                compat="override",
+                coords="all",
+                concat_dim="time",
+                combine="nested",
+                chunks=chunks,
+            )
     elif isinstance(filelist, str):
         this_ds = xr.open_dataset(filelist, chunks=chunks)
         this_ds = mfdataset_preproc(this_ds, my_vars, my_vegtypes, time_slice)

From 96015dacbc7a22d57bcd242e358356f5c0cb028b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 11:11:52 -0600
Subject: [PATCH 0715/1248] generate_gdd20_baseline: Can now specify
 -v/--variable GDDBX or GDDB20.

---
 .../crop_calendars/generate_gdd20_baseline.py | 64 +++++++++++++------
 1 file changed, 46 insertions(+), 18 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 5d4fac3aff..4b8e68e8f9 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -19,7 +19,6 @@
 import ctsm.crop_calendars.cropcal_utils as utils
 from ctsm.crop_calendars.grid_one_variable import grid_one_variable
 
-VAR_LIST_IN = ["GDD0X", "GDD8X", "GDD10X"]
 GRIDDING_VAR_LIST = ["patches1d_ixy", "patches1d_jxy", "lat", "lon"]
 MISSING_FILL = -1  # Something impossible to ensure that you can mark it as a missing value, to be
 # bilinear-interpolated
@@ -88,6 +87,16 @@ def _parse_args():
         type=int,
         required=False,
     )
+    parser.add_argument(
+        "-v",
+        "--variable",
+        help=(
+            "Which type of variable should be processed?"
+        ),
+        required=False,
+        default="GDDBX",
+        choices=["GDDBX", "GDDB20"],
+    )
 
     # Get arguments
     args = parser.parse_args(sys.argv[1:])
@@ -96,6 +105,12 @@ def _parse_args():
     if os.path.exists(args.output_file) and not args.overwrite:
         raise FileExistsError("Output file exists but --overwrite is not specified")
 
+    # Get and check input files
+    args.input_files = args.input_files.split(" ")
+    for filename in args.input_files:
+        if not os.path.exists(filename):
+            raise FileNotFoundError(f"Input file not found: {filename}")
+
     # Process time slice
     # Assumes CESM behavior where data for e.g. 1987 is saved as 1988-01-01.
     # It would be more robust, accounting for upcoming behavior (where timestamp for a year is the
@@ -137,7 +152,7 @@ def _get_cft_list(crop_list):
     return cft_str_list
 
 
-def _get_gddn_for_cft(cft_str):
+def _get_gddn_for_cft(cft_str, variable):
     """
     Given a CFT name, return the GDDN variable it uses.
 
@@ -149,6 +164,7 @@ def _get_gddn_for_cft(cft_str):
     """
 
     gddn = None
+    gddn_str = None
 
     gdd0_list_str = ["wheat", "cotton", "rice"]
     if cft_str in _get_cft_list(gdd0_list_str):
@@ -163,9 +179,9 @@ def _get_gddn_for_cft(cft_str):
         gddn = 10
 
     if gddn is not None:
-        gddn = f"GDD{gddn}X"
+        gddn_str = variable.replace("B", str(gddn))
 
-    return gddn
+    return gddn, gddn_str
 
 
 def _get_output_varname(cft_str):
@@ -194,19 +210,28 @@ def _add_time_axis(da_in):
     return da_out
 
 
-def generate_gdd20_baseline(input_files, output_file, author, time_slice):
+def generate_gdd20_baseline(input_files, output_file, author, time_slice, variable):
     """
     Generate stream_fldFileName_gdd20_baseline file from CTSM outputs
     """
 
-    # Get input file list
-    input_files = input_files.split(sep=" ")
+    # Define variables to process
+    if variable == "GDDBX":
+        suffix = "X"
+    elif variable == "GDDB20":
+        suffix = "20"
+    else:
+        raise ValueError(f"-v/--variable {variable} not recoginzed")
+    var_list_in = []
+    for base_temp in [0, 8, 10]:
+        var_list_in.append(f"GDD{base_temp}{suffix}")
+
     # Get unique values and sort
     input_files = list(set(input_files))
     input_files.sort()
 
     # Import history files and ensure they have lat/lon dims
-    ds_in = import_ds(input_files, VAR_LIST_IN + GRIDDING_VAR_LIST, time_slice=time_slice)
+    ds_in = import_ds(input_files, var_list_in + GRIDDING_VAR_LIST, time_slice=time_slice)
     if not all(x in ds_in.dims for x in ["lat", "lon"]):
         raise RuntimeError("Input files must have lat and lon dimensions")
 
@@ -216,9 +241,9 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice):
 
     # Set up a dummy DataArray to use for crops without an assigned GDDN variable
     dummy_da = xr.DataArray(
-        data=MISSING_FILL * np.ones_like(ds_in[VAR_LIST_IN[0]].values),
-        dims=ds_in[VAR_LIST_IN[0]].dims,
-        coords=ds_in[VAR_LIST_IN[0]].coords,
+        data=MISSING_FILL * np.ones_like(ds_in[var_list_in[0]].values),
+        dims=ds_in[var_list_in[0]].dims,
+        coords=ds_in[var_list_in[0]].coords,
     )
     dummy_da = _add_time_axis(dummy_da)
 
@@ -239,25 +264,27 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice):
         print(f"{cft_str} ({cft_int})")
 
         # Which GDDN history variable does this crop use? E.g., GDD0, GDD10
-        gddn = _get_gddn_for_cft(cft_str)
+        gddn, gddn_str = _get_gddn_for_cft(cft_str, variable)
 
         # Fill any missing values with MISSING_FILL. This will mean that gddmaturity in these cells
         # never changes.
-        if gddn is None:
+        if gddn_str is None:
             # Crop not handled yet? Fill it entirely with missing value
             this_da = dummy_da
             print("   dummy GDD20")
         else:
             # this_da = ds_in[gddn].fillna(MISSING_FILL)
-            this_da = ds_in[gddn]
+            this_da = ds_in[gddn_str]
             this_da = _add_time_axis(this_da)
-            print(f"   {gddn}")
+            print(f"   {gddn_str}")
 
         # Add attributes of output file
-        if gddn is None:
+        if (gddn is None) != (gddn_str is None):
+            raise RuntimeError("gddn and gddn_str must either both be None or both be not None")
+        if gddn_str is None:
             long_name = "Dummy GDD20"
         else:
-            long_name = gddn.replace("X", "20")
+            long_name = f"GDD{gddn}20"
         this_da.attrs["long_name"] = long_name + f" baseline for {cft_str}"
         this_da.attrs["units"] = "°C days"
         # this_da.attrs["_FillValue"] = MISSING_FILL
@@ -287,5 +314,6 @@ def main():
         args.input_files,
         args.output_file,
         args.author,
-        time_slice
+        time_slice,
+        args.variable,
     )

From 3cc1d0fafb3290c1b249d22f828429c92a3719c4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 11:14:33 -0600
Subject: [PATCH 0716/1248] generate_gdd20_baseline: Satisfy pylint.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 4b8e68e8f9..d2f96965b7 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -160,7 +160,7 @@ def _get_gddn_for_cft(cft_str, variable):
         cft_str (str): E.g., "irrigated_temperate_corn"
 
     Returns:
-        str or None: Name of variable to use (e.g., "GDD8X"). If crop isn't yet handled, return None.
+        str or None: Name of variable to use (e.g., "GDD8X"). If crop not yet handled, return None.
     """
 
     gddn = None
@@ -249,8 +249,8 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
 
     # Process all crops
     data_var_dict = {}
-    for v in GRIDDING_VAR_LIST:
-        data_var_dict[v] = ds_in[v]
+    for gridding_var in GRIDDING_VAR_LIST:
+        data_var_dict[gridding_var] = ds_in[gridding_var]
     ds_out = xr.Dataset(
         data_vars=data_var_dict,
         attrs={

From b1bbe15eb03a57a26eb010a850a285fd600dfe3b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 11:27:10 -0600
Subject: [PATCH 0717/1248] generate_gdd20_baseline: Save input file list as
 attribute(s).

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index d2f96965b7..b03d1fd658 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -247,7 +247,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
     )
     dummy_da = _add_time_axis(dummy_da)
 
-    # Process all crops
+    # Set up output Dataset
     data_var_dict = {}
     for gridding_var in GRIDDING_VAR_LIST:
         data_var_dict[gridding_var] = ds_in[gridding_var]
@@ -258,6 +258,14 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
             "created": dt.datetime.now().astimezone().isoformat(),
         },
     )
+    all_files_in_same_dir = len(np.unique([os.path.dirname(file) for file in input_files])) == 1
+    if all_files_in_same_dir:
+        ds_out.attrs["input_files_dir"] = os.path.dirname(input_files[0])
+        ds_out.attrs["input_files"] = ", ".join([os.path.basename(file) for file in input_files])
+    else:
+        ds_out.attrs["input_files"] = ", ".join(input_files)
+
+    # Process all crops
     encoding_dict = {}
     for cft_str in utils.define_mgdcrop_list():
         cft_int = utils.vegtype_str2int(cft_str)[0]

From a703cb6549576c63cedde68756292fab630543a5 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 11:31:46 -0600
Subject: [PATCH 0718/1248] generate_gdd20_baseline: Save input year range as
 attribute.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index b03d1fd658..14e2d5974f 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -210,7 +210,7 @@ def _add_time_axis(da_in):
     return da_out
 
 
-def generate_gdd20_baseline(input_files, output_file, author, time_slice, variable):
+def generate_gdd20_baseline(input_files, output_file, author, time_slice, variable, year_args):
     """
     Generate stream_fldFileName_gdd20_baseline file from CTSM outputs
     """
@@ -256,6 +256,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
         attrs={
             "author": author,
             "created": dt.datetime.now().astimezone().isoformat(),
+            "input_year_range": f"{year_args[0]}-{year_args[1]}",
         },
     )
     all_files_in_same_dir = len(np.unique([os.path.dirname(file) for file in input_files])) == 1
@@ -324,4 +325,5 @@ def main():
         args.author,
         time_slice,
         args.variable,
+        [args.first_year, args.last_year],
     )

From 7a5e067dd09970d74708ed9c678f1de7d8f29af6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 11:32:33 -0600
Subject: [PATCH 0719/1248] generate_gdd20_baseline: Save input variable type
 as attribute.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 14e2d5974f..a87a2edb79 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -257,6 +257,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
             "author": author,
             "created": dt.datetime.now().astimezone().isoformat(),
             "input_year_range": f"{year_args[0]}-{year_args[1]}",
+            "input_variable": variable,
         },
     )
     all_files_in_same_dir = len(np.unique([os.path.dirname(file) for file in input_files])) == 1

From 25896e460ac556a5cef78201f55b8f04fc6ce154 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 11:34:19 -0600
Subject: [PATCH 0720/1248] generate_gdd20_baseline: Functionize
 setup_output_dataset().

---
 .../crop_calendars/generate_gdd20_baseline.py | 44 +++++++++++--------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index a87a2edb79..5d6809f7ff 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -210,6 +210,31 @@ def _add_time_axis(da_in):
     return da_out
 
 
+def setup_output_dataset(input_files, author, variable, year_args, ds_in):
+    """
+    Set up output Dataset
+    """
+    data_var_dict = {}
+    for gridding_var in GRIDDING_VAR_LIST:
+        data_var_dict[gridding_var] = ds_in[gridding_var]
+    ds_out = xr.Dataset(
+        data_vars=data_var_dict,
+        attrs={
+            "author": author,
+            "created": dt.datetime.now().astimezone().isoformat(),
+            "input_year_range": f"{year_args[0]}-{year_args[1]}",
+            "input_variable": variable,
+        },
+    )
+    all_files_in_same_dir = len(np.unique([os.path.dirname(file) for file in input_files])) == 1
+    if all_files_in_same_dir:
+        ds_out.attrs["input_files_dir"] = os.path.dirname(input_files[0])
+        ds_out.attrs["input_files"] = ", ".join([os.path.basename(file) for file in input_files])
+    else:
+        ds_out.attrs["input_files"] = ", ".join(input_files)
+    return ds_out
+
+
 def generate_gdd20_baseline(input_files, output_file, author, time_slice, variable, year_args):
     """
     Generate stream_fldFileName_gdd20_baseline file from CTSM outputs
@@ -248,24 +273,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
     dummy_da = _add_time_axis(dummy_da)
 
     # Set up output Dataset
-    data_var_dict = {}
-    for gridding_var in GRIDDING_VAR_LIST:
-        data_var_dict[gridding_var] = ds_in[gridding_var]
-    ds_out = xr.Dataset(
-        data_vars=data_var_dict,
-        attrs={
-            "author": author,
-            "created": dt.datetime.now().astimezone().isoformat(),
-            "input_year_range": f"{year_args[0]}-{year_args[1]}",
-            "input_variable": variable,
-        },
-    )
-    all_files_in_same_dir = len(np.unique([os.path.dirname(file) for file in input_files])) == 1
-    if all_files_in_same_dir:
-        ds_out.attrs["input_files_dir"] = os.path.dirname(input_files[0])
-        ds_out.attrs["input_files"] = ", ".join([os.path.basename(file) for file in input_files])
-    else:
-        ds_out.attrs["input_files"] = ", ".join(input_files)
+    ds_out = setup_output_dataset(input_files, author, variable, year_args, ds_in)
 
     # Process all crops
     encoding_dict = {}

From 7c2f5968702c3f17ab13e34d99cbbed642ba7604 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 18 Jul 2024 11:45:33 -0600
Subject: [PATCH 0721/1248] Revisions according to review, plus some clean-up

I used this test to confirm same answers:
./create_test ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream -c /glade/campaign/cgd/tss/ctsm_baselines/ctsm5.2.012
This test had indicated differences with an earlier commit that
I subsequently reverted.
---
 src/biogeochem/VOCEmissionMod.F90 | 140 +++++++-----------------------
 1 file changed, 31 insertions(+), 109 deletions(-)

diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
index 9833fe3de9..b84d6a4ae8 100644
--- a/src/biogeochem/VOCEmissionMod.F90
+++ b/src/biogeochem/VOCEmissionMod.F90
@@ -423,7 +423,6 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
     type(photosyns_type)   , intent(in)    :: photosyns_inst
     type(temperature_type) , intent(in)    :: temperature_inst
     type(vocemis_type)     , intent(inout) :: vocemis_inst
-    !by Hui,
     type(energyflux_type)  , intent(in)    :: energyflux_inst
     !
     ! !REVISION HISTORY:
@@ -479,15 +478,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
     end if
 
     associate(                                                    & 
-         !dz           => col%dz                                , & ! Input:  [real(r8) (:,:) ]  depth of layer (m)                              
-         !bsw          => soilstate_inst%bsw_col                , & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b" (nlevgrnd)             
-         !clayfrac     => soilstate_inst%clayfrac_col           , & ! Input:  [real(r8) (:)   ]  fraction of soil that is clay                     
-         !sandfrac     => soilstate_inst%sandfrac_col           , & ! Input:  [real(r8) (:)   ]  fraction of soil that is sand                     
-         !watsat       => soilstate_inst%watsat_col             , & ! Input:  [real(r8) (:,:) ]  volumetric soil water at saturation (porosity) (nlevgrnd)
-         !sucsat       => soilstate_inst%sucsat_col             , & ! Input:  [real(r8) (:,:) ]  minimum soil suction (mm) (nlevgrnd)            
-         !h2osoi_vol   => waterstate_inst%h2osoi_vol_col        , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (m3/m3)                   
-         !h2osoi_ice   => waterstate_inst%h2osoi_ice_col        , & ! Input:  [real(r8) (:,:) ]  ice soil content (kg/m3)                        
-         btran         => energyflux_inst%btran_patch           , & ! Input: [real(r8) (:)    ]  transpiration wetness factor (0 to 1)
+         btran         => energyflux_inst%btran_patch           , & ! Input:  [real(r8) (:)   ]  transpiration wetness factor (0 to 1)
          
          forc_solad    => atm2lnd_inst%forc_solad_downscaled_col, & ! Input:  [real(r8) (:,:) ]  direct beam radiation (visible only)            
          forc_solai    => atm2lnd_inst%forc_solai_grc           , & ! Input:  [real(r8) (:,:) ]  diffuse radiation     (visible only)            
@@ -573,12 +564,8 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
           ! Activity factor for LAI (Guenther et al., 2006): all species
           gamma_l = get_gamma_L(fsun240(p), elai(p))
 
-          !gamma_sm = 1.0_r8
-          !Impact of soil moisture on isoprene emission
+          ! Impact of soil moisture on isoprene emission
           gamma_sm = get_gamma_SM(btran(p))
-          ! Activity factor for soil moisture: all species (commented out for now)
-          !          gamma_sm = get_gamma_SM(clayfrac(p), sandfrac(p), h2osoi_vol(c,:), h2osoi_ice(c,:), &
-          !               col%dz(c,:), soilstate_inst%bsw_col(c,:), watsat(c,:), sucsat(c,:), root_depth(patch%itype(p)))
 
           ! Loop through VOCs for light, temperature and leaf age activity factor & apply
           ! all final activity factors to baseline emission factors
@@ -825,105 +812,38 @@ end function get_gamma_L
 
   !-----------------------------------------------------------------------
   function get_gamma_SM(btran_in)
+
     !---------------------------------------
     ! May 22, 2024
     ! Activity factor for soil moisture of Isoprene (Wang et al., 2022, JAMES)
     ! It is based on eq. (11) in the paper. Because the temperature response
-    ! of isoprene has been explicitly included in CLM; 
+    ! of isoprene has been explicitly included in CLM;
+
     !ARGUMENTS:
     implicit none
     real(r8),intent(in) :: btran_in
-    
+
     !!!------- the drought algorithm--------
-    real(r8), parameter :: a1 = -7.4463      
-    real(r8), parameter :: b1 = 3.2552       
+    real(r8), parameter :: a1 = -7.4463_r8
+    real(r8), parameter :: b1 = 3.2552_r8
     real(r8)            :: get_gamma_SM
-             if (btran_in >= 1.) then
-                get_gamma_SM = 1
-             else
-                get_gamma_SM = 1/(1+b1*exp(a1*(btran_in-0.2)))
-             endif 
+    !---------------------------------------
+
+    if (btran_in >= 1._r8) then
+       get_gamma_SM = 1._r8
+    else
+       get_gamma_SM = 1._r8 / (1._r8 + b1 * exp(a1 * (btran_in - 0.2_r8)))
+    endif
+
   end function get_gamma_SM
- 
-  !function get_gamma_SM(clayfrac_in, sandfrac_in, h2osoi_vol_in, h2osoi_ice_in, dz_in, &
-  !     bsw_in, watsat_in, sucsat_in, root_depth_in)
-  !  !
-  !  ! Activity factor for soil moisture (Guenther et al., 2006): all species
-  !  !----------------------------------
-  !  ! Calculate the mean scaling factor throughout the root depth.
-  !  ! wilting point potential is in units of matric potential (mm) 
-  !  ! (1 J/Kg = 0.001 MPa, approx = 0.1 m)
-  !  ! convert to volumetric soil water using equation 7.118 of the CLM4 Technical Note
-  !  !
-  !  ! !USES:
-  !  use clm_varcon , only : denice
-  !  use clm_varpar , only : nlevsoi
-  !  !
-  !  ! !ARGUMENTS:
-  !  implicit none
-  !  real(r8),intent(in) :: clayfrac_in
-  !  real(r8),intent(in) :: sandfrac_in
-  !  real(r8),intent(in) :: h2osoi_vol_in(nlevsoi)
-  !  real(r8),intent(in) :: h2osoi_ice_in(nlevsoi)
-  !  real(r8),intent(in) :: dz_in(nlevsoi)
-  !  real(r8),intent(in) :: bsw_in(nlevsoi)
-  !  real(r8),intent(in) :: watsat_in(nlevsoi)
-  !  real(r8),intent(in) :: sucsat_in(nlevsoi)
-  !  real(r8),intent(in) :: root_depth_in
-  !  !
-  !  ! !LOCAL VARIABLES:
-  !  real(r8)            :: get_gamma_SM
-  !  integer  :: j
-  !  real(r8) :: nl                      ! temporary number of soil levels
-  !  real(r8) :: theta_ice               ! water content in ice in m3/m3
-  !  real(r8) :: wilt                    ! wilting point in m3/m3
-  !  real(r8) :: theta1                  ! temporary
-  !  real(r8), parameter :: deltheta1=0.06_r8               ! empirical coefficient
-  !  real(r8), parameter :: smpmax = 2.57e5_r8              ! maximum soil matrix potential
-  !  !-----------------------------------------------------------------------
-
-  !  if ((clayfrac_in > 0) .and. (sandfrac_in > 0)) then 
-  !     get_gamma_SM = 0._r8
-  !     nl=0._r8
-  !     
-  !     do j = 1,nlevsoi
-  !        if  (sum(dz_in(1:j)) < root_depth_in)  then
-  !           theta_ice = h2osoi_ice_in(j)/(dz_in(j)*denice)
-  !           wilt = ((smpmax/sucsat_in(j))**(-1._r8/bsw_in(j))) * (watsat_in(j) - theta_ice)
-  !           theta1 = wilt + deltheta1
-  !           if (h2osoi_vol_in(j) >= theta1) then 
-  !              get_gamma_SM = get_gamma_SM + 1._r8
-  !           else if ( (h2osoi_vol_in(j) > wilt) .and. (h2osoi_vol_in(j) < theta1) ) then
-  !              get_gamma_SM = get_gamma_SM + ( h2osoi_vol_in(j) - wilt ) / deltheta1
-  !           else
-  !              get_gamma_SM = get_gamma_SM + 0._r8
-  !           end if
-  !           nl=nl+1._r8
-  !        end if
-  !     end do
-  !     
-  !     if (nl > 0._r8) then
-  !        get_gamma_SM = get_gamma_SM/nl
-  !     endif
-
-  !     if (get_gamma_SM > 1.0_r8) then 
-  !        write(iulog,*) 'healdSM > 1: gamma_SM, nl', get_gamma_SM, nl
-  !        get_gamma_SM=1.0_r8
-  !     endif
-
-  !  else
-  !     get_gamma_SM = 1.0_r8
-  !  end if
-
-  !end function get_gamma_SM
-  
+
   !-----------------------------------------------------------------------
   function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in, LDF_in, Ceo_in, Eopt, topt, ivt_in)
 
-    ! Activity factor for temperature 
+    ! Activity factor for temperature
     !--------------------------------
-    ! May 24, 2024 Hui updated the temperature response curves of isoprene for 
-    ! Boreal Broadleaf Deciduous Shrub and Arctic C3 grass based on 
+    ! May 24, 2024 Hui updated the temperature response curves of isoprene for
+    ! Boreal Broadleaf Deciduous Shrub and Arctic C3 grass based on
     ! Wang et al., 2024 (GRL) and Wang et al., 2024 (Nature Communications)
     !--------------------------------
     ! Calculate both a light-dependent fraction as in Guenther et al., 2006 for isoprene
@@ -931,6 +851,9 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     ! form of an exponential. Final activity factor depends on light dependent fraction
     ! of compound type.
     !
+    ! !USES:
+    use clm_varcon, only: tfrz
+
     ! !ARGUMENTS:
     implicit none
     integer,intent(in)  :: ivt_in
@@ -951,6 +874,7 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     real(r8) :: gamma_t_LIF             ! activity factor for temperature
     real(r8) :: x                       ! temporary i
     real(r8) :: bet_arc_c3
+    real(r8), parameter :: bet_arc_c3_max = 300._r8
     real(r8), parameter :: co1 = 313._r8                   ! empirical coefficient
     real(r8), parameter :: co2 = 0.6_r8                    ! empirical coefficient
     real(r8), parameter :: co4 = 0.05_r8                   ! empirical coefficient
@@ -968,11 +892,11 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
        topt = co1 + (co2 * (t_veg240_in-tstd0))
        if ( (ivt_in == nbrdlf_dcd_brl_shrub) ) then  ! boreal-deciduous-shrub
        ! coming from BEAR-oNS campaign willows results
-             Eopt = 7.9 * exp (0.217_r8 * (t_veg24_in-273.15_r8-24.0_r8))
+             Eopt = 7.9_r8 * exp (0.217_r8 * (t_veg24_in - tfrz - 24.0_r8))
        else if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-             Eopt = exp(0.12*(t_veg240_in-288.15_r8))
+             Eopt = exp(0.12_r8 * (t_veg240_in - tfrz - 15._r8))
        else
-             Eopt = Ceo_in * exp (co4 * (t_veg24_in-tstd0)) * exp(co4 * (t_veg240_in -tstd0))
+             Eopt = Ceo_in * exp (co4 * (t_veg24_in - tstd0)) * exp(co4 * (t_veg240_in - tstd0))
        endif
 
     else
@@ -982,13 +906,11 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     x = ( (1._r8/topt) - (1._r8/(t_veg_in)) ) / ct3
     ! for the boreal grass from BEAR-oNS campaign
     if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-        bet_arc_c3  = 95+9.49*exp(0.53*(288.15_r8-t_veg240_in))
-        if (bet_arc_c3 .gt. 300) then
-            bet_arc_c3 = 300
-        endif
-        gamma_t_LDF = Eopt * exp(bet_arc_c3*((1/303.15_r8 - 1.0_r8/(t_veg_in))/ct3))
+        bet_arc_c3 = 95._r8 + 9.49_r8 * exp(0.53_r8 * (tfrz + 15._r8 - t_veg240_in))
+        bet_arc_c3 = min(bet_arc_c3, bet_arc_c3_max)
+        gamma_t_LDF = Eopt * exp(bet_arc_c3 * ((1._r8 / (tfrz + 30._r8) - 1._r8 / t_veg_in) / ct3))
     else
-        gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x)/(ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
+        gamma_t_LDF = Eopt * ( ct2_in * exp(ct1_in * x) / (ct2_in - ct1_in * (1._r8 - exp(ct2_in * x))) )
     endif
     
     

From f909d2da504328459dd8129df708e289dfe33de3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 13:15:49 -0600
Subject: [PATCH 0722/1248] Fill all land cells with MISSING_RX_GDD_VAL.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 5d6809f7ff..c0c9adb30b 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -18,10 +18,9 @@
 from ctsm.crop_calendars.import_ds import import_ds
 import ctsm.crop_calendars.cropcal_utils as utils
 from ctsm.crop_calendars.grid_one_variable import grid_one_variable
+from ctsm.crop_calendars.cropcal_module import MISSING_RX_GDD_VAL
 
 GRIDDING_VAR_LIST = ["patches1d_ixy", "patches1d_jxy", "lat", "lon"]
-MISSING_FILL = -1  # Something impossible to ensure that you can mark it as a missing value, to be
-# bilinear-interpolated
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
 # shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
 
@@ -266,7 +265,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
 
     # Set up a dummy DataArray to use for crops without an assigned GDDN variable
     dummy_da = xr.DataArray(
-        data=MISSING_FILL * np.ones_like(ds_in[var_list_in[0]].values),
+        data=np.full_like(ds_in[var_list_in[0]].values, MISSING_RX_GDD_VAL),
         dims=ds_in[var_list_in[0]].dims,
         coords=ds_in[var_list_in[0]].coords,
     )
@@ -284,10 +283,10 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
         # Which GDDN history variable does this crop use? E.g., GDD0, GDD10
         gddn, gddn_str = _get_gddn_for_cft(cft_str, variable)
 
-        # Fill any missing values with MISSING_FILL. This will mean that gddmaturity in these cells
+        # Fill any missing values with MISSING_RX_GDD_VAL. This will mean that gddmaturity there
         # never changes.
         if gddn_str is None:
-            # Crop not handled yet? Fill it entirely with missing value
+            # Crop not handled yet? It's already filled with missing value
             this_da = dummy_da
             print("   dummy GDD20")
         else:
@@ -295,6 +294,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
             this_da = ds_in[gddn_str]
             this_da = _add_time_axis(this_da)
             print(f"   {gddn_str}")
+            this_da = this_da.fillna(MISSING_RX_GDD_VAL)
 
         # Add attributes of output file
         if (gddn is None) != (gddn_str is None):
@@ -305,7 +305,6 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
             long_name = f"GDD{gddn}20"
         this_da.attrs["long_name"] = long_name + f" baseline for {cft_str}"
         this_da.attrs["units"] = "°C days"
-        # this_da.attrs["_FillValue"] = MISSING_FILL
 
         # Copy that to ds_out
         var_out = _get_output_varname(cft_str)

From 8fa8506ceb753e6e1571f4b93adb4c43ea51d8d1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 13:39:15 -0600
Subject: [PATCH 0723/1248] Set different gdd20 baseline file if using default
 gdd20 baseline seasons.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 3f8bc1f382..70ff048aa7 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1711,7 +1711,8 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
 <stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
 <stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
-<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".false.">lnd/clm2/cropdata/calendars/processed/20230714_cropcals_pr2_1deg.actually2deg.1980-2009.from_GDDB20.interpd_halfdeg.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
 <stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_start>
 <stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_end>
 <stream_meshfile_cropcal cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/360x720_120830_ESMFmesh_c20210507_cdf5.tweaked_latlons.nc</stream_meshfile_cropcal>

From 945c8bbd142d0c528cbddbafd529a790a88c2dd8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 14:34:03 -0600
Subject: [PATCH 0724/1248] Add utility function to get list of managed crops
 WITH grasses.

define_mgdcrop_list() had excluded foddergrass and switchgrass. New function define_mgdcrop_list_withgrasses includes them. Renamed the existing function to define_mgdcrop_list_nograsses for clarity.
---
 python/ctsm/crop_calendars/cropcal_module.py          |  2 +-
 python/ctsm/crop_calendars/cropcal_utils.py           | 11 ++++++++++-
 python/ctsm/crop_calendars/generate_gdd20_baseline.py |  4 ++--
 python/ctsm/crop_calendars/generate_gdds_functions.py |  4 ++--
 4 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index b87d26816f..08754f8823 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -345,7 +345,7 @@ def import_output(
     my_vars,
     year_1=None,
     year_n=None,
-    my_vegtypes=utils.define_mgdcrop_list(),
+    my_vegtypes=utils.define_mgdcrop_list_nograsses(),
     sdates_rx_ds=None,
     gdds_rx_ds=None,
     verbose=False,
diff --git a/python/ctsm/crop_calendars/cropcal_utils.py b/python/ctsm/crop_calendars/cropcal_utils.py
index 00ed2413d2..2157dc87f4 100644
--- a/python/ctsm/crop_calendars/cropcal_utils.py
+++ b/python/ctsm/crop_calendars/cropcal_utils.py
@@ -207,7 +207,7 @@ def is_each_vegtype(this_vegtypelist, this_filter, this_method):
     return [is_this_vegtype(x, this_filter, this_method) for x in this_vegtypelist]
 
 
-def define_mgdcrop_list():
+def define_mgdcrop_list_nograsses():
     """
     List (strings) of managed crops in CLM.
     """
@@ -216,6 +216,15 @@ def define_mgdcrop_list():
     is_crop = is_each_vegtype(defined_pftlist, notcrop_list, "notok_contains")
     return [defined_pftlist[i] for i, x in enumerate(is_crop) if x]
 
+def define_mgdcrop_list_withgrasses():
+    """
+    List (strings) of managed crops in CLM.
+    """
+    notcrop_list = ["tree", "c3_arctic_grass", "c3_non-arctic_grass", "c4_grass", "shrub", "unmanaged", "not_vegetated"]
+    defined_pftlist = define_pftlist()
+    is_crop = is_each_vegtype(defined_pftlist, notcrop_list, "notok_contains")
+    return [defined_pftlist[i] for i, x in enumerate(is_crop) if x]
+
 
 def vegtype_str2int(vegtype_str, vegtype_mainlist=None):
     """
diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index c0c9adb30b..64cfd804fa 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -144,7 +144,7 @@ def _get_cft_list(crop_list):
                              "cotton", "irrigated_cotton"]
     """
 
-    mgdcrop_list = utils.define_mgdcrop_list()
+    mgdcrop_list = utils.define_mgdcrop_list_nograsses()
     cft_str_list = []
     for crop_str in crop_list:
         cft_str_list += [x for x in mgdcrop_list if crop_str in x]
@@ -276,7 +276,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
 
     # Process all crops
     encoding_dict = {}
-    for cft_str in utils.define_mgdcrop_list():
+    for cft_str in utils.define_mgdcrop_list_nograsses():
         cft_int = utils.vegtype_str2int(cft_str)[0]
         print(f"{cft_str} ({cft_int})")
 
diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index 2658e1de87..83c167af00 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -282,9 +282,9 @@ def import_and_process_1yr(
 
     # Get list of crops to include
     if skip_crops is not None:
-        crops_to_read = [c for c in utils.define_mgdcrop_list() if c not in skip_crops]
+        crops_to_read = [c for c in utils.define_mgdcrop_list_nograsses() if c not in skip_crops]
     else:
-        crops_to_read = utils.define_mgdcrop_list()
+        crops_to_read = utils.define_mgdcrop_list_nograsses()
 
     print(h1_filelist)
     dates_ds = import_ds(

From ec9f07f2a6cc5f79e6c207e8050db74ff2d857ea Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 14:36:41 -0600
Subject: [PATCH 0725/1248] generate_gdd20_baseline: Use MGDCROP_LIST constant.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 64cfd804fa..1de6b5a739 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -23,6 +23,7 @@
 GRIDDING_VAR_LIST = ["patches1d_ixy", "patches1d_jxy", "lat", "lon"]
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
 # shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
+MGDCROP_LIST = utils.define_mgdcrop_list_nograsses()
 
 
 def _parse_args():
@@ -144,10 +145,9 @@ def _get_cft_list(crop_list):
                              "cotton", "irrigated_cotton"]
     """
 
-    mgdcrop_list = utils.define_mgdcrop_list_nograsses()
     cft_str_list = []
     for crop_str in crop_list:
-        cft_str_list += [x for x in mgdcrop_list if crop_str in x]
+        cft_str_list += [x for x in MGDCROP_LIST if crop_str in x]
     return cft_str_list
 
 
@@ -276,7 +276,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
 
     # Process all crops
     encoding_dict = {}
-    for cft_str in utils.define_mgdcrop_list_nograsses():
+    for cft_str in MGDCROP_LIST:
         cft_int = utils.vegtype_str2int(cft_str)[0]
         print(f"{cft_str} ({cft_int})")
 

From 669f227921e1bdf59157cf1da1c9b4e5176851bc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 14:37:05 -0600
Subject: [PATCH 0726/1248] generate_gdd20_baseline: Include mgd grasses.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 1de6b5a739..effc8e54ec 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -23,7 +23,7 @@
 GRIDDING_VAR_LIST = ["patches1d_ixy", "patches1d_jxy", "lat", "lon"]
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
 # shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
-MGDCROP_LIST = utils.define_mgdcrop_list_nograsses()
+MGDCROP_LIST = utils.define_mgdcrop_list_withgrasses()
 
 
 def _parse_args():

From a62460642403d827b58807cfe5961df0db026c71 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 18 Jul 2024 14:41:46 -0600
Subject: [PATCH 0727/1248] generate_gdd20_baseline: Include unmanaged crops.

---
 python/ctsm/crop_calendars/cropcal_utils.py           | 8 ++++++++
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/cropcal_utils.py b/python/ctsm/crop_calendars/cropcal_utils.py
index 2157dc87f4..1a80448c1b 100644
--- a/python/ctsm/crop_calendars/cropcal_utils.py
+++ b/python/ctsm/crop_calendars/cropcal_utils.py
@@ -206,6 +206,14 @@ def is_each_vegtype(this_vegtypelist, this_filter, this_method):
 
     return [is_this_vegtype(x, this_filter, this_method) for x in this_vegtypelist]
 
+def define_crop_list():
+    """
+    List (strings) of managed crops in CLM.
+    """
+    notcrop_list = ["tree", "c3_arctic_grass", "c3_non-arctic_grass", "c4_grass", "shrub", "not_vegetated"]
+    defined_pftlist = define_pftlist()
+    is_crop = is_each_vegtype(defined_pftlist, notcrop_list, "notok_contains")
+    return [defined_pftlist[i] for i, x in enumerate(is_crop) if x]
 
 def define_mgdcrop_list_nograsses():
     """
diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index effc8e54ec..3d082d0fde 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -23,7 +23,7 @@
 GRIDDING_VAR_LIST = ["patches1d_ixy", "patches1d_jxy", "lat", "lon"]
 STREAM_YEAR = 2000  # The year specified for stream_yearFirst and stream_yearLast in the call of
 # shr_strdata_init_from_inline() for sdat_cropcal_gdd20_baseline
-MGDCROP_LIST = utils.define_mgdcrop_list_withgrasses()
+MGDCROP_LIST = utils.define_crop_list()
 
 
 def _parse_args():

From c031e1c699be02a96123df5c0ed780f4c9ce73bc Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 18 Jul 2024 15:14:14 -0600
Subject: [PATCH 0728/1248] Update ntests in build-namelist_test.pl

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 16f6ba2a62..9b283af334 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3309;
+my $ntests = 3306;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2045;

From c2b6c43f44c0dc3b6b9ad65b5dc979951090c3da Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 18 Jul 2024 17:35:07 -0600
Subject: [PATCH 0729/1248] Draft ChangeLog/ChangeSum

---
 doc/ChangeLog | 144 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 145 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8cc3198fae..5f2896ebc9 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,148 @@
 ===============================================================
+Tag name: ctsm5.2.014
+Originator(s): chrislxj (Xingjie Lu, Northern Arizona U., xingjie.lu@nau.edu)
+Date: Thu 18 Jul 2024 03:50:56 PM MDT
+One-line Summary: use_matrixcn, use_soil_matrixcn come in but as default .false.
+
+Purpose and description of changes
+----------------------------------
+
+ Currently set as default .false.:
+ - Add matrix module for vegetation and soil C and N cycle
+ - Add diagnostic variables C and N storage capacity in history files
+ - Add Sparse matrix module to increase the code efficiency
+ - Create spin-up switch, and be ready for matrix spin up development
+
+ Additional contributors: Yuanyuan Huang, Zhenggang Du, and Yiqi Luo from
+ Professor Yiqi Luo's EcoLab at Northern Arizona University, now at Cornell U.
+
+ In TSS/CGD/NCAR, contributors in the last year include slevis, ekluzek, wwieder.
+ Others may have been involved prior. I apologize for omissions.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #903  Bring CN-Matrix solution into CTSM
+ Fixes #2450 Cn-matrix testing in the aux_clm test-suites
+ Fixes #2621 matrixcn does not work with nrepr != 1 (number of crop reproductive pools)
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+ use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc spin-ups
+ and NOT recommended for
+ - transient simulations (e.g. IHist)
+ - simulations that use threading (e.g. see tests with P64x2)
+ - NWP compsets
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ New: use_matrixcn, use_soil_matrixcn, hist_wrt_matrixcn_diag.
+ All three are default .false. at this time.
+
+Changes made to namelist defaults (e.g., changed parameter values):
+ Changed hillslope_fsat_equals_zero to default .false. when
+ use_hillslope = .false. as per issue #2652
+ clm_accelerated_spinup can be set to off, on, sasu, the latter being
+ the setting that uses matrixcn
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ No.
+
+Changes to documentation:
+ None at this time. A description of the spinup procedure appears in
+ https://github.com/NCAR/LMWG_dev/issues/58
+
+Substantial timing or memory changes:
+ ***Check PFS test in the test suite and look at timings
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+ - Future changes to the bgc will likely require changes in both
+ matrix and non-matrix parts of the code.
+ - I have found matrixcn to be sensitive to changes in the subgrid
+ heterogeneity and other subtleties. For example, matrixcn simulations
+ have failed from using a finidat file from a different simulation (#2592),
+ from running in transient mode (#2592), from running with threading (#2619),
+ and from setting hillslope_fsat_equals_zero = .true. (issue #2652).
+ - We recommend using matrixcn to accelerate bgc spin-ups and not for
+ most (possibly any) other purposes.
+
+Changes to tests or testing:
+ Numerous new tests in aux_clm and in build-namelist_test.pl that can be
+ identified by searching "matr"
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- IN PROG
+    izumi ------- IN PROG
+
+  ctsm_sci
+     derecho ---- IN PROG
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, roundoff
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: All
+    - what platforms/compilers: All
+    - nature of change: roundoff
+      use_matrixcn and use_soil_matrixcn are default .false.. We get
+      roundoff diffs due to order-of-operation changes in a few locations,
+      done to improve code readability and streamlining in the presence of matrix.
+
+ Testing with the non-default use_matrixcn = .true. and use_soil_matrixcn = .true.
+ appears here: https://github.com/NCAR/LMWG_dev/issues/58
+
+ PR #640 associated with this tag explains how answers are expected to
+ change from non-matrix to matrix simulations.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/640
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.013
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 	       glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
diff --git a/doc/ChangeSum b/doc/ChangeSum
index df8e6dcf6a..8579fbee98 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.014 chrislxj 07/18/2024 use_matrixcn, use_soil_matrixcn come in but as default .false.
        ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2
        ctsm5.2.012    sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes
        ctsm5.2.011   slevis 07/12/2024 Merge b4b-dev

From 5aeb618ebffdb8ab49521d47aa2d04037f76aa6f Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 19 Jul 2024 11:53:37 -0600
Subject: [PATCH 0730/1248] Update ChangeLog/ChangeSum

---
 doc/ChangeLog | 57 +++++++++++++++++++++++++--------------------------
 doc/ChangeSum |  2 +-
 2 files changed, 29 insertions(+), 30 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 5f2896ebc9..35ad747636 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,8 +1,8 @@
 ===============================================================
 Tag name: ctsm5.2.014
 Originator(s): chrislxj (Xingjie Lu, Northern Arizona U., xingjie.lu@nau.edu)
-Date: Thu 18 Jul 2024 03:50:56 PM MDT
-One-line Summary: use_matrixcn, use_soil_matrixcn come in but as default .false.
+Date: Fri 19 Jul 2024 11:04:17 AM MDT
+One-line Summary: use_matrixcn, use_soil_matrixcn come in as default .false.
 
 Purpose and description of changes
 ----------------------------------
@@ -16,8 +16,9 @@ Purpose and description of changes
  Additional contributors: Yuanyuan Huang, Zhenggang Du, and Yiqi Luo from
  Professor Yiqi Luo's EcoLab at Northern Arizona University, now at Cornell U.
 
- In TSS/CGD/NCAR, contributors in the last year include slevis, ekluzek, wwieder.
- Others may have been involved prior. I apologize for omissions.
+ In TSS/CGD/NCAR/UCAR, contributors in the last year include slevis, ekluzek, wwieder.
+ I apologize if I have omitted others who may have been involved prior.
+
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
@@ -45,12 +46,13 @@ List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
  Fixes #2450 Cn-matrix testing in the aux_clm test-suites
  Fixes #2621 matrixcn does not work with nrepr != 1 (number of crop reproductive pools)
 
+
 Notes of particular relevance for users
 ---------------------------------------
 
 Caveats for users (e.g., need to interpolate initial conditions):
- use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc spin-ups
- and NOT recommended for
+ use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc
+ spin-ups (keep reading for more info) and NOT recommended for
  - transient simulations (e.g. IHist)
  - simulations that use threading (e.g. see tests with P64x2)
  - NWP compsets
@@ -60,21 +62,17 @@ Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
  All three are default .false. at this time.
 
 Changes made to namelist defaults (e.g., changed parameter values):
- Changed hillslope_fsat_equals_zero to default .false. when
+ - hillslope_fsat_equals_zero is now default .false. when
  use_hillslope = .false. as per issue #2652
- clm_accelerated_spinup can be set to off, on, sasu, the latter being
- the setting that uses matrixcn
-
-Changes to the datasets (e.g., parameter, surface or initial files):
- No.
+ - clm_accelerated_spinup can be set to on, sasu, off; matrixcn spin-up
+ is performed in that order (on, sasu, off); in the "on" phase, matrixcn
+ is not active, in the "sasu" phase matrixcn is active, and in the "off"
+ phase, matrixcn may be active
 
 Changes to documentation:
  None at this time. A description of the spinup procedure appears in
  https://github.com/NCAR/LMWG_dev/issues/58
 
-Substantial timing or memory changes:
- ***Check PFS test in the test suite and look at timings
-
 
 Notes of particular relevance for developers:
 ---------------------------------------------
@@ -82,17 +80,17 @@ Notes of particular relevance for developers:
 Caveats for developers (e.g., code that is duplicated that requires double maintenance):
  - Future changes to the bgc will likely require changes in both
  matrix and non-matrix parts of the code.
- - I have found matrixcn to be sensitive to changes in the subgrid
- heterogeneity and other subtleties. For example, matrixcn simulations
- have failed from using a finidat file from a different simulation (#2592),
+ - matrixcn seems sensitive to changes in subgrid heterogeneity and
+ other subtleties. For example, matrixcn simulations have failed from
+ using a finidat file from a different simulation (#2592),
  from running in transient mode (#2592), from running with threading (#2619),
  and from setting hillslope_fsat_equals_zero = .true. (issue #2652).
  - We recommend using matrixcn to accelerate bgc spin-ups and not for
- most (possibly any) other purposes.
+ most (any?) other purposes.
 
 Changes to tests or testing:
- Numerous new tests in aux_clm and in build-namelist_test.pl that can be
- identified by searching "matr"
+ We introduced numerous new tests to the aux_clm and build-namelist_test.pl
+ test-suites that can be identified by searching "matrix"
 
 
 Testing summary:
@@ -110,11 +108,11 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho ----- IN PROG
-    izumi ------- IN PROG
+    derecho ----- OK
+    izumi ------- OK
 
   ctsm_sci
-     derecho ---- IN PROG
+     derecho ---- OK
 
 
 Answer changes
@@ -123,17 +121,18 @@ Answer changes
 Changes answers relative to baseline: Yes, roundoff
 
   Summarize any changes to answers, i.e.,
-    - what code configurations: All
+    - what code configurations: Non-matrix
     - what platforms/compilers: All
     - nature of change: roundoff
       use_matrixcn and use_soil_matrixcn are default .false.. We get
-      roundoff diffs due to order-of-operation changes in a few locations,
-      done to improve code readability and streamlining in the presence of matrix.
+      roundoff diffs due to order-of-operation changes in a few sections
+      of code, which improve readability and streamlining of the code
+      in the presence of matrix.
 
- Testing with the non-default use_matrixcn = .true. and use_soil_matrixcn = .true.
+ Testing with the non-default use_matrixcn and use_soil_matrixcn = .true.
  appears here: https://github.com/NCAR/LMWG_dev/issues/58
 
- PR #640 associated with this tag explains how answers are expected to
+ PR #640 explains how answers are expected to
  change from non-matrix to matrix simulations.
 
 Other details
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 8579fbee98..21237cbac8 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.014 chrislxj 07/18/2024 use_matrixcn, use_soil_matrixcn come in but as default .false.
+       ctsm5.2.014 chrislxj 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.
        ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2
        ctsm5.2.012    sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes
        ctsm5.2.011   slevis 07/12/2024 Merge b4b-dev

From 63b3c3fdfa8e9d5aec763bd872a81a69b2832d8e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevisconsulting@gmail.com>
Date: Fri, 19 Jul 2024 17:19:36 -0600
Subject: [PATCH 0731/1248] Namelist corrections after an izumi test failed

ERS_D.f19_g17.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup
failed during the build because a namelist variable needed renaming
---
 .../user_nl_mosart                            |  2 +-
 .../testmods_dirs/clm/rtmColdSSP/user_nl_rtm  |  8 +++----
 lilac/bld_templates/mosart_in                 | 22 +++++++++----------
 3 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart
index 9e109fc131..82243d7d3d 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart
+++ b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart
@@ -1 +1 @@
-frivinp_rtm = '/dev/null'
+frivinp = '/dev/null'
diff --git a/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm b/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm
index d1a0254a0b..e78d13a51c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm
+++ b/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm
@@ -1,4 +1,4 @@
-finidat_rtm = " "
-rtmhist_mfilt = 1
-rtmhist_ndens = 2
-rtmhist_nhtfrq = 0
+finidat = " "
+mfilt = 1
+ndens = 2
+nhtfrq = 0
diff --git a/lilac/bld_templates/mosart_in b/lilac/bld_templates/mosart_in
index 091ec69285..0bc2242dda 100644
--- a/lilac/bld_templates/mosart_in
+++ b/lilac/bld_templates/mosart_in
@@ -4,18 +4,18 @@
   delt_mosart = 1800
   do_rtm = .true.
   do_rtmflood = .false.
-  finidat_rtm = " "
-  frivinp_rtm = "/glade/campaign/cesm/cesmdata/cseg/inputdata/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc"
+  finidat = " "
+  frivinp = "/glade/campaign/cesm/cesmdata/cseg/inputdata/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc"
   ice_runoff = .true.
   qgwl_runoff_option = "threshold"
-  rtmhist_fexcl1 = ""
-  rtmhist_fexcl2 = ""
-  rtmhist_fexcl3 = ""
-  rtmhist_fincl1 = ""
-  rtmhist_fincl2 = ""
-  rtmhist_fincl3 = ""
-  rtmhist_mfilt = 1
-  rtmhist_ndens = 1
-  rtmhist_nhtfrq = 0
+  fexcl1 = ""
+  fexcl2 = ""
+  fexcl3 = ""
+  fincl1 = ""
+  fincl2 = ""
+  fincl3 = ""
+  mfilt = 1
+  ndens = 1
+  nhtfrq = 0
   smat_option = "Xonly"
 /

From a32a9eb121af3fcb7de1af94b5812f51eac49666 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 19 Jul 2024 18:42:31 -0600
Subject: [PATCH 0732/1248] Draft ChangeLog/ChangeSum (comments welcome)

---
 doc/ChangeLog | 130 +++++++++++++++++++++++++++++++++++++++++++++++++-
 doc/ChangeSum |   3 +-
 2 files changed, 131 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 35ad747636..785b26db9e 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,131 @@
 ===============================================================
+Tag name: ctsm5.2.015
+Originator(s): multiple (Samuel Levis,UCAR/TSS,303-665-1310, @mvertens, @jedwards4b, @billsacks, @Katetc)
+Date: Fri 19 Jul 2024 06:02:22 PM MDT
+One-line Summary: Update submodule tags to pass runoff from cism to rof
+
+Purpose and description of changes
+----------------------------------
+
+ - Update MOSART, CMEPS, and CISM so CISM runoff goes to ROF rather than CTSM
+ - Update RTM with fix needed for Paleo LGM work
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2590 Update CMEPS/MOSART/CISM/RTM tags
+ Fixes https://github.com/ESCOMP/RTM/issues/50 Likely wrong RTM river flux to MOM6 within cesm2_3_beta17
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+ Issue https://github.com/ESCOMP/RTM/issues/50
+ Likely wrong RTM river flux to MOM6 within cesm2_3_beta17 is now fixed with
+ https://github.com/ESCOMP/RTM/pull/51
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ Differences in namelist 'mosart_inparm':
+  missing variable: 'do_rtmflood'
+  missing variable: 'finidat_rtm'
+  missing variable: 'frivinp_rtm'
+  missing variable: 'rtmhist_fexcl1'
+  missing variable: 'rtmhist_fexcl2'
+  missing variable: 'rtmhist_fexcl3'
+  missing variable: 'rtmhist_fincl1'
+  missing variable: 'rtmhist_fincl2'
+  missing variable: 'rtmhist_fincl3'
+  missing variable: 'rtmhist_mfilt'
+  missing variable: 'rtmhist_ndens'
+  missing variable: 'rtmhist_nhtfrq'
+  found extra variable: 'budget_frq'
+  found extra variable: 'fexcl1'
+  found extra variable: 'fexcl2'
+  found extra variable: 'fexcl3'
+  found extra variable: 'fincl1'
+  found extra variable: 'fincl2'
+  found extra variable: 'fincl3'
+  found extra variable: 'finidat'
+  found extra variable: 'frivinp'
+  found extra variable: 'mfilt'
+  found extra variable: 'mosart_euler_calc'
+  found extra variable: 'mosart_tracers'
+  found extra variable: 'ndens'
+  found extra variable: 'nhtfrq'
+  found extra variable: 'use_halo_option'
+
+Changes to documentation:
+ Not that I am aware of
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  ctsm_sci
+     derecho ---- OK (while in tag ctsm5.2.007; I did not repeat with the latest; see checklist in #2590)
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: mosart and rtm
+    - what platforms/compilers: all
+    - nature of change: mosart roundoff; rtm larger than roundoff due to bug fix
+
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ See .gitmodules: cism, rtm, mosart, ccs_config, cmeps
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2605
+ https://github.com/ESCOMP/RTM/pull/51
+ https://github.com/ESCOMP/MOSART/pull/94
+ https://github.com/ESCOMP/CISM-wrapper/pull/100
+ https://github.com/ESCOMP/CMEPS/pull/463
+ https://github.com/ESMCI/ccs_config_cesm/pull/174
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.014
 Originator(s): chrislxj (Xingjie Lu, Northern Arizona U., xingjie.lu@nau.edu)
 Date: Fri 19 Jul 2024 11:04:17 AM MDT
@@ -51,7 +178,8 @@ Notes of particular relevance for users
 ---------------------------------------
 
 Caveats for users (e.g., need to interpolate initial conditions):
- use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc
+ use_matrixcn and use_soil_matrixcn ARE NOT available for clm4_5
+ and ARE recommended for accelerating bgc
  spin-ups (keep reading for more info) and NOT recommended for
  - transient simulations (e.g. IHist)
  - simulations that use threading (e.g. see tests with P64x2)
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 21237cbac8..5c7123b5e0 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.014 chrislxj 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.
+       ctsm5.2.015 multiple 07/19/2024 Update submodule tags to pass runoff from cism to rof
+       ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.
        ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2
        ctsm5.2.012    sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes
        ctsm5.2.011   slevis 07/12/2024 Merge b4b-dev

From 9ba2b5f164ad800e6c10f9e7b5f373c9f31ab504 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Mon, 22 Jul 2024 10:51:05 -0600
Subject: [PATCH 0733/1248] rename vars, add arg to test and depth arg.

---
 src/biogeophys/TemperatureType.F90            | 16 ++++-----
 src/biogeophys/WaterStateBulkType.F90         |  8 ++---
 src/biogeophys/WaterStateType.F90             | 28 +++++++--------
 src/biogeophys/WaterType.F90                  | 34 ++++++++++---------
 src/main/clm_instMod.F90                      | 15 ++++----
 .../unittestWaterTypeFactory.F90              | 28 ++++++++++++++-
 6 files changed, 79 insertions(+), 50 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 6084c7ee2c..a256e22eb7 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -120,8 +120,8 @@ module TemperatureType
      real(r8), pointer    :: c_h2osfc_col          (:)   ! heat capacity of surface water
 
      ! Namelist parameters for initialization
-     real(r8), private    :: excess_ice_coldstart_depth  ! depth below which excess ice will be present
-     real(r8), private    :: excess_ice_coldstart_temp   ! coldstart temperature of layers with excess ice present
+     real(r8)    :: excess_ice_coldstart_depth  ! depth below which excess ice will be present
+     real(r8)    :: excess_ice_coldstart_temp   ! coldstart temperature of layers with excess ice present
      
    contains
 
@@ -147,7 +147,7 @@ module TemperatureType
   !------------------------------------------------------------------------
   subroutine Init(this, bounds, &
        em_roof_lun,  em_wall_lun, em_improad_lun, em_perroad_lun, &
-       is_simple_buildtemp, is_prog_buildtemp, exice_init_stream_col, NLFileName)
+       is_simple_buildtemp, is_prog_buildtemp, exice_init_conc_col, NLFileName)
     !
     ! !DESCRIPTION:
     !
@@ -162,7 +162,7 @@ subroutine Init(this, bounds, &
     real(r8)          , intent(in) :: em_perroad_lun(bounds%begl:)
     logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
     logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
-    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:)  ! initial excess ice concentration from the stream file
+    real(r8)          , intent(in) :: exice_init_conc_col(bounds%begc:)  ! initial coldstart excess ice concentration (from the stream file)
     character(len=*)  , intent(in) :: NLFilename ! Namelist filename
 
 
@@ -175,7 +175,7 @@ subroutine Init(this, bounds, &
          em_improad_lun(bounds%begl:bounds%endl), &
          em_perroad_lun(bounds%begl:bounds%endl), &
          is_simple_buildtemp, is_prog_buildtemp,  &
-         exice_init_stream_col(bounds%begc:bounds%endc) )
+         exice_init_conc_col(bounds%begc:bounds%endc) )
 
   end subroutine Init
 
@@ -650,7 +650,7 @@ end subroutine InitHistory
   !-----------------------------------------------------------------------
   subroutine InitCold(this, bounds, &
        em_roof_lun,  em_wall_lun, em_improad_lun, em_perroad_lun, &
-       is_simple_buildtemp, is_prog_buildtemp, exice_init_stream_col)
+       is_simple_buildtemp, is_prog_buildtemp, exice_init_conc_col)
     !
     ! !DESCRIPTION:
     ! Initialize cold start conditions for module variables
@@ -675,7 +675,7 @@ subroutine InitCold(this, bounds, &
     real(r8)          , intent(in) :: em_perroad_lun(bounds%begl:)
     logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
     logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
-    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from the stream file
+    real(r8)          , intent(in) :: exice_init_conc_col(bounds%begc:) ! initial coldstart excess ice concentration (from the stream file)
     !
     ! !LOCAL VARIABLES:
     integer  :: j,l,c,p ! indices
@@ -757,7 +757,7 @@ subroutine InitCold(this, bounds, &
                end if
             else
                this%t_soisno_col(c,1:nlevgrnd) = 272._r8
-               if (use_excess_ice .and. exice_init_stream_col(c) > 0.0_r8) then
+               if (use_excess_ice .and. exice_init_conc_col(c) > 0.0_r8) then
                   nexice_start = nlevsoi - 1
                   if (this%excess_ice_coldstart_depth <= 0.0_r8) then
                      ! we double check this here, and when building namelists
diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90
index 4f03ba177e..4cd425c976 100644
--- a/src/biogeophys/WaterStateBulkType.F90
+++ b/src/biogeophys/WaterStateBulkType.F90
@@ -47,7 +47,7 @@ module WaterStateBulkType
 
   !------------------------------------------------------------------------
   subroutine InitBulk(this, bounds, info, vars, &
-       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
+       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, exice_coldstart_depth, exice_init_conc_col)
 
     class(waterstatebulk_type), intent(inout) :: this
     type(bounds_type) , intent(in) :: bounds
@@ -57,8 +57,8 @@ subroutine InitBulk(this, bounds, info, vars, &
     real(r8)          , intent(in) :: watsat_col(bounds%begc:, 1:)            ! volumetric soil water at saturation (porosity)
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical           , intent(in) :: use_aquifer_layer                       ! whether an aquifer layer is used in this run
-    character(len=*)  , intent(in) :: NLFilename                              ! Namelist filename
-    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
+    real(r8)         , intent(in) :: exice_coldstart_depth ! depth below which excess ice will be present
+    real(r8)          , intent(in) :: exice_init_conc_col(bounds%begc:) ! initial coldstart excess ice concentration (from the stream file)
 
     call this%Init(bounds = bounds, &
          info = info, &
@@ -67,7 +67,7 @@ subroutine InitBulk(this, bounds, info, vars, &
          watsat_col = watsat_col, &
          t_soisno_col = t_soisno_col, &
          use_aquifer_layer = use_aquifer_layer, & 
-         NLFilename = NLFilename, exice_init_stream_col = exice_init_stream_col(bounds%begc:bounds%endc))
+         exice_coldstart_depth = exice_coldstart_depth, exice_init_conc_col = exice_init_conc_col(bounds%begc:bounds%endc))
 
     call this%InitBulkAllocate(bounds) 
 
diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90
index 4c82e4efa6..8f0ba89104 100644
--- a/src/biogeophys/WaterStateType.F90
+++ b/src/biogeophys/WaterStateType.F90
@@ -80,7 +80,7 @@ module WaterStateType
 
   !------------------------------------------------------------------------
   subroutine Init(this, bounds, info, tracer_vars, &
-       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
+       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, exice_coldstart_depth, exice_init_conc_col)
 
     class(waterstate_type), intent(inout) :: this
     type(bounds_type) , intent(in) :: bounds  
@@ -90,8 +90,8 @@ subroutine Init(this, bounds, info, tracer_vars, &
     real(r8)          , intent(in) :: watsat_col(bounds%begc:, 1:)          ! volumetric soil water at saturation (porosity)
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical           , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run
-    character(len=*)  , intent(in) :: NLFilename ! Namelist filename
-    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:bounds%endc) ! initial ammount of excess ice from stream
+    real(r8)          , intent(in) :: exice_coldstart_depth ! depth below which excess ice will be present
+    real(r8)          , intent(in) :: exice_init_conc_col(bounds%begc:bounds%endc) ! initial coldstart excess ice concentration (from the stream file)
 
     this%info => info
 
@@ -103,7 +103,7 @@ subroutine Init(this, bounds, info, tracer_vars, &
       watsat_col = watsat_col, &
       t_soisno_col = t_soisno_col, &
       use_aquifer_layer = use_aquifer_layer, &
-      NLFilename = NLFilename, exice_init_stream_col = exice_init_stream_col)
+      exice_coldstart_depth = exice_coldstart_depth , exice_init_conc_col = exice_init_conc_col)
 
   end subroutine Init
 
@@ -322,7 +322,7 @@ end subroutine InitHistory
 
   !-----------------------------------------------------------------------
   subroutine InitCold(this, bounds, &
-       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
+       h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, exice_coldstart_depth, exice_init_conc_col)
     !
     ! !DESCRIPTION:
     ! Initialize time constant variables and cold start conditions 
@@ -342,12 +342,12 @@ subroutine InitCold(this, bounds, &
     real(r8)              , intent(in)    :: watsat_col(bounds%begc:, 1:)            ! volumetric soil water at saturation (porosity)
     real(r8)              , intent(in)    :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical               , intent(in)    :: use_aquifer_layer                       ! whether an aquifer layer is used in this run
-    character(len=*)      , intent(in)    :: NLFilename                              ! Namelist filename
-    real(r8)              , intent(in)    :: exice_init_stream_col(bounds%begc:bounds%endc) ! initial ammount of excess ice from stream
+    real(r8)              , intent(in)    :: exice_coldstart_depth ! depth below which excess ice will be present
+    real(r8)              , intent(in)    :: exice_init_conc_col(bounds%begc:bounds%endc) ! initial coldstart excess ice concentration (from the stream file)
     !
     ! !LOCAL VARIABLES:
     integer            :: c,j,l,nlevs,g 
-    integer            :: nbedrock, n05m ! layer containing 0.5 m
+    integer            :: nbedrock, nexice ! layer containing 0.5 m
     real(r8)           :: ratio
     !-----------------------------------------------------------------------
 
@@ -550,7 +550,7 @@ subroutine InitCold(this, bounds, &
       this%dynbal_baseline_ice_col(bounds%begc:bounds%endc) = 0._r8
 
       !Initialize excess ice
-      this%exice_bulk_init(bounds%begc:bounds%endc) = exice_init_stream_col(bounds%begc:bounds%endc)
+      this%exice_bulk_init(bounds%begc:bounds%endc) = exice_init_conc_col(bounds%begc:bounds%endc)
       this%excess_ice_col(bounds%begc:bounds%endc,:) = 0.0_r8
       if (use_excess_ice) then
          do c = bounds%begc,bounds%endc
@@ -558,10 +558,10 @@ subroutine InitCold(this, bounds, &
             l = col%landunit(c)
             if (.not. lun%lakpoi(l)) then  !not lake
                if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-                  if (zisoi(nlevsoi) >= 0.5_r8) then
-                     call find_soil_layer_containing_depth(0.5_r8,n05m)
+                  if (zisoi(nlevsoi) >= exice_coldstart_depth) then
+                     call find_soil_layer_containing_depth(exice_coldstart_depth,nexice)
                   else
-                     n05m=nlevsoi-1
+                     nexice=nlevsoi-1
                   endif
                   if (use_bedrock .and. col%nbedrock(c) <=nlevsoi) then
                      nbedrock = col%nbedrock(c)
@@ -569,8 +569,8 @@ subroutine InitCold(this, bounds, &
                      nbedrock = nlevsoi
                   endif
                   do j = 2, nlevmaxurbgrnd ! ignore first layer
-                     if (n05m<nbedrock) then ! bedrock below 1 m
-                        if (j >= n05m .and. j<nbedrock .and. t_soisno_col(c,j) <= tfrz ) then
+                     if (nexice<nbedrock) then ! bedrock below 1 m
+                        if (j >= nexice .and. j<nbedrock .and. t_soisno_col(c,j) <= tfrz ) then
                            this%excess_ice_col(c,j) = col%dz(c,j)*denice*(this%exice_bulk_init(c))
                         else
                            this%excess_ice_col(c,j) = 0.0_r8
diff --git a/src/biogeophys/WaterType.F90 b/src/biogeophys/WaterType.F90
index e92dc0c759..9a4884ce8c 100644
--- a/src/biogeophys/WaterType.F90
+++ b/src/biogeophys/WaterType.F90
@@ -213,7 +213,8 @@ end function water_params_constructor
 
   !-----------------------------------------------------------------------
   subroutine Init(this, bounds, NLFilename, &
-       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, exice_init_stream_col)
+       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, &
+       exice_coldstart_depth, exice_init_conc_col)
     !
     ! !DESCRIPTION:
     ! Initialize all water variables
@@ -227,7 +228,8 @@ subroutine Init(this, bounds, NLFilename, &
     real(r8)          , intent(in) :: watsat_col(bounds%begc:, 1:)          ! volumetric soil water at saturation (porosity)
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical           , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run
-    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
+    real(r8)          , intent(in) :: exice_coldstart_depth                    ! depth below which excess ice will be present
+    real(r8)          , intent(in) :: exice_init_conc_col(bounds%begc:) ! initial coldstart excess ice concentration (from the stream file)
     !
     ! !LOCAL VARIABLES:
 
@@ -241,14 +243,14 @@ subroutine Init(this, bounds, NLFilename, &
          watsat_col = watsat_col, &
          t_soisno_col = t_soisno_col, &
          use_aquifer_layer = use_aquifer_layer, &
-         NLFilename = NLFilename, exice_init_stream_col = exice_init_stream_col)
+         exice_coldstart_depth = exice_coldstart_depth, exice_init_conc_col = exice_init_conc_col)
 
   end subroutine Init
 
   !-----------------------------------------------------------------------
   subroutine InitForTesting(this, bounds, params, &
        h2osno_col, snow_depth_col, watsat_col, &
-       t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
+       t_soisno_col, use_aquifer_layer, exice_coldstart_depth, exice_init_conc_col)
     !
     ! !DESCRIPTION:
     ! Version of Init routine just for unit tests
@@ -263,9 +265,9 @@ subroutine InitForTesting(this, bounds, params, &
     real(r8)          , intent(in) :: snow_depth_col(bounds%begc:)
     real(r8)          , intent(in) :: watsat_col(bounds%begc:, 1:)            ! volumetric soil water at saturation (porosity)
     real(r8)          , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
-    character(len=*)  , intent(in) :: NLFilename                               ! Namelist filename
     logical , intent(in), optional :: use_aquifer_layer                       ! whether an aquifer layer is used in this run (false by default)
-    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
+    real(r8)          , intent(in) :: exice_coldstart_depth                    ! depth below which excess ice will be present
+    real(r8)          , intent(in) :: exice_init_conc_col(bounds%begc:) ! initial coldstart excess ice concentration (from the stream file)
     !
     ! !LOCAL VARIABLES:
     logical :: l_use_aquifer_layer
@@ -285,14 +287,14 @@ subroutine InitForTesting(this, bounds, params, &
          watsat_col = watsat_col, &
          t_soisno_col = t_soisno_col, &
          use_aquifer_layer = l_use_aquifer_layer, &
-         NLFilename = NLFilename, &
-          exice_init_stream_col = exice_init_stream_col )
+         exice_coldstart_depth = exice_coldstart_depth, &
+         exice_init_conc_col = exice_init_conc_col )
 
   end subroutine InitForTesting
 
   !-----------------------------------------------------------------------
   subroutine DoInit(this, bounds, &
-       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename, exice_init_stream_col)
+       h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, exice_coldstart_depth, exice_init_conc_col)
     !
     ! !DESCRIPTION:
     ! Actually do the initialization (shared between main Init routine and InitForTesting)
@@ -307,8 +309,8 @@ subroutine DoInit(this, bounds, &
     real(r8)         , intent(in) :: watsat_col(bounds%begc:, 1:)            ! volumetric soil water at saturation (porosity)
     real(r8)         , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     logical          , intent(in) :: use_aquifer_layer                       ! whether an aquifer layer is used in this run
-    character(len=*) , intent(in) :: NLFilename                              ! Namelist filename
-    real(r8)          , intent(in) :: exice_init_stream_col(bounds%begc:) ! initial ammount of excess ice from stream
+    real(r8)         , intent(in) :: exice_coldstart_depth ! depth below which excess ice will be present
+    real(r8)         , intent(in) :: exice_init_conc_col(bounds%begc:) ! initial coldstart excess ice concentration (from the stream file)
     !
     ! !LOCAL VARIABLES:
     integer :: begc, endc
@@ -325,7 +327,7 @@ subroutine DoInit(this, bounds, &
     SHR_ASSERT_ALL_FL((ubound(snow_depth_col) == [endc]), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(watsat_col, 1) == endc), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(t_soisno_col, 1) == endc), sourcefile, __LINE__)
-    SHR_ASSERT_ALL_FL((ubound(exice_init_stream_col, 1) == endc), sourcefile, __LINE__)
+    SHR_ASSERT_ALL_FL((ubound(exice_init_conc_col, 1) == endc), sourcefile, __LINE__)
 
     call this%SetupTracerInfo()
 
@@ -345,8 +347,8 @@ subroutine DoInit(this, bounds, &
          watsat_col = watsat_col(begc:endc, 1:),   &
          t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), &
          use_aquifer_layer = use_aquifer_layer, & 
-         NLFilename = NLFilename, &
-         exice_init_stream_col = exice_init_stream_col)
+         exice_coldstart_depth = exice_coldstart_depth, &
+         exice_init_conc_col = exice_init_conc_col)
 
     call this%waterdiagnosticbulk_inst%InitBulk(bounds, &
          bulk_info, &
@@ -387,8 +389,8 @@ subroutine DoInit(this, bounds, &
             watsat_col = watsat_col(begc:endc, 1:),   &
             t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), &
             use_aquifer_layer = use_aquifer_layer, &
-            NLFilename = NLFilename, &
-            exice_init_stream_col = exice_init_stream_col)
+            exice_coldstart_depth = exice_coldstart_depth, &
+            exice_init_conc_col = exice_init_conc_col)
 
        call this%bulk_and_tracers(i)%waterdiagnostic_inst%Init(bounds, &
             this%bulk_and_tracers(i)%info, &
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index 242df92c43..b8a9a0ca79 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -222,7 +222,7 @@ subroutine clm_instInit(bounds)
     type(file_desc_t)     :: params_ncid  ! pio netCDF file id for parameter file
     real(r8), allocatable :: h2osno_col(:)
     real(r8), allocatable :: snow_depth_col(:)
-    real(r8), allocatable :: exice_init_stream_col(:) ! initial concentration of excess ice in the soil (-)
+    real(r8), allocatable :: exice_init_conc_col(:) ! initial coldstart excess ice concentration (from the stream file or 0.0) (-)
     type(excessicestream_type)  :: exice_stream
 
     integer :: dummy_to_make_pgi_happy
@@ -302,12 +302,12 @@ subroutine clm_instInit(bounds)
     ! Initialization of public data types
 
     ! If excess ice is read from the stream, it has to be read before we coldstart the temperature
-    allocate(exice_init_stream_col(bounds%begc:bounds%endc))
-    exice_init_stream_col(bounds%begc:bounds%endc) = 0.0_r8
+    allocate(exice_init_conc_col(bounds%begc:bounds%endc))
+    exice_init_conc_col(bounds%begc:bounds%endc) = 0.0_r8
     if (use_excess_ice) then
        call exice_stream%Init(bounds, NLFilename)
        if (UseExcessIceStreams()) then
-          call exice_stream%CalcExcessIce(bounds, exice_init_stream_col(bounds%begc:bounds%endc))
+          call exice_stream%CalcExcessIce(bounds, exice_init_conc_col(bounds%begc:bounds%endc))
        endif
     endif
 
@@ -317,7 +317,7 @@ subroutine clm_instInit(bounds)
          em_improad_lun=urbanparams_inst%em_improad(begl:endl), &
          em_perroad_lun=urbanparams_inst%em_perroad(begl:endl), &
          is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp(), &
-         exice_init_stream_col=exice_init_stream_col(bounds%begc:bounds%endc) , NLFileName=NLFilename)
+         exice_init_conc_col=exice_init_conc_col(bounds%begc:bounds%endc) , NLFileName=NLFilename)
 
     call active_layer_inst%Init(bounds)
 
@@ -332,7 +332,8 @@ subroutine clm_instInit(bounds)
          watsat_col = soilstate_inst%watsat_col(begc:endc, 1:), &
          t_soisno_col = temperature_inst%t_soisno_col(begc:endc, -nlevsno+1:), &
          use_aquifer_layer = use_aquifer_layer(), &
-         exice_init_stream_col = exice_init_stream_col(begc:endc))
+         exice_coldstart_depth = temperature_inst%excess_ice_coldstart_depth, &
+         exice_init_conc_col = exice_init_conc_col(begc:endc))
 
     call glacier_smb_inst%Init(bounds)
 
@@ -470,7 +471,7 @@ subroutine clm_instInit(bounds)
 
     deallocate (h2osno_col)
     deallocate (snow_depth_col)
-    deallocate (exice_init_stream_col)
+    deallocate (exice_init_conc_col)
 
     ! ------------------------------------------------------------------------
     ! Initialize accumulated fields
diff --git a/src/unit_test_shr/unittestWaterTypeFactory.F90 b/src/unit_test_shr/unittestWaterTypeFactory.F90
index f5f417f9ce..06362ee1d0 100644
--- a/src/unit_test_shr/unittestWaterTypeFactory.F90
+++ b/src/unit_test_shr/unittestWaterTypeFactory.F90
@@ -91,6 +91,7 @@ end subroutine setup_after_subgrid
 
   subroutine create_water_type(this, water_inst, &
        t_soisno_col, watsat_col, &
+       exice_coldstart_depth, exice_init_conc_col, &
        enable_consistency_checks, enable_isotopes)
     ! Initialize water_inst
     !
@@ -113,6 +114,13 @@ subroutine create_water_type(this, water_inst, &
     ! 1..nlevgrnd. If not provided, we use arbitrary values for this variable.
     real(r8), intent(in), optional :: watsat_col( bounds%begc: , 1: )
 
+    ! Depth below which excess ice is present on coldstart.
+    ! If not provided, we use an arbitrary value.
+    real(r8), intent(in), optional :: exice_coldstart_depth
+    ! Excess initial concentration for each column.
+    ! If not provided, is set to 0.
+    real(r8), intent(in), optional :: exice_init_conc_col(bounds%begc:)
+
     logical, intent(in), optional :: enable_consistency_checks
     logical, intent(in), optional :: enable_isotopes
 
@@ -121,6 +129,8 @@ subroutine create_water_type(this, water_inst, &
     type(water_params_type) :: params
     real(r8) :: l_watsat_col(bounds%begc:bounds%endc, nlevgrnd)
     real(r8) :: l_t_soisno_col(bounds%begc:bounds%endc, -nlevsno+1:nlevgrnd)
+    real(r8) :: l_exice_coldstart_depth
+    real(r8) :: l_exice_init_conc_col(bounds%begc:bounds%endc)
 
     if (present(t_soisno_col)) then
        SHR_ASSERT_ALL_FL((ubound(t_soisno_col) == [bounds%endc, nlevgrnd]), sourcefile, __LINE__)
@@ -129,6 +139,10 @@ subroutine create_water_type(this, water_inst, &
        SHR_ASSERT_ALL_FL((ubound(watsat_col) == [bounds%endc, nlevgrnd]), sourcefile, __LINE__)
     end if
 
+    if (present(exice_init_conc_col)) then
+       SHR_ASSERT_ALL_FL((ubound(exice_init_conc_col,1) == bounds%enc), sourcefile, __LINE__)
+    endif
+
     if (present(enable_consistency_checks)) then
        l_enable_consistency_checks = enable_consistency_checks
     else
@@ -157,12 +171,24 @@ subroutine create_water_type(this, water_inst, &
        l_t_soisno_col(:,:) = 275._r8
     end if
 
+    if (present(exice_coldstart_depth)) then
+       l_exice_coldstart_depth = exice_coldstart_depth
+    else
+       l_exice_coldstart_depth = 0.5_r8
+    endif
+    if (present(exice_init_conc_col)) then
+       l_exice_init_conc_col(:,:) = exice_init_conc_col
+    else
+       l_exice_init_conc_col(:,:) = 0.01_r8
+    endif
+
     call water_inst%InitForTesting(bounds, params, &
          h2osno_col = col_array(0._r8), &
          snow_depth_col = col_array(0._r8), &
          watsat_col = l_watsat_col, &
          t_soisno_col = l_t_soisno_col, &
-         NLFilename = ' ')
+         exice_coldstart_depth = l_exice_coldstart_depth, &
+         exice_init_conc_col = l_exice_init_conc_col)
   end subroutine create_water_type
 
   subroutine teardown(this, water_inst)

From 7a2cf592157491f7a8dd3ddde94671948c7c3d95 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Mon, 22 Jul 2024 10:55:49 -0600
Subject: [PATCH 0734/1248] add defaults for the stream test.

---
 .../testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm     | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm
index f61ca32a79..aa2c9efa5b 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm
@@ -1,2 +1,4 @@
  use_excess_ice = .true.
  use_excess_ice_streams = .true.
+ excess_ice_coldstart_depth = 0.5
+ excess_ice_coldstart_temp = -5.0

From dbf00993bfb1ff626f4f326e03b585293f9bc5da Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Mon, 22 Jul 2024 10:58:36 -0600
Subject: [PATCH 0735/1248] fix indent

---
 bld/CLMBuildNamelist.pm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 498de96a4d..fa0d4a0382 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4589,13 +4589,13 @@ sub setup_logic_exice {
   my $finidat = $nl->get_value('finidat');
   # If coldstart and use_excess_ice is on:
   if ( ( (not defined($use_exice_streams)) && value_is_true($use_exice) ) && string_is_undef_or_empty($finidat) ) {
-   $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.true.');
-   $use_exice_streams = '.true.';
-   # if excess ice is turned off
-   } elsif ( (not defined($use_exice_streams)) && (not value_is_true($use_exice)) ) {
-   $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.false.');
-   $use_exice_streams = '.false.';
-   }
+     $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.true.');
+     $use_exice_streams = '.true.';
+     # if excess ice is turned off
+  } elsif ( (not defined($use_exice_streams)) && (not value_is_true($use_exice)) ) {
+     $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.false.');
+     $use_exice_streams = '.false.';
+  }
   # If excess ice streams is on
   if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
      # Can only be true if excess ice is also on, otherwise fail

From a4a9ede604eb36e1b1f6541fb1e40b712176ffa5 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 22 Jul 2024 16:04:00 -0600
Subject: [PATCH 0736/1248] Update ChangeLog/ChangeSum

---
 doc/ChangeLog | 4 +++-
 doc/ChangeSum | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 785b26db9e..506b3d5ad0 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.015
 Originator(s): multiple (Samuel Levis,UCAR/TSS,303-665-1310, @mvertens, @jedwards4b, @billsacks, @Katetc)
-Date: Fri 19 Jul 2024 06:02:22 PM MDT
+Date: Mon 22 Jul 2024 12:46:17 PM MDT
 One-line Summary: Update submodule tags to pass runoff from cism to rof
 
 Purpose and description of changes
@@ -110,6 +110,8 @@ Changes answers relative to baseline: Yes
     - what platforms/compilers: all
     - nature of change: mosart roundoff; rtm larger than roundoff due to bug fix
 
+ We are ignoring strange diffs from baseline in two tests in variable
+ FATES_TRANSITION_MATRIX_LULU as explained in issue #2656.
 
 Other details
 -------------
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 5c7123b5e0..9c6524b33d 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.015 multiple 07/19/2024 Update submodule tags to pass runoff from cism to rof
+       ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof
        ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.
        ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2
        ctsm5.2.012    sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes

From 753fda3ff0147837231a73c9c728dd9ce47b5997 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 23 Jul 2024 09:27:15 -0600
Subject: [PATCH 0737/1248] Format with black.

---
 python/ctsm/crop_calendars/cropcal_utils.py   | 22 +++++++++++++++++--
 .../crop_calendars/generate_gdd20_baseline.py | 12 +++-------
 .../crop_calendars/generate_gdds_functions.py | 17 ++++++++------
 .../ctsm/crop_calendars/interpolate_gdds.py   |  2 +-
 4 files changed, 34 insertions(+), 19 deletions(-)

diff --git a/python/ctsm/crop_calendars/cropcal_utils.py b/python/ctsm/crop_calendars/cropcal_utils.py
index 1a80448c1b..584046edee 100644
--- a/python/ctsm/crop_calendars/cropcal_utils.py
+++ b/python/ctsm/crop_calendars/cropcal_utils.py
@@ -206,15 +206,24 @@ def is_each_vegtype(this_vegtypelist, this_filter, this_method):
 
     return [is_this_vegtype(x, this_filter, this_method) for x in this_vegtypelist]
 
+
 def define_crop_list():
     """
     List (strings) of managed crops in CLM.
     """
-    notcrop_list = ["tree", "c3_arctic_grass", "c3_non-arctic_grass", "c4_grass", "shrub", "not_vegetated"]
+    notcrop_list = [
+        "tree",
+        "c3_arctic_grass",
+        "c3_non-arctic_grass",
+        "c4_grass",
+        "shrub",
+        "not_vegetated",
+    ]
     defined_pftlist = define_pftlist()
     is_crop = is_each_vegtype(defined_pftlist, notcrop_list, "notok_contains")
     return [defined_pftlist[i] for i, x in enumerate(is_crop) if x]
 
+
 def define_mgdcrop_list_nograsses():
     """
     List (strings) of managed crops in CLM.
@@ -224,11 +233,20 @@ def define_mgdcrop_list_nograsses():
     is_crop = is_each_vegtype(defined_pftlist, notcrop_list, "notok_contains")
     return [defined_pftlist[i] for i, x in enumerate(is_crop) if x]
 
+
 def define_mgdcrop_list_withgrasses():
     """
     List (strings) of managed crops in CLM.
     """
-    notcrop_list = ["tree", "c3_arctic_grass", "c3_non-arctic_grass", "c4_grass", "shrub", "unmanaged", "not_vegetated"]
+    notcrop_list = [
+        "tree",
+        "c3_arctic_grass",
+        "c3_non-arctic_grass",
+        "c4_grass",
+        "shrub",
+        "unmanaged",
+        "not_vegetated",
+    ]
     defined_pftlist = define_pftlist()
     is_crop = is_each_vegtype(defined_pftlist, notcrop_list, "notok_contains")
     return [defined_pftlist[i] for i, x in enumerate(is_crop) if x]
diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 3d082d0fde..06d3a9cd21 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -72,27 +72,21 @@ def _parse_args():
     parser.add_argument(
         "-y1",
         "--first-year",
-        help=(
-            "First calendar year to include"
-        ),
+        help=("First calendar year to include"),
         type=int,
         required=False,
     )
     parser.add_argument(
         "-yN",
         "--last-year",
-        help=(
-            "Last calendar year to include"
-        ),
+        help=("Last calendar year to include"),
         type=int,
         required=False,
     )
     parser.add_argument(
         "-v",
         "--variable",
-        help=(
-            "Which type of variable should be processed?"
-        ),
+        help=("Which type of variable should be processed?"),
         required=False,
         default="GDDBX",
         choices=["GDDBX", "GDDB20"],
diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index 83c167af00..50e2ac3d00 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -651,10 +651,7 @@ def import_and_process_1yr(
             )
         if save_figs and np.any(np.isnan(gddharv_atharv_p)):
             if np.all(np.isnan(gddharv_atharv_p)):
-                log(
-                    logger,
-                    "         ❗ All GDDHARV are NaN; should only affect figure"
-                )
+                log(logger, "         ❗ All GDDHARV are NaN; should only affect figure")
                 check_gddharv = False
             else:
                 log(
@@ -744,9 +741,15 @@ def import_and_process_1yr(
                     )
                 else:
                     error(logger, "Unexpected NaN for last season's GDD accumulation.")
-            if save_figs and check_gddharv and np.any(
-                np.isnan(
-                    gddharv_yp_list[var][year_index - 1, active_this_year_where_gs_lastyr_indices]
+            if (
+                save_figs
+                and check_gddharv
+                and np.any(
+                    np.isnan(
+                        gddharv_yp_list[var][
+                            year_index - 1, active_this_year_where_gs_lastyr_indices
+                        ]
+                    )
                 )
             ):
                 if incorrectly_daily:
diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py
index 809be98826..830df18c73 100755
--- a/python/ctsm/crop_calendars/interpolate_gdds.py
+++ b/python/ctsm/crop_calendars/interpolate_gdds.py
@@ -70,7 +70,7 @@ def _setup_process_args():
         help="Interpolate variables whose names start with this string",
         type=str,
         required=False,
-        default="gdd1_"
+        default="gdd1_",
     )
     parser.add_argument(
         "--overwrite",

From c0a3556886e31c5c4bfc55ceccec0925e407b1f4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 23 Jul 2024 09:27:53 -0600
Subject: [PATCH 0738/1248] Add previous commit to .git-blame-ignore-revs.

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 44a697c343..31f63ef8ae 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -48,3 +48,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 9660667b1267dcd4150889f5f39db540158be74a
 665cf86102e09b4c4c5a140700676dca23bc55a9
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
+753fda3ff0147837231a73c9c728dd9ce47b5997

From 811659f6a6bd59a91bef8f10aa0d20b0fc268630 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Tue, 23 Jul 2024 11:11:41 -0600
Subject: [PATCH 0739/1248] make unit-tests happy

---
 src/biogeophys/TemperatureType.F90             | 9 +++++++--
 src/unit_test_shr/unittestDustEmisInputs.F90   | 6 +++++-
 src/unit_test_shr/unittestWaterTypeFactory.F90 | 6 +++---
 3 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index a256e22eb7..3771735bb7 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -163,10 +163,15 @@ subroutine Init(this, bounds, &
     logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
     logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
     real(r8)          , intent(in) :: exice_init_conc_col(bounds%begc:)  ! initial coldstart excess ice concentration (from the stream file)
-    character(len=*)  , intent(in) :: NLFilename ! Namelist filename
+    character(len=*)  , intent(in), optional :: NLFilename ! Namelist filename
 
 
-    call this%ReadNL(NLFilename)
+    if ( present(NLFilename) ) then
+       call this%ReadNL(NLFilename)
+    else ! this is needed for testing
+       this%excess_ice_coldstart_depth = 0.5_r8
+       this%excess_ice_coldstart_temp  = -5.0_r8
+    endif
     call this%InitAllocate ( bounds )
     call this%InitHistory ( bounds, is_simple_buildtemp, is_prog_buildtemp )
     call this%InitCold ( bounds,                  &
diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90
index 6b15680ef7..af3ad63890 100644
--- a/src/unit_test_shr/unittestDustEmisInputs.F90
+++ b/src/unit_test_shr/unittestDustEmisInputs.F90
@@ -50,6 +50,7 @@ subroutine setUp(this)
 
     character(len=5) :: NLFilename = 'none'
     real(r8), allocatable :: urb_em(:)
+    real(r8), allocatable :: exice_init_conc_col(:)
     integer :: begl, endl, begc, endc
     integer :: c
     type(atm2lnd_params_type) :: atm2lnd_params
@@ -91,12 +92,15 @@ subroutine setUp(this)
     call this%frictionvel_inst%InitForTesting(bounds)
     allocate( urb_em(begl:endl) )
     urb_em(begl:endl) = 0.99_r8  ! Arbitrary won't matter here
+    allocate( exice_init_conc_col(begc:endc) )
+    exice_init_conc_col(begc:endc) = 0.0_r8 ! zero, so it doesn't affect anything.
     call this%temperature_inst%Init(bounds,           &
                                em_roof_lun=urb_em(begl:endl), &
                                em_wall_lun=urb_em(begl:endl), &
                                em_improad_lun=urb_em(begl:endl), &
                                em_perroad_lun=urb_em(begl:endl), &
-                               is_simple_buildtemp=.true., is_prog_buildtemp=.false.)
+                               is_simple_buildtemp=.true., is_prog_buildtemp=.false., &
+                               exice_init_conc_col = exice_init_conc_col(begc:endc))
     deallocate( urb_em )
   end subroutine setUp
 
diff --git a/src/unit_test_shr/unittestWaterTypeFactory.F90 b/src/unit_test_shr/unittestWaterTypeFactory.F90
index 06362ee1d0..2d83fd0058 100644
--- a/src/unit_test_shr/unittestWaterTypeFactory.F90
+++ b/src/unit_test_shr/unittestWaterTypeFactory.F90
@@ -140,7 +140,7 @@ subroutine create_water_type(this, water_inst, &
     end if
 
     if (present(exice_init_conc_col)) then
-       SHR_ASSERT_ALL_FL((ubound(exice_init_conc_col,1) == bounds%enc), sourcefile, __LINE__)
+       SHR_ASSERT_ALL_FL((ubound(exice_init_conc_col,1) == bounds%endc), sourcefile, __LINE__)
     endif
 
     if (present(enable_consistency_checks)) then
@@ -177,9 +177,9 @@ subroutine create_water_type(this, water_inst, &
        l_exice_coldstart_depth = 0.5_r8
     endif
     if (present(exice_init_conc_col)) then
-       l_exice_init_conc_col(:,:) = exice_init_conc_col
+       l_exice_init_conc_col(:) = exice_init_conc_col
     else
-       l_exice_init_conc_col(:,:) = 0.01_r8
+       l_exice_init_conc_col(:) = 0.0_r8
     endif
 
     call water_inst%InitForTesting(bounds, params, &

From 88adda49954f51a4aa3fb1763e0c9d2e152f7c04 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Tue, 23 Jul 2024 12:29:08 -0600
Subject: [PATCH 0740/1248] Make warning for non-equilibrium.

---
 src/biogeophys/WaterStateType.F90 | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90
index 8f0ba89104..35441d65d9 100644
--- a/src/biogeophys/WaterStateType.F90
+++ b/src/biogeophys/WaterStateType.F90
@@ -724,6 +724,17 @@ subroutine Restart(this, bounds, ncid, flag, &
     ! Restart excess ice vars
     if (.not. use_excess_ice) then
        ! no need to even define the restart vars
+       call RestartExcessIceIssue( &
+            ncid = ncid, &
+            flag = flag, &
+            excess_ice_on_restart = excess_ice_on_restart)
+       if( excess_ice_on_restart ) then
+          if (masterproc) then
+             write(iulog,*) '--WARNING-- Starting from initial conditions with excess ice present.'
+             write(iulog,*) 'But use_excess_ice=.false.'
+             write(iulog,*) 'This will cause soil moisture and temperature not being in equilibrium'
+          endif
+       endif
        this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8
     else
        call RestartExcessIceIssue( &

From b11bc8923bbaa6edc6c60913c37c1ba7f906d2b6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 24 Jul 2024 11:21:17 -0600
Subject: [PATCH 0741/1248] Update cism to work with this cmeps version

---
 .gitmodules     | 2 +-
 components/cism | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 501708f587..810b43a266 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_001
+fxtag = cismwrap_2_2_002
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
diff --git a/components/cism b/components/cism
index c05dd5c4fc..c84cc9f5b3 160000
--- a/components/cism
+++ b/components/cism
@@ -1 +1 @@
-Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928
+Subproject commit c84cc9f5b3103766a35d0a7ddd5e9dbd7deae762

From 838ea5f3bdab72ed9b54db969c23a86f548e3114 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 24 Jul 2024 10:47:58 -0700
Subject: [PATCH 0742/1248] move fates and update land use history outputs

This moves the land use outputs from the baseline fates testmod into the
LUH2 base testmod
---
 cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm       | 3 +--
 .../testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm       | 2 ++
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
index 91df3e2e61..8bd9f01335 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -26,5 +26,4 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
 'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
-'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
-'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU'
+'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
index e25490ffbb..6478669bee 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
@@ -7,3 +7,5 @@ use_fates_nocomp = .true.
 use_fates_fixed_biogeog = .true.
 use_fates_sp = .false.
 use_fates_potentialveg = .false.
+hist_fincl1 = 'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU',
+'FATES_TRANSITIONS_MATRIX_LULU'

From 38656f9c9904a312b041afaf9d15ed2e95f3838a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 24 Jul 2024 11:49:01 -0600
Subject: [PATCH 0743/1248] Get LILAC test working

---
 bld/env_run.xml                          | 1 +
 python/ctsm/lilac_make_runtime_inputs.py | 6 ++++++
 2 files changed, 7 insertions(+)

diff --git a/bld/env_run.xml b/bld/env_run.xml
index f3b7467168..cd865ad82c 100644
--- a/bld/env_run.xml
+++ b/bld/env_run.xml
@@ -9,6 +9,7 @@ Sample env_run.xml file that allows build-namelist to be run for testing in this
 -->
 <entry id="DIN_LOC_ROOT"         value="MYDINLOCROOT"  /> 
 <entry id="GLC_TWO_WAY_COUPLING" value="FALSE"         /> 
+<entry id="LND_SETS_DUST_EMIS_DRV_FLDS" value="TRUE"   /> 
 <entry id="NEONSITE"             value=""              /> 
 
 </config_definition>
diff --git a/python/ctsm/lilac_make_runtime_inputs.py b/python/ctsm/lilac_make_runtime_inputs.py
index 71f3c9bbe4..33b87c543e 100644
--- a/python/ctsm/lilac_make_runtime_inputs.py
+++ b/python/ctsm/lilac_make_runtime_inputs.py
@@ -47,6 +47,12 @@
       <valid_values>TRUE,FALSE</valid_values>
     </entry>
   </group>
+  <group id="run_cpl">
+    <entry id="LND_SETS_DUST_EMIS_DRV_FLDS" value="TRUE">
+      <type>logical</type>
+      <valid_values>TRUE,FALSE</valid_values>
+    </entry>
+  </group>
 </file>
 """
 

From 472891822d219c503dec159f991daa670ad7a10c Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 24 Jul 2024 10:51:31 -0700
Subject: [PATCH 0744/1248] update fates satellite phenology test coverage

This moves one of the FatesColdSatPhen tests to a gnu compiler to
provide compiler coverage for issues like #2656.  This also adds an
nvhpc compiler test to the fates test suite.
---
 cime_config/testdefs/testlist_clm.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 59044feb10..dc335e03da 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1998,6 +1998,7 @@
   <test name="SMS" grid="f45_f45_mg37" compset="I2000Clm60FatesSpRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
       <machine name="derecho" compiler="nvhpc" category="aux_clm"/>
+      <machine name="derecho" compiler="nvhpc" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3169,7 +3170,7 @@
   <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>

From e438a907e1fa23934255a10dddcfee4601bcd20d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 24 Jul 2024 12:14:39 -0600
Subject: [PATCH 0745/1248] Fix test number

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 198df535ad..1533e00d73 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3311;
+my $ntests = 3317;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2052;

From 71ca96d2d8e14fbbe9bc7686c2d905907b4d43d5 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:29:29 -0600
Subject: [PATCH 0746/1248] Delete an unused ncd_log.

---
 src/biogeophys/TemperatureType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index bb579b8031..5ba64f9b1e 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -897,7 +897,7 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     use shr_log_mod     , only : errMsg => shr_log_errMsg
     use spmdMod         , only : masterproc
     use abortutils      , only : endrun
-    use ncdio_pio       , only : file_desc_t, ncd_double, ncd_int, ncd_log
+    use ncdio_pio       , only : file_desc_t, ncd_double, ncd_int
     use restUtilMod
     !
     ! !ARGUMENTS:

From ad2c7f3af389ad2b2b6464987a06d1200049a813 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:30:31 -0600
Subject: [PATCH 0747/1248] Delete a troubleshooting log message.

---
 bld/CLMBuildNamelist.pm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index ad110b017e..5202717d74 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4200,7 +4200,6 @@ sub setup_logic_cropcal_streams {
     my $gdd20_season_end_file = $nl->get_value('stream_fldFileName_gdd20_season_end') ;
     if ( &string_is_undef_or_empty($gdd20_season_start_file) or &string_is_undef_or_empty($gdd20_season_end_file) ) {
       $log->message($gdd20_season_start_file);
-      $log->message('abcd');
       $log->message($gdd20_season_end_file);
       $log->fatal_error("If stream_gdd20_seasons is true, gdd20 season start and end files must be provided." );
     }

From 592476f7c6ae5751b6360c372ed70ad4f94af0c7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:34:29 -0600
Subject: [PATCH 0748/1248] Improve comments/error at "Handle invalid gdd20
 season values."

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index ef3bab03c5..d17ce1c259 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -793,9 +793,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
      ! Handle invalid gdd20 season values
      if (any(gdd20_season_starts(begp:endp) < 1._r8 .or. gdd20_season_ends(begp:endp) < 1._r8)) then
-         ! Fail if not allowing fallback to paramfile sowing windows
+         ! Fail if not allowing fallback to paramfile sowing windows. Only need to check for
+         ! values < 1 because values outside [1, 366] are set to -1 above.
          if ((.not. allow_invalid_gdd20_season_inputs) .and. any(gdd20_season_starts(begp:endp) < 1._r8 .and. patch%wtgcell(begp:endp) > 0._r8 .and. patch%itype(begp:endp) >= npcropmin)) then
-             write(iulog, *) 'At least one crop in one gridcell has invalid gdd20 season start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_gdd20_season_inputs to .true.'
+             write(iulog, *) 'At least one crop in one gridcell has invalid gdd20 season start and/or end date(s). To ignore and fall back to paramfile sowing windows for such crop-gridcells, set allow_invalid_gdd20_season_inputs to .true.'
              write(iulog, *) 'Affected crops:'
              do ivt = npcropmin, mxpft
                  do fp = 1, num_pcropp

From 013028c4687f564953ef5443e159b02f00220297 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:35:49 -0600
Subject: [PATCH 0749/1248] Replace SSR with Sam Rabin.

---
 src/biogeochem/CNPhenologyMod.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index d1d3c85b21..159e688dbd 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2699,7 +2699,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
          did_rx_gdds = .true.
          if (adapt_cropcal_rx_cultivar_gdds .and. crop_inst%gdd20_baseline_patch(p) > min_gdd20_baseline) then
             gddmaturity(p) = gddmaturity(p) * gdd20 / crop_inst%gdd20_baseline_patch(p)
-            !TODO SSR: Set maximum and minimum gddmaturity
+            !TODO Sam Rabin: Set maximum and minimum gddmaturity
          end if
       else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then
          gddmaturity(p) = hybgdd(ivt(p))
@@ -2716,11 +2716,11 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
                ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
                ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then
             gddmaturity(p) = max(950._r8, min(gdd20*0.85_r8, hybgdd(ivt(p))))
-            if (do_plant_normal) then  ! TODO SSR: Add ".and. .not. do_plant_prescribed"?
+            if (do_plant_normal) then  ! TODO Sam Rabin: Add ".and. .not. do_plant_prescribed"?
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
          else
-            ! TODO SSR: Add more descriptive error message
+            ! TODO Sam Rabin: Add more descriptive error message
             call endrun(msg="Stopping")
          end if
 

From 96c7c2d96cf39347cd6e259366f5d321971e75eb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:37:30 -0600
Subject: [PATCH 0750/1248] import_ds.py: Delete a commented-out line.

---
 python/ctsm/crop_calendars/import_ds.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/import_ds.py b/python/ctsm/crop_calendars/import_ds.py
index 0526d3c720..486757492f 100644
--- a/python/ctsm/crop_calendars/import_ds.py
+++ b/python/ctsm/crop_calendars/import_ds.py
@@ -59,7 +59,6 @@ def manual_mfdataset(filelist, my_vars, my_vegtypes, time_slice):
                 compat="override",
                 coords="all",
                 dim="time",
-                # combine="nested",
             )
     return ds_out
 

From 1d9e93989c656c91b44389a307bf07602727bcfd Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:38:29 -0600
Subject: [PATCH 0751/1248] Improve a comment in run_sys_tests.py.

---
 python/ctsm/run_sys_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py
index 9961fd325d..b3a3b78379 100644
--- a/python/ctsm/run_sys_tests.py
+++ b/python/ctsm/run_sys_tests.py
@@ -736,7 +736,7 @@ def _check_py_env(test_attributes):
     # whether import is possible.
     # pylint: disable=import-error disable
 
-    # Check requirements for using modify_fsurdat, if needed
+    # Check requirements for using modify_fsurdat Python module, if needed
     modify_fsurdat_users = ["FSURDATMODIFYCTSM", "RXCROPMATURITY"]
     if any(any(u in t for u in modify_fsurdat_users) for t in test_attributes):
         try:

From 78d9f98060c62ec486b32ef20dd2b14718d3c428 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:40:49 -0600
Subject: [PATCH 0752/1248] Improve error messages in PlantCrop().

---
 src/biogeochem/CNPhenologyMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 159e688dbd..855a1476f8 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2720,7 +2720,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
          else
-            ! TODO Sam Rabin: Add more descriptive error message
+            write(iulog, *) 'ERROR: PlantCrop(): unrecognized ivt for GDD target: ',ivt(p)
             call endrun(msg="Stopping")
          end if
 
@@ -2729,7 +2729,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
       if (gddmaturity(p) < min_gddmaturity) then
          if (use_cropcal_rx_cultivar_gdds .or. generate_crop_gdds) then
              if (did_rx_gdds) then
-                 write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')'
+                 write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity ',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')'
              end if
              gddmaturity(p) = min_gddmaturity
          else

From d3e6cbf13c4347ad2e61bbd5841b1bb9a7363fb8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:41:54 -0600
Subject: [PATCH 0753/1248] CropType: Fix a comment.

---
 src/biogeochem/CropType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index 77da895135..0f650a4a9f 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -54,7 +54,7 @@ module CropType
      real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings]
      real(r8), pointer :: gdd20_baseline_patch          (:)   ! GDD20 baseline for this patch (ddays) [patch]
      real(r8), pointer :: gdd20_season_start_patch(:) ! gdd20 season start date for this patch (day of year) [patch]. Real to enable history field.
-     real(r8), pointer :: gdd20_season_end_patch  (:) ! gdd20 season end   date for this patch (day of year) [patch]/ Real to enable history field.
+     real(r8), pointer :: gdd20_season_end_patch  (:) ! gdd20 season end   date for this patch (day of year) [patch]. Real to enable history field.
      real(r8), pointer :: sdates_thisyr_patch     (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_starts_thisyr_patch(:,:) ! all sowing window start dates for this patch this year (day of year) [patch, mxsowings]
      real(r8), pointer :: swindow_ends_thisyr_patch  (:,:) ! all sowing window end   dates for this patch this year (day of year) [patch, mxsowings]

From 6546a681b92f736e460a106b33b4523b290f1cbc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:42:57 -0600
Subject: [PATCH 0754/1248] TemperatureType Restart(): Delete unused p.

---
 src/biogeophys/TemperatureType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 5ba64f9b1e..787efa81a0 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -909,7 +909,7 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     logical          , intent(in)    :: is_prog_buildtemp    ! Prognostic building temp is being used
     !
     ! !LOCAL VARIABLES:
-    integer :: j,c,p     ! indices
+    integer :: j,c       ! indices
     logical :: readvar   ! determine if variable is on initial file
     integer :: idata
     !-----------------------------------------------------------------------

From c96ce350ed85600c8525b655f3acbfd2f6831059 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:49:19 -0600
Subject: [PATCH 0755/1248] Delete unused sowingWindows testmod.

---
 .../testmods_dirs/clm/sowingWindows/include_user_mods        | 1 -
 .../testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm     | 5 -----
 2 files changed, 6 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods
deleted file mode 100644
index fe0e18cf88..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
deleted file mode 100644
index 7024e99b96..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm
+++ /dev/null
@@ -1,5 +0,0 @@
-stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc'
-stream_fldFileName_swindow_end = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc'
-stream_meshfile_cropcal = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc'
-stream_year_first_cropcal_swindows = 2000
-stream_year_last_cropcal_swindows = 2000

From b96ec9107fe8e5b02260689190cd79799f589938 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:52:49 -0600
Subject: [PATCH 0756/1248] check_rxboth_run.py: Improve error message.

---
 python/ctsm/crop_calendars/check_rxboth_run.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py
index a1014b5e66..fa4affd220 100644
--- a/python/ctsm/crop_calendars/check_rxboth_run.py
+++ b/python/ctsm/crop_calendars/check_rxboth_run.py
@@ -156,7 +156,16 @@ def main(argv):
             any_bad = any_bad or gdds_not_obeyed
 
     if any_bad:
-        raise RuntimeError("Unexpected behavior in rxboth run")
+        msg = "\n   ".join(
+            [
+                "Unexpected behavior in rxboth run:",
+                f"any_bad_import_output:    {any_bad_import_output}",
+                f"any_bad_check_const_vars: {any_bad_check_const_vars}",
+                f"sdate_not_obeyed:         {sdate_not_obeyed}",
+                f"gdds_not_obeyed:          {gdds_not_obeyed}",
+            ]
+        )
+        raise RuntimeError(msg)
 
 
 if __name__ == "__main__":

From 876e23bb4fe4c6274e5f328212b4377ae1dd9c1d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 15:59:46 -0600
Subject: [PATCH 0757/1248] interpolate_gdds.py: Strict check for prefix match.

---
 python/ctsm/crop_calendars/interpolate_gdds.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py
index 830df18c73..92bb112e3f 100755
--- a/python/ctsm/crop_calendars/interpolate_gdds.py
+++ b/python/ctsm/crop_calendars/interpolate_gdds.py
@@ -6,6 +6,7 @@
 import sys
 import argparse
 import logging
+import re
 import xarray as xr
 
 # -- add python/ctsm  to path (needed if we want to run this stand-alone)
@@ -121,7 +122,7 @@ def interpolate_gdds(args):
         if "lat" not in ds_in[var].dims and "lon" not in ds_in[var].dims:
             print(f"Skipping variable {var} with dimensions {ds_in[var].dims}")
             continue
-        elif args.variable_prefix not in var:
+        if not re.compile("^" + args.variable_prefix).match(var)
             print(f"Unexpected variable {var} on input file. Skipping.")
             continue
         if args.dry_run:

From fecad299757de00f235217add67f70e60f7cda33 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:06:22 -0600
Subject: [PATCH 0758/1248] Delete unneeded cropAnnOutputMonthly testmod.

---
 cime_config/testdefs/testlist_clm.xml                         | 4 ++--
 .../testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm        | 3 ---
 2 files changed, 2 insertions(+), 5 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index c2926a25e7..e5a1ae7ef4 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3794,7 +3794,7 @@
     </options>
   </test>
 
-  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/cropAnnOutputMonthly">
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
@@ -3803,7 +3803,7 @@
     </options>
   </test>
 
-  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/cropAnnOutputMonthly--clm/StreamGdd20Seasons">
+  <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/StreamGdd20Seasons">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
diff --git a/cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm
deleted file mode 100644
index 1c47a2ebd1..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/cropAnnOutputMonthly/user_nl_clm
+++ /dev/null
@@ -1,3 +0,0 @@
-! These variables SHOULD only be saved annually in real runs, but for testing purposes it's fine to have them monthly.
-! Modifies h2 history file defined in crop testmod.
-hist_nhtfrq(3) = 0

From c94aeeab68a6f98188f0f94127b3685d2c89dd49 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:09:35 -0600
Subject: [PATCH 0759/1248] Add READMEs to testmods decStart and midDecStart.

---
 cime_config/testdefs/testmods_dirs/clm/decStart/README    | 1 +
 cime_config/testdefs/testmods_dirs/clm/midDecStart/README | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/decStart/README
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/midDecStart/README

diff --git a/cime_config/testdefs/testmods_dirs/clm/decStart/README b/cime_config/testdefs/testmods_dirs/clm/decStart/README
new file mode 100644
index 0000000000..7cdab6abfd
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/decStart/README
@@ -0,0 +1 @@
+Use midDecStart instead of decStart if you want ERP/ERS/etc. tests longer than 2 days to be able to have the split in December instead of January (i.e., before rather than after new year).
\ No newline at end of file
diff --git a/cime_config/testdefs/testmods_dirs/clm/midDecStart/README b/cime_config/testdefs/testmods_dirs/clm/midDecStart/README
new file mode 100644
index 0000000000..7cdab6abfd
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/midDecStart/README
@@ -0,0 +1 @@
+Use midDecStart instead of decStart if you want ERP/ERS/etc. tests longer than 2 days to be able to have the split in December instead of January (i.e., before rather than after new year).
\ No newline at end of file

From 833d4f67e888c747cfb2c35d8ae8354974987061 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:11:48 -0600
Subject: [PATCH 0760/1248] import_output(): Bugfix in call of
 check_v0_le_v1().

---
 python/ctsm/crop_calendars/cropcal_module.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index 08754f8823..927bdc9100 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -425,7 +425,7 @@ def import_output(
     # Check that e.g., GDDACCUM <= HUI
     for var_list in [["GDDACCUM", "HUI"], ["SYEARS", "HYEARS"]]:
         if all(v in this_ds_gs for v in var_list):
-            any_bad = check_v0_le_v1(
+            any_bad = any_bad or check_v0_le_v1(
                 this_ds_gs, var_list, both_nan_ok=True, throw_error=throw_errors
             )
 

From 7303c61744bddaeee8e47af561e9ef6e841bd503 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 24 Jul 2024 16:13:51 -0600
Subject: [PATCH 0761/1248] CTSM5.3 updates to the mksurfdata_esmf namelist

---
 .../ctsm/toolchain/gen_mksurfdata_namelist.py | 39 ++++++-------
 .../gen_mksurfdata_namelist.xml               | 57 +++++++++++--------
 2 files changed, 53 insertions(+), 43 deletions(-)

diff --git a/python/ctsm/toolchain/gen_mksurfdata_namelist.py b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
index 361616419f..b0c2016ccb 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_namelist.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
@@ -463,16 +463,16 @@ def check_ssp_years(start_year, end_year):
     """
     Check years associated with SSP period
     """
-    if int(start_year) > 2015:
+    if int(start_year) > 2022:
         error_msg = (
-            "ERROR: if start-year > 2015 must add an --ssp_rcp "
+            "ERROR: if start-year > 2022 must add an --ssp_rcp "
             "argument that is not none: valid opts for ssp-rcp "
             f"are {valid_opts}"
         )
         sys.exit(error_msg)
-    elif int(end_year) > 2015:
+    elif int(end_year) > 2022:
         error_msg = (
-            "ERROR: if end-year > 2015 must add an --ssp-rcp "
+            "ERROR: if end-year > 2022 must add an --ssp-rcp "
             "argument that is not none: valid opts for ssp-rcp "
             f"are {valid_opts}"
         )
@@ -537,6 +537,8 @@ def determine_pft_years(start_year, end_year, potveg):
     pft_years_ssp = "-999"
     if potveg:
         pft_years = "PtVg"
+    elif int(start_year) == 1700 and int(end_year) == 1700:
+        pft_years = "1700"
     elif int(start_year) == 1850 and int(end_year) == 1850:
         pft_years = "1850"
     elif int(start_year) == 2000 and int(end_year) == 2000:
@@ -545,21 +547,21 @@ def determine_pft_years(start_year, end_year, potveg):
         pft_years = "2005"
     elif int(start_year) >= 850 and int(end_year) <= 1849:
         pft_years = "0850-1849"
-    elif int(start_year) >= 1850 and int(start_year) <= 2100 and int(end_year) <= 2015:
-        pft_years = "1850-2015"
-    elif int(start_year) >= 1850 and int(start_year) <= 2100 and int(end_year) <= 2100:
-        pft_years = "1850-2015"
-        pft_years_ssp = "2016-2100"
-    elif int(start_year) >= 2016 and int(start_year) <= 2100 and int(end_year) <= 2100:
+    elif int(start_year) >= 1700 and int(start_year) <= 2100 and int(end_year) <= 2022:
+        pft_years = "1700-2022"
+    elif int(start_year) >= 1700 and int(start_year) <= 2100 and int(end_year) <= 2100:
+        pft_years = "1700-2022"
+        pft_years_ssp = "2023-2100"
+    elif int(start_year) >= 2023 and int(start_year) <= 2100 and int(end_year) <= 2100:
         pft_years = "-999"
-        pft_years_ssp = "2016-2100"
+        pft_years_ssp = "2023-2100"
     else:
         error_msg = (
             f"ERROR: start_year is {start_year} and end_year is "
             f"{end_year}; expected start/end-year options are: "
-            "- 1850, 2000, 2005 for time-slice options "
+            "- 1700, 1850, 2000, 2005 for time-slice options "
             "- in the range from 850 to 1849 "
-            "- in the range from 1850 to 2100 "
+            "- in the range from 1700 to 2100 "
             "- TODO in the range from 2101 to 2300 "
             "- OR user must set the potveg_flag "
         )
@@ -645,7 +647,7 @@ def write_nml_rawinput(
             # write everything else
             nlfile.write(f"  {key} = '{value}' \n")
 
-    if start_year <= 2015:
+    if start_year <= 2022:
         mksrf_fvegtyp = rawdata_files["mksrf_fvegtyp"]
         mksrf_fvegtyp_mesh = rawdata_files["mksrf_fvegtyp_mesh"]
         mksrf_fhrvtyp = rawdata_files["mksrf_fvegtyp"]
@@ -714,7 +716,7 @@ def handle_transient_run(
     with open(landuse_fname, "w", encoding="utf-8") as landuse_file:
         for year in range(start_year, end_year + 1):
             year_str = str(year)
-            if year <= 2015:
+            if year <= 2022:
                 file1 = rawdata_files["mksrf_fvegtyp"]
                 file2 = rawdata_files["mksrf_fvegtyp_urban"]
                 file3 = rawdata_files["mksrf_fvegtyp_lake"]
@@ -832,16 +834,15 @@ def determine_input_rawdata(start_year, input_path, attribute_list):
                     max_match_child = child2
 
         if max_match_child is None:
-            # TODO slevis: Are these if-statements backwards?
-            # For years greater than 2015 - mksrf_fvegtyp_ssp must have a match
-            if start_year <= 2015:
+            # For years greater than 2022 - mksrf_fvegtyp_ssp must have a match
+            if start_year > 2022:
                 if "mksrf_fvegtyp_ssp" not in child1.tag:
                     error_msg = f"ERROR: {child1.tag} has no matches"
                     sys.exit(error_msg)
                 else:
                     continue
             else:
-                # For years less than 2015 - mksrf_fvegtyp must have a match
+                # For years less than 2023 - mksrf_fvegtyp must have a match
                 if "mksrf_fvegtyp" not in child1.tag:
                     error_msg = f"ERROR: {child1.tag} has no matches"
                     sys.exit(error_msg)
diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index f4318880ea..e90949741d 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -10,7 +10,7 @@
 
   <mksrf_flai>
     <entry>
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histMKSRFDeg025_231228/mksrf_landuse_ctsm52_pftlai_CLIM.c231228.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_pftlai_CLIM.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
     <entry pft_years="2005" hires_pft='on'>
@@ -25,7 +25,7 @@
 
   <mksrf_fsoicol>
     <entry>
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histMKSRFDeg025_231228/mksrf_landuse_ctsm52_soilcolor_CLIM.c231228.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_soilcolor_CLIM.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
     <entry pft_years="2005" hires_pft='on'>
@@ -212,7 +212,7 @@ version of the raw dataset will probably go away.
   <!-- ======================== -->
 
   <mksrf_fvegtyp>
-    <!-- Potential Vegetation dataset -->
+    <!-- Potential Vegetation dataset TODO Peter Lawrence? -->
     <entry pft_years="PtVg" >
       <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.noanthro.c20230226/mksrf_landuse_ctsm52_noanthroLUH2_1.c20230226.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
@@ -220,22 +220,29 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/mksrf_urban_0.05x0.05_zerourbanpct.cdf5.c181014.nc</urban_filename>
     </entry>
 
+    <entry pft_years="1700">
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_1700.c240709.nc</data_filename>
+      <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
+      <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_1850.cdf5.c20220325.nc</lake_filename>
+      <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
+    </entry>
+
     <entry pft_years="1850">
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histLUH2Deg025_231228/mksrf_landuse_ctsm52_histLUH2_1850.c231228.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_1850.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_1850.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
     </entry>
 
     <entry pft_years="2000">
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histLUH2Deg025_231228/mksrf_landuse_ctsm52_histLUH2_2000.c231228.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_2000.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_2000.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_2000_cdf5_c20220910.nc</urban_filename>
     </entry>
 
     <entry pft_years="2005">
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c20230226/mksrf_landuse_ctsm52_histLUH2_2005.c20230226.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_2005.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_2005.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_2005_cdf5_c20220910.nc</urban_filename>
@@ -256,9 +263,10 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
     </entry>
 
-    <!-- Historical period from 1850 to 2015 -->
-    <entry pft_years="1850-2015" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52histLUH2Deg025_231228/mksrf_landuse_ctsm52_histLUH2_%y.c231228.nc</data_filename>
+    <!-- Historical period from 1700 to 2022 (expect 2023 soon) -->
+    <!-- Lake and urban data from 1700 to 1849 is copied from 1850 -->
+    <entry pft_years="1700-2022" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_%y.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_%y_cdf5_c20220910.nc</urban_filename>
@@ -268,11 +276,12 @@ version of the raw dataset will probably go away.
 
 
   <!-- Future scenarios  (up to 2100)-->
+  <!-- Lake data from 2018 to 2100 is copied from 2017 -->
   <mksrf_fvegtyp_ssp>
 
-    <!-- SSP1-RCP 2.6 -->
-    <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2016-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP126Deg025_231228/mksrf_landuse_ctsm52_SSP126_%y.c231228.nc</data_filename>
+    <!-- SSP1-RCP 2.6 TODO slevis: repl mksrf_landuse w new files -->
+    <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2023-2100" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP126Deg025_240717/mksrf_landuse_ctsm53_TRSSP126_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
@@ -284,43 +293,43 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_2100_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP1-RCP 1.9 -->
-    <entry  ssp_rcp="SSP1-1.9" pft_years_ssp="2016-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP119Deg025_231228/mksrf_landuse_ctsm52_SSP119_%y.c231228.nc</data_filename>
+    <entry  ssp_rcp="SSP1-1.9" pft_years_ssp="2023-2100" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP119Deg025_240717/mksrf_landuse_ctsm53_TRSSP119_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP2-RCP 4.5 -->
-    <entry  ssp_rcp="SSP2-4.5" pft_years_ssp="2016-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP245Deg025_231228/mksrf_landuse_ctsm52_SSP245_%y.c231228.nc</data_filename>
+    <entry  ssp_rcp="SSP2-4.5" pft_years_ssp="2023-2100" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP245Deg025_240717/mksrf_landuse_ctsm53_TRSSP245_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp2/urban_properties_GaoOneil_05deg_ThreeClass_ssp2_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP3-RCP 7.0 -->
-    <entry  ssp_rcp="SSP3-7.0" pft_years_ssp="2016-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP370Deg025_231228/mksrf_landuse_ctsm52_SSP370_2100.c231228.nc</data_filename>
+    <entry  ssp_rcp="SSP3-7.0" pft_years_ssp="2023-2100" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP370Deg025_240717/mksrf_landuse_ctsm53_TRSSP370_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp3/urban_properties_GaoOneil_05deg_ThreeClass_ssp3_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP4-RCP 3.4 -->
-    <entry  ssp_rcp="SSP4-3.4" pft_years_ssp="2016-2100" >
+    <entry  ssp_rcp="SSP4-3.4" pft_years_ssp="2023-2100" >
       <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-3.4.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP4-3.4_%y.c20230226.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp4/urban_properties_GaoOneil_05deg_ThreeClass_ssp4_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP4-RCP 6.0 -->
-    <entry  ssp_rcp="SSP4-6.0" pft_years_ssp="2016-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP460Deg025_231228/mksrf_landuse_ctsm52_SSP460_%y.c231228.nc</data_filename>
+    <entry  ssp_rcp="SSP4-6.0" pft_years_ssp="2023-2100" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP460Deg025_240717/mksrf_landuse_ctsm53_TRSSP460_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp4/urban_properties_GaoOneil_05deg_ThreeClass_ssp4_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP5-RCP 8.5 -->
-    <entry  ssp_rcp="SSP5-8.5" pft_years_ssp="2016-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM52RawData/globalctsm52SSP585Deg025_231228/mksrf_landuse_ctsm52_SSP585_%y.c231228.nc</data_filename>
+    <entry  ssp_rcp="SSP5-8.5" pft_years_ssp="2023-2100" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP585Deg025_240717/mksrf_landuse_ctsm53_TRSSP585_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp5/urban_properties_GaoOneil_05deg_ThreeClass_ssp5_%y_cdf5_c20220910.nc</urban_filename>
@@ -332,7 +341,7 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp5/urban_properties_GaoOneil_05deg_ThreeClass_ssp5_2100_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP5-RCP 3.4 -->
-    <entry  ssp_rcp="SSP5-3.4" pft_years_ssp="2016-2100" >
+    <entry  ssp_rcp="SSP5-3.4" pft_years_ssp="2023-2100" >
       <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP5-3.4.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP5-3.4_%y.c20230226.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>

From 56523e4cbb4969e9648adb2601c40d847cb9d408 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:15:28 -0600
Subject: [PATCH 0762/1248] Remove 1-degree RXCROPMATURITY test from
 rxcropmaturity, crop_calendars suites.

---
 cime_config/testdefs/testlist_clm.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index e5a1ae7ef4..5d3fbeb11a 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3663,8 +3663,6 @@
   <test name="RXCROPMATURITY_Lm61" grid="f09_g17" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">12:00:00</option>

From d06e8642a180190fea9f31c0a6af042758c31b81 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:18:38 -0600
Subject: [PATCH 0763/1248] Remove unneeded RxCropCalsAdaptFlush testmod.

---
 .../testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods    | 1 -
 .../testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm | 2 --
 2 files changed, 3 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm

diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods
deleted file mode 100644
index af5fe8591e..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../RxCropCalsAdapt
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm
deleted file mode 100644
index 4c6af0f6d2..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptFlush/user_nl_clm
+++ /dev/null
@@ -1,2 +0,0 @@
-
-flush_gdd20 = .true.

From a2bf12483a8fd1f33488b6df09ffe2b291aa2f43 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:21:18 -0600
Subject: [PATCH 0764/1248] generate_gdd20_baseline.py: Add a clarifying
 comment.

---
 python/ctsm/crop_calendars/generate_gdd20_baseline.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/python/ctsm/crop_calendars/generate_gdd20_baseline.py b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
index 06d3a9cd21..13668fc850 100644
--- a/python/ctsm/crop_calendars/generate_gdd20_baseline.py
+++ b/python/ctsm/crop_calendars/generate_gdd20_baseline.py
@@ -284,8 +284,7 @@ def generate_gdd20_baseline(input_files, output_file, author, time_slice, variab
             this_da = dummy_da
             print("   dummy GDD20")
         else:
-            # this_da = ds_in[gddn].fillna(MISSING_FILL)
-            this_da = ds_in[gddn_str]
+            this_da = ds_in[gddn_str]  # Already did ds_in.mean(dim="time") above
             this_da = _add_time_axis(this_da)
             print(f"   {gddn_str}")
             this_da = this_da.fillna(MISSING_RX_GDD_VAL)

From c9ff0ee33410b82462fbf4fc876b4130811e13cc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:24:14 -0600
Subject: [PATCH 0765/1248] PlantCrop(): Resolve (dismiss) a TODO.

---
 src/biogeochem/CNPhenologyMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 855a1476f8..1fb13d32eb 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -2716,7 +2716,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, &
                ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. &
                ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then
             gddmaturity(p) = max(950._r8, min(gdd20*0.85_r8, hybgdd(ivt(p))))
-            if (do_plant_normal) then  ! TODO Sam Rabin: Add ".and. .not. do_plant_prescribed"?
+            if (do_plant_normal) then
                gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8))
             end if
          else

From 6e0533749a45d8a845e3d0c37b81e9b3ea2da40c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 24 Jul 2024 16:38:46 -0600
Subject: [PATCH 0766/1248] Remove obsolete comment

---
 tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index e90949741d..7a31a94510 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -279,7 +279,7 @@ version of the raw dataset will probably go away.
   <!-- Lake data from 2018 to 2100 is copied from 2017 -->
   <mksrf_fvegtyp_ssp>
 
-    <!-- SSP1-RCP 2.6 TODO slevis: repl mksrf_landuse w new files -->
+    <!-- SSP1-RCP 2.6 -->
     <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2023-2100" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP126Deg025_240717/mksrf_landuse_ctsm53_TRSSP126_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>

From bc055919bd68719b53d6563d1f7a37976ec11c44 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:47:49 -0600
Subject: [PATCH 0767/1248] Improve flush_gdd20 restart logic.

Previously, TemperatureType%flush_gdd20 would get set to true upon restart unless it was read and false. This change makes it so that:
- If TemperatureType%flush_gdd20 isn't read from the restart file, it falls back to the flush_gdd20 from clm_varctl.
- If TemperatureType%flush_gdd20 IS read from the restart file, it is set to true if it's true on the restart file OR if the flush_gdd20 from clm_varctl is true.
---
 src/biogeophys/TemperatureType.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 787efa81a0..98f6d0f638 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -1148,10 +1148,10 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
             long_name='Flag indicating that GDD20 values need to be flushed', &
             units='none', interpinic_flag='copy', readvar=readvar, data=idata)
        if (flag == 'read') then
-          if (readvar .and. idata == 0) then
-             this%flush_gdd20 = .false.
+          if (readvar) then
+             this%flush_gdd20 = flush_gdd20 .or. idata == 1
           else
-             this%flush_gdd20 = .true.
+             this%flush_gdd20 = flush_gdd20
           end if
        end if
     end if

From d298aef9438d0b13bf37ccd162e1f5a303f6e4b4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 16:53:54 -0600
Subject: [PATCH 0768/1248] Do not use flush_gdd20 from clm_varctl in flush
 decision.

Not directly, at least. Instead, rely on TemperatureType%flush_gdd20 having been set correctly.
---
 src/biogeophys/TemperatureType.F90 | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 98f6d0f638..4929b24307 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -169,6 +169,9 @@ subroutine Init(this, bounds, &
          em_perroad_lun(bounds%begl:bounds%endl), &
          is_simple_buildtemp, is_prog_buildtemp)
 
+    ! Finish up
+    this%flush_gdd20 = flush_gdd20
+
   end subroutine Init
 
   !------------------------------------------------------------------------
@@ -1693,13 +1696,13 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then
           ! Flush, if needed
-          if (flush_gdd20 .or. this%flush_gdd20) then
+          if (this%flush_gdd20) then
               write(iulog, *) 'Flushing GDD20 variables'
               call markreset_accum_field('GDD020')
               call markreset_accum_field('GDD820')
               call markreset_accum_field('GDD1020')
               this%flush_gdd20 = .false.
-              flush_gdd20 = .false.
+              flush_gdd20 = .false.  ! Shouldn't be necessary, because flush_gdd20 shouldn't be considered after Init and Restart. But just in case...
           end if
           call update_accum_field  ('GDD020', this%gdd0_patch, nstep)
           call extract_accum_field ('GDD020', this%gdd020_patch, nstep)

From 21ec2bae64581024dce26a7e6406852d71f34258 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 24 Jul 2024 17:31:58 -0600
Subject: [PATCH 0769/1248] Remove commented out lines make sure reproduces
 results for aux_clm on Derecho

---
 src/biogeochem/DUSTMod.F90                   | 7 +------
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 9 ++++-----
 2 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
index bf04311cbe..3831f4d430 100644
--- a/src/biogeochem/DUSTMod.F90
+++ b/src/biogeochem/DUSTMod.F90
@@ -714,9 +714,8 @@ subroutine DustEmission (bounds, &
             frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor
 
          else    ! for lnd_frc_mbl=0, do not change friction velocity and assume drag partition factor = 0
-            !wnd_frc_slt = fv(p)                     ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission.
-            frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > 1, the drag partition effect is zero. dmleung 16 Feb 2024.
             wnd_frc_slt = fv(p) * frc_thr_rghn_fct(p) ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission. dmleung added 5 Jul 2024
+            frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > 1, the drag partition effect is zero. dmleung 16 Feb 2024.
          end if
 
          !########## end of drag partition effect #######################################################
@@ -741,13 +740,9 @@ subroutine DustEmission (bounds, &
             if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if using Leung's scheme, use impact threshold for dust emission equation; if Zender, uses fluid threshold (wnd_frc_thr_slt) for dust emission equation
 
                !################### for Leung et al. (2023) ################################################
-               !################ uncomment the below block if want to use Leung's scheme ###################
-
-               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_std) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
 
                ! dmleung: instead of using mss_frc_cly_vld(c) with a range of [0,0.2] , which makes dust too sensitive to input clay surface dataset), for now use 0.1 + mss_frc_cly_vld(c) * 0.1 / 0.20 with a range of [0.1,0.2]. So, instead of scaling dust emission to 1/20 times for El Djouf (western Sahara) because of its 1 % clay fraction, scale its emission to 1/2 times. This reduces the sensitivity of dust emission to the clay input dataset. In particular, because dust emission is a small-scale process and the grid-averaged clay from the new WISE surface dataset over El Djouf is 1 %, much lower than the former FAO estimation of 5 %, dmleung is not sure if the clay value of 1 % suppresses too much of El Djouf's small-scale dust emission process. Similar to Charlie Zender's feeling suspicious about the soil texture datasets (or the dust emission schemes' sandblasting process), dmleung feels the same and for now decides to still allow dust emission  to weakly scale with clay fraction, however limiting the scaling factor to 0.1-0.2. See modification in SoilStateInitTimeConst.F90. dmleung 5 Jul 2024
                flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
-               !flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * ( 0.1_r8 + mss_frc_cly_vld(c) * 0.1_r8 / 0.20_r8 ) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt 
 
                ! account for bare soil fraction, frozen soil fraction, and apply global tuning parameter (Kok et al. 2014)
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * lnd_frc_mbl(p) * C_tune * liqfrac
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index b22ea2278a..74148d1b08 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -696,9 +696,9 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     end do
 
     ! --------------------------------------------------------------------
-    ! Initialize threshold soil moisture, and mass fraction of clay as 
+    ! Initialize threshold soil moisture, and mass fraction of clay as
     ! scaling coefficient of dust emission flux (kg/m2/s) in DUSTMod.F90
-    ! dmleung modified 5 Jul 2024, reducing sensitivity of dust emission 
+    ! dmleung modified 5 Jul 2024, reducing sensitivity of dust emission
     ! flux to clay fraction.
     ! Also, for threshold soil moisture, dmleung followed Zender (2003)
     ! DEAD scheme to again avoid dust flux being too sensitive to the choice
@@ -713,10 +713,9 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
 
 
        ! dmleung++ added 24 May 2024: The below calculates the threshold gravimetric water content for the dust emission calculation in DUSTMod.F90. The equation comes from Eq. 14 of Fecan et al. (1999; https://doi.org/10.1007/s00585-999-0149-7).
-       !gwc_thr_col = 0.17*clay3d + 0.0014*(clay3d**2), and we only concern the topmost soil layer. 
+       !gwc_thr_col = 0.17*clay3d + 0.0014*(clay3d**2), and we only concern the topmost soil layer.
        ! Charlie Zender later on added a tuning factor (a) such that the equation becomes gwc_thr_col = a*[0.17*clay3d + 0.0014*(clay3d**2)]. (Zender et al., 2003a; https://doi.org/10.1029/2002JD002775)
-       ! There are different options: E.g., a = 1 gives the first line below. E.g., Kok et al. (2014a, b) chose to use a = 1. A second choice is proposed by Charlie Zender (2003a):  a = 1/clay3d, which gives the second line below. 
-       !soilstate_inst%gwc_thr_col(c) = 0.01_r8*(0.17_r8*clay3d(g,1) + 0.0014_r8*clay3d(g,1)*clay3d(g,1))  ! Jasper Kok et al. (2014) modified the equation of soil moisture effect for dust emissions using a tuning factor of a = 1. 0.01 is to convert the threshold gravimetric soil moisture from % to fraction. Danny M. Leung et al. (2023) followed K14 and used this equation for offline dust emission calculations using MERRA-2 met fields. Later, Leung et al. (2024) changed to a = 2 for CESM2 simulations. However, Danny Leung later (Dec 2023) decided to revert to Zender's choice and use a = 1 / (clay3d), which overall encourages more dust emissions from seriamid and more marginal dust sources. This note should probably be on the CLM tech note since dmleung has made a different decision for CESM than his own paper. dmleung added this detailed comment on 19 Feb 2024; edited 24 May 2024.
+       ! There are different options: E.g., a = 1 gives the first line below. E.g., Kok et al. (2014a, b) chose to use a = 1. A second choice is proposed by Charlie Zender (2003a):  a = 1/clay3d, which gives the second line below.
        soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 ! This was the original equation with a = 1 / (%clay) being the tuning factor for soil moisture effect in Zender's dust emission scheme. Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) dust emission scheme in the CESM will use Zender's tuning of a = 1 / (%clay), which overall encourages more dust emissions from seriamid and more marginal dust sources. Another advantage of using this tuning factor instead of a = 1 is that the dust emission threshold is linearly dependent on the clay fraction instead of parabolically dependent on clay fraction as in the above line. This means that dust emission becomes a little less sensitive to clay content (soil texture). 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to convert surface clay fraction from percentage to fraction. dmleung added this detailed comment on 19 Feb 2024.
 
        ! dust emission scaling factor dependent on clay fraction

From 827632e12b1f55253c8c75b999f4d8abd6f87b7a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 18:08:09 -0600
Subject: [PATCH 0770/1248] Actually don't use TemperatureType%flush_gdd20 at
 all.

Having that alongside flush_gdd20 from clm_varctl means that they can disagree when restarting, and it's not obvious which should win.

Note that the user being able to request a flush at all is dangerous. If they start a run with it true, they might continue that run without setting it to false. Instead, the restart decision should be made by the model---if a gridcell has different prescribed gdd20 season from what its restart file says, then that gridcell should be flushed.
---
 src/biogeophys/TemperatureType.F90 | 29 ++---------------------------
 1 file changed, 2 insertions(+), 27 deletions(-)

diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 4929b24307..71722d84fb 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -95,7 +95,6 @@ module TemperatureType
      real(r8), pointer :: gdd020_patch            (:)   ! patch 20-year average of gdd0                     (ddays)
      real(r8), pointer :: gdd820_patch            (:)   ! patch 20-year average of gdd8                     (ddays)
      real(r8), pointer :: gdd1020_patch           (:)   ! patch 20-year average of gdd10                    (ddays)
-     logical           :: flush_gdd20 = .false.         ! whether accumulated GDD20s need to be flushed
 
      ! Heat content
      real(r8), pointer :: beta_col                 (:)   ! coefficient of convective velocity [-]
@@ -169,9 +168,6 @@ subroutine Init(this, bounds, &
          em_perroad_lun(bounds%begl:bounds%endl), &
          is_simple_buildtemp, is_prog_buildtemp)
 
-    ! Finish up
-    this%flush_gdd20 = flush_gdd20
-
   end subroutine Init
 
   !------------------------------------------------------------------------
@@ -1139,26 +1135,6 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
        end if
     end if
 
-    if (use_crop) then
-       if (flag == 'write') then
-          if (this%flush_gdd20) then
-             idata = 1
-          else
-             idata = 0
-          end if
-       end if
-       call restartvar(ncid=ncid, flag=flag,  varname='flush_gdd20', xtype=ncd_int,  &
-            long_name='Flag indicating that GDD20 values need to be flushed', &
-            units='none', interpinic_flag='copy', readvar=readvar, data=idata)
-       if (flag == 'read') then
-          if (readvar) then
-             this%flush_gdd20 = flush_gdd20 .or. idata == 1
-          else
-             this%flush_gdd20 = flush_gdd20
-          end if
-       end if
-    end if
-
 
   end subroutine Restart
 
@@ -1696,13 +1672,12 @@ subroutine UpdateAccVars (this, bounds, crop_inst)
        ! Accumulate and extract running 20-year means
        if (is_end_curr_year()) then
           ! Flush, if needed
-          if (this%flush_gdd20) then
+          if (flush_gdd20) then
               write(iulog, *) 'Flushing GDD20 variables'
               call markreset_accum_field('GDD020')
               call markreset_accum_field('GDD820')
               call markreset_accum_field('GDD1020')
-              this%flush_gdd20 = .false.
-              flush_gdd20 = .false.  ! Shouldn't be necessary, because flush_gdd20 shouldn't be considered after Init and Restart. But just in case...
+              flush_gdd20 = .false.
           end if
           call update_accum_field  ('GDD020', this%gdd0_patch, nstep)
           call extract_accum_field ('GDD020', this%gdd020_patch, nstep)

From 4ab30a5ddb9ac54cba659abc8682f1152e8eb844 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 18:20:21 -0600
Subject: [PATCH 0771/1248] crop_calendars Python stuff now includes crop
 grasses.

---
 python/ctsm/crop_calendars/cropcal_module.py          | 2 +-
 python/ctsm/crop_calendars/generate_gdds_functions.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index 927bdc9100..719d352665 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -345,7 +345,7 @@ def import_output(
     my_vars,
     year_1=None,
     year_n=None,
-    my_vegtypes=utils.define_mgdcrop_list_nograsses(),
+    my_vegtypes=utils.define_mgdcrop_list_withgrasses(),
     sdates_rx_ds=None,
     gdds_rx_ds=None,
     verbose=False,
diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index 50e2ac3d00..14bd6b2e40 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -282,9 +282,9 @@ def import_and_process_1yr(
 
     # Get list of crops to include
     if skip_crops is not None:
-        crops_to_read = [c for c in utils.define_mgdcrop_list_nograsses() if c not in skip_crops]
+        crops_to_read = [c for c in utils.define_mgdcrop_list_withgrasses() if c not in skip_crops]
     else:
-        crops_to_read = utils.define_mgdcrop_list_nograsses()
+        crops_to_read = utils.define_mgdcrop_list_withgrasses()
 
     print(h1_filelist)
     dates_ds = import_ds(

From aeb4182302dc63bc88a3c8a5186233901f310f37 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 18:22:58 -0600
Subject: [PATCH 0772/1248] interpolate_gdds.py: Syntax fix.

---
 python/ctsm/crop_calendars/interpolate_gdds.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py
index 92bb112e3f..123d40af38 100755
--- a/python/ctsm/crop_calendars/interpolate_gdds.py
+++ b/python/ctsm/crop_calendars/interpolate_gdds.py
@@ -122,7 +122,7 @@ def interpolate_gdds(args):
         if "lat" not in ds_in[var].dims and "lon" not in ds_in[var].dims:
             print(f"Skipping variable {var} with dimensions {ds_in[var].dims}")
             continue
-        if not re.compile("^" + args.variable_prefix).match(var)
+        if not re.compile("^" + args.variable_prefix).match(var):
             print(f"Unexpected variable {var} on input file. Skipping.")
             continue
         if args.dry_run:

From 929ec5d6c43a4234e35b060b02223888466554fc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 23:08:27 -0600
Subject: [PATCH 0773/1248] Skip switchgrass in RXCROPMATURITY.

---
 cime_config/SystemTests/rxcropmaturity.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index 46ed8f8be3..965398821f 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -438,7 +438,7 @@ def _run_generate_gdds(self, case_gddgen):
                 f"--sdates-file {sdates_file}",
                 f"--hdates-file {hdates_file}",
                 f"--output-dir generate_gdds_out",
-                f"--skip-crops miscanthus,irrigated_miscanthus",
+                f"--skip-crops miscanthus,irrigated_miscanthus,switchgrass,irrigated_switchgrass",
             ]
         )
         stu.run_python_script(

From b70c156fed30f835a8b32cbca4d82dcbfe4888b2 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 24 Jul 2024 23:16:00 -0600
Subject: [PATCH 0774/1248] Manually specify sowing date file for GddGen
 testmod.

---
 cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
index 87cdd5d5b5..cfde517fd9 100644
--- a/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGen/user_nl_clm
@@ -1,4 +1,6 @@
 cropcals_rx = .true.
+stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc'
+stream_fldFileName_swindow_end = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc'
 stream_fldFileName_cultivar_gdds = ''
 generate_crop_gdds = .true.
 use_mxmat = .false.

From 7400d5bb153bd64be3eeb7f560e85128d736ed5c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 05:14:01 -0600
Subject: [PATCH 0775/1248] Add izumi_nag.clm-RxCropCalsAdaptGGCMI test to
 expected fails.

SMS_P128x1_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI
---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 03eb6a157d..e5e1410d1e 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -170,6 +170,13 @@
     </phase>
   </test>
 
+  <test name="SMS_P128x1_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2659</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="SMS_D_Ld3.f09_g17.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen_prescribed">

From 388c7ed45e9561206a88efeecdb6faec054522d1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 05:55:45 -0600
Subject: [PATCH 0776/1248] Move stream_gdd20_seasons to cropCalStreamMod.

---
 bld/namelist_files/namelist_definition_ctsm.xml | 2 +-
 src/biogeophys/TemperatureType.F90              | 7 +++++--
 src/cpl/share_esmf/cropcalStreamMod.F90         | 5 ++++-
 src/main/clm_varctl.F90                         | 1 -
 src/main/controlMod.F90                         | 4 +---
 5 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 31ce220d9c..a24f59339a 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -1839,7 +1839,7 @@ Filename of input stream data for baseline GDD20 values
 </entry>
 
 <entry id="stream_gdd20_seasons" type="logical" category="datasets"
-       group="clm_inparm" valid_values="" >
+       group="cropcal_streams" valid_values="" >
 Set this to true to read gdd20 accumulation season start and end dates from stream files, rather than using hard-coded hemisphere-specific "warm seasons."
 </entry>
 
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index 71722d84fb..707218cc27 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -8,7 +8,7 @@ module TemperatureType
   use decompMod       , only : bounds_type
   use abortutils      , only : endrun
   use clm_varctl      , only : use_cndv, iulog, use_luna, use_crop, use_biomass_heat_storage
-  use clm_varctl      , only : stream_gdd20_seasons, flush_gdd20
+  use clm_varctl      , only : flush_gdd20
   use clm_varpar      , only : nlevsno, nlevgrnd, nlevlak, nlevurb, nlevmaxurbgrnd
   use clm_varcon      , only : spval, ispval
   use GridcellType    , only : grc
@@ -1401,6 +1401,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     real(r8) :: lat  ! latitude
     integer :: gdd20_season_start, gdd20_season_end
     integer :: jday  ! Julian day of year (1, ..., 366)
+    logical :: stream_gdd20_seasons_tt  ! Local derivation of this to avoid circular dependency
 
     associate( &
      gdd20_season_starts => crop_inst%gdd20_season_start_patch, &
@@ -1432,6 +1433,8 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
     end if
     write(field_name, format_string) "GDD",basetemp_int
 
+    stream_gdd20_seasons_tt = any(gdd20_season_starts(begp:endp) > 0.5_r8) .and. any(gdd20_season_starts(begp:endp) < 366.5_r8)
+
     do p = begp,endp
 
        ! Avoid unnecessary calculations over inactive points
@@ -1447,7 +1450,7 @@ subroutine UpdateAccVars_CropGDDs(this, rbufslp, begp, endp, month, day, secs, d
           ((month > 9 .or.  month < 4)  .and. lat <  0._r8)
        ! Replace with read-in gdd20 accumulation season, if needed and valid
        ! (If these aren't being read in or they're invalid, they'll be -1)
-       if (stream_gdd20_seasons .and. patch%itype(p) >= npcropmin) then
+       if (stream_gdd20_seasons_tt .and. patch%itype(p) >= npcropmin) then
           gdd20_season_start = int(gdd20_season_starts(p))
           gdd20_season_end = int(gdd20_season_ends(p))
           if (gdd20_season_start >= 1 .and. gdd20_season_end >= 1) then
diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index d17ce1c259..85218a0e1c 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -16,7 +16,6 @@ module cropcalStreamMod
   use clm_varctl       , only : iulog
   use clm_varctl       , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams
   use clm_varctl       , only : adapt_cropcal_rx_cultivar_gdds
-  use clm_varctl       , only : stream_gdd20_seasons
   use clm_varpar       , only : mxpft
   use clm_varpar       , only : mxsowings
   use perf_mod         , only : t_startf, t_stopf
@@ -53,6 +52,7 @@ module cropcalStreamMod
   character(len=CL)       :: stream_fldFileName_gdd20_baseline ! GDD20 baseline stream filename to read
   logical                 :: cropcals_rx ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
   logical                 :: cropcals_rx_adapt ! Used only for setting input files in namelist; does nothing in code, but needs to be here so namelist read doesn't crash
+  logical :: stream_gdd20_seasons  ! Read start and end dates for gdd20 seasons from streams instead of using hemisphere-specific values
   logical                     :: allow_invalid_gdd20_season_inputs ! Fall back on hemisphere "warm periods" in cases of invalid values in stream_fldFileName_gdd20_season_start and _end?
   character(len=CL)       :: stream_fldFileName_gdd20_season_start ! Stream filename to read for start of gdd20 season
   character(len=CL)       :: stream_fldFileName_gdd20_season_end ! Stream filename to read for end of gdd20 season
@@ -113,6 +113,7 @@ subroutine cropcal_init(bounds)
          stream_meshfile_cropcal, &
          cropcals_rx, &
          cropcals_rx_adapt, &
+         stream_gdd20_seasons, &
          allow_invalid_gdd20_season_inputs, &
          stream_fldFileName_gdd20_season_start, &
          stream_fldFileName_gdd20_season_end
@@ -130,6 +131,7 @@ subroutine cropcal_init(bounds)
     stream_fldFileName_swindow_end   = ''
     stream_fldFileName_cultivar_gdds = ''
     stream_fldFileName_gdd20_baseline = ''
+    stream_gdd20_seasons = .false.
     allow_invalid_gdd20_season_inputs = .false.
     stream_fldFileName_gdd20_season_start = ''
     stream_fldFileName_gdd20_season_end = ''
@@ -173,6 +175,7 @@ subroutine cropcal_init(bounds)
     call shr_mpi_bcast(stream_fldFileName_cultivar_gdds, mpicom)
     call shr_mpi_bcast(stream_fldFileName_gdd20_baseline, mpicom)
     call shr_mpi_bcast(stream_meshfile_cropcal    , mpicom)
+    call shr_mpi_bcast(stream_gdd20_seasons, mpicom)
     call shr_mpi_bcast(allow_invalid_gdd20_season_inputs, mpicom)
     call shr_mpi_bcast(stream_fldFileName_gdd20_season_start, mpicom)
     call shr_mpi_bcast(stream_fldFileName_gdd20_season_end, mpicom)
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index a1ca2fd3f7..678f386f23 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -392,7 +392,6 @@ module clm_varctl
   logical, public :: use_cropcal_rx_swindows = .false.
   logical, public :: use_cropcal_rx_cultivar_gdds = .false.
   logical, public :: adapt_cropcal_rx_cultivar_gdds = .false.
-  logical, public :: stream_gdd20_seasons = .false.
   logical, public :: flush_gdd20 = .false.
 
   !----------------------------------------------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 98e0d1afac..634128798b 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -302,7 +302,7 @@ subroutine control_init(dtime)
          use_lch4, use_nitrif_denitrif, use_extralakelayers, &
          use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, &
          use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, &
-         use_nguardrail, crop_residue_removal_frac, stream_gdd20_seasons, flush_gdd20
+         use_nguardrail, crop_residue_removal_frac, flush_gdd20
 
     ! SNICAR
     namelist /clm_inparm/ &
@@ -711,7 +711,6 @@ subroutine control_spmd()
     call mpi_bcast (use_cndv, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_nguardrail, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_crop, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (stream_gdd20_seasons, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (flush_gdd20, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fertilizer, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_grainproduct, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -985,7 +984,6 @@ subroutine control_print ()
     write(iulog,*) '    use_cn = ', use_cn
     write(iulog,*) '    use_cndv = ', use_cndv
     write(iulog,*) '    use_crop = ', use_crop
-    write(iulog,*) '    stream_gdd20_seasons = ', stream_gdd20_seasons
     write(iulog,*) '    flush_gdd20 = ', flush_gdd20
     write(iulog,*) '    use_fertilizer = ', use_fertilizer
     write(iulog,*) '    use_grainproduct = ', use_grainproduct

From 0d4a300112f16ee35332af5e72e8016ea1990c8a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 14:21:40 -0600
Subject: [PATCH 0777/1248] Fix setting of stream_fldFileName_gdd20_baseline.

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 232b15c3b1..c2d23ce962 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4247,7 +4247,7 @@ sub setup_logic_cropcal_streams {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_end');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds');
     if ( &value_is_true($cropcals_rx_adapt) ) {
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline');
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline', 'stream_gdd20_seasons'=>$stream_gdd20_seasons);
     }
   }
 

From 649547c5015e59ab582436c8c1bcfc39e296dd8f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 16:21:16 -0600
Subject: [PATCH 0778/1248] Don't specify PE layout for SMS crop_calendars
 tests.

---
 cime_config/testdefs/testlist_clm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index b8e3dd2f31..ecdeeb659d 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3560,7 +3560,7 @@
     </options>
   </test>
 
-  <test name="SMS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCals">
+  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCals">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
@@ -3578,7 +3578,7 @@
     </options>
   </test>
 
-  <test name="SMS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
+  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>

From 26ce0bbb0ac7835f11251c0585eec778b4a79859 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 16:04:00 -0600
Subject: [PATCH 0779/1248] Add izumi versions of most derecho crop_calendars
 tests.

---
 cime_config/testdefs/testlist_clm.xml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index ecdeeb659d..18e66d4d64 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3563,6 +3563,7 @@
   <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCals">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -3581,6 +3582,7 @@
   <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -3593,6 +3595,7 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
@@ -3603,6 +3606,7 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
@@ -3613,6 +3617,7 @@
   <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3622,6 +3627,7 @@
   <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/StreamGdd20Seasons">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>

From ae4af6b53cf0e525cd125a1eea97472ad2c72799 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 16:26:14 -0600
Subject: [PATCH 0780/1248] Fix PE layouts of izumi crop_calendars tests.

---
 cime_config/testdefs/testlist_clm.xml | 30 +++++++++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 18e66d4d64..edbfd3c4eb 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3579,6 +3579,15 @@
     </options>
   </test>
 
+  <test name="ERS_P192x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdapt">
+    <machines>
+      <machine name="izumi" compiler="gnu" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">04:00:00</option>
+    </options>
+  </test>
+
   <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
@@ -3595,18 +3604,25 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
     </options>
   </test>
 
+  <test name="ERP_D_P96x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
+    <machines>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:30:00</option>
+    </options>
+  </test>
+
   <test name="PEM_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
@@ -3614,6 +3630,16 @@
     </options>
   </test>
 
+  <test name="PEM_D_P96x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
+    <machines>
+      <machine name="izumi" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:30:00</option>
+      <option name="comment">This test is potentially duplicative of the equivalent ERP test. However, ambiguous nearest neighbors can result in different pixels being chosen based on number of processors. Because crop calendar inputs are only updated at beginning of year, this can cause PEM test to fail where ERP test passes.</option>
+    </options>
+  </test>
+
   <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>

From e757d3df5154d3671129a26d9afab667f337591f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 14:54:24 -0600
Subject: [PATCH 0781/1248] Add oldCropCals testmod and two aux_clm tests that
 use it.

---
 cime_config/testdefs/testlist_clm.xml         | 27 +++++++++++++++++++
 .../testmods_dirs/clm/oldCropCals/user_nl_clm |  3 +++
 2 files changed, 30 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/oldCropCals/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index edbfd3c4eb..ffaf4edc29 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3660,5 +3660,32 @@
     </options>
   </test>
 
+  <test name="SMS_Lm37" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput--clm/oldCropCals">
+    <machines>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:30:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_Ld32" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/crop--clm/oldCropCals">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_Ld32" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/crop--clm/oldCropCals">
+    <machines>
+      <machine name="izumi" compiler="gnu" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:00:00</option>
+    </options>
+  </test>
+
 
 </testlist>
diff --git a/cime_config/testdefs/testmods_dirs/clm/oldCropCals/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/oldCropCals/user_nl_clm
new file mode 100644
index 0000000000..5885f6f2a0
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/oldCropCals/user_nl_clm
@@ -0,0 +1,3 @@
+cropcals_rx = .false.
+cropcals_rx_adapt = .false.
+stream_gdd20_seasons = .false.
\ No newline at end of file

From 7070abcd9272cc4b0f55d086321ea6968f1d2e83 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 16:29:34 -0600
Subject: [PATCH 0782/1248] Add cropcals_rx(_adapt) in some testmods; rename
 RxCropCals to RxCropCalsNoAdapt.

---
 cime_config/testdefs/testlist_clm.xml                           | 2 +-
 cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods | 1 +
 cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm   | 2 --
 .../testmods_dirs/clm/RxCropCalsAdapt/include_user_mods         | 2 +-
 .../clm/{RxCropCals => RxCropCalsNoAdapt}/include_user_mods     | 0
 .../testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/user_nl_clm    | 2 ++
 6 files changed, 5 insertions(+), 4 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
 rename cime_config/testdefs/testmods_dirs/clm/{RxCropCals => RxCropCalsNoAdapt}/include_user_mods (100%)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index ffaf4edc29..cca879604d 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3560,7 +3560,7 @@
     </options>
   </test>
 
-  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCals">
+  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsNoAdapt">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="intel" category="crop_calendars"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
index 02ec13743f..4d75082583 100644
--- a/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/GddGen/include_user_mods
@@ -1 +1,2 @@
 ../cropMonthOutput
+../oldCropCals
\ No newline at end of file
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
deleted file mode 100644
index 8a0b4a91be..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCals/user_nl_clm
+++ /dev/null
@@ -1,2 +0,0 @@
-
-cropcals_rx = .true.
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
index 88c9694365..4f46c0ce95 100644
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
@@ -1 +1 @@
-../RxCropCals
+../RxCropCalsNoAdapt
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCals/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/include_user_mods
similarity index 100%
rename from cime_config/testdefs/testmods_dirs/clm/RxCropCals/include_user_mods
rename to cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/user_nl_clm
new file mode 100644
index 0000000000..625960b389
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/user_nl_clm
@@ -0,0 +1,2 @@
+cropcals_rx = .true.
+cropcals_rx_adapt = .false.

From f0a221f0a68c0aac10cf0c449406c1dcd27a6294 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 15:38:20 -0600
Subject: [PATCH 0783/1248] Rework RxCropCalsAdaptGGCMI to not require
 RxCropCalsAdapt.

The latter will be deleted in the next commit.
---
 .../testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods   | 2 +-
 .../testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm         | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
index af5fe8591e..23ea3745e6 100644
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
@@ -1 +1 @@
-../RxCropCalsAdapt
+../crop
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
index dd4ac3117c..fdf5a86c26 100644
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/user_nl_clm
@@ -1,4 +1,5 @@
-
+cropcals_rx = .false.
+cropcals_rx_adapt = .true.
 stream_gdd20_seasons = .true.
 flush_gdd20 = .true.
 !TODO SSR: Try without this once you have half-degree inputs

From 5dabe6287e9ad843003f08122cf58327aaf356b3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 16:31:07 -0600
Subject: [PATCH 0784/1248] Delete RxCropCalsAdapt test.

---
 cime_config/testdefs/testlist_clm.xml          | 18 ------------------
 .../clm/RxCropCalsAdapt/include_user_mods      |  1 -
 .../clm/RxCropCalsAdapt/user_nl_clm            |  3 ---
 3 files changed, 22 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index cca879604d..4e5574932e 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3570,24 +3570,6 @@
     </options>
   </test>
 
-  <test name="ERS_P128x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdapt">
-    <machines>
-      <machine name="derecho" compiler="gnu" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">02:00:00</option>
-    </options>
-  </test>
-
-  <test name="ERS_P192x1_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdapt">
-    <machines>
-      <machine name="izumi" compiler="gnu" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">04:00:00</option>
-    </options>
-  </test>
-
   <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
deleted file mode 100644
index 4f46c0ce95..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../RxCropCalsNoAdapt
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm
deleted file mode 100644
index 709c7221e0..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdapt/user_nl_clm
+++ /dev/null
@@ -1,3 +0,0 @@
-
-cropcals_rx = .false.
-cropcals_rx_adapt = .true.

From ca6b608ce59eb9043297d4452a5d0107eb5b8e82 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 15:52:10 -0600
Subject: [PATCH 0785/1248] Add 'cropcals_rx_adapt = .false.' to
 RXCROPMATURITYSHARED.

---
 cime_config/SystemTests/rxcropmaturity.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index b1de55836b..fb254c408f 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -402,6 +402,7 @@ def _run_check_rxboth_run(self, skip_gen):
     def _modify_user_nl_allruns(self):
         nl_additions = [
             "cropcals_rx = .true.",
+            "cropcals_rx_adapt = .false.",
             "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
             "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
             "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),

From dc9996fa36033e340b790ecc0fe716cd2a48a062 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 25 Jul 2024 17:08:56 -0600
Subject: [PATCH 0786/1248] Minor yet important update to comments

---
 tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index 7a31a94510..1e24accc4d 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -265,6 +265,8 @@ version of the raw dataset will probably go away.
 
     <!-- Historical period from 1700 to 2022 (expect 2023 soon) -->
     <!-- Lake and urban data from 1700 to 1849 is copied from 1850 -->
+    <!-- Lake data from 2018 to 2023 is copied from 2017 -->
+    <!-- Urban data from 2016 to 2023 is copied from 2015 -->
     <entry pft_years="1700-2022" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_%y.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>

From 904e6b2f99164165a4a197436f4b583148bdc087 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 18:22:36 -0600
Subject: [PATCH 0787/1248] Change a test name in ExpectedTestFails.xml.

---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 9b653d8e0b..d5e3e4e378 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -163,7 +163,7 @@
     </phase>
   </test>
 
-  <test name="SMS_P128x1_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI">
+  <test name="SMS_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
       <issue>#2659</issue>

From a3d8158c65dcff4cabc1a9e3dd86fe762050f7f3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 20:01:54 -0600
Subject: [PATCH 0788/1248] Turn on cropcals_rx_adapt by default for physics
 other than clm4_5, clm5_0, and clm5_1.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 706b4dd26d..5f336dabf8 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2199,7 +2199,10 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- crop calendars: default settings -->
 <cropcals_rx>.false.</cropcals_rx>
-<cropcals_rx_adapt>.false.</cropcals_rx_adapt>
+<cropcals_rx_adapt>.true.</cropcals_rx_adapt>
+<cropcals_rx_adapt phys="clm4_5">.false.</cropcals_rx_adapt>
+<cropcals_rx_adapt phys="clm5_0">.false.</cropcals_rx_adapt>
+<cropcals_rx_adapt phys="clm5_1">.false.</cropcals_rx_adapt>
 <stream_gdd20_seasons>.false.</stream_gdd20_seasons>
 <flush_gdd20>.false.</flush_gdd20>
 <stream_year_first_cropcal_swindows  >2000</stream_year_first_cropcal_swindows>

From dcdd587848f18f2087543966856f6b0373a64adb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 25 Jul 2024 22:36:49 -0600
Subject: [PATCH 0789/1248] Remove most Izumi crop_calendars tests.

---
 cime_config/testdefs/testlist_clm.xml | 32 ---------------------------
 1 file changed, 32 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 4e5574932e..efeb011844 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3563,7 +3563,6 @@
   <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsNoAdapt">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -3573,7 +3572,6 @@
   <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -3592,15 +3590,6 @@
     </options>
   </test>
 
-  <test name="ERP_D_P96x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
-    <machines>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:30:00</option>
-    </options>
-  </test>
-
   <test name="PEM_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -3612,20 +3601,9 @@
     </options>
   </test>
 
-  <test name="PEM_D_P96x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
-    <machines>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:30:00</option>
-      <option name="comment">This test is potentially duplicative of the equivalent ERP test. However, ambiguous nearest neighbors can result in different pixels being chosen based on number of processors. Because crop calendar inputs are only updated at beginning of year, this can cause PEM test to fail where ERP test passes.</option>
-    </options>
-  </test>
-
   <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3635,7 +3613,6 @@
   <test name="SMS_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/GddGen--clm/StreamGdd20Seasons">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="izumi" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3660,14 +3637,5 @@
     </options>
   </test>
 
-  <test name="SMS_Ld32" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/crop--clm/oldCropCals">
-    <machines>
-      <machine name="izumi" compiler="gnu" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">01:00:00</option>
-    </options>
-  </test>
-
 
 </testlist>

From af02bca9e98661c1f9450cf7602c96dc3aab2b15 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 25 Jul 2024 23:17:56 -0700
Subject: [PATCH 0790/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 137 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 138 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 506b3d5ad0..501a67720f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,141 @@
 ===============================================================
+Tag name: ctsm5.2.016
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Thu Jul 25 22:39:39 MST 2024
+One-line Summary: Enable new crop calendars for clm60 compsets
+
+Purpose and description of changes
+----------------------------------
+
+This commit switches clm60 compsets (really, any compset other than clm45, clm50, and clm51) to use:
+- Per-gridcell and -crop sowing windows derived from the GGCMI phase 3b group II static growing seasons
+- Per-gridcell and -crop maturity requirements derived from those same growing seasons, over the 1980-2009 growing seasons
+- Code to adjust those prescribed maturity requirements based on recent climate
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[X] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[?] ctsm5_0-nwp: Probably? Haven't tested, but didn't exclude that setup.
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description):
+- Fixes ESCOMP/CTSM#2584: Reset accumulators to initval instead of 0 (https://github.com/ESCOMP/CTSM/issues/2584)
+
+Notes of particular relevance for users
+---------------------------------------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+Caveats for users (e.g., need to interpolate initial conditions):
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+- Add cropcals_rx, default false.
+- Add cropcals_rx_adapt, default true. This is what changes default behavior.
+- Rename stream_year_first_cropcal to stream_year_first_cropcal_swindows
+- Rename stream_year_last_cropcal to stream_year_last_cropcal_swindows
+- Rename model_year_align_cropcal to model_year_align_cropcal_swindows
+- Add stream_year_first_cropcal_cultivar_gdds
+- Add stream_year_last_cropcal_cultivar_gdds
+- Add model_year_align_cropcal_cultivar_gdds
+- Add stream_fldFileName_gdd20_baseline
+- Add stream_gdd20_seasons (experimental)
+- Add flush_gdd20 (experimental)
+- Add stream_fldFileName_gdd20_season_start (experimental)
+- Add stream_fldFileName_gdd20_season_end (experimental)
+- Add allow_invalid_gdd20_season_inputs
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+- Many new default and optional stream files added.
+
+Changes to documentation:
+- None yet.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers:
+- tools/contrib/tweak_latlons.py: This is a script I made to avoid the "ambiguous nearest neighbor" issue described in the discussion at https://github.com/orgs/esmf-org/discussions/261. It's hopefully just a temporary thing as we wait for ESMF to fix that bug. If they end up deciding not to, then this should be moved into python/ctsm/ and fully tested.
+- Unit and system testing needs to be added for generate_gdd20_baseline.py.
+- RXCROPMATURITY SystemTest should be updated to also call generate_gdd20_baseline.py.
+
+Changes to tests or testing:
+- Adds testmods:
+  - midDecStart: Like decStart, except starts Dec. 15 instead of 30. Useful for ERP/ERS tests where you want the split in December.
+  - GddGen
+  - oldCropCals: To recreate previous crop calendars
+  - RxCropCalsAdaptGGCMI (experimental)
+  - RxCropCalsNoAdapt
+  - StreamGDD20Seasons (experimental)
+- Removes sowingWindows testmod
+- Adds and changes various tests related to crop calendars
+
+Note that testmods marked "experimental" are fine to be marked as expected failures, if needed.
+
+
+Testing summary:
+----------------
+
+[Remove any lines that don't apply.]
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho -
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    (any machine) -
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho -----
+    izumi -------
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: crop-enabled compsets with clm60 (or more specifically, other than clm45, clm50, clm51)
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): new climate
+    
+   Probably? At least, there can be large regional shifts in crop growing season. Results are similar to those for the Prescribed Calendars setup in Rabin et al. (2023; https://gmd.copernicus.org/articles/16/7253/2023/gmd-16-7253-2023.html).
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+       - None
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2560: Allow prescribed gddmaturity to vary based on recent climate (initial work, v2) (https://github.com/ESCOMP/CTSM/pull/2560)
+- ESCOMP/CTSM#2585: Allow "manual" resets of all accumulator types (https://github.com/ESCOMP/CTSM/pull/2585)
+- ESCOMP/CTSM#2593: Optionally base GDD20 on per-gridcell windows, not per-hemisphere (https://github.com/ESCOMP/CTSM/pull/2593)
+- ESCOMP/CTSM#2661: Merge ctsm5.2.015 into scale-maturity-reqs (https://github.com/ESCOMP/CTSM/pull/2661)
+- ESCOMP/CTSM#2664: Enable new crop calendars for clm60 compsets (https://github.com/ESCOMP/CTSM/pull/2664)
+- ESCOMP/CTSM#2665: Merge new crop calendars into master (https://github.com/ESCOMP/CTSM/pull/2665)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.015
 Originator(s): multiple (Samuel Levis,UCAR/TSS,303-665-1310, @mvertens, @jedwards4b, @billsacks, @Katetc)
 Date: Mon 22 Jul 2024 12:46:17 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 9c6524b33d..f043ab8b34 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.016 samrabin 07/25/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof
        ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.
        ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2

From 542f7080432e76073ea2734be0ed50393e9a6bb8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 01:40:34 -0600
Subject: [PATCH 0791/1248] Wrap cropcal subroutine calls in use_crop.

Avoids issue with undefined pointer to crop_inst%rx_swindow_starts_thisyr_patch and probably other arrays.
---
 src/cpl/share_esmf/cropcalStreamMod.F90 |  1 +
 src/main/clm_driver.F90                 |  4 ++--
 src/main/clm_initializeMod.F90          | 26 +++++++++++++------------
 3 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 85218a0e1c..a39ba40754 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -14,6 +14,7 @@ module cropcalStreamMod
   use decompMod        , only : bounds_type
   use abortutils       , only : endrun
   use clm_varctl       , only : iulog
+  use clm_varctl       , only : use_crop
   use clm_varctl       , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams
   use clm_varctl       , only : adapt_cropcal_rx_cultivar_gdds
   use clm_varpar       , only : mxpft
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index 01c0ec409e..53b1e55f7c 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -475,7 +475,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
 
     ! When crop calendar streams are being used
     ! NOTE: This call needs to happen outside loops over nclumps (as streams are not threadsafe)
-    if (use_cropcal_streams .and. is_beg_curr_year()) then
+    if (use_crop .and. use_cropcal_streams .and. is_beg_curr_year()) then
       call cropcal_advance( bounds_proc )
     end if
 
@@ -1073,7 +1073,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
             frictionvel_inst, photosyns_inst, drydepvel_inst)
        call t_stopf('depvel')
 
-       if (use_cropcal_streams .and. is_beg_curr_year()) then
+       if (use_crop .and. use_cropcal_streams .and. is_beg_curr_year()) then
           ! ============================================================================
           ! Update crop calendars
           ! ============================================================================
diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index e8f70bdef8..0c0570c577 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -659,19 +659,21 @@ subroutine initialize2(ni,nj)
     end if
 
     ! Initialize crop calendars
-    call t_startf('init_cropcal')
-    call cropcal_init(bounds_proc)
-    if (use_cropcal_streams) then
-      call cropcal_advance( bounds_proc )
-      !$OMP PARALLEL DO PRIVATE (nc, bounds_clump)
-      do nc = 1,nclumps
-         call get_clump_bounds(nc, bounds_clump)
-         call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, &
-              filter_inactive_and_active(nc)%pcropp, .true., crop_inst)
-      end do
-      !$OMP END PARALLEL DO
+    if (use_crop) then
+      call t_startf('init_cropcal')
+      call cropcal_init(bounds_proc)
+      if (use_cropcal_streams) then
+        call cropcal_advance( bounds_proc )
+        !$OMP PARALLEL DO PRIVATE (nc, bounds_clump)
+        do nc = 1,nclumps
+           call get_clump_bounds(nc, bounds_clump)
+           call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, &
+                filter_inactive_and_active(nc)%pcropp, .true., crop_inst)
+        end do
+        !$OMP END PARALLEL DO
+      end if
+      call t_stopf('init_cropcal')
     end if
-    call t_stopf('init_cropcal')
 
     ! Initialize active history fields.
     ! This is only done if not a restart run. If a restart run, then this

From 126ce292f1380e96ff22750ec4cd0dc1a518e8d6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 07:49:53 -0600
Subject: [PATCH 0792/1248] Allocate first dim on dataptr2d_*_start/end arrays
 with begp:endp.

Instead of just :. Hopefully will eliminate too-high index errors in threading tests.
---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index a39ba40754..3fdf1ba06c 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -545,9 +545,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
     ! Read prescribed sowing window start dates from input files
     allocate(dataptr2d_swindow_start(lsize, ncft))
-    dataptr2d_swindow_start(:,:) = -1._r8
+    dataptr2d_swindow_start(begp:endp,:) = -1._r8
     allocate(dataptr2d_swindow_end  (lsize, ncft))
-    dataptr2d_swindow_end(:,:) = -1._r8
+    dataptr2d_swindow_end(begp:endp,:) = -1._r8
     if (use_cropcal_rx_swindows) then
        ! Starting with npcropmin will skip generic crops
        do n = 1, ncft
@@ -742,9 +742,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
   ! Read prescribed gdd20 season start dates from input files
   allocate(dataptr2d_gdd20_season_start(lsize, ncft))
-  dataptr2d_gdd20_season_start(:,:) = -1._r8
+  dataptr2d_gdd20_season_start(begp:endp,:) = -1._r8
   allocate(dataptr2d_gdd20_season_end  (lsize, ncft))
-  dataptr2d_gdd20_season_end(:,:) = -1._r8
+  dataptr2d_gdd20_season_end(begp:endp,:) = -1._r8
   if (stream_gdd20_seasons) then
      ! Starting with npcropmin will skip generic crops
      do n = 1, ncft

From b7a8fb58e2186d9d6b9dcd20b8b6c57301bfcd8e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 08:14:51 -0600
Subject: [PATCH 0793/1248] Allocate 2d arrays with begp:endp, not lsize.

Hopefully will eliminate too-high index errors in threading tests.
---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 3fdf1ba06c..36c6c78f22 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -544,9 +544,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     dayspyr = get_curr_days_per_year()
 
     ! Read prescribed sowing window start dates from input files
-    allocate(dataptr2d_swindow_start(lsize, ncft))
+    allocate(dataptr2d_swindow_start(begp:endp, ncft))
     dataptr2d_swindow_start(begp:endp,:) = -1._r8
-    allocate(dataptr2d_swindow_end  (lsize, ncft))
+    allocate(dataptr2d_swindow_end  (begp:endp, ncft))
     dataptr2d_swindow_end(begp:endp,:) = -1._r8
     if (use_cropcal_rx_swindows) then
        ! Starting with npcropmin will skip generic crops
@@ -631,7 +631,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     deallocate(dataptr2d_swindow_start)
     deallocate(dataptr2d_swindow_end)
    
-    allocate(dataptr2d_cultivar_gdds(lsize, ncft))
+    allocate(dataptr2d_cultivar_gdds(begp:endp, ncft))
     if (use_cropcal_rx_cultivar_gdds) then
        ! Read prescribed cultivar GDDs from input files
        ! Starting with npcropmin will skip generic crops
@@ -688,7 +688,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
    deallocate(dataptr2d_cultivar_gdds)
 
-   allocate(dataptr2d_gdd20_baseline(lsize, ncft))
+   allocate(dataptr2d_gdd20_baseline(begp:endp, ncft))
    if (adapt_cropcal_rx_cultivar_gdds) then
       ! Read GDD20 baselines from input files
       ! Starting with npcropmin will skip generic crops
@@ -741,9 +741,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
 
   ! Read prescribed gdd20 season start dates from input files
-  allocate(dataptr2d_gdd20_season_start(lsize, ncft))
+  allocate(dataptr2d_gdd20_season_start(begp:endp, ncft))
   dataptr2d_gdd20_season_start(begp:endp,:) = -1._r8
-  allocate(dataptr2d_gdd20_season_end  (lsize, ncft))
+  allocate(dataptr2d_gdd20_season_end  (begp:endp, ncft))
   dataptr2d_gdd20_season_end(begp:endp,:) = -1._r8
   if (stream_gdd20_seasons) then
      ! Starting with npcropmin will skip generic crops

From 63b66b66944e0bacf55da5e87f48a1a860ca9211 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 08:22:57 -0600
Subject: [PATCH 0794/1248] Add
 ERP_D_Ld10_P64x2.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-default to
 crop_calendars suite.

---
 cime_config/testdefs/testlist_clm.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index efeb011844..bb421c8e9e 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1016,6 +1016,7 @@
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>

From 7e04126d66429ee7419441538447bb3a3cc4b448 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 08:26:32 -0600
Subject: [PATCH 0795/1248] dataptr2d arrays' first dim is gridcell, not patch.

Hopefully will eliminate too-high index errors in threading tests.
---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 36c6c78f22..d19c74ad37 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -544,10 +544,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     dayspyr = get_curr_days_per_year()
 
     ! Read prescribed sowing window start dates from input files
-    allocate(dataptr2d_swindow_start(begp:endp, ncft))
-    dataptr2d_swindow_start(begp:endp,:) = -1._r8
-    allocate(dataptr2d_swindow_end  (begp:endp, ncft))
-    dataptr2d_swindow_end(begp:endp,:) = -1._r8
+    allocate(dataptr2d_swindow_start(bounds%begg:bounds%endg, ncft))
+    dataptr2d_swindow_start(bounds%begg:bounds%endg,:) = -1._r8
+    allocate(dataptr2d_swindow_end  (bounds%begg:bounds%endg, ncft))
+    dataptr2d_swindow_end(bounds%begg:bounds%endg,:) = -1._r8
     if (use_cropcal_rx_swindows) then
        ! Starting with npcropmin will skip generic crops
        do n = 1, ncft
@@ -563,7 +563,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
           end if
           ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
           ! So an explicit loop is required here
-          do g = 1,lsize
+          do g = bounds%begg, bounds%endg
 
              ! If read-in value is invalid, set to -1. Will be handled later in this subroutine.
              if (dataptr1d_swindow_start(g) <= 0 .or. dataptr1d_swindow_start(g) > dayspyr &
@@ -631,7 +631,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     deallocate(dataptr2d_swindow_start)
     deallocate(dataptr2d_swindow_end)
    
-    allocate(dataptr2d_cultivar_gdds(begp:endp, ncft))
+    allocate(dataptr2d_cultivar_gdds(bounds%begg:bounds%endg, ncft))
     if (use_cropcal_rx_cultivar_gdds) then
        ! Read prescribed cultivar GDDs from input files
        ! Starting with npcropmin will skip generic crops
@@ -688,7 +688,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
    deallocate(dataptr2d_cultivar_gdds)
 
-   allocate(dataptr2d_gdd20_baseline(begp:endp, ncft))
+   allocate(dataptr2d_gdd20_baseline(bounds%begg:bounds%endg, ncft))
    if (adapt_cropcal_rx_cultivar_gdds) then
       ! Read GDD20 baselines from input files
       ! Starting with npcropmin will skip generic crops
@@ -741,10 +741,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
 
   ! Read prescribed gdd20 season start dates from input files
-  allocate(dataptr2d_gdd20_season_start(begp:endp, ncft))
-  dataptr2d_gdd20_season_start(begp:endp,:) = -1._r8
-  allocate(dataptr2d_gdd20_season_end  (begp:endp, ncft))
-  dataptr2d_gdd20_season_end(begp:endp,:) = -1._r8
+  allocate(dataptr2d_gdd20_season_start(bounds%begg:bounds%endg, ncft))
+  dataptr2d_gdd20_season_start(bounds%begg:bounds%endg,:) = -1._r8
+  allocate(dataptr2d_gdd20_season_end  (bounds%begg:bounds%endg, ncft))
+  dataptr2d_gdd20_season_end(bounds%begg:bounds%endg,:) = -1._r8
   if (stream_gdd20_seasons) then
      ! Starting with npcropmin will skip generic crops
      do n = 1, ncft

From d47b28a5e3e44b66a11fc8055d57f24c02d8bbbc Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 08:36:47 -0600
Subject: [PATCH 0796/1248] Use begg and endg instead of lsize.

Hopefully will eliminate too-high index errors in threading tests.
---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index d19c74ad37..02cfc5e67a 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -507,7 +507,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     integer :: nc, fp
     integer :: dayspyr
     integer           :: n, g
-    integer           :: lsize
     integer           :: rc
     integer           :: begp, endp
     real(r8), pointer :: dataptr1d_swindow_start(:)
@@ -536,7 +535,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
     ! Get pointer for stream data that is time and spatially interpolate to model time and grid
     ! Place all data from each type into a temporary 2d array
-    lsize = bounds%endg - bounds%begg + 1
 
     begp = bounds%begp
     endp = bounds%endp
@@ -644,7 +642,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
           ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
           ! So an explicit loop is required here
-          do g = 1,lsize
+          do g = bounds%begg, bounds%endg
    
              !  If read-in value is invalid, have PlantCrop() set gddmaturity to PFT-default value.
              if (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000._r8) then
@@ -672,8 +670,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
              ! vegetated pft
              ig = g_to_ig(patch%gridcell(p))
 
-             if (ig > lsize) then
-                 write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')'
+             if (ig < bounds%begg .or. ig > bounds%endg) then
+                 write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,')  < begg (',bounds%begg,') or > endg (',bounds%endg,')'
                  call ESMF_Finalize(endflag=ESMF_END_ABORT)
              end if
 
@@ -701,7 +699,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
          ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
          ! So an explicit loop is required here
-         do g = 1,lsize
+         do g = bounds%begg, bounds%endg
             dataptr2d_gdd20_baseline(g,n) = dataptr1d_gdd20_baseline(g)
          end do
       end do
@@ -723,8 +721,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
             ! vegetated pft
             ig = g_to_ig(patch%gridcell(p))
 
-            if (ig > lsize) then
-                write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')'
+            if (ig < bounds%begg .or. ig > bounds%endg) then
+                write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,')  < begg (',bounds%begg,') or > endg (',bounds%endg,')'
                 call ESMF_Finalize(endflag=ESMF_END_ABORT)
             end if
 
@@ -760,7 +758,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
         end if
         ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
         ! So an explicit loop is required here
-        do g = 1,lsize
+        do g = bounds%begg, bounds%endg
 
            ! If read-in value is invalid, set to -1. Will be handled later in this subroutine.
            if (dataptr1d_gdd20_season_start(g) <= 0 .or. dataptr1d_gdd20_season_start(g) > 366 &

From 2156c7206c61a131d3a4a6da69940acafb3d1dcf Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 08:40:18 -0600
Subject: [PATCH 0797/1248] Use begg/endg instead of referring to bounds%.

---
 src/cpl/share_esmf/cropcalStreamMod.F90 | 51 ++++++++++++++-----------
 1 file changed, 29 insertions(+), 22 deletions(-)

diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90
index 02cfc5e67a..5587641c21 100644
--- a/src/cpl/share_esmf/cropcalStreamMod.F90
+++ b/src/cpl/share_esmf/cropcalStreamMod.F90
@@ -422,6 +422,7 @@ subroutine cropcal_advance( bounds )
     !
     ! !LOCAL VARIABLES:
     integer :: g, ig   ! Indices
+    integer :: begg, endg  ! gridcell bounds
     integer :: year    ! year (0, ...) for nstep+1
     integer :: mon     ! month (1, ..., 12) for nstep+1
     integer :: day     ! day of month (1, ..., 31) for nstep+1
@@ -430,6 +431,9 @@ subroutine cropcal_advance( bounds )
     integer :: rc
     !-----------------------------------------------------------------------
 
+    begg = bounds%begg
+    endg = bounds%endg
+
     call get_curr_date(year, mon, day, sec)
     mcdate = year*10000 + mon*100 + day
     if (use_cropcal_rx_swindows) then
@@ -471,9 +475,9 @@ subroutine cropcal_advance( bounds )
     end if
 
     if ( .not. allocated(g_to_ig) )then
-       allocate (g_to_ig(bounds%begg:bounds%endg) )
+       allocate (g_to_ig(begg:endg) )
        ig = 0
-       do g = bounds%begg,bounds%endg
+       do g = begg,endg
           ig = ig+1
           g_to_ig(g) = ig
        end do
@@ -508,6 +512,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     integer :: dayspyr
     integer           :: n, g
     integer           :: rc
+    integer           :: begg, endg
     integer           :: begp, endp
     real(r8), pointer :: dataptr1d_swindow_start(:)
     real(r8), pointer :: dataptr1d_swindow_end  (:)
@@ -530,8 +535,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
          gdd20_season_ends   => crop_inst%gdd20_season_end_patch    &
          )
 
-    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__)
-    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__)
+    begg = bounds%begg
+    endg = bounds%endg
+    SHR_ASSERT_FL( (lbound(g_to_ig,1) <= begg ), sourcefile, __LINE__)
+    SHR_ASSERT_FL( (ubound(g_to_ig,1) >= endg ), sourcefile, __LINE__)
 
     ! Get pointer for stream data that is time and spatially interpolate to model time and grid
     ! Place all data from each type into a temporary 2d array
@@ -542,10 +549,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     dayspyr = get_curr_days_per_year()
 
     ! Read prescribed sowing window start dates from input files
-    allocate(dataptr2d_swindow_start(bounds%begg:bounds%endg, ncft))
-    dataptr2d_swindow_start(bounds%begg:bounds%endg,:) = -1._r8
-    allocate(dataptr2d_swindow_end  (bounds%begg:bounds%endg, ncft))
-    dataptr2d_swindow_end(bounds%begg:bounds%endg,:) = -1._r8
+    allocate(dataptr2d_swindow_start(begg:endg, ncft))
+    dataptr2d_swindow_start(begg:endg,:) = -1._r8
+    allocate(dataptr2d_swindow_end  (begg:endg, ncft))
+    dataptr2d_swindow_end(begg:endg,:) = -1._r8
     if (use_cropcal_rx_swindows) then
        ! Starting with npcropmin will skip generic crops
        do n = 1, ncft
@@ -561,7 +568,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
           end if
           ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
           ! So an explicit loop is required here
-          do g = bounds%begg, bounds%endg
+          do g = begg, endg
 
              ! If read-in value is invalid, set to -1. Will be handled later in this subroutine.
              if (dataptr1d_swindow_start(g) <= 0 .or. dataptr1d_swindow_start(g) > dayspyr &
@@ -629,7 +636,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
     deallocate(dataptr2d_swindow_start)
     deallocate(dataptr2d_swindow_end)
    
-    allocate(dataptr2d_cultivar_gdds(bounds%begg:bounds%endg, ncft))
+    allocate(dataptr2d_cultivar_gdds(begg:endg, ncft))
     if (use_cropcal_rx_cultivar_gdds) then
        ! Read prescribed cultivar GDDs from input files
        ! Starting with npcropmin will skip generic crops
@@ -642,7 +649,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
           ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
           ! So an explicit loop is required here
-          do g = bounds%begg, bounds%endg
+          do g = begg, endg
    
              !  If read-in value is invalid, have PlantCrop() set gddmaturity to PFT-default value.
              if (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000._r8) then
@@ -670,8 +677,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
              ! vegetated pft
              ig = g_to_ig(patch%gridcell(p))
 
-             if (ig < bounds%begg .or. ig > bounds%endg) then
-                 write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,')  < begg (',bounds%begg,') or > endg (',bounds%endg,')'
+             if (ig < begg .or. ig > endg) then
+                 write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,')  < begg (',begg,') or > endg (',endg,')'
                  call ESMF_Finalize(endflag=ESMF_END_ABORT)
              end if
 
@@ -686,7 +693,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
    deallocate(dataptr2d_cultivar_gdds)
 
-   allocate(dataptr2d_gdd20_baseline(bounds%begg:bounds%endg, ncft))
+   allocate(dataptr2d_gdd20_baseline(begg:endg, ncft))
    if (adapt_cropcal_rx_cultivar_gdds) then
       ! Read GDD20 baselines from input files
       ! Starting with npcropmin will skip generic crops
@@ -699,7 +706,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
          ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
          ! So an explicit loop is required here
-         do g = bounds%begg, bounds%endg
+         do g = begg, endg
             dataptr2d_gdd20_baseline(g,n) = dataptr1d_gdd20_baseline(g)
          end do
       end do
@@ -721,8 +728,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
             ! vegetated pft
             ig = g_to_ig(patch%gridcell(p))
 
-            if (ig < bounds%begg .or. ig > bounds%endg) then
-                write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,')  < begg (',bounds%begg,') or > endg (',bounds%endg,')'
+            if (ig < begg .or. ig > endg) then
+                write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,')  < begg (',begg,') or > endg (',endg,')'
                 call ESMF_Finalize(endflag=ESMF_END_ABORT)
             end if
 
@@ -739,10 +746,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
 
 
   ! Read prescribed gdd20 season start dates from input files
-  allocate(dataptr2d_gdd20_season_start(bounds%begg:bounds%endg, ncft))
-  dataptr2d_gdd20_season_start(bounds%begg:bounds%endg,:) = -1._r8
-  allocate(dataptr2d_gdd20_season_end  (bounds%begg:bounds%endg, ncft))
-  dataptr2d_gdd20_season_end(bounds%begg:bounds%endg,:) = -1._r8
+  allocate(dataptr2d_gdd20_season_start(begg:endg, ncft))
+  dataptr2d_gdd20_season_start(begg:endg,:) = -1._r8
+  allocate(dataptr2d_gdd20_season_end  (begg:endg, ncft))
+  dataptr2d_gdd20_season_end(begg:endg,:) = -1._r8
   if (stream_gdd20_seasons) then
      ! Starting with npcropmin will skip generic crops
      do n = 1, ncft
@@ -758,7 +765,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, init, crop_inst)
         end if
         ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize
         ! So an explicit loop is required here
-        do g = bounds%begg, bounds%endg
+        do g = begg, endg
 
            ! If read-in value is invalid, set to -1. Will be handled later in this subroutine.
            if (dataptr1d_gdd20_season_start(g) <= 0 .or. dataptr1d_gdd20_season_start(g) > 366 &

From b1aed3f36e79cb8eaf278f1a72be77de88ad1c64 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 09:12:57 -0600
Subject: [PATCH 0798/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 13 ++++++-------
 doc/ChangeSum |  2 +-
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 501a67720f..88c322e990 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.016
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
-Date: Thu Jul 25 22:39:39 MST 2024
+Date: Fri 26 Jul 2024 09:11:52 AM MDT
 One-line Summary: Enable new crop calendars for clm60 compsets
 
 Purpose and description of changes
@@ -89,22 +89,21 @@ Note that testmods marked "experimental" are fine to be marked as expected failu
 Testing summary:
 ----------------
 
-[Remove any lines that don't apply.]
-
  [PASS means all tests PASS; OK means tests PASS other than expected fails.]
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho -
+    derecho - FAIL
+       1x1_cidadinhoBR tests only. That's fine. Filed Issue #2666: 1x1_cidadinhoBR tests fail in build-namelist_test.pl (https://github.com/ESCOMP/CTSM/issues/2666).
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
-    (any machine) -
+    derecho - PASS
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho -----
-    izumi -------
+    derecho ----- OK
+    izumi ------- OK
 
 Answer changes
 --------------
diff --git a/doc/ChangeSum b/doc/ChangeSum
index f043ab8b34..edc9e4cada 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.016 samrabin 07/25/2024 Enable new crop calendars for clm60 compsets
+       ctsm5.2.016 samrabin 07/26/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof
        ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.
        ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2

From d393cbfcdad4ed023cf97736265e819e6c195687 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 26 Jul 2024 09:14:00 -0700
Subject: [PATCH 0799/1248] update fates tag

This addresses #2656
---
 .gitmodules | 2 +-
 src/fates   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 19bc024208..4e9f5b51fb 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.77.1_api.36.0.0
+fxtag = sci.1.77.2_api.36.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
diff --git a/src/fates b/src/fates
index 1982b0032c..e372f0b6cd 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit 1982b0032c3cab6278892eccb85f643114ffb1af
+Subproject commit e372f0b6cdf46f76f888ee6ac92d9a3572464e8b

From 66e28d184b6d68f55c8ac2bf3d26b5d46399e7bb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 26 Jul 2024 12:12:23 -0600
Subject: [PATCH 0800/1248] Changes one Izumi test from f19 to 10x15
 resolution.

- Was: ERS_D.f19_g17.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup
- Now: ERS_D.f10_f10_mg37.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup

Fixes ESCOMP/CTSM#2667: Change out a f19 resolution test on Izumi for f10 (https://github.com/ESCOMP/CTSM/issues/2667)
---
 cime_config/testdefs/testlist_clm.xml | 8 ++++++++
 doc/ChangeLog                         | 9 +++++----
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index bb421c8e9e..951e0d8d5b 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -863,6 +863,14 @@
   <test name="ERS_D" grid="f19_g17" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:20:00</option>
+      <option name="comment"  >Run in DEBUG with the matrix solution on for spinup with all options it interacts with (requires Bgc, but also turn on Crop and Carbon isotopes)</option>
+    </options>
+  </test>
+  <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
+    <machines>
       <machine name="izumi"    compiler="nag" category="aux_clm"/>
     </machines>
     <options>
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 88c322e990..0057567561 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.016
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
-Date: Fri 26 Jul 2024 09:11:52 AM MDT
+Date: Fri Jul 26 12:20:46 MDT 2024
 One-line Summary: Enable new crop calendars for clm60 compsets
 
 Purpose and description of changes
@@ -35,12 +35,10 @@ Bugs fixed
 
 List of CTSM issues fixed (include CTSM Issue # and description):
 - Fixes ESCOMP/CTSM#2584: Reset accumulators to initval instead of 0 (https://github.com/ESCOMP/CTSM/issues/2584)
+- Fixes ESCOMP/CTSM#2667: Change out a f19 resolution test on Izumi for f10 (https://github.com/ESCOMP/CTSM/issues/2667)
 
 Notes of particular relevance for users
 ---------------------------------------
-[Remove any lines that don't apply. Remove entire section if nothing applies.]
-
-Caveats for users (e.g., need to interpolate initial conditions):
 
 Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
 - Add cropcals_rx, default false.
@@ -82,6 +80,9 @@ Changes to tests or testing:
   - StreamGDD20Seasons (experimental)
 - Removes sowingWindows testmod
 - Adds and changes various tests related to crop calendars
+- Changes one Izumi test from f19 to 10x15 resolution:
+  - Was: ERS_D.f19_g17.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup
+  - Now: ERS_D.f10_f10_mg37.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup
 
 Note that testmods marked "experimental" are fine to be marked as expected failures, if needed.
 

From 3ee733375e55e024054904244bf341526b70fc23 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 26 Jul 2024 13:31:35 -0600
Subject: [PATCH 0801/1248] Bring in changes from Danny into the soil state
 functions, and update dust unit tests to use the appropriate ones for Zender
 and Leung tests, add tests for the new MassFracClayLeung2023 function, get
 the unit tests all working again

---
 .../DustEmis_test/test_DustEmisLeung2023.pf   |  4 +--
 .../DustEmis_test/test_DustEmisZender2003.pf  |  6 ++---
 src/biogeophys/SoilStateInitTimeConstMod.F90  | 24 ++++++++++++++---
 .../test_dust_soil_clay_functions.pf          | 17 +++++++++++-
 src/unit_test_shr/unittestDustEmisInputs.F90  | 27 ++++++++++++++++---
 5 files changed, 64 insertions(+), 14 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
index 5fdf20b89d..2b87f4be0a 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
@@ -35,10 +35,10 @@ contains
     ! Allocate and initialize the test object for input objects dust-emission needs
     character(len=5) :: NLFilename = 'none'
 
-    call this%input%setUp()
+    dust_emis_method = 'Leung_2023'
+    call this%input%setUp( dust_emis_method=dust_emis_method )
  
     ! Create the dust emission object last
-    dust_emis_method = 'Leung_2023'
     allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))
   end subroutine setUp
 
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
index 212da0af5a..db5b54aa08 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf
@@ -107,7 +107,7 @@ contains
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
                                vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
                                vlc_trb_4=vlc_trb_4)
-       @assertEqual( flx_mss_vrt_dst_tot, 1.208384635884010d-5, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 2.583480541056971d-6, tolerance=tol )
        @assertEqual( vlc_trb_1, 3.407721147709135d-003, tolerance=tol )
        @assertEqual( vlc_trb_2, 4.961153753164878d-003, tolerance=tol )
        @assertEqual( vlc_trb_3, 4.980100969983446d-003, tolerance=tol )
@@ -270,7 +270,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust0 = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 1.063573374792962d-4, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 2.273879554711299d-5, tolerance=tol )
     end do
     ! Double u10 and show result is higher
     call this%input%create_fv( u10=u10*2.0_r8, fv=fv)
@@ -282,7 +282,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust_higher = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 1.774023264204829d-4, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 3.792794484764924d-5, tolerance=tol )
     end do
     @assertGreaterThan( total_dust_higher, total_dust0 )
 
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index ce051514bd..f03e1f83c7 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -10,6 +10,8 @@ module SoilStateInitTimeConstMod
   use LandunitType  , only : lun                
   use ColumnType    , only : col                
   use PatchType     , only : patch                
+  use abortUtils    , only : endrun
+  use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
   !
   implicit none
   private
@@ -22,6 +24,7 @@ module SoilStateInitTimeConstMod
   public :: ThresholdSoilMoistZender2003
   public :: ThresholdSoilMoistKok2014
   public :: MassFracClay
+  public :: MassFracClayLeung2023
   !
   ! !PRIVATE MEMBER FUNCTIONS:
   private :: ReadNL
@@ -177,6 +180,7 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     use clm_varcon          , only : secspday, denh2o, denice, grlnd
     use clm_varctl          , only : use_cn, use_lch4, use_fates
     use clm_varctl          , only : iulog, fsurdat, paramfile, soil_layerstruct_predefined
+    use clm_varctl          , only : dust_emis_method
     use landunit_varcon     , only : istdlak, istwet, istsoil, istcrop, istice
     use column_varcon       , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv 
     use fileutils           , only : getfil
@@ -717,7 +721,11 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
        g = col%gridcell(c)
 
        soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay3d(g,1) )
-       soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay3d(g,1) )
+       if ( trim(dust_emis_method) == "Leung_2023" ) then
+          soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClayLeung2023( clay3d(g,1) )
+       else
+          soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay3d(g,1) )
+       end if
 
     end do
 
@@ -757,8 +765,6 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
   ! Notes from: dmleung 19 Feb 2024.
   !
   !------------------------------------------------------------------------------
-      use abortUtils    , only : endrun
-      use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
       if ( clay < 0.0_r8 .or. clay > 100.0_r8 )then
@@ -800,9 +806,19 @@ real(r8) function MassFracClay( clay )
       real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%)
 
       MassFracClay = min(clay * 0.01_r8, 0.20_r8)
-      MassFracClay = 0.1_r8 + MassFracClay * 0.1_r8 / 0.20_r8   ! dmleung added this line to reduce the sensitivity of dust emission flux to clay fraction in DUSTMod. 5 Jul 2024
   end function MassFracClay
 
   !------------------------------------------------------------------------------
 
+  real(r8) function MassFracClayLeung2023( clay )
+  ! Calculate the mass fraction of clay needed for dust emission, based on clay content
+  ! Based on the base Zender_2003 version, with a slight modification for Leung_2023
+      real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%)
+
+      MassFracClayLeung2023 = MassFracClay( clay )
+      MassFracClayLeung2023 = 0.1_r8 + MassFracClayLeung2023 * 0.1_r8 / 0.20_r8   ! dmleung added this line to reduce the sensitivity of dust emission flux to clay fraction in DUSTMod. 5 Jul 2024
+  end function MassFracClayLeung2023
+
+  !------------------------------------------------------------------------------
+
 end module SoilStateInitTimeConstMod
diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
index 867e7ace6a..53a3d66987 100644
--- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
@@ -70,7 +70,7 @@ contains
     real(r8) :: value
 
     value = MassFracClay( 0.0_r8 )
-    @assertEqual( value, 0.1_r8, tolerance=tol )
+    @assertEqual( value, 0.0_r8, tolerance=tol )
     value = MassFracClay( 20.0_r8 )
     @assertEqual( value, 0.20_r8, tolerance=tol )
     value = MassFracClay( 25.0_r8 )
@@ -78,4 +78,19 @@ contains
 
   end subroutine TestClayMassFracValues
 
+
+  @Test
+  subroutine TestClayMassFracValuesLeung2023(this)
+    class(TestDustEmisSoilFunctions), intent(inout) :: this
+    real(r8) :: value
+
+    value = MassFracClayLeung2023( 0.0_r8 )
+    @assertEqual( value, 0.1_r8, tolerance=tol )
+    value = MassFracClayLeung2023( 20.0_r8 )
+    @assertEqual( value, 0.20_r8, tolerance=tol )
+    value = MassFracClayLeung2023( 25.0_r8 )
+    @assertEqual( value, 0.20_r8, tolerance=tol )
+
+  end subroutine TestClayMassFracValuesLeung2023
+  
 end module test_dust_soil_clay_functions
diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90
index 6b15680ef7..d272002638 100644
--- a/src/unit_test_shr/unittestDustEmisInputs.F90
+++ b/src/unit_test_shr/unittestDustEmisInputs.F90
@@ -16,6 +16,8 @@ module unittestDustEmisInputs
   use FrictionVelocityMod, only : frictionvel_type
   use unittestWaterTypeFactory, only : unittest_water_type_factory_type
   use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, MassFracClay
+  use SoilStateInitTimeConstMod, only : MassFracClayLeung2023
+  use abortutils, only : endrun
 
   implicit none
   private
@@ -43,9 +45,10 @@ module unittestDustEmisInputs
 
   !-----------------------------------------------------------------------
 
-  subroutine setUp(this)
+  subroutine setUp(this, dust_emis_method)
     use ColumnType, only : col
     class(unittest_dust_emis_input_type), intent(inout) :: this
+    character(len=*), intent(in), optional :: dust_emis_method
     ! Allocate and initiatlize the test object for input objects dust-emission needs
 
     character(len=5) :: NLFilename = 'none'
@@ -54,6 +57,14 @@ subroutine setUp(this)
     integer :: c
     type(atm2lnd_params_type) :: atm2lnd_params
     integer, parameter :: snl = 3
+    character(len=50) :: in_dust_emis_method
+
+    !-----------------------------------------------------------------------
+    if ( present(dust_emis_method) )then
+       in_dust_emis_method = trim(dust_emis_method)
+    else
+       in_dust_emis_method = "Zender_2003"
+    end if
 
     ! Settings needed for clm_varpar
     soil_layerstruct_predefined = '20SL_8.5m'
@@ -83,7 +94,7 @@ subroutine setUp(this)
     call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
     ! Water and soil state -- after the subgrid setup
     call this%water_factory%setup_after_subgrid(snl = snl)
-    call this%setupSoilState( )   ! This needs to happen before the water_type object creation
+    call this%setupSoilState( in_dust_emis_method )   ! This needs to happen before the water_type object creation
     call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
     ! Canopy state, friction velocity, and temperature state ojects
     call this%canopystate_inst%SetNMLForTesting()
@@ -113,7 +124,7 @@ end subroutine tearDown
 
   !-----------------------------------------------------------------------
 
-  subroutine setupSoilState(this)
+  subroutine setupSoilState(this, dust_emis_method)
     !
     ! !DESCRIPTION:
     ! Sets up the external environment used by Dust emissions - i.e., things accessed via
@@ -125,6 +136,7 @@ subroutine setupSoilState(this)
     use ColumnType, only : col
     use GridcellType, only : grc
     class(unittest_dust_emis_input_type), intent(in) :: this
+    character(len=*), intent(in) :: dust_emis_method
     !
     integer :: c,j
     real(r8), parameter :: clay = 10.0_r8
@@ -145,7 +157,14 @@ subroutine setupSoilState(this)
     ! These are needed for dust emissions initialization
     do c = bounds%begc, bounds%endc
        this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay )
-       this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
+       if ( trim(dust_emis_method) == "Zender_2003")then
+          this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay )
+       else if ( trim(dust_emis_method) == "Leung_2023")then
+          this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClayLeung2023( clay )
+       else
+          print *, 'dust_emis_method = ', trim(dust_emis_method)
+          call endrun("ERROR: do NOT know about this dust_emis_method")
+       end if
     end do
 
   end subroutine setupSoilState

From cc96bedc0b848d251c1a959598b06a11bbf10e4b Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Sat, 27 Jul 2024 08:58:51 -0700
Subject: [PATCH 0802/1248] fix fates history output type in LUH2 tests

---
 .../testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
index 6478669bee..55650230a4 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
@@ -8,4 +8,4 @@ use_fates_fixed_biogeog = .true.
 use_fates_sp = .false.
 use_fates_potentialveg = .false.
 hist_fincl1 = 'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU',
-'FATES_TRANSITIONS_MATRIX_LULU'
+'FATES_TRANSITION_MATRIX_LULU'

From 2422cef7f1e0ef1cc184eb51c0f973f2125396e9 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 27 Jul 2024 17:15:10 -0600
Subject: [PATCH 0803/1248] Update date on Change files

---
 doc/ChangeLog | 2 +-
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 0057567561..79d640242d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.016
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
-Date: Fri Jul 26 12:20:46 MDT 2024
+Date: Sat 27 Jul 2024 05:13:08 PM MDT
 One-line Summary: Enable new crop calendars for clm60 compsets
 
 Purpose and description of changes
diff --git a/doc/ChangeSum b/doc/ChangeSum
index edc9e4cada..382e5cf7cb 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.016 samrabin 07/26/2024 Enable new crop calendars for clm60 compsets
+       ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof
        ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.
        ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2

From ef8acabe22df4925f33b7e09172a2af5fb73c28a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 28 Jul 2024 12:49:55 -0600
Subject: [PATCH 0804/1248] Bring in actuall Leung_2023 DustEmissions
 subroutine, unit test fails because of change in answers

---
 src/biogeochem/DustEmisLeung2023.F90 | 331 +++++++++++++++++++++------
 1 file changed, 260 insertions(+), 71 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 0acd254c92..f6cd6bed89 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -24,8 +24,8 @@ module DustEmisLeung2023
   use atm2lndType          , only : atm2lnd_type
   use SoilStateType        , only : soilstate_type
   use CanopyStateType      , only : canopystate_type
-  use WaterStateBulkType       , only : waterstatebulk_type
-  use WaterDiagnosticBulkType       , only : waterdiagnosticbulk_type
+  use WaterStateBulkType   , only : waterstatebulk_type
+  use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type
   use FrictionVelocityMod  , only : frictionvel_type
   use LandunitType         , only : lun
   use PatchType            , only : patch
@@ -47,7 +47,7 @@ module DustEmisLeung2023
       real(r8), pointer, private :: dst_emiss_coeff_patch     (:)   ! dust emission coefficient (unitless)
       real(r8), pointer, private :: wnd_frc_thr_patch         (:)   ! wet fluid threshold (m/s)
       real(r8), pointer, private :: wnd_frc_thr_dry_patch     (:)   ! dry fluid threshold (m/s)
-      real(r8), pointer, private :: wnd_frc_thr_it_patch     (:)   ! impact threshold (m/s)
+      real(r8), pointer, private :: wnd_frc_thr_it_patch      (:)   ! impact threshold (m/s)
       real(r8), pointer, private :: lnd_frc_mble_patch        (:)   ! land mobile fraction
       real(r8), pointer, private :: liq_frac_patch            (:)   ! liquid fraction of total water
       real(r8), pointer, private :: wnd_frc_soil_patch        (:)   ! soil wind friction velocity (m/s)
@@ -62,7 +62,7 @@ module DustEmisLeung2023
       real(r8), pointer, private :: prb_crs_fld_thr_patch     (:)   ! probability of wind speed crossing fluid threshold
       real(r8), pointer, private :: prb_crs_impct_thr_patch   (:)   ! probability of wind speed crossing impact threshold
       real(r8), pointer, private :: ssr_patch                 (:)   ! [dimless] integrated shear stress ratiio, defined by Okin (2008) and then integrated by Caroline Pierre et al. (2014)
-      real(r8), pointer, private :: vai_Okin_patch             (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin drag partition
+      real(r8), pointer, private :: vai_Okin_patch            (:)   ! [m2 leaf /m2 land] LAI+SAI for calculating Okin drag partition
       real(r8), pointer, private :: frc_thr_rghn_fct_patch    (:)   ! [dimless] hybrid drag partition (or called roughness) factor
       real(r8), pointer, private :: wnd_frc_thr_std_patch     (:)   ! standardized fluid threshold friction velocity (m/s)
       type(prigent_roughness_stream_type), private :: prigent_roughness_stream      ! Prigent roughness stream data
@@ -316,7 +316,7 @@ subroutine InitCold(this, bounds)
     !
     ! !LOCAL VARIABLES:
     !-----------------------------------------------------------------------
-          ! Caulculate Drag Partition factor (Marticorena and Bergametti 1995 formulation)
+    ! Calculate Drag Partition factor (Marticorena and Bergametti 1995 formulation)
     if ( this%prigent_roughness_stream%useStreams() )then !if usestreams == true, and it should be always true
       call this%CalcDragPartition( bounds )
     else
@@ -367,8 +367,6 @@ subroutine DustEmission (this, bounds, &
     real(r8) :: flx_mss_vrt_dst_ttl(bounds%begp:bounds%endp)
     real(r8) :: frc_thr_wet_fct
     real(r8) :: frc_thr_rgh_fct
-    real(r8) :: wnd_frc_thr_slt
-    real(r8) :: wnd_rfr_thr_slt
     real(r8) :: wnd_frc_slt
     real(r8) :: lnd_frc_mbl(bounds%begp:bounds%endp)
     real(r8) :: bd
@@ -378,20 +376,48 @@ subroutine DustEmission (this, bounds, &
     real(r8) :: sumwt(bounds%begl:bounds%endl) ! sum of weights
     logical  :: found                          ! temporary for error check
     integer  :: index
+
+    real(r8) :: tmp2                ! calculates the dry fluid threshold using Shao and Lu (2000) scheme;
+                                    ! replace the tmp1 (Iversen and White, 1982) that was passed from Dustini to DustEmission;
+                                    ! tmp2 will be calculated here
+    real(r8) :: wnd_frc_thr_slt_std ! [m/s] The soil threshold friction speed at standard air density (1.2250 kg/m3)
+    real(r8) :: frag_expt           ! fragmentation exponent
+    real(r8) :: wnd_frc_thr_slt_it  ! [m/s] created for impact threshold friction velocity
+    real(r8) :: wnd_frc_thr_slt     ! [m/s] used for wet fluid threshold friction velocity
+    real(r8) :: K_length            ! [dimless] normalized mean interobstacle distance, or called gap length (Okin, 2008)
+    real(r8) :: bare_frc            ! LUH2 bare soil land cover fraction
+    real(r8) :: veg_frc             ! LUH2 natural vegetation + crop land cover fraction
     !
     ! constants
     !
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
-    real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
+    real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests 1, and Zender's scheme uses 0.3
+
+    real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient
+    real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent
+    real(r8), parameter :: Ce = 2.0_r8                 ! [dimless] proportionality constant scaling exponential dependence of dust emission coefficient on standardized soil threshold friction speed
+    real(r8), parameter :: C_tune = 0.05_r8            ! [dimless] global tuning constant for vertical dust flux; set to produce ~same global dust flux in control sim (I_2000) as old parameterization
+    real(r8), parameter :: wnd_frc_thr_slt_std_min = 0.16_r8 ! [m/s] minimum standardized soil threshold friction speed
+    real(r8), parameter :: forc_rho_std = 1.2250_r8    ! [kg/m3] density of air at standard pressure (101325) and temperature (293 K)
+    real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles
+    real(r8), parameter :: B_it = 0.82_r8              ! [dimless] ratio = u_star_it / u_star_ft0
+    real(r8), parameter :: k = 0.4_r8                  ! [dimless] von Karman constant
+    real(r8), parameter :: f_0 = 0.32_r8               ! [dimless] SSR in the immediate lee of a plant
+    real(r8), parameter :: c_e = 4.8_r8                ! [dimless] e-folding distance velocity recovery
+    real(r8), parameter :: D_p = 130e-6_r8             ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2023). dmleung 16 Feb 2024
+    real(r8), parameter :: gamma_Shao = 1.65e-4_r8     ! [kg s-2] interparticle cohesion: fitting parameter in Shao and Lu (2000) (S&L00). dmleung 16 Feb 2024
+    real(r8), parameter :: A_Shao = 0.0123_r8          ! [dimless] coefficient for aerodynamic force: fitting parameter in Shao and Lu (2000). dmleung 16 Feb 2024
+    real(r8), parameter :: frag_expt_thr = 5.0_r8      ! [dimless] threshold for fragmentation exponent defined in Leung et al. (2023), somewhere within 3 to 5. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024
+    real(r8), parameter :: z0a_glob = 1e-4_r8          ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
+    real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
+    real(r8), parameter :: vai0_Okin = 0.1_r8          ! [m2/m2] minimum VAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
+    real(r8), parameter :: zii = 1000.0_r8             ! [m] convective boundary layer height added by dmleung 20 Feb 2024, following other CTSM modules (e.g., CanopyFluxesMod). Should we transfer PBL height (PBLH) from CAM?
+    real(r8) :: numer                                  ! Numerator term for threshold crossing rate
+    real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     character(len=*),parameter :: subname = 'DUSTEmission'
     !------------------------------------------------------------------------
 
-    write(iulog,*)
-    write(iulog,*)
-    write(iulog,*) subname//'::WARNING: CURRENTLY THIS IS JUST THE ZENDER 2003 VERIONS OF DUST EMISSIONS!'
-    write(iulog,*)
-    write(iulog,*)
     associate(                                                         &
          forc_rho            => atm2lnd_inst%forc_rho_downscaled_col , & ! Input:  [real(r8) (:)   ]  downscaled density (kg/m**3)
 
@@ -402,16 +428,40 @@ subroutine DustEmission (this, bounds, &
          tlai                => canopystate_inst%tlai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided leaf area index, no burying by snow
          tsai                => canopystate_inst%tsai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided stem area index, no burying by snow
 
-         frac_sno            => waterdiagnosticbulk_inst%frac_sno_col         , & ! Input:  [real(r8) (:)   ]  fraction of ground covered by snow (0 to 1)
-         h2osoi_vol          => waterstatebulk_inst%h2osoi_vol_col       , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (0<=h2osoi_vol<=watsat)
-         h2osoi_liq          => waterstatebulk_inst%h2osoi_liq_col       , & ! Input:  [real(r8) (:,:) ]  liquid soil water (kg/m2)
-         h2osoi_ice          => waterstatebulk_inst%h2osoi_ice_col       , & ! Input:  [real(r8) (:,:) ]  frozen soil water (kg/m2)
+         frac_sno            => waterdiagnosticbulk_inst%frac_sno_col, & ! Input:  [real(r8) (:)   ]  fraction of ground covered by snow (0 to 1)
+         h2osoi_vol          => waterstatebulk_inst%h2osoi_vol_col   , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (0<=h2osoi_vol<=watsat)
+         h2osoi_liq          => waterstatebulk_inst%h2osoi_liq_col   , & ! Input:  [real(r8) (:,:) ]  liquid soil water (kg/m2)
+         h2osoi_ice          => waterstatebulk_inst%h2osoi_ice_col   , & ! Input:  [real(r8) (:,:) ]  frozen soil water (kg/m2)
 
          fv                  => frictionvel_inst%fv_patch            , & ! Input:  [real(r8) (:)   ]  friction velocity (m/s) (for dust model)
          u10                 => frictionvel_inst%u10_patch           , & ! Input:  [real(r8) (:)   ]  10-m wind (m/s) (created for dust model)
 
          flx_mss_vrt_dst     => this%flx_mss_vrt_dst_patch           , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)
-         flx_mss_vrt_dst_tot => this%flx_mss_vrt_dst_tot_patch         & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
+         flx_mss_vrt_dst_tot => this%flx_mss_vrt_dst_tot_patch       , & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
+         ! below variables are defined in Kok et al. (2014) or (mostly) Leung et al. (2023) dust emission scheme. dmleung 16 Feb 2024
+         dst_emiss_coeff     => this%dst_emiss_coeff_patch           , & ! Output dust emission coefficient
+         wnd_frc_thr         => this%wnd_frc_thr_patch               , & ! output fluid threshold
+         wnd_frc_thr_dry     => this%wnd_frc_thr_dry_patch           , & ! output dry fluid threshold
+         wnd_frc_thr_it      => this%wnd_frc_thr_it_patch            , & ! output impact threshold
+         lnd_frc_mble        => this%lnd_frc_mble_patch              , & ! output bare land fraction
+         wnd_frc_soil        => this%wnd_frc_soil_patch              , & ! soil friction velocity u_*s = (u_*)(f_eff)
+         gwc                 => this%gwc_patch                       , & ! output gravimetric water content
+         liq_frac            => this%liq_frac_patch                  , & ! output fraction of liquid moisture
+         intrmtncy_fct       => this%intrmtncy_fct_patch             , & ! output intermittency factor eta (fraction of time that dust emission is active within a timestep)
+         stblty              => this%stblty_patch                    , & ! stability in similarity theory (no need to output)
+         u_mean_slt          => this%u_mean_slt_patch                , & ! output mean wind speed at 0.1 m height translated from friction velocity using the log law of the wall, assuming neutral condition
+         u_sd_slt            => this%u_sd_slt_patch                  , & ! output standard deviation of wind speed from similarity theory
+         u_fld_thr           => this%u_fld_thr_patch                 , & ! output fluid threshold wind speed at 0.1 m height translated from the log law of the wall
+         u_impct_thr         => this%u_impct_thr_patch               , & ! output impact threshold wind speed at 0.1 m height translated from the log law of the wall
+         thr_crs_rate        => this%thr_crs_rate_patch              , & ! output threshold crossing rate in Comola 2019 intermittency parameterization
+         prb_crs_fld_thr     => this%prb_crs_fld_thr_patch           , & ! output probability of instantaneous wind crossing fluid threshold in Comola 2019 intermittency parameterization
+         prb_crs_impct_thr   => this%prb_crs_impct_thr_patch         , & ! output probability of instantaneous wind crossing impact threshold in Comola 2019 intermittency parameterization
+         ssr                 => this%ssr_patch                       , & ! output vegetation drag partition factor in Okin 2008 vegetation roughness effect (called shear stress ratio, SSR in Okin 2008)
+         vai_Okin            => this%vai_Okin_patch                  , & ! vegetation area index for calculating Okin-Pierre vegetation drag partitioning. vai=0 in the ssr equation will lead to infinity, so a small value is added into this vai dmleung defined. (no need to output) 16 Feb 2024
+         frc_thr_rghn_fct    => this%frc_thr_rghn_fct_patch          , & ! output hybrid/total drag partition factor considering both rock and vegetation drag partition factors.
+         wnd_frc_thr_std     => this%wnd_frc_thr_std_patch           , & ! standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
+         dpfct_rock          => this%dpfct_rock_patch                , & ! output rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
+         obu                 => frictionvel_inst%obu_patch             & ! Input:  [real(r8) (:)   ] Monin-Obukhov length from the friction Velocity module          obu                 => frictionvel_inst%obu_patch             & ! Input:  [real(r8) (:)   ] Monin-Obukhov length from the friction Velocity module 
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -486,11 +536,33 @@ subroutine DustEmission (this, bounds, &
          end if
       end do
 
+      ! dmleung add output for bare_frc and veg_frc here if wanted !!!!----------------------
+
       ! reset history output variables before next if-statement to avoid output = inf
 
       do fp = 1,num_nolakep
          p = filter_nolakep(fp)
          flx_mss_vrt_dst_tot(p) = 0.0_r8
+         dst_emiss_coeff(p) = 0.0_r8
+         wnd_frc_thr(p) = 0.0_r8
+         wnd_frc_thr_dry(p) = 0.0_r8
+         lnd_frc_mble(p) = 0.0_r8
+         wnd_frc_soil(p) = 0.0_r8
+         gwc(p) = 0.0_r8
+         liq_frac(p) = 0.0_r8
+         u_mean_slt(p) = 0.0_r8
+         u_sd_slt(p) = 0.0_r8
+         stblty(p)   = 0.0_r8
+         u_fld_thr(p) = 0.0_r8
+         u_impct_thr(p) = 0.0_r8
+         thr_crs_rate(p) = 0.0_r8
+         prb_crs_fld_thr(p) = 0.0_r8
+         prb_crs_impct_thr(p) = 0.0_r8
+         intrmtncy_fct(p) = 0.0_r8
+         ssr(p) = 0.0_r8
+         vai_Okin(p) = 0.0_r8
+         frc_thr_rghn_fct(p) = 0.0_r8
+         wnd_frc_thr_std(p) = 0.0_r8
       end do
       do n = 1, ndst
          do fp = 1,num_nolakep
@@ -505,86 +577,203 @@ subroutine DustEmission (this, bounds, &
          l = patch%landunit(p)
          g = patch%gridcell(p)
 
-         ! only perform the following calculations if lnd_frc_mbl is non-zero
-
-         if (lnd_frc_mbl(p) > 0.0_r8) then
+         !--------------------------------------------------------------------------------------------------
+         ! put dust emission calculation here to output threshold friction velocity for the whole globe,
+         ! not just when lnd_frc_mbl = 0. Danny M. Leung 27 Nov 2021
+          
+         !####################################################################################################
+         ! calculate soil moisture effect for dust emission threshold
+         ! following Fecan, Marticorena et al. (1999)
+         ! also see Zender et al. (2003) for DUST emission scheme and Kok et al. (2014b) for K14 emission scheme in CESM
+         bd = (1._r8-watsat(c,1))*dns_slt      ![kg m-3] Bulk density of dry surface soil (dmleung changed from 2700 to dns_slt, soil particle density, on 16 Feb 2024. Note that dn s_slt=2650 kg m-3 so the value is changed by a tiny bit from 2700 to 2650. dns_slt has been here for many years so dns_slt should be used here instead of explicitly typing the value out. dmleung 16 Feb 2024)
+
+         ! use emission threshold to calculate standardized threshold and dust emission coefficient
+
+         ! Here convert h2osoi_vol (H2OSOI) at the topmost CTSM soil layer from volumetric (m3 water / m3 soil) to gravimetric soil moisture (kg water / kg soil)
+         gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
+         if (gwc_sfc > gwc_thr(c)) then
+            frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)   ! dmleung's comment: this is an empirical equation by Fecan, Marticorena et al. (1999) on relating the soil moisture factor on enhancing dust emission threshold to gravimetric soil moisture. 1.21 and 0.68 are fitting parameters in the regression done by Fecan; 100 is to convert gracimetric soil moisture from fraction (kg water / kg soil) to percentage. Note that gwc_thr was defined in SoilStateInitConst.F90 as a fraction. 1.0_r8 means there is no soil moisture effect on enhancing dust emission threhsold. dmleung 16 Feb 2024.
+         else
+            frc_thr_wet_fct = 1.0_r8
+         end if
 
-            ! the following comes from subr. frc_thr_rgh_fct_get
-            ! purpose: compute factor by which surface roughness increases threshold
-            !          friction velocity (currently a constant)
+         ! output moisture variables
+         gwc(p) = gwc_sfc     ! output surface gravimetric water content
+
+         ! slevis: adding liqfrac here, because related to effects from soil water
+         liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
+         ! dmleung: output liquid fraction
+         liq_frac(p) = liqfrac
+
+         !#######################################################################################################
+         ! calculate Shao & Lu (2000) dust emission threshold scheme here
+         ! use tmp1 from DUSTini for Iversen and White I&W (1982) (~75 um is optimal); use tmp2 for S&L (2000) (~80 um is optimal)
+         ! see Danny M. Leung et al. (2023)
+         !#######################################################################################################
+         tmp2 = sqrt(A_Shao * (dns_slt*grav*D_p + gamma_Shao/D_p))  ! calculate S&L (2000) scheme here for threshold; gamma = 1.65e-4 following S&L00, D_p = 127 um ~ 130 um following Leung et al. (2023). dmleung use defined parameters instead of typing numerical values 16 Feb 2024
+         wnd_frc_thr_dry(p) = tmp2 / sqrt(forc_rho(c))    ! dry fluid threshold
+         wnd_frc_thr_slt = tmp2 / sqrt(forc_rho(c)) * frc_thr_wet_fct !* frc_thr_rgh_fct   ! fluid threshold. dmleung commented out frc_thr_rgh_fct since it is used to modify the wind, not the wind threshold.
+         wnd_frc_thr_slt_it = B_it * tmp2 / sqrt(forc_rho(c)) ! define impact threshold
+
+         ! the above formula is true for Iversen and White (1982) and Shao and Lu (2000) scheme
+         wnd_frc_thr(p) = wnd_frc_thr_slt          ! output fluid threshold
+         wnd_frc_thr_it(p) = wnd_frc_thr_slt_it    ! output impact threshold
+
+         !##############################################################################################
+         ! dmleung: here, calculate quantities relevant to the fluid threshold
+         ! standardized fluid threshold
+         wnd_frc_thr_slt_std = wnd_frc_thr_slt * sqrt(forc_rho(c) / forc_rho_std) ! standardized soil threshold friction speed (defined using fluid threshold)
+         wnd_frc_thr_std(p) = wnd_frc_thr_slt_std          ! output standardized fluid threshold
+         ! dust emission coefficient or soil erodibility coefficient (this is analogous to the soil erodibility map or prefenertial source filter in Zender; see zendersoilerodstream)
+         dst_emiss_coeff(p) = Cd0 * exp(-Ce * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min) ! save dust emission coefficient here for all grids
+
+         ! framentation exponent (dependent on fluid threshold)
+         frag_expt = (Ca * (wnd_frc_thr_slt_std - wnd_frc_thr_slt_std_min) / wnd_frc_thr_slt_std_min)  ! fragmentation exponent, defined in Kok et al. (2014a)
+         if (frag_expt > frag_expt_thr) then   ! set fragmentation exponent to be 3 or 5 at maximum, to avoid local AOD blowup
+            frag_expt = frag_expt_thr
+         end if
 
-            frc_thr_rgh_fct = 1.0_r8
+         !##############################################################################################
+         !################ drag partition effect, and soil-surface friction velocity ###################
+         ! subsection on computing vegetation drag partition and hybrid drag partition factors
+         ! in Leung et al. (2023), drag partition effect is applied on the wind instead of the threshold
+         !##############################################################################################
+         ! the following comes from subr. frc_thr_rgh_fct_get
+         ! purpose: compute factor by which surface roughness increases threshold
+         !          friction velocity (currently a constant)
+
+         if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
+            !if (lnd_frc_mbl(p) > 0.0_r8  .AND. ttlai(p)<=1_r8) then
+            ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
+            !lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
+            !lai(p) = ttlai(p) + lai0_Okin     ! ttlai = tlai+tsai. Okin-Pierre's equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
+            !if (lai(p) > 1_r8) then
+            !   lai(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
+            !end if              !
+
+            !if (ttlai(p) + vai0_Okin <= 1_r8) then
+            !   vai_Okin(p) = ttlai(p) + vai0_Okin     ! ttlai = vai = tlai+tsai. Okin-Pierre's equation is undefined at vai=0, and VAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
+            !end if                                    ! In the Okin-Pierre formulation, VAI has to be 0 < VAI <= 1.
+
+            vai_Okin(p) = tlai_lu(l)+vai0_Okin       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
+            if (vai_Okin(p) > 1_r8) then
+               vai_Okin(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1) 
+            end if
 
-            ! the following comes from subr. frc_thr_wet_fct_get
-            ! purpose: compute factor by which soil moisture increases threshold friction velocity
-            ! adjust threshold velocity for inhibition by moisture
-            ! modified 4/5/2002 (slevis) to use gravimetric instead of volumetric
-            ! water content
 
-            bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
-            gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
-            if (gwc_sfc > gwc_thr(c)) then
-               frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)
+            ! calculate Okin's shear stress ratio (SSR, which is vegetation drag partition factor) using Pierre's equation
+            K_length = 2_r8 * (1_r8/vai_Okin(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
+            ssr(p) = (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023). This line is Pierre's formulation.
+
+            ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
+            if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
+               if (patch%itype(p) == noveg) then ! if bare, uses rock drag partition factor
+                  if (dpfct_rock(p) /= dpfct_rock(p)) then ! dmleung added 24 May 2024: dpfct_rock(p) could be NaN; CLM could run when DEBUG=FALSE in env_build.xml but dies when DEBUG=TRUE (usually when checking if wnd_frc_slt > wnd_frc_thr_slt_it and if numer/denom < 30._r8 below)
+                     !write(iulog,*) 'dpfct_rock(p) == NaN; dpfct_rock(p) = ', dpfct_rock(p)
+                     frc_thr_rgh_fct = 0.001_r8 ! Set drag partition effect to be a very small value (or zero) such that there is no emission whenever dpfct_rock(p) = NaN; dmleung 24 May 2024
+                  else
+                     !write(iulog,*) 'dpfct_rock(p) = ', dpfct_rock(p)
+                     frc_thr_rgh_fct = dpfct_rock(p)
+                  end if
+               !frc_thr_rgh_fct = dpfct_rock(p) ! This should be the original code when dpfct_rock(p) has values everywhere
+               else   ! if vegetation, uses vegetation drag partition factor
+                  frc_thr_rgh_fct = ssr(p)
+               end if
             else
-               frc_thr_wet_fct = 1.0_r8
+               frc_thr_rgh_fct = 1.0_r8
             end if
 
-            ! slevis: adding liqfrac here, because related to effects from soil water
+            wnd_frc_slt = fv(p) * frc_thr_rgh_fct   ! wnd_frc_slt is the drag-parition-modified wind speed and will be used in the dust emission equation below
+
+            frc_thr_rghn_fct(p) = frc_thr_rgh_fct   ! save and output hybrid drag partition factor
 
-            liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
+         else    ! for lnd_frc_mbl=0, do not change friction velocity and assume drag partition factor = 0
+            wnd_frc_slt = fv(p) * frc_thr_rghn_fct(p) ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission. dmleung added 5 Jul 2024
+            frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > 1, the drag partition effect is zero. dmleung 16 Feb 2024.
+         end if
+
+         !########## end of drag partition effect #######################################################
 
-            ! the following lines come from subr. dst_mbl
-            ! purpose: adjust threshold friction velocity to acct for moisture and
-            !          roughness. The ratio saltation_factor / sqrt(forc_rho) comes from
-            !          subr. wnd_frc_thr_slt_get which computes dry threshold
-            !          friction velocity for saltation
+         ! save soil friction velocity and roughness effect before the if-statement
+         wnd_frc_soil(p) = wnd_frc_slt  ! save soil friction velocity for CLM output, which has drag partition and Owen effect
+         ! 20 Feb 2024: dmleung notes that Leung does not consider the Owen's effect. This is Jasper Kok's decision. The Owen's effect should be in Zender's DUST emission scheme.
 
-            wnd_frc_thr_slt = this%saltation_factor / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
+         ! save land mobile fraction
+         lnd_frc_mble(p) = lnd_frc_mbl(p)  ! save land mobile fraction first, before the if-statement
+         ! only perform the following calculations if lnd_frc_mbl is non-zero
+
+         if (lnd_frc_mbl(p) > 0.0_r8) then  ! if bare land fraction is larger than 0 then calculate the dust emission equation
 
             ! reset these variables which will be updated in the following if-block
 
-            wnd_frc_slt = fv(p)
             flx_mss_hrz_slt_ttl = 0.0_r8
             flx_mss_vrt_dst_ttl(p) = 0.0_r8
 
-            ! the following line comes from subr. dst_mbl
-            ! purpose: threshold saltation wind speed
+            ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
+            ! purpose: compute vertically integrated streamwise mass flux of particles
 
-            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)
+            if (wnd_frc_slt > wnd_frc_thr_slt_it) then! if using Leung's scheme, use impact threshold for dust emission equation; if Zender, uses fluid threshold (wnd_frc_thr_slt) for dust emission equation
 
-            ! the following if-block comes from subr. wnd_frc_slt_get
-            ! purpose: compute the saltating friction velocity
-            ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
+               !################### for Leung et al. (2023) ################################################
+               ! dmleung: instead of using mss_frc_cly_vld(c) with a range of [0,0.2] , which makes dust too sensitive to input clay surface dataset), for now use 0.1 + mss_frc_cly_vld(c) * 0.1 / 0.20 with a range of [0.1,0.2]. So, instead of scaling dust emission to 1/20 times for El Djouf (western Sahara) because of its 1 % clay fraction, scale its emission to 1/2 times. This reduces the sensitivity of dust emission to the clay input dataset. In particular, because dust emission is a small-scale process and the grid-averaged clay from the new WISE surface dataset over El Djouf is 1 %, much lower than the former FAO estimation of 5 %, dmleung is not sure if the clay value of 1 % suppresses too much of El Djouf's small-scale dust emission process. Similar to Charlie Zender's feeling suspicious about the soil texture datasets (or the dust emission schemes' sandblasting process), dmleung feels the same and for now decides to still allow dust emission  to weakly scale with clay fraction, however limiting the scaling factor to 0.1-0.2. See modification in SoilStateInitTimeConst.F90. dmleung 5 Jul 2024
+               flx_mss_vrt_dst_ttl(p) = dst_emiss_coeff(p) * mss_frc_cly_vld(c) * forc_rho(c) * ((wnd_frc_slt**2.0_r8 - wnd_frc_thr_slt_it**2.0_r8) / wnd_frc_thr_slt_it) * (wnd_frc_slt / wnd_frc_thr_slt_it)**frag_expt  ! Leung et al. (2022) uses Kok et al. (2014) dust emission euqation for emission flux
 
-            if (u10(p) >= wnd_rfr_thr_slt) then
-               wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
-               wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
-               wnd_frc_slt = fv(p) + wnd_frc_slt_dlt
+               ! account for bare soil fraction, frozen soil fraction, and apply global tuning parameter (Kok et al. 2014)
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * lnd_frc_mbl(p) * C_tune * liqfrac
+               !########################################################################################
             end if
 
-            ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
-            ! purpose: compute vertically integrated streamwise mass flux of particles
+            !############## Danny M. Leung added the intermittency calculation #################################
+            ! subsection for intermittency factor calculation (only used by Leung's scheme, not Zender's scheme)
+            ! Leung et al. (2023) uses the Comola et al. (2019) intermittency scheme for the calculation of intermittent dust emissions.
+            ! This part takes care of the sub-timestep, high-frequency (< 1 minute period) turblent wind fluctuations occuring at the planetary boundary layer (PBL) near surface. Subtimestep wind gusts and episodes are important for generating emissions in marginal dust source regions, such as semiarid areas and high-latitude polar deserts.
+            ! 2 Dec 2021: assume no buoyancy contribution to the wind fluctuation (u_sd_slt), so no obul(p) is needed. It is shown to be important for the wind fluctuations contribute little to the intermittency factor. We might add this back in the future revisions.
+            ! 20 Feb 2024: dmleung notes that dmleung may revise Comola's scheme in the future to improve Comola's formulation of the statistical parameterization.
 
-            if (wnd_frc_slt > wnd_frc_thr_slt) then
-               wnd_frc_rat = wnd_frc_thr_slt / wnd_frc_slt
-               flx_mss_hrz_slt_ttl = cst_slt * forc_rho(c) * (wnd_frc_slt**3.0_r8) * &
-                    (1.0_r8 - wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) / grav
+            ! mean lowpass-filtered wind speed at hgt_sal = 0.1 m saltation height (assuming aerodynamic roughness length z0a_glob = 1e-4 m globally for ease; also assuming neutral condition)
+            u_mean_slt(p) = (wnd_frc_slt/k) * log(hgt_sal / z0a_glob)  ! translating from ustar (velocity scale) to actual wind
 
-               ! the following loop originates from subr. dst_mbl
-               ! purpose: apply land sfc and veg limitations and global tuning factor
-               ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect
-               ! of frozen soil
+            !stblty(p) = 0_r8   ! -dmleung 2 Dec 2021: use stability = 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
+            stblty(p) = zii / obu(p)   ! -dmleung 20 Feb 2024: use obu from CTSM and PBL height = zii (= 1000_r8) which is default in CTSM. Should we transfer PBL height from CAM?
+            if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
+               u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
+            else
+               u_sd_slt(p) = wnd_frc_slt * (0.001_r8)**0.333_r8   ! should have used 0 theoretically; used 0.001 here to avoid undefined values
+            end if
 
-               flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * &
-                    flx_mss_fdg_fct * liqfrac
+            ! threshold velocities
+            ! Here wnd_frc_thr_slt is the fluid threshold; wnd_frc_thr_dry(p) is the dry fluid threshold; B_it*wnd_frc_thr_dry(p) is the impact threshold
+            ! fluid threshold wind at 0.1 m saltation height
+            u_fld_thr(p) = (wnd_frc_thr_slt/k) * log(hgt_sal / z0a_glob)  ! assume a globally constant z0a value for the log law of the wall, but it can be z0m from CLM or, better, z0a from Prigent's roughness dataset. Danny M. Leung et al. (2023) chose to assume a global constant z0a = 1e-4 m. dmleung 20 Feb 2024
+            ! impact threshold wind at 0.1 m saltation height
+            u_impct_thr(p) = (wnd_frc_thr_slt_it/k) * log(hgt_sal / z0a_glob)
+
+            ! threshold crossing rate
+            numer = (u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p)))
+            denom = (2.0_r8 * u_sd_slt(p)**2.0_r8) ! note that u_sd_slt should be always positive
+            ! Truncate to zero if the expression inside exp is becoming too large
+            if ( numer/denom < 30._r8 ) then  ! set numer/denom to be < 30 given exp(30) below is already very large; also denom itself should be non-zero and non-negative given the standard deviation (u_sd_slt) of the subtimestep wind fluctuation is non-negative. dmleung 28 May 2024
+               thr_crs_rate(p) = (exp((u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2.0_r8 * u_sd_slt(p)**2.0_r8)) + 1.0_r8)**(-1.0_r8)
+            else
+               thr_crs_rate(p) = 0.0_r8
             end if
 
-            ! the following comes from subr. flx_mss_vrt_dst_ttl_MaB95_get
-            ! purpose: diagnose total vertical mass flux of dust from vertically
-            !          integrated streamwise mass flux
+            ! probability that lowpass-filtered wind speed does not exceed u_ft
+            prb_crs_fld_thr(p) = 0.5_r8 * (1.0_r8 + erf((u_fld_thr(p) - u_mean_slt(p)) / ( sqrt(2.0_r8) * u_sd_slt(p))))
+            ! probability that lowpass-filtered wind speed does not exceed u_it
+            prb_crs_impct_thr(p) = 0.5_r8 * (1.0_r8 + erf((u_impct_thr(p) - u_mean_slt(p)) / ( sqrt(2.0_r8) * u_sd_slt(p))))
+
+            ! intermittency factor (eta; ranging from 0 to 1)
+            intrmtncy_fct(p) = 1.0_r8 - prb_crs_fld_thr(p) + thr_crs_rate(p) * (prb_crs_fld_thr(p) - prb_crs_impct_thr(p))
+
+            ! multiply dust emission flux by intermittency factor
+            if (intrmtncy_fct(p) /= intrmtncy_fct(p)) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p)
+            else
+               flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * intrmtncy_fct(p)  ! multiply dust flux by intermittency
+            end if
 
-            dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )
-            flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
+            !############ end the intermittency subsection here; only use for Leung's scheme  ##########################
 
          end if   ! lnd_frc_mbl > 0.0
 

From 667003d404dd4b9ca63efce0c3a0a115c0b42651 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 28 Jul 2024 16:59:51 -0600
Subject: [PATCH 0805/1248] Fix several of the Leung 2023 unit tests because of
 change in answers, still two fail

---
 src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
index 2b87f4be0a..e18e00e269 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
@@ -107,7 +107,7 @@ contains
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
                                vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
                                vlc_trb_4=vlc_trb_4)
-       @assertEqual( flx_mss_vrt_dst_tot, 1.208384635884010d-5, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 1.305341724414137d-006, tolerance=tol )
        @assertEqual( vlc_trb_1, 3.407721147709135d-003, tolerance=tol )
        @assertEqual( vlc_trb_2, 4.961153753164878d-003, tolerance=tol )
        @assertEqual( vlc_trb_3, 4.980100969983446d-003, tolerance=tol )
@@ -270,7 +270,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust0 = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 1.063573374792962d-4, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 1.064145669761461d-5, tolerance=tol )
     end do
     ! Double u10 and show result is higher
     call this%input%create_fv( u10=u10*2.0_r8, fv=fv)
@@ -282,7 +282,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust_higher = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 1.774023264204829d-4, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 1.064145669761461d-5, tolerance=tol )
     end do
     @assertGreaterThan( total_dust_higher, total_dust0 )
 

From 0f9fee7ea3b3f6732e2f0dd7bf75f7f6536b3cfa Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Jul 2024 11:42:44 -0600
Subject: [PATCH 0806/1248] LILAC needs to read and handle the drv_flds_in file
 as dust emission settings are required and it's namelist must be read

---
 cime_config/SystemTests/lilacsmoke.py    | 2 +-
 python/ctsm/lilac_make_runtime_inputs.py | 1 -
 src/CMakeLists.txt                       | 1 +
 src/cpl/lilac/lnd_comp_esmf.F90          | 5 +++++
 4 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/cime_config/SystemTests/lilacsmoke.py b/cime_config/SystemTests/lilacsmoke.py
index 1287301ba2..5bdbb31ec1 100644
--- a/cime_config/SystemTests/lilacsmoke.py
+++ b/cime_config/SystemTests/lilacsmoke.py
@@ -38,7 +38,7 @@
 
 logger = logging.getLogger(__name__)
 
-_LILAC_RUNTIME_FILES = ["lnd_in", "lnd_modelio.nml", "lilac_in"]
+_LILAC_RUNTIME_FILES = ["lnd_in", "lnd_modelio.nml", "drv_flds_in", "lilac_in"]
 
 
 class LILACSMOKE(SystemTestsCommon):
diff --git a/python/ctsm/lilac_make_runtime_inputs.py b/python/ctsm/lilac_make_runtime_inputs.py
index 33b87c543e..e751f6c931 100644
--- a/python/ctsm/lilac_make_runtime_inputs.py
+++ b/python/ctsm/lilac_make_runtime_inputs.py
@@ -307,7 +307,6 @@ def buildnml(cime_path, rundir):
     # remove temporary files in rundir
     os.remove(os.path.join(rundir, "config_cache.xml"))
     os.remove(os.path.join(rundir, "env_lilac.xml"))
-    os.remove(os.path.join(rundir, "drv_flds_in"))
     os.remove(infile)
 
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9388e65bc2..5b0f6c9b1b 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -107,5 +107,6 @@ add_subdirectory(${CLM_ROOT}/src/init_interp/test clm_init_interp_test)
 add_subdirectory(${CLM_ROOT}/src/self_tests/test clm_self_tests_test)
 
 # Add driver unit test directories
+# (these should be moved to the appropriate submodule)
 add_subdirectory(${CLM_ROOT}/src/drv_test drv_test)
 
diff --git a/src/cpl/lilac/lnd_comp_esmf.F90 b/src/cpl/lilac/lnd_comp_esmf.F90
index 298aa730c0..6c8bb2a491 100644
--- a/src/cpl/lilac/lnd_comp_esmf.F90
+++ b/src/cpl/lilac/lnd_comp_esmf.F90
@@ -114,6 +114,8 @@ subroutine lnd_init(comp, import_state, export_state, clock, rc)
     use ESMF              , only : ESMF_StateAdd
     use ESMF              , only : operator(==)
 
+    use shr_dust_emis_mod , only : shr_dust_emis_readnl
+
     ! input/output variables
     type(ESMF_GridComp)  :: comp         ! CLM gridded component
     type(ESMF_State)     :: import_state ! CLM import state
@@ -270,6 +272,9 @@ subroutine lnd_init(comp, import_state, export_state, clock, rc)
     ! Fill in the value for model_meshfile in lnd_comp_shr used by the stream routines in share_esmf/
     model_meshfile = trim(lnd_mesh_filename)
 
+    ! Reading in the drv_flds_in namelist is required for dust emissions
+    call shr_dust_emis_readnl( mpicom, "drv_flds_in")
+
     !----------------------
     ! Obtain caseid and start type from attributes in import state
     !----------------------

From 6d07a80bb6a4d0238863907c92a8f984480e72ad Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Mon, 29 Jul 2024 11:50:48 -0600
Subject: [PATCH 0807/1248] pass physics and proper defaults.

---
 bld/CLMBuildNamelist.pm                       | 15 +++++++++------
 bld/namelist_files/namelist_defaults_ctsm.xml |  4 ++--
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index fa0d4a0382..77fb8a679f 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1815,7 +1815,7 @@ sub process_namelist_inline_logic {
   #################################
   # namelist group: exice_streams #
   #################################
-  setup_logic_exice($opts, $nl_flags, $definition, $defaults, $nl);
+  setup_logic_exice($opts, $nl_flags, $definition, $defaults, $nl, $physv);
 
   ##########################################
   # namelist group: clm_temperature_inparm #
@@ -2322,7 +2322,6 @@ sub setup_logic_soilstate {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'organic_frac_squared' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_bedrock',
               'use_fates'=>$nl_flags->{'use_fates'}, 'vichydro'=>$nl_flags->{'vichydro'} );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice'); # excess ice flag should be read before stream vars
 
   my $var1 = "soil_layerstruct_predefined";
   my $var2 = "soil_layerstruct_userdefined";
@@ -4583,7 +4582,8 @@ sub setup_logic_exice {
   #
   # excess ice streams
   #
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); 
   my $use_exice = $nl->get_value( 'use_excess_ice' );
   my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' );
   my $finidat = $nl->get_value('finidat');
@@ -4642,10 +4642,13 @@ sub setup_logic_coldstart_temp {
 
   # set initial temperatures for excess ice gridcells:
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_temp');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_depth');
-
   my $use_exice = $nl->get_value( 'use_excess_ice' );
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_temp',
+             'use_excess_ice'=>$use_exice);
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_depth',
+             'use_excess_ice'=>$use_exice);
+
   my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' );
   my $exice_cs_temp = $nl->get_value( 'excess_ice_coldstart_temp' );
   my $exice_cs_depth = $nl->get_value( 'excess_ice_coldstart_depth' );
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 47f9802aff..7ce2235a84 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2058,8 +2058,8 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- =========================================  -->
 
 <use_excess_ice>.false.</use_excess_ice>
-<excess_ice_coldstart_temp>0.0</excess_ice_coldstart_temp>
-<excess_ice_coldstart_depth>1.0</excess_ice_coldstart_depth>
+<excess_ice_coldstart_temp>-1.0</excess_ice_coldstart_temp>
+<excess_ice_coldstart_depth>0.5</excess_ice_coldstart_depth>
 <excess_ice_coldstart_temp use_excess_ice=".true.">-3.15</excess_ice_coldstart_temp>
 <excess_ice_coldstart_depth use_excess_ice=".true.">0.5</excess_ice_coldstart_depth>
 <stream_fldfilename_exice use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc</stream_fldfilename_exice>

From 7208b6671a7dde13624ecca56bc0e165a111ac9b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Jul 2024 16:36:29 -0600
Subject: [PATCH 0808/1248] Fix grammar

---
 bld/namelist_files/namelist_definition_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 575d72856f..a987fc1300 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -2826,12 +2826,12 @@ If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020)
 
 <entry id="excess_ice_coldstart_temp" type="real" category="clm_physics"
        group="clm_temperature_inparm" >
-Initial soil temperature to use for gridcells with excess ice present during a run starting with coldstart (deg C). Value is only apply if use_excess_ice is true.
+Initial soil temperature to use for gridcells with excess ice present during a run starting with coldstart (deg C). Value only applys if use_excess_ice is true.
 </entry>
 
 <entry id="excess_ice_coldstart_depth" type="real" category="clm_physics"
        group="clm_temperature_inparm" >
-Soil depth below which initial excess ice concentration will be applied during a run starting with coldstart (m). Value is only apply if use_excess_ice is true. 
+Soil depth below which initial excess ice concentration will be applied during a run starting with coldstart (m). Value only applys if use_excess_ice is true. 
 If this is set below depth of the soil depth, only the last soil layer will get excess ice.
 </entry>
 

From 17c748bad564c560cf305549b744c7c82c13b5c5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Jul 2024 17:06:26 -0600
Subject: [PATCH 0809/1248] Fix 1x1_cidadinhoBR tests by specifying
 2000_control for it and 1850_control for smallville

---
 bld/unit_testers/build-namelist_test.pl | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index c92f428d82..d6291c94de 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1532,7 +1532,11 @@ sub cat_and_create_namelistinfile {
 # Check for crop resolutions
 my @crop1850_res = ( "1x1_smallvilleIA", "1x1_cidadinhoBR" );
 foreach my $res ( @crop1850_res ) {
-   $options = "-bgc bgc -crop -res $res -use_case 1850_control -envxml_dir .";
+   my $use_case = "1850_control";
+   if ( $res =~ /1x1_cidadinhoBR/ ) {
+      $use_case = "2000_control";
+   }
+   $options = "-bgc bgc -crop -res $res -use_case $use_case -envxml_dir .";
    &make_env_run();
    eval{ system( "$bldnml $options  > $tempfile 2>&1 " ); };
    is( $@, '', "$options" );

From 0903d70234eab143bdb5f48959fed725e6766422 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Jul 2024 18:00:13 -0600
Subject: [PATCH 0810/1248] This looks wrong, but is actually correct in order
 to get this to work through initialization, otherwise it fails thinking
 stremas are off

---
 src/cpl/share_esmf/PrigentRoughnessStreamType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90 b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
index 564891bcac..2e78704614 100644
--- a/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/cpl/share_esmf/PrigentRoughnessStreamType.F90
@@ -184,7 +184,7 @@ logical function UseStreams(this)
           UseStreams = .true.
        end if
     else
-       UseStreams = .false.  ! Prigent streams are off without a filename given
+       UseStreams = .true.
     end if
   end function UseStreams
 

From a58ad0fba8030617211b3e7d36167cc0a70631d6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 29 Jul 2024 18:01:35 -0600
Subject: [PATCH 0811/1248] Get unit tests all working by adjusting the Leung
 2023 test by what's doing on inside the Leung 2023 code

---
 .../test/DustEmis_test/test_DustEmisLeung2023.pf | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
index e18e00e269..e6634d9ad7 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
@@ -234,7 +234,7 @@ contains
    patch%itype(bounds%begp:bounds%endp) = 1
    call this%input%create_atm2lnd()
    call this%input%create_fv( )
-   this%input%canopystate_inst%tlai_patch(:) = 0.3_r8
+   this%input%canopystate_inst%tlai_patch(:) = 1.0_r8
    call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
                      this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
                      this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
@@ -250,8 +250,8 @@ contains
   !-----------------------------------------------------------------------
 
   @Test
-  subroutine check_dust_emis_increasing_wind(this)
-    ! Check dust emissions with increasing wind
+  subroutine check_dust_emis_increasing_fv(this)
+    ! Check dust emissions with increasing friction velocity
     class(TestDustEmisLeung2023), intent(inout) :: this
     integer :: p, c
     real(r8) :: flx_mss_vrt_dst_tot
@@ -259,7 +259,7 @@ contains
     real(r8) :: u10 = 10._r8
     real(r8) :: total_dust0, total_dust_higher
 
-    ! Run baseline u10
+    ! Run baseline fv
     call this%input%create_atm2lnd()
     call this%input%create_fv( u10=u10, fv=fv )
     call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
@@ -272,8 +272,8 @@ contains
        total_dust0 = flx_mss_vrt_dst_tot
        @assertEqual( flx_mss_vrt_dst_tot, 1.064145669761461d-5, tolerance=tol )
     end do
-    ! Double u10 and show result is higher
-    call this%input%create_fv( u10=u10*2.0_r8, fv=fv)
+    ! Double fv and show result is higher
+    call this%input%create_fv( u10=u10, fv=fv*2.0_r8)
     call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
                       this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
                       this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
@@ -282,11 +282,11 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust_higher = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 1.064145669761461d-5, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 8.309603073613188d-5, tolerance=tol )
     end do
     @assertGreaterThan( total_dust_higher, total_dust0 )
 
-  end subroutine check_dust_emis_increasing_wind
+  end subroutine check_dust_emis_increasing_fv
 
   !-----------------------------------------------------------------------
 

From a8ff15afcd6e4c7f813c4cd9b93605b8ddc7f216 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Tue, 30 Jul 2024 08:01:23 -0600
Subject: [PATCH 0812/1248] add error when user sets streams to false and exice
 to true on coldstart

---
 bld/CLMBuildNamelist.pm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 77fb8a679f..ca99c131b0 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4595,6 +4595,11 @@ sub setup_logic_exice {
   } elsif ( (not defined($use_exice_streams)) && (not value_is_true($use_exice)) ) {
      $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.false.');
      $use_exice_streams = '.false.';
+  # Checking for cold clm_start_type and not finidat here since finidat can be not set set in branch/hybrid runs and
+  # These cases are handled in the restart routines in the model
+  } elsif ( defined($use_exice_streams) && (not value_is_true($use_exice_streams)) && value_is_true($use_exice) &&
+          ( $nl_flags->{'clm_start_type'} eq "'cold'" || $nl_flags->{'clm_start_type'} eq "'arb_ic'" )) {
+     $log->fatal_error("use_excess_ice_streams can NOT be FALSE when use_excess_ice is TRUE on the cold start" );
   }
   # If excess ice streams is on
   if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {

From 4d4fe83b759c972c9f4e8d0ad9422d1cd36c7693 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Jul 2024 08:38:44 -0600
Subject: [PATCH 0813/1248] Fix test numbers

---
 bld/unit_testers/build-namelist_test.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index d6291c94de..5bccb3b77c 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3317;
+my $ntests = 3329;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2052;
+   $ntests += 1999;
 }
 plan( tests=>$ntests );
 

From cdb36a0f681d02a2c5720940c169a559783a3e9b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Jul 2024 08:39:36 -0600
Subject: [PATCH 0814/1248] Update change files

---
 doc/ChangeLog | 115 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 116 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 79d640242d..8c01174329 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,119 @@
 ===============================================================
+Tag name: ctsm5.2.017
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Tue 30 Jul 2024 08:39:20 AM MDT
+One-line Summary: Dust emissions control moved to cmeps
+
+Purpose and description of changes
+----------------------------------
+
+Remove the dust emissions namelist items from CTSM and use the namelist in the drv_flds_in for CMEPS.
+
+This updates CTSM to use the namelist control in CMEPS (in ESCOMP/CMEPS#429). So the CMEPS external needs to be updated, and the
+namelist control in CTSM changed to use CMEPS rather than the internal CTSM control settings and the CTSM ones removed.
+
+The new XML variable:
+
+   LND_SETS_DUST_EMIS_DRV_FLDS
+
+controls whether dust emission settings are set by CTSM or by CAM. Only one or the other can set them, and it's required so when CAM
+and CTSM are running together they need to know which one will select.
+
+This required some changes for LILAC. The drv_flds_in namelist file is now required for LILAC, and read for dust emissions
+(and dust emissions only) at the LILAC lnd_comp_esmf.F90 level.
+
+Add a unit test for the CMEPS code to make sure it's working correctly. This validates the code both for CAM and CTSM.
+
+Fix the cidinahoBR test in the build-namelist unit tester.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+
+  Fixes #2376 -- Update CTSM with CMEPS that controls dust emission options
+  Fixes #2150 -- Ability to flip between different dust emission methods
+  Fixes #2524 -- Add option to NOT set dust emission settings when coupled to CAM
+  Fixes #2666 -- cidinahoBR test in build-namelist 
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+   dust_emis_method can NOT be set to Leung_2023 -- yet.
+   See below about LND_SETS_DUST_EMIS_DRV_FLDS
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+  CTSM namelist items moved to the dust_emis_inparm namelist in drv_flds_in:
+  zender_soil_erod_source and dust_emis_method
+
+  New logical XML variable:
+     LND_SETS_DUST_EMIS_DRV_FLDS
+  If TRUE CTSM sets the dust emission namelist, otherwise CAM will (when coupled to CAM) 
+  If you are NOT coupled to CAM and LND_SETS_DUST_EMIS_DRV_FLDS==FALSE, the model will abort
+  trying to read the dust_emis_inparm namelist in drv_flds_in.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   Added a PF unit test for CMEPS dust emission code. This should be moved to CMEPS, but still run here.
+   Control design in DustEmisFactory, uses a Functional Programming design pattern with pure functions
+   from CMEPS for CTSM to know the drv_flds_in settings. Design notes were added in that regard.
+
+Testing summary: Regular
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS (1006 are different because of the namelist changes)
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+  #2545 -- Dust emission control moved to CMEPS
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.016
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Sat 27 Jul 2024 05:13:08 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 382e5cf7cb..15a67bcf04 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.017     erik 07/30/2024 Dust emissions control moved to cmeps
        ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof
        ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false.

From f28ecdb5cbd3ab3ab28ffd149ef54761055e926e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Jul 2024 08:44:59 -0600
Subject: [PATCH 0815/1248] Add note about the fails compared to baselines

---
 doc/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8c01174329..aeb7b2972f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -105,6 +105,12 @@ Answer changes
 
 Changes answers relative to baseline: No bit-for-bit
 
+  The following tests compared different to baseline because of reproducability issues:
+     ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings
+     SMS_D.1x1_brazil.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdDryDepSatPhen
+     SMS_D.1x1_brazil.I2000Clm60FatesSpCruRsGs.derecho_gnu.clm-FatesColdMeganSatPhen
+  The CN-MATRIX issue is because of #2619 and FATES because of #2656
+
 Other details
 -------------
 

From e5656454d59db3b2f414993bfb41d18ca54ba1b3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 30 Jul 2024 21:26:45 -0600
Subject: [PATCH 0816/1248] Add more excess ice tests for fail conditions, the
 last two don't pass as they aren't setup yet

---
 bld/unit_testers/build-namelist_test.pl | 31 ++++++++++++++++++++++---
 1 file changed, 28 insertions(+), 3 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 53c71ae0e9..b9d20cbba9 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3254;
+my $ntests = 3263;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2001;
+   $ntests += 1965;
 }
 plan( tests=>$ntests );
 
@@ -322,7 +322,7 @@ sub cat_and_create_namelistinfile {
                          "-res 0.9x1.25 -namelist '&a irrigate=.true./'", "-res 0.9x1.25 -verbose", "-res 0.9x1.25 -ssp_rcp SSP2-4.5", "-res 0.9x1.25 -test", "-res 0.9x1.25 -sim_year 1850",
                          "-res 0.9x1.25 -namelist '&a use_lai_streams=.true.,use_soil_moisture_streams=.true./'",
                          "-res 0.9x1.25 -namelist '&a use_excess_ice=.true. use_excess_ice_streams=.true./'",
-                         "-res 0.9x1.25 -namelist '&a use_excess_ice=.true. use_excess_ice_streams=.false./'",
+                         "-res 0.9x1.25 --clm_start_type cold -namelist '&a use_excess_ice=.true. use_excess_ice_streams=.true./'",
                          "-res 0.9x1.25 -use_case 1850_control",
                          "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'",
                          "-res 1x1_brazil",
@@ -542,6 +542,21 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "coldstart exice on wo stream"=>{ options=>"-res 0.9x1.25 -envxml_dir . --clm_start_type cold",
+                                     namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm6_0",
+                                   },
+     "coldstart exice on bad temp" =>{ options=>"-res 0.9x1.25 -envxml_dir . --clm_start_type cold",
+                                     namelst=>"use_excess_ice=.true., use_excess_ice_streams = .true., excess_ice_coldstart_temp=0.0",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm6_0",
+                                   },
+     "coldstart exice on bad depth" =>{ options=>"-res 0.9x1.25 -envxml_dir . --clm_start_type cold",
+                                     namelst=>"use_excess_ice=.true., use_excess_ice_streams = .true., excess_ice_coldstart_depth=0.0",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm6_0",
+                                   },
      "clm50CNDVwtransient"       =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1295,6 +1310,16 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
+     "Set coldtemp wo coldstart" =>{ options=>"-envxml_dir . --clm_start_type startup",
+                                     namelst=>"use_excess_ice=.true.,excess_ice_coldstart_temp=-10.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm6_0",
+                                   },
+     "Set colddepth wo coldstart" =>{ options=>"-envxml_dir . --clm_start_type startup",
+                                     namelst=>"use_excess_ice=.true.,excess_ice_coldstart_depth=0.5",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm6_0",
+                                   },
      "NotNEONbutNEONlightres"    =>{ options=>"--res CLM_USRDAT --clm_usr_name regional --envxml_dir . --bgc bgc --light_res 106x174",
                                      namelst=>"fsurdat='build-namelist_test.pl'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

From e3605abe8fb9e614873fe273967ab6554209b27c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 31 Jul 2024 14:28:18 -0600
Subject: [PATCH 0817/1248] Change the checks a bit, the coldstart temps always
 need to be set even if excess ice is off

---
 bld/CLMBuildNamelist.pm | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index ca99c131b0..ee82afdb17 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4645,9 +4645,22 @@ sub setup_logic_coldstart_temp {
 
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  # set initial temperatures for excess ice gridcells:
+  # set initial temperatures for excess ice gridcells: needs to be set whether excess ice is on or not
 
   my $use_exice = $nl->get_value( 'use_excess_ice' );
+  my $finidat = $nl->get_value('finidat');
+
+  my @list = ( "excess_ice_coldstart_temp", "excess_ice_coldstart_depth" );
+
+  # Only needs to be set if it's a coldstart
+  if ( ! string_is_undef_or_empty($finidat) ) {
+     foreach my $var ( @list ) {
+        my $val = $nl->get_value( $var );
+        if ( defined($val) ) {
+           $log->warning("$var only needs to be set if this is a cold-start, although InitCold is always called");
+        }
+     }
+  }
 
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_temp',
              'use_excess_ice'=>$use_exice);
@@ -4658,15 +4671,12 @@ sub setup_logic_coldstart_temp {
   my $exice_cs_temp = $nl->get_value( 'excess_ice_coldstart_temp' );
   my $exice_cs_depth = $nl->get_value( 'excess_ice_coldstart_depth' );
 
-  if (defined($use_exice) && value_is_true($use_exice)) {
-     # Checking this setting only needed IF excess ice streams are on get the stream defaults
-     if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
-      if (defined($exice_cs_depth) && $exice_cs_depth <= 0.0 ) {
-        $log->fatal_error("excess_ice_coldstart_depth is <= 0.0" );
-      }
-      if (defined($exice_cs_temp) && $exice_cs_temp >= 0.0 ) {
-        $log->fatal_error("excess_ice_coldstart_temp is >= 0.0, no excess ice will be present in this run" );
-      }
+  if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
+     if (defined($exice_cs_depth) && $exice_cs_depth <= 0.0 ) {
+       $log->fatal_error("excess_ice_coldstart_depth is <= 0.0" );
+     }
+     if (defined($exice_cs_temp) && $exice_cs_temp >= 0.0 ) {
+       $log->fatal_error("excess_ice_coldstart_temp is >= 0.0, no excess ice will be present in this run" );
      }
   }
 }

From 18df0661ea867a1b2e8cc75027be5ddaf0ea5753 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 31 Jul 2024 14:59:17 -0600
Subject: [PATCH 0818/1248] Save use_excice_streams to nl_flags so it doesn't
 have to be set to false when not needed

---
 bld/CLMBuildNamelist.pm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index ee82afdb17..ab70d698f4 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4593,7 +4593,6 @@ sub setup_logic_exice {
      $use_exice_streams = '.true.';
      # if excess ice is turned off
   } elsif ( (not defined($use_exice_streams)) && (not value_is_true($use_exice)) ) {
-     $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.false.');
      $use_exice_streams = '.false.';
   # Checking for cold clm_start_type and not finidat here since finidat can be not set set in branch/hybrid runs and
   # These cases are handled in the restart routines in the model
@@ -4601,6 +4600,9 @@ sub setup_logic_exice {
           ( $nl_flags->{'clm_start_type'} eq "'cold'" || $nl_flags->{'clm_start_type'} eq "'arb_ic'" )) {
      $log->fatal_error("use_excess_ice_streams can NOT be FALSE when use_excess_ice is TRUE on the cold start" );
   }
+
+  # Put use_exice_streams into nl_flags so can be referenced later
+  $nl_flags->{'use_excice_streams'} = $use_exice_streams;
   # If excess ice streams is on
   if (defined($use_exice_streams) && value_is_true($use_exice_streams)) {
      # Can only be true if excess ice is also on, otherwise fail
@@ -4652,7 +4654,7 @@ sub setup_logic_coldstart_temp {
 
   my @list = ( "excess_ice_coldstart_temp", "excess_ice_coldstart_depth" );
 
-  # Only needs to be set if it's a coldstart
+  # Only needs to be set by the user if it's a coldstart
   if ( ! string_is_undef_or_empty($finidat) ) {
      foreach my $var ( @list ) {
         my $val = $nl->get_value( $var );
@@ -4667,7 +4669,7 @@ sub setup_logic_coldstart_temp {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'excess_ice_coldstart_depth',
              'use_excess_ice'=>$use_exice);
 
-  my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' );
+  my $use_exice_streams = $nl_flags->{'use_excice_streams'};
   my $exice_cs_temp = $nl->get_value( 'excess_ice_coldstart_temp' );
   my $exice_cs_depth = $nl->get_value( 'excess_ice_coldstart_depth' );
 

From 797444f1a5878c138ac6e198000f5ed292a992cf Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 31 Jul 2024 16:51:57 -0600
Subject: [PATCH 0819/1248] Start the ChangeLog

---
 doc/ChangeLog | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 105 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index aeb7b2972f..f3bf5c91c1 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,108 @@
 ===============================================================
+Tag name: ctsm5.2.018
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Wed 31 Jul 2024 04:38:36 PM MDT
+One-line Summary: Fix/excess ice cold start
+
+Purpose and description of changes
+----------------------------------
+
+Changed the way soil temperature is initialized when excess ice is on and the model starts from cold.
+
+Specific notes
+
+Added 2 parameters: excess_ice_coldstart_depth and excess_ice_coldstart_temp which control top depth and soil temperature for soil layers in columns where excess ice is present. Other columns get their default soil temperature.
+
+excessicestream_type has been taken out of waterstate_type and its routines are called directly in clm_inst%Init. Checks for UseExcessIceStreams() are still in place in WaterStateType.F90 for double-checking.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2384 -- Cold start temperature init when excess ice is on
+ Fixes #2373 -- SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro fails
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+  Added: excess_ice_coldstart_temp and excess_ice_coldstart_depth
+
+Changes made to namelist defaults (e.g., changed parameter values):
+  Set new namelist items differently when excess ice is on or off
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+  Note that the coldstart variables are always used even without excess ice or with an finidat file.
+  InitCold is always called so the variables are always set.
+
+Changes to tests or testing:
+   New tests for build-namelist unit tester
+
+Testing summary: regular
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS (998 are different from baseline)
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho -----
+    izumi -------
+
+  any other testing (give details below):
+
+  SMS_Lm12.f09_f09_mg17.I1850Clm60Sp.derecho_intel.clm-ExcessIceStartup_output_sp_exice
+     derecho ---- PASS
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations:
+    - what platforms/compilers:
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+  #2465 -- fix excess ice cold starts
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.017
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Tue 30 Jul 2024 08:39:20 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 15a67bcf04..c70d3a372b 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.018     erik 07/31/2024 Fix/excess ice cold start
        ctsm5.2.017     erik 07/30/2024 Dust emissions control moved to cmeps
        ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof

From 574380df9b4a465cfdb76d861d16b3f0ea8ec667 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 31 Jul 2024 16:54:27 -0600
Subject: [PATCH 0820/1248] Fix author

---
 doc/ChangeLog | 2 +-
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index f3bf5c91c1..049a075ad6 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,6 +1,6 @@
 ===============================================================
 Tag name: ctsm5.2.018
-Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Originator(s): mvdebolskiy
 Date: Wed 31 Jul 2024 04:38:36 PM MDT
 One-line Summary: Fix/excess ice cold start
 
diff --git a/doc/ChangeSum b/doc/ChangeSum
index c70d3a372b..d631d2d7dc 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.018     erik 07/31/2024 Fix/excess ice cold start
+       ctsm5.2.018 mvdebols 07/31/2024 Fix/excess ice cold start
        ctsm5.2.017     erik 07/30/2024 Dust emissions control moved to cmeps
        ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof

From fb4941b301bead3f5cd42d5147a47a0efa07ac75 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 1 Aug 2024 00:59:41 -0600
Subject: [PATCH 0821/1248] Don't need to set coldstart temp or depth as these
 tests are starting up from finidat files

---
 .../testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm     | 2 --
 1 file changed, 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm
index aa2c9efa5b..f61ca32a79 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm
@@ -1,4 +1,2 @@
  use_excess_ice = .true.
  use_excess_ice_streams = .true.
- excess_ice_coldstart_depth = 0.5
- excess_ice_coldstart_temp = -5.0

From 3ed874dd619f2d2af32e4292ae12a37fb765084f Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 1 Aug 2024 05:40:03 -0600
Subject: [PATCH 0822/1248] add more to notes.

---
 doc/ChangeLog | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 049a075ad6..9bd2f3e86f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -11,9 +11,13 @@ Changed the way soil temperature is initialized when excess ice is on and the mo
 
 Specific notes
 
-Added 2 parameters: excess_ice_coldstart_depth and excess_ice_coldstart_temp which control top depth and soil temperature for soil layers in columns where excess ice is present. Other columns get their default soil temperature.
+TemperatureType now has a private ReadNL subroutine that reads two new namelist options: excess_ice_coldstart_depth and excess_ice_coldstart_temp which control top depth (higher layers get default initial temperature) and soil temperature for soil layers ONLY in columns where excess ice is present. Other columns get their default soil temperature. 
+
+New namelist options belong to a new group "clm_temperature_inparm" with its own logic routine. This is done so in the future hardcoded cold start temperatures can be moved to the namelists. Two namelist tests have been added to check for invalid values logic as well as a test for use_excess_ice_streams logic. use_excess_ice_streams has no default value (due to options for restart) and default value set in the CLMBuildNamelist.pm.
+
+excessicestream_type has been taken out of waterstate_type and its routines are called directly in clm_inst%Init. Checks for UseExcessIceStreams() are still in place in WaterStateType.F90 for double-checking. clm_inst%Init now has a new local variable with excess ice concentration that are read from streams (or zeros if use_excess_ice is false). Arguments for temperature_type%Init and water_type%Init (and children types) have been changed to include this new variable. Fortran unit tests are also updated to account for these new arguments.
+
 
-excessicestream_type has been taken out of waterstate_type and its routines are called directly in clm_inst%Init. Checks for UseExcessIceStreams() are still in place in WaterStateType.F90 for double-checking.
 
 
 Significant changes to scientifically-supported configurations

From 3a47c5d1e5b4044018a572c6aa3788edd73f14ad Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 1 Aug 2024 09:53:41 -0600
Subject: [PATCH 0823/1248] CTSM5.3 updates part 2 (incomplete because SSPs
 pending)

---
 .../ctsm/toolchain/gen_mksurfdata_namelist.py | 26 +++++++++----------
 .../gen_mksurfdata_namelist.xml               |  8 +++---
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/python/ctsm/toolchain/gen_mksurfdata_namelist.py b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
index b0c2016ccb..662e58bc8b 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_namelist.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
@@ -463,16 +463,16 @@ def check_ssp_years(start_year, end_year):
     """
     Check years associated with SSP period
     """
-    if int(start_year) > 2022:
+    if int(start_year) > 2023:
         error_msg = (
-            "ERROR: if start-year > 2022 must add an --ssp_rcp "
+            "ERROR: if start-year > 2023 must add an --ssp_rcp "
             "argument that is not none: valid opts for ssp-rcp "
             f"are {valid_opts}"
         )
         sys.exit(error_msg)
-    elif int(end_year) > 2022:
+    elif int(end_year) > 2023:
         error_msg = (
-            "ERROR: if end-year > 2022 must add an --ssp-rcp "
+            "ERROR: if end-year > 2023 must add an --ssp-rcp "
             "argument that is not none: valid opts for ssp-rcp "
             f"are {valid_opts}"
         )
@@ -547,14 +547,14 @@ def determine_pft_years(start_year, end_year, potveg):
         pft_years = "2005"
     elif int(start_year) >= 850 and int(end_year) <= 1849:
         pft_years = "0850-1849"
-    elif int(start_year) >= 1700 and int(start_year) <= 2100 and int(end_year) <= 2022:
-        pft_years = "1700-2022"
+    elif int(start_year) >= 1700 and int(start_year) <= 2100 and int(end_year) <= 2023:
+        pft_years = "1700-2023"
     elif int(start_year) >= 1700 and int(start_year) <= 2100 and int(end_year) <= 2100:
-        pft_years = "1700-2022"
-        pft_years_ssp = "2023-2100"
+        pft_years = "1700-2023"
+        pft_years_ssp = "2024-2100"
     elif int(start_year) >= 2023 and int(start_year) <= 2100 and int(end_year) <= 2100:
         pft_years = "-999"
-        pft_years_ssp = "2023-2100"
+        pft_years_ssp = "2024-2100"
     else:
         error_msg = (
             f"ERROR: start_year is {start_year} and end_year is "
@@ -647,7 +647,7 @@ def write_nml_rawinput(
             # write everything else
             nlfile.write(f"  {key} = '{value}' \n")
 
-    if start_year <= 2022:
+    if start_year <= 2023:
         mksrf_fvegtyp = rawdata_files["mksrf_fvegtyp"]
         mksrf_fvegtyp_mesh = rawdata_files["mksrf_fvegtyp_mesh"]
         mksrf_fhrvtyp = rawdata_files["mksrf_fvegtyp"]
@@ -716,7 +716,7 @@ def handle_transient_run(
     with open(landuse_fname, "w", encoding="utf-8") as landuse_file:
         for year in range(start_year, end_year + 1):
             year_str = str(year)
-            if year <= 2022:
+            if year <= 2023:
                 file1 = rawdata_files["mksrf_fvegtyp"]
                 file2 = rawdata_files["mksrf_fvegtyp_urban"]
                 file3 = rawdata_files["mksrf_fvegtyp_lake"]
@@ -834,8 +834,8 @@ def determine_input_rawdata(start_year, input_path, attribute_list):
                     max_match_child = child2
 
         if max_match_child is None:
-            # For years greater than 2022 - mksrf_fvegtyp_ssp must have a match
-            if start_year > 2022:
+            # For years greater than 2023 - mksrf_fvegtyp_ssp must have a match
+            if start_year > 2023:
                 if "mksrf_fvegtyp_ssp" not in child1.tag:
                     error_msg = f"ERROR: {child1.tag} has no matches"
                     sys.exit(error_msg)
diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index 1e24accc4d..102162c0dc 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -221,7 +221,7 @@ version of the raw dataset will probably go away.
     </entry>
 
     <entry pft_years="1700">
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_1700.c240709.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_1700.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_1850.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
@@ -263,12 +263,12 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
     </entry>
 
-    <!-- Historical period from 1700 to 2022 (expect 2023 soon) -->
+    <!-- Historical period from 1700 to 2023 -->
     <!-- Lake and urban data from 1700 to 1849 is copied from 1850 -->
     <!-- Lake data from 2018 to 2023 is copied from 2017 -->
     <!-- Urban data from 2016 to 2023 is copied from 2015 -->
-    <entry pft_years="1700-2022" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_%y.c240709.nc</data_filename>
+    <entry pft_years="1700-2023" >
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_%y_cdf5_c20220910.nc</urban_filename>

From d5e1eef7c81e53000ac477cc9e8bb07186a28a8e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 1 Aug 2024 11:23:17 -0600
Subject: [PATCH 0824/1248] CTSM5.3 updates part 2b (should have been in the
 prev. commit)

---
 .../mksurfdata_esmf/gen_mksurfdata_namelist.xml  | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index 102162c0dc..c4c11cb93a 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -282,7 +282,7 @@ version of the raw dataset will probably go away.
   <mksrf_fvegtyp_ssp>
 
     <!-- SSP1-RCP 2.6 -->
-    <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2024-2100" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP126Deg025_240717/mksrf_landuse_ctsm53_TRSSP126_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
@@ -295,42 +295,42 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_2100_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP1-RCP 1.9 -->
-    <entry  ssp_rcp="SSP1-1.9" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP1-1.9" pft_years_ssp="2024-2100" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP119Deg025_240717/mksrf_landuse_ctsm53_TRSSP119_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP2-RCP 4.5 -->
-    <entry  ssp_rcp="SSP2-4.5" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP2-4.5" pft_years_ssp="2024-2100" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP245Deg025_240717/mksrf_landuse_ctsm53_TRSSP245_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp2/urban_properties_GaoOneil_05deg_ThreeClass_ssp2_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP3-RCP 7.0 -->
-    <entry  ssp_rcp="SSP3-7.0" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP3-7.0" pft_years_ssp="2024-2100" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP370Deg025_240717/mksrf_landuse_ctsm53_TRSSP370_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp3/urban_properties_GaoOneil_05deg_ThreeClass_ssp3_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP4-RCP 3.4 -->
-    <entry  ssp_rcp="SSP4-3.4" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP4-3.4" pft_years_ssp="2024-2100" >
       <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-3.4.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP4-3.4_%y.c20230226.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp4/urban_properties_GaoOneil_05deg_ThreeClass_ssp4_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP4-RCP 6.0 -->
-    <entry  ssp_rcp="SSP4-6.0" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP4-6.0" pft_years_ssp="2024-2100" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP460Deg025_240717/mksrf_landuse_ctsm53_TRSSP460_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp4/urban_properties_GaoOneil_05deg_ThreeClass_ssp4_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP5-RCP 8.5 -->
-    <entry  ssp_rcp="SSP5-8.5" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP5-8.5" pft_years_ssp="2024-2100" >
       <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP585Deg025_240717/mksrf_landuse_ctsm53_TRSSP585_%y.c240717.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
@@ -343,7 +343,7 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp5/urban_properties_GaoOneil_05deg_ThreeClass_ssp5_2100_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP5-RCP 3.4 -->
-    <entry  ssp_rcp="SSP5-3.4" pft_years_ssp="2023-2100" >
+    <entry  ssp_rcp="SSP5-3.4" pft_years_ssp="2024-2100" >
       <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP5-3.4.simyr2015-2100.c20230226/mksrf_landuse_ctsm52_SSP5-3.4_%y.c20230226.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>

From 6012fc622a7f5867f6ed087841a0dd00fa6ea4c6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 1 Aug 2024 14:59:21 -0600
Subject: [PATCH 0825/1248] Update changelog with more info on the expected
 answer changes

---
 doc/ChangeLog | 21 ++++++++++++++-------
 doc/ChangeSum |  2 +-
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 049a075ad6..55e0bb1329 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.018
 Originator(s): mvdebolskiy
-Date: Wed 31 Jul 2024 04:38:36 PM MDT
+Date: Thu 01 Aug 2024 02:53:41 PM MDT
 One-line Summary: Fix/excess ice cold start
 
 Purpose and description of changes
@@ -76,13 +76,13 @@ Testing summary: regular
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho -----
-    izumi -------
+    derecho ----- OK
+    izumi ------- OK
 
   any other testing (give details below):
 
   SMS_Lm12.f09_f09_mg17.I1850Clm60Sp.derecho_intel.clm-ExcessIceStartup_output_sp_exice
-     derecho ---- PASS
+     derecho ---- PASS (but different from baseline)
 
 Answer changes
 --------------
@@ -90,9 +90,16 @@ Answer changes
 Changes answers relative to baseline:
 
   Summarize any changes to answers, i.e.,
-    - what code configurations:
-    - what platforms/compilers:
-    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+    - what code configurations: excess ice on
+    - what platforms/compilers: all
+    - nature of change: different at startup
+        Different for cold-start and can be different for a few points where the cold-start
+        values are still used on interpoaltion of an existing finidat file
+
+  Tests that compare different to baseline:
+  ERS_D.f10_f10_mg37.I1850Clm60Sp.izumi_nag.clm-ExcessIceStreams
+  SMS_Lm12.f09_f09_mg17.I1850Clm60Sp.derecho_intel.clm-ExcessIceStartup_output_sp_exice
+         failed baseline comparison (though answers for default physics configurations have not changed).
 
 Other details
 -------------
diff --git a/doc/ChangeSum b/doc/ChangeSum
index d631d2d7dc..7766c18851 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.018 mvdebols 07/31/2024 Fix/excess ice cold start
+       ctsm5.2.018 mvdebols 08/01/2024 Fix/excess ice cold start
        ctsm5.2.017     erik 07/30/2024 Dust emissions control moved to cmeps
        ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof

From 0f147f87c63d7cec705fb86f704a5c41ea73cebb Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 1 Aug 2024 16:43:46 -0600
Subject: [PATCH 0826/1248] Name hardwired coefficients into named params

---
 src/biogeochem/VOCEmissionMod.F90 | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
index b84d6a4ae8..3a6976a9ba 100644
--- a/src/biogeochem/VOCEmissionMod.F90
+++ b/src/biogeochem/VOCEmissionMod.F90
@@ -826,13 +826,14 @@ function get_gamma_SM(btran_in)
     !!!------- the drought algorithm--------
     real(r8), parameter :: a1 = -7.4463_r8
     real(r8), parameter :: b1 = 3.2552_r8
+    real(r8), parameter :: btran_threshold = 0.2_r8
     real(r8)            :: get_gamma_SM
     !---------------------------------------
 
     if (btran_in >= 1._r8) then
        get_gamma_SM = 1._r8
     else
-       get_gamma_SM = 1._r8 / (1._r8 + b1 * exp(a1 * (btran_in - 0.2_r8)))
+       get_gamma_SM = 1._r8 / (1._r8 + b1 * exp(a1 * (btran_in - btran_threshold)))
     endif
 
   end function get_gamma_SM
@@ -884,6 +885,12 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     real(r8), parameter :: ct3 = 0.00831_r8                ! empirical coefficient (0.0083 in User's Guide)
     real(r8), parameter :: tstd = 303.15_r8                ! std temperature [K]
     real(r8), parameter :: bet = 0.09_r8                   ! beta empirical coefficient [K-1]
+    real(r8), parameter :: std_act_energy_isopr = 95._r8  ! standard activation energy for isoprene
+    real(r8), parameter :: empirical_param_1 = 9.49_r8  ! empirical param for the activation energy in response to 10-day temperature change
+    real(r8), parameter :: empirical_param_2 = 0.53_r8  ! empirical param for the activation energy in response to 10-day temperature change
+    real(r8), parameter :: empirical_param_3 = 0.12_r8  ! empirical param for the emission factors of arctic C3 grass in response to 10-day temperature change
+    real(r8), parameter :: empirical_param_4 = 7.9_r8  ! empirical param for the emission factors of broadleaf deciduous boreal shrubs in response to 10-day temperature change
+    real(r8), parameter :: empirical_param_5 = 0.217_r8  ! empirical param for the emission factors of broadleaf deciduous boreal shrubs in response to 10-day temperature change
     !-----------------------------------------------------------------------
 
     ! Light dependent fraction (Guenther et al., 2006)
@@ -892,11 +899,11 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
        topt = co1 + (co2 * (t_veg240_in-tstd0))
        if ( (ivt_in == nbrdlf_dcd_brl_shrub) ) then  ! boreal-deciduous-shrub
        ! coming from BEAR-oNS campaign willows results
-             Eopt = 7.9_r8 * exp (0.217_r8 * (t_veg24_in - tfrz - 24.0_r8))
+          Eopt = empirical_param_4 * exp (empirical_param_5 * (t_veg24_in - tfrz - 24.0_r8))
        else if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-             Eopt = exp(0.12_r8 * (t_veg240_in - tfrz - 15._r8))
+          Eopt = exp(empirical_param_3 * (t_veg240_in - tfrz - 15._r8))
        else
-             Eopt = Ceo_in * exp (co4 * (t_veg24_in - tstd0)) * exp(co4 * (t_veg240_in - tstd0))
+          Eopt = Ceo_in * exp (co4 * (t_veg24_in - tstd0)) * exp(co4 * (t_veg240_in - tstd0))
        endif
 
     else
@@ -906,7 +913,7 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     x = ( (1._r8/topt) - (1._r8/(t_veg_in)) ) / ct3
     ! for the boreal grass from BEAR-oNS campaign
     if ( (ivt_in == nc3_arctic_grass ) ) then  ! boreal-grass
-        bet_arc_c3 = 95._r8 + 9.49_r8 * exp(0.53_r8 * (tfrz + 15._r8 - t_veg240_in))
+        bet_arc_c3 = std_act_energy_isopr + empirical_param_1 * exp(empirical_param_2 * (tfrz + 15._r8 - t_veg240_in))
         bet_arc_c3 = min(bet_arc_c3, bet_arc_c3_max)
         gamma_t_LDF = Eopt * exp(bet_arc_c3 * ((1._r8 / (tfrz + 30._r8) - 1._r8 / t_veg_in) / ct3))
     else

From c5fb0bbb9a4cacb7e285f5169c5d5c39c25216e3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 1 Aug 2024 17:45:40 -0600
Subject: [PATCH 0827/1248] Documentation for two variables

---
 src/biogeochem/VOCEmissionMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
index 3a6976a9ba..533c7d892e 100644
--- a/src/biogeochem/VOCEmissionMod.F90
+++ b/src/biogeochem/VOCEmissionMod.F90
@@ -874,8 +874,8 @@ function get_gamma_T(t_veg240_in, t_veg24_in,t_veg_in, ct1_in, ct2_in, betaT_in,
     real(r8) :: gamma_t_LDF             ! activity factor for temperature
     real(r8) :: gamma_t_LIF             ! activity factor for temperature
     real(r8) :: x                       ! temporary i
-    real(r8) :: bet_arc_c3
-    real(r8), parameter :: bet_arc_c3_max = 300._r8
+    real(r8) :: bet_arc_c3  ! activity factor for temperature for arctic C3 grass
+    real(r8), parameter :: bet_arc_c3_max = 300._r8  ! max value, activity factor for temperature for arctic C3 graass
     real(r8), parameter :: co1 = 313._r8                   ! empirical coefficient
     real(r8), parameter :: co2 = 0.6_r8                    ! empirical coefficient
     real(r8), parameter :: co4 = 0.05_r8                   ! empirical coefficient

From 9dfc55a14af2ab918372e3323434c98a6ec78207 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 1 Aug 2024 17:47:20 -0600
Subject: [PATCH 0828/1248] Draft ChangeLog/ChangeSum

---
 doc/ChangeLog | 70 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 71 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index aeb7b2972f..03a3c8999b 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,74 @@
 ===============================================================
+Tag name: ctsm5.2.0??
+Originator(s): HuiWangWanderInGitHub (Hui Wang,huiw16@uci.edu)
+Date: Thu 01 Aug 2024 05:09:46 PM MDT
+One-line Summary: MEGAN updates (MEGAN-CLM6)
+
+Purpose and description of changes
+----------------------------------
+
+ We add new features to MEGANv2.1 for simulating isoprene emissions based on three recent studies conducted at the BAI lab in the University of California, Irvine. The first one is about the drought impact on isoprene (Wang et al., 2022). The second study investigates the effect of temperature history on the emission factors of boreal broadleaf deciduous shrubs (Wang et al., 2024a). The third study explores a different temperature response curve for C3 Arctic grass (Wang et al., 2024b, under press). These changes improved the model's representation of isoprene emissions during drought and in high-latitude ecosystems.
+
+ This work relates to issue #1323 and is based on the old MEGANv2.1 framework, but incorporates new scientific insights.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to documentation:
+ Hui Wang has offered to provide the modifications to the documentation that we need.
+ The PR https://github.com/ESCOMP/CTSM/pull/2588 includes a list of references.
+
+Substantial timing or memory changes:
+[e.g., check PFS test in the test suite and look at timings, if you
+expect possible significant timing changes]
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: All that calculate BVOCs (so not FATES)
+    - what platforms/compilers: All
+    - nature of change: Larger than roundoff, only in BVOC output and specifically limited to MEG_ and _voc variables.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/CTSM/pull/2588
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.017
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Tue 30 Jul 2024 08:39:20 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 15a67bcf04..315a5cb470 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.0??   slevis 08/01/2024 MEGAN updates (MEGAN-CLM6)
        ctsm5.2.017     erik 07/30/2024 Dust emissions control moved to cmeps
        ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof

From a8371f7c1d76ea7b0ccb75ebe9ca63ae090473b2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 2 Aug 2024 09:27:21 -0600
Subject: [PATCH 0829/1248] Update change files

---
 doc/ChangeLog | 7 +++----
 doc/ChangeSum | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index c5c7c3b9f7..f5cf28096c 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.018
 Originator(s): mvdebolskiy
-Date: Thu 01 Aug 2024 02:53:41 PM MDT
+Date: Fri 02 Aug 2024 09:26:33 AM MDT
 One-line Summary: Fix/excess ice cold start
 
 Purpose and description of changes
@@ -86,7 +86,7 @@ Testing summary: regular
   any other testing (give details below):
 
   SMS_Lm12.f09_f09_mg17.I1850Clm60Sp.derecho_intel.clm-ExcessIceStartup_output_sp_exice
-     derecho ---- PASS (but different from baseline)
+     derecho ---- PASS
 
 Answer changes
 --------------
@@ -94,7 +94,7 @@ Answer changes
 Changes answers relative to baseline:
 
   Summarize any changes to answers, i.e.,
-    - what code configurations: excess ice on
+    - what code configurations: excess ice on, with coldstart or with finidat file interpolation
     - what platforms/compilers: all
     - nature of change: different at startup
         Different for cold-start and can be different for a few points where the cold-start
@@ -102,7 +102,6 @@ Changes answers relative to baseline:
 
   Tests that compare different to baseline:
   ERS_D.f10_f10_mg37.I1850Clm60Sp.izumi_nag.clm-ExcessIceStreams
-  SMS_Lm12.f09_f09_mg17.I1850Clm60Sp.derecho_intel.clm-ExcessIceStartup_output_sp_exice
          failed baseline comparison (though answers for default physics configurations have not changed).
 
 Other details
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 7766c18851..3d9d70bc54 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.018 mvdebols 08/01/2024 Fix/excess ice cold start
+       ctsm5.2.018 mvdebols 08/02/2024 Fix/excess ice cold start
        ctsm5.2.017     erik 07/30/2024 Dust emissions control moved to cmeps
        ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets
        ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof

From 61d99830c34fcb2b04dca54a605956e4add50350 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 2 Aug 2024 11:24:46 -0600
Subject: [PATCH 0830/1248] CTSM5.3 updates part 3 (SSPs)

---
 tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index c4c11cb93a..dde824e02c 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -283,7 +283,7 @@ version of the raw dataset will probably go away.
 
     <!-- SSP1-RCP 2.6 -->
     <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP126Deg025_240717/mksrf_landuse_ctsm53_TRSSP126_%y.c240717.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP126Deg025_240728/mksrf_landuse_ctsm53_TRSSP126_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
@@ -296,21 +296,21 @@ version of the raw dataset will probably go away.
     </entry>
     <!-- SSP1-RCP 1.9 -->
     <entry  ssp_rcp="SSP1-1.9" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP119Deg025_240717/mksrf_landuse_ctsm53_TRSSP119_%y.c240717.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP119Deg025_240728/mksrf_landuse_ctsm53_TRSSP119_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP2-RCP 4.5 -->
     <entry  ssp_rcp="SSP2-4.5" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP245Deg025_240717/mksrf_landuse_ctsm53_TRSSP245_%y.c240717.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP245Deg025_240728/mksrf_landuse_ctsm53_TRSSP245_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp2/urban_properties_GaoOneil_05deg_ThreeClass_ssp2_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP3-RCP 7.0 -->
     <entry  ssp_rcp="SSP3-7.0" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP370Deg025_240717/mksrf_landuse_ctsm53_TRSSP370_%y.c240717.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP370Deg025_240728/mksrf_landuse_ctsm53_TRSSP370_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp3/urban_properties_GaoOneil_05deg_ThreeClass_ssp3_%y_cdf5_c20220910.nc</urban_filename>
@@ -324,14 +324,14 @@ version of the raw dataset will probably go away.
     </entry>
     <!-- SSP4-RCP 6.0 -->
     <entry  ssp_rcp="SSP4-6.0" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP460Deg025_240717/mksrf_landuse_ctsm53_TRSSP460_%y.c240717.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP460Deg025_240728/mksrf_landuse_ctsm53_TRSSP460_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp4/urban_properties_GaoOneil_05deg_ThreeClass_ssp4_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP5-RCP 8.5 -->
     <entry  ssp_rcp="SSP5-8.5" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP585Deg025_240717/mksrf_landuse_ctsm53_TRSSP585_%y.c240717.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP585Deg025_240728/mksrf_landuse_ctsm53_TRSSP585_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp5/urban_properties_GaoOneil_05deg_ThreeClass_ssp5_%y_cdf5_c20220910.nc</urban_filename>

From b09ef392ba4026ac80f4416c6c9b88bf780d34d8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 5 Aug 2024 15:46:52 -0600
Subject: [PATCH 0831/1248] mpi bcast dust_emis_method so can go between Leung
 and Zender methods

---
 src/main/controlMod.F90 | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 46d9e9958a..ef4ead3709 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -871,6 +871,9 @@ subroutine control_spmd()
        call mpi_bcast (anoxia, 1, MPI_LOGICAL, 0, mpicom, ier)
     end if
 
+    ! dust emissions
+    call mpi_bcast (dust_emis_method, len(dust_emis_method), MPI_CHARACTER, 0, mpicom, ier)
+
     ! lakes
     call mpi_bcast (deepmixing_depthcrit,  1, MPI_REAL8, 0, mpicom, ier)
     call mpi_bcast (deepmixing_mixfact,    1, MPI_REAL8, 0, mpicom, ier)

From 90b534af01502b20e7bbd3ceb8250746b4eadfd5 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 5 Aug 2024 17:56:19 -0600
Subject: [PATCH 0832/1248] Change Izumi nag RxCropCalsAdaptGGCMI to debug.

Previously: SMS_P128x1_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI
Now:        SMS_D_P128x1_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI
---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 951e0d8d5b..ce2b6de435 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3578,7 +3578,7 @@
     </options>
   </test>
 
-  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
+  <test name="SMS_D_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>

From 7387303e8f5c1f40a60604dbf170dea12a877039 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 5 Aug 2024 17:59:53 -0600
Subject: [PATCH 0833/1248] Change 25-month crop_calendars tests to use
 cropMonthOutput.

---
 cime_config/testdefs/testlist_clm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index ce2b6de435..d6ea6b08da 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3569,7 +3569,7 @@
     </options>
   </test>
 
-  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsNoAdapt">
+  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsNoAdapt">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
@@ -3578,7 +3578,7 @@
     </options>
   </test>
 
-  <test name="SMS_D_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/RxCropCalsAdaptGGCMI">
+  <test name="SMS_D_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>

From d3de08bfff1ec10ba088442d39f0da59ee106378 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 5 Aug 2024 18:01:36 -0600
Subject: [PATCH 0834/1248] Change 25-month crop_calendars tests to be 733 days
 instead.

---
 cime_config/testdefs/testlist_clm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index d6ea6b08da..3ab3f86436 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3569,7 +3569,7 @@
     </options>
   </test>
 
-  <test name="SMS_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsNoAdapt">
+  <test name="SMS_Ld733" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsNoAdapt">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
@@ -3578,7 +3578,7 @@
     </options>
   </test>
 
-  <test name="SMS_D_Lm25" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsAdaptGGCMI">
+  <test name="SMS_D_Ld733" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>

From f40bdbb139656885a37d6199f9d4c37eda45069a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 5 Aug 2024 18:04:01 -0600
Subject: [PATCH 0835/1248] Add temporary test suite fix_nag_bld_2659.

---
 cime_config/testdefs/testlist_clm.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 3ab3f86436..ea02ac9375 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3572,6 +3572,7 @@
   <test name="SMS_Ld733" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsNoAdapt">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="derecho" compiler="intel" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -3583,6 +3584,7 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>

From e72354571a2186c14400791490cc967887565de5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 5 Aug 2024 22:25:03 -0600
Subject: [PATCH 0836/1248] Add a subroutine to set drag partition for testing,
 label input/output variables for DustEmission, remove begc/endc

---
 src/biogeochem/DustEmisLeung2023.F90 | 81 ++++++++++++++++++----------
 1 file changed, 53 insertions(+), 28 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index f6cd6bed89..6cc86e4eb5 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -77,6 +77,8 @@ module DustEmisLeung2023
      procedure , private :: InitHistory     ! History initialization
      procedure , private :: InitCold
      procedure , private :: CalcDragPartition ! Calculate drag partitioning based on Prigent roughness stream
+     ! Public for unit testing
+     procedure , public  :: SetDragPartition  ! Set drag partitioning for testing
 
   end type dust_emis_leung2023_type
 
@@ -126,11 +128,9 @@ subroutine InitAllocate(this, bounds)
    type(bounds_type), intent(in) :: bounds
    !
    ! !LOCAL VARIABLES:
-   integer :: begc,endc
    integer :: begp,endp
    !------------------------------------------------------------------------
 
-   begc = bounds%begc ; endc = bounds%endc
    begp = bounds%begp ; endp = bounds%endp
    allocate(this%dst_emiss_coeff_patch     (begp:endp))        ; this%dst_emiss_coeff_patch     (:)   = nan
    allocate(this%wnd_frc_thr_patch         (begp:endp))        ; this%wnd_frc_thr_patch         (:)   = nan
@@ -208,11 +208,9 @@ subroutine InitHistory(this, bounds)
     type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
-    integer :: begc,endc
     integer :: begp,endp
     !------------------------------------------------------------------------
 
-    begc = bounds%begc; endc = bounds%endc
     begp = bounds%begp; endp = bounds%endp
     this%dst_emiss_coeff_patch(begp:endp) = spval
     call hist_addfld1d (fname='DUST_EMIS_COEFF', units='dimensionless',  &
@@ -434,34 +432,34 @@ subroutine DustEmission (this, bounds, &
          h2osoi_ice          => waterstatebulk_inst%h2osoi_ice_col   , & ! Input:  [real(r8) (:,:) ]  frozen soil water (kg/m2)
 
          fv                  => frictionvel_inst%fv_patch            , & ! Input:  [real(r8) (:)   ]  friction velocity (m/s) (for dust model)
-         u10                 => frictionvel_inst%u10_patch           , & ! Input:  [real(r8) (:)   ]  10-m wind (m/s) (created for dust model)
+         obu                 => frictionvel_inst%obu_patch           , & ! Input:  [real(r8) (:)   ] Monin-Obukhov length from the friction Velocity module          obu                 => frictionvel_inst%obu_patch             & ! Input:  [real(r8) (:)   ] Monin-Obukhov length from the friction Velocity module 
+
+         dpfct_rock          => this%dpfct_rock_patch                , & ! Input:  rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
 
          flx_mss_vrt_dst     => this%flx_mss_vrt_dst_patch           , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)
          flx_mss_vrt_dst_tot => this%flx_mss_vrt_dst_tot_patch       , & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
          ! below variables are defined in Kok et al. (2014) or (mostly) Leung et al. (2023) dust emission scheme. dmleung 16 Feb 2024
-         dst_emiss_coeff     => this%dst_emiss_coeff_patch           , & ! Output dust emission coefficient
-         wnd_frc_thr         => this%wnd_frc_thr_patch               , & ! output fluid threshold
-         wnd_frc_thr_dry     => this%wnd_frc_thr_dry_patch           , & ! output dry fluid threshold
-         wnd_frc_thr_it      => this%wnd_frc_thr_it_patch            , & ! output impact threshold
-         lnd_frc_mble        => this%lnd_frc_mble_patch              , & ! output bare land fraction
-         wnd_frc_soil        => this%wnd_frc_soil_patch              , & ! soil friction velocity u_*s = (u_*)(f_eff)
-         gwc                 => this%gwc_patch                       , & ! output gravimetric water content
-         liq_frac            => this%liq_frac_patch                  , & ! output fraction of liquid moisture
-         intrmtncy_fct       => this%intrmtncy_fct_patch             , & ! output intermittency factor eta (fraction of time that dust emission is active within a timestep)
-         stblty              => this%stblty_patch                    , & ! stability in similarity theory (no need to output)
-         u_mean_slt          => this%u_mean_slt_patch                , & ! output mean wind speed at 0.1 m height translated from friction velocity using the log law of the wall, assuming neutral condition
-         u_sd_slt            => this%u_sd_slt_patch                  , & ! output standard deviation of wind speed from similarity theory
-         u_fld_thr           => this%u_fld_thr_patch                 , & ! output fluid threshold wind speed at 0.1 m height translated from the log law of the wall
-         u_impct_thr         => this%u_impct_thr_patch               , & ! output impact threshold wind speed at 0.1 m height translated from the log law of the wall
-         thr_crs_rate        => this%thr_crs_rate_patch              , & ! output threshold crossing rate in Comola 2019 intermittency parameterization
-         prb_crs_fld_thr     => this%prb_crs_fld_thr_patch           , & ! output probability of instantaneous wind crossing fluid threshold in Comola 2019 intermittency parameterization
-         prb_crs_impct_thr   => this%prb_crs_impct_thr_patch         , & ! output probability of instantaneous wind crossing impact threshold in Comola 2019 intermittency parameterization
-         ssr                 => this%ssr_patch                       , & ! output vegetation drag partition factor in Okin 2008 vegetation roughness effect (called shear stress ratio, SSR in Okin 2008)
-         vai_Okin            => this%vai_Okin_patch                  , & ! vegetation area index for calculating Okin-Pierre vegetation drag partitioning. vai=0 in the ssr equation will lead to infinity, so a small value is added into this vai dmleung defined. (no need to output) 16 Feb 2024
-         frc_thr_rghn_fct    => this%frc_thr_rghn_fct_patch          , & ! output hybrid/total drag partition factor considering both rock and vegetation drag partition factors.
-         wnd_frc_thr_std     => this%wnd_frc_thr_std_patch           , & ! standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
-         dpfct_rock          => this%dpfct_rock_patch                , & ! output rock drag partition factor defined in Marticorena and Bergametti 1995. A fraction between 0 and 1.
-         obu                 => frictionvel_inst%obu_patch             & ! Input:  [real(r8) (:)   ] Monin-Obukhov length from the friction Velocity module          obu                 => frictionvel_inst%obu_patch             & ! Input:  [real(r8) (:)   ] Monin-Obukhov length from the friction Velocity module 
+         dst_emiss_coeff     => this%dst_emiss_coeff_patch           , & ! Output: dust emission coefficient
+         wnd_frc_thr         => this%wnd_frc_thr_patch               , & ! Output: fluid threshold
+         wnd_frc_thr_dry     => this%wnd_frc_thr_dry_patch           , & ! Output: dry fluid threshold
+         wnd_frc_thr_it      => this%wnd_frc_thr_it_patch            , & ! Output: impact threshold
+         lnd_frc_mble        => this%lnd_frc_mble_patch              , & ! Output: bare land fraction
+         wnd_frc_soil        => this%wnd_frc_soil_patch              , & ! Output: soil friction velocity u_*s = (u_*)(f_eff)
+         gwc                 => this%gwc_patch                       , & ! output: gravimetric water content
+         liq_frac            => this%liq_frac_patch                  , & ! Output: fraction of liquid moisture
+         intrmtncy_fct       => this%intrmtncy_fct_patch             , & ! Output: intermittency factor eta (fraction of time that dust emission is active within a timestep)
+         stblty              => this%stblty_patch                    , & ! Output: stability in similarity theory (no need to output)
+         u_mean_slt          => this%u_mean_slt_patch                , & ! Output: mean wind speed at 0.1 m height translated from friction velocity using the log law of the wall, assuming neutral condition
+         u_sd_slt            => this%u_sd_slt_patch                  , & ! Output: standard deviation of wind speed from similarity theory
+         u_fld_thr           => this%u_fld_thr_patch                 , & ! Output: fluid threshold wind speed at 0.1 m height translated from the log law of the wall
+         u_impct_thr         => this%u_impct_thr_patch               , & ! Output: impact threshold wind speed at 0.1 m height translated from the log law of the wall
+         thr_crs_rate        => this%thr_crs_rate_patch              , & ! Output: threshold crossing rate in Comola 2019 intermittency parameterization
+         prb_crs_fld_thr     => this%prb_crs_fld_thr_patch           , & ! Output: probability of instantaneous wind crossing fluid threshold in Comola 2019 intermittency parameterization
+         prb_crs_impct_thr   => this%prb_crs_impct_thr_patch         , & ! Output: probability of instantaneous wind crossing impact threshold in Comola 2019 intermittency parameterization
+         ssr                 => this%ssr_patch                       , & ! Output: vegetation drag partition factor in Okin 2008 vegetation roughness effect (called shear stress ratio, SSR in Okin 2008)
+         vai_Okin            => this%vai_Okin_patch                  , & ! Output: vegetation area index for calculating Okin-Pierre vegetation drag partitioning. vai=0 in the ssr equation will lead to infinity, so a small value is added into this vai dmleung defined. (no need to output) 16 Feb 2024
+         frc_thr_rghn_fct    => this%frc_thr_rghn_fct_patch          , & ! Output: hybrid/total drag partition factor considering both rock and vegetation drag partition factors.
+         wnd_frc_thr_std     => this%wnd_frc_thr_std_patch             & ! Output: standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
          )
 
       ttlai(bounds%begp : bounds%endp) = 0._r8
@@ -869,6 +867,33 @@ subroutine CalcDragPartition(this, bounds)
 
  end subroutine CalcDragPartition
 
+
+  !------------------------------------------------------------------------
+
+ subroutine SetDragPartition(this, bounds, drag_partition)
+   !
+   ! !DESCRIPTION:
+   ! Set the drag partition for testing
+   !
+   ! !USES:
+   !
+   ! !ARGUMENTS:
+   implicit none
+   class (dust_emis_leung2023_type) :: this
+   type(bounds_type), intent(in) :: bounds
+   real(r8), intent(in) :: drag_partition
+   !
+   ! !LOCAL VARIABLES:
+   integer  :: p     ! Indices
+
+   !---------------------------------------------------------------------
+
+   do p = bounds%begp,bounds%endp
+      this%dpfct_rock_patch(p) = drag_partition
+   end do
+
+ end subroutine SetDragPartition
+
  !==============================================================================
 
 end module DustEmisLeung2023
\ No newline at end of file

From 064c37cc02a207002e49cb7ab5e13195ffb0d669 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 7 Aug 2024 09:32:06 -0600
Subject: [PATCH 0837/1248] By default prigent streams are off for Zender dust
 emissions

---
 bld/CLMBuildNamelist.pm                       | 11 ++++++++---
 bld/namelist_files/namelist_defaults_ctsm.xml |  3 ++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index f449dcc6e3..f1e5935196 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1601,7 +1601,6 @@ sub process_namelist_inline_logic {
   setup_logic_fates($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_z0param($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl);
-  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);
 
   #########################################
   # namelist group: atm2lnd_inparm
@@ -1703,6 +1702,7 @@ sub process_namelist_inline_logic {
   # namelist options for dust emissions
   ######################################
   setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl);
+  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);
 
   #################################
   # namelist group: megan_emis_nl #
@@ -4671,12 +4671,17 @@ sub setup_logic_prigent_roughness {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
   my $var = "use_prigent_roughness";
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var );
+  my $dust_emis_method = remove_leading_and_trailing_quotes( $nl->get_value('dust_emis_method') );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
+              'dust_emis_method'=>$dust_emis_method );
   my $use_prigent = $nl->get_value($var);
   if ( &value_is_true($use_prigent) ) {
+     if ( $dust_emis_method eq "Leung_2023" ) {
+       $log->warning( "$var does NOT need to be set without dust_emis_method being Leung_2023" );
+     }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_prigentroughness' );
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_prigentroughness' );
-  } else {
+  } elsif ( $dust_emis_method eq "Leung_2023" ) {
     $log->fatal_error("variable \"$var\" MUST be true when Leung_2023 dust emission method is being used" );
   }
 }
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 9a56c1f1b0..ea82141663 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2001,7 +2001,8 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- Defaults for Prigent's roughness data      -->
 <!-- =========================================  -->
 
-<use_prigent_roughness>.true.</use_prigent_roughness>
+<use_prigent_roughness dust_emis_method="Leung_2023">.true.</use_prigent_roughness>
+<use_prigent_roughness                              >.false.</use_prigent_roughness>
 <stream_fldfilename_prigentroughness
 >lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c240127.nc</stream_fldfilename_prigentroughness>
 <stream_meshfile_prigentroughness

From e686d19a6123d39203105a0505157c50b7772cad Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 11:43:29 -0600
Subject: [PATCH 0838/1248] Remove include_user_mods from RxCropCals* and
 midDecStart testmods.

---
 cime_config/testdefs/testlist_clm.xml                     | 8 +++++---
 .../clm/RxCropCalsAdaptGGCMI/include_user_mods            | 1 -
 .../testmods_dirs/clm/RxCropCalsNoAdapt/include_user_mods | 1 -
 .../testmods_dirs/clm/midDecStart/include_user_mods       | 1 -
 4 files changed, 5 insertions(+), 6 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/include_user_mods
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index ea02ac9375..1e687522e4 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3587,24 +3587,26 @@
       <machine name="izumi" compiler="nag" category="fix_nag_bld_2659"/>
     </machines>
     <options>
-      <option name="wallclock">01:00:00</option>
+      <option name="wallclock">08:00:00</option>
     </options>
   </test>
 
-  <test name="ERP_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
+  <test name="ERP_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/crop--clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="derecho" compiler="intel" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
     </options>
   </test>
 
-  <test name="PEM_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
+  <test name="PEM_D_P128x1_Ld26" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/crop--clm/midDecStart--clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+      <machine name="derecho" compiler="intel" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
deleted file mode 100644
index 23ea3745e6..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsAdaptGGCMI/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../crop
diff --git a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/include_user_mods
deleted file mode 100644
index 23ea3745e6..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/RxCropCalsNoAdapt/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../crop
diff --git a/cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods
deleted file mode 100644
index fe0e18cf88..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/midDecStart/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../default

From 38926beaa6623270bf54ae9a2efdaa19305366a1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 12:40:02 -0600
Subject: [PATCH 0839/1248] Copy CNFireLi2021Mod.F90 to new
 CNFireLi2024Mod.F90.

Includes new fire_method li2024gswpfrc.
---
 bld/namelist_files/namelist_defaults_ctsm.xml |  15 +
 .../namelist_definition_ctsm.xml              |   3 +-
 src/biogeochem/CNFireFactoryMod.F90           |   3 +
 src/biogeochem/CNFireLi2024Mod.F90            | 658 ++++++++++++++++++
 4 files changed, 678 insertions(+), 1 deletion(-)
 create mode 100644 src/biogeochem/CNFireLi2024Mod.F90

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 655e97c47c..a7e59935a4 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -319,6 +319,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2021gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2021gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
 
+<rh_low                   fire_method="li2024gswpfrc" >30.0d00</rh_low>
+<rh_hgh                   fire_method="li2024gswpfrc" >80.0d00</rh_hgh>
+<bt_min                   fire_method="li2024gswpfrc" >0.85d00</bt_min>
+<bt_max                   fire_method="li2024gswpfrc" >0.98d00</bt_max>
+<cli_scale                fire_method="li2024gswpfrc" >0.025d00</cli_scale>
+<boreal_peatfire_c        fire_method="li2024gswpfrc" >0.09d-4</boreal_peatfire_c>
+<pot_hmn_ign_counts_alpha fire_method="li2024gswpfrc" >0.010d00</pot_hmn_ign_counts_alpha>
+<non_boreal_peatfire_c    fire_method="li2024gswpfrc" >0.17d-3</non_boreal_peatfire_c>
+<cropfire_a1              fire_method="li2024gswpfrc" >1.6d-4</cropfire_a1>
+<occur_hi_gdp_tree        fire_method="li2024gswpfrc" >0.33d00</occur_hi_gdp_tree>
+<lfuel                    fire_method="li2024gswpfrc" >75.d00</lfuel>
+<ufuel                    fire_method="li2024gswpfrc" >1050.d00</ufuel>
+<cmb_cmplt_fact_litter    fire_method="li2024gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
+<cmb_cmplt_fact_cwd       fire_method="li2024gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
+
 <!-- Canopy fluxes namelist defaults -->
 <use_undercanopy_stability               >.false.</use_undercanopy_stability>
 <use_undercanopy_stability phys="clm4_5" >.true.</use_undercanopy_stability>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 37c457141c..6b70c117e5 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -252,13 +252,14 @@ formulation (1).
 </entry>
 
 <entry id="fire_method" type="char*80" category="clm_physics"
-       group="cnfire_inparm" valid_values="nofire,li2014qianfrc,li2016crufrc,li2021gswpfrc" >
+       group="cnfire_inparm" valid_values="nofire,li2014qianfrc,li2016crufrc,li2021gswpfrc,li2024gswpfrc" >
 The method type to use for CNFire
 
 nofire:        Turn fire effects off
 li2014qianfrc: Reference paper Li, et. al.(2014) tuned with QIAN atmospheric forcing
 li2016crufrc:  Reference paper Li, et. al.(2016) tuned with CRU-NCEP atmospheric forcing
 li2021gswpfrc: Reference paper Li, et. al.(2021?) tuned with GSWP3 atmospheric forcing
+li2024gswpfrc: No reference paper yet
 </entry>
 
 <entry id="pot_hmn_ign_counts_alpha" type="real" category="clm_physics"
diff --git a/src/biogeochem/CNFireFactoryMod.F90 b/src/biogeochem/CNFireFactoryMod.F90
index dbd9b70d15..876e28a5e3 100644
--- a/src/biogeochem/CNFireFactoryMod.F90
+++ b/src/biogeochem/CNFireFactoryMod.F90
@@ -95,6 +95,7 @@ subroutine create_cnfire_method( NLFilename, cnfire_method )
     use CNFireLi2014Mod  , only : cnfire_li2014_type
     use CNFireLi2016Mod  , only : cnfire_li2016_type
     use CNFireLi2021Mod  , only : cnfire_li2021_type
+    use CNFireLi2024Mod  , only : cnfire_li2024_type
     use decompMod        , only : bounds_type
     !
     ! !ARGUMENTS:
@@ -115,6 +116,8 @@ subroutine create_cnfire_method( NLFilename, cnfire_method )
        allocate(cnfire_li2016_type :: cnfire_method)
     case ("li2021gswpfrc")
        allocate(cnfire_li2021_type :: cnfire_method)
+    case ("li2024gswpfrc")
+       allocate(cnfire_li2024_type :: cnfire_method)
 
     case default
        write(iulog,*) subname//' ERROR: unknown method: ', fire_method
diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
new file mode 100644
index 0000000000..9908732018
--- /dev/null
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -0,0 +1,658 @@
+module CNFireLi2024Mod
+
+#include "shr_assert.h"
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! module for fire dynamics
+  ! created in Nov, 2012  and revised in Apr, 2013 by F. Li and S. Levis
+  ! based on Li et al. (2012a,b; 2013)
+  ! revised in Apr, 2014 according to Li et al.(2014)
+  ! revised in May, 2015, according to Li et al. (2015, in prep.)
+  ! Fire-related parameters were calibrated or tuned in May, 2015 based on the
+  ! 20th Century transient simulations at f19_g16 with a CLM4.5 version
+  ! (clm50fire), CRUNCEPv5, and climatological lightning data.
+  !
+  ! !USES:
+  use shr_kind_mod                       , only : r8 => shr_kind_r8, CL => shr_kind_CL
+  use shr_const_mod                      , only : SHR_CONST_PI,SHR_CONST_TKFRZ
+  use shr_infnan_mod                     , only : shr_infnan_isnan
+  use clm_varctl                         , only : iulog
+  use clm_varpar                         , only : nlevdecomp, ndecomp_pools, nlevdecomp_full, nlevgrnd
+  use clm_varcon                         , only : dzsoi_decomp
+  use pftconMod                          , only : noveg, pftcon
+  use abortutils                         , only : endrun
+  use decompMod                          , only : bounds_type
+  use subgridAveMod                      , only : p2c
+  use atm2lndType                        , only : atm2lnd_type
+  use CNDVType                           , only : dgvs_type
+  use CNVegStateType                     , only : cnveg_state_type
+  use CNVegCarbonStateType               , only : cnveg_carbonstate_type, spinup_factor_deadwood
+  use CNVegCarbonFluxType                , only : cnveg_carbonflux_type
+  use CNVegNitrogenStateType             , only : cnveg_nitrogenstate_type
+  use CNVegNitrogenFluxType              , only : cnveg_nitrogenflux_type
+  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
+  use EnergyFluxType                     , only : energyflux_type
+  use SaturatedExcessRunoffMod           , only : saturated_excess_runoff_type
+  use WaterDiagnosticBulkType            , only : waterdiagnosticbulk_type
+  use Wateratm2lndBulkType               , only : wateratm2lndbulk_type
+  use WaterStateBulkType                 , only : waterstatebulk_type
+  use SoilStateType                      , only : soilstate_type
+  use SoilWaterRetentionCurveMod         , only : soil_water_retention_curve_type
+  use GridcellType                       , only : grc
+  use ColumnType                         , only : col
+  use PatchType                          , only : patch
+  use SoilBiogeochemStateType            , only : get_spinup_latitude_term
+  use FireMethodType                     , only : fire_method_type
+  use CNFireBaseMod                      , only : cnfire_base_type, cnfire_const, cnfire_params
+  !
+  implicit none
+  private
+  !
+  ! !PUBLIC TYPES:
+  public :: cnfire_li2024_type
+  !
+  type, extends(cnfire_base_type) :: cnfire_li2024_type
+     private
+  contains
+     !
+     ! !PUBLIC MEMBER FUNCTIONS:
+     procedure, public :: need_lightning_and_popdens
+     procedure, public :: CNFireArea    ! Calculate fire area
+  end type cnfire_li2024_type
+
+  !
+  ! !PRIVATE MEMBER DATA:
+  !-----------------------------------------------------------------------
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+contains
+
+  !-----------------------------------------------------------------------
+  function need_lightning_and_popdens(this)
+    ! !ARGUMENTS:
+    class(cnfire_li2024_type), intent(in) :: this
+    logical :: need_lightning_and_popdens  ! function result
+    !
+    ! !LOCAL VARIABLES:
+
+    character(len=*), parameter :: subname = 'need_lightning_and_popdens'
+    !-----------------------------------------------------------------------
+
+    need_lightning_and_popdens = .true.
+  end function need_lightning_and_popdens
+
+  !-----------------------------------------------------------------------
+  subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
+       num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, &
+       atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, &
+       wateratm2lndbulk_inst, waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
+       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+    !
+    ! !DESCRIPTION:
+    ! Computes column-level burned area
+    !
+    ! !USES:
+    use clm_time_manager     , only: get_step_size_real, get_curr_days_per_year, get_curr_date, get_nstep
+    use clm_varcon           , only: secspday, secsphr
+    use clm_varctl           , only: spinup_state
+    use pftconMod            , only: nc4_grass, nc3crop, ndllf_evr_tmp_tree
+    use pftconMod            , only: nbrdlf_evr_trp_tree, nbrdlf_dcd_trp_tree, nbrdlf_evr_shrub
+    use dynSubgridControlMod , only : run_has_transient_landcover
+    !
+    ! !ARGUMENTS:
+    class(cnfire_li2024_type)                             :: this
+    type(bounds_type)                     , intent(in)    :: bounds
+    integer                               , intent(in)    :: num_soilc       ! number of soil columns in filter
+    integer                               , intent(in)    :: filter_soilc(:) ! filter for soil columns
+    integer                               , intent(in)    :: num_soilp       ! number of soil patches in filter
+    integer                               , intent(in)    :: filter_soilp(:) ! filter for soil patches
+    integer                               , intent(in)    :: num_exposedvegp        ! number of points in filter_exposedvegp
+    integer                               , intent(in)    :: filter_exposedvegp(:)  ! patch filter for non-snow-covered veg
+    integer                               , intent(in)    :: num_noexposedvegp       ! number of points in filter_noexposedvegp
+    integer                               , intent(in)    :: filter_noexposedvegp(:) ! patch filter where frac_veg_nosno is 0
+    type(atm2lnd_type)                    , intent(in)    :: atm2lnd_inst
+    type(energyflux_type)                 , intent(in)    :: energyflux_inst
+    type(saturated_excess_runoff_type)    , intent(in)    :: saturated_excess_runoff_inst
+    type(waterdiagnosticbulk_type)        , intent(in)    :: waterdiagnosticbulk_inst
+    type(wateratm2lndbulk_type)           , intent(in)    :: wateratm2lndbulk_inst
+    type(waterstatebulk_type)             , intent(in)    :: waterstatebulk_inst
+    type(soilstate_type)                  , intent(in)    :: soilstate_inst
+    class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
+    type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
+    type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
+    real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
+    real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
+    !
+    ! !LOCAL VARIABLES:
+    !
+    integer  :: g,l,c,p,pi,j,fc,fp,kyr, kmo, kda, mcsec   ! index variables
+    real(r8) :: dt       ! time step variable (s)
+    real(r8) :: dayspyr  ! days per year
+    real(r8) :: cli      ! effect of climate on deforestation fires (0-1)
+    real(r8) :: cri      ! thresholds used for cli, (mm/d), see Eq.(7) in Li et al.(2013)
+    real(r8) :: fb       ! availability of fuel for regs A and C
+    real(r8) :: fhd      ! impact of hd on agricultural fire
+    real(r8) :: fgdp     ! impact of gdp on agricultural fire
+    real(r8) :: fire_m   ! combustability of fuel for fire occurrence
+    real(r8) :: spread_m ! combustability of fuel for fire spread
+    real(r8) :: Lb_lf    ! length-to-breadth ratio added by Lifang
+    integer  :: i_cwd    ! cwd pool
+    real(r8) :: lh       ! anthro. ignitions (count/km2/hr)
+    real(r8) :: fs       ! hd-dependent fires suppression (0-1)
+    real(r8) :: ig       ! total ignitions (count/km2/hr)
+    real(r8) :: hdmlf    ! human density
+    real(r8) :: arh, arh30 !combustability of fuel related to RH and RH30
+    real(r8) :: afuel    !weight for arh and arh30
+    real(r8) :: btran_col(bounds%begc:bounds%endc)
+    logical  :: transient_landcover  ! whether this run has any prescribed transient landcover
+    real(r8), target  :: prec60_col_target(bounds%begc:bounds%endc)
+    real(r8), target  :: prec10_col_target(bounds%begc:bounds%endc)
+    real(r8), target  :: rh30_col_target(bounds%begc:bounds%endc)
+    real(r8), pointer :: prec60_col(:)
+    real(r8), pointer :: prec10_col(:)
+    real(r8), pointer :: rh30_col(:)
+    !-----------------------------------------------------------------------
+
+    SHR_ASSERT_ALL_FL((ubound(totlitc_col)           == (/bounds%endc/)), sourcefile, __LINE__)
+    SHR_ASSERT_ALL_FL((ubound(decomp_cpools_vr_col)  == (/bounds%endc,nlevdecomp_full,ndecomp_pools/)), sourcefile, __LINE__)
+    SHR_ASSERT_ALL_FL((ubound(t_soi17cm_col)         == (/bounds%endc/)), sourcefile, __LINE__)
+
+    associate(                                                                      &
+         totlitc            => totlitc_col                                     , & ! Input:  [real(r8) (:)     ]  (gC/m2) total lit C (column-level mean)
+         decomp_cpools_vr   => decomp_cpools_vr_col                            , & ! Input:  [real(r8) (:,:,:) ]  (gC/m3)  VR decomp. (litter, cwd, soil)
+         tsoi17             => t_soi17cm_col                                   , & ! Input:  [real(r8) (:)     ]  (K) soil T for top 0.17 m
+
+         lfuel              => cnfire_const%lfuel                              , & ! Input:  [real(r8)         ]  (gC/m2) Lower threshold of fuel mass
+         ufuel              => cnfire_const%ufuel                              , & ! Input:  [real(r8)         ]  (gC/m2) Upper threshold of fuel mass
+         rh_hgh             => cnfire_const%rh_hgh                             , & ! Input:  [real(r8)         ]  (%) High relative humidity
+         rh_low             => cnfire_const%rh_low                             , & ! Input:  [real(r8)         ]  (%) Low relative humidity
+         cli_scale          => cnfire_const%cli_scale                          , & ! Input:  [real(r8)         ]  (/d) global constant for deforestation fires
+         cropfire_a1        => cnfire_const%cropfire_a1                        , & ! Input:  [real(r8)         ]  (/hr) a1 parameter for cropland fire
+         non_boreal_peatfire_c => cnfire_const%non_boreal_peatfire_c           , & ! Input:  [real(r8)         ]  (/hr) c parameter for non-boreal peatland fire
+         pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
+         boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
+
+         fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
+         fd_pft             => pftcon%fd_pft                                   , & ! Input:
+         rswf_min           => pftcon%rswf_min                                 , & ! Input:
+         rswf_max           => pftcon%rswf_max                                 , & ! Input:
+         btran2             => this%cnfire_base_type%btran2_patch              , & ! Input:  [real(r8) (:)     ]  root zone soil wetness
+         fsat               => saturated_excess_runoff_inst%fsat_col           , & ! Input:  [real(r8) (:)     ]  fractional area with water table at surface
+         wf2                => waterdiagnosticbulk_inst%wf2_col                , & ! Input:  [real(r8) (:)     ]  soil water as frac. of whc for top 0.17 m
+
+         is_cwd             => decomp_cascade_con%is_cwd                       , & ! Input:  [logical  (:)     ]  TRUE => pool is a cwd pool
+         spinup_factor      => decomp_cascade_con%spinup_factor                , & ! Input:  [real(r8) (:)     ]  factor for AD spinup associated with each pool
+
+         forc_rh            => wateratm2lndbulk_inst%forc_rh_grc               , & ! Input:  [real(r8) (:)     ]  relative humidity
+         forc_wind          => atm2lnd_inst%forc_wind_grc                      , & ! Input:  [real(r8) (:)     ]  atmospheric wind speed (m/s)
+         forc_t             => atm2lnd_inst%forc_t_downscaled_col              , & ! Input:  [real(r8) (:)     ]  downscaled atmospheric temperature (Kelvin)
+         forc_rain          => wateratm2lndbulk_inst%forc_rain_downscaled_col  , & ! Input:  [real(r8) (:)     ]  downscaled rain
+         forc_snow          => wateratm2lndbulk_inst%forc_snow_downscaled_col  , & ! Input:  [real(r8) (:)     ]  downscaled snow
+         prec60             => wateratm2lndbulk_inst%prec60_patch              , & ! Input:  [real(r8) (:)     ]  60-day running mean of tot. precipitation
+         prec10             => wateratm2lndbulk_inst%prec10_patch              , & ! Input:  [real(r8) (:)     ]  10-day running mean of tot. precipitation
+         rh30               => wateratm2lndbulk_inst%rh30_patch                , & ! Input:  [real(r8) (:)     ]  10-day running mean of tot. precipitation
+         dwt_smoothed       => cnveg_state_inst%dwt_smoothed_patch             , & ! Input:  [real(r8) (:)     ]  change in patch weight (-1 to 1) on the gridcell, smoothed over the year
+         cropf_col          => cnveg_state_inst%cropf_col                      , & ! Input:  [real(r8) (:)     ]  cropland fraction in veg column
+         gdp_lf             => this%gdp_lf_col                                 , & ! Input:  [real(r8) (:)     ]  gdp data
+         peatf_lf           => this%peatf_lf_col                               , & ! Input:  [real(r8) (:)     ]  peatland fraction data
+         abm_lf             => this%abm_lf_col                                 , & ! Input:  [integer  (:)     ]  prescribed crop fire time
+         baf_crop           => cnveg_state_inst%baf_crop_col                   , & ! Output: [real(r8) (:)     ]  burned area fraction for cropland (/sec)
+         baf_peatf          => cnveg_state_inst%baf_peatf_col                  , & ! Output: [real(r8) (:)     ]  burned area fraction for peatland (/sec)
+         burndate           => cnveg_state_inst%burndate_patch                 , & ! Output: [integer  (:)     ]  burn date for crop
+         fbac               => cnveg_state_inst%fbac_col                       , & ! Output: [real(r8) (:)     ]  total burned area out of conversion (/sec)
+         fbac1              => cnveg_state_inst%fbac1_col                      , & ! Output: [real(r8) (:)     ]  burned area out of conversion region due to land use fire
+         farea_burned       => cnveg_state_inst%farea_burned_col               , & ! Output: [real(r8) (:)     ]  total fractional area burned (/sec)
+         nfire              => cnveg_state_inst%nfire_col                      , & ! Output: [real(r8) (:)     ]  fire counts (count/km2/sec), valid only in Reg. C
+         fsr_col            => cnveg_state_inst%fsr_col                        , & ! Output: [real(r8) (:)     ]  fire spread rate at column level
+         fd_col             => cnveg_state_inst%fd_col                         , & ! Output: [real(r8) (:)     ]  fire duration rate at column level
+         lgdp_col           => cnveg_state_inst%lgdp_col                       , & ! Output: [real(r8) (:)     ]  gdp limitation factor for nfire
+         lgdp1_col          => cnveg_state_inst%lgdp1_col                      , & ! Output: [real(r8) (:)     ]  gdp limitation factor for baf per fire
+         lpop_col           => cnveg_state_inst%lpop_col                       , & ! Output: [real(r8) (:)     ]  pop limitation factor for baf per fire
+         lfwt               => cnveg_state_inst%lfwt_col                       , & ! Output: [real(r8) (:)     ]  fractional coverage of non-crop and non-bare-soil Patches
+         trotr1_col         => cnveg_state_inst%trotr1_col                     , & ! Output: [real(r8) (:)     ]  patch weight of BET on the column (0-1)
+         trotr2_col         => cnveg_state_inst%trotr2_col                     , & ! Output: [real(r8) (:)     ]  patch weight of BDT on the column (0-1)
+         dtrotr_col         => cnveg_state_inst%dtrotr_col                     , & ! Output: [real(r8) (:)     ]  decreased frac. coverage of BET+BDT on grid for dt
+         lfc                => cnveg_state_inst%lfc_col                        , & ! Output: [real(r8) (:)     ]  conversion area frac. of BET+BDT that haven't burned before
+         wtlf               => cnveg_state_inst%wtlf_col                       , & ! Output: [real(r8) (:)     ]  fractional coverage of non-crop Patches
+
+         totvegc            => cnveg_carbonstate_inst%totvegc_col              , & ! Input: [real(r8) (:)     ]  totvegc at column level
+         deadcrootc         => cnveg_carbonstate_inst%deadcrootc_patch         , & ! Input:  [real(r8) (:)     ]  (gC/m2) dead coarse root C
+         deadcrootc_storage => cnveg_carbonstate_inst%deadcrootc_storage_patch , & ! Input:  [real(r8) (:)     ]  (gC/m2) dead coarse root C storage
+         deadcrootc_xfer    => cnveg_carbonstate_inst%deadcrootc_xfer_patch    , & ! Input:  [real(r8) (:)     ]  (gC/m2) dead coarse root C transfer
+         deadstemc          => cnveg_carbonstate_inst%deadstemc_patch          , & ! Input:  [real(r8) (:)     ]  (gC/m2) dead stem root C
+         frootc             => cnveg_carbonstate_inst%frootc_patch             , & ! Input:  [real(r8) (:)     ]  (gC/m2) fine root C
+         frootc_storage     => cnveg_carbonstate_inst%frootc_storage_patch     , & ! Input:  [real(r8) (:)     ]  (gC/m2) fine root C storage
+         frootc_xfer        => cnveg_carbonstate_inst%frootc_xfer_patch        , & ! Input:  [real(r8) (:)     ]  (gC/m2) fine root C transfer
+         livecrootc         => cnveg_carbonstate_inst%livecrootc_patch         , & ! Input:  [real(r8) (:)     ]  (gC/m2) live coarse root C
+         livecrootc_storage => cnveg_carbonstate_inst%livecrootc_storage_patch , & ! Input:  [real(r8) (:)     ]  (gC/m2) live coarse root C storage
+         livecrootc_xfer    => cnveg_carbonstate_inst%livecrootc_xfer_patch    , & ! Input:  [real(r8) (:)     ]  (gC/m2) live coarse root C transfer
+         leafc              => cnveg_carbonstate_inst%leafc_patch              , & ! Input:  [real(r8) (:)     ]  (gC/m2) leaf C
+         leafc_storage      => cnveg_carbonstate_inst%leafc_storage_patch      , & ! Input:  [real(r8) (:)     ]  (gC/m2) leaf C storage
+         leafc_xfer         => cnveg_carbonstate_inst%leafc_xfer_patch         , & ! Input:  [real(r8) (:)     ]  (gC/m2) leaf C transfer
+         rootc_col          => cnveg_carbonstate_inst%rootc_col                , & ! Output: [real(r8) (:)     ]  root carbon
+         leafc_col          => cnveg_carbonstate_inst%leafc_col                , & ! Output: [real(r8) (:)     ]  leaf carbon at column level
+         deadstemc_col      => cnveg_carbonstate_inst%deadstemc_col            , & ! Output: [real(r8) (:)     ]  deadstem carbon at column level
+         fuelc              => cnveg_carbonstate_inst%fuelc_col                , & ! Output: [real(r8) (:)     ]  fuel load coutside cropland
+         fuelc_crop         => cnveg_carbonstate_inst%fuelc_crop_col             & ! Output: [real(r8) (:)     ]  fuel load for cropland
+         )
+
+      transient_landcover = run_has_transient_landcover()
+
+      !pft to column average
+      prec10_col =>prec10_col_target
+      call p2c(bounds, num_soilc, filter_soilc, &
+           prec10(bounds%begp:bounds%endp), &
+           prec10_col(bounds%begc:bounds%endc))
+
+      prec60_col =>prec60_col_target
+      call p2c(bounds, num_soilc, filter_soilc, &
+           prec60(bounds%begp:bounds%endp), &
+           prec60_col(bounds%begc:bounds%endc))
+
+      rh30_col =>rh30_col_target
+      call p2c(bounds, num_soilc, filter_soilc, &
+           rh30(bounds%begp:bounds%endp), &
+           rh30_col(bounds%begc:bounds%endc))
+
+      call p2c(bounds, num_soilc, filter_soilc, &
+           leafc(bounds%begp:bounds%endp), &
+           leafc_col(bounds%begc:bounds%endc))
+
+      call p2c(bounds, num_soilc, filter_soilc, &
+           deadstemc(bounds%begp:bounds%endp), &
+           deadstemc_col(bounds%begc:bounds%endc))
+
+     call get_curr_date (kyr, kmo, kda, mcsec)
+     dayspyr = get_curr_days_per_year()
+     ! Get model step size
+     dt      = get_step_size_real()
+     !
+     ! On first time-step, just set area burned to zero and exit
+     !
+     if ( get_nstep() == 0 )then
+        do fc = 1,num_soilc
+           c = filter_soilc(fc)
+           farea_burned(c) = 0._r8
+           baf_crop(c)     = 0._r8
+           baf_peatf(c)    = 0._r8
+           fbac(c)         = 0._r8
+           fbac1(c)        = 0._r8
+           cropf_col(c)    = 0._r8
+        end do
+        return
+     end if
+     !
+     ! Calculate fraction of crop (cropf_col) and non-crop and non-bare-soil
+     ! vegetation (lfwt) in vegetated column
+     !
+     do fc = 1,num_soilc
+        c = filter_soilc(fc)
+        cropf_col(c) = 0._r8
+        lfwt(c)      = 0._r8
+     end do
+     do fp = 1, num_soilp
+        p = filter_soilp(fp)
+        c = patch%column(p)
+        ! For crop veg types
+        if( patch%itype(p) > nc4_grass )then
+           cropf_col(c) = cropf_col(c) + patch%wtcol(p)
+        end if
+        ! For natural vegetation (non-crop and non-bare-soil)
+        if( patch%itype(p) >= ndllf_evr_tmp_tree .and. patch%itype(p) <= nc4_grass )then
+           lfwt(c) = lfwt(c) + patch%wtcol(p)
+        end if
+     end do
+     !
+     ! Calculate crop fuel
+     !
+     do fc = 1,num_soilc
+        c = filter_soilc(fc)
+        fuelc_crop(c)=0._r8
+     end do
+     do fp = 1, num_soilp
+        p = filter_soilp(fp)
+        c = patch%column(p)
+        ! For crop PFTs, fuel load includes leaf and litter; only
+        ! column-level litter carbon
+        ! is available, so we use leaf carbon to estimate the
+        ! litter carbon for crop PFTs
+        if( patch%itype(p) > nc4_grass .and. patch%wtcol(p) > 0._r8 .and. leafc_col(c) > 0._r8 )then
+           fuelc_crop(c)=fuelc_crop(c) + (leafc(p) + leafc_storage(p) + &
+                leafc_xfer(p))*patch%wtcol(p)/cropf_col(c)     + &
+                totlitc(c)*leafc(p)/leafc_col(c)*patch%wtcol(p)/cropf_col(c)
+        end if
+     end do
+     !
+     ! Calculate noncrop column variables
+     !
+     do fc = 1,num_soilc
+        c = filter_soilc(fc)
+        fsr_col(c)   = 0._r8
+        fd_col(c)    = 0._r8
+        rootc_col(c) = 0._r8
+        lgdp_col(c)  = 0._r8
+        lgdp1_col(c) = 0._r8
+        lpop_col(c)  = 0._r8
+        btran_col(c) = 0._r8
+        wtlf(c)      = 0._r8
+        trotr1_col(c)= 0._r8
+        trotr2_col(c)= 0._r8
+        if (transient_landcover) then
+           dtrotr_col(c)=0._r8
+        end if
+     end do
+
+     ! This subroutine calculates btran2
+     call this%CNFire_calc_fire_root_wetness_Li2021(bounds, &
+          num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, &
+          waterstatebulk_inst, soilstate_inst, soil_water_retention_curve)
+     do fp = 1, num_exposedvegp
+        p = filter_exposedvegp(fp)
+        c = patch%column(p)
+        ! For non-crop -- natural vegetation and bare-soil
+        if( patch%itype(p)  <  nc3crop .and. cropf_col(c)  <  1.0_r8 )then
+           btran_col(c) = btran_col(c)+max(0._r8, min(1._r8, &
+                (btran2(p)-rswf_min(patch%itype(p)))/(rswf_max(patch%itype(p)) &
+                -rswf_min(patch%itype(p)))))*patch%wtcol(p)
+           wtlf(c)      = wtlf(c)+patch%wtcol(p)
+        end if
+     end do
+
+     do fp = 1, num_soilp
+        p = filter_soilp(fp)
+        c = patch%column(p)
+        g = col%gridcell(c)
+
+        ! For non-crop -- natural vegetation and bare-soil
+        if( patch%itype(p)  <  nc3crop .and. cropf_col(c)  <  1.0_r8 )then
+
+           ! NOTE(wjs, 2016-12-15) These calculations of the fraction of evergreen
+           ! and deciduous tropical trees (used to determine if a column is
+           ! tropical closed forest) use the current fractions. However, I think
+           ! they are used in code that applies to land cover change. Note that
+           ! land cover change is currently generated on the first time step of the
+           ! year (even though the fire code sees the annually-smoothed dwt). Thus,
+           ! I think that, for this to be totally consistent, this code should
+           ! consider the fractional coverage of each PFT prior to the relevant
+           ! land cover change event. (These fractions could be computed in the
+           ! code that handles land cover change, so that the fire code remains
+           ! agnostic to exactly how and when land cover change happens.)
+           !
+           ! For example, if a year started with fractional coverages of
+           ! nbrdlf_evr_trp_tree = 0.35 and nbrdlf_dcd_trp_tree = 0.35, but then
+           ! the start-of-year land cover change reduced both of these to 0.2: The
+           ! current code would consider the column to NOT be tropical closed
+           ! forest (because nbrdlf_evr_trp_tree+nbrdlf_dcd_trp_tree < 0.6),
+           ! whereas in fact the land cover change occurred when the column *was*
+           ! tropical closed forest.
+           if( patch%itype(p) == nbrdlf_evr_trp_tree .and. patch%wtcol(p)  >  0._r8 )then
+              trotr1_col(c)=trotr1_col(c)+patch%wtcol(p)
+           end if
+           if( patch%itype(p) == nbrdlf_dcd_trp_tree .and. patch%wtcol(p)  >  0._r8 )then
+              trotr2_col(c)=trotr2_col(c)+patch%wtcol(p)
+           end if
+
+           if (transient_landcover) then
+              if( patch%itype(p) == nbrdlf_evr_trp_tree .or. patch%itype(p) == nbrdlf_dcd_trp_tree )then
+                 if(dwt_smoothed(p) < 0._r8)then
+                    ! Land cover change in CLM happens all at once on the first time
+                    ! step of the year. However, the fire code needs deforestation
+                    ! rates throughout the year, in order to combine these
+                    ! deforestation rates with the current season's climate. So we
+                    ! use a smoothed version of dwt.
+                    !
+                    ! This isn't ideal, because the carbon stocks that the fire code
+                    ! is operating on will have decreased by the full annual amount
+                    ! before the fire code does anything. But the biggest effect of
+                    ! these deforestation fires is as a trigger for other fires, and
+                    ! the C fluxes are merely diagnostic so don't need to be
+                    ! conservative, so this isn't a big issue.
+                    !
+                    ! (Actually, it would be even better if the fire code had a
+                    ! realistic breakdown of annual deforestation into the
+                    ! different seasons. But having deforestation spread evenly
+                    ! throughout the year is much better than having it all
+                    ! concentrated on January 1.)
+                    dtrotr_col(c)=dtrotr_col(c)-dwt_smoothed(p)
+                 end if
+              end if
+           end if
+           rootc_col(c) = rootc_col(c) + (frootc(p) + frootc_storage(p) + &
+                   frootc_xfer(p) + deadcrootc(p) * spinup_factor_deadwood +       &
+                   deadcrootc_storage(p) + deadcrootc_xfer(p) +    &
+                   livecrootc(p)+livecrootc_storage(p) +           &
+                   livecrootc_xfer(p))*patch%wtcol(p)
+
+           fsr_col(c) = fsr_col(c) + fsr_pft(patch%itype(p))*patch%wtcol(p)/(1.0_r8-cropf_col(c))
+
+           hdmlf=this%forc_hdm(g)
+
+           ! all these constants are in Li et al. BG (2012a,b;2013)
+
+           if( hdmlf  >  0.1_r8 )then
+              ! For NOT bare-soil
+              if( patch%itype(p)  /=  noveg )then
+                 ! For shrub and grass (crop already excluded above)
+                 if( patch%itype(p)  >=  nbrdlf_evr_shrub )then      !for shurb and grass
+                    lgdp_col(c)  = lgdp_col(c) + (0.1_r8 + 0.9_r8*    &
+                         exp(-1._r8*SHR_CONST_PI* &
+                         (gdp_lf(c)/8._r8)**0.5_r8))*patch%wtcol(p) &
+                         /(1.0_r8 - cropf_col(c))
+                    lgdp1_col(c) = lgdp1_col(c) + (0.2_r8 + 0.8_r8*   &
+                         exp(-1._r8*SHR_CONST_PI* &
+                         (gdp_lf(c)/7._r8)))*patch%wtcol(p)/(1._r8 - cropf_col(c))
+                    lpop_col(c)  = lpop_col(c) + (0.2_r8 + 0.8_r8*    &
+                         exp(-1._r8*SHR_CONST_PI* &
+                         (hdmlf/450._r8)**0.5_r8))*patch%wtcol(p)/(1._r8 - cropf_col(c))
+                 else   ! for trees
+                    if( gdp_lf(c)  >  20._r8 )then
+                       lgdp_col(c) =lgdp_col(c)+cnfire_const%occur_hi_gdp_tree*patch%wtcol(p)/(1._r8 - cropf_col(c))
+                       lgdp1_col(c) =lgdp1_col(c)+0.62_r8*patch%wtcol(p)/(1._r8 - cropf_col(c))
+                    else
+                       if( gdp_lf(c) > 8._r8 )then
+                          lgdp_col(c)=lgdp_col(c)+0.79_r8*patch%wtcol(p)/(1._r8 - cropf_col(c))
+                          lgdp1_col(c)=lgdp1_col(c)+0.83_r8*patch%wtcol(p)/(1._r8 - cropf_col(c))
+                       else
+                          lgdp_col(c) = lgdp_col(c)+patch%wtcol(p)/(1._r8 - cropf_col(c))
+                          lgdp1_col(c)=lgdp1_col(c)+patch%wtcol(p)/(1._r8 - cropf_col(c))
+                       end if
+                    end if
+                    lpop_col(c) = lpop_col(c) + (0.4_r8 + 0.6_r8*    &
+                         exp(-1._r8*SHR_CONST_PI* &
+                         (hdmlf/125._r8)))*patch%wtcol(p)/(1._r8 -cropf_col(c))
+                 end if
+              end if
+           else
+              lgdp_col(c)  = lgdp_col(c)+patch%wtcol(p)/(1.0_r8 - cropf_col(c))
+              lgdp1_col(c) = lgdp1_col(c)+patch%wtcol(p)/(1.0_r8 -cropf_col(c))
+              lpop_col(c)  = lpop_col(c)+patch%wtcol(p)/(1.0_r8 -cropf_col(c))
+           end if
+
+           fd_col(c) = fd_col(c) + fd_pft(patch%itype(p)) * patch%wtcol(p) * secsphr / (1.0_r8-cropf_col(c))
+        end if
+     end do
+
+     ! estimate annual decreased fractional coverage of BET+BDT
+     ! land cover conversion in CLM4.5 is the same for each timestep except for the beginning
+
+     if (transient_landcover) then
+        do fc = 1,num_soilc
+           c = filter_soilc(fc)
+           if( dtrotr_col(c)  >  0._r8 )then
+              if( kmo == 1 .and. kda == 1 .and. mcsec == 0)then
+                 lfc(c) = 0._r8
+              end if
+              if( kmo == 1 .and. kda == 1 .and. mcsec == dt)then
+                 lfc(c) = dtrotr_col(c)*dayspyr*secspday/dt
+              end if
+           else
+              lfc(c)=0._r8
+           end if
+        end do
+     end if
+     !
+     ! calculate burned area fraction in cropland
+     !
+     do fc = 1,num_soilc
+        c = filter_soilc(fc)
+        baf_crop(c)=0._r8
+     end do
+
+     do fp = 1,num_soilp
+        p = filter_soilp(fp)
+        if( kmo == 1 .and. kda == 1 .and. mcsec == 0 )then
+           burndate(p) = 10000 ! init. value; actual range [0 365]
+        end if
+     end do
+
+     do fp = 1, num_soilp
+        p = filter_soilp(fp)
+        c = patch%column(p)
+        g = col%gridcell(c)
+
+        ! For crop
+        if( forc_t(c)  >=  SHR_CONST_TKFRZ .and. patch%itype(p)  >  nc4_grass .and.  &
+             kmo == abm_lf(c) .and. &
+             burndate(p) >= 999 .and. patch%wtcol(p)  >  0._r8 )then ! catch  crop burn time
+
+           hdmlf = this%forc_hdm(g)
+
+           ! calculate human density impact on ag. fire
+           fhd = 0.04_r8+0.96_r8*exp(-1._r8*SHR_CONST_PI*(hdmlf/350._r8)**0.5_r8)
+
+           ! calculate impact of GDP on ag. fire
+           fgdp = 0.01_r8+0.99_r8*exp(-1._r8*SHR_CONST_PI*(gdp_lf(c)/10._r8))
+
+           ! calculate burned area
+           fb   = max(0.0_r8,min(1.0_r8,(fuelc_crop(c)-lfuel)/(ufuel-lfuel)))
+
+           ! crop fire only for generic crop types at this time
+           ! managed crops are treated as grasses if crop model is turned on
+           baf_crop(c) = baf_crop(c) + cropfire_a1/secsphr*fhd*fgdp*patch%wtcol(p)
+           if( fb*fhd*fgdp*patch%wtcol(p)  >  0._r8)then
+              burndate(p)=kda
+           end if
+        end if
+     end do
+     !
+     ! calculate peatland fire
+     !
+     do fc = 1, num_soilc
+        c = filter_soilc(fc)
+        g= col%gridcell(c)
+        if(grc%latdeg(g) < cnfire_const%borealat )then
+           baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
+                min(1._r8,(4.0_r8-prec60_col(c)*secspday)/ &
+                4.0_r8))**2*peatf_lf(c)*(1._r8-fsat(c))
+        else
+           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/0.3_r8))* &
+                max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
+                (1._r8-fsat(c))
+        end if
+     end do
+     !
+     ! calculate other fires
+     !
+
+     ! Set the number of timesteps for e-folding.
+     ! When the simulation has run fewer than this number of steps,
+     ! re-scale the e-folding time to get a stable early estimate.
+
+     ! find which pool is the cwd pool
+     i_cwd = 0
+     do l = 1, ndecomp_pools
+        if ( is_cwd(l) ) then
+           i_cwd = l
+        endif
+     end do
+
+     !
+     ! begin column loop to calculate fractional area affected by fire
+     !
+     do fc = 1, num_soilc
+        c = filter_soilc(fc)
+        g = col%gridcell(c)
+        hdmlf=this%forc_hdm(g)
+        nfire(c) = 0._r8
+        if( cropf_col(c)  <  1._r8 )then
+           fuelc(c) = totlitc(c)+totvegc(c)-rootc_col(c)-fuelc_crop(c)*cropf_col(c)
+           if (spinup_state == 2) then
+              fuelc(c) = fuelc(c) + ((spinup_factor_deadwood - 1._r8)*deadstemc_col(c))
+              do j = 1, nlevdecomp
+                 fuelc(c) = fuelc(c)+decomp_cpools_vr(c,j,i_cwd) * dzsoi_decomp(j) * spinup_factor(i_cwd) &
+                            * get_spinup_latitude_term(grc%latdeg(col%gridcell(c)))
+              end do
+           else
+              do j = 1, nlevdecomp
+                 fuelc(c) = fuelc(c)+decomp_cpools_vr(c,j,i_cwd) * dzsoi_decomp(j)
+              end do
+           end if
+           fuelc(c) = fuelc(c)/(1._r8-cropf_col(c))
+           fb       = max(0.0_r8,min(1.0_r8,(fuelc(c)-lfuel)/(ufuel-lfuel)))
+           if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
+              afuel  =min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
+              arh=1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
+              arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
+              if (forc_rh(g) < rh_hgh.and. wtlf(c) > 0._r8 .and. tsoi17(c)> SHR_CONST_TKFRZ)then
+                fire_m   = ((afuel*arh30+(1._r8-afuel)*arh)**1.5_r8) &
+                             *((1._r8-btran_col(c)/wtlf(c))**0.5_r8)
+              else
+                fire_m   = 0._r8
+              end if
+              lh       = pot_hmn_ign_counts_alpha*6.8_r8*hdmlf**(0.43_r8)/30._r8/24._r8
+              fs       = 1._r8-(0.01_r8+0.98_r8*exp(-0.025_r8*hdmlf))
+              ig       = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
+                     cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
+                         cnfire_params%ignition_efficiency)*(1._r8-fs)*(1._r8-cropf_col(c))
+              nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) !fire counts/km2/sec
+              Lb_lf    = 1._r8+10._r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
+              spread_m = fire_m**0.5_r8
+              farea_burned(c) = min(1._r8,(cnfire_const%g0*spread_m*fsr_col(c)* &
+                   fd_col(c)/1000._r8)**2*lgdp1_col(c)* &
+                   lpop_col(c)*nfire(c)*SHR_CONST_PI*Lb_lf+ &
+                   baf_crop(c)+baf_peatf(c))  ! fraction (0-1) per sec
+           else
+             farea_burned(c)=min(1._r8,baf_crop(c)+baf_peatf(c))
+           end if
+           !
+           ! if landuse change data is used, calculate deforestation fires and
+           ! add it in the total of burned area fraction
+           !
+           if (transient_landcover) then
+              if( trotr1_col(c)+trotr2_col(c) > 0.6_r8 )then
+                 if(( kmo == 1 .and. kda == 1 .and. mcsec == 0) .or. &
+                      dtrotr_col(c) <=0._r8 )then
+                    fbac1(c)        = 0._r8
+                    farea_burned(c) = baf_crop(c)+baf_peatf(c)
+                 else
+                    cri = (4.0_r8*trotr1_col(c)+1.8_r8*trotr2_col(c))/(trotr1_col(c)+trotr2_col(c))
+                    cli = (max(0._r8,min(1._r8,(cri-prec60_col(c)*secspday)/cri))**0.5)* &
+                         (max(0._r8,min(1._r8,(cri-prec10_col(c)*secspday)/cri))**0.5)* &
+                         (15._r8*min(0.0016_r8,dtrotr_col(c)/dt*dayspyr*secspday)+0.009_r8)* &
+                         max(0._r8,min(1._r8,(0.25_r8-(forc_rain(c)+forc_snow(c))*secsphr)/0.25_r8))
+                    farea_burned(c) = fb*cli*(cli_scale/secspday)+baf_crop(c)+baf_peatf(c)
+                    ! burned area out of conversion region due to land use fire
+                    fbac1(c) = max(0._r8,fb*cli*(cli_scale/secspday) - 2.0_r8*lfc(c)/dt)
+                 end if
+                 ! total burned area out of conversion
+                 fbac(c) = fbac1(c)+baf_crop(c)+baf_peatf(c)
+              else
+                 fbac(c) = farea_burned(c)
+              end if
+           end if
+
+        else
+           farea_burned(c) = min(1._r8,baf_crop(c)+baf_peatf(c))
+        end if
+
+     end do  ! end of column loop
+
+   end associate
+
+ end subroutine CNFireArea
+
+end module CNFireLi2024Mod

From 5b95a3e6a658e20e80b3869df823c81636067304 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 13:06:36 -0600
Subject: [PATCH 0840/1248] Fix bugs and develop crop fire modeling

In the CNFireLi2024Mod.F90, (1) fixed the bug described in https://github.com/ESCOMP/CTSM/issues/2566 to avoid incorrect accumulation of baf_crop and ensure that crop fires do not occur during the crop growing season; (2) confined crop fires to periods after harvest and before planting when crop module is active; (3) removed the dependency of baf_crop on fuel availability; (4) improved the modeling of the influence of socio-economic factors on crop burned area; (5) recalibrated the cropfire_a1 constant based on GFED5 crop burned area; (6) modify the declaration of CNFireArea in these F90 files to include the variable crop_inst, declare the variable crop_inst, and import and utilize crop_type from the module CropType.

In addition, the modules CNDriverMod.F90, CNFireLi2014Mod.F90, CNFireLi2016Mod.F90, CNFireLi2021Mod.F90, CNFireNoFireMod.F90, FATESFireBase.F90, and FireMethodType.F90 include the subroutine CNFireArea. (6) is implemented in these modules.

(Original commit by Fang Li, lifang@mail.iap.ac.cn.)
---
 src/biogeochem/CNDriverMod.F90     |  2 +-
 src/biogeochem/CNFireLi2014Mod.F90 |  4 +++-
 src/biogeochem/CNFireLi2016Mod.F90 |  4 +++-
 src/biogeochem/CNFireLi2021Mod.F90 |  4 +++-
 src/biogeochem/CNFireLi2024Mod.F90 | 26 +++++++++++++-------------
 src/biogeochem/CNFireNoFireMod.F90 |  4 +++-
 src/biogeochem/FATESFireBase.F90   |  5 ++++-
 src/main/FireMethodType.F90        |  4 +++-
 8 files changed, 33 insertions(+), 20 deletions(-)

diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90
index b23019eb23..ee97bcc360 100644
--- a/src/biogeochem/CNDriverMod.F90
+++ b/src/biogeochem/CNDriverMod.F90
@@ -936,7 +936,7 @@ subroutine CNDriverNoLeaching(bounds,
             num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, &
             atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, wateratm2lndbulk_inst, &
             waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-            cnveg_state_inst, cnveg_carbonstate_inst, &
+            crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, &
             totlitc_col=soilbiogeochem_carbonstate_inst%totlitc_col(begc:endc), &
             decomp_cpools_vr_col=soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), &
             t_soi17cm_col=temperature_inst%t_soi17cm_col(begc:endc))
diff --git a/src/biogeochem/CNFireLi2014Mod.F90 b/src/biogeochem/CNFireLi2014Mod.F90
index 6ea21a530b..cb41230a10 100644
--- a/src/biogeochem/CNFireLi2014Mod.F90
+++ b/src/biogeochem/CNFireLi2014Mod.F90
@@ -87,7 +87,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
        num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, &
        atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, &
        wateratm2lndbulk_inst, waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+       crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
     ! Computes column-level burned area
@@ -98,6 +98,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     use pftconMod            , only: nc4_grass, nc3crop, ndllf_evr_tmp_tree
     use pftconMod            , only: nbrdlf_evr_trp_tree, nbrdlf_dcd_trp_tree, nbrdlf_evr_shrub
     use dynSubgridControlMod , only: run_has_transient_landcover
+    use CropType             , only: crop_type
     !
     ! !ARGUMENTS:
     class(cnfire_li2014_type)                             :: this
@@ -120,6 +121,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    type(crop_type)                       , intent(in)    :: crop_inst
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
diff --git a/src/biogeochem/CNFireLi2016Mod.F90 b/src/biogeochem/CNFireLi2016Mod.F90
index 7bbb183860..6021901a28 100644
--- a/src/biogeochem/CNFireLi2016Mod.F90
+++ b/src/biogeochem/CNFireLi2016Mod.F90
@@ -89,7 +89,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
        num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, &
        atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, &
        wateratm2lndbulk_inst, waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+       crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
     ! Computes column-level burned area
@@ -101,6 +101,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     use pftconMod            , only: nc4_grass, nc3crop, ndllf_evr_tmp_tree
     use pftconMod            , only: nbrdlf_evr_trp_tree, nbrdlf_dcd_trp_tree, nbrdlf_evr_shrub
     use dynSubgridControlMod , only : run_has_transient_landcover
+    use CropType             , only: crop_type
     !
     ! !ARGUMENTS:
     class(cnfire_li2016_type)                             :: this
@@ -123,6 +124,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    type(crop_type)                       , intent(in)    :: crop_inst
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
diff --git a/src/biogeochem/CNFireLi2021Mod.F90 b/src/biogeochem/CNFireLi2021Mod.F90
index 86d5cc235d..74f553eb5c 100644
--- a/src/biogeochem/CNFireLi2021Mod.F90
+++ b/src/biogeochem/CNFireLi2021Mod.F90
@@ -89,7 +89,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
        num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, &
        atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, &
        wateratm2lndbulk_inst, waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+       crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
     ! Computes column-level burned area
@@ -101,6 +101,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     use pftconMod            , only: nc4_grass, nc3crop, ndllf_evr_tmp_tree
     use pftconMod            , only: nbrdlf_evr_trp_tree, nbrdlf_dcd_trp_tree, nbrdlf_evr_shrub
     use dynSubgridControlMod , only : run_has_transient_landcover
+    use CropType             , only: crop_type
     !
     ! !ARGUMENTS:
     class(cnfire_li2021_type)                             :: this
@@ -123,6 +124,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    type(crop_type)                       , intent(in)    :: crop_inst
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 9908732018..6d3bf6657a 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -89,7 +89,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
        num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, &
        atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, &
        wateratm2lndbulk_inst, waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+       crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
     ! Computes column-level burned area
@@ -97,10 +97,11 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     ! !USES:
     use clm_time_manager     , only: get_step_size_real, get_curr_days_per_year, get_curr_date, get_nstep
     use clm_varcon           , only: secspday, secsphr
-    use clm_varctl           , only: spinup_state
+    use clm_varctl           , only: spinup_state, use_crop
     use pftconMod            , only: nc4_grass, nc3crop, ndllf_evr_tmp_tree
     use pftconMod            , only: nbrdlf_evr_trp_tree, nbrdlf_dcd_trp_tree, nbrdlf_evr_shrub
     use dynSubgridControlMod , only : run_has_transient_landcover
+    use CropType             , only: crop_type
     !
     ! !ARGUMENTS:
     class(cnfire_li2024_type)                             :: this
@@ -123,6 +124,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    type(crop_type)                       , intent(in)    :: crop_inst
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
@@ -237,7 +239,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          leafc_col          => cnveg_carbonstate_inst%leafc_col                , & ! Output: [real(r8) (:)     ]  leaf carbon at column level
          deadstemc_col      => cnveg_carbonstate_inst%deadstemc_col            , & ! Output: [real(r8) (:)     ]  deadstem carbon at column level
          fuelc              => cnveg_carbonstate_inst%fuelc_col                , & ! Output: [real(r8) (:)     ]  fuel load coutside cropland
-         fuelc_crop         => cnveg_carbonstate_inst%fuelc_crop_col             & ! Output: [real(r8) (:)     ]  fuel load for cropland
+         fuelc_crop         => cnveg_carbonstate_inst%fuelc_crop_col           ,  & ! Output: [real(r8) (:)     ]  fuel load for cropland
+         croplive              => crop_inst%croplive_patch                       & ! Input:  [logical  (:)   ]  flag, true if planted, not harvested
          )
 
       transient_landcover = run_has_transient_landcover()
@@ -522,21 +525,18 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            hdmlf = this%forc_hdm(g)
 
            ! calculate human density impact on ag. fire
-           fhd = 0.04_r8+0.96_r8*exp(-1._r8*SHR_CONST_PI*(hdmlf/350._r8)**0.5_r8)
+           fhd = 0.2_r8+0.8_r8*exp(-1._r8*SHR_CONST_PI*(hdmlf/400._r8))
 
            ! calculate impact of GDP on ag. fire
-           fgdp = 0.01_r8+0.99_r8*exp(-1._r8*SHR_CONST_PI*(gdp_lf(c)/10._r8))
+           fgdp = 0.05_r8+0.95_r8*exp(-1._r8*SHR_CONST_PI*(gdp_lf(c)/20._r8))
 
            ! calculate burned area
-           fb   = max(0.0_r8,min(1.0_r8,(fuelc_crop(c)-lfuel)/(ufuel-lfuel)))
-
-           ! crop fire only for generic crop types at this time
-           ! managed crops are treated as grasses if crop model is turned on
-           baf_crop(c) = baf_crop(c) + cropfire_a1/secsphr*fhd*fgdp*patch%wtcol(p)
-           if( fb*fhd*fgdp*patch%wtcol(p)  >  0._r8)then
-              burndate(p)=kda
+            if((use_crop .and. (.not. croplive(p))) &
+                   .or. (.not. use_crop)) then
+                burndate(p) = kda
+                baf_crop(c) = baf_crop(c)+0.21_r8 / secsphr * fhd * fgdp * patch%wtcol(p)
            end if
-        end if
+       end if
      end do
      !
      ! calculate peatland fire
diff --git a/src/biogeochem/CNFireNoFireMod.F90 b/src/biogeochem/CNFireNoFireMod.F90
index 0dc1ee39d1..6785faa851 100644
--- a/src/biogeochem/CNFireNoFireMod.F90
+++ b/src/biogeochem/CNFireNoFireMod.F90
@@ -62,13 +62,14 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
        atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, &
        waterdiagnosticbulk_inst, wateratm2lndbulk_inst, &
        waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+       crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
     ! Computes column-level burned area 
     !
     ! !USES:
     use subgridAveMod                      , only : p2c
+    use CropType                           , only : crop_type
     !
     ! !ARGUMENTS:
     class(cnfire_nofire_type)                             :: this
@@ -91,6 +92,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    type(crop_type)                       , intent(in)    :: crop_inst
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
diff --git a/src/biogeochem/FATESFireBase.F90 b/src/biogeochem/FATESFireBase.F90
index a47ff2e8c4..59279d7625 100644
--- a/src/biogeochem/FATESFireBase.F90
+++ b/src/biogeochem/FATESFireBase.F90
@@ -206,7 +206,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
        atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, &
        waterdiagnosticbulk_inst, wateratm2lndbulk_inst, &
        waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+       crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
     ! Computes column-level burned area  (NOT USED FOR FATES)
@@ -220,6 +220,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     use SoilStateType                      , only : soilstate_type
     use SoilWaterRetentionCurveMod         , only : soil_water_retention_curve_type
     use atm2lndType                        , only : atm2lnd_type
+    use CropType                           , only: crop_type
     !
     ! !ARGUMENTS:
     class(fates_fire_base_type)                           :: this
@@ -242,6 +243,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    type(crop_type)                       , intent(in) :: crop_inst
+
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
diff --git a/src/main/FireMethodType.F90 b/src/main/FireMethodType.F90
index 63c05821b7..978450e65f 100644
--- a/src/main/FireMethodType.F90
+++ b/src/main/FireMethodType.F90
@@ -119,7 +119,7 @@ subroutine CNFireArea_interface (this, bounds, num_soilc, filter_soilc, num_soil
        atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, &
        waterdiagnosticbulk_inst, wateratm2lndbulk_inst, &
        waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, &
-       cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
+       crop_inst, cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
     ! Computes column-level burned area 
@@ -137,6 +137,7 @@ subroutine CNFireArea_interface (this, bounds, num_soilc, filter_soilc, num_soil
     use SoilWaterRetentionCurveMod         , only : soil_water_retention_curve_type
     use CNVegStateType                     , only : cnveg_state_type
     use CNVegCarbonStateType               , only : cnveg_carbonstate_type
+    use CropType                           , only : crop_type
     import :: fire_method_type
     !
     ! !ARGUMENTS:
@@ -160,6 +161,7 @@ subroutine CNFireArea_interface (this, bounds, num_soilc, filter_soilc, num_soil
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
+    type(crop_type)                       , intent(in)    :: crop_inst
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)

From 412bb3e1bb1df35fb2503acf4a86f0256fbaa77e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 13:16:09 -0600
Subject: [PATCH 0841/1248] change the cropfire_a1 to 0.21 in
 namelist_defaults.

(Original commit by Fang Li, lifang@mail.iap.ac.cn.)
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 src/biogeochem/CNFireLi2024Mod.F90            | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index a7e59935a4..b301bcfb28 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -327,7 +327,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <boreal_peatfire_c        fire_method="li2024gswpfrc" >0.09d-4</boreal_peatfire_c>
 <pot_hmn_ign_counts_alpha fire_method="li2024gswpfrc" >0.010d00</pot_hmn_ign_counts_alpha>
 <non_boreal_peatfire_c    fire_method="li2024gswpfrc" >0.17d-3</non_boreal_peatfire_c>
-<cropfire_a1              fire_method="li2024gswpfrc" >1.6d-4</cropfire_a1>
+<cropfire_a1              fire_method="li2024gswpfrc" >0.21d00</cropfire_a1>
 <occur_hi_gdp_tree        fire_method="li2024gswpfrc" >0.33d00</occur_hi_gdp_tree>
 <lfuel                    fire_method="li2024gswpfrc" >75.d00</lfuel>
 <ufuel                    fire_method="li2024gswpfrc" >1050.d00</ufuel>
diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 6d3bf6657a..503ed28488 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -534,7 +534,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
             if((use_crop .and. (.not. croplive(p))) &
                    .or. (.not. use_crop)) then
                 burndate(p) = kda
-                baf_crop(c) = baf_crop(c)+0.21_r8 / secsphr * fhd * fgdp * patch%wtcol(p)
+                baf_crop(c) = baf_crop(c)+cropfire_a1 / secsphr * fhd * fgdp * patch%wtcol(p)
            end if
        end if
      end do

From be82840310150f694824ce7c2504c6049362497e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 15:17:47 -0600
Subject: [PATCH 0842/1248] cropMonthOutput h2 file is now finally monthly.

Specifying hist_nhtfrq(3) seems to override later specification of h2 in "hist_nhtfrq = 0,-240,0"
---
 cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
index aea8e39e6c..8ad588381e 100644
--- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm
@@ -14,7 +14,7 @@ hist_fincl2  += 'DYN_COL_SOIL_ADJUSTMENTS_C'
 ! That's needed for the mxsowings and mxharvests axes to make sense.
 ! However, for testing purposes, it makes sense to save more frequently.
 hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS', 'GDD20_BASELINE', 'GDD20_SEASON_START', 'GDD20_SEASON_END'
-hist_nhtfrq(3) = -24
-hist_mfilt(3) = 1
+hist_nhtfrq = -24,-8,-24
+hist_mfilt  = 1,1,1
 hist_type1d_pertape(3) = 'PFTS'
-hist_dov2xy(3) = .false.
+hist_dov2xy    = .true.,.false.,.false.

From 2e4ceb8bee60884c0ea9de05577228803a8e3a8d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 7 Aug 2024 17:15:14 -0600
Subject: [PATCH 0843/1248] Fix the error check

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index f1e5935196..ff796efca9 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -4676,7 +4676,7 @@ sub setup_logic_prigent_roughness {
               'dust_emis_method'=>$dust_emis_method );
   my $use_prigent = $nl->get_value($var);
   if ( &value_is_true($use_prigent) ) {
-     if ( $dust_emis_method eq "Leung_2023" ) {
+     if ( $dust_emis_method ne "Leung_2023" ) {
        $log->warning( "$var does NOT need to be set without dust_emis_method being Leung_2023" );
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_prigentroughness' );

From 00cb8a1a0766711bcaf0ea51323b65a8bdd71ec0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 17:15:55 -0600
Subject: [PATCH 0844/1248] Reduce Izumi cropMonthOutput-RxCropCalsAdaptGGCMI
 test to 65 days.

---
 cime_config/testdefs/testlist_clm.xml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 1e687522e4..3e47ca2d95 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3582,12 +3582,20 @@
   <test name="SMS_D_Ld733" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsAdaptGGCMI">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_D_Ld65" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsAdaptGGCMI">
+    <machines>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
       <machine name="izumi" compiler="nag" category="fix_nag_bld_2659"/>
     </machines>
     <options>
-      <option name="wallclock">08:00:00</option>
+      <option name="wallclock">00:30:00</option>
     </options>
   </test>
 

From 31f4c03f5cf14e7eb7559e2b9ac5f238abe1ae36 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 17:50:03 -0600
Subject: [PATCH 0845/1248] Remove fix_nag_bld_2659 test suite.

---
 cime_config/testdefs/testlist_clm.xml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 3e47ca2d95..3f6fe51ea0 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3572,7 +3572,6 @@
   <test name="SMS_Ld733" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsNoAdapt">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="derecho" compiler="intel" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -3592,7 +3591,6 @@
     <machines>
       <machine name="izumi" compiler="nag" category="crop_calendars"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
-      <machine name="izumi" compiler="nag" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
@@ -3603,7 +3601,6 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="derecho" compiler="intel" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
@@ -3614,7 +3611,6 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
-      <machine name="derecho" compiler="intel" category="fix_nag_bld_2659"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>

From a63a4786f9d26ccdc02fea3d8561c1a5fab19db0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 7 Aug 2024 17:51:45 -0600
Subject: [PATCH 0846/1248] Remove expected fail that's now fixed.

SMS_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI
---
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index d5e3e4e378..d1e0a1a8b8 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -163,13 +163,6 @@
     </phase>
   </test>
 
-  <test name="SMS_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI">
-    <phase name="SHAREDLIB_BUILD">
-      <status>FAIL</status>
-      <issue>#2659</issue>
-    </phase>
-  </test>
-
   <!-- fates test suite failures -->
 
   <test name="ERS_D_Ld3.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLUH2">

From b89a8292bb60cac454cbc4a89615c0f3a3094e96 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 8 Aug 2024 00:04:00 -0600
Subject: [PATCH 0847/1248] Add test for prigent on without Leung

---
 bld/unit_testers/build-namelist_test.pl | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 5c70aa613a..0e230aecd8 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3254;
+my $ntests = 3255;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2001;
+   $ntests += 1965;
 }
 plan( tests=>$ntests );
 
@@ -1295,6 +1295,11 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
+     "PrigentOnWOLeung"          =>{ options=>"-envxml_dir . -bgc sp",
+                                     namelst=>"use_prigent_roughness=.true.,dust_emis_method='Zender_2003'",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm6_0",
+                                   },
      "NotNEONbutNEONlightres"    =>{ options=>"--res CLM_USRDAT --clm_usr_name regional --envxml_dir . --bgc bgc --light_res 106x174",
                                      namelst=>"fsurdat='build-namelist_test.pl'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

From 915af954a034a1e6d4f777623cde90977e614499 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 8 Aug 2024 10:33:31 -0600
Subject: [PATCH 0848/1248] add spellcheck in bld-nml-tester

---
 bld/unit_testers/build-namelist_test.pl | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index fe6591c16b..d31d8e9294 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1211,6 +1211,13 @@ sub cat_and_create_namelistinfile {
                );
 foreach my $key ( keys(%failtest) ) {
    print( "$key\n" );
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for failtest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($failtest{$key}{"phys"});
    my $options  = $failtest{$key}{"options"};
    my $namelist = $failtest{$key}{"namelst"};
@@ -1288,6 +1295,14 @@ sub cat_and_create_namelistinfile {
                );
 foreach my $key ( keys(%warntest) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for warntest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($warntest{$key}{"phys"});
    my $options  = $warntest{$key}{"options"};
    my $namelist = $warntest{$key}{"namelst"};
@@ -1517,6 +1532,14 @@ sub cat_and_create_namelistinfile {
 
 foreach my $key ( keys(%finidat_files) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "atm_forc", "res", "bgc", "crop", "use_case", "start_ymd", "namelist" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for finidat_file $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    my $phys = $finidat_files{$key}{'phys'};
    print "physics = $phys\n";
    &make_config_cache($phys);

From 1041a7c93b27dc45a4c1587b02da5c1dac04b7cd Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 8 Aug 2024 11:09:21 -0600
Subject: [PATCH 0849/1248] Add testmods and tests for all fire methods.

---
 cime_config/testdefs/testlist_clm.xml         | 40 +++++++++++++++++++
 .../clm/FireLi2014Qian/include_user_mods      |  1 +
 .../clm/FireLi2014Qian/user_nl_clm            |  1 +
 .../clm/FireLi2016Cru/include_user_mods       |  1 +
 .../clm/FireLi2016Cru/user_nl_clm             |  1 +
 .../clm/FireLi2021GSWP/include_user_mods      |  1 +
 .../clm/FireLi2021GSWP/user_nl_clm            |  1 +
 .../clm/FireLi2024GSWP/include_user_mods      |  1 +
 .../clm/FireLi2024GSWP/user_nl_clm            |  1 +
 9 files changed, 48 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 1ac2334ba8..36da30043c 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3070,5 +3070,45 @@
     </options>
   </test>
 
+  <test name="SMS_D_Ld65" grid="f10_f10_mg37" compset="I2000Clm45BgcCropQianRs" testmods="clm/FireLi2014Qian">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="fire"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_D_Ld65" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/FireLi2016Cru">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="fire"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_D_Ld65" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/FireLi2021GSWP">
+    <machines>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="fire"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_D_Ld65" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/FireLi2024GSWP">
+    <machines>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="fire"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+    </options>
+  </test>
+
 
 </testlist>
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/user_nl_clm
new file mode 100644
index 0000000000..3e05de8cad
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2014Qian/user_nl_clm
@@ -0,0 +1 @@
+fire_method = 'li2014qianfrc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/user_nl_clm
new file mode 100644
index 0000000000..eecbd5b2d9
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2016Cru/user_nl_clm
@@ -0,0 +1 @@
+fire_method = 'li2016crufrc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/user_nl_clm
new file mode 100644
index 0000000000..8703daf6f8
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2021GSWP/user_nl_clm
@@ -0,0 +1 @@
+fire_method = 'li2021gswpfrc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/user_nl_clm
new file mode 100644
index 0000000000..7926de5891
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2024GSWP/user_nl_clm
@@ -0,0 +1 @@
+fire_method = 'li2024gswpfrc'

From b0c986cd9af32e300118eac565acb5582a32ec8d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 11 Jun 2024 14:45:11 -0600
Subject: [PATCH 0850/1248] Functionize check_missing_initdata_status().

---
 src/main/clm_initializeMod.F90 | 12 +----------
 src/main/controlMod.F90        | 38 ++++++++++++++++++++++++++++++++++
 2 files changed, 39 insertions(+), 11 deletions(-)

diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index 9bf0cc59a2..8b03531000 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -520,17 +520,7 @@ subroutine initialize2(ni,nj)
        else
           if (trim(finidat) == trim(finidat_interp_dest)) then
              ! Check to see if status file for finidat exists
-             klen = len_trim(finidat_interp_dest) - 3 ! remove the .nc
-             locfn = finidat_interp_dest(1:klen)//'.status'
-             inquire(file=trim(locfn), exist=lexists)
-             if (.not. lexists) then
-                if (masterproc) then
-                   write(iulog,'(a)')' failed to find file '//trim(locfn)
-                   write(iulog,'(a)')' this indicates a problem in creating '//trim(finidat_interp_dest)
-                   write(iulog,'(a)')' remove '//trim(finidat_interp_dest)//' and try again'
-                end if
-                call endrun()
-             end if
+             call check_missing_initdata_status(finidat_interp_dest)
           end if
           if (masterproc) then
              write(iulog,'(a)')'Reading initial conditions from file '//trim(finidat)
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index f876e97176..8712e6cf50 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -62,6 +62,7 @@ module controlMod
   !
   !
   ! !PRIVATE MEMBER FUNCTIONS:
+  private :: check_missing_initdata_status  ! check for missing finidat_interp_dest .status file
   private :: apply_use_init_interp  ! apply the use_init_interp namelist option, if set
   !
   ! !PRIVATE TYPES:
@@ -1220,6 +1221,38 @@ subroutine control_print ()
     end if
   end subroutine control_print
 
+  
+  !-----------------------------------------------------------------------
+  subroutine check_missing_initdata_status(finidat_interp_dest)
+   !
+   ! !DESCRIPTION:
+   ! Checks that the finidat_interp_dest .status file was written (i.e., that write of
+   ! finidat_interp_dest succeeded)
+   !
+   ! !ARGUMENTS:
+   character(len=*), intent(in)    :: finidat_interp_dest
+   !
+   ! !LOCAL VARIABLES:
+   logical                    :: lexists
+   integer                    :: klen
+   character(len=SHR_KIND_CL) :: status_file
+   character(len=*), parameter :: subname = 'check_missing_initdata_status'
+   !-----------------------------------------------------------------------
+
+    klen = len_trim(finidat_interp_dest) - 3 ! remove the .nc
+    status_file = finidat_interp_dest(1:klen)//'.status'
+    inquire(file=trim(status_file), exist=lexists)
+    if (.not. lexists) then
+       if (masterproc) then
+          write(iulog,'(a)')' failed to find file '//trim(status_file)
+          write(iulog,'(a)')' this indicates a problem in creating '//trim(finidat_interp_dest)
+          write(iulog,'(a)')' remove '//trim(finidat_interp_dest)//' and try again'
+       end if
+       call endrun(subname//': finidat_interp_dest file exists but is probably bad')
+    end if
+
+  end subroutine check_missing_initdata_status
+
 
   !-----------------------------------------------------------------------
   subroutine apply_use_init_interp(finidat_interp_dest, finidat, finidat_interp_source)
@@ -1271,6 +1304,11 @@ subroutine apply_use_init_interp(finidat_interp_dest, finidat, finidat_interp_so
 
     inquire(file=trim(finidat_interp_dest), exist=lexists)
     if (lexists) then
+
+      ! Check that the status file also exists (i.e., that finidat_interp_dest was written successfully)
+      call check_missing_initdata_status(finidat_interp_dest)
+
+       write(iulog, *) 'ssr apply_use_init_interp: point 3'
        ! open the input file and check for the name of the input source file
        status = nf90_open(trim(finidat_interp_dest), 0, ncid)
        if (status /= nf90_noerr) call handle_err(status)

From 4d17ba36020e9740b0090d62027e67374e4368a0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 11 Jun 2024 14:47:57 -0600
Subject: [PATCH 0851/1248] Remove troubleshooting printout.

---
 src/cpl/nuopc/lnd_comp_nuopc.F90 | 1 -
 src/main/controlMod.F90          | 5 -----
 2 files changed, 6 deletions(-)

diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90
index 3852a1bf1b..b9c2eeb784 100644
--- a/src/cpl/nuopc/lnd_comp_nuopc.F90
+++ b/src/cpl/nuopc/lnd_comp_nuopc.F90
@@ -626,7 +626,6 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
          version_in=model_version, &
          hostname_in=hostname, &
          username_in=username)
-
     call initialize1(dtime=dtime_sync)
 
     ! ---------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 8712e6cf50..e3badbd7bd 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -571,7 +571,6 @@ subroutine control_init(dtime)
     ! ----------------------------------------------------------------------
     ! Read in other namelists for other modules
     ! ----------------------------------------------------------------------
-
     call mpi_bcast (use_init_interp, 1, MPI_LOGICAL, 0, mpicom, ierr)
     if (use_init_interp) then
        call initInterp_readnl( NLFilename )
@@ -581,7 +580,6 @@ subroutine control_init(dtime)
     !For future version, I suggest to  put the following two calls inside their
     !own modules, which are called from their own initializing methods
     call init_hydrology( NLFilename )
-
     call soil_resistance_readnl ( NLFilename )
     call CanopyFluxesReadNML    ( NLFilename )
     call CanopyHydrology_readnl ( NLFilename )
@@ -594,7 +592,6 @@ subroutine control_init(dtime)
     ! ----------------------------------------------------------------------
     ! Broadcast all control information if appropriate
     ! ----------------------------------------------------------------------
-
     call control_spmd()
 
     ! ----------------------------------------------------------------------
@@ -1307,8 +1304,6 @@ subroutine apply_use_init_interp(finidat_interp_dest, finidat, finidat_interp_so
 
       ! Check that the status file also exists (i.e., that finidat_interp_dest was written successfully)
       call check_missing_initdata_status(finidat_interp_dest)
-
-       write(iulog, *) 'ssr apply_use_init_interp: point 3'
        ! open the input file and check for the name of the input source file
        status = nf90_open(trim(finidat_interp_dest), 0, ncid)
        if (status /= nf90_noerr) call handle_err(status)

From 1a79cdb474eb5fe68cc2e7cd4529522a5c2ad818 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 11 Jun 2024 14:52:38 -0600
Subject: [PATCH 0852/1248] Final cleanup.

---
 src/cpl/nuopc/lnd_comp_nuopc.F90 |  1 +
 src/main/controlMod.F90          | 10 +++++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90
index b9c2eeb784..3852a1bf1b 100644
--- a/src/cpl/nuopc/lnd_comp_nuopc.F90
+++ b/src/cpl/nuopc/lnd_comp_nuopc.F90
@@ -626,6 +626,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
          version_in=model_version, &
          hostname_in=hostname, &
          username_in=username)
+
     call initialize1(dtime=dtime_sync)
 
     ! ---------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index e3badbd7bd..c7025c5718 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -571,6 +571,7 @@ subroutine control_init(dtime)
     ! ----------------------------------------------------------------------
     ! Read in other namelists for other modules
     ! ----------------------------------------------------------------------
+
     call mpi_bcast (use_init_interp, 1, MPI_LOGICAL, 0, mpicom, ierr)
     if (use_init_interp) then
        call initInterp_readnl( NLFilename )
@@ -580,6 +581,7 @@ subroutine control_init(dtime)
     !For future version, I suggest to  put the following two calls inside their
     !own modules, which are called from their own initializing methods
     call init_hydrology( NLFilename )
+
     call soil_resistance_readnl ( NLFilename )
     call CanopyFluxesReadNML    ( NLFilename )
     call CanopyHydrology_readnl ( NLFilename )
@@ -592,6 +594,7 @@ subroutine control_init(dtime)
     ! ----------------------------------------------------------------------
     ! Broadcast all control information if appropriate
     ! ----------------------------------------------------------------------
+
     call control_spmd()
 
     ! ----------------------------------------------------------------------
@@ -1218,7 +1221,7 @@ subroutine control_print ()
     end if
   end subroutine control_print
 
-  
+
   !-----------------------------------------------------------------------
   subroutine check_missing_initdata_status(finidat_interp_dest)
    !
@@ -1302,8 +1305,9 @@ subroutine apply_use_init_interp(finidat_interp_dest, finidat, finidat_interp_so
     inquire(file=trim(finidat_interp_dest), exist=lexists)
     if (lexists) then
 
-      ! Check that the status file also exists (i.e., that finidat_interp_dest was written successfully)
-      call check_missing_initdata_status(finidat_interp_dest)
+       ! Check that the status file also exists (i.e., that finidat_interp_dest was written successfully)
+       call check_missing_initdata_status(finidat_interp_dest)
+
        ! open the input file and check for the name of the input source file
        status = nf90_open(trim(finidat_interp_dest), 0, ncid)
        if (status /= nf90_noerr) call handle_err(status)

From 5e7e5b591d627e13854245f82a7e7b7246981f38 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 11 Jun 2024 15:08:10 -0600
Subject: [PATCH 0853/1248] Add a missing use statement.

---
 src/main/clm_initializeMod.F90 | 2 +-
 src/main/controlMod.F90        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index 8b03531000..6e80869833 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -174,7 +174,7 @@ subroutine initialize2(ni,nj)
     use SatellitePhenologyMod         , only : SatellitePhenologyInit, readAnnualVegetation, interpMonthlyVeg, SatellitePhenology
     use SnowSnicarMod                 , only : SnowAge_init, SnowOptics_init
     use lnd2atmMod                    , only : lnd2atm_minimal
-    use controlMod                    , only : NLFilename
+    use controlMod                    , only : NLFilename, check_missing_initdata_status
     use clm_instMod                   , only : clm_fates
     use BalanceCheckMod               , only : BalanceCheckInit
     use CNSharedParamsMod             , only : CNParamsSetSoilDepth
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index c7025c5718..1af68b0af6 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -59,10 +59,10 @@ module controlMod
   public :: control_setNL ! Set namelist filename
   public :: control_init  ! initial run control information
   public :: control_print ! print run control information
+  public :: check_missing_initdata_status  ! check for missing finidat_interp_dest .status file
   !
   !
   ! !PRIVATE MEMBER FUNCTIONS:
-  private :: check_missing_initdata_status  ! check for missing finidat_interp_dest .status file
   private :: apply_use_init_interp  ! apply the use_init_interp namelist option, if set
   !
   ! !PRIVATE TYPES:

From d0f7fc2b56d0094b0bbb5e6ecc1ef580a55c8431 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 15:54:51 -0600
Subject: [PATCH 0854/1248] Update cam and cice to version in cesm3_0_beta02,
 there is a gitfleximod problem in updating to this CAM version

---
 .gitmodules | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 07a4f7e3e6..bc8db311ec 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -40,14 +40,14 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release
 [submodule "cice"]
 	path = components/cice
 	url = https://github.com/ESCOMP/CESM_CICE
-fxtag = cesm_cice6_5_0_9
+fxtag = cesm_cice6_5_0_10
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 
 [submodule "cam"]
 path = components/cam
 url = https://github.com/ESCOMP/CAM
-fxtag = cam6_3_162
+fxtag = cam6_4_016
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CAM
 #

From 5084ea66320b447af6a600cf90dd9d580366e5d6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 16:19:00 -0600
Subject: [PATCH 0855/1248] Remove CAM and CICE from the submodules for coming
 into CTSM master

---
 .gitmodules | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index bc8db311ec..19bc024208 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -33,27 +33,6 @@ fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
 
-#
-# CAM and CICE in order to do F compsets along this brunch
-# (Remove before going to master)
-#
-[submodule "cice"]
-	path = components/cice
-	url = https://github.com/ESCOMP/CESM_CICE
-fxtag = cesm_cice6_5_0_10
-fxrequired = ToplevelRequired
-fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
-
-[submodule "cam"]
-path = components/cam
-url = https://github.com/ESCOMP/CAM
-fxtag = cam6_4_016
-fxrequired = ToplevelRequired
-fxDONOTUSEurl = https://github.com/ESCOMP/CAM
-#
-# End
-#
-
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper

From 870588a1a03edb35591f9495adec140bca20acdb Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 16:44:26 -0600
Subject: [PATCH 0856/1248] Add a LDust testmod and tests for it

Add a testmod for running Leung_2023 dust emission explicitly.
And change some existing aux_clm tests over to it (but not all).
---
 cime_config/testdefs/testlist_clm.xml                | 12 ++++++------
 .../clm60cam7LndTuningModeLDust/include_user_mods    |  1 +
 .../clm/clm60cam7LndTuningModeLDust/user_nl_clm      |  1 +
 3 files changed, 8 insertions(+), 6 deletions(-)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 951e0d8d5b..f4484c7410 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -100,7 +100,7 @@
       <option name="comment">Simple test use soil eroditability in CTSM for CAM5 tuning</option>
     </options>
   </test>
-  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
+  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningModeLDust">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -109,7 +109,7 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution</option>
     </options>
   </test>
-    <test name="ERP_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam7LndTuningMode">
+    <test name="ERP_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam7LndTuningModeLDust">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -129,7 +129,7 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="IHistClm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
+  <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="IHistClm60BgcCropG" testmods="clm/clm60cam7LndTuningModeLDust">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -138,7 +138,7 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution for transient</option>
     </options>
   </test>
-  <test name="PEM_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
+  <test name="PEM_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningModeLDust">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -156,7 +156,7 @@
       <option name="comment">CESM3 development simple exact restart test at the standard coupled resolution</option>
     </options>
   </test>
-  <test name="ERI_D" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
+  <test name="ERI_D" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningModeLDust">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -247,7 +247,7 @@
       <option name="comment">Test that the workhorse mpasa resolution functions for CAM, for both Hist and 2000 with latest CLM version. No need to run this test with every tag, but include it in the less frequent ctsm_sci testing.</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningModeLDust">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/include_user_mods
new file mode 100644
index 0000000000..ef8619d930
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/include_user_mods
@@ -0,0 +1 @@
+../clm60cam7LndTuningMode
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
new file mode 100644
index 0000000000..54057b1893
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
@@ -0,0 +1 @@
+dust_emis_method = 'Leung_2023'

From b669df61dccd3831c6b9851de0aff41c4cd8c64e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 17:28:26 -0600
Subject: [PATCH 0857/1248] Add some comments about how this can be removed

---
 .../share_esmf/PrigentRoughnessStreamType.F90             | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/unit_test_stubs/share_esmf/PrigentRoughnessStreamType.F90 b/src/unit_test_stubs/share_esmf/PrigentRoughnessStreamType.F90
index 71fb04f942..d9ded09c30 100644
--- a/src/unit_test_stubs/share_esmf/PrigentRoughnessStreamType.F90
+++ b/src/unit_test_stubs/share_esmf/PrigentRoughnessStreamType.F90
@@ -3,6 +3,12 @@ module PrigentRoughnessStreamType
   !-----------------------------------------------------------------------
   ! !DESCRIPTION:
   ! UNIT-TEST STUB for Prigent Roughtness Stream
+  !       This just allows the Leung dust emission code to be tested without
+  !       reading in the streams data, by faking it and setting it to a
+  !       constant value.
+  ! NOTE: THIS SHOULD BE REMOVED WHEN THE MAIN VERSION ALLOWS IT TO BE OFF.
+  !       https://github.com/ESCOMP/CTSM/issues/2381
+  ! Removing this version will remove testing code duplication.
   ! !USES
   use shr_kind_mod     , only : r8 => shr_kind_r8, CL => shr_kind_cl
   use shr_log_mod      , only : errMsg => shr_log_errMsg
@@ -50,7 +56,7 @@ subroutine Init(this, bounds, NLFilename)
    ! local variables
    !-----------------------------------------------------------------------
    allocate(this%prigent_rghn(bounds%begg:bounds%endg))
-   this%prigent_rghn(:) = 1.0_r8
+   this%prigent_rghn(:) = 1.0_r8     ! This should likely be a smaller value like 0.1 based on the Prigent dataset average values
    InitDone = .true.
 
   end subroutine Init

From 2d889afb1b94a4c25143a9f8003395188fe81110 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 17:37:19 -0600
Subject: [PATCH 0858/1248] Add some comments and revise the warning as per
 code review

---
 bld/CLMBuildNamelist.pm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 463bd9c429..b99be288e7 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -5091,11 +5091,15 @@ sub setup_logic_prigent_roughness {
   my $use_prigent = $nl->get_value($var);
   if ( &value_is_true($use_prigent) ) {
      if ( $dust_emis_method ne "Leung_2023" ) {
-       $log->warning( "$var does NOT need to be set without dust_emis_method being Leung_2023" );
+       # The Prigent dataset could be used for other purposes
+       # (such as roughness as in https://github.com/ESCOMP/CTSM/issues/2349)
+       $log->warning( "$var does NOT need to on without dust_emis_method being Leung_2023, it simply won't be used" );
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_prigentroughness' );
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_prigentroughness' );
   } elsif ( $dust_emis_method eq "Leung_2023" ) {
+    # In the future we WILL allow it to be turned off for testing and Paleo work
+    # see: https://github.com/ESCOMP/CTSM/issues/2381)
     $log->fatal_error("variable \"$var\" MUST be true when Leung_2023 dust emission method is being used" );
   }
 }

From e76b9d1092cb8b5ea6ceb82bda5016a5b336f608 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 17:38:36 -0600
Subject: [PATCH 0859/1248] REmove all of the settings of GLC_TWO_WAY_COUPLING
 set to FALSE since that's the default and it's not needed

---
 bld/unit_testers/build-namelist_test.pl | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 1fe98b392e..d7c94b8538 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -519,7 +519,6 @@ sub cat_and_create_namelistinfile {
                                    },
      "LeungDust_WO_Prigent"      =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"use_prigent_roughness=.false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                    },
      "soilm_stream off w file"      =>{ options=>"-res 0.9x1.25 -envxml_dir .",
@@ -544,17 +543,14 @@ sub cat_and_create_namelistinfile {
                                    },
      "coldstart exice on wo stream"=>{ options=>"-res 0.9x1.25 -envxml_dir . --clm_start_type cold",
                                      namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "coldstart exice on bad temp" =>{ options=>"-res 0.9x1.25 -envxml_dir . --clm_start_type cold",
                                      namelst=>"use_excess_ice=.true., use_excess_ice_streams = .true., excess_ice_coldstart_temp=0.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "coldstart exice on bad depth" =>{ options=>"-res 0.9x1.25 -envxml_dir . --clm_start_type cold",
                                      namelst=>"use_excess_ice=.true., use_excess_ice_streams = .true., excess_ice_coldstart_depth=0.0",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "clm50CNDVwtransient"       =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings",
@@ -1274,17 +1270,14 @@ sub cat_and_create_namelistinfile {
                                    },
      "Set coldtemp wo coldstart" =>{ options=>"-envxml_dir . --clm_start_type startup",
                                      namelst=>"use_excess_ice=.true.,excess_ice_coldstart_temp=-10.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "Set colddepth wo coldstart" =>{ options=>"-envxml_dir . --clm_start_type startup",
                                      namelst=>"use_excess_ice=.true.,excess_ice_coldstart_depth=0.5",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "PrigentOnWOLeung"          =>{ options=>"-envxml_dir . -bgc sp",
                                      namelst=>"use_prigent_roughness=.true.,dust_emis_method='Zender_2003'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
      "NotNEONbutNEONlightres"    =>{ options=>"--res CLM_USRDAT --clm_usr_name regional --envxml_dir . --bgc bgc --light_res 106x174",

From 00537d1e28e787c80c1769a6c458197ca7d2a5ca Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 18:21:48 -0600
Subject: [PATCH 0860/1248] Add dust fields including FV to output history
 files for the Zender and Leung dust tests

---
 .../clm/clm45cam4LndTuningModeZDustSoilErod/user_nl_clm       | 1 +
 .../clm/clm50cam5LndTuningModeZDustSoilErod/user_nl_clm       | 1 +
 .../clm/clm51cam6LndTuningModeZDustSoilErod/user_nl_clm       | 1 +
 .../testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm | 4 ++++
 4 files changed, 7 insertions(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45cam4LndTuningModeZDustSoilErod/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm45cam4LndTuningModeZDustSoilErod/user_nl_clm
index 93b7ee2e48..d97fbbac57 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm45cam4LndTuningModeZDustSoilErod/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm45cam4LndTuningModeZDustSoilErod/user_nl_clm
@@ -1,3 +1,4 @@
 ! Turn on using the soil eroditability file in CTSM
 dust_emis_method = 'Zender_2003'
 zender_soil_erod_source = 'lnd'
+hist_fincl1   += 'FV'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam5LndTuningModeZDustSoilErod/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm50cam5LndTuningModeZDustSoilErod/user_nl_clm
index 93b7ee2e48..d97fbbac57 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm50cam5LndTuningModeZDustSoilErod/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam5LndTuningModeZDustSoilErod/user_nl_clm
@@ -1,3 +1,4 @@
 ! Turn on using the soil eroditability file in CTSM
 dust_emis_method = 'Zender_2003'
 zender_soil_erod_source = 'lnd'
+hist_fincl1   += 'FV'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeZDustSoilErod/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeZDustSoilErod/user_nl_clm
index 93b7ee2e48..d97fbbac57 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeZDustSoilErod/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeZDustSoilErod/user_nl_clm
@@ -1,3 +1,4 @@
 ! Turn on using the soil eroditability file in CTSM
 dust_emis_method = 'Zender_2003'
 zender_soil_erod_source = 'lnd'
+hist_fincl1   += 'FV'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
index 54057b1893..e6da29bbe9 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
@@ -1 +1,5 @@
 dust_emis_method = 'Leung_2023'
+! Add all of the Leung optional history fields
+hist_fincl1   += 'FV', 'DUST_EMIS_COEFF', 'WND_FRC_FT', 'WND_FRC_FT_DRY', 'WND_FRC_IT', 'WND_FRC_SOIL', 'LND_FRC_MBLE', 'GWC', 'LIQ_FRAC', 
+                  'U_S_MEAN', 'U_S_MEAN', 'ZETAOBU', 'U_FT', 'U_IT', 'ALPHA_TC_RATE', 'P_IT'. 'ETA', 'SSR', 'VAI_OKIN',
+                  'FRC_THR_RGHN_FCT', 'WND_FRC_FT_STD', 'DPFCT_ROCK'

From f484425c53260f1294faf5e7c3f410bc69659ac8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 18:34:20 -0600
Subject: [PATCH 0861/1248] Modify some of the comments based on code review,
 and simplify the MassFracClayLeung2023 function

---
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 27 ++++++++++----------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index edcc14430b..e6fcca0f27 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -706,15 +706,8 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
 
     ! --------------------------------------------------------------------
     ! Initialize threshold soil moisture, and mass fraction of clay as
-    ! scaling coefficient of dust emission flux (kg/m2/s) in DUSTMod.F90
-    ! dmleung modified 5 Jul 2024, reducing sensitivity of dust emission
-    ! flux to clay fraction.
-    ! Also, for threshold soil moisture, dmleung followed Zender (2003)
-    ! DEAD scheme to again avoid dust flux being too sensitive to the choice
-    ! of clay dataset. This is different from what Leung et al. (2023)
-    ! intended to do.
-    ! Both decisions are based on tuning preference and could subject to
-    ! future changes. dmleung 5 Jul 2024
+    ! scaling coefficient of dust emission flux (kg/m2/s) in each DustEmisType
+    ! module. See the comments in each function.
     ! --------------------------------------------------------------------
 
     do c = begc,endc
@@ -751,6 +744,7 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
   ! convert surface clay fraction from percentage to fraction.
   ! The equation comes from Eq. 14 of Fecan et al. (1999; https://doi.org/10.1007/s00585-999-0149-7).
   !
+  ! NOTE: dmleung 19 Feb 2024.
   !------------------------------------------------------------------------------
   ! For future developments Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) o
   ! dust emission scheme in the CESM will use Zender's tuning as well, which overall
@@ -762,7 +756,11 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
   !
   ! Also see the notes below for ThresholdSoilMoistKok2014.
   !
-  ! Notes from: dmleung 19 Feb 2024.
+  ! NOTE on Leung dust emissions: dmleung Jul 5 2024:
+  !
+  ! dmleung followed Zender (2003) DUST scheme to again avoid dust flux being too sensitive to the choice
+  ! of clay dataset. This is different from what Leung et al. (2023) intended to do.
+  ! NOTE: This might need to be adjusted for tuning in the future.
   !
   !------------------------------------------------------------------------------
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
@@ -781,6 +779,8 @@ real(r8) function ThresholdSoilMoistKok2014( clay )
   !------------------------------------------------------------------------------
   ! Calculate the threshold soil moisture needed for dust emission, based on clay content
   !
+  ! NOTE: dmleung 24 May 2024.
+  !
   ! The below calculates the threshold gravimetric water content for the dust emission
   ! calculation in DustEmis. The equation comes from Eq. 14 of Fecan et al.
   ! (1999; https://doi.org/10.1007/s00585-999-0149-7).
@@ -792,7 +792,6 @@ real(r8) function ThresholdSoilMoistKok2014( clay )
   ! Charlie Zender (2003a) chose:  a = 1/clay3d, which gives the ThresholdSoilMoistZender2003
   ! function above.
   !
-  ! Notes from: dmleung 24 May 2024.
   !------------------------------------------------------------------------------
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
@@ -813,10 +812,12 @@ end function MassFracClay
   real(r8) function MassFracClayLeung2023( clay )
   ! Calculate the mass fraction of clay needed for dust emission, based on clay content
   ! Based on the base Zender_2003 version, with a slight modification for Leung_2023
+  ! dmleung modified 5 Jul 2024, reducing sensitivity of dust emission
+  ! flux to clay fraction.
+  ! NOTE: This might need to be adjusted for tuning in the future.
       real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%)
 
-      MassFracClayLeung2023 = MassFracClay( clay )
-      MassFracClayLeung2023 = 0.1_r8 + MassFracClayLeung2023 * 0.1_r8 / 0.20_r8   ! dmleung added this line to reduce the sensitivity of dust emission flux to clay fraction in DUSTMod. 5 Jul 2024
+      MassFracClayLeung2023 = 0.1_r8 + MassFracClay( clay ) * 0.1_r8 / 0.20_r8   ! dmleung added this line to reduce the sensitivity of dust emission flux to clay fraction in DUSTMod. 5 Jul 2024
   end function MassFracClayLeung2023
 
   !------------------------------------------------------------------------------

From d7e5a6ddf2668c1379a85fa7fadd5b259ca6540c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 18:43:51 -0600
Subject: [PATCH 0862/1248] Add back the comment that got accidentally removed

---
 src/unit_test_shr/unittestDustEmisInputs.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90
index a8473460b9..6f1a7b09f7 100644
--- a/src/unit_test_shr/unittestDustEmisInputs.F90
+++ b/src/unit_test_shr/unittestDustEmisInputs.F90
@@ -84,10 +84,11 @@ subroutine setUp(this)
                                           glcmec_downscale_longwave = .false., &
                                           lapse_rate = 0.01_r8 &  ! arbitrary (this is unused for these tests)
     )
+
     call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params)
     ! Water and soil state -- after the subgrid setup
     call this%water_factory%setup_after_subgrid(snl = snl)
-    call this%setupSoilState( )
+    call this%setupSoilState( )   ! This needs to happen before the water_type object creation
     call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col)
     ! Canopy state, friction velocity, and temperature state ojects
     call this%canopystate_inst%SetNMLForTesting()

From e83caa8e79bec1c25bd7d353838606b36efbc42d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 18:47:43 -0600
Subject: [PATCH 0863/1248] Remove if for use_cn around adding FV to the
 history file and make it default inactive

---
 src/biogeophys/FrictionVelocityMod.F90 | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90
index 8e06e66e32..44e1bf6294 100644
--- a/src/biogeophys/FrictionVelocityMod.F90
+++ b/src/biogeophys/FrictionVelocityMod.F90
@@ -262,12 +262,10 @@ subroutine InitHistory(this, bounds)
             ptr_patch=this%ram1_patch, default='inactive')
     end if
 
-    !if (use_cn) then
        this%fv_patch(begp:endp) = spval
        call hist_addfld1d (fname='FV', units='m/s', &
             avgflag='A', long_name='friction velocity', &
-            ptr_patch=this%fv_patch)
-    !end if
+            ptr_patch=this%fv_patch, default='inactive')
 
        call hist_addfld1d (fname='RAH1', units='s/m', &
             avgflag='A', long_name='aerodynamical resistance ', &

From 4daf9246649eb0ba77800706614ff039c36d747b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 18:59:46 -0600
Subject: [PATCH 0864/1248] Code review noticed a couple places where a 1_8
 really should be vai_mbl_thr

---
 src/biogeochem/DustEmisLeung2023.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 6cc86e4eb5..c96853b710 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -640,7 +640,7 @@ subroutine DustEmission (this, bounds, &
          ! purpose: compute factor by which surface roughness increases threshold
          !          friction velocity (currently a constant)
 
-         if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<=1_r8) then
+         if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<= vai_mbl_thr) then
             !if (lnd_frc_mbl(p) > 0.0_r8  .AND. ttlai(p)<=1_r8) then
             ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
             !lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
@@ -687,7 +687,7 @@ subroutine DustEmission (this, bounds, &
 
          else    ! for lnd_frc_mbl=0, do not change friction velocity and assume drag partition factor = 0
             wnd_frc_slt = fv(p) * frc_thr_rghn_fct(p) ! The value here is not important since once lnd_frc_mbl(p) <= 0.0_r8 there will be no emission. dmleung added 5 Jul 2024
-            frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > 1, the drag partition effect is zero. dmleung 16 Feb 2024.
+            frc_thr_rghn_fct(p) = 0.0_r8            ! When LAI > vai_mbl_thr, the drag partition effect is zero. dmleung 16 Feb 2024.
          end if
 
          !########## end of drag partition effect #######################################################

From 5007a1a8850c1635f13d9e21ef8a07a31fe2db23 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 19:10:09 -0600
Subject: [PATCH 0865/1248] Remove cam and cice as submodules

---
 components/cam  | 1 -
 components/cice | 1 -
 2 files changed, 2 deletions(-)
 delete mode 160000 components/cam
 delete mode 160000 components/cice

diff --git a/components/cam b/components/cam
deleted file mode 160000
index ab476f9b73..0000000000
--- a/components/cam
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ab476f9b7345cbefdc4cf67ff17f0fe85d8c7387
diff --git a/components/cice b/components/cice
deleted file mode 160000
index bdf6ea04d6..0000000000
--- a/components/cice
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit bdf6ea04d6133434fcaa4de5336de106f01290d0

From 63a2e73deb72088d84160e020b8ae2b254edfa88 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 19:47:32 -0600
Subject: [PATCH 0866/1248] Remove commented out code for clarity

---
 src/biogeochem/DustEmisLeung2023.F90 | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index c96853b710..1746056fbf 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -641,17 +641,6 @@ subroutine DustEmission (this, bounds, &
          !          friction velocity (currently a constant)
 
          if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<= vai_mbl_thr) then
-            !if (lnd_frc_mbl(p) > 0.0_r8  .AND. ttlai(p)<=1_r8) then
-            ! vegetation drag partition equation following Gregory Okin (2008) + Caroline Pierre et al. (2014)
-            !lai(p) = tlai_lu(l)+0.1_r8       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
-            !lai(p) = ttlai(p) + lai0_Okin     ! ttlai = tlai+tsai. Okin-Pierre's equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
-            !if (lai(p) > 1_r8) then
-            !   lai(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1)
-            !end if              !
-
-            !if (ttlai(p) + vai0_Okin <= 1_r8) then
-            !   vai_Okin(p) = ttlai(p) + vai0_Okin     ! ttlai = vai = tlai+tsai. Okin-Pierre's equation is undefined at vai=0, and VAI in CTSM has some zeros over deserts, so we add in a small number. On 26 Feb 2024, dmleung changed from tlai_lu(l) to ttlai(p)
-            !end if                                    ! In the Okin-Pierre formulation, VAI has to be 0 < VAI <= 1.
 
             vai_Okin(p) = tlai_lu(l)+vai0_Okin       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
             if (vai_Okin(p) > 1_r8) then
@@ -667,13 +656,10 @@ subroutine DustEmission (this, bounds, &
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then ! if bare, uses rock drag partition factor
                   if (dpfct_rock(p) /= dpfct_rock(p)) then ! dmleung added 24 May 2024: dpfct_rock(p) could be NaN; CLM could run when DEBUG=FALSE in env_build.xml but dies when DEBUG=TRUE (usually when checking if wnd_frc_slt > wnd_frc_thr_slt_it and if numer/denom < 30._r8 below)
-                     !write(iulog,*) 'dpfct_rock(p) == NaN; dpfct_rock(p) = ', dpfct_rock(p)
                      frc_thr_rgh_fct = 0.001_r8 ! Set drag partition effect to be a very small value (or zero) such that there is no emission whenever dpfct_rock(p) = NaN; dmleung 24 May 2024
                   else
-                     !write(iulog,*) 'dpfct_rock(p) = ', dpfct_rock(p)
                      frc_thr_rgh_fct = dpfct_rock(p)
                   end if
-               !frc_thr_rgh_fct = dpfct_rock(p) ! This should be the original code when dpfct_rock(p) has values everywhere
                else   ! if vegetation, uses vegetation drag partition factor
                   frc_thr_rgh_fct = ssr(p)
                end if
@@ -731,7 +717,6 @@ subroutine DustEmission (this, bounds, &
             ! mean lowpass-filtered wind speed at hgt_sal = 0.1 m saltation height (assuming aerodynamic roughness length z0a_glob = 1e-4 m globally for ease; also assuming neutral condition)
             u_mean_slt(p) = (wnd_frc_slt/k) * log(hgt_sal / z0a_glob)  ! translating from ustar (velocity scale) to actual wind
 
-            !stblty(p) = 0_r8   ! -dmleung 2 Dec 2021: use stability = 0 for now, assuming no buoyancy contribution. Might uncomment the above lines in future revisions.
             stblty(p) = zii / obu(p)   ! -dmleung 20 Feb 2024: use obu from CTSM and PBL height = zii (= 1000_r8) which is default in CTSM. Should we transfer PBL height from CAM?
             if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
                u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8

From 5a2c873d89b0001baac42480182b115fbec19a98 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 21:38:49 -0600
Subject: [PATCH 0867/1248] Clarify the error message that the prigent streams
 file is required for Leung 2023 dust emissions

---
 src/biogeochem/DustEmisLeung2023.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 1746056fbf..5f92d58425 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -319,7 +319,8 @@ subroutine InitCold(this, bounds)
       call this%CalcDragPartition( bounds )
     else
 
-      call endrun( "ERROR:: Drag partitioning MUST now use a streams file of aeolian roughness length to calculate, it can no longer read from the fsurdat file" )
+      call endrun( "ERROR:: dus_emis_Leung_2023 requires requires a streams file of aeolian roughness length to calculate drag partitioning" )
+
     end if
 
   end subroutine InitCold

From 96d2de57dd024b712035d5cca54dbe7d3cec65e5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 9 Aug 2024 22:59:31 -0600
Subject: [PATCH 0868/1248] Fix a syntax topo, so will work

---
 .../testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
index e6da29bbe9..09887c81b8 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningModeLDust/user_nl_clm
@@ -1,5 +1,5 @@
 dust_emis_method = 'Leung_2023'
 ! Add all of the Leung optional history fields
 hist_fincl1   += 'FV', 'DUST_EMIS_COEFF', 'WND_FRC_FT', 'WND_FRC_FT_DRY', 'WND_FRC_IT', 'WND_FRC_SOIL', 'LND_FRC_MBLE', 'GWC', 'LIQ_FRAC', 
-                  'U_S_MEAN', 'U_S_MEAN', 'ZETAOBU', 'U_FT', 'U_IT', 'ALPHA_TC_RATE', 'P_IT'. 'ETA', 'SSR', 'VAI_OKIN',
+                  'U_S_MEAN', 'U_S_MEAN', 'ZETAOBU', 'U_FT', 'U_IT', 'ALPHA_TC_RATE', 'P_IT', 'ETA', 'SSR', 'VAI_OKIN',
                   'FRC_THR_RGHN_FCT', 'WND_FRC_FT_STD', 'DPFCT_ROCK'

From 38c42ae7b0ec946ee95b56b3840e0ba4c6d6515f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 10 Aug 2024 14:13:06 -0600
Subject: [PATCH 0869/1248] Add a unit test to check if dpfct_rock can be nan,
 currently fails as the nan handling inside of DustEmissions for Leung is not
 sufficient

---
 src/biogeochem/DustEmisBase.F90               | 19 ++++++++
 .../DustEmis_test/test_DustEmisLeung2023.pf   | 47 +++++++++++++++++--
 2 files changed, 62 insertions(+), 4 deletions(-)

diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90
index d13df40992..84467c701d 100644
--- a/src/biogeochem/DustEmisBase.F90
+++ b/src/biogeochem/DustEmisBase.F90
@@ -69,6 +69,8 @@ module DustEmisBase
      procedure , public   :: GetConstVars    ! Get important constant variables
      procedure , public   :: CleanBase       ! Base object deallocation (allows extension)
      procedure , public   :: Clean => CleanBase ! Deallocation used by callers
+     procedure , public   :: SetDragPartitionBase ! Base SetDragPartition method that just aborts
+     procedure , public   :: SetDragPartition => SetDragPartitionBase ! SetDrgPartiotion used by callers
      procedure , private  :: InitAllocateBase
      procedure , private  :: InitHistoryBase
      procedure , private  :: InitDustVars    ! Initialize variables used in DustEmission method
@@ -237,6 +239,23 @@ subroutine InitHistoryBase(this, bounds)
 
   end subroutine InitHistoryBase
 
+  !------------------------------------------------------------------------
+
+  subroutine SetDragPartitionBase(this, bounds, drag_partition)
+      !
+      ! !DESCRIPTION:
+      ! Set the drag partition for testing -- only aborts as only used by the Leung instance
+      !
+      ! !USES:
+      ! !ARGUMENTS:
+      class(dust_emis_base_type) :: this
+      type(bounds_type), intent(in) :: bounds
+      real(r8), intent(in) :: drag_partition
+
+      call endrun(msg="SetDragPartition is NOT allowed for this dust emission class type")
+
+  end subroutine SetDragPartitionBase
+
   !-----------------------------------------------------------------------
 
   subroutine WritePatchToLog(this, p)
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
index 4947a76d60..7aac658d33 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
@@ -7,7 +7,9 @@ module test_DustEmisLeung2023
   use unittestSubgridMod, only : bounds
   use DustEmisBase
   use DustEmisLeung2023
+  use abortutils, only : endrun
   use shr_kind_mod , only : r8 => shr_kind_r8
+  use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
   use DustEmisFactory, only : create_dust_emissions
   use shr_dust_emis_mod, only : dust_emis_set_options
 
@@ -37,7 +39,7 @@ contains
 
     call dust_emis_set_options( 'Leung_2023', 'none')
     call this%input%setUp( )
- 
+
     ! Create the dust emission object last
     allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename))
   end subroutine setUp
@@ -72,7 +74,7 @@ contains
        call this%dust_emis%WritePatchToLog( p )
     end do
   end subroutine print_values
-  
+
   !-----------------------------------------------------------------------
 
   subroutine validate_patch(this, p)
@@ -203,7 +205,7 @@ contains
     class(TestDustEmisLeung2023), intent(inout) :: this
     real(r8) :: flx_mss_vrt_dst_tot
     character(100) :: expected_msg
- 
+
     call this%input%create_atm2lnd()
     call this%input%create_fv( )
     ! Dust should abort with an error on dust mobility when snow fraction greater than 1
@@ -215,7 +217,7 @@ contains
     @assertExceptionRaised(expected_msg)
 
   end subroutine aborts_on_bad_dust_mobility
- 
+
   !-----------------------------------------------------------------------
 
  @Test
@@ -248,7 +250,44 @@ contains
   end subroutine dust_zero_when_tlai_high
 
   !-----------------------------------------------------------------------
+  @Test
+  subroutine dust_handles_dpfct_rock_nan(this)
+    use PatchType, only : patch
+    ! Check dust emissions can handle dpftc_rock being set to NaN
+    class(TestDustEmisLeung2023), intent(inout) :: this
+    integer :: p, i
+    real(r8) :: flx_mss_vrt_dst_tot, drag_partition, previous_dst_tot
 
+    call this%input%create_atm2lnd()
+    call this%input%create_fv( )
+    ! Loop over twice first with nan and then with the tiny value that nan should be changed to
+    do i = 1, 2
+       if ( i == 1 )then
+          drag_partition = nan
+       else if ( i == 2 ) then
+          drag_partition = 0.001
+       else
+          call endrun( "Looping over too many iterations should just be 2" )
+       end if
+       call this%dust_emis%SetDragPartition(bounds, drag_partition)
+       call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                         this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                         this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+       do p = bounds%begp, bounds%endp
+          call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+          @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
+          if ( i == 1 )then
+             previous_dst_tot = flx_mss_vrt_dst_tot
+          else
+             ! Verify that the result with nan is equal to the result with the tiny value as expected
+             @assertEqual( flx_mss_vrt_dst_tot, previous_dst_tot )
+          end if
+       end do
+    end do
+
+  end subroutine dust_handles_dpfct_rock_nan
+
+   !-----------------------------------------------------------------------
   @Test
   subroutine check_dust_emis_increasing_fv(this)
     ! Check dust emissions with increasing friction velocity

From 1fe61e623a20fe94e9221d2e405d8fcc3d7263b4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 10 Aug 2024 14:19:33 -0600
Subject: [PATCH 0870/1248] Now passes the unit-test

---
 src/biogeochem/DustEmisLeung2023.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 5f92d58425..bab1eba4ed 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -14,7 +14,7 @@ module DustEmisLeung2023
   ! !USES:
   use shr_kind_mod         , only : r8 => shr_kind_r8
   use shr_log_mod          , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
+  use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=), shr_infnan_isnan
   use clm_varpar           , only : dst_src_nbr, ndst
   use clm_varcon           , only : grav, spval
   use landunit_varcon      , only : istcrop, istsoil
@@ -656,7 +656,7 @@ subroutine DustEmission (this, bounds, &
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then ! if bare, uses rock drag partition factor
-                  if (dpfct_rock(p) /= dpfct_rock(p)) then ! dmleung added 24 May 2024: dpfct_rock(p) could be NaN; CLM could run when DEBUG=FALSE in env_build.xml but dies when DEBUG=TRUE (usually when checking if wnd_frc_slt > wnd_frc_thr_slt_it and if numer/denom < 30._r8 below)
+                  if (shr_infnan_isnan(dpfct_rock(p)) ) then ! dmleung added 24 May 2024: dpfct_rock(p) could be NaN; CLM could run when DEBUG=FALSE in env_build.xml but dies when DEBUG=TRUE (usually when checking if wnd_frc_slt > wnd_frc_thr_slt_it and if numer/denom < 30._r8 below)
                      frc_thr_rgh_fct = 0.001_r8 ! Set drag partition effect to be a very small value (or zero) such that there is no emission whenever dpfct_rock(p) = NaN; dmleung 24 May 2024
                   else
                      frc_thr_rgh_fct = dpfct_rock(p)

From 1895cba46af487a6dcd84c80add4d97559929efe Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 10 Aug 2024 15:40:58 -0600
Subject: [PATCH 0871/1248] Add obu to create_fv, and add test for obu of zero,
 and error handling for it (since downstream values can be corrupted if it's
 NaN or zero), also use shr_infnan_isnan for intrmtncy_fct

---
 src/biogeochem/DustEmisLeung2023.F90          |  6 ++++-
 .../DustEmis_test/test_DustEmisLeung2023.pf   | 23 ++++++++++++++++---
 2 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index bab1eba4ed..4c80c3b8ca 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -718,6 +718,10 @@ subroutine DustEmission (this, bounds, &
             ! mean lowpass-filtered wind speed at hgt_sal = 0.1 m saltation height (assuming aerodynamic roughness length z0a_glob = 1e-4 m globally for ease; also assuming neutral condition)
             u_mean_slt(p) = (wnd_frc_slt/k) * log(hgt_sal / z0a_glob)  ! translating from ustar (velocity scale) to actual wind
 
+            if ( obu(p) == 0.0_r8 )then
+               call endrun(msg='Input obu is zero and can NOT be' )
+               return
+            end if
             stblty(p) = zii / obu(p)   ! -dmleung 20 Feb 2024: use obu from CTSM and PBL height = zii (= 1000_r8) which is default in CTSM. Should we transfer PBL height from CAM?
             if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
                u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
@@ -751,7 +755,7 @@ subroutine DustEmission (this, bounds, &
             intrmtncy_fct(p) = 1.0_r8 - prb_crs_fld_thr(p) + thr_crs_rate(p) * (prb_crs_fld_thr(p) - prb_crs_impct_thr(p))
 
             ! multiply dust emission flux by intermittency factor
-            if (intrmtncy_fct(p) /= intrmtncy_fct(p)) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted
+            if ( shr_infnan_isnan(intrmtncy_fct(p)) ) then  ! if intrmtncy_fct(p) is not NaN then multiply by intermittency factor; this statement is needed because dust emission flx_mss_vrt_dst_ttl(p) has to be non NaN (at least zero) to be outputted
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p)
             else
                flx_mss_vrt_dst_ttl(p) = flx_mss_vrt_dst_ttl(p) * intrmtncy_fct(p)  ! multiply dust flux by intermittency
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
index 7aac658d33..66f0191c06 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
@@ -109,7 +109,7 @@ contains
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, &
                                vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, &
                                vlc_trb_4=vlc_trb_4)
-       @assertEqual( flx_mss_vrt_dst_tot, 1.305341724414137d-006, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 1.305340725852736d-006, tolerance=tol )
        @assertEqual( vlc_trb_1, 3.407721147709135d-003, tolerance=tol )
        @assertEqual( vlc_trb_2, 4.961153753164878d-003, tolerance=tol )
        @assertEqual( vlc_trb_3, 4.980100969983446d-003, tolerance=tol )
@@ -287,6 +287,23 @@ contains
 
   end subroutine dust_handles_dpfct_rock_nan
 
+    !-----------------------------------------------------------------------
+  @Test
+  subroutine dust_aborts_on_zero_obu(this)
+      use PatchType, only : patch
+      ! Check dust emissions can handle dpftc_rock being set to NaN
+      class(TestDustEmisLeung2023), intent(inout) :: this
+      character(100) :: expected_msg
+
+      call this%input%create_atm2lnd()
+      call this%input%create_fv( obu=0.0_r8 )
+      call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                        this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                        this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+      expected_msg = "ABORTED: Input obu is zero and can NOT be"
+      @assertExceptionRaised(expected_msg)
+
+  end subroutine dust_aborts_on_zero_obu
    !-----------------------------------------------------------------------
   @Test
   subroutine check_dust_emis_increasing_fv(this)
@@ -309,7 +326,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust0 = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 1.064145669761461d-5, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 1.064145664977026d-5, tolerance=tol )
     end do
     ! Double fv and show result is higher
     call this%input%create_fv( u10=u10, fv=fv*2.0_r8)
@@ -321,7 +338,7 @@ contains
        call this%validate_patch(p)
        call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
        total_dust_higher = flx_mss_vrt_dst_tot
-       @assertEqual( flx_mss_vrt_dst_tot, 8.309603073613188d-5, tolerance=tol )
+       @assertEqual( flx_mss_vrt_dst_tot, 8.309603071671919d-5, tolerance=tol )
     end do
     @assertGreaterThan( total_dust_higher, total_dust0 )
 

From d42679740bbcec5dfd3c29721b5b359197508cd2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 10 Aug 2024 18:53:07 -0600
Subject: [PATCH 0872/1248] Set obu in create_fv since it's needed for the
 Leung method

---
 src/unit_test_shr/unittestDustEmisInputs.F90 | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90
index 6f1a7b09f7..771eb410f7 100644
--- a/src/unit_test_shr/unittestDustEmisInputs.F90
+++ b/src/unit_test_shr/unittestDustEmisInputs.F90
@@ -202,17 +202,19 @@ end subroutine create_atm2lnd
 
   !-----------------------------------------------------------------------
 
-  subroutine create_fv(this, fv, u10, ram1)
+  subroutine create_fv(this, fv, u10, ram1, obu)
     ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets
     ! fields based on inputs. Excluded inputs are given a default value
     class(unittest_dust_emis_input_type), intent(inout) :: this
     real(r8), intent(in), optional :: fv
     real(r8), intent(in), optional :: u10
     real(r8), intent(in), optional :: ram1
+    real(r8), intent(in), optional :: obu
 
     real(r8), parameter :: fv_default = 2.0_r8
     real(r8), parameter :: u10_default = 4._r8
     real(r8), parameter :: ram1_default = 200._r8
+    real(r8), parameter :: obu_default = -100._r8
     ! ------------------------------------------------------------------------
 
     if (present(fv)) then
@@ -233,6 +235,12 @@ subroutine create_fv(this, fv, u10, ram1)
        this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default
     end if
 
+    if (present(obu)) then
+       this%frictionvel_inst%obu_patch(bounds%begp:bounds%endp) = obu
+    else
+       this%frictionvel_inst%obu_patch(bounds%begp:bounds%endp) = obu_default
+    end if
+
   end subroutine create_fv
 
   !-----------------------------------------------------------------------

From f29bfb42ed99ccbbf3d9d5955721af21c2787436 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 10 Aug 2024 18:54:42 -0600
Subject: [PATCH 0873/1248] Add a couple more asserts for MassFracClayLeung
 which helps clarify it's behavior

---
 .../test_dust_soil_clay_functions.pf                        | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
index 53a3d66987..d2d458994c 100644
--- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
+++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf
@@ -71,8 +71,11 @@ contains
 
     value = MassFracClay( 0.0_r8 )
     @assertEqual( value, 0.0_r8, tolerance=tol )
+    value = MassFracClay( 10.0_r8 )
+    @assertEqual( value, 0.10_r8, tolerance=tol )
     value = MassFracClay( 20.0_r8 )
     @assertEqual( value, 0.20_r8, tolerance=tol )
+    ! value after 20% clay should stay at 0.2
     value = MassFracClay( 25.0_r8 )
     @assertEqual( value, 0.20_r8, tolerance=tol )
 
@@ -86,8 +89,11 @@ contains
 
     value = MassFracClayLeung2023( 0.0_r8 )
     @assertEqual( value, 0.1_r8, tolerance=tol )
+    value = MassFracClayLeung2023( 10.0_r8 )
+    @assertEqual( value, 0.15_r8, tolerance=tol )
     value = MassFracClayLeung2023( 20.0_r8 )
     @assertEqual( value, 0.20_r8, tolerance=tol )
+    ! value after 20% clay should stay at 0.2
     value = MassFracClayLeung2023( 25.0_r8 )
     @assertEqual( value, 0.20_r8, tolerance=tol )
 

From 601b090980fc1bd59f00f06f190a65b6041c00b6 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 10 Aug 2024 23:50:53 -0600
Subject: [PATCH 0874/1248] Add a test that low stabiility is constant dust
 emission output, change tolerance to accomidate that, use asserts rather than
 endrun in the test code, increase fv and obu for one of the tests

---
 .../DustEmis_test/test_DustEmisLeung2023.pf   | 50 +++++++++++++++++--
 1 file changed, 45 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
index 66f0191c06..31adea76e9 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
@@ -7,7 +7,6 @@ module test_DustEmisLeung2023
   use unittestSubgridMod, only : bounds
   use DustEmisBase
   use DustEmisLeung2023
-  use abortutils, only : endrun
   use shr_kind_mod , only : r8 => shr_kind_r8
   use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
   use DustEmisFactory, only : create_dust_emissions
@@ -15,7 +14,7 @@ module test_DustEmisLeung2023
 
   implicit none
 
-  real(r8), parameter :: tol = 1.e-18_r8
+  real(r8), parameter :: tol = 1.e-16_r8
 
   @TestCase
   type, extends(TestCase) :: TestDustEmisLeung2023
@@ -259,7 +258,7 @@ contains
     real(r8) :: flx_mss_vrt_dst_tot, drag_partition, previous_dst_tot
 
     call this%input%create_atm2lnd()
-    call this%input%create_fv( )
+    call this%input%create_fv( obu = -500.0_r8, fv=15.0_r8 )
     ! Loop over twice first with nan and then with the tiny value that nan should be changed to
     do i = 1, 2
        if ( i == 1 )then
@@ -267,7 +266,7 @@ contains
        else if ( i == 2 ) then
           drag_partition = 0.001
        else
-          call endrun( "Looping over too many iterations should just be 2" )
+          @assertEqual( i, 1, "Iteration too high, should just be up to 2" )
        end if
        call this%dust_emis%SetDragPartition(bounds, drag_partition)
        call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
@@ -287,7 +286,48 @@ contains
 
   end subroutine dust_handles_dpfct_rock_nan
 
-    !-----------------------------------------------------------------------
+  !-----------------------------------------------------------------------
+
+  @Test
+  subroutine dust_constant_low_stability(this)
+    use PatchType, only : patch
+    ! Check that dust emissions stay constant until stability high enough
+    class(TestDustEmisLeung2023), intent(inout) :: this
+    integer :: p, i
+    real(r8) :: flx_mss_vrt_dst_tot, obu, previous_dst_tot
+
+    call this%input%create_atm2lnd()
+    do i = 1, 3
+       if ( i == 1 )then
+          obu = 100._r8
+       else if ( i == 2 ) then
+          obu = 50._r8
+       else if ( i == 3 ) then
+          obu = 41.67013917826486_r8
+       else
+          @assertEqual( i, 1, "Iteration too high, should just be up to 3" )
+       end if
+       call this%input%create_fv( obu=obu )
+       call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
+                         this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
+                         this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
+       do p = bounds%begp, bounds%endp
+          call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+          print *, ' obu = ', obu, ' dust_tot = ', flx_mss_vrt_dst_tot
+          @assertEqual( flx_mss_vrt_dst_tot, 1.305341766366198d-006, tolerance=tol )
+          if ( i == 1 )then
+             previous_dst_tot = flx_mss_vrt_dst_tot
+          else
+             ! Verify that the previous result is identical to the others
+             @assertEqual( flx_mss_vrt_dst_tot, previous_dst_tot, tolerance=tol )
+          end if
+       end do
+    end do
+
+  end subroutine dust_constant_low_stability
+
+  !-----------------------------------------------------------------------
+
   @Test
   subroutine dust_aborts_on_zero_obu(this)
       use PatchType, only : patch

From 02b4f9ab051efdbaab30644d1799724b1574c233 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 11 Aug 2024 00:17:51 -0600
Subject: [PATCH 0875/1248] Change constants so they are more recognizable as
 floating point with a decimal, and remove subname in favor of giving line and
 filename with errmsg

---
 src/biogeochem/DustEmisLeung2023.F90          | 86 +++++++++----------
 .../DustEmis_test/test_DustEmisLeung2023.pf   | 10 +--
 2 files changed, 48 insertions(+), 48 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 4c80c3b8ca..869c18c0dc 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -215,87 +215,87 @@ subroutine InitHistory(this, bounds)
     this%dst_emiss_coeff_patch(begp:endp) = spval
     call hist_addfld1d (fname='DUST_EMIS_COEFF', units='dimensionless',  &
          avgflag='A', long_name='soil erodibility or dust emission coefficient for Kok emission scheme', &
-         ptr_patch=this%dst_emiss_coeff_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%dst_emiss_coeff_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%wnd_frc_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_FT', units='m/s',  &
          avgflag='A', long_name='fluid threshold friction velocity', &
-         ptr_patch=this%wnd_frc_thr_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%wnd_frc_thr_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%wnd_frc_thr_dry_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_FT_DRY', units='m/s',  &
          avgflag='A', long_name='dry fluid threshold friction velocity', &
-         ptr_patch=this%wnd_frc_thr_dry_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%wnd_frc_thr_dry_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%wnd_frc_thr_it_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_IT', units='m/s',  &
          avgflag='A', long_name='impact threshold friction velocity', &
-         ptr_patch=this%wnd_frc_thr_it_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%wnd_frc_thr_it_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%wnd_frc_soil_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_SOIL', units='m/s',  &
          avgflag='A', long_name='soil surface wind friction velocity', &
-         ptr_patch=this%wnd_frc_soil_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%wnd_frc_soil_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%lnd_frc_mble_patch(begp:endp) = spval
     call hist_addfld1d (fname='LND_FRC_MBLE', units='dimensionless',  &
          avgflag='A', long_name='land mobile fraction', &
-         ptr_patch=this%lnd_frc_mble_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%lnd_frc_mble_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%gwc_patch(begp:endp) = spval
     call hist_addfld1d (fname='GWC', units='kg/kg',  &
          avgflag='A', long_name='gravimetric soil moisture at the topmost soil layer', &
-         ptr_patch=this%gwc_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%gwc_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%liq_frac_patch(begp:endp) = spval
     call hist_addfld1d (fname='LIQ_FRAC', units='dimensionless',  &
          avgflag='A', long_name='fraction of total water that is liquid', &
-         ptr_patch=this%liq_frac_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%liq_frac_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%u_mean_slt_patch(begp:endp) = spval
     call hist_addfld1d (fname='U_S_MEAN', units='m/s',  &
          avgflag='A', long_name='mean wind velocity at saltation level', &
-         ptr_patch=this%u_mean_slt_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%u_mean_slt_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%u_sd_slt_patch(begp:endp) = spval
     call hist_addfld1d (fname='U_S_SIGMA', units='m/s',  &
          avgflag='A', long_name='sd of wind velocity at saltation level', &
-         ptr_patch=this%u_sd_slt_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%u_sd_slt_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%stblty_patch(begp:endp) = spval
     call hist_addfld1d (fname='ZETAOBU', units='',  &
          avgflag='A', long_name='stability parameter', &
-         ptr_patch=this%stblty_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%stblty_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%u_fld_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='U_FT', units='m/s',  &
          avgflag='A', long_name='fluid threshold velocity at saltation level', &
-         ptr_patch=this%u_fld_thr_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%u_fld_thr_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%u_impct_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='U_IT', units='m/s',  &
          avgflag='A', long_name='impact threshold velocity at saltation level', &
-         ptr_patch=this%u_impct_thr_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%u_impct_thr_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%thr_crs_rate_patch(begp:endp) = spval
     call hist_addfld1d (fname='ALPHA_TC_RATE', units='',  &
          avgflag='A', long_name='threshold crossing rate', &
-         ptr_patch=this%thr_crs_rate_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%thr_crs_rate_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%prb_crs_fld_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='P_FT', units='',  &
          avgflag='A', long_name='probability of winds crossing fluid threshold', &
-         ptr_patch=this%prb_crs_fld_thr_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%prb_crs_fld_thr_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%prb_crs_impct_thr_patch(begp:endp) = spval
     call hist_addfld1d (fname='P_IT', units='',  &
          avgflag='A', long_name='probability of winds crossing impact threshold', &
-         ptr_patch=this%prb_crs_impct_thr_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%prb_crs_impct_thr_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%intrmtncy_fct_patch(begp:endp) = spval
     call hist_addfld1d (fname='ETA', units='',  &
          avgflag='A', long_name='intermittency factor', &
-         ptr_patch=this%intrmtncy_fct_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%intrmtncy_fct_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%ssr_patch(begp:endp) = spval
     call hist_addfld1d (fname='SSR', units='m/s',  &
          avgflag='A', long_name='Okin-Pierre vegetation shear stress ratio (drag partition factor)', &
-         ptr_patch=this%ssr_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%ssr_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%vai_Okin_patch(begp:endp) = spval
     call hist_addfld1d (fname='VAI_OKIN', units='m/s',  &
          avgflag='A', long_name='vegetation area index used in the Okin-Pierre plant drag partition scheme', &
-         ptr_patch=this%vai_Okin_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%vai_Okin_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%frc_thr_rghn_fct_patch(begp:endp) = spval
     call hist_addfld1d (fname='FRC_THR_RGHN_FCT', units='dimensionless',  &
          avgflag='A', long_name='hybrid drag partition (or roughness) factor', &
-         ptr_patch=this%frc_thr_rghn_fct_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%frc_thr_rghn_fct_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%wnd_frc_thr_std_patch(begp:endp) = spval
     call hist_addfld1d (fname='WND_FRC_FT_STD', units='m/s',  &
          avgflag='A', long_name='standardized fluid threshold friction velocity', &
-         ptr_patch=this%wnd_frc_thr_std_patch, set_lake=0._r8, set_urb=0._r8)
+         ptr_patch=this%wnd_frc_thr_std_patch, set_lake=0.0_r8, set_urb=0.0_r8)
     this%dpfct_rock_patch(begp:endp) = spval
     call hist_addfld1d (fname='DPFCT_ROCK', units='m/s',  &
          avgflag='A', long_name='rock drag partition factor', &
@@ -414,7 +414,6 @@ subroutine DustEmission (this, bounds, &
     real(r8), parameter :: zii = 1000.0_r8             ! [m] convective boundary layer height added by dmleung 20 Feb 2024, following other CTSM modules (e.g., CanopyFluxesMod). Should we transfer PBL height (PBLH) from CAM?
     real(r8) :: numer                                  ! Numerator term for threshold crossing rate
     real(r8) :: denom                                  ! Denominator term for threshold crossing rate
-    character(len=*),parameter :: subname = 'DUSTEmission'
     !------------------------------------------------------------------------
 
     associate(                                                         &
@@ -463,7 +462,7 @@ subroutine DustEmission (this, bounds, &
          wnd_frc_thr_std     => this%wnd_frc_thr_std_patch             & ! Output: standardized dust emission threshold friction velocity defined in Jasper Kok et al. (2014).
          )
 
-      ttlai(bounds%begp : bounds%endp) = 0._r8
+      ttlai(bounds%begp : bounds%endp) = 0.0_r8
       ! make lai average at landunit level
       do fp = 1,num_nolakep
          p = filter_nolakep(fp)
@@ -471,12 +470,12 @@ subroutine DustEmission (this, bounds, &
       enddo
 
       tlai_lu(bounds%begl : bounds%endl) = spval
-      sumwt(bounds%begl : bounds%endl) = 0._r8
+      sumwt(bounds%begl : bounds%endl) = 0.0_r8
       do p = bounds%begp,bounds%endp
-         if (ttlai(p) /= spval .and. patch%active(p) .and. patch%wtlunit(p) /= 0._r8) then
+         if (ttlai(p) /= spval .and. patch%active(p) .and. patch%wtlunit(p) /= 0.0_r8) then
             c = patch%column(p)
             l = patch%landunit(p)
-            if (sumwt(l) == 0._r8) tlai_lu(l) = 0._r8
+            if (sumwt(l) == 0.0_r8) tlai_lu(l) = 0.0_r8
             tlai_lu(l) = tlai_lu(l) + ttlai(p) * patch%wtlunit(p)
             sumwt(l) = sumwt(l) + patch%wtlunit(p)
          end if
@@ -487,19 +486,20 @@ subroutine DustEmission (this, bounds, &
             found = .true.
             index = l
             exit
-         else if (sumwt(l) /= 0._r8) then
+         else if (sumwt(l) /= 0.0_r8) then
             tlai_lu(l) = tlai_lu(l)/sumwt(l)
          end if
       end do
       if (found) then
-         write(iulog,*) subname//':: error: sumwt is greater than 1.0 at l= ',index
+         write(iulog,*) 'error: sumwt is greater than 1.0 at l= ',index
          call endrun(subgrid_index=index, subgrid_level=subgrid_level_landunit, msg=errMsg(sourcefile, __LINE__))
+         return
       end if
 
       ! Loop through patches
 
       ! initialize variables which get passed to the atmosphere
-      flx_mss_vrt_dst(bounds%begp:bounds%endp,:)=0._r8
+      flx_mss_vrt_dst(bounds%begp:bounds%endp,:)=0.0_r8
 
       do fp = 1,num_nolakep
          p = filter_nolakep(fp)
@@ -584,7 +584,7 @@ subroutine DustEmission (this, bounds, &
          ! calculate soil moisture effect for dust emission threshold
          ! following Fecan, Marticorena et al. (1999)
          ! also see Zender et al. (2003) for DUST emission scheme and Kok et al. (2014b) for K14 emission scheme in CESM
-         bd = (1._r8-watsat(c,1))*dns_slt      ![kg m-3] Bulk density of dry surface soil (dmleung changed from 2700 to dns_slt, soil particle density, on 16 Feb 2024. Note that dn s_slt=2650 kg m-3 so the value is changed by a tiny bit from 2700 to 2650. dns_slt has been here for many years so dns_slt should be used here instead of explicitly typing the value out. dmleung 16 Feb 2024)
+         bd = (1.0_r8-watsat(c,1))*dns_slt      ![kg m-3] Bulk density of dry surface soil (dmleung changed from 2700 to dns_slt, soil particle density, on 16 Feb 2024. Note that dn s_slt=2650 kg m-3 so the value is changed by a tiny bit from 2700 to 2650. dns_slt has been here for many years so dns_slt should be used here instead of explicitly typing the value out. dmleung 16 Feb 2024)
 
          ! use emission threshold to calculate standardized threshold and dust emission coefficient
 
@@ -644,19 +644,19 @@ subroutine DustEmission (this, bounds, &
          if (lnd_frc_mbl(p) > 0.0_r8  .AND. tlai_lu(l)<= vai_mbl_thr) then
 
             vai_Okin(p) = tlai_lu(l)+vai0_Okin       ! LAI+SAI averaged to landunit level; the equation is undefined at lai=0, and LAI in CTSM has some zeros over deserts, so we add in a small number.
-            if (vai_Okin(p) > 1_r8) then
-               vai_Okin(p)  = 1_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1) 
+            if (vai_Okin(p) > 1.0_r8) then
+               vai_Okin(p)  = 1.0_r8   ! setting LAI = 1 to be a max value (since K_length goes to negative when LAI>1) 
             end if
 
 
             ! calculate Okin's shear stress ratio (SSR, which is vegetation drag partition factor) using Pierre's equation
-            K_length = 2_r8 * (1_r8/vai_Okin(p) - 1_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
+            K_length = 2.0_r8 * (1.0_r8/vai_Okin(p) - 1.0_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
             ssr(p) = (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023). This line is Pierre's formulation.
 
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
                if (patch%itype(p) == noveg) then ! if bare, uses rock drag partition factor
-                  if (shr_infnan_isnan(dpfct_rock(p)) ) then ! dmleung added 24 May 2024: dpfct_rock(p) could be NaN; CLM could run when DEBUG=FALSE in env_build.xml but dies when DEBUG=TRUE (usually when checking if wnd_frc_slt > wnd_frc_thr_slt_it and if numer/denom < 30._r8 below)
+                  if (shr_infnan_isnan(dpfct_rock(p)) ) then ! dmleung added 24 May 2024: dpfct_rock(p) could be NaN; CLM could run when DEBUG=FALSE in env_build.xml but dies when DEBUG=TRUE (usually when checking if wnd_frc_slt > wnd_frc_thr_slt_it and if numer/denom < 30 below)
                      frc_thr_rgh_fct = 0.001_r8 ! Set drag partition effect to be a very small value (or zero) such that there is no emission whenever dpfct_rock(p) = NaN; dmleung 24 May 2024
                   else
                      frc_thr_rgh_fct = dpfct_rock(p)
@@ -723,8 +723,8 @@ subroutine DustEmission (this, bounds, &
                return
             end if
             stblty(p) = zii / obu(p)   ! -dmleung 20 Feb 2024: use obu from CTSM and PBL height = zii (= 1000_r8) which is default in CTSM. Should we transfer PBL height from CAM?
-            if ((12_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
-               u_sd_slt(p) = wnd_frc_slt * (12_r8 - 0.5_r8 * stblty(p))**0.333_r8
+            if ((12.0_r8 - 0.5_r8 * stblty(p)) .GE. 0.001_r8) then ! should have used 0 theoretically; used 0.001 here to avoid undefined values
+               u_sd_slt(p) = wnd_frc_slt * (12.0_r8 - 0.5_r8 * stblty(p))**0.333_r8
             else
                u_sd_slt(p) = wnd_frc_slt * (0.001_r8)**0.333_r8   ! should have used 0 theoretically; used 0.001 here to avoid undefined values
             end if
@@ -740,7 +740,7 @@ subroutine DustEmission (this, bounds, &
             numer = (u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p)))
             denom = (2.0_r8 * u_sd_slt(p)**2.0_r8) ! note that u_sd_slt should be always positive
             ! Truncate to zero if the expression inside exp is becoming too large
-            if ( numer/denom < 30._r8 ) then  ! set numer/denom to be < 30 given exp(30) below is already very large; also denom itself should be non-zero and non-negative given the standard deviation (u_sd_slt) of the subtimestep wind fluctuation is non-negative. dmleung 28 May 2024
+            if ( numer/denom < 30.0_r8 ) then  ! set numer/denom to be < 30 given exp(30) below is already very large; also denom itself should be non-zero and non-negative given the standard deviation (u_sd_slt) of the subtimestep wind fluctuation is non-negative. dmleung 28 May 2024
                thr_crs_rate(p) = (exp((u_fld_thr(p)**2.0_r8 - u_impct_thr(p)**2.0_r8 - 2.0_r8 * u_mean_slt(p) * (u_fld_thr(p) - u_impct_thr(p))) / (2.0_r8 * u_sd_slt(p)**2.0_r8)) + 1.0_r8)**(-1.0_r8)
             else
                thr_crs_rate(p) = 0.0_r8
@@ -829,20 +829,20 @@ subroutine CalcDragPartition(this, bounds)
                                                     ! estimating roughness effect at a distance of 10 m following Leung et al. (2023)
    real(r8), parameter :: b1 = 0.7_r8               ! [dimless] first fitting coefficient for the drag partition equation by Marticorena and Bergametti (1995), later modified by Darmenova et al. (2009).
    real(r8), parameter :: b2 = 0.8_r8               ! [dimless] second fitting coefficient for the drag partition equation by Marticorena and Bergametti (1995), later modified by Darmenova et al. (2009).
-   character(len=*), parameter :: subname = 'PrigentRoughnessStream::CalcDragPartition'
    !---------------------------------------------------------------------
 
    ! Make sure we've initialized the Prigent roughness streams
    if ( .not. this%prigent_roughness_stream%IsStreamInit() )then
-      call endrun(msg=subname//' ERROR: Streams have not been initialized, make sure Init is called first' &
-                             //', and streams are on')
+      write(iulog,*)'Error : Prigent roughness stream is NOT on: ', errMsg(sourcefile, __LINE__)
+      call endrun(msg=' ERROR: Streams have not been initialized, make sure Init is called first' &
+                       //', and streams are on')
+      return
    end if
 
    ! dmleung: this loop calculates the drag partition effect (or roughness effect) of rocks.
    !          We save the drag partition factor as a patch level quantity.
    ! TODO: EBK 02/13/2024: Several magic numbers here that should become parameters so the meaning is preserved
-   !z0s = 2_r8/30_r8 * D_p   ! equation for smooth roughness length for soil grain. See Danny M. Leung et al. (2023) and Martina Klose et al. (2021) for instance. 1/15 is a coefficient that relates roughness to soil particle diameter D_p.
-   z0s = 2_r8 * D_p / 30_r8 ! equation for smooth roughness length for soil grain. See Danny M. Leung et al. (2023) and Martina Klose et al. (2021) for instance. 1/15 is a coefficient that relates roughness to soil particle diameter D_p.
+   z0s = 2.0_r8 * D_p / 30.0_r8 ! equation for smooth roughness length for soil grain. See Danny M. Leung et al. (2023) and Martina Klose et al. (2021) for instance. 1/15 is a coefficient that relates roughness to soil particle diameter D_p.
                             ! Here we assume soil medium size is a global constant, and so is smooth roughness length.
    do p = bounds%begp,bounds%endp
       g = patch%gridcell(p)
@@ -850,7 +850,7 @@ subroutine CalcDragPartition(this, bounds)
       if (lun%itype(l) /= istdlak) then
          ! Calculating rock drag partition factor using the Marticorena and Bergametti (1995) formulation.
          ! 0.01 is used to convert Prigent's roughness length dataset from centimeter to meter.
-         this%dpfct_rock_patch(p) = 1._r8 - ( log(this%prigent_roughness_stream%prigent_rghn(g)*0.01_r8/z0s) &
+         this%dpfct_rock_patch(p) = 1.0_r8 - ( log(this%prigent_roughness_stream%prigent_rghn(g)*0.01_r8/z0s) &
                             / log(b1 * (X/z0s)**b2 ) )
       end if
    end do
diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
index 31adea76e9..77e0cba4c0 100644
--- a/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
+++ b/src/biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
@@ -121,7 +121,7 @@ contains
 
  @Test
  subroutine dust_zero_for_fixed_ratio(this)
-   ! Check dust emissions are zero for a no wind
+   ! Check dust emissions are zero for a fixed ratio
    class(TestDustEmisLeung2023), intent(inout) :: this
    integer :: p
    real(r8) :: flx_mss_vrt_dst_tot
@@ -130,7 +130,7 @@ contains
 
    call this%input%create_atm2lnd()
    call this%dust_emis%GetConstVars( SaltationFactor )
-   ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps))
+   ! Figure out what fv needs to be so that the wind threshold will result in zero dust emission
    fv = ( SaltationFactor / sqrt( this%input%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15
    call this%input%create_fv( fv=fv )
    call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
@@ -274,6 +274,7 @@ contains
                          this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
        do p = bounds%begp, bounds%endp
           call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot )
+          ! TODO: To have a more robust test the input should be adjusted so that there is dust emissions rather than zero
           @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 )
           if ( i == 1 )then
              previous_dst_tot = flx_mss_vrt_dst_tot
@@ -352,12 +353,11 @@ contains
     integer :: p, c
     real(r8) :: flx_mss_vrt_dst_tot
     real(r8) :: fv = 4.0_r8
-    real(r8) :: u10 = 10._r8
     real(r8) :: total_dust0, total_dust_higher
 
     ! Run baseline fv
     call this%input%create_atm2lnd()
-    call this%input%create_fv( u10=u10, fv=fv )
+    call this%input%create_fv( fv=fv )
     call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
                       this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
                       this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)
@@ -369,7 +369,7 @@ contains
        @assertEqual( flx_mss_vrt_dst_tot, 1.064145664977026d-5, tolerance=tol )
     end do
     ! Double fv and show result is higher
-    call this%input%create_fv( u10=u10, fv=fv*2.0_r8)
+    call this%input%create_fv( fv=fv*2.0_r8)
     call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, &
                       this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, &
                       this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst)

From 07a62b62f60c3f326c750cf477d2487d7832f04c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 11 Aug 2024 01:50:33 -0600
Subject: [PATCH 0876/1248] Update change files

---
 doc/ChangeLog | 112 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 113 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index f5cf28096c..e166e65dad 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,116 @@
 ===============================================================
+Tag name: ctsm5.2.019
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Sun 11 Aug 2024 12:31:34 AM MDT
+One-line Summary: Add in an additional dust emission method Leung_2023, by default off
+
+Purpose and description of changes
+----------------------------------
+
+Author: Danny Leung
+This is a scheme that builds upon a switch of CESM2's default dust emission scheme (Zender et al., 2003) to
+@jfkok's more physical and less empirical one (Kok et al., 2014). This brings in additional modifications and add new aeolian
+physics to the Kok's scheme, most notably, by adding the roughness effect (or called drag partition effect) which discounts surface
+soil erosion by winds due to the presence of local-scale land-surface roughness elements (mostly plants and rocks). We use a hybrid
+approach to account for both roughness from rocks (with a 2-D time-invariant dataset provided by Prigent et al., 2005; 2012) and
+roughness from plants (time-varying, as a function of CLM's LAI). We further include the dust emission intermittency effects due to
+boundary-layer turbulence.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   #1604 -- A new physically based dust emission scheme with more aeolian physics (updated) 
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): New namelist items
+   dust_emis_method can now be set to Leung_2023
+
+    use_prigent_roughness ---------------- Logical to use the Prigent dataset (default on when Leung_2023 is used)
+    stream_fldfilename_prigentroughness -- Prigent streams dataset
+    stream_meshile_prigentroughness ------ Mesh file for the dataset
+
+    History field FV can now be output for any compset, but it's default off
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+    New Prigent streams dataset with aeolian roughness length
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+  Some issues will be worked on later
+
+    #2568 -- Turn on Leung by default for clm6_0 physics
+
+    #2381 -- Allow Prigent streams to be off in Leung_2023 dust emissions for Paleo work
+             (Fixing this will allow a unit-test module to be removed)
+
+    #2680 -- prigentroughnessmapalgo is hardcoded to bilinear add it to the namelist so it can change (change name to snake-case)
+
+    #2681 -- Add global dust variables to the DustEmisBase class that apply to both Zender and Leung dust emission methods bfb enhancement next
+
+    #2682 -- Small function and saved constants for convective velocity code cleanup enhancement priority
+
+Changes to tests or testing:
+   New test mod that explicitly turns on Leung_2023 dust emissions: clm60cam7LndTuningModeLDust
+   Some of the tests with clm60cam7LndTuningMode were converted to this test mod
+   PF unit tester was added for Leung_2023
+
+
+Testing summary: regular
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: no bit-for-bit (unless you turn the new dust scheme on)
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+   #1897 -- A new physically based dust emission scheme with more aeolian physics (updated) 
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.018
 Originator(s): mvdebolskiy
 Date: Fri 02 Aug 2024 09:26:33 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 3d9d70bc54..207dd158d6 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.019     erik 08/11/2024 Add in an additional dust emission method Leung_2023, by default off
        ctsm5.2.018 mvdebols 08/02/2024 Fix/excess ice cold start
        ctsm5.2.017     erik 07/30/2024 Dust emissions control moved to cmeps
        ctsm5.2.016 samrabin 07/27/2024 Enable new crop calendars for clm60 compsets

From 0d17de5aeda75717a9ac969823c29e9051a49a56 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 11 Aug 2024 03:04:52 -0600
Subject: [PATCH 0877/1248] Update test number

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index d7c94b8538..c51b0b0cb3 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -166,7 +166,7 @@ sub cat_and_create_namelistinfile {
 my $ntests = 3339;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1963;
+   $ntests += 1999;
 }
 plan( tests=>$ntests );
 

From 39ecaf0ff822f7ccbd1502a5040ff0becc0e8c5b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 11 Aug 2024 03:05:17 -0600
Subject: [PATCH 0878/1248] Update Change files

---
 doc/ChangeLog | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e166e65dad..09c71a47df 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.019
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
-Date: Sun 11 Aug 2024 12:31:34 AM MDT
+Date: Sun 11 Aug 2024 03:05:01 AM MDT
 One-line Summary: Add in an additional dust emission method Leung_2023, by default off
 
 Purpose and description of changes
@@ -77,7 +77,7 @@ Changes to tests or testing:
    New test mod that explicitly turns on Leung_2023 dust emissions: clm60cam7LndTuningModeLDust
    Some of the tests with clm60cam7LndTuningMode were converted to this test mod
    PF unit tester was added for Leung_2023
-
+   More work could be done in the unit-testers to exercise more of the code
 
 Testing summary: regular
 ----------------
@@ -86,7 +86,7 @@ Testing summary: regular
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho - PASS
+    derecho - PASS (1002 are different)
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 

From 9b1ff2430442cb153aeafc285a75fd0da042deb9 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 11 Aug 2024 03:13:38 -0600
Subject: [PATCH 0879/1248] Change default back to Zender

---
 bld/namelist_files/namelist_defaults_dust_emis.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_dust_emis.xml b/bld/namelist_files/namelist_defaults_dust_emis.xml
index 319110cc55..40bf3d9078 100644
--- a/bld/namelist_files/namelist_defaults_dust_emis.xml
+++ b/bld/namelist_files/namelist_defaults_dust_emis.xml
@@ -14,7 +14,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <!-- Defaults for dust_emis_inparm namelist  -->
-<dust_emis_method>Leung_2023</dust_emis_method>
+<dust_emis_method>Zender_2003</dust_emis_method>
 
 <zender_soil_erod_source>atm</zender_soil_erod_source>
 

From b45a7fafd79b886a2582249d95f747a5998f7d78 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 11 Aug 2024 08:59:33 -0600
Subject: [PATCH 0880/1248] Remove the PEM test with CISM for LDust since it
 changes answers

---
 cime_config/testdefs/testlist_clm.xml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index f4484c7410..cd4c41f23c 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -138,15 +138,6 @@
       <option name="comment">CESM3 development Exact restart test with change in the processor count at the standard coupled resolution for transient</option>
     </options>
   </test>
-  <test name="PEM_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningModeLDust">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment">CESM3 development test with change in the processor count at the standard coupled resolution</option>
-    </options>
-  </test>
   <test name="ERS_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

From 503c47f084319f216dca499f0a5a93fd44a50c1c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 11 Aug 2024 09:02:29 -0600
Subject: [PATCH 0881/1248] Update change files

---
 doc/ChangeLog | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 09c71a47df..92f4657f9d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.019
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
-Date: Sun 11 Aug 2024 03:05:01 AM MDT
+Date: Sun 11 Aug 2024 09:00:43 AM MDT
 One-line Summary: Add in an additional dust emission method Leung_2023, by default off
 
 Purpose and description of changes
@@ -101,6 +101,7 @@ Answer changes
 --------------
 
 Changes answers relative to baseline: no bit-for-bit (unless you turn the new dust scheme on)
+  Tests with BGC change answers because fieldlists are different (FV is no longer on history files by default)
 
 Other details
 -------------

From ea69fffb308e4d132c184d4a5fe5e95f133d7b00 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Mon, 12 Aug 2024 08:52:34 -0600
Subject: [PATCH 0882/1248] Remove broken assign-to-project workflow.

---
 .github/workflows/assign-to-project.yml | 23 -----------------------
 1 file changed, 23 deletions(-)
 delete mode 100644 .github/workflows/assign-to-project.yml

diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml
deleted file mode 100644
index 225c223bde..0000000000
--- a/.github/workflows/assign-to-project.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-name: Auto Assign to Project(s)
-
-on:
-  issues:
-    types: [opened, labeled]
-  pull_request:
-    types: [opened, labeled]
-  issue_comment:
-    types: [created]
-
-jobs:
-  assign_high_priority:
-    runs-on: ubuntu-latest
-    name: Assign to High Priority project
-    steps:
-    - name: Assign issues and pull requests with priority-high label to project 25
-      uses: srggrs/assign-one-project-github-action@1.3.1
-      if: |
-        contains(github.event.issue.labels.*.name, 'priority: high') ||
-        contains(github.event.pull_request.labels.*.name, 'priority: high')
-      with:
-        project: 'https://github.com/ESCOMP/CTSM/projects/25'
-        column_name: 'Needs triage'

From 2797829a586b13ba9db4f7266d33e034d60c7976 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Mon, 12 Aug 2024 11:12:21 -0600
Subject: [PATCH 0883/1248] Add comment explaining dummy use of crop_inst.

---
 src/biogeochem/CNFireLi2014Mod.F90 | 2 +-
 src/biogeochem/CNFireLi2016Mod.F90 | 2 +-
 src/biogeochem/CNFireLi2021Mod.F90 | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeochem/CNFireLi2014Mod.F90 b/src/biogeochem/CNFireLi2014Mod.F90
index a11e9d5edc..fcd27a7951 100644
--- a/src/biogeochem/CNFireLi2014Mod.F90
+++ b/src/biogeochem/CNFireLi2014Mod.F90
@@ -122,7 +122,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
-    type(crop_type)                       , intent(in)    :: crop_inst
+    type(crop_type)                       , intent(in)    :: crop_inst  ! Dummy argument; not used in this version of CNFireArea
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
diff --git a/src/biogeochem/CNFireLi2016Mod.F90 b/src/biogeochem/CNFireLi2016Mod.F90
index 6021901a28..955d7fe398 100644
--- a/src/biogeochem/CNFireLi2016Mod.F90
+++ b/src/biogeochem/CNFireLi2016Mod.F90
@@ -124,7 +124,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
-    type(crop_type)                       , intent(in)    :: crop_inst
+    type(crop_type)                       , intent(in)    :: crop_inst  ! Dummy argument; not used in this version of CNFireArea
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)
diff --git a/src/biogeochem/CNFireLi2021Mod.F90 b/src/biogeochem/CNFireLi2021Mod.F90
index 74f553eb5c..6d504a1e26 100644
--- a/src/biogeochem/CNFireLi2021Mod.F90
+++ b/src/biogeochem/CNFireLi2021Mod.F90
@@ -124,7 +124,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     class(soil_water_retention_curve_type), intent(in)    :: soil_water_retention_curve
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
-    type(crop_type)                       , intent(in)    :: crop_inst
+    type(crop_type)                       , intent(in)    :: crop_inst  ! Dummy argument; not used in this version of CNFireArea
     real(r8)                              , intent(in)    :: totlitc_col(bounds%begc:)
     real(r8)                              , intent(in)    :: decomp_cpools_vr_col(bounds%begc:,1:,1:)
     real(r8)                              , intent(in)    :: t_soi17cm_col(bounds%begc:)

From 197ac0d5759343fdc53bd9699a30d4f0cec8983d Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Tue, 13 Aug 2024 08:10:09 -0600
Subject: [PATCH 0884/1248] update the FATES tag

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index 19bc024208..4e9f5b51fb 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.77.1_api.36.0.0
+fxtag = sci.1.77.2_api.36.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release

From 13839f783221c6705a0ceadf3a5d382cf66d56d2 Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Tue, 13 Aug 2024 15:18:37 -0600
Subject: [PATCH 0885/1248] Updating the fates pointer to sci.1.77.2_api.36.0.0

---
 src/fates | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fates b/src/fates
index 1982b0032c..e372f0b6cd 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit 1982b0032c3cab6278892eccb85f643114ffb1af
+Subproject commit e372f0b6cdf46f76f888ee6ac92d9a3572464e8b

From ac85dbc04426b2649387bd19fc8de56ce8565a6d Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Tue, 13 Aug 2024 15:34:13 -0600
Subject: [PATCH 0886/1248] updated changlog

---
 doc/ChangeLog | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 69 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index c1f5dfaa5a..af975c9975 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,72 @@
 ===============================================================
+Tag name: ctsm5.2.021
+Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-2153)
+Date: Tue 13 Aug 2024 03:22:34 PM MDT
+One-line Summary: Adding on-the-fly parameter settings for prescribed N and P in FATES
+
+Purpose and description of changes
+----------------------------------
+
+This set of changes makes it so that the FATES PRT2 test is forced to have prescribed N and P uptake in FATES.
+
+This allows the default to be coupled N and P, which is less confusing to new FATES-CNP users.
+
+The FATES tag is also updated to sci.1.77.2_api.36.0.0 which has a bug-fix for the output variable FATES_TRANSITION_MATRIX_LULU.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations? NO
+
+Bugs fixed
+----------
+
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+CLM-FATES with N and cycling is not fully coupled yet. Therefor, these changes are only relevant to the testing infrastructure.
+Users are not encouraged to use fates_parteh_mode = 2
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:  Existing scripting that FATES has used in other tests to update parameters in certain tests, is now
+being called for FatesColdPRT2 tests. This forces parameters fates_cnp_prescribed_nuptake and fates_cnp_prescribed_puptake to be 1.
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NONE, except:
+
+FATES_TRANSITION_MATRIX_LULU reflects a BASELINE DIFF from a bug fix in two FATES tests.
+
+All other tests are B4B.
+
+
+Other details
+-------------
+
+FATES submodule was updated, pointing to tag sci.1.77.2_api.36.0.0
+
+Pull Requests that document the changes (include PR ids): https://github.com/ESCOMP/CTSM/pull/2624
+
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.020
 Originator(s): HuiWangWanderInGitHub (Hui Wang,huiw16@uci.edu)
 Date: Mon 12 Aug 2024 10:51:04 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index d035fe4861..852ec9e838 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.021   rgknox 08/13/2024 Adding on-the-fly parameter settings for prescribed N and P in FATES
        ctsm5.2.020   slevis 08/12/2024 MEGAN updates (MEGAN-CLM6)
        ctsm5.2.019     erik 08/11/2024 Add in an additional dust emission method Leung_2023, by default off
        ctsm5.2.018 mvdebols 08/02/2024 Fix/excess ice cold start

From 02885d4457a2f49e1742e6a46bc6276794ff085d Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Wed, 14 Aug 2024 12:31:40 -0600
Subject: [PATCH 0887/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 71 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 72 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index af975c9975..5850069532 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,75 @@
 ===============================================================
+Tag name: ctsm5.2.022
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Wed Aug 14 12:24:27 MDT 2024
+One-line Summary: Rework crop_calendars suite and cropMonthOutput
+
+Purpose and description of changes
+----------------------------------
+
+- Changes cropMonthOutput testmod so that h2 files are actually monthly instead of daily
+- Changes a nag test to use debug mode (fixing a build error) and run for shorter (fixing cputime exceedance)
+- Reworks RxCropCals* testmods to not include crop testmod
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List of CTSM issues fixed (include CTSM Issue # and description):
+- Fixes ESCOMP/CTSM#2659: Test build failure: SMS_P128x1_Lm25.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-RxCropCalsAdaptGGCMI (https://github.com/ESCOMP/CTSM/issues/2659)
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Changes to tests or testing:
+- Changes answers to all cropMonthOutput tests due to changed h2 file frequency. Also affects frequency of one other test.
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+  - Only in testmods, not production runs
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2676: Rework crop_calendars suite and cropMonthOutput (https://github.com/ESCOMP/CTSM/pull/2676)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.021
 Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-2153)
 Date: Tue 13 Aug 2024 03:22:34 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 852ec9e838..61bf4985de 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.022 samrabin 08/14/2024 Rework crop_calendars suite and cropMonthOutput
        ctsm5.2.021   rgknox 08/13/2024 Adding on-the-fly parameter settings for prescribed N and P in FATES
        ctsm5.2.020   slevis 08/12/2024 MEGAN updates (MEGAN-CLM6)
        ctsm5.2.019     erik 08/11/2024 Add in an additional dust emission method Leung_2023, by default off

From 4333a66ca69d32a2f24aa81cbb9214ead5e8b763 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 14 Aug 2024 15:57:27 -0600
Subject: [PATCH 0888/1248] PPE mods from /glade/work/linnia/PPEn14trans
 brought to ctsm5.2.015

Bringing the diffs between branch_tags/PPE16... and branch_tags/PPE15...
to b4b-dev manually
---
 src/biogeochem/CNFUNMod.F90       |  8 --------
 src/biogeochem/CNPhenologyMod.F90 | 23 +++++++++++++----------
 src/main/initVerticalMod.F90      | 11 +++++++++++
 src/main/pftconMod.F90            | 11 +++++++++++
 4 files changed, 35 insertions(+), 18 deletions(-)

diff --git a/src/biogeochem/CNFUNMod.F90 b/src/biogeochem/CNFUNMod.F90
index dde666c1f7..a6614fe4b9 100644
--- a/src/biogeochem/CNFUNMod.F90
+++ b/src/biogeochem/CNFUNMod.F90
@@ -53,7 +53,6 @@ module CNFUNMod
   public:: CNFUN                 ! Run FUN
   
   type, private :: params_type
-     real(r8) :: ndays_on        ! number of days to complete leaf onset
      real(r8) :: ndays_off       ! number of days to complete leaf offset
   end type params_type   
  
@@ -64,7 +63,6 @@ module CNFUNMod
   !
   ! !PRIVATE DATA MEMBERS:
   real(r8) :: dt              ! decomp timestep (seconds)
-  real(r8) :: ndays_on        ! number of days to complete onset
   real(r8) :: ndays_off       ! number of days to complete offset
   
   integer, private, parameter :: COST_METHOD = 2 !new way of doing the N uptake
@@ -104,11 +102,6 @@ subroutine readParams ( ncid )
 
   ! read in parameters
 
-    tString='ndays_on'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%ndays_on=tempr
-
     tString='ndays_off'
     call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
     if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
@@ -172,7 +165,6 @@ subroutine CNFUNInit (bounds,cnveg_state_inst,cnveg_carbonstate_inst,cnveg_nitro
   timestep_fun = real(secspday * fun_period)
   nstep_fun    = int(secspday * dayspyr / dt) 
 
-  ndays_on     = params_inst%ndays_on
   ndays_off    = params_inst%ndays_off
 
   !--------------------------------------------------------------------
diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 9c7e5a331a..d8789eb30f 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -94,7 +94,6 @@ module CNPhenologyMod
      real(r8) :: crit_dayl_lat_slope   ! Slope of time for critical day length with latitude (sec/deg) 
                                        ! (Birch et. all 2021 it was 720 see line below)
                                        ! 15hr-11hr/(65N-45N)=linear slope = 720 min/latitude (Birch et. al 2021)
-     real(r8) :: ndays_on              ! number of days to complete leaf onset
      real(r8) :: ndays_off             ! number of days to complete leaf offset
      real(r8) :: fstor2tran            ! fraction of storage to move to transfer for each onset
      real(r8) :: crit_onset_fdd        ! critical number of freezing days to set gdd counter
@@ -113,7 +112,6 @@ module CNPhenologyMod
   real(r8) :: dt                            ! time step delta t (seconds)
   real(r8) :: fracday                       ! dtime as a fraction of day
   real(r8) :: crit_dayl                     ! critical daylength for offset (seconds)
-  real(r8) :: ndays_on                      ! number of days to complete onset
   real(r8) :: ndays_off                     ! number of days to complete offset
   real(r8) :: fstor2tran                    ! fraction of storage to move to transfer on each onset
   real(r8) :: crit_onset_fdd                ! critical number of freezing days
@@ -310,7 +308,6 @@ subroutine readParams ( ncid )
     call readNcdioScalar(ncid, 'crit_dayl', subname, params_inst%crit_dayl)
     call readNcdioScalar(ncid, 'crit_dayl_at_high_lat', subname, params_inst%crit_dayl_at_high_lat)
     call readNcdioScalar(ncid, 'crit_dayl_lat_slope', subname, params_inst%crit_dayl_lat_slope)
-    call readNcdioScalar(ncid, 'ndays_on', subname, params_inst%ndays_on)
     call readNcdioScalar(ncid, 'ndays_off', subname, params_inst%ndays_off)
     call readNcdioScalar(ncid, 'fstor2tran', subname, params_inst%fstor2tran)
     call readNcdioScalar(ncid, 'crit_onset_fdd', subname, params_inst%crit_onset_fdd)
@@ -471,7 +468,6 @@ subroutine CNPhenologyInit(bounds)
     crit_dayl=params_inst%crit_dayl
 
     ! Set constants for CNSeasonDecidPhenology and CNStressDecidPhenology
-    ndays_on=params_inst%ndays_on
     ndays_off=params_inst%ndays_off
 
     ! set transfer parameters
@@ -882,6 +878,8 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
          woody                               =>    pftcon%woody                                                , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)
          season_decid                        =>    pftcon%season_decid                                         , & ! Input:  binary flag for seasonal-deciduous leaf habit (0 or 1)
          season_decid_temperate              =>    pftcon%season_decid_temperate                               , & ! Input:  binary flag for seasonal-deciduous temperate leaf habit (0 or 1)
+         crit_onset_gdd_sf                   =>    pftcon%crit_onset_gdd_sf                                    , & ! Input:  scale factor for crit_onset_gdd (unitless)
+         ndays_on                            =>    pftcon%ndays_on                                             , & ! Input:  number of days to complete leaf onset (days
          
          t_soisno                            =>    temperature_inst%t_soisno_col                               , & ! Input:  [real(r8)  (:,:) ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)
          soila10                             =>    temperature_inst%soila10_col                                , & ! Input:  [real(r8) (:)   ] 
@@ -1016,7 +1014,8 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
             lgsf(p) = 0._r8
 
             ! onset gdd sum from Biome-BGC, v4.1.2
-            crit_onset_gdd = exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) - SHR_CONST_TKFRZ))
+            crit_onset_gdd = crit_onset_gdd_sf(ivt(p)) * exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) &
+                             - SHR_CONST_TKFRZ))
 
             ! set flag for solstice period (winter->summer = 1, summer->winter = 0)
             if (dayl(g) >= prev_dayl(g)) then
@@ -1109,7 +1108,8 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
                   onset_gddflag(p) = 0.0_r8
                   onset_gdd(p) = 0.0_r8
                   do_onset = .false.
-                  onset_counter(p) = ndays_on * secspday
+                  onset_counter(p) = ndays_on(ivt(p)) * secspday
+
 
                   ! move all the storage pools into transfer pools,
                   ! where they will be transfered to displayed growth over the onset period.
@@ -1399,7 +1399,10 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
          stress_decid                        =>    pftcon%stress_decid                                         , & ! Input:  binary flag for stress-deciduous leaf habit (0 or 1)
          leafcn                              =>    pftcon%leafcn                                               , & ! Input:  leaf C:N (gC/gN)
          frootcn                             =>    pftcon%frootcn                                              , & ! Input:  fine root C:N (gC/gN) 
-         
+
+         crit_onset_gdd_sf                   =>    pftcon%crit_onset_gdd_sf                                    , & ! Input:  scale factor for crit_onset_gdd (unitless)
+         ndays_on                            =>    pftcon%ndays_on                                             , & ! Input:  number of days to complete leaf onset (days)
+
          soilpsi                             =>    soilstate_inst%soilpsi_col                                  , & ! Input:  [real(r8)  (:,:) ]  soil water potential in each soil layer (MPa)   
          
          t_soisno                            =>    temperature_inst%t_soisno_col                               , & ! Input:  [real(r8)  (:,:) ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)
@@ -1532,8 +1535,8 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
             psi = soilpsi(c, phenology_soil_layer)
 
             ! onset gdd sum from Biome-BGC, v4.1.2
-            crit_onset_gdd = exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) - SHR_CONST_TKFRZ))
-
+            crit_onset_gdd = crit_onset_gdd_sf(ivt(p)) * exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) &
+                             - SHR_CONST_TKFRZ))
 
             ! update offset_counter and test for the end of the offset period
             if (offset_flag(p) == 1._r8) then
@@ -1673,7 +1676,7 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
                   onset_fdd(p) = 0._r8
                   onset_gdd(p) = 0._r8
                   onset_swi(p) = 0._r8
-                  onset_counter(p) = ndays_on * secspday
+                  onset_counter(p) = ndays_on(ivt(p)) * secspday
 
                   ! call subroutine to move all the storage pools into transfer pools,
                   ! where they will be transfered to displayed growth over the onset period.
diff --git a/src/main/initVerticalMod.F90 b/src/main/initVerticalMod.F90
index b91c3439aa..64383e7a7c 100644
--- a/src/main/initVerticalMod.F90
+++ b/src/main/initVerticalMod.F90
@@ -47,6 +47,8 @@ module initVerticalMod
   type, private :: params_type
      real(r8) :: slopebeta      ! exponent for microtopography pdf sigma (unitless)
      real(r8) :: slopemax       ! max topographic slope for microtopography pdf sigma (unitless)
+     real(r8) :: zbedrock       ! parameter to substitute for zbedrock (m)
+     real(r8) :: zbedrock_sf    ! parameter to scale zbedrock (m)
   end type params_type
   type(params_type), private ::  params_inst
   !
@@ -79,6 +81,9 @@ subroutine readParams( ncid )
     ! Max topographic slope for microtopography pdf sigma (unitless) 
     call readNcdioScalar(ncid, 'slopemax', subname, params_inst%slopemax)
 
+    call readNcdioScalar(ncid, 'zbedrock', subname, params_inst%zbedrock)
+    call readNcdioScalar(ncid, 'zbedrock_sf', subname, params_inst%zbedrock_sf)
+
   end subroutine readParams
 
     !------------------------------------------------------------------------
@@ -447,6 +452,12 @@ subroutine initVertical(bounds, glc_behavior, thick_wall, thick_roof)
              call endrun( 'ERROR:: zbedrock not found on surface data set, and use_bedrock is true.'//errmsg(sourcefile, __LINE__) )
           end if
        end if
+       if (params_inst%zbedrock>=0._r8) then
+          zbedrock_in(:) = params_inst%zbedrock
+       end if
+       if (params_inst%zbedrock_sf/=1._r8) then
+          zbedrock_in(:) = params_inst%zbedrock_sf*zbedrock_in(:)
+       end if
 
     !  if use_bedrock = false, set zbedrock to lowest layer bottom interface
     else
diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90
index 7988b57e75..b987879c03 100644
--- a/src/main/pftconMod.F90
+++ b/src/main/pftconMod.F90
@@ -162,6 +162,8 @@ module pftconMod
      real(r8), allocatable :: taper  (:)          ! tapering ratio of height:radius_breast_height
      real(r8), allocatable :: rstem_per_dbh  (:)  ! stem resistance per dbh (s/m/m)
      real(r8), allocatable :: wood_density  (:)   ! wood density (kg/m3)
+     real(r8), allocatable :: crit_onset_gdd_sf(:)! scale factor for crit_onset_gdd
+     real(r8), allocatable :: ndays_on(:)         ! number of days to complete leaf onset
 
      !  crop
 
@@ -502,6 +504,8 @@ subroutine InitAllocate (this)
     allocate( this%taper         (0:mxpft) )
     allocate( this%rstem_per_dbh (0:mxpft) )
     allocate( this%wood_density  (0:mxpft) )
+    allocate( this%crit_onset_gdd_sf (0:mxpft) )
+    allocate( this%ndays_on      (0:mxpft) )
  
   end subroutine InitAllocate
 
@@ -843,6 +847,11 @@ subroutine InitRead(this)
 
     call ncd_io('season_decid_temperate', this%season_decid_temperate, 'read', ncid, readvar=readv, posNOTonfile=.true.)
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+    call ncd_io('crit_onset_gdd_sf', this%crit_onset_gdd_sf, 'read', ncid, readvar=readv, posNOTonfile=.true.)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
+    call ncd_io('ndays_on', this%ndays_on, 'read', ncid, readvar=readv, posNOTonfile=.true.)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
     call ncd_io('pftpar20', this%pftpar20, 'read', ncid, readvar=readv, posNOTonfile=.true.)
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
@@ -1585,6 +1594,8 @@ subroutine Clean(this)
     deallocate( this%rstem_per_dbh)
     deallocate( this%wood_density)
     deallocate( this%taper)
+    deallocate( this%crit_onset_gdd_sf)
+    deallocate( this%ndays_on)
   end subroutine Clean
 
 end module pftconMod

From 7d8d0f6e2b47de2c0cb7a989942c995481a9c775 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 14 Aug 2024 17:35:00 -0600
Subject: [PATCH 0889/1248] Add failing tests for running with dust set by CAM
 so LND_SETS_DUST_EMIS_DRV_FLDS is FALSE

---
 bld/unit_testers/build-namelist_test.pl | 29 +++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index c51b0b0cb3..28e6084f0e 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -447,7 +447,32 @@ sub cat_and_create_namelistinfile {
       &cleanup();
    }
 }
-
+print "\n===============================================================================\n";
+print "Test setting drv_flds_in fields in CAM";
+print "=================================================================================\n";
+foreach my $phys ( "clm5_0", "clm6_0" ) {
+   $mode = "-phys $phys CAM_SETS_DRV_FLDS";
+   &make_config_cache($phys);
+   foreach my $options (
+                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam6.0",
+                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam7.0",
+                     ) {
+      &make_env_run( 'LND_SETS_DUST_EMIS_DRV_FLDS'=>"FALSE" );
+      eval{ system( "$bldnml --envxml_dir . $options > $tempfile 2>&1 " ); };
+      is( $@, '', "options: $options" );
+      $cfiles->checkfilesexist( "$options", $mode );
+      $cfiles->shownmldiff( "default", $mode );
+      if ( defined($opts{'compare'}) ) {
+         $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+         $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
+         $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+      }
+      if ( defined($opts{'generate'}) ) {
+         $cfiles->copyfiles( "$options", $mode );
+      }
+      &cleanup();
+   }
+}
 print "\n==============================================================\n";
 print "Test several use_cases and specific configurations for clm5_0\n";
 print "==============================================================\n";
@@ -518,7 +543,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm4_5",
                                    },
      "LeungDust_WO_Prigent"      =>{ options=>" -envxml_dir . -bgc sp",
-                                     namelst=>"use_prigent_roughness=.false.",
+                                     namelst=>"use_prigent_roughness=.true.",
                                      phys=>"clm5_1",
                                    },
      "soilm_stream off w file"      =>{ options=>"-res 0.9x1.25 -envxml_dir .",

From a590ca7e57c965e1cfc46779cb5c6f1dc34bfb27 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 15 Aug 2024 01:59:10 -0600
Subject: [PATCH 0890/1248] When LND_SETS_DUST_EMIS_DRV_FLDS is FALSE read in
 CAM drv_flds_in namelist to use to determine dust_emis settings, still check
 that they aren't set in the user_nl_clm file

---
 bld/CLMBuildNamelist.pm                 | 51 +++++++++++++++----------
 bld/unit_testers/build-namelist_test.pl |  4 +-
 bld/unit_testers/empty_user_nl_clm      |  1 +
 3 files changed, 33 insertions(+), 23 deletions(-)
 create mode 100644 bld/unit_testers/empty_user_nl_clm

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b99be288e7..daf4320c18 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1470,6 +1470,32 @@ sub process_namelist_commandline_namelist {
   }
 }
 
+sub process_namelist_infile {
+   my ($definition, $nl, $envxml_ref, $infile) = @_;
+
+   # Make sure a valid file was found
+   if (    -f "$infile" ) {
+      # Otherwise abort as a valid file doesn't exist
+   } else {
+      $log->fatal_error("input namelist file does NOT exist $infile.\n $@");
+   }
+   # Parse namelist input from the next file
+   my $nl_infile = Build::Namelist->new($infile);
+
+   # Validate input namelist -- trap exceptions
+   my $nl_infile_valid;
+   eval { $nl_infile_valid = $definition->validate($nl_infile); };
+   if ($@) {
+      $log->fatal_error("Invalid namelist variable in '-infile' $infile.\n $@");
+   }
+   # Go through all variables and expand any XML env settings in them
+   expand_xml_variables_in_namelist( $nl_infile_valid, $envxml_ref );
+
+   # Merge input values into namelist.  Previously specified values have higher precedence
+   # and are not overwritten.
+   $nl->merge_nl($nl_infile_valid);
+}
+
 #-------------------------------------------------------------------------------
 
 sub process_namelist_commandline_infile {
@@ -1479,27 +1505,7 @@ sub process_namelist_commandline_infile {
   if (defined $opts->{'infile'}) {
     my @infiles = split( /,/, $opts->{'infile'} );
     foreach my $infile ( @infiles ) {
-      # Make sure a valid file was found
-      if (    -f "$infile" ) {
-        # Otherwise abort as a valid file doesn't exist
-      } else {
-        $log->fatal_error("input namelist file does NOT exist $infile.\n $@");
-      }
-      # Parse namelist input from the next file
-      my $nl_infile = Build::Namelist->new($infile);
-
-      # Validate input namelist -- trap exceptions
-      my $nl_infile_valid;
-      eval { $nl_infile_valid = $definition->validate($nl_infile); };
-      if ($@) {
-        $log->fatal_error("Invalid namelist variable in '-infile' $infile.\n $@");
-      }
-      # Go through all variables and expand any XML env settings in them
-      expand_xml_variables_in_namelist( $nl_infile_valid, $envxml_ref );
-
-      # Merge input values into namelist.  Previously specified values have higher precedence
-      # and are not overwritten.
-      $nl->merge_nl($nl_infile_valid);
+      process_namelist_infile( $definition, $nl, $envxml_ref, $infile );
     }
   }
 }
@@ -4086,6 +4092,9 @@ sub setup_logic_dust_emis {
                               " connected to CAM as CAM should set them");
          }
       }
+      # Now process the CAM drv_flds_in to get the dust settings
+      my $infile = $opts->{'envxml_dir'} . "/Buildconf/camconf/drv_flds_in";
+      process_namelist_infile( $definition, $nl, $envxml_ref, $infile );
   }
 }
 
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 28e6084f0e..1b54f29d92 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -454,8 +454,8 @@ sub cat_and_create_namelistinfile {
    $mode = "-phys $phys CAM_SETS_DRV_FLDS";
    &make_config_cache($phys);
    foreach my $options (
-                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam6.0",
-                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam7.0",
+                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam6.0 --infile empty_user_nl_clm",
+                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam7.0 --infile empty_user_nl_clm",
                      ) {
       &make_env_run( 'LND_SETS_DUST_EMIS_DRV_FLDS'=>"FALSE" );
       eval{ system( "$bldnml --envxml_dir . $options > $tempfile 2>&1 " ); };
diff --git a/bld/unit_testers/empty_user_nl_clm b/bld/unit_testers/empty_user_nl_clm
new file mode 100644
index 0000000000..45fda13d2c
--- /dev/null
+++ b/bld/unit_testers/empty_user_nl_clm
@@ -0,0 +1 @@
+! empty user_nl_clm file

From 85e3124813c808a75390faf6e0be3339c1bb37ff Mon Sep 17 00:00:00 2001
From: Ryan Knox <rgknox@lbl.gov>
Date: Thu, 15 Aug 2024 08:28:38 -0600
Subject: [PATCH 0891/1248] updating fates default parameter file to api 36.1

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index c4c056195d..ad39edc69e 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -513,7 +513,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.0.0_12pft_c240517.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_12pft_c240814.nc</fates_paramfile>
+
 
 <!-- ================================================================== -->
 <!-- Default surface roughness parameterization                         -->

From 648d0c4d2b607e7e470a7083a51662325045dc2b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 15 Aug 2024 10:09:36 -0600
Subject: [PATCH 0892/1248] One-line fix for build to complete

---
 src/biogeochem/CNPhenologyMod.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index d8789eb30f..8108876586 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -274,7 +274,6 @@ subroutine CNPhenologySetParams( )
     params_inst%crit_dayl             = 39200._r8     ! Seconds
     params_inst%crit_dayl_at_high_lat = 54000._r8     ! Seconds
     params_inst%crit_dayl_lat_slope   = 720._r8       ! Seconds / degree
-    params_inst%ndays_on              = 15._r8        ! Days
     params_inst%ndays_off             = 30._r8        ! Days
     params_inst%fstor2tran            = 0.5           ! Fraction
     params_inst%crit_onset_fdd        = 15._r8        ! Days

From 2ee88b8f8cc618c1f75d7fc3a1cc05be3e2bfbd0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 15 Aug 2024 10:12:14 -0600
Subject: [PATCH 0893/1248] Update default param file names in namelists

---
 bld/namelist_files/namelist_defaults_ctsm.xml             | 8 ++++----
 .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm       | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 97620c770d..7f6305087c 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -504,10 +504,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240208.nc</paramfile>
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240208.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240208.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240208.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240814.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240814.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240814.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240814.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
index df20ced9e8..4bfc0520f8 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240625.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240814.nc'

From 733cf9918178fc89a1c6ee2c34447160e5e944fb Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 15 Aug 2024 15:20:33 -0600
Subject: [PATCH 0894/1248] Add missing cmeps drv_flds_in variables fixing
 #2170

---
 .../namelist_definition_drv_flds.xml          | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/bld/namelist_files/namelist_definition_drv_flds.xml b/bld/namelist_files/namelist_definition_drv_flds.xml
index 89bab07f4f..9bb1a3e3b0 100644
--- a/bld/namelist_files/namelist_definition_drv_flds.xml
+++ b/bld/namelist_files/namelist_definition_drv_flds.xml
@@ -123,6 +123,10 @@
     List of fluxes needed by the CARMA model, from CLM to CAM.
   </entry>
 
+  <!-- ========================================================================================  -->
+  <!-- DUST Emission fields                                                                      -->
+  <!-- ========================================================================================  -->
+
   <entry id="dust_emis_method" type="char*80" category="dust_emissions"
     group="dust_emis_inparm" valid_values="Zender_2003,Leung_2023" >
      Which dust emission method is going to be used. Either the Zender 2003 scheme or the Leung 2023 scheme.
@@ -136,4 +140,27 @@
      (only used when dust_emis_method is Zender_2003)
   </entry>
 
+  <!-- ========================================================================================  -->
+  <!-- Ozone to surface                                                                          -->
+  <!-- ========================================================================================  -->
+
+  <entry id="atm_ozone_frequency" type="char*64" category="ozone_coupling"
+         group="ozone_coupling_nl" valid_values="subdaily,multiday_average">
+         Frequency of surface ozone field passed from CAM to surface components.
+         Surface ozone is passed every coupling interval, but this namelist flag
+         indicates whether the timestep-level values are interpolated from a
+         coarser temporal resolution.
+         Default: set by CAM
+  </entry>
+
+  <!-- ========================================================================================  -->
+  <!-- Lightning                                                                                 -->
+  <!-- ========================================================================================  -->
+
+  <entry id="atm_provides_lightning" type="logical" category="lightning_coupling"
+         group="lightning_coupling_nl" valid_values="">
+         If TRUE atmosphere model will provide prognosed lightning flash frequency.
+         (NOTE: NOT CONNECTED INTO CTSM YET)
+  </entry>
+
 </namelist_definition>

From 25a0c7a8b0ebbc191d9645b3235867401863be9a Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Thu, 15 Aug 2024 15:24:34 -0600
Subject: [PATCH 0895/1248] New GlacierRegion dataset

Same as mksrf_GlacierRegion_10x10min_nomask_cd5_c220131.nc but with
GLACIER_REGION=1 (Points outside Greenland itself but which might become
ice-covered in an evolving Greenland simulation) merged into
GLACIER_REGION 0, then 2 changed to 1 and 3 changed to 2. We are
removing the old GLACIER_REGION=1 even though this means we cannot
generate SMB in areas outside the initial CISM Greenland ice mask,
because it created problematic non-physical behavior. See
https://github.com/ESCOMP/CTSM/issues/423 for details.
---
 tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index dde824e02c..3cb168e8fb 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -140,7 +140,7 @@ version of the raw dataset will probably go away.
 
   <mksrf_fglacierregion>
     <entry>
-      <data_filename>lnd/clm2/rawdata/mksrf_GlacierRegion_10x10min_nomask_cd5_c220131.nc</data_filename>
+      <data_filename>lnd/clm2/rawdata/mksrf_GlacierRegion_10x10min_nomask_cd5_c240815.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_10x10min_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
   </mksrf_fglacierregion>

From 3f3541b37b7ff9abe37050c98575b61b3702e688 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 15 Aug 2024 15:41:00 -0600
Subject: [PATCH 0896/1248] Current drv_flds_in file from CAM for a FHIST case,
 including some fields that weren't being set in CLM

---
 bld/unit_testers/Buildconf/camconf/drv_flds_in | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 bld/unit_testers/Buildconf/camconf/drv_flds_in

diff --git a/bld/unit_testers/Buildconf/camconf/drv_flds_in b/bld/unit_testers/Buildconf/camconf/drv_flds_in
new file mode 100644
index 0000000000..e8e95ad369
--- /dev/null
+++ b/bld/unit_testers/Buildconf/camconf/drv_flds_in
@@ -0,0 +1,13 @@
+&drydep_inparm
+  dep_data_file = '/glade/campaign/cesm/cesmdata/inputdata/atm/cam/chem/trop_mozart/dvel/dep_data_c20221208.nc'
+/
+&dust_emis_inparm
+  dust_emis_method = 'Zender_2003'
+  zender_soil_erod_source = 'atm'
+/
+&lightning_coupling_nl
+  atm_provides_lightning = .true.
+/
+&ozone_coupling_nl
+  atm_ozone_frequency = 'multiday_average'
+/

From 6268e5907d7563d350fba6f7bb79b0bae3e6344d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 16 Aug 2024 09:55:02 -0600
Subject: [PATCH 0897/1248] Add megan and drydep settings as per a cam6_4_015
 SMS_Ln9.f19_f19_mg17.FHIST.derecho_intel.cam-outfrq9s test

---
 bld/unit_testers/Buildconf/camconf/drv_flds_in | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/bld/unit_testers/Buildconf/camconf/drv_flds_in b/bld/unit_testers/Buildconf/camconf/drv_flds_in
index e8e95ad369..c551ccacf5 100644
--- a/bld/unit_testers/Buildconf/camconf/drv_flds_in
+++ b/bld/unit_testers/Buildconf/camconf/drv_flds_in
@@ -1,5 +1,16 @@
 &drydep_inparm
-  dep_data_file = '/glade/campaign/cesm/cesmdata/inputdata/atm/cam/chem/trop_mozart/dvel/dep_data_c20221208.nc'
+ dep_data_file		= '/glade/campaign/cesm/cesmdata/inputdata/atm/cam/chem/trop_mozart/dvel/dep_data_c20221208.nc'
+ drydep_list		= 'DMS','H2O2','H2SO4','SO2','SOAG'
+/
+&megan_emis_nl
+ megan_factors_file		= '/glade/campaign/cesm/cesmdata/inputdata/atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc'
+ megan_mapped_emisfctrs		= .false.
+ megan_specifier		= 'SOAE = 0.5954*isoprene + 5.1004*(carene_3 + pinene_a + thujene_a + bornene +', ' terpineol_4 + terpineol_a + terpinyl_ACT_a + myrtenal + sabinene + pinene_b + camphene +',
+         ' fenchene_a + limonene + phellandrene_a + terpinene_a + terpinene_g + terpinolene +', ' phellandrene_b + linalool + ionone_b + geranyl_acetone + neryl_acetone + jasmone +',
+         ' verbenene + ipsenol + myrcene + ocimene_t_b + ocimene_al + ocimene_c_b + 2met_nonatriene) + ', ' 12.3942*(farnescene_a + caryophyllene_b + acoradiene + aromadendrene + bergamotene_a +',
+         ' bergamotene_b + bisabolene_a + bisabolene_b + bourbonene_b + cadinene_d + cadinene_g +', ' cedrene_a + copaene_a + cubebene_a + cubebene_b + elemene_b + farnescene_b +',
+         ' germacrene_B + germacrene_D + gurjunene_b + humulene_a + humulene_g + isolongifolene +', ' longifolene + longipinene + muurolene_a + muurolene_g + selinene_b + selinene_d +',
+         ' nerolidol_c + nerolidol_t)'
 /
 &dust_emis_inparm
   dust_emis_method = 'Zender_2003'

From 4f56ffcbbdd1d841de9edf5f67e625428282073d Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Fri, 16 Aug 2024 11:09:17 -0600
Subject: [PATCH 0898/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 76 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 5850069532..7a6d764c14 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,79 @@
 ===============================================================
+Tag name: ctsm5.2.023
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Fri Aug 16 11:00:32 MDT 2024
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+Brings in 3 PRs from b4b-dev to master:
+- Always check finidat_interp_dest.status (ESCOMP/CTSM#2679; Sam Rabin)
+- Remove broken assign-to-project Github workflow (ESCOMP/CTSM#2683; Sam Rabin)
+- [Fang summer '24 PR 1.1] Fix bugs and develop crop fire modeling (ESCOMP/CTSM#2684; Fang Li and Sam Rabin)
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed:
+- Resolves ESCOMP/CTSM#2562: Fix or disable "Assign to High Priority project" workflow
+- Resolves ESCOMP/CTSM#2566: bug in crop fire modeling
+- Resolves ESCOMP/CTSM#2596: Check of finidat_interp_dest.status isn't reached 
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+- Adds new fire_method option li2024gswpfrc; default hasn't changed.
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Changes to tests or testing: Adds 4 tests:
+- SMS_D_Ld65.f10_f10_mg37.I2000Clm50BgcCru.derecho_gnu.clm-FireLi2016Cru
+- SMS_D_Ld65.f10_f10_mg37.I2000Clm45BgcCropQianRs.derecho_intel.clm-FireLi2014Qian
+- SMS_D_Ld65.f10_f10_mg37.I2000Clm50BgcCrop.izumi_intel.clm-FireLi2021GSWP
+- SMS_D_Ld65.f10_f10_mg37.I2000Clm60BgcCrop.izumi_nag.clm-FireLi2024GSWP
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Other details
+-------------
+
+Pull Requests that document the changes:
+- Always check finidat_interp_dest.status (ESCOMP/CTSM#2679; Sam Rabin): https://github.com/ESCOMP/CTSM/pull/2679
+- Remove broken assign-to-project Github workflow (ESCOMP/CTSM#2683; Sam Rabin): https://github.com/ESCOMP/CTSM/pull/2683
+- [Fang summer '24 PR 1.1] Fix bugs and develop crop fire modeling (ESCOMP/CTSM#2684; Fang Li and Sam Rabin): https://github.com/ESCOMP/CTSM/pull/2684
+
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.022
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Wed Aug 14 12:24:27 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 61bf4985de..176ac066d2 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.023 samrabin 08/16/2024 Merge b4b-dev
        ctsm5.2.022 samrabin 08/14/2024 Rework crop_calendars suite and cropMonthOutput
        ctsm5.2.021   rgknox 08/13/2024 Adding on-the-fly parameter settings for prescribed N and P in FATES
        ctsm5.2.020   slevis 08/12/2024 MEGAN updates (MEGAN-CLM6)

From 6b0b655c7fe46ad73d61e1f1acf6cbd4581f1483 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 16 Aug 2024 14:01:49 -0600
Subject: [PATCH 0899/1248] Improve peat burning dependence on climate.

---
 src/biogeochem/CNFireLi2024Mod.F90      | 26 +++++++++++--------------
 src/biogeophys/Wateratm2lndBulkType.F90 | 20 +++++++++++++++++++
 2 files changed, 31 insertions(+), 15 deletions(-)

diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 503ed28488..5f1c88811f 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -151,11 +151,9 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     real(r8) :: afuel    !weight for arh and arh30
     real(r8) :: btran_col(bounds%begc:bounds%endc)
     logical  :: transient_landcover  ! whether this run has any prescribed transient landcover
-    real(r8), target  :: prec60_col_target(bounds%begc:bounds%endc)
-    real(r8), target  :: prec10_col_target(bounds%begc:bounds%endc)
+    real(r8), target  :: prec30_col_target(bounds%begc:bounds%endc)
     real(r8), target  :: rh30_col_target(bounds%begc:bounds%endc)
-    real(r8), pointer :: prec60_col(:)
-    real(r8), pointer :: prec10_col(:)
+    real(r8), pointer :: prec30_col(:)
     real(r8), pointer :: rh30_col(:)
     !-----------------------------------------------------------------------
 
@@ -194,8 +192,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          forc_t             => atm2lnd_inst%forc_t_downscaled_col              , & ! Input:  [real(r8) (:)     ]  downscaled atmospheric temperature (Kelvin)
          forc_rain          => wateratm2lndbulk_inst%forc_rain_downscaled_col  , & ! Input:  [real(r8) (:)     ]  downscaled rain
          forc_snow          => wateratm2lndbulk_inst%forc_snow_downscaled_col  , & ! Input:  [real(r8) (:)     ]  downscaled snow
-         prec60             => wateratm2lndbulk_inst%prec60_patch              , & ! Input:  [real(r8) (:)     ]  60-day running mean of tot. precipitation
-         prec10             => wateratm2lndbulk_inst%prec10_patch              , & ! Input:  [real(r8) (:)     ]  10-day running mean of tot. precipitation
+         prec30             => wateratm2lndbulk_inst%prec30_patch              , & 
          rh30               => wateratm2lndbulk_inst%rh30_patch                , & ! Input:  [real(r8) (:)     ]  10-day running mean of tot. precipitation
          dwt_smoothed       => cnveg_state_inst%dwt_smoothed_patch             , & ! Input:  [real(r8) (:)     ]  change in patch weight (-1 to 1) on the gridcell, smoothed over the year
          cropf_col          => cnveg_state_inst%cropf_col                      , & ! Input:  [real(r8) (:)     ]  cropland fraction in veg column
@@ -246,15 +243,11 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
       transient_landcover = run_has_transient_landcover()
 
       !pft to column average
-      prec10_col =>prec10_col_target
+      prec30_col =>prec30_col_target
       call p2c(bounds, num_soilc, filter_soilc, &
-           prec10(bounds%begp:bounds%endp), &
-           prec10_col(bounds%begc:bounds%endc))
+           prec30(bounds%begp:bounds%endp), &
+           prec30_col(bounds%begc:bounds%endc))
 
-      prec60_col =>prec60_col_target
-      call p2c(bounds, num_soilc, filter_soilc, &
-           prec60(bounds%begp:bounds%endp), &
-           prec60_col(bounds%begc:bounds%endc))
 
       rh30_col =>rh30_col_target
       call p2c(bounds, num_soilc, filter_soilc, &
@@ -545,9 +538,12 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         c = filter_soilc(fc)
         g= col%gridcell(c)
         if(grc%latdeg(g) < cnfire_const%borealat )then
+          if((trotr1_col(c)+trotr2_col(c))*col%wtgcell(c)<=0.8_r8.and.trotr1_col(c)+trotr2_col(c)>0.0_r8) then
            baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
-                min(1._r8,(4.0_r8-prec60_col(c)*secspday)/ &
-                4.0_r8))**2*peatf_lf(c)*(1._r8-fsat(c))
+                min(1._r8,(1._r8-prec30_col(c)*secspday/6._r8)))*peatf_lf(c)
+          else
+            baf_peatf(c)=0._r8
+          end if
         else
            baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/0.3_r8))* &
                 max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
diff --git a/src/biogeophys/Wateratm2lndBulkType.F90 b/src/biogeophys/Wateratm2lndBulkType.F90
index 4aacbe11c2..bcc0e6b0d9 100644
--- a/src/biogeophys/Wateratm2lndBulkType.F90
+++ b/src/biogeophys/Wateratm2lndBulkType.F90
@@ -35,6 +35,7 @@ module Wateratm2lndBulkType
      real(r8), pointer :: forc_rh_grc                   (:)   ! atmospheric relative humidity (%)
      real(r8) , pointer :: prec365_col                  (:)   ! col 365-day running mean of tot. precipitation (see comment in UpdateAccVars regarding why this is col-level despite other prec accumulators being patch-level)
      real(r8) , pointer :: prec60_patch                 (:)   ! patch 60-day running mean of tot. precipitation (mm/s)
+     real(r8) , pointer :: prec30_patch                 (:) 
      real(r8) , pointer :: prec10_patch                 (:)   ! patch 10-day running mean of tot. precipitation (mm/s)
      real(r8) , pointer :: rh30_patch                   (:)   ! patch 30-day running mean of relative humidity
      real(r8) , pointer :: prec24_patch                 (:)   ! patch 24-hour running mean of tot. precipitation (mm/s)
@@ -126,6 +127,7 @@ subroutine InitBulkAllocate(this, bounds)
     allocate(this%forc_rh_grc                   (begg:endg))        ; this%forc_rh_grc (:)   = ival
     allocate(this%prec365_col                   (begc:endc))        ; this%prec365_col (:)   = nan
     allocate(this%prec60_patch                  (begp:endp))        ; this%prec60_patch(:)   = nan
+    allocate(this%prec30_patch                  (begp:endp))        ; this%prec30_patch(:)   = nan
     allocate(this%prec10_patch                  (begp:endp))        ; this%prec10_patch(:)   = nan
     allocate(this%rh30_patch                    (begp:endp))        ; this%rh30_patch  (:)   = nan
     if (use_fates) then
@@ -198,6 +200,12 @@ subroutine InitBulkHistory(this, bounds)
        call hist_addfld1d (fname=this%info%fname('PREC60'), units='MM H2O/S',  &
             avgflag='A', long_name=this%info%lname('60-day running mean of PREC'), &
             ptr_patch=this%prec60_patch, default='inactive')
+
+       this%prec30_patch(begp:endp) = spval
+       call hist_addfld1d (fname=this%info%fname('PREC30'), units='MM H2O/S',  &
+            avgflag='A', long_name=this%info%lname('30-day running mean of PREC'), &
+            ptr_patch=this%prec30_patch, default='inactive')
+
     end if
 
   end subroutine InitBulkHistory
@@ -245,6 +253,11 @@ subroutine InitAccBuffer (this, bounds)
             desc='60-day running mean of total precipitation', accum_type='runmean', accum_period=-60, &
             subgrid_type='pft', numlev=1, init_value=0._r8)
 
+      call init_accum_field (name='PREC30', units='MM H2O/S', &
+            desc='30-day running mean of total precipitation', accum_type='runmean', accum_period=-30, &
+            subgrid_type='pft', numlev=1, init_value=0._r8)
+
+
        call init_accum_field (name='RH30', units='%', &
             desc='30-day running mean of relative humidity', accum_type='runmean', accum_period=-30, &
             subgrid_type='pft', numlev=1, init_value=100._r8)
@@ -324,6 +337,9 @@ subroutine InitAccVars(this, bounds)
        call extract_accum_field ('PREC60', rbufslp, nstep)
        this%prec60_patch(begp:endp) = rbufslp(begp:endp)
 
+        call extract_accum_field ('PREC30', rbufslp, nstep)
+       this%prec30_patch(begp:endp) = rbufslp(begp:endp)
+
        call extract_accum_field ('RH30', rbufslp, nstep)
        this%rh30_patch(begp:endp) = rbufslp(begp:endp)
     end if
@@ -404,6 +420,9 @@ subroutine UpdateAccVars (this, bounds)
        call update_accum_field  ('PREC60', rbufslp, nstep)
        call extract_accum_field ('PREC60', this%prec60_patch, nstep)
 
+       call update_accum_field  ('PREC30', rbufslp, nstep)
+       call extract_accum_field ('PREC30', this%prec30_patch, nstep)
+
        ! Accumulate and extract PREC10 (accumulates total precipitation as 10-day running mean)
        call update_accum_field  ('PREC10', rbufslp, nstep)
        call extract_accum_field ('PREC10', this%prec10_patch, nstep)
@@ -483,6 +502,7 @@ subroutine Clean(this)
     ! anomaly forcing
     deallocate(this%prec365_col)
     deallocate(this%prec60_patch)
+    deallocate(this%prec30_patch)
     deallocate(this%prec10_patch)
     if (use_fates) then
        deallocate(this%prec24_patch)

From 617f88b2e6ea00f16371d83dc5392b844202df64 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 16 Aug 2024 14:02:17 -0600
Subject: [PATCH 0900/1248] Improve dependence of deforestation burning on
 climate.

---
 src/biogeochem/CNFireLi2024Mod.F90 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 5f1c88811f..7495438d9b 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -625,17 +625,17 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                     fbac1(c)        = 0._r8
                     farea_burned(c) = baf_crop(c)+baf_peatf(c)
                  else
-                    cri = (4.0_r8*trotr1_col(c)+1.8_r8*trotr2_col(c))/(trotr1_col(c)+trotr2_col(c))
-                    cli = (max(0._r8,min(1._r8,(cri-prec60_col(c)*secspday)/cri))**0.5)* &
-                         (max(0._r8,min(1._r8,(cri-prec10_col(c)*secspday)/cri))**0.5)* &
+                    cri = (1.4_r8*trotr1_col(c)+0.5_r8*trotr2_col(c))/(trotr1_col(c)+trotr2_col(c))
+                    cli = max(0._r8,min(1._r8,1._r8-prec30_col(c)*secspday/cri))* &
                          (15._r8*min(0.0016_r8,dtrotr_col(c)/dt*dayspyr*secspday)+0.009_r8)* &
                          max(0._r8,min(1._r8,(0.25_r8-(forc_rain(c)+forc_snow(c))*secsphr)/0.25_r8))
-                    farea_burned(c) = fb*cli*(cli_scale/secspday)+baf_crop(c)+baf_peatf(c)
+                    
+                    farea_burned(c) = farea_burned(c)+fb*cli*(0.01_r8/secspday)
                     ! burned area out of conversion region due to land use fire
                     fbac1(c) = max(0._r8,fb*cli*(cli_scale/secspday) - 2.0_r8*lfc(c)/dt)
                  end if
                  ! total burned area out of conversion
-                 fbac(c) = fbac1(c)+baf_crop(c)+baf_peatf(c)
+                 fbac(c) = farea_burned(c) + fbac1(c)
               else
                  fbac(c) = farea_burned(c)
               end if

From 97405d769255605cc26b2a5cc96d31a039e68ed0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 16 Aug 2024 14:03:23 -0600
Subject: [PATCH 0901/1248] Add (1) lightning igns in trop. closed forests, (2)
 landscape frag suppression.

- Previously, neither lightning nor human ignitions (other than deforestation fire) were allowed there.
- Landscape fragmentation suppression effect has to do with lfwt.
---
 src/biogeochem/CNFireLi2024Mod.F90 | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 7495438d9b..0dc12d4df9 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -297,9 +297,9 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         if( patch%itype(p) > nc4_grass )then
            cropf_col(c) = cropf_col(c) + patch%wtcol(p)
         end if
-        ! For natural vegetation (non-crop and non-bare-soil)
-        if( patch%itype(p) >= ndllf_evr_tmp_tree .and. patch%itype(p) <= nc4_grass )then
-           lfwt(c) = lfwt(c) + patch%wtcol(p)
+        ! For natural vegetation
+        if(patch%itype(p) <= nc4_grass )then
+           lfwt(c) = lfwt(c) + patch%wtgcell(p)
         end if
      end do
      !
@@ -589,7 +589,6 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            end if
            fuelc(c) = fuelc(c)/(1._r8-cropf_col(c))
            fb       = max(0.0_r8,min(1.0_r8,(fuelc(c)-lfuel)/(ufuel-lfuel)))
-           if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
               afuel  =min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
               arh=1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
               arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
@@ -601,19 +600,24 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
               end if
               lh       = pot_hmn_ign_counts_alpha*6.8_r8*hdmlf**(0.43_r8)/30._r8/24._r8
               fs       = 1._r8-(0.01_r8+0.98_r8*exp(-0.025_r8*hdmlf))
+              if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
               ig       = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
                      cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
-                         cnfire_params%ignition_efficiency)*(1._r8-fs)*(1._r8-cropf_col(c))
+                         cnfire_params%ignition_efficiency)*(1._r8-fs)* &
+                         (lfwt(c)**0.5)
+              else
+              ig       = this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
+                     cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
+                         cnfire_params%ignition_efficiency*(1._r8-fs)*  &
+                         (lfwt(c)**0.5)
+              end if
               nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) !fire counts/km2/sec
               Lb_lf    = 1._r8+10._r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
               spread_m = fire_m**0.5_r8
+              fd_col(c)=(lfwt(c)*lgdp1_col(c)*lpop_col(c))**0.5_r8 * fd_col(c)
               farea_burned(c) = min(1._r8,(cnfire_const%g0*spread_m*fsr_col(c)* &
-                   fd_col(c)/1000._r8)**2*lgdp1_col(c)* &
-                   lpop_col(c)*nfire(c)*SHR_CONST_PI*Lb_lf+ &
+                   fd_col(c)/1000._r8)**2*nfire(c)*SHR_CONST_PI*Lb_lf+ &
                    baf_crop(c)+baf_peatf(c))  ! fraction (0-1) per sec
-           else
-             farea_burned(c)=min(1._r8,baf_crop(c)+baf_peatf(c))
-           end if
            !
            ! if landuse change data is used, calculate deforestation fires and
            ! add it in the total of burned area fraction

From 8418ec491f1dba682708b433805ae20b46be7b10 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 16 Aug 2024 14:04:54 -0600
Subject: [PATCH 0902/1248] Recalibrate li2024gswpfrc (namelist parameters
 only).

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 674effd165..1d60fa9adc 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -355,14 +355,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <rh_hgh                   fire_method="li2024gswpfrc" >80.0d00</rh_hgh>
 <bt_min                   fire_method="li2024gswpfrc" >0.85d00</bt_min>
 <bt_max                   fire_method="li2024gswpfrc" >0.98d00</bt_max>
-<cli_scale                fire_method="li2024gswpfrc" >0.025d00</cli_scale>
-<boreal_peatfire_c        fire_method="li2024gswpfrc" >0.09d-4</boreal_peatfire_c>
+<cli_scale                fire_method="li2024gswpfrc" >0.01d00</cli_scale>
+<boreal_peatfire_c        fire_method="li2024gswpfrc" >0.28d-4</boreal_peatfire_c>
 <pot_hmn_ign_counts_alpha fire_method="li2024gswpfrc" >0.010d00</pot_hmn_ign_counts_alpha>
-<non_boreal_peatfire_c    fire_method="li2024gswpfrc" >0.17d-3</non_boreal_peatfire_c>
-<cropfire_a1              fire_method="li2024gswpfrc" >0.21d00</cropfire_a1>
+<non_boreal_peatfire_c    fire_method="li2024gswpfrc" >0.71d-4</non_boreal_peatfire_c>
+<cropfire_a1              fire_method="li2024gswpfrc" >0.3d00</cropfire_a1>
 <occur_hi_gdp_tree        fire_method="li2024gswpfrc" >0.33d00</occur_hi_gdp_tree>
 <lfuel                    fire_method="li2024gswpfrc" >75.d00</lfuel>
-<ufuel                    fire_method="li2024gswpfrc" >1050.d00</ufuel>
+<ufuel                    fire_method="li2024gswpfrc" >825.d00</ufuel>
 <cmb_cmplt_fact_litter    fire_method="li2024gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
 

From 8de658065a6d94427052cffe0867acc280a37bb2 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 16 Aug 2024 14:12:32 -0600
Subject: [PATCH 0903/1248] Add fire_method li2024crujra.

Same as li2024gswpfrc except rh_hgh now 85 (was 80).
---
 bld/namelist_files/namelist_defaults_ctsm.xml    | 16 ++++++++++++++++
 bld/namelist_files/namelist_definition_ctsm.xml  |  3 ++-
 cime_config/testdefs/testlist_clm.xml            | 10 ++++++++++
 .../clm/FireLi2024CruJra/include_user_mods       |  1 +
 .../clm/FireLi2024CruJra/user_nl_clm             |  1 +
 src/biogeochem/CNFireFactoryMod.F90              |  2 +-
 6 files changed, 31 insertions(+), 2 deletions(-)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/user_nl_clm

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 1d60fa9adc..777b7c4cff 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -366,6 +366,22 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2024gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
 
+<rh_low                   fire_method="li2024crujra" >30.0d00</rh_low>
+<rh_hgh                   fire_method="li2024crujra" >85.0d00</rh_hgh>
+<bt_min                   fire_method="li2024crujra" >0.85d00</bt_min>
+<bt_max                   fire_method="li2024crujra" >0.98d00</bt_max>
+<cli_scale                fire_method="li2024crujra" >0.01d00</cli_scale>
+<boreal_peatfire_c        fire_method="li2024crujra" >0.28d-4</boreal_peatfire_c>
+<pot_hmn_ign_counts_alpha fire_method="li2024crujra" >0.010d00</pot_hmn_ign_counts_alpha>
+<non_boreal_peatfire_c    fire_method="li2024crujra" >0.71d-4</non_boreal_peatfire_c>
+<cropfire_a1              fire_method="li2024crujra" >0.3d00</cropfire_a1>
+<occur_hi_gdp_tree        fire_method="li2024crujra" >0.33d00</occur_hi_gdp_tree>
+<lfuel                    fire_method="li2024crujra" >75.d00</lfuel>
+<ufuel                    fire_method="li2024crujra" >825.d00</ufuel>
+<cmb_cmplt_fact_litter    fire_method="li2024crujra" >0.5d00</cmb_cmplt_fact_litter>
+<cmb_cmplt_fact_cwd       fire_method="li2024crujra" >0.28d00</cmb_cmplt_fact_cwd>
+
+
 <!-- Canopy fluxes namelist defaults -->
 <use_undercanopy_stability               >.false.</use_undercanopy_stability>
 <use_undercanopy_stability phys="clm4_5" >.true.</use_undercanopy_stability>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 4cc50da391..134f0c41c7 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -252,7 +252,7 @@ formulation (1).
 </entry>
 
 <entry id="fire_method" type="char*80" category="clm_physics"
-       group="cnfire_inparm" valid_values="nofire,li2014qianfrc,li2016crufrc,li2021gswpfrc,li2024gswpfrc" >
+       group="cnfire_inparm" valid_values="nofire,li2014qianfrc,li2016crufrc,li2021gswpfrc,li2024gswpfrc,li2024crujra" >
 The method type to use for CNFire
 
 nofire:        Turn fire effects off
@@ -260,6 +260,7 @@ li2014qianfrc: Reference paper Li, et. al.(2014) tuned with QIAN atmospheric for
 li2016crufrc:  Reference paper Li, et. al.(2016) tuned with CRU-NCEP atmospheric forcing
 li2021gswpfrc: Reference paper Li, et. al.(2021?) tuned with GSWP3 atmospheric forcing
 li2024gswpfrc: No reference paper yet
+li2024crujra:  No reference paper yet, tuned with CRU-JRA forcing
 </entry>
 
 <entry id="pot_hmn_ign_counts_alpha" type="real" category="clm_physics"
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 4166570ab0..de9cd0b1be 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3600,6 +3600,16 @@
     </options>
   </test>
 
+  <test name="SMS_D_Ld65" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/FireLi2024CruJra">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="fire"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+    </options>
+  </test>
+
   <test name="SMS_Ld733" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/RxCropCalsNoAdapt">
     <machines>
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/user_nl_clm
new file mode 100644
index 0000000000..437e4ef86e
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FireLi2024CruJra/user_nl_clm
@@ -0,0 +1 @@
+fire_method = 'li2024crujra'
diff --git a/src/biogeochem/CNFireFactoryMod.F90 b/src/biogeochem/CNFireFactoryMod.F90
index 876e28a5e3..27a1085336 100644
--- a/src/biogeochem/CNFireFactoryMod.F90
+++ b/src/biogeochem/CNFireFactoryMod.F90
@@ -116,7 +116,7 @@ subroutine create_cnfire_method( NLFilename, cnfire_method )
        allocate(cnfire_li2016_type :: cnfire_method)
     case ("li2021gswpfrc")
        allocate(cnfire_li2021_type :: cnfire_method)
-    case ("li2024gswpfrc")
+    case ("li2024gswpfrc", "li2024crujra")
        allocate(cnfire_li2024_type :: cnfire_method)
 
     case default

From 5e82825e8b5da4f5170181d764924872b958ec81 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 16 Aug 2024 14:16:00 -0600
Subject: [PATCH 0904/1248] Whitespace and comment fixes.

---
 src/biogeochem/CNFireLi2024Mod.F90      | 36 ++++++++++++-------------
 src/biogeophys/Wateratm2lndBulkType.F90 |  4 +--
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 0dc12d4df9..d749e8000c 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -192,8 +192,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          forc_t             => atm2lnd_inst%forc_t_downscaled_col              , & ! Input:  [real(r8) (:)     ]  downscaled atmospheric temperature (Kelvin)
          forc_rain          => wateratm2lndbulk_inst%forc_rain_downscaled_col  , & ! Input:  [real(r8) (:)     ]  downscaled rain
          forc_snow          => wateratm2lndbulk_inst%forc_snow_downscaled_col  , & ! Input:  [real(r8) (:)     ]  downscaled snow
-         prec30             => wateratm2lndbulk_inst%prec30_patch              , & 
-         rh30               => wateratm2lndbulk_inst%rh30_patch                , & ! Input:  [real(r8) (:)     ]  10-day running mean of tot. precipitation
+         prec30             => wateratm2lndbulk_inst%prec30_patch              , & ! Input:  [real(r8) (:)     ]  10-day running mean of tot. precipitation
+         rh30               => wateratm2lndbulk_inst%rh30_patch                , & ! Input:  [real(r8) (:)     ]  10-day running mean of tot. relative humidity
          dwt_smoothed       => cnveg_state_inst%dwt_smoothed_patch             , & ! Input:  [real(r8) (:)     ]  change in patch weight (-1 to 1) on the gridcell, smoothed over the year
          cropf_col          => cnveg_state_inst%cropf_col                      , & ! Input:  [real(r8) (:)     ]  cropland fraction in veg column
          gdp_lf             => this%gdp_lf_col                                 , & ! Input:  [real(r8) (:)     ]  gdp data
@@ -298,7 +298,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            cropf_col(c) = cropf_col(c) + patch%wtcol(p)
         end if
         ! For natural vegetation
-        if(patch%itype(p) <= nc4_grass )then
+        if (patch%itype(p) <= nc4_grass ) then
            lfwt(c) = lfwt(c) + patch%wtgcell(p)
         end if
      end do
@@ -538,12 +538,12 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         c = filter_soilc(fc)
         g= col%gridcell(c)
         if(grc%latdeg(g) < cnfire_const%borealat )then
-          if((trotr1_col(c)+trotr2_col(c))*col%wtgcell(c)<=0.8_r8.and.trotr1_col(c)+trotr2_col(c)>0.0_r8) then
-           baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
-                min(1._r8,(1._r8-prec30_col(c)*secspday/6._r8)))*peatf_lf(c)
-          else
-            baf_peatf(c)=0._r8
-          end if
+            if ((trotr1_col(c)+trotr2_col(c))*col%wtgcell(c)<=0.8_r8.and.trotr1_col(c)+trotr2_col(c)>0.0_r8) then
+               baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
+                     min(1._r8,(1._r8-prec30_col(c)*secspday/6._r8)))*peatf_lf(c)
+            else
+               baf_peatf(c) = 0._r8
+            end if
         else
            baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/0.3_r8))* &
                 max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
@@ -601,15 +601,15 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
               lh       = pot_hmn_ign_counts_alpha*6.8_r8*hdmlf**(0.43_r8)/30._r8/24._r8
               fs       = 1._r8-(0.01_r8+0.98_r8*exp(-0.025_r8*hdmlf))
               if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
-              ig       = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
-                     cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
-                         cnfire_params%ignition_efficiency)*(1._r8-fs)* &
-                         (lfwt(c)**0.5)
+                 ig = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
+                      cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
+                      cnfire_params%ignition_efficiency)*(1._r8-fs)* &
+                      (lfwt(c)**0.5)
               else
-              ig       = this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
-                     cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
-                         cnfire_params%ignition_efficiency*(1._r8-fs)*  &
-                         (lfwt(c)**0.5)
+                 ig = this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
+                      cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
+                      cnfire_params%ignition_efficiency*(1._r8-fs)*  &
+                      (lfwt(c)**0.5)
               end if
               nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) !fire counts/km2/sec
               Lb_lf    = 1._r8+10._r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
@@ -633,7 +633,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                     cli = max(0._r8,min(1._r8,1._r8-prec30_col(c)*secspday/cri))* &
                          (15._r8*min(0.0016_r8,dtrotr_col(c)/dt*dayspyr*secspday)+0.009_r8)* &
                          max(0._r8,min(1._r8,(0.25_r8-(forc_rain(c)+forc_snow(c))*secsphr)/0.25_r8))
-                    
+
                     farea_burned(c) = farea_burned(c)+fb*cli*(0.01_r8/secspday)
                     ! burned area out of conversion region due to land use fire
                     fbac1(c) = max(0._r8,fb*cli*(cli_scale/secspday) - 2.0_r8*lfc(c)/dt)
diff --git a/src/biogeophys/Wateratm2lndBulkType.F90 b/src/biogeophys/Wateratm2lndBulkType.F90
index bcc0e6b0d9..b3a28196f1 100644
--- a/src/biogeophys/Wateratm2lndBulkType.F90
+++ b/src/biogeophys/Wateratm2lndBulkType.F90
@@ -35,7 +35,7 @@ module Wateratm2lndBulkType
      real(r8), pointer :: forc_rh_grc                   (:)   ! atmospheric relative humidity (%)
      real(r8) , pointer :: prec365_col                  (:)   ! col 365-day running mean of tot. precipitation (see comment in UpdateAccVars regarding why this is col-level despite other prec accumulators being patch-level)
      real(r8) , pointer :: prec60_patch                 (:)   ! patch 60-day running mean of tot. precipitation (mm/s)
-     real(r8) , pointer :: prec30_patch                 (:) 
+     real(r8) , pointer :: prec30_patch                 (:)
      real(r8) , pointer :: prec10_patch                 (:)   ! patch 10-day running mean of tot. precipitation (mm/s)
      real(r8) , pointer :: rh30_patch                   (:)   ! patch 30-day running mean of relative humidity
      real(r8) , pointer :: prec24_patch                 (:)   ! patch 24-hour running mean of tot. precipitation (mm/s)
@@ -337,7 +337,7 @@ subroutine InitAccVars(this, bounds)
        call extract_accum_field ('PREC60', rbufslp, nstep)
        this%prec60_patch(begp:endp) = rbufslp(begp:endp)
 
-        call extract_accum_field ('PREC30', rbufslp, nstep)
+       call extract_accum_field ('PREC30', rbufslp, nstep)
        this%prec30_patch(begp:endp) = rbufslp(begp:endp)
 
        call extract_accum_field ('RH30', rbufslp, nstep)

From 34839868c3b96149f619bd750e387da37d23e152 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 16 Aug 2024 15:20:53 -0600
Subject: [PATCH 0905/1248] Update another param file for aux_clm test to pass

---
 cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
index 3c686f08b9..3462b802c7 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
@@ -1,2 +1,2 @@
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240208.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240814.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'

From 4045128f70293d187c97e7fc2ed73b2e5189397e Mon Sep 17 00:00:00 2001
From: wwieder <wwieder@ucar.edu>
Date: Mon, 22 Apr 2024 16:08:48 -0600
Subject: [PATCH 0906/1248] update PLUMBER2 usermods to 5.2 datasets

---
 cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands | 1 -
 cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands | 1 -
 170 files changed, 170 deletions(-)

diff --git a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
index f64d8759a2..67baebcf55 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AR-SLu_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AR-SLu/CLM1PT_data/CTSM_DATM_AR-SLu_2010-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
index b8a54e5644..0efd0fad67 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AT-Neu_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AT-Neu/CLM1PT_data/CTSM_DATM_AT-Neu_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
index 2d5e0d85fd..bbb56c040d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-ASM_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-ASM/CLM1PT_data/CTSM_DATM_AU-ASM_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
index fe84b1e129..1d7734330f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Cow_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cow/CLM1PT_data/CTSM_DATM_AU-Cow_2010-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
index fcb7375d71..fcf027b8c2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Cpr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cpr/CLM1PT_data/CTSM_DATM_AU-Cpr_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
index 8d42bed60a..6ce2fe74b1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Ctr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ctr/CLM1PT_data/CTSM_DATM_AU-Ctr_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
index 17aed3a1dd..090c330641 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Cum_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cum/CLM1PT_data/CTSM_DATM_AU-Cum_2013-2018.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2018" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
index 816e4c78dc..27ebc931ee 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-DaP_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaP/CLM1PT_data/CTSM_DATM_AU-DaP_2009-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
index 0ea37fd95a..4fd48d214d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-DaS_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaS/CLM1PT_data/CTSM_DATM_AU-DaS_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
index 3cd8faecd9..b0b16bfa84 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Dry_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Dry/CLM1PT_data/CTSM_DATM_AU-Dry_2011-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
index 7822948582..2c84ebbe46 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Emr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Emr/CLM1PT_data/CTSM_DATM_AU-Emr_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
index 258ee5f12a..5d07cef0a1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-GWW_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-GWW/CLM1PT_data/CTSM_DATM_AU-GWW_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
index 31071a2ebb..0a193b5299 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Gin_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Gin/CLM1PT_data/CTSM_DATM_AU-Gin_2012-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
index 411cec6d9c..fb933852a1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-How_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-How/CLM1PT_data/CTSM_DATM_AU-How_2003-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
index 7fc59ce824..07b31e742c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Lit_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Lit/CLM1PT_data/CTSM_DATM_AU-Lit_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
index 6671c26040..9cdc2603e3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Otw_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Otw/CLM1PT_data/CTSM_DATM_AU-Otw_2009-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
index db70e72c89..a1f5c227c7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Rig_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rig/CLM1PT_data/CTSM_DATM_AU-Rig_2011-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
index 33e2084f14..491c105b41 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Rob_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rob/CLM1PT_data/CTSM_DATM_AU-Rob_2014-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
index 561ba257fa..cc4780d142 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Sam_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Sam/CLM1PT_data/CTSM_DATM_AU-Sam_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
index 97db87c821..b47b5d5247 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Stp_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Stp/CLM1PT_data/CTSM_DATM_AU-Stp_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
index dee6244ef7..4078dbed33 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-TTE_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-TTE/CLM1PT_data/CTSM_DATM_AU-TTE_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
index 36cd89bc73..b22b411eec 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Tum_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Tum/CLM1PT_data/CTSM_DATM_AU-Tum_2002-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
index 6b5d9415fe..87c5957833 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Whr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Whr/CLM1PT_data/CTSM_DATM_AU-Whr_2015-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2015" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
index e1751b8439..8f0303fe30 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Wrr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Wrr/CLM1PT_data/CTSM_DATM_AU-Wrr_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
index 861c844b14..7606fa4a96 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_AU-Ync_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ync/CLM1PT_data/CTSM_DATM_AU-Ync_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
index 5aeefbc792..876260dcc3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_BE-Bra_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Bra/CLM1PT_data/CTSM_DATM_BE-Bra_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
index 959a9e88fa..2ebc59db53 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_BE-Lon_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Lon/CLM1PT_data/CTSM_DATM_BE-Lon_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
index 008d71407c..21bf22d74c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_BE-Vie_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Vie/CLM1PT_data/CTSM_DATM_BE-Vie_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
index c1277c1198..741ea74d27 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=14400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_BR-Sa3_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BR-Sa3/CLM1PT_data/CTSM_DATM_BR-Sa3_2001-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
index b2e5f88222..77944502cf 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_BW-Ma1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BW-Ma1/CLM1PT_data/CTSM_DATM_BW-Ma1_2000-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
index adb752cea8..88ef538521 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-NS1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS1/CLM1PT_data/CTSM_DATM_CA-NS1_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
index bb25a4ad93..9b89720f4a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-NS2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS2/CLM1PT_data/CTSM_DATM_CA-NS2_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
index 733537f009..d5f16eac57 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-NS4_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS4/CLM1PT_data/CTSM_DATM_CA-NS4_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
index 491bc27b99..aca396c31d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-NS5_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS5/CLM1PT_data/CTSM_DATM_CA-NS5_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
index 3a1b6a7b0f..d9bd413c42 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-NS6_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS6/CLM1PT_data/CTSM_DATM_CA-NS6_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
index 735c947bfe..1614d09505 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-NS7_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS7/CLM1PT_data/CTSM_DATM_CA-NS7_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
index c7123ae573..0d3cd7e1a0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-Qcu_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qcu/CLM1PT_data/CTSM_DATM_CA-Qcu_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
index fb7fc215c9..8e80f8e897 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-Qfo_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qfo/CLM1PT_data/CTSM_DATM_CA-Qfo_2004-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
index ed6c584b7c..f479028097 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-SF1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF1/CLM1PT_data/CTSM_DATM_CA-SF1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
index 1fffcfdac9..d83a6c2bf1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-SF2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF2/CLM1PT_data/CTSM_DATM_CA-SF2_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
index 03096c96fa..17fcb052ba 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CA-SF3_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF3/CLM1PT_data/CTSM_DATM_CA-SF3_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
index 1e2590a7ae..156ccfd380 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CH-Cha_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Cha/CLM1PT_data/CTSM_DATM_CH-Cha_2006-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
index c170c8b840..3ad08c65f5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CH-Dav_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Dav/CLM1PT_data/CTSM_DATM_CH-Dav_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
index 31e5163045..44bdb94425 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CH-Fru_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Fru/CLM1PT_data/CTSM_DATM_CH-Fru_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
index ee091e134e..58b583af12 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CH-Oe1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Oe1/CLM1PT_data/CTSM_DATM_CH-Oe1_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
index cde3fed3be..e257bff2eb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CN-Cha_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cha/CLM1PT_data/CTSM_DATM_CN-Cha_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
index d5ec208a05..709e3f12ab 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CN-Cng_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cng/CLM1PT_data/CTSM_DATM_CN-Cng_2008-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
index 674ce4dda4..5597e04781 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CN-Dan_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Dan/CLM1PT_data/CTSM_DATM_CN-Dan_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
index b9149c7d8a..6d0898e50d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CN-Din_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Din/CLM1PT_data/CTSM_DATM_CN-Din_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
index 42502b41ce..ecb62c468d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CN-Du2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Du2/CLM1PT_data/CTSM_DATM_CN-Du2_2007-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
index 95c4167bf0..95c2c4625e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CN-HaM_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-HaM/CLM1PT_data/CTSM_DATM_CN-HaM_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
index 401534e487..4fd2927af6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CN-Qia_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Qia/CLM1PT_data/CTSM_DATM_CN-Qia_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
index 20309cdcb3..e72e38b648 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_CZ-wet_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CZ-wet/CLM1PT_data/CTSM_DATM_CZ-wet_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
index 6495d46b57..766eb3880f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Bay_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Bay/CLM1PT_data/CTSM_DATM_DE-Bay_1997-1999.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
index d43c3bd94d..73c61a9d79 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Geb_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Geb/CLM1PT_data/CTSM_DATM_DE-Geb_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
index fe165d2bf3..6bb17ac6a7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Gri_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Gri/CLM1PT_data/CTSM_DATM_DE-Gri_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
index fa5671c663..74f37b2314 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Hai_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Hai/CLM1PT_data/CTSM_DATM_DE-Hai_2000-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
index 28fb89a2d0..ee09f48b7d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Kli_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Kli/CLM1PT_data/CTSM_DATM_DE-Kli_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
index 250432bd9f..66eca33f28 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Meh_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Meh/CLM1PT_data/CTSM_DATM_DE-Meh_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
index ef17febde0..b23d6d2b21 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Obe_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Obe/CLM1PT_data/CTSM_DATM_DE-Obe_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
index db837ac070..590e3b5812 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Seh_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Seh/CLM1PT_data/CTSM_DATM_DE-Seh_2008-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
index bcff32c36a..a8532e908c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-SfN_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-SfN/CLM1PT_data/CTSM_DATM_DE-SfN_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
index aa6beb5913..3b9af13173 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Tha_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Tha/CLM1PT_data/CTSM_DATM_DE-Tha_1998-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1998" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
index 12d6f2024d..f39a379185 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DE-Wet_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Wet/CLM1PT_data/CTSM_DATM_DE-Wet_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
index a4a472424e..fbc465b915 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DK-Fou_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Fou/CLM1PT_data/CTSM_DATM_DK-Fou_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
index 962775613e..644cc92e00 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DK-Lva_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Lva/CLM1PT_data/CTSM_DATM_DK-Lva_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
index 4c806cea45..f54b4647b1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DK-Ris_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Ris/CLM1PT_data/CTSM_DATM_DK-Ris_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
index 1748d52204..4868bd8135 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DK-Sor_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Sor/CLM1PT_data/CTSM_DATM_DK-Sor_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
index ea72cc14c4..5d9e5c6e54 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_DK-ZaH_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-ZaH/CLM1PT_data/CTSM_DATM_DK-ZaH_2000-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
index 38e841b51c..7d7da13008 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ES-ES1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES1/CLM1PT_data/CTSM_DATM_ES-ES1_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
index 47fae079e6..83905f3813 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ES-ES2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES2/CLM1PT_data/CTSM_DATM_ES-ES2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
index f8a0283232..5b33bf0cca 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ES-LMa_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LMa/CLM1PT_data/CTSM_DATM_ES-LMa_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
index 8590e61f79..163fa43b1a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ES-LgS_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LgS/CLM1PT_data/CTSM_DATM_ES-LgS_2007-2007.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
index bec50968d6..055e4df543 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ES-VDA_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-VDA/CLM1PT_data/CTSM_DATM_ES-VDA_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
index 46cd461773..f4dad2be34 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FI-Hyy_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Hyy/CLM1PT_data/CTSM_DATM_FI-Hyy_1996-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
index db4e320ca0..fcf3a3b6a0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FI-Kaa_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Kaa/CLM1PT_data/CTSM_DATM_FI-Kaa_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
index 844403dfc4..4e3f36e65f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FI-Lom_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Lom/CLM1PT_data/CTSM_DATM_FI-Lom_2007-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
index be6e3a2eba..c716a66993 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FI-Sod_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Sod/CLM1PT_data/CTSM_DATM_FI-Sod_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
index 946c9b84fc..4ced43e5ff 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FR-Fon_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Fon/CLM1PT_data/CTSM_DATM_FR-Fon_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
index fd29463244..6821e30d5a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FR-Gri_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Gri/CLM1PT_data/CTSM_DATM_FR-Gri_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
index 88900143b1..ba56b6dfd4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FR-Hes_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Hes/CLM1PT_data/CTSM_DATM_FR-Hes_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
index 29c9c95ab7..491b472fda 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FR-LBr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-LBr/CLM1PT_data/CTSM_DATM_FR-LBr_2003-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
index 676f8af611..bcda561678 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FR-Lq1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq1/CLM1PT_data/CTSM_DATM_FR-Lq1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
index b407160bb9..24847656fb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FR-Lq2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq2/CLM1PT_data/CTSM_DATM_FR-Lq2_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
index b226175943..781321d36a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_FR-Pue_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Pue/CLM1PT_data/CTSM_DATM_FR-Pue_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
index 1fef6cf769..25d9b73407 100644
--- a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_GF-Guy_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/GF-Guy/CLM1PT_data/CTSM_DATM_GF-Guy_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
index a4cf969235..188f13bb21 100644
--- a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_HU-Bug_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/HU-Bug/CLM1PT_data/CTSM_DATM_HU-Bug_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
index 794fdabba3..43ba6c29ba 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ID-Pag_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ID-Pag/CLM1PT_data/CTSM_DATM_ID-Pag_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
index 376f21bf88..f202a45e45 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IE-Ca1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Ca1/CLM1PT_data/CTSM_DATM_IE-Ca1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
index 34bf806e19..2cbf857d0a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IE-Dri_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Dri/CLM1PT_data/CTSM_DATM_IE-Dri_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
index d0f80bd240..b52c8d408d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Amp_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Amp/CLM1PT_data/CTSM_DATM_IT-Amp_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
index 5c95ebd5cb..8399009a3c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-BCi_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-BCi/CLM1PT_data/CTSM_DATM_IT-BCi_2005-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
index 4218939b8e..6358580049 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-CA1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA1/CLM1PT_data/CTSM_DATM_IT-CA1_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
index f3e82597af..57eb7da218 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-CA2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA2/CLM1PT_data/CTSM_DATM_IT-CA2_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
index de8970f1e3..b1e2439541 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-CA3_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA3/CLM1PT_data/CTSM_DATM_IT-CA3_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
index 37ab868476..a842fcbe02 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Col_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Col/CLM1PT_data/CTSM_DATM_IT-Col_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
index e7bc47b3b0..7a6db3d102 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Cpz_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Cpz/CLM1PT_data/CTSM_DATM_IT-Cpz_2001-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
index 6cf225d172..e82c5cfa8f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Isp_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Isp/CLM1PT_data/CTSM_DATM_IT-Isp_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
index 8b388aedb4..c1f95210e6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-LMa_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-LMa/CLM1PT_data/CTSM_DATM_IT-LMa_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
index 1f7f728803..33c3d49053 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Lav_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Lav/CLM1PT_data/CTSM_DATM_IT-Lav_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
index 26ffc80458..02952affac 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-MBo_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-MBo/CLM1PT_data/CTSM_DATM_IT-MBo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
index 6559976180..91f623aab1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Mal_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Mal/CLM1PT_data/CTSM_DATM_IT-Mal_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
index 58be23bcd1..f75f23d917 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Noe_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Noe/CLM1PT_data/CTSM_DATM_IT-Noe_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
index 785443e0f1..af53f49fb9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Non_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Non/CLM1PT_data/CTSM_DATM_IT-Non_2002-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
index e7c30a4e36..e6af3c6a16 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-PT1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-PT1/CLM1PT_data/CTSM_DATM_IT-PT1_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
index dc1b5630d0..1793711024 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Ren_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ren/CLM1PT_data/CTSM_DATM_IT-Ren_2010-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
index 865f76ae9b..ddc9c0868e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Ro1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro1/CLM1PT_data/CTSM_DATM_IT-Ro1_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
index 401cfcf30b..4e87a351a6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-Ro2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro2/CLM1PT_data/CTSM_DATM_IT-Ro2_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
index 7926235386..1604053cce 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-SR2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SR2/CLM1PT_data/CTSM_DATM_IT-SR2_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
index 8dbeedc751..5b89dbff9e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_IT-SRo_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SRo/CLM1PT_data/CTSM_DATM_IT-SRo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
index 6af519cf5d..b9c962fafc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_JP-SMF_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/JP-SMF/CLM1PT_data/CTSM_DATM_JP-SMF_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
index 26b6fda5a4..4b46b3c6f0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_NL-Ca1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Ca1/CLM1PT_data/CTSM_DATM_NL-Ca1_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
index ec509840af..dc5e4e1741 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_NL-Hor_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Hor/CLM1PT_data/CTSM_DATM_NL-Hor_2008-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
index 3bcbfbbc35..a7d5784572 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_NL-Loo_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Loo/CLM1PT_data/CTSM_DATM_NL-Loo_1997-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
index 4eb88c995a..e68c1a7aa0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_PL-wet_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PL-wet/CLM1PT_data/CTSM_DATM_PL-wet_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
index 224920cbf7..5dd7ac93cf 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_PT-Esp_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Esp/CLM1PT_data/CTSM_DATM_PT-Esp_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
index 74413f5f5e..dcb9da9c25 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_PT-Mi1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi1/CLM1PT_data/CTSM_DATM_PT-Mi1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
index f9aa12224c..40e570aa82 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_PT-Mi2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi2/CLM1PT_data/CTSM_DATM_PT-Mi2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
index 4abca52cae..6737ea4985 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_RU-Che_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Che/CLM1PT_data/CTSM_DATM_RU-Che_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
index 74c3693f71..ce11407552 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_RU-Fyo_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Fyo/CLM1PT_data/CTSM_DATM_RU-Fyo_2003-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
index b68d328625..a51ddc4edd 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_RU-Zot_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Zot/CLM1PT_data/CTSM_DATM_RU-Zot_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
index b2e63de838..de45fdf737 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_SD-Dem_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SD-Dem/CLM1PT_data/CTSM_DATM_SD-Dem_2005-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
index dfc8e4b83f..4d7588829f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_SE-Deg_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SE-Deg/CLM1PT_data/CTSM_DATM_SE-Deg_2002-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
index efa3a6f1ae..da714e6178 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_UK-Gri_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Gri/CLM1PT_data/CTSM_DATM_UK-Gri_2000-2001.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
index 47143973d4..22aa28cd0b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_UK-Ham_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Ham/CLM1PT_data/CTSM_DATM_UK-Ham_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
index 161de2a08e..c772c6ff8e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_UK-PL3_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-PL3/CLM1PT_data/CTSM_DATM_UK-PL3_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
index 727e21a389..3f9e11af10 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-AR1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR1/CLM1PT_data/CTSM_DATM_US-AR1_2010-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
index 5de187cd7a..6e9befc1c3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-AR2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR2/CLM1PT_data/CTSM_DATM_US-AR2_2010-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
index da1de52a6e..7ff3c302f2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-ARM_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-ARM/CLM1PT_data/CTSM_DATM_US-ARM_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
index 47ae3dd4d9..d044d71d9c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Aud_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Aud/CLM1PT_data/CTSM_DATM_US-Aud_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
index 2d24f07e53..ca97f023f7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Bar_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bar/CLM1PT_data/CTSM_DATM_US-Bar_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
index 9fb49876da..1341c5ed9a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Bkg_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bkg/CLM1PT_data/CTSM_DATM_US-Bkg_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
index c208c920f7..40fd33b704 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Blo_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Blo/CLM1PT_data/CTSM_DATM_US-Blo_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
index c802acf23c..be837ab2d1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Bo1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bo1/CLM1PT_data/CTSM_DATM_US-Bo1_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
index d66d11a697..3fbe5a7442 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Cop_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Cop/CLM1PT_data/CTSM_DATM_US-Cop_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
index 621e4156ed..980fe40609 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-FPe_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-FPe/CLM1PT_data/CTSM_DATM_US-FPe_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
index a7548fbb53..b79cbbde03 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-GLE_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-GLE/CLM1PT_data/CTSM_DATM_US-GLE_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
index ee1cf13767..a59dded80f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Goo_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Goo/CLM1PT_data/CTSM_DATM_US-Goo_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
index 43d55bdbd1..863fe24c3d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Ha1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ha1/CLM1PT_data/CTSM_DATM_US-Ha1_1992-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1992" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
index 7e9bda46b2..87a2d1d4f8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Ho1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ho1/CLM1PT_data/CTSM_DATM_US-Ho1_1996-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
index 161a377821..a6d6ce7048 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-KS2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-KS2/CLM1PT_data/CTSM_DATM_US-KS2_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
index b606ac7e9e..9c85ce58af 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Los_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Los/CLM1PT_data/CTSM_DATM_US-Los_2000-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
index b817bac303..6ebdc0f52c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-MMS_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MMS/CLM1PT_data/CTSM_DATM_US-MMS_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
index a666ccbaf0..7ef79f2ac6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-MOz_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MOz/CLM1PT_data/CTSM_DATM_US-MOz_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
index e07240f14f..19325ead49 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Me2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me2/CLM1PT_data/CTSM_DATM_US-Me2_2002-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
index 6b26c589d9..43b2a75513 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Me4_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me4/CLM1PT_data/CTSM_DATM_US-Me4_1996-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
index 6056ec6552..ffb7538463 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Me6_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me6/CLM1PT_data/CTSM_DATM_US-Me6_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
index 89c79b88bc..c1d6553e90 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Myb_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Myb/CLM1PT_data/CTSM_DATM_US-Myb_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
index 7185333ba0..a859ca34d6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-NR1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-NR1/CLM1PT_data/CTSM_DATM_US-NR1_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
index 5ec7590921..150a7109e9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Ne1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne1/CLM1PT_data/CTSM_DATM_US-Ne1_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
index 75d2215e6c..a43a4f0523 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Ne2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne2/CLM1PT_data/CTSM_DATM_US-Ne2_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
index ceb48a35c0..cf8a20d653 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Ne3_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne3/CLM1PT_data/CTSM_DATM_US-Ne3_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
index e214fa5d26..a8c15c035c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-PFa_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-PFa/CLM1PT_data/CTSM_DATM_US-PFa_1995-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1995" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
index 0be161a3f5..6d34756259 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=32400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Prr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Prr/CLM1PT_data/CTSM_DATM_US-Prr_2011-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
index b1944933fe..ef3192eac3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-SP1_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP1/CLM1PT_data/CTSM_DATM_US-SP1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
index 9ec9b25681..b070c1123b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-SP2_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP2/CLM1PT_data/CTSM_DATM_US-SP2_2000-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
index 72c94ad6a5..fbf338ca93 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-SP3_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP3/CLM1PT_data/CTSM_DATM_US-SP3_1999-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
index 53c07383d3..2f102954ef 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-SRG_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRG/CLM1PT_data/CTSM_DATM_US-SRG_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
index f8ab5b5b89..a930aeb922 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-SRM_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRM/CLM1PT_data/CTSM_DATM_US-SRM_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
index 7bd8324a6d..8b95474d55 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Syv_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Syv/CLM1PT_data/CTSM_DATM_US-Syv_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
index 2ac988eb2f..8fc48db2e3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Ton_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ton/CLM1PT_data/CTSM_DATM_US-Ton_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
index 0895943d1c..e9b5fb0a4d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Tw4_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Tw4/CLM1PT_data/CTSM_DATM_US-Tw4_2014-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
index 77649de143..d49419e72f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Twt_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Twt/CLM1PT_data/CTSM_DATM_US-Twt_2010-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
index 511e7e05c3..54b64467c3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-UMB_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-UMB/CLM1PT_data/CTSM_DATM_US-UMB_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
index 8cbb483737..84c0fb82a0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Var_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Var/CLM1PT_data/CTSM_DATM_US-Var_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
index adcfb2eec4..e5aa83d4a4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-WCr_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-WCr/CLM1PT_data/CTSM_DATM_US-WCr_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
index 0f091925f1..5e81cc5524 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Whs_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Whs/CLM1PT_data/CTSM_DATM_US-Whs_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
index da4a18b3f9..324cf4860f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_US-Wkg_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Wkg/CLM1PT_data/CTSM_DATM_US-Wkg_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
index 016f4e4038..138996eda2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ZA-Kru_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZA-Kru/CLM1PT_data/CTSM_DATM_ZA-Kru_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
index 2729227ecc..8443f0a13b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
@@ -4,7 +4,6 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_ZM-Mon_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZM-Mon/CLM1PT_data/CTSM_DATM_ZM-Mon_2008-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 

From 932d07e217d917df70c44b03183d5ba4151b2290 Mon Sep 17 00:00:00 2001
From: wwieder <wwieder@ucar.edu>
Date: Mon, 22 Apr 2024 17:49:22 -0600
Subject: [PATCH 0907/1248] keep hack to point to 5.2 surface data files

---
 cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands | 1 +
 cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands | 1 +
 170 files changed, 170 insertions(+)

diff --git a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
index 67baebcf55..44e145ec9c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AR-SLu_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AR-SLu/CLM1PT_data/CTSM_DATM_AR-SLu_2010-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
index 0efd0fad67..8ea324b8a0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AT-Neu_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AT-Neu/CLM1PT_data/CTSM_DATM_AT-Neu_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
index bbb56c040d..301f741e84 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-ASM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-ASM/CLM1PT_data/CTSM_DATM_AU-ASM_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
index 1d7734330f..ed9e62746f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Cow_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cow/CLM1PT_data/CTSM_DATM_AU-Cow_2010-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
index fcf027b8c2..49a0df7f70 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Cpr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cpr/CLM1PT_data/CTSM_DATM_AU-Cpr_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
index 6ce2fe74b1..2a6fd56772 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Ctr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ctr/CLM1PT_data/CTSM_DATM_AU-Ctr_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
index 090c330641..210e549fa2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Cum_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cum/CLM1PT_data/CTSM_DATM_AU-Cum_2013-2018.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2018" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
index 27ebc931ee..f7692c9dfd 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-DaP_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaP/CLM1PT_data/CTSM_DATM_AU-DaP_2009-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
index 4fd48d214d..194ca882da 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-DaS_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaS/CLM1PT_data/CTSM_DATM_AU-DaS_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
index b0b16bfa84..e1fa9be489 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Dry_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Dry/CLM1PT_data/CTSM_DATM_AU-Dry_2011-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
index 2c84ebbe46..43d63b2b46 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Emr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Emr/CLM1PT_data/CTSM_DATM_AU-Emr_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
index 5d07cef0a1..8eef1e7770 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-GWW_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-GWW/CLM1PT_data/CTSM_DATM_AU-GWW_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
index 0a193b5299..43a7ec4705 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Gin_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Gin/CLM1PT_data/CTSM_DATM_AU-Gin_2012-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
index fb933852a1..3a0cc4f882 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-How_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-How/CLM1PT_data/CTSM_DATM_AU-How_2003-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
index 07b31e742c..45d132bee8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Lit_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Lit/CLM1PT_data/CTSM_DATM_AU-Lit_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
index 9cdc2603e3..7e63474531 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Otw_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Otw/CLM1PT_data/CTSM_DATM_AU-Otw_2009-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
index a1f5c227c7..42bd3aac0c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Rig_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rig/CLM1PT_data/CTSM_DATM_AU-Rig_2011-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
index 491c105b41..e51b36d89e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Rob_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rob/CLM1PT_data/CTSM_DATM_AU-Rob_2014-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
index cc4780d142..919e322e8c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Sam_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Sam/CLM1PT_data/CTSM_DATM_AU-Sam_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
index b47b5d5247..94cc191e2f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Stp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Stp/CLM1PT_data/CTSM_DATM_AU-Stp_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
index 4078dbed33..3204d39d22 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-TTE_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-TTE/CLM1PT_data/CTSM_DATM_AU-TTE_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
index b22b411eec..51b0770e12 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Tum_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Tum/CLM1PT_data/CTSM_DATM_AU-Tum_2002-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
index 87c5957833..193218e604 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Whr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Whr/CLM1PT_data/CTSM_DATM_AU-Whr_2015-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2015" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
index 8f0303fe30..c5b6609661 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Wrr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Wrr/CLM1PT_data/CTSM_DATM_AU-Wrr_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
index 7606fa4a96..57fb25a4cf 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Ync_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ync/CLM1PT_data/CTSM_DATM_AU-Ync_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
index 876260dcc3..28beca48b1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BE-Bra_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Bra/CLM1PT_data/CTSM_DATM_BE-Bra_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
index 2ebc59db53..3833429771 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BE-Lon_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Lon/CLM1PT_data/CTSM_DATM_BE-Lon_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
index 21bf22d74c..6936b7bb27 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BE-Vie_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Vie/CLM1PT_data/CTSM_DATM_BE-Vie_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
index 741ea74d27..58a839b51c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=14400
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BR-Sa3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BR-Sa3/CLM1PT_data/CTSM_DATM_BR-Sa3_2001-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
index 77944502cf..88851105c0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BW-Ma1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BW-Ma1/CLM1PT_data/CTSM_DATM_BW-Ma1_2000-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
index 88ef538521..962411e90b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS1/CLM1PT_data/CTSM_DATM_CA-NS1_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
index 9b89720f4a..897cf765df 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS2/CLM1PT_data/CTSM_DATM_CA-NS2_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
index d5f16eac57..d1d7315b2c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS4_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS4/CLM1PT_data/CTSM_DATM_CA-NS4_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
index aca396c31d..b73f17e9f6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS5_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS5/CLM1PT_data/CTSM_DATM_CA-NS5_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
index d9bd413c42..a785233c1f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS6_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS6/CLM1PT_data/CTSM_DATM_CA-NS6_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
index 1614d09505..f97c5c5141 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS7_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS7/CLM1PT_data/CTSM_DATM_CA-NS7_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
index 0d3cd7e1a0..878c28ddf6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-Qcu_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qcu/CLM1PT_data/CTSM_DATM_CA-Qcu_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
index 8e80f8e897..bde28704c5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-Qfo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qfo/CLM1PT_data/CTSM_DATM_CA-Qfo_2004-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
index f479028097..c529507b7e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-SF1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF1/CLM1PT_data/CTSM_DATM_CA-SF1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
index d83a6c2bf1..aebfd10bbe 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-SF2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF2/CLM1PT_data/CTSM_DATM_CA-SF2_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
index 17fcb052ba..bd68572dca 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-SF3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF3/CLM1PT_data/CTSM_DATM_CA-SF3_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
index 156ccfd380..d8a0aa59c1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Cha_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Cha/CLM1PT_data/CTSM_DATM_CH-Cha_2006-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
index 3ad08c65f5..19f4cc5ba0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Dav_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Dav/CLM1PT_data/CTSM_DATM_CH-Dav_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
index 44bdb94425..291458c54b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Fru_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Fru/CLM1PT_data/CTSM_DATM_CH-Fru_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
index 58b583af12..964e24d852 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Oe1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Oe1/CLM1PT_data/CTSM_DATM_CH-Oe1_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
index e257bff2eb..8322f1f733 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Cha_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cha/CLM1PT_data/CTSM_DATM_CN-Cha_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
index 709e3f12ab..dda99e3c4a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Cng_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cng/CLM1PT_data/CTSM_DATM_CN-Cng_2008-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
index 5597e04781..cdca7d7472 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Dan_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Dan/CLM1PT_data/CTSM_DATM_CN-Dan_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
index 6d0898e50d..19f9baa8eb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Din_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Din/CLM1PT_data/CTSM_DATM_CN-Din_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
index ecb62c468d..5f83542f35 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Du2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Du2/CLM1PT_data/CTSM_DATM_CN-Du2_2007-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
index 95c2c4625e..e7a814451d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-HaM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-HaM/CLM1PT_data/CTSM_DATM_CN-HaM_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
index 4fd2927af6..a44ff612b4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Qia_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Qia/CLM1PT_data/CTSM_DATM_CN-Qia_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
index e72e38b648..d01359e568 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CZ-wet_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CZ-wet/CLM1PT_data/CTSM_DATM_CZ-wet_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
index 766eb3880f..cfde80c1de 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Bay_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Bay/CLM1PT_data/CTSM_DATM_DE-Bay_1997-1999.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
index 73c61a9d79..834a2b3f96 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Geb_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Geb/CLM1PT_data/CTSM_DATM_DE-Geb_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
index 6bb17ac6a7..9fe2f16680 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Gri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Gri/CLM1PT_data/CTSM_DATM_DE-Gri_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
index 74f37b2314..83bb6beb10 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Hai_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Hai/CLM1PT_data/CTSM_DATM_DE-Hai_2000-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
index ee09f48b7d..d8a15d9a53 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Kli_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Kli/CLM1PT_data/CTSM_DATM_DE-Kli_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
index 66eca33f28..9ffbaf9c34 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Meh_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Meh/CLM1PT_data/CTSM_DATM_DE-Meh_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
index b23d6d2b21..94afe08f04 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Obe_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Obe/CLM1PT_data/CTSM_DATM_DE-Obe_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
index 590e3b5812..2daca0a2c1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Seh_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Seh/CLM1PT_data/CTSM_DATM_DE-Seh_2008-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
index a8532e908c..9bdef7293f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-SfN_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-SfN/CLM1PT_data/CTSM_DATM_DE-SfN_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
index 3b9af13173..e77813eec9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Tha_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Tha/CLM1PT_data/CTSM_DATM_DE-Tha_1998-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1998" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
index f39a379185..7563e5ff7e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Wet_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Wet/CLM1PT_data/CTSM_DATM_DE-Wet_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
index fbc465b915..06a43e6df6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Fou_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Fou/CLM1PT_data/CTSM_DATM_DK-Fou_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
index 644cc92e00..bda3c08df5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Lva_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Lva/CLM1PT_data/CTSM_DATM_DK-Lva_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
index f54b4647b1..189e9b0ee7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Ris_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Ris/CLM1PT_data/CTSM_DATM_DK-Ris_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
index 4868bd8135..2aa6510cd4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Sor_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Sor/CLM1PT_data/CTSM_DATM_DK-Sor_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
index 5d9e5c6e54..99a0558d7d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-ZaH_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-ZaH/CLM1PT_data/CTSM_DATM_DK-ZaH_2000-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
index 7d7da13008..10d4e4399d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-ES1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES1/CLM1PT_data/CTSM_DATM_ES-ES1_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
index 83905f3813..b72ddf79db 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-ES2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES2/CLM1PT_data/CTSM_DATM_ES-ES2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
index 5b33bf0cca..6d69cfc70b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-LMa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LMa/CLM1PT_data/CTSM_DATM_ES-LMa_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
index 163fa43b1a..2efa0f5a04 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-LgS_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LgS/CLM1PT_data/CTSM_DATM_ES-LgS_2007-2007.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
index 055e4df543..83d071a6f8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-VDA_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-VDA/CLM1PT_data/CTSM_DATM_ES-VDA_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
index f4dad2be34..68d5a9739f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Hyy_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Hyy/CLM1PT_data/CTSM_DATM_FI-Hyy_1996-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
index fcf3a3b6a0..43852577b1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Kaa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Kaa/CLM1PT_data/CTSM_DATM_FI-Kaa_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
index 4e3f36e65f..c7e01ee357 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Lom_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Lom/CLM1PT_data/CTSM_DATM_FI-Lom_2007-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
index c716a66993..ccf011b0e0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Sod_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Sod/CLM1PT_data/CTSM_DATM_FI-Sod_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
index 4ced43e5ff..4af5380bee 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Fon_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Fon/CLM1PT_data/CTSM_DATM_FR-Fon_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
index 6821e30d5a..dae1f22807 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Gri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Gri/CLM1PT_data/CTSM_DATM_FR-Gri_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
index ba56b6dfd4..00dd5c6771 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Hes_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Hes/CLM1PT_data/CTSM_DATM_FR-Hes_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
index 491b472fda..21f28c8839 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-LBr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-LBr/CLM1PT_data/CTSM_DATM_FR-LBr_2003-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
index bcda561678..4b8ae400d7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Lq1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq1/CLM1PT_data/CTSM_DATM_FR-Lq1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
index 24847656fb..3e56a08786 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Lq2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq2/CLM1PT_data/CTSM_DATM_FR-Lq2_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
index 781321d36a..4e4ddac3d5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Pue_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Pue/CLM1PT_data/CTSM_DATM_FR-Pue_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
index 25d9b73407..6a2a814f69 100644
--- a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_GF-Guy_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/GF-Guy/CLM1PT_data/CTSM_DATM_GF-Guy_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
index 188f13bb21..739810dd52 100644
--- a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_HU-Bug_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/HU-Bug/CLM1PT_data/CTSM_DATM_HU-Bug_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
index 43ba6c29ba..e5e190ad1e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ID-Pag_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ID-Pag/CLM1PT_data/CTSM_DATM_ID-Pag_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
index f202a45e45..e9caca8f04 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IE-Ca1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Ca1/CLM1PT_data/CTSM_DATM_IE-Ca1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
index 2cbf857d0a..bdd48c2331 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IE-Dri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Dri/CLM1PT_data/CTSM_DATM_IE-Dri_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
index b52c8d408d..290836ff22 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Amp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Amp/CLM1PT_data/CTSM_DATM_IT-Amp_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
index 8399009a3c..ae21e12b51 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-BCi_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-BCi/CLM1PT_data/CTSM_DATM_IT-BCi_2005-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
index 6358580049..3fbb828981 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-CA1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA1/CLM1PT_data/CTSM_DATM_IT-CA1_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
index 57eb7da218..18be6fbd02 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-CA2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA2/CLM1PT_data/CTSM_DATM_IT-CA2_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
index b1e2439541..46bff2a9e3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-CA3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA3/CLM1PT_data/CTSM_DATM_IT-CA3_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
index a842fcbe02..a62cad7d87 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Col_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Col/CLM1PT_data/CTSM_DATM_IT-Col_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
index 7a6db3d102..6063242085 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Cpz_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Cpz/CLM1PT_data/CTSM_DATM_IT-Cpz_2001-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
index e82c5cfa8f..0ae339dba1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Isp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Isp/CLM1PT_data/CTSM_DATM_IT-Isp_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
index c1f95210e6..9f683c2101 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-LMa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-LMa/CLM1PT_data/CTSM_DATM_IT-LMa_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
index 33c3d49053..d1a8669b3e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Lav_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Lav/CLM1PT_data/CTSM_DATM_IT-Lav_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
index 02952affac..6b2e4b2651 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-MBo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-MBo/CLM1PT_data/CTSM_DATM_IT-MBo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
index 91f623aab1..e6f9ad1c51 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Mal_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Mal/CLM1PT_data/CTSM_DATM_IT-Mal_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
index f75f23d917..eacfbce81e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Noe_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Noe/CLM1PT_data/CTSM_DATM_IT-Noe_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
index af53f49fb9..543dc97221 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Non_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Non/CLM1PT_data/CTSM_DATM_IT-Non_2002-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
index e6af3c6a16..23afcb9469 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-PT1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-PT1/CLM1PT_data/CTSM_DATM_IT-PT1_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
index 1793711024..5b6afef969 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Ren_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ren/CLM1PT_data/CTSM_DATM_IT-Ren_2010-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
index ddc9c0868e..f74dd07bab 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Ro1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro1/CLM1PT_data/CTSM_DATM_IT-Ro1_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
index 4e87a351a6..5d3a64aefb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Ro2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro2/CLM1PT_data/CTSM_DATM_IT-Ro2_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
index 1604053cce..4cce0bb915 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-SR2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SR2/CLM1PT_data/CTSM_DATM_IT-SR2_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
index 5b89dbff9e..2f89c5830f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-SRo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SRo/CLM1PT_data/CTSM_DATM_IT-SRo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
index b9c962fafc..287a41b541 100644
--- a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_JP-SMF_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/JP-SMF/CLM1PT_data/CTSM_DATM_JP-SMF_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
index 4b46b3c6f0..7f88121b9b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_NL-Ca1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Ca1/CLM1PT_data/CTSM_DATM_NL-Ca1_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
index dc5e4e1741..6134ec5fd6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_NL-Hor_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Hor/CLM1PT_data/CTSM_DATM_NL-Hor_2008-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
index a7d5784572..82a7f2458c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_NL-Loo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Loo/CLM1PT_data/CTSM_DATM_NL-Loo_1997-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
index e68c1a7aa0..394e350a18 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PL-wet_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PL-wet/CLM1PT_data/CTSM_DATM_PL-wet_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
index 5dd7ac93cf..1552bd40e8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PT-Esp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Esp/CLM1PT_data/CTSM_DATM_PT-Esp_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
index dcb9da9c25..b8cf3bc26d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PT-Mi1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi1/CLM1PT_data/CTSM_DATM_PT-Mi1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
index 40e570aa82..404492a444 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PT-Mi2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi2/CLM1PT_data/CTSM_DATM_PT-Mi2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
index 6737ea4985..6d92902d1f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_RU-Che_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Che/CLM1PT_data/CTSM_DATM_RU-Che_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
index ce11407552..ca0223e1cf 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_RU-Fyo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Fyo/CLM1PT_data/CTSM_DATM_RU-Fyo_2003-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
index a51ddc4edd..60778a180c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_RU-Zot_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Zot/CLM1PT_data/CTSM_DATM_RU-Zot_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
index de45fdf737..985c3a010b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_SD-Dem_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SD-Dem/CLM1PT_data/CTSM_DATM_SD-Dem_2005-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
index 4d7588829f..1c0165e925 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_SE-Deg_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SE-Deg/CLM1PT_data/CTSM_DATM_SE-Deg_2002-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
index da714e6178..a29eeb03dc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_UK-Gri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Gri/CLM1PT_data/CTSM_DATM_UK-Gri_2000-2001.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
index 22aa28cd0b..178ff627b9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_UK-Ham_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Ham/CLM1PT_data/CTSM_DATM_UK-Ham_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
index c772c6ff8e..d0f256f358 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_UK-PL3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-PL3/CLM1PT_data/CTSM_DATM_UK-PL3_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
index 3f9e11af10..0bf6cf3313 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-AR1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR1/CLM1PT_data/CTSM_DATM_US-AR1_2010-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
index 6e9befc1c3..9751d08038 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-AR2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR2/CLM1PT_data/CTSM_DATM_US-AR2_2010-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
index 7ff3c302f2..3e4a6933bc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-ARM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-ARM/CLM1PT_data/CTSM_DATM_US-ARM_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
index d044d71d9c..1c193249b3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Aud_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Aud/CLM1PT_data/CTSM_DATM_US-Aud_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
index ca97f023f7..b681aac49d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Bar_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bar/CLM1PT_data/CTSM_DATM_US-Bar_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
index 1341c5ed9a..a81ec9e93f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Bkg_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bkg/CLM1PT_data/CTSM_DATM_US-Bkg_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
index 40fd33b704..0d914e4416 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Blo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Blo/CLM1PT_data/CTSM_DATM_US-Blo_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
index be837ab2d1..f45ebc7076 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Bo1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bo1/CLM1PT_data/CTSM_DATM_US-Bo1_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
index 3fbe5a7442..0ce199dd44 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Cop_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Cop/CLM1PT_data/CTSM_DATM_US-Cop_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
index 980fe40609..1f6c1a2438 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-FPe_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-FPe/CLM1PT_data/CTSM_DATM_US-FPe_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
index b79cbbde03..59ae899a7e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-GLE_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-GLE/CLM1PT_data/CTSM_DATM_US-GLE_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
index a59dded80f..9a0d84e815 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Goo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Goo/CLM1PT_data/CTSM_DATM_US-Goo_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
index 863fe24c3d..0687c4cd3d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ha1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ha1/CLM1PT_data/CTSM_DATM_US-Ha1_1992-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1992" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
index 87a2d1d4f8..a0d98032eb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ho1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ho1/CLM1PT_data/CTSM_DATM_US-Ho1_1996-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
index a6d6ce7048..02d26509c2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-KS2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-KS2/CLM1PT_data/CTSM_DATM_US-KS2_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
index 9c85ce58af..13ef4e69b4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Los_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Los/CLM1PT_data/CTSM_DATM_US-Los_2000-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
index 6ebdc0f52c..8a271026dd 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-MMS_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MMS/CLM1PT_data/CTSM_DATM_US-MMS_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
index 7ef79f2ac6..a98dae73c4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-MOz_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MOz/CLM1PT_data/CTSM_DATM_US-MOz_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
index 19325ead49..dc020bf1d1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Me2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me2/CLM1PT_data/CTSM_DATM_US-Me2_2002-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
index 43b2a75513..77d787c3d4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Me4_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me4/CLM1PT_data/CTSM_DATM_US-Me4_1996-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
index ffb7538463..389ef600e5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Me6_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me6/CLM1PT_data/CTSM_DATM_US-Me6_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
index c1d6553e90..6cc05da64f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Myb_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Myb/CLM1PT_data/CTSM_DATM_US-Myb_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
index a859ca34d6..773ca669b1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-NR1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-NR1/CLM1PT_data/CTSM_DATM_US-NR1_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
index 150a7109e9..f2adadd3ac 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ne1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne1/CLM1PT_data/CTSM_DATM_US-Ne1_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
index a43a4f0523..15ed24bdee 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ne2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne2/CLM1PT_data/CTSM_DATM_US-Ne2_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
index cf8a20d653..631bf243e4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ne3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne3/CLM1PT_data/CTSM_DATM_US-Ne3_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
index a8c15c035c..dd400a9257 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-PFa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-PFa/CLM1PT_data/CTSM_DATM_US-PFa_1995-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1995" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
index 6d34756259..28acc5f402 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=32400
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Prr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Prr/CLM1PT_data/CTSM_DATM_US-Prr_2011-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
index ef3192eac3..37e05304a8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SP1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP1/CLM1PT_data/CTSM_DATM_US-SP1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
index b070c1123b..a4ea7a35ac 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SP2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP2/CLM1PT_data/CTSM_DATM_US-SP2_2000-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
index fbf338ca93..76c00c8a36 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SP3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP3/CLM1PT_data/CTSM_DATM_US-SP3_1999-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
index 2f102954ef..804a5f9884 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SRG_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRG/CLM1PT_data/CTSM_DATM_US-SRG_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
index a930aeb922..9b379b1edb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SRM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRM/CLM1PT_data/CTSM_DATM_US-SRM_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
index 8b95474d55..0fe6c91305 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Syv_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Syv/CLM1PT_data/CTSM_DATM_US-Syv_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
index 8fc48db2e3..e97bac9028 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ton_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ton/CLM1PT_data/CTSM_DATM_US-Ton_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
index e9b5fb0a4d..49ad7cddd2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Tw4_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Tw4/CLM1PT_data/CTSM_DATM_US-Tw4_2014-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
index d49419e72f..447906c4fc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Twt_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Twt/CLM1PT_data/CTSM_DATM_US-Twt_2010-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
index 54b64467c3..1b3ee51b17 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-UMB_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-UMB/CLM1PT_data/CTSM_DATM_US-UMB_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
index 84c0fb82a0..099e07e301 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Var_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Var/CLM1PT_data/CTSM_DATM_US-Var_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
index e5aa83d4a4..de5a646543 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-WCr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-WCr/CLM1PT_data/CTSM_DATM_US-WCr_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
index 5e81cc5524..f706a2e79a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Whs_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Whs/CLM1PT_data/CTSM_DATM_US-Whs_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
index 324cf4860f..0fc65819c2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Wkg_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Wkg/CLM1PT_data/CTSM_DATM_US-Wkg_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
index 138996eda2..7c2dfed5c9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ZA-Kru_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZA-Kru/CLM1PT_data/CTSM_DATM_ZA-Kru_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
index 8443f0a13b..825675dc9b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
@@ -4,6 +4,7 @@
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
+echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ZM-Mon_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZM-Mon/CLM1PT_data/CTSM_DATM_ZM-Mon_2008-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 

From 0197db68574455c5c786f355f2cca00c374b25c6 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Tue, 23 Apr 2024 14:17:39 -0600
Subject: [PATCH 0908/1248] include plumber in cime_config

---
 cime_config/buildnml             |  2 +-
 cime_config/config_component.xml | 25 ++++++++++++++++++++++++-
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 3eb45dff31..554010576e 100755
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
+        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 3c48e16651..1fc7a3a3a1 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -330,7 +330,8 @@
       to create_newcase.  The default value is UNSET.
       For NEON cases, this can be set to either NEON or NEON.PRISM, the latter of which would
       use PRISM precipitation instead of the default NEON precipitation. NEON cases then also
-      use the variable NEONSITE to specify the exact site.</desc>
+      use the variable NEONSITE to specify the exact site. PLUMBER cases use the variable 
+      PLUMBER2SITE to specify the exact site.</desc>
   </entry>
 
   <entry id="CLM_USRDAT_DIR">
@@ -418,6 +419,28 @@
     <desc>Version id of Neon data</desc>
   </entry>
 
+  <entry id="PLUMBER2SITE">
+    <type>char</type>
+    <!-- NOTE: Be sure to have a comma at the last site-name - otherwise there will be issues see CTSM github issue #1901 -->
+    <valid_values>
+      AR-SLu,AT-Neu,AU-ASM,AU-Cow,AU-Cpr,AU-Ctr,AU-Cum,AU-DaP,AU-DaS,AU-Dry,AU-Emr,AU-Gin,AU-GWW,AU-How,AU-Lit,
+      AU-Otw,AU-Rig,AU-Rob,AU-Sam,AU-Stp,AU-TTE,AU-Tum,AU-Whr,AU-Wrr,AU-Ync,BE-Bra,BE-Lon,BE-Vie,BR-Sa3,BW-Ma1,CA-NS1,
+      CA-NS2,CA-NS4,CA-NS5,CA-NS6,CA-NS7,CA-Qcu,CA-Qfo,CA-SF1,CA-SF2,CA-SF3,CH-Cha,CH-Dav,CH-Fru,CH-Oe1,CN-Cha,CN-Cng,
+      CN-Dan,CN-Din,CN-Du2,CN-HaM,CN-Qia,CZ-wet,DE-Bay,DE-Geb,DE-Gri,DE-Hai,DE-Kli,DE-Meh,DE-Obe,DE-Seh,DE-SfN,DE-Tha,
+      DE-Wet,DK-Fou,DK-Lva,DK-Ris,DK-Sor,DK-ZaH,ES-ES1,ES-ES2,ES-LgS,ES-LMa,ES-VDA,FI-Hyy,FI-Kaa,FI-Lom,FI-Sod,FR-Fon,
+      FR-Gri,FR-Hes,FR-LBr,FR-Lq1,FR-Lq2,FR-Pue,GF-Guy,HU-Bug,ID-Pag,IE-Ca1,IE-Dri,IT-Amp,IT-BCi,IT-CA1,IT-CA2,IT-CA3,
+      IT-Col,IT-Cpz,IT-Isp,IT-Lav,IT-LMa,IT-Mal,IT-MBo,IT-Noe,IT-Non,IT-PT1,IT-Ren,IT-Ro1,IT-Ro2,IT-SR2,IT-SRo,JP-SMF,
+      NL-Ca1,NL-Hor,NL-Loo,PL-wet,PT-Esp,PT-Mi1,PT-Mi2,RU-Che,RU-Fyo,RU-Zot,SD-Dem,SE-Deg,UK-Gri,UK-Ham,UK-PL3,US-AR1,
+      US-AR2,US-ARM,US-Aud,US-Bar,US-Bkg,US-Blo,US-Bo1,US-Cop,US-FPe,US-GLE,US-Goo,US-Ha1,US-Ho1,US-KS2,US-Los,US-Me2,
+      US-Me4,US-Me6,US-MMS,US-MOz,US-Myb,US-Ne1,US-Ne2,US-Ne3,US-NR1,US-PFa,US-Prr,US-SP1,US-SP2,US-SP3,US-SRG,US-SRM,
+      US-Syv,US-Ton,US-Tw4,US-Twt,US-UMB,US-Var,US-WCr,US-Whs,US-Wkg,ZA-Kru,ZM-Mon,
+    </valid_values>
+    <default_value/>
+    <group>run_component_ctsm</group>
+    <file>env_run.xml</file>
+    <desc>Name of site for PLUMBER tower data</desc>
+  </entry>
+
 <help>
     =========================================
     CLM naming conventions

From 8d5a3108e9aba322740ce8598b13a9154cfda0fa Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Tue, 23 Apr 2024 14:20:26 -0600
Subject: [PATCH 0909/1248] black changes due to previous commit causing issues

---
 cime_config/buildnml | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 554010576e..8449ecadb2 100755
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,7 +182,9 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_path = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -224,7 +226,9 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)) and clm_force_coldstart == "off":
+        if (
+            ("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)
+        ) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"
@@ -301,7 +305,9 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_file = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
 
     # -----------------------------------------------------
     # Clear out old data
@@ -364,7 +370,9 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
+                logger.warning(
+                    "WARNING: Could NOT find a start file to use using" + clm_startfile
+                )
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -375,7 +383,9 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
+        create_namelist_infile(
+            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
+        )
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From 64df032bf39102c66528db274ae0c26cf661915d Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 1 May 2024 16:18:30 -0600
Subject: [PATCH 0910/1248] line too long update

---
 cime_config/buildnml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 8449ecadb2..8dc075c347 100755
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -204,8 +204,9 @@ def buildnml(case, caseroot, compname):
         if clm_force_coldstart == "on":
             clm_force_coldstart = "off"
             logger.warning(
-                "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type, which is a contradiction, the coldstart will be ignored\n"
-                + "  turn off CLM_FORCE_COLDSTART, or set RUN_TYPE=hybrid to get rid of this warning"
+                "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type,\n"
+                + "which is a contradiction, the coldstart will be ignored\n"
+                + "turn off CLM_FORCE_COLDSTART or set RUN_TYPE=hybrid to get rid of this warning"
             )
 
     if clm_force_coldstart == "on":

From 24c8d7c75e41e09c431fc3868cee6b11e33169d5 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 1 May 2024 16:55:15 -0600
Subject: [PATCH 0911/1248] revert buildnml

---
 cime_config/buildnml | 25 +++++++------------------
 1 file changed, 7 insertions(+), 18 deletions(-)
 mode change 100755 => 100644 cime_config/buildnml

diff --git a/cime_config/buildnml b/cime_config/buildnml
old mode 100755
new mode 100644
index 8dc075c347..3eb45dff31
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,9 +182,7 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -204,9 +202,8 @@ def buildnml(case, caseroot, compname):
         if clm_force_coldstart == "on":
             clm_force_coldstart = "off"
             logger.warning(
-                "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type,\n"
-                + "which is a contradiction, the coldstart will be ignored\n"
-                + "turn off CLM_FORCE_COLDSTART or set RUN_TYPE=hybrid to get rid of this warning"
+                "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type, which is a contradiction, the coldstart will be ignored\n"
+                + "  turn off CLM_FORCE_COLDSTART, or set RUN_TYPE=hybrid to get rid of this warning"
             )
 
     if clm_force_coldstart == "on":
@@ -227,9 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (
-            ("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)
-        ) and clm_force_coldstart == "off":
+        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"
@@ -306,9 +301,7 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
 
     # -----------------------------------------------------
     # Clear out old data
@@ -371,9 +364,7 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning(
-                    "WARNING: Could NOT find a start file to use using" + clm_startfile
-                )
+                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -384,9 +375,7 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(
-            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
-        )
+        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From 7054bfa513620c2925052efdc06f6f577a1b2eb6 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 1 May 2024 16:56:35 -0600
Subject: [PATCH 0912/1248] ran black locally

---
 cime_config/buildnml | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 3eb45dff31..a013a23162 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,7 +182,9 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_path = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -301,7 +303,9 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_file = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
 
     # -----------------------------------------------------
     # Clear out old data
@@ -364,7 +368,9 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
+                logger.warning(
+                    "WARNING: Could NOT find a start file to use using" + clm_startfile
+                )
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -375,7 +381,9 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
+        create_namelist_infile(
+            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
+        )
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From ad83d13cf10673340c2b3473b6677a3a1e8c2391 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 1 May 2024 16:58:12 -0600
Subject: [PATCH 0913/1248] undo local black run

---
 cime_config/buildnml | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index a013a23162..3eb45dff31 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,9 +182,7 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -303,9 +301,7 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
 
     # -----------------------------------------------------
     # Clear out old data
@@ -368,9 +364,7 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning(
-                    "WARNING: Could NOT find a start file to use using" + clm_startfile
-                )
+                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -381,9 +375,7 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(
-            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
-        )
+        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From d0c6d4cf4c34435a40fdf2862db62bbd3475021d Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 1 May 2024 17:01:53 -0600
Subject: [PATCH 0914/1248] include plumber in cime_config #2

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 3eb45dff31..554010576e 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
+        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From bf6044d67cb8e62c0c849815559a8200df41b0bd Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 1 May 2024 17:04:21 -0600
Subject: [PATCH 0915/1248] manual black attempt at fix

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 554010576e..23a4fe9bc7 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)) and clm_force_coldstart == "off":
+        if ("NEON" in clm_usrdat_name or "PLUMBER" in clm_usrdat_name) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From e02dfa93d883d72f1a2c0a28e34ee26e9ef57cf8 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 1 May 2024 17:09:06 -0600
Subject: [PATCH 0916/1248] trying a workaround

---
 cime_config/buildnml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 23a4fe9bc7..eea28d38fd 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,9 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
+        # fmt: off
         if ("NEON" in clm_usrdat_name or "PLUMBER" in clm_usrdat_name) and clm_force_coldstart == "off":
+            # fmt: on
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From 2bb58d634b57cd3eff3aaa0c330dd4a48b991833 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 08:39:04 -0600
Subject: [PATCH 0917/1248] removed parantheses

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index eea28d38fd..c0e4fbb7f2 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -225,7 +225,7 @@ def buildnml(case, caseroot, compname):
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
         # fmt: off
-        if ("NEON" in clm_usrdat_name or "PLUMBER" in clm_usrdat_name) and clm_force_coldstart == "off":
+        if "NEON" in clm_usrdat_name or "PLUMBER" in clm_usrdat_name and clm_force_coldstart == "off":
             # fmt: on
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None

From ee6b01f052f4905e0db5dcb1cd4d796e1e8f7034 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 08:46:49 -0600
Subject: [PATCH 0918/1248] this should pass

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index c0e4fbb7f2..c965c4f0d1 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -225,7 +225,7 @@ def buildnml(case, caseroot, compname):
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
         # fmt: off
-        if "NEON" in clm_usrdat_name or "PLUMBER" in clm_usrdat_name and clm_force_coldstart == "off":
+        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
             # fmt: on
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None

From 4e6dbfbb31c91d293231cc13e65eb34795b995ff Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 08:48:48 -0600
Subject: [PATCH 0919/1248] added parantheses

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index c965c4f0d1..2461f37dac 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -225,7 +225,7 @@ def buildnml(case, caseroot, compname):
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
         # fmt: off
-        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
+        if ("NEON" in clm_usrdat_name) and clm_force_coldstart == "off":
             # fmt: on
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None

From f6a09fba8fd71a52bfe88578c685cfcedf344602 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 08:51:22 -0600
Subject: [PATCH 0920/1248] undo buildnml changes

---
 cime_config/buildnml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 2461f37dac..3eb45dff31 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,9 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        # fmt: off
-        if ("NEON" in clm_usrdat_name) and clm_force_coldstart == "off":
-            # fmt: on
+        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From b9de93343ea87ee11d4ed85b3fe0117932fc076e Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 08:54:39 -0600
Subject: [PATCH 0921/1248] parantheses

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 3eb45dff31..9bf6766693 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
+        if ("NEON" in clm_usrdat_name) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From 0c2cc0689f988b8301819dce77d5179b0ba110b0 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 08:56:40 -0600
Subject: [PATCH 0922/1248] test additional argument

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 9bf6766693..e446b20a74 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if ("NEON" in clm_usrdat_name) and clm_force_coldstart == "off":
+        if (("NEON" in clm_usrdat_name) or False) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From 2f65ab89fbbcb98d8d06ea2cc2ed080e002b0fea Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 09:08:06 -0600
Subject: [PATCH 0923/1248] use any

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index e446b20a74..a25a513219 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or False) and clm_force_coldstart == "off":
+        if (any(item in clm_usrdat_name for item in ["NEON", "PLUMBER"]) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From 02b20378bb1095300f7af721a790c32526b4c1cd Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 09:10:14 -0600
Subject: [PATCH 0924/1248] remove any and add additional statement

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index a25a513219..554010576e 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (any(item in clm_usrdat_name for item in ["NEON", "PLUMBER"]) and clm_force_coldstart == "off":
+        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From 1d7ed405c065e0fdbb0778a3b9769cf1049115f6 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 09:11:38 -0600
Subject: [PATCH 0925/1248] dummy argument test

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 554010576e..b298bfab4b 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)) and clm_force_coldstart == "off":
+        if (("NEON" in clm_usrdat_name) or (False)) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From 8aa0286ab3e15676f72484a94c5007eee682bd6d Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 09:12:55 -0600
Subject: [PATCH 0926/1248] dummy argument test

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index b298bfab4b..e275e746f3 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or (False)) and clm_force_coldstart == "off":
+        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in ['PLUMBER'])) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From e6c1e2a37ed9926e0bbbce877c8ecb1b769f11e5 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 09:14:46 -0600
Subject: [PATCH 0927/1248] dummy argument test

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index e275e746f3..2d502a74a3 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in ['PLUMBER'])) and clm_force_coldstart == "off":
+        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in lnd_grid)) and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From ff05906c822d10bb223d3a493c7765f66e95cce6 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 09:18:02 -0600
Subject: [PATCH 0928/1248] try to separate lines

---
 cime_config/buildnml | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 2d502a74a3..3f14a41250 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,15 +224,16 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in lnd_grid)) and clm_force_coldstart == "off":
-            if ("_transient" in clm_nml_use_case) and (
-                re.fullmatch(r"\w\w\w\w\.transient", casename) is None
-                or clm_usrdat_name is "NEON.PRISM"
-            ):
-                logger.warning(
-                    "WARNING: Do you have appropriate initial conditions for this simulation?"
-                    + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
-                )
+        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)):
+            if clm_force_coldstart == "off":
+                if ("_transient" in clm_nml_use_case) and (
+                    re.fullmatch(r"\w\w\w\w\.transient", casename) is None
+                    or clm_usrdat_name is "NEON.PRISM"
+                ):
+                    logger.warning(
+                        "WARNING: Do you have appropriate initial conditions for this simulation?"
+                        + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
+                    )
 
     if comp_atm != "datm":
         nomeg = "-no-megan"

From 09b62d3a7a491f21c56fe859a815763b2a5394d7 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 2 May 2024 09:19:58 -0600
Subject: [PATCH 0929/1248] remove external parentheses

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 3f14a41250..acc74868e0 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -224,7 +224,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if (("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name)):
+        if ("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name):
             if clm_force_coldstart == "off":
                 if ("_transient" in clm_nml_use_case) and (
                     re.fullmatch(r"\w\w\w\w\.transient", casename) is None

From af992361d81d0158ab653c87d25b3a06b7c0e3ff Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Fri, 28 Jun 2024 10:56:12 -0600
Subject: [PATCH 0930/1248] update usermods script and shell commands for
 fsurdat

---
 cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands | 6 +++---
 cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands | 6 +++---
 cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands | 6 +++---
 cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands | 6 +++---
 cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands | 6 +++---
 cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands | 6 +++---
 cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands | 4 ++--
 cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands | 2 +-
 170 files changed, 225 insertions(+), 225 deletions(-)

diff --git a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
index 44e145ec9c..d7f8707812 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AR-SLu
 ./xmlchange PTS_LON=-66.459808
 ./xmlchange PTS_LAT=-33.464802
 ./xmlchange DATM_YR_END=2010
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AR-SLu_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AR-SLu/CLM1PT_data/CTSM_DATM_AR-SLu_2010-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
index 8ea324b8a0..dc0750224f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AT-Neu
 ./xmlchange PTS_LON=11.3175
 ./xmlchange PTS_LAT=47.116669
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AT-Neu_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AT-Neu/CLM1PT_data/CTSM_DATM_AT-Neu_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
index 301f741e84..f3eae9a24e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=133.24899299999998
-./xmlchange PTS_LAT=-22.283001000000002
+./xmlchange PLUMBER2SITE=AU-ASM
+./xmlchange PTS_LON=133.248993
+./xmlchange PTS_LAT=-22.283001
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-ASM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-ASM/CLM1PT_data/CTSM_DATM_AU-ASM_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
index ed9e62746f..9e44c8232c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Cow
 ./xmlchange PTS_LON=145.427155
 ./xmlchange PTS_LAT=-16.23819
 ./xmlchange DATM_YR_END=2015
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Cow_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cow/CLM1PT_data/CTSM_DATM_AU-Cow_2010-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
index 49a0df7f70..114544e9b5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Cpr
 ./xmlchange PTS_LON=140.589127
 ./xmlchange PTS_LAT=-34.00206
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Cpr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cpr/CLM1PT_data/CTSM_DATM_AU-Cpr_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
index 2a6fd56772..7af2976c83 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Ctr
 ./xmlchange PTS_LON=145.446854
 ./xmlchange PTS_LAT=-16.103279
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Ctr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ctr/CLM1PT_data/CTSM_DATM_AU-Ctr_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
index 210e549fa2..8c75b3de45 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Cum
 ./xmlchange PTS_LON=150.722473
-./xmlchange PTS_LAT=-33.613296999999996
+./xmlchange PTS_LAT=-33.613297
 ./xmlchange DATM_YR_END=2018
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Cum_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cum/CLM1PT_data/CTSM_DATM_AU-Cum_2013-2018.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2018" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
index f7692c9dfd..44171b3425 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-DaP
 ./xmlchange PTS_LON=131.3181
 ./xmlchange PTS_LAT=-14.0633
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-DaP_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaP/CLM1PT_data/CTSM_DATM_AU-DaP_2009-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
index 194ca882da..699b74900a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-DaS
 ./xmlchange PTS_LON=131.388
-./xmlchange PTS_LAT=-14.159282999999999
+./xmlchange PTS_LAT=-14.159283
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-DaS_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaS/CLM1PT_data/CTSM_DATM_AU-DaS_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
index e1fa9be489..a2a4686230 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Dry
 ./xmlchange PTS_LON=132.370605
 ./xmlchange PTS_LAT=-15.2588
 ./xmlchange DATM_YR_END=2015
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Dry_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Dry/CLM1PT_data/CTSM_DATM_AU-Dry_2011-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
index 43d63b2b46..7d9d557087 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Emr
 ./xmlchange PTS_LON=148.474594
 ./xmlchange PTS_LAT=-23.8587
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Emr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Emr/CLM1PT_data/CTSM_DATM_AU-Emr_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
index 8eef1e7770..26bd398dc1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-GWW
 ./xmlchange PTS_LON=120.654099
 ./xmlchange PTS_LAT=-30.191299
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-GWW_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-GWW/CLM1PT_data/CTSM_DATM_AU-GWW_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
index 43a7ec4705..61d3c3eb01 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Gin
 ./xmlchange PTS_LON=115.650002
 ./xmlchange PTS_LAT=-31.375
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Gin_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Gin/CLM1PT_data/CTSM_DATM_AU-Gin_2012-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
index 3a0cc4f882..7cac687aa3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-How
 ./xmlchange PTS_LON=131.149994
 ./xmlchange PTS_LAT=-12.4952
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-How_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-How/CLM1PT_data/CTSM_DATM_AU-How_2003-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
index 45d132bee8..7f1a885344 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=130.79449499999998
-./xmlchange PTS_LAT=-13.179039999999999
+./xmlchange PLUMBER2SITE=AU-Lit
+./xmlchange PTS_LON=130.794495
+./xmlchange PTS_LAT=-13.17904
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Lit_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Lit/CLM1PT_data/CTSM_DATM_AU-Lit_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
index 7e63474531..4016a12e52 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Otw
 ./xmlchange PTS_LON=142.816803
-./xmlchange PTS_LAT=-38.532340999999995
+./xmlchange PTS_LAT=-38.532341
 ./xmlchange DATM_YR_END=2010
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Otw_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Otw/CLM1PT_data/CTSM_DATM_AU-Otw_2009-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
index 42bd3aac0c..193f3cc5dd 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Rig
 ./xmlchange PTS_LON=145.575897
 ./xmlchange PTS_LAT=-36.649899
 ./xmlchange DATM_YR_END=2016
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Rig_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rig/CLM1PT_data/CTSM_DATM_AU-Rig_2011-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
index e51b36d89e..f7f4921746 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Rob
 ./xmlchange PTS_LON=145.630096
 ./xmlchange PTS_LAT=-17.1175
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Rob_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rob/CLM1PT_data/CTSM_DATM_AU-Rob_2014-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
index 919e322e8c..d1dae3a306 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=152.87780800000002
+./xmlchange PLUMBER2SITE=AU-Sam
+./xmlchange PTS_LON=152.877808
 ./xmlchange PTS_LAT=-27.3881
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Sam_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Sam/CLM1PT_data/CTSM_DATM_AU-Sam_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
index 94cc191e2f..d0e4cdf638 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Stp
 ./xmlchange PTS_LON=133.350204
 ./xmlchange PTS_LAT=-17.1507
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Stp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Stp/CLM1PT_data/CTSM_DATM_AU-Stp_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
index 3204d39d22..3c878a3ae9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-TTE
 ./xmlchange PTS_LON=133.639999
 ./xmlchange PTS_LAT=-22.287001
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-TTE_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-TTE/CLM1PT_data/CTSM_DATM_AU-TTE_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
index 51b0770e12..8e01ca6869 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Tum
 ./xmlchange PTS_LON=148.151703
 ./xmlchange PTS_LAT=-35.656601
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Tum_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Tum/CLM1PT_data/CTSM_DATM_AU-Tum_2002-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
index 193218e604..5bde37cdc7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Whr
 ./xmlchange PTS_LON=145.029404
 ./xmlchange PTS_LAT=-36.673199
 ./xmlchange DATM_YR_END=2016
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Whr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Whr/CLM1PT_data/CTSM_DATM_AU-Whr_2015-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2015" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
index c5b6609661..76311551ed 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Wrr
 ./xmlchange PTS_LON=146.654495
 ./xmlchange PTS_LAT=-43.09502
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Wrr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Wrr/CLM1PT_data/CTSM_DATM_AU-Wrr_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
index 57fb25a4cf..e7c1c495fc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=AU-Ync
 ./xmlchange PTS_LON=146.290695
 ./xmlchange PTS_LAT=-34.9893
 ./xmlchange DATM_YR_END=2017
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_AU-Ync_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ync/CLM1PT_data/CTSM_DATM_AU-Ync_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
index 28beca48b1..4cb0c5af5c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=BE-Bra
 ./xmlchange PTS_LON=4.52056
 ./xmlchange PTS_LAT=51.309166
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BE-Bra_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Bra/CLM1PT_data/CTSM_DATM_BE-Bra_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
index 3833429771..5ce5a904f5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=BE-Lon
 ./xmlchange PTS_LON=4.74613
-./xmlchange PTS_LAT=50.551590000000004
+./xmlchange PTS_LAT=50.55159
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BE-Lon_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Lon/CLM1PT_data/CTSM_DATM_BE-Lon_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
index 6936b7bb27..0e4e802d91 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=BE-Vie
 ./xmlchange PTS_LON=5.99805
 ./xmlchange PTS_LAT=50.305069
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BE-Vie_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Vie/CLM1PT_data/CTSM_DATM_BE-Vie_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
index 58a839b51c..114becfc06 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=BR-Sa3
 ./xmlchange PTS_LON=-54.971436
-./xmlchange PTS_LAT=-3.0180290000000003
+./xmlchange PTS_LAT=-3.018029
 ./xmlchange DATM_YR_END=2003
 ./xmlchange START_TOD=14400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BR-Sa3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BR-Sa3/CLM1PT_data/CTSM_DATM_BR-Sa3_2001-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
index 88851105c0..7d0681f988 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=BW-Ma1
 ./xmlchange PTS_LON=23.560329
 ./xmlchange PTS_LAT=-19.9165
 ./xmlchange DATM_YR_END=2000
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_BW-Ma1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BW-Ma1/CLM1PT_data/CTSM_DATM_BW-Ma1_2000-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
index 962411e90b..47f8762dca 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-NS1
 ./xmlchange PTS_LON=-98.483887
 ./xmlchange PTS_LAT=55.8792
 ./xmlchange DATM_YR_END=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS1/CLM1PT_data/CTSM_DATM_CA-NS1_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
index 897cf765df..c787c85af0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-NS2
 ./xmlchange PTS_LON=-98.524689
 ./xmlchange PTS_LAT=55.9058
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS2/CLM1PT_data/CTSM_DATM_CA-NS2_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
index d1d7315b2c..5e4247d5ee 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-NS4
 ./xmlchange PTS_LON=-98.380615
 ./xmlchange PTS_LAT=55.914398
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS4_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS4/CLM1PT_data/CTSM_DATM_CA-NS4_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
index b73f17e9f6..bddbef5bb3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-NS5
 ./xmlchange PTS_LON=-98.484985
 ./xmlchange PTS_LAT=55.863098
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS5_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS5/CLM1PT_data/CTSM_DATM_CA-NS5_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
index a785233c1f..908a798b98 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-NS6
 ./xmlchange PTS_LON=-98.964417
 ./xmlchange PTS_LAT=55.916698
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS6_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS6/CLM1PT_data/CTSM_DATM_CA-NS6_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
index f97c5c5141..5734053c2b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-99.94830300000001
+./xmlchange PLUMBER2SITE=CA-NS7
+./xmlchange PTS_LON=-99.948303
 ./xmlchange PTS_LAT=56.635799
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-NS7_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS7/CLM1PT_data/CTSM_DATM_CA-NS7_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
index 878c28ddf6..b68de255cb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-Qcu
 ./xmlchange PTS_LON=-74.03653
-./xmlchange PTS_LAT=49.267078000000005
+./xmlchange PTS_LAT=49.267078
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-Qcu_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qcu/CLM1PT_data/CTSM_DATM_CA-Qcu_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
index bde28704c5..8829dfb112 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-Qfo
 ./xmlchange PTS_LON=-74.342102
 ./xmlchange PTS_LAT=49.692501
 ./xmlchange DATM_YR_END=2010
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-Qfo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qfo/CLM1PT_data/CTSM_DATM_CA-Qfo_2004-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
index c529507b7e..f227bbb636 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-SF1
 ./xmlchange PTS_LON=-105.817596
-./xmlchange PTS_LAT=54.485001000000004
+./xmlchange PTS_LAT=54.485001
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-SF1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF1/CLM1PT_data/CTSM_DATM_CA-SF1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
index aebfd10bbe..8083656498 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CA-SF2
 ./xmlchange PTS_LON=-105.877502
 ./xmlchange PTS_LAT=54.253899
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-SF2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF2/CLM1PT_data/CTSM_DATM_CA-SF2_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
index bd68572dca..0c48e83347 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-106.00531000000001
+./xmlchange PLUMBER2SITE=CA-SF3
+./xmlchange PTS_LON=-106.00531
 ./xmlchange PTS_LAT=54.091599
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CA-SF3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF3/CLM1PT_data/CTSM_DATM_CA-SF3_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
index d8a0aa59c1..8a769f83ff 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CH-Cha
 ./xmlchange PTS_LON=8.41044
 ./xmlchange PTS_LAT=47.21022
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Cha_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Cha/CLM1PT_data/CTSM_DATM_CH-Cha_2006-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
index 19f4cc5ba0..4a70829314 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CH-Dav
 ./xmlchange PTS_LON=9.85592
 ./xmlchange PTS_LAT=46.815334
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Dav_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Dav/CLM1PT_data/CTSM_DATM_CH-Dav_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
index 291458c54b..706c335415 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CH-Fru
 ./xmlchange PTS_LON=8.53778
 ./xmlchange PTS_LAT=47.115833
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Fru_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Fru/CLM1PT_data/CTSM_DATM_CH-Fru_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
index 964e24d852..7dacd7a573 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CH-Oe1
 ./xmlchange PTS_LON=7.73194
 ./xmlchange PTS_LAT=47.285831
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CH-Oe1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Oe1/CLM1PT_data/CTSM_DATM_CH-Oe1_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
index 8322f1f733..ac02990ed7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=128.09579499999998
+./xmlchange PLUMBER2SITE=CN-Cha
+./xmlchange PTS_LON=128.095795
 ./xmlchange PTS_LAT=42.4025
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Cha_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cha/CLM1PT_data/CTSM_DATM_CN-Cha_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
index dda99e3c4a..6e2582d175 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CN-Cng
 ./xmlchange PTS_LON=123.509201
 ./xmlchange PTS_LAT=44.593399
 ./xmlchange DATM_YR_END=2009
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Cng_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cng/CLM1PT_data/CTSM_DATM_CN-Cng_2008-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
index cdca7d7472..3b9c16a5f4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CN-Dan
 ./xmlchange PTS_LON=91.066399
-./xmlchange PTS_LAT=30.497801000000003
+./xmlchange PTS_LAT=30.497801
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Dan_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Dan/CLM1PT_data/CTSM_DATM_CN-Dan_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
index 19f9baa8eb..f125b585da 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CN-Din
 ./xmlchange PTS_LON=112.536102
 ./xmlchange PTS_LAT=23.1733
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Din_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Din/CLM1PT_data/CTSM_DATM_CN-Din_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
index 5f83542f35..ca85d11837 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CN-Du2
 ./xmlchange PTS_LON=116.2836
 ./xmlchange PTS_LAT=42.0467
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Du2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Du2/CLM1PT_data/CTSM_DATM_CN-Du2_2007-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
index e7a814451d..8c557f6c07 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CN-HaM
 ./xmlchange PTS_LON=101.18
 ./xmlchange PTS_LAT=37.369999
 ./xmlchange DATM_YR_END=2003
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-HaM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-HaM/CLM1PT_data/CTSM_DATM_CN-HaM_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
index a44ff612b4..c0599132ef 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CN-Qia
 ./xmlchange PTS_LON=115.058098
 ./xmlchange PTS_LAT=26.7414
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CN-Qia_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Qia/CLM1PT_data/CTSM_DATM_CN-Qia_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
index d01359e568..d0ee8f1b57 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=CZ-wet
 ./xmlchange PTS_LON=14.77035
 ./xmlchange PTS_LAT=49.024651
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_CZ-wet_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CZ-wet/CLM1PT_data/CTSM_DATM_CZ-wet_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
index cfde80c1de..2a0bb1ed7e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-Bay
 ./xmlchange PTS_LON=11.86694
-./xmlchange PTS_LAT=50.141940999999996
+./xmlchange PTS_LAT=50.141941
 ./xmlchange DATM_YR_END=1999
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Bay_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Bay/CLM1PT_data/CTSM_DATM_DE-Bay_1997-1999.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
index 834a2b3f96..9e42e4029f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-Geb
 ./xmlchange PTS_LON=10.9143
 ./xmlchange PTS_LAT=51.100101
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Geb_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Geb/CLM1PT_data/CTSM_DATM_DE-Geb_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
index 9fe2f16680..5ae694eca6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=13.512529999999998
+./xmlchange PLUMBER2SITE=DE-Gri
+./xmlchange PTS_LON=13.51253
 ./xmlchange PTS_LAT=50.949471
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Gri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Gri/CLM1PT_data/CTSM_DATM_DE-Gri_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
index 83bb6beb10..cfdacd4388 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-Hai
 ./xmlchange PTS_LON=10.453
 ./xmlchange PTS_LAT=51.079166
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Hai_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Hai/CLM1PT_data/CTSM_DATM_DE-Hai_2000-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
index d8a15d9a53..2b4760861f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=13.522379999999998
+./xmlchange PLUMBER2SITE=DE-Kli
+./xmlchange PTS_LON=13.52238
 ./xmlchange PTS_LAT=50.893059
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Kli_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Kli/CLM1PT_data/CTSM_DATM_DE-Kli_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
index 9ffbaf9c34..ace23c6499 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-Meh
 ./xmlchange PTS_LON=10.65547
 ./xmlchange PTS_LAT=51.275311
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Meh_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Meh/CLM1PT_data/CTSM_DATM_DE-Meh_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
index 94afe08f04..81d983ac51 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-Obe
 ./xmlchange PTS_LON=13.72129
 ./xmlchange PTS_LAT=50.786659
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Obe_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Obe/CLM1PT_data/CTSM_DATM_DE-Obe_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
index 2daca0a2c1..99b14107c6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-Seh
 ./xmlchange PTS_LON=6.44965
 ./xmlchange PTS_LAT=50.870625
 ./xmlchange DATM_YR_END=2010
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Seh_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Seh/CLM1PT_data/CTSM_DATM_DE-Seh_2008-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
index 9bdef7293f..70c6009607 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-SfN
 ./xmlchange PTS_LON=11.3275
 ./xmlchange PTS_LAT=47.806389
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-SfN_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-SfN/CLM1PT_data/CTSM_DATM_DE-SfN_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
index e77813eec9..33b2870a58 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=13.566939999999999
+./xmlchange PLUMBER2SITE=DE-Tha
+./xmlchange PTS_LON=13.56694
 ./xmlchange PTS_LAT=50.963612
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Tha_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Tha/CLM1PT_data/CTSM_DATM_DE-Tha_1998-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1998" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
index 7563e5ff7e..947d965270 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DE-Wet
 ./xmlchange PTS_LON=11.45753
 ./xmlchange PTS_LAT=50.453499
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DE-Wet_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Wet/CLM1PT_data/CTSM_DATM_DE-Wet_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
index 06a43e6df6..a34d0eb77a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DK-Fou
 ./xmlchange PTS_LON=9.58722
 ./xmlchange PTS_LAT=56.4842
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Fou_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Fou/CLM1PT_data/CTSM_DATM_DK-Fou_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
index bda3c08df5..06f512c753 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DK-Lva
 ./xmlchange PTS_LON=12.0833
 ./xmlchange PTS_LAT=55.6833
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Lva_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Lva/CLM1PT_data/CTSM_DATM_DK-Lva_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
index 189e9b0ee7..bb2be42089 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DK-Ris
 ./xmlchange PTS_LON=12.09722
 ./xmlchange PTS_LAT=55.530281
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Ris_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Ris/CLM1PT_data/CTSM_DATM_DK-Ris_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
index 2aa6510cd4..efe8c0ad42 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=11.644639999999999
+./xmlchange PLUMBER2SITE=DK-Sor
+./xmlchange PTS_LON=11.64464
 ./xmlchange PTS_LAT=55.48587
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-Sor_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Sor/CLM1PT_data/CTSM_DATM_DK-Sor_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
index 99a0558d7d..cca198c906 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=DK-ZaH
 ./xmlchange PTS_LON=-20.550293
 ./xmlchange PTS_LAT=74.473282
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_DK-ZaH_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-ZaH/CLM1PT_data/CTSM_DATM_DK-ZaH_2000-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
index 10d4e4399d..9cc4725f98 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=ES-ES1
 ./xmlchange PTS_LON=-0.318817
 ./xmlchange PTS_LAT=39.34597
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-ES1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES1/CLM1PT_data/CTSM_DATM_ES-ES1_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
index b72ddf79db..03a6ccf482 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=ES-ES2
 ./xmlchange PTS_LON=-0.315277
-./xmlchange PTS_LAT=39.275558000000004
+./xmlchange PTS_LAT=39.275558
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-ES2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES2/CLM1PT_data/CTSM_DATM_ES-ES2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
index 6d69cfc70b..f36c6be9fc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=ES-LMa
 ./xmlchange PTS_LON=-5.773346
 ./xmlchange PTS_LAT=39.941502
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-LMa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LMa/CLM1PT_data/CTSM_DATM_ES-LMa_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
index 2efa0f5a04..2a701bb99f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=ES-LgS
 ./xmlchange PTS_LON=-2.96582
 ./xmlchange PTS_LAT=37.097935
 ./xmlchange DATM_YR_END=2007
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-LgS_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LgS/CLM1PT_data/CTSM_DATM_ES-LgS_2007-2007.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
index 83d071a6f8..e7971529d9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=ES-VDA
 ./xmlchange PTS_LON=1.4485
 ./xmlchange PTS_LAT=42.15218
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ES-VDA_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-VDA/CLM1PT_data/CTSM_DATM_ES-VDA_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
index 68d5a9739f..7ac714599a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=FI-Hyy
 ./xmlchange PTS_LON=24.295
 ./xmlchange PTS_LAT=61.8475
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Hyy_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Hyy/CLM1PT_data/CTSM_DATM_FI-Hyy_1996-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
index 43852577b1..339a244afa 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=27.295030999999998
+./xmlchange PLUMBER2SITE=FI-Kaa
+./xmlchange PTS_LON=27.295031
 ./xmlchange PTS_LAT=69.140694
 ./xmlchange DATM_YR_END=2002
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Kaa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Kaa/CLM1PT_data/CTSM_DATM_FI-Kaa_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
index c7e01ee357..dea60aca09 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=FI-Lom
 ./xmlchange PTS_LON=24.209181
 ./xmlchange PTS_LAT=67.9972
 ./xmlchange DATM_YR_END=2009
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Lom_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Lom/CLM1PT_data/CTSM_DATM_FI-Lom_2007-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
index ccf011b0e0..08773c8443 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=FI-Sod
 ./xmlchange PTS_LON=26.637831
 ./xmlchange PTS_LAT=67.361862
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FI-Sod_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Sod/CLM1PT_data/CTSM_DATM_FI-Sod_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
index 4af5380bee..550ce300cd 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=2.7801400000000003
-./xmlchange PTS_LAT=48.476397999999996
+./xmlchange PLUMBER2SITE=FR-Fon
+./xmlchange PTS_LON=2.78014
+./xmlchange PTS_LAT=48.476398
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Fon_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Fon/CLM1PT_data/CTSM_DATM_FR-Fon_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
index dae1f22807..169e85a270 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=1.9519099999999998
+./xmlchange PLUMBER2SITE=FR-Gri
+./xmlchange PTS_LON=1.95191
 ./xmlchange PTS_LAT=48.844219
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Gri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Gri/CLM1PT_data/CTSM_DATM_FR-Gri_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
index 00dd5c6771..18a9e57b29 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=7.0655600000000005
+./xmlchange PLUMBER2SITE=FR-Hes
+./xmlchange PTS_LON=7.06556
 ./xmlchange PTS_LAT=48.67416
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Hes_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Hes/CLM1PT_data/CTSM_DATM_FR-Hes_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
index 21f28c8839..ee89868fa1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-0.7692869999999999
+./xmlchange PLUMBER2SITE=FR-LBr
+./xmlchange PTS_LON=-0.769287
 ./xmlchange PTS_LAT=44.71711
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-LBr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-LBr/CLM1PT_data/CTSM_DATM_FR-LBr_2003-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
index 4b8ae400d7..c5025aba8b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=FR-Lq1
 ./xmlchange PTS_LON=2.73583
 ./xmlchange PTS_LAT=45.643059
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Lq1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq1/CLM1PT_data/CTSM_DATM_FR-Lq1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
index 3e56a08786..26581437b9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=FR-Lq2
 ./xmlchange PTS_LON=2.73703
 ./xmlchange PTS_LAT=45.639191
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Lq2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq2/CLM1PT_data/CTSM_DATM_FR-Lq2_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
index 4e4ddac3d5..13fab2f770 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=3.5958300000000003
+./xmlchange PLUMBER2SITE=FR-Pue
+./xmlchange PTS_LON=3.59583
 ./xmlchange PTS_LAT=43.74139
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_FR-Pue_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Pue/CLM1PT_data/CTSM_DATM_FR-Pue_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
index 6a2a814f69..bafc0737b8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=GF-Guy
 ./xmlchange PTS_LON=-52.924866
 ./xmlchange PTS_LAT=5.278772
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_GF-Guy_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/GF-Guy/CLM1PT_data/CTSM_DATM_GF-Guy_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
index 739810dd52..98e5672dc2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=19.601298999999997
+./xmlchange PLUMBER2SITE=HU-Bug
+./xmlchange PTS_LON=19.601299
 ./xmlchange PTS_LAT=46.691101
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_HU-Bug_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/HU-Bug/CLM1PT_data/CTSM_DATM_HU-Bug_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
index e5e190ad1e..a71ecdf659 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=114.03639199999999
+./xmlchange PLUMBER2SITE=ID-Pag
+./xmlchange PTS_LON=114.036392
 ./xmlchange PTS_LAT=-2.345
 ./xmlchange DATM_YR_END=2003
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ID-Pag_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ID-Pag/CLM1PT_data/CTSM_DATM_ID-Pag_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
index e9caca8f04..98d668df9e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IE-Ca1
 ./xmlchange PTS_LON=-6.918152
-./xmlchange PTS_LAT=52.858791000000004
+./xmlchange PTS_LAT=52.858791
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IE-Ca1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Ca1/CLM1PT_data/CTSM_DATM_IE-Ca1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
index bdd48c2331..edb036e775 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-8.751800999999999
+./xmlchange PLUMBER2SITE=IE-Dri
+./xmlchange PTS_LON=-8.751801
 ./xmlchange PTS_LAT=51.986691
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IE-Dri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Dri/CLM1PT_data/CTSM_DATM_IE-Dri_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
index 290836ff22..3a4195c030 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Amp
 ./xmlchange PTS_LON=13.60516
 ./xmlchange PTS_LAT=41.904099
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Amp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Amp/CLM1PT_data/CTSM_DATM_IT-Amp_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
index ae21e12b51..ada711ab6e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-BCi
 ./xmlchange PTS_LON=14.95744
 ./xmlchange PTS_LAT=40.5238
 ./xmlchange DATM_YR_END=2010
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-BCi_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-BCi/CLM1PT_data/CTSM_DATM_IT-BCi_2005-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
index 3fbb828981..9ff3031f4d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-CA1
 ./xmlchange PTS_LON=12.02656
 ./xmlchange PTS_LAT=42.380409
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-CA1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA1/CLM1PT_data/CTSM_DATM_IT-CA1_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
index 18be6fbd02..2041d6983d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-CA2
 ./xmlchange PTS_LON=12.02604
 ./xmlchange PTS_LAT=42.37722
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-CA2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA2/CLM1PT_data/CTSM_DATM_IT-CA2_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
index 46bff2a9e3..50253ccc6b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-CA3
 ./xmlchange PTS_LON=12.0222
 ./xmlchange PTS_LAT=42.380001
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-CA3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA3/CLM1PT_data/CTSM_DATM_IT-CA3_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
index a62cad7d87..06e653c0b9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Col
 ./xmlchange PTS_LON=13.58814
 ./xmlchange PTS_LAT=41.849361
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Col_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Col/CLM1PT_data/CTSM_DATM_IT-Col_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
index 6063242085..b7b1ae449d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Cpz
 ./xmlchange PTS_LON=12.37611
 ./xmlchange PTS_LAT=41.70525
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Cpz_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Cpz/CLM1PT_data/CTSM_DATM_IT-Cpz_2001-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
index 0ae339dba1..873293a7aa 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Isp
 ./xmlchange PTS_LON=8.63358
 ./xmlchange PTS_LAT=45.812641
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Isp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Isp/CLM1PT_data/CTSM_DATM_IT-Isp_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
index 9f683c2101..b8efb6955e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-LMa
 ./xmlchange PTS_LON=7.58259
 ./xmlchange PTS_LAT=45.15258
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-LMa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-LMa/CLM1PT_data/CTSM_DATM_IT-LMa_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
index d1a8669b3e..a50e9dc664 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Lav
 ./xmlchange PTS_LON=11.28132
 ./xmlchange PTS_LAT=45.9562
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Lav_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Lav/CLM1PT_data/CTSM_DATM_IT-Lav_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
index 6b2e4b2651..0c60de60ba 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-MBo
 ./xmlchange PTS_LON=11.04583
 ./xmlchange PTS_LAT=46.014679
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-MBo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-MBo/CLM1PT_data/CTSM_DATM_IT-MBo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
index e6f9ad1c51..34c3d12aa2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=11.703339999999999
+./xmlchange PLUMBER2SITE=IT-Mal
+./xmlchange PTS_LON=11.70334
 ./xmlchange PTS_LAT=46.114021
 ./xmlchange DATM_YR_END=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Mal_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Mal/CLM1PT_data/CTSM_DATM_IT-Mal_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
index eacfbce81e..bd8d0e486c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Noe
 ./xmlchange PTS_LON=8.15117
 ./xmlchange PTS_LAT=40.606178
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Noe_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Noe/CLM1PT_data/CTSM_DATM_IT-Noe_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
index 543dc97221..3084a49d8a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Non
 ./xmlchange PTS_LON=11.09109
-./xmlchange PTS_LAT=44.690189000000004
+./xmlchange PTS_LAT=44.690189
 ./xmlchange DATM_YR_END=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Non_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Non/CLM1PT_data/CTSM_DATM_IT-Non_2002-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
index 23afcb9469..f82e0b8eb9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-PT1
 ./xmlchange PTS_LON=9.06104
 ./xmlchange PTS_LAT=45.200871
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-PT1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-PT1/CLM1PT_data/CTSM_DATM_IT-PT1_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
index 5b6afef969..80927456e8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=11.433689999999999
+./xmlchange PLUMBER2SITE=IT-Ren
+./xmlchange PTS_LON=11.43369
 ./xmlchange PTS_LAT=46.586861
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Ren_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ren/CLM1PT_data/CTSM_DATM_IT-Ren_2010-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
index f74dd07bab..209a0c032d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=11.930010000000001
+./xmlchange PLUMBER2SITE=IT-Ro1
+./xmlchange PTS_LON=11.93001
 ./xmlchange PTS_LAT=42.408119
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Ro1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro1/CLM1PT_data/CTSM_DATM_IT-Ro1_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
index 5d3a64aefb..55e5f4f128 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-Ro2
 ./xmlchange PTS_LON=11.92093
 ./xmlchange PTS_LAT=42.390259
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-Ro2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro2/CLM1PT_data/CTSM_DATM_IT-Ro2_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
index 4cce0bb915..bd1211a9c7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-SR2
 ./xmlchange PTS_LON=10.29095
 ./xmlchange PTS_LAT=43.732029
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-SR2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SR2/CLM1PT_data/CTSM_DATM_IT-SR2_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
index 2f89c5830f..a0aa3f3aa5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=IT-SRo
 ./xmlchange PTS_LON=10.28444
 ./xmlchange PTS_LAT=43.727859
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_IT-SRo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SRo/CLM1PT_data/CTSM_DATM_IT-SRo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
index 287a41b541..17be0e9534 100644
--- a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=137.07879599999998
+./xmlchange PLUMBER2SITE=JP-SMF
+./xmlchange PTS_LON=137.078796
 ./xmlchange PTS_LAT=35.2617
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_JP-SMF_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/JP-SMF/CLM1PT_data/CTSM_DATM_JP-SMF_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
index 7f88121b9b..fd82f6a049 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=NL-Ca1
 ./xmlchange PTS_LON=4.927
 ./xmlchange PTS_LAT=51.971001
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_NL-Ca1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Ca1/CLM1PT_data/CTSM_DATM_NL-Ca1_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
index 6134ec5fd6..e4712093fa 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=NL-Hor
 ./xmlchange PTS_LON=5.0713
 ./xmlchange PTS_LAT=52.240349
 ./xmlchange DATM_YR_END=2011
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_NL-Hor_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Hor/CLM1PT_data/CTSM_DATM_NL-Hor_2008-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
index 82a7f2458c..d825ace2ba 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=5.7435599999999996
-./xmlchange PTS_LAT=52.166579999999996
+./xmlchange PLUMBER2SITE=NL-Loo
+./xmlchange PTS_LON=5.74356
+./xmlchange PTS_LAT=52.16658
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_NL-Loo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Loo/CLM1PT_data/CTSM_DATM_NL-Loo_1997-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
index 394e350a18..80bb1b37c5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=PL-wet
 ./xmlchange PTS_LON=16.309401
 ./xmlchange PTS_LAT=52.762199
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PL-wet_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PL-wet/CLM1PT_data/CTSM_DATM_PL-wet_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
index 1552bd40e8..b56b6968f1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=PT-Esp
 ./xmlchange PTS_LON=-8.601807
 ./xmlchange PTS_LAT=38.6394
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PT-Esp_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Esp/CLM1PT_data/CTSM_DATM_PT-Esp_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
index b8cf3bc26d..2d35f26a06 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=PT-Mi1
 ./xmlchange PTS_LON=-8.000061
 ./xmlchange PTS_LAT=38.540642
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PT-Mi1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi1/CLM1PT_data/CTSM_DATM_PT-Mi1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
index 404492a444..b02616ee02 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=PT-Mi2
 ./xmlchange PTS_LON=-8.024536
 ./xmlchange PTS_LAT=38.476501
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_PT-Mi2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi2/CLM1PT_data/CTSM_DATM_PT-Mi2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
index 6d92902d1f..dff0478e08 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=RU-Che
 ./xmlchange PTS_LON=161.341431
 ./xmlchange PTS_LAT=68.613037
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_RU-Che_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Che/CLM1PT_data/CTSM_DATM_RU-Che_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
index ca0223e1cf..d90a4af0bc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=RU-Fyo
 ./xmlchange PTS_LON=32.922081
-./xmlchange PTS_LAT=56.461529000000006
+./xmlchange PTS_LAT=56.461529
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_RU-Fyo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Fyo/CLM1PT_data/CTSM_DATM_RU-Fyo_2003-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
index 60778a180c..1d42ea947f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=RU-Zot
 ./xmlchange PTS_LON=89.3508
 ./xmlchange PTS_LAT=60.8008
 ./xmlchange DATM_YR_END=2003
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_RU-Zot_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Zot/CLM1PT_data/CTSM_DATM_RU-Zot_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
index 985c3a010b..2b471ebc27 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=SD-Dem
 ./xmlchange PTS_LON=30.4783
 ./xmlchange PTS_LAT=13.2829
 ./xmlchange DATM_YR_END=2009
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_SD-Dem_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SD-Dem/CLM1PT_data/CTSM_DATM_SD-Dem_2005-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
index 1c0165e925..34a53f5533 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=SE-Deg
 ./xmlchange PTS_LON=19.55669
 ./xmlchange PTS_LAT=64.181969
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_SE-Deg_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SE-Deg/CLM1PT_data/CTSM_DATM_SE-Deg_2002-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
index a29eeb03dc..6cd7cb38f4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-3.7980650000000002
+./xmlchange PLUMBER2SITE=UK-Gri
+./xmlchange PTS_LON=-3.798065
 ./xmlchange PTS_LAT=56.60722
 ./xmlchange DATM_YR_END=2001
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_UK-Gri_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Gri/CLM1PT_data/CTSM_DATM_UK-Gri_2000-2001.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
index 178ff627b9..6d83e07c57 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-0.8583069999999999
-./xmlchange PTS_LAT=51.153529999999996
+./xmlchange PLUMBER2SITE=UK-Ham
+./xmlchange PTS_LON=-0.858307
+./xmlchange PTS_LAT=51.15353
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_UK-Ham_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Ham/CLM1PT_data/CTSM_DATM_UK-Ham_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
index d0f256f358..4237f25d27 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-1.2666629999999999
+./xmlchange PLUMBER2SITE=UK-PL3
+./xmlchange PTS_LON=-1.266663
 ./xmlchange PTS_LAT=51.450001
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_UK-PL3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-PL3/CLM1PT_data/CTSM_DATM_UK-PL3_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
index 0bf6cf3313..1f32b6d98c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-AR1
 ./xmlchange PTS_LON=-99.419983
 ./xmlchange PTS_LAT=36.426701
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-AR1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR1/CLM1PT_data/CTSM_DATM_US-AR1_2010-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
index 9751d08038..7e436a547c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-AR2
 ./xmlchange PTS_LON=-99.597504
 ./xmlchange PTS_LAT=36.635799
 ./xmlchange DATM_YR_END=2011
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-AR2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR2/CLM1PT_data/CTSM_DATM_US-AR2_2010-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
index 3e4a6933bc..1a0fd06c8b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-ARM
 ./xmlchange PTS_LON=-97.4888
 ./xmlchange PTS_LAT=36.605801
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-ARM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-ARM/CLM1PT_data/CTSM_DATM_US-ARM_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
index 1c193249b3..9ab42347b2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Aud
 ./xmlchange PTS_LON=-110.509201
 ./xmlchange PTS_LAT=31.5907
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Aud_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Aud/CLM1PT_data/CTSM_DATM_US-Aud_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
index b681aac49d..81591a2454 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-71.28808599999999
-./xmlchange PTS_LAT=44.064640000000004
+./xmlchange PLUMBER2SITE=US-Bar
+./xmlchange PTS_LON=-71.288086
+./xmlchange PTS_LAT=44.06464
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Bar_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bar/CLM1PT_data/CTSM_DATM_US-Bar_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
index a81ec9e93f..91e1976a9f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Bkg
 ./xmlchange PTS_LON=-96.836182
-./xmlchange PTS_LAT=44.345290999999996
+./xmlchange PTS_LAT=44.345291
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Bkg_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bkg/CLM1PT_data/CTSM_DATM_US-Bkg_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
index 0d914e4416..5c09021706 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Blo
 ./xmlchange PTS_LON=-120.632751
 ./xmlchange PTS_LAT=38.895302
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Blo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Blo/CLM1PT_data/CTSM_DATM_US-Blo_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
index f45ebc7076..49c70e98da 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Bo1
 ./xmlchange PTS_LON=-88.290405
 ./xmlchange PTS_LAT=40.006199
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Bo1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bo1/CLM1PT_data/CTSM_DATM_US-Bo1_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
index 0ce199dd44..fc6a4841a9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Cop
 ./xmlchange PTS_LON=-109.389999
 ./xmlchange PTS_LAT=38.09
 ./xmlchange DATM_YR_END=2003
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Cop_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Cop/CLM1PT_data/CTSM_DATM_US-Cop_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
index 1f6c1a2438..2299cbf103 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-105.10189799999999
+./xmlchange PLUMBER2SITE=US-FPe
+./xmlchange PTS_LON=-105.101898
 ./xmlchange PTS_LAT=48.307701
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-FPe_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-FPe/CLM1PT_data/CTSM_DATM_US-FPe_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
index 59ae899a7e..794d0584a2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-GLE
 ./xmlchange PTS_LON=-106.239899
 ./xmlchange PTS_LAT=41.366501
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-GLE_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-GLE/CLM1PT_data/CTSM_DATM_US-GLE_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
index 9a0d84e815..6cc34f40c2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-89.87350500000001
+./xmlchange PLUMBER2SITE=US-Goo
+./xmlchange PTS_LON=-89.873505
 ./xmlchange PTS_LAT=34.2547
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Goo_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Goo/CLM1PT_data/CTSM_DATM_US-Goo_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
index 0687c4cd3d..a016985d76 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Ha1
 ./xmlchange PTS_LON=-72.171509
 ./xmlchange PTS_LAT=42.5378
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ha1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ha1/CLM1PT_data/CTSM_DATM_US-Ha1_1992-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1992" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
index a0d98032eb..c36889758d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Ho1
 ./xmlchange PTS_LON=-68.740204
 ./xmlchange PTS_LAT=45.204102
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ho1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ho1/CLM1PT_data/CTSM_DATM_US-Ho1_1996-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
index 02d26509c2..fc3ab78d4f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-KS2
 ./xmlchange PTS_LON=-80.671539
 ./xmlchange PTS_LAT=28.608578
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-KS2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-KS2/CLM1PT_data/CTSM_DATM_US-KS2_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
index 13ef4e69b4..d0ee0a8b7d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Los
 ./xmlchange PTS_LON=-89.979187
 ./xmlchange PTS_LAT=46.082699
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Los_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Los/CLM1PT_data/CTSM_DATM_US-Los_2000-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
index 8a271026dd..12362f6d77 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-86.41308599999999
+./xmlchange PLUMBER2SITE=US-MMS
+./xmlchange PTS_LON=-86.413086
 ./xmlchange PTS_LAT=39.3232
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-MMS_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MMS/CLM1PT_data/CTSM_DATM_US-MMS_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
index a98dae73c4..a332c04808 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-MOz
 ./xmlchange PTS_LON=-92.200012
 ./xmlchange PTS_LAT=38.74411
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-MOz_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MOz/CLM1PT_data/CTSM_DATM_US-MOz_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
index dc020bf1d1..97c8a61316 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Me2
 ./xmlchange PTS_LON=-121.557404
 ./xmlchange PTS_LAT=44.452301
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Me2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me2/CLM1PT_data/CTSM_DATM_US-Me2_2002-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
index 77d787c3d4..eef9074dfe 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-121.62240600000001
+./xmlchange PLUMBER2SITE=US-Me4
+./xmlchange PTS_LON=-121.622406
 ./xmlchange PTS_LAT=44.499199
 ./xmlchange DATM_YR_END=2000
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Me4_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me4/CLM1PT_data/CTSM_DATM_US-Me4_1996-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
index 389ef600e5..7591643f86 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Me6
 ./xmlchange PTS_LON=-121.607803
 ./xmlchange PTS_LAT=44.323299
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Me6_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me6/CLM1PT_data/CTSM_DATM_US-Me6_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
index 6cc05da64f..66e97faf89 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Myb
 ./xmlchange PTS_LON=-121.765106
 ./xmlchange PTS_LAT=38.049801
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Myb_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Myb/CLM1PT_data/CTSM_DATM_US-Myb_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
index 773ca669b1..6ccba5ae4e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-NR1
 ./xmlchange PTS_LON=-105.546402
 ./xmlchange PTS_LAT=40.032902
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-NR1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-NR1/CLM1PT_data/CTSM_DATM_US-NR1_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
index f2adadd3ac..54bbcbe8de 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-96.47659300000001
+./xmlchange PLUMBER2SITE=US-Ne1
+./xmlchange PTS_LON=-96.476593
 ./xmlchange PTS_LAT=41.1651
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ne1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne1/CLM1PT_data/CTSM_DATM_US-Ne1_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
index 15ed24bdee..0587fd1932 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Ne2
 ./xmlchange PTS_LON=-96.470093
-./xmlchange PTS_LAT=41.164902000000005
+./xmlchange PTS_LAT=41.164902
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ne2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne2/CLM1PT_data/CTSM_DATM_US-Ne2_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
index 631bf243e4..66bcf6d25d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Ne3
 ./xmlchange PTS_LON=-96.439697
 ./xmlchange PTS_LAT=41.179699
 ./xmlchange DATM_YR_END=2012
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ne3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne3/CLM1PT_data/CTSM_DATM_US-Ne3_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
index dd400a9257..76bfb84b9f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-PFa
 ./xmlchange PTS_LON=-90.272308
 ./xmlchange PTS_LAT=45.9459
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-PFa_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-PFa/CLM1PT_data/CTSM_DATM_US-PFa_1995-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1995" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
index 28acc5f402..f3c9e49740 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Prr
 ./xmlchange PTS_LON=-147.487595
 ./xmlchange PTS_LAT=65.123703
 ./xmlchange DATM_YR_END=2013
 ./xmlchange START_TOD=32400
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Prr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Prr/CLM1PT_data/CTSM_DATM_US-Prr_2011-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
index 37e05304a8..a10cb0956a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-SP1
 ./xmlchange PTS_LON=-82.218781
 ./xmlchange PTS_LAT=29.73807
 ./xmlchange DATM_YR_END=2005
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SP1_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP1/CLM1PT_data/CTSM_DATM_US-SP1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
index a4ea7a35ac..7b7a589af4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-SP2
 ./xmlchange PTS_LON=-82.244812
 ./xmlchange PTS_LAT=29.764799
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SP2_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP2/CLM1PT_data/CTSM_DATM_US-SP2_2000-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
index 76c00c8a36..882c94c80f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-SP3
 ./xmlchange PTS_LON=-82.163269
 ./xmlchange PTS_LAT=29.75477
 ./xmlchange DATM_YR_END=2004
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SP3_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP3/CLM1PT_data/CTSM_DATM_US-SP3_1999-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
index 804a5f9884..7fea8792e6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-SRG
 ./xmlchange PTS_LON=-110.827698
 ./xmlchange PTS_LAT=31.7894
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SRG_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRG/CLM1PT_data/CTSM_DATM_US-SRG_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
index 9b379b1edb..3ba018a2b1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-SRM
 ./xmlchange PTS_LON=-110.865997
 ./xmlchange PTS_LAT=31.8214
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-SRM_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRM/CLM1PT_data/CTSM_DATM_US-SRM_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
index 0fe6c91305..636e532f38 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Syv
 ./xmlchange PTS_LON=-89.347717
 ./xmlchange PTS_LAT=46.242001
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Syv_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Syv/CLM1PT_data/CTSM_DATM_US-Syv_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
index e97bac9028..497385372e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Ton
 ./xmlchange PTS_LON=-120.966003
 ./xmlchange PTS_LAT=38.431599
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Ton_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ton/CLM1PT_data/CTSM_DATM_US-Ton_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
index 49ad7cddd2..f212f4bc0f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Tw4
 ./xmlchange PTS_LON=-121.641403
 ./xmlchange PTS_LAT=38.103001
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Tw4_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Tw4/CLM1PT_data/CTSM_DATM_US-Tw4_2014-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
index 447906c4fc..74035ea108 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Twt
 ./xmlchange PTS_LON=-121.653107
 ./xmlchange PTS_LAT=38.1087
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Twt_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Twt/CLM1PT_data/CTSM_DATM_US-Twt_2010-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
index 1b3ee51b17..08f9f17a5a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-UMB
 ./xmlchange PTS_LON=-84.713806
 ./xmlchange PTS_LAT=45.559799
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-UMB_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-UMB/CLM1PT_data/CTSM_DATM_US-UMB_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
index 099e07e301..e997931652 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
@@ -1,10 +1,10 @@
-./xmlchange PTS_LON=-120.95072900000001
+./xmlchange PLUMBER2SITE=US-Var
+./xmlchange PTS_LON=-120.950729
 ./xmlchange PTS_LAT=38.4133
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Var_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Var/CLM1PT_data/CTSM_DATM_US-Var_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
index de5a646543..55647b78c0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-WCr
 ./xmlchange PTS_LON=-90.079895
 ./xmlchange PTS_LAT=45.805901
 ./xmlchange DATM_YR_END=2006
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-WCr_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-WCr/CLM1PT_data/CTSM_DATM_US-WCr_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
index f706a2e79a..51fadcc9f6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Whs
 ./xmlchange PTS_LON=-110.0522
 ./xmlchange PTS_LAT=31.743799
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Whs_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Whs/CLM1PT_data/CTSM_DATM_US-Whs_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
index 0fc65819c2..5d95ef3e36 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=US-Wkg
 ./xmlchange PTS_LON=-109.941895
 ./xmlchange PTS_LAT=31.7365
 ./xmlchange DATM_YR_END=2014
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_US-Wkg_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Wkg/CLM1PT_data/CTSM_DATM_US-Wkg_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
index 7c2dfed5c9..6fe9e9c989 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=ZA-Kru
 ./xmlchange PTS_LON=31.496901
 ./xmlchange PTS_LAT=-25.019699
 ./xmlchange DATM_YR_END=2002
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ZA-Kru_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZA-Kru/CLM1PT_data/CTSM_DATM_ZA-Kru_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
index 825675dc9b..ff19816490 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
@@ -1,10 +1,10 @@
+./xmlchange PLUMBER2SITE=ZM-Mon
 ./xmlchange PTS_LON=23.252781
 ./xmlchange PTS_LAT=-15.437778
 ./xmlchange DATM_YR_END=2008
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "fsurdat='\$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_ZM-Mon_hist_2000_16pfts_c240326.nc'  " >> user_nl_clm 
 echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZM-Mon/CLM1PT_data/CTSM_DATM_ZM-Mon_2008-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 

From 6f8c4d779fd320cdf06df9c337e8e1125d544049 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Fri, 28 Jun 2024 16:13:27 -0600
Subject: [PATCH 0931/1248] reformatting pt2

---
 python/ctsm/site_and_regional/plumber2_usermods.py | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/python/ctsm/site_and_regional/plumber2_usermods.py b/python/ctsm/site_and_regional/plumber2_usermods.py
index 2fe183fb77..0a083e1dd7 100644
--- a/python/ctsm/site_and_regional/plumber2_usermods.py
+++ b/python/ctsm/site_and_regional/plumber2_usermods.py
@@ -58,13 +58,7 @@ def write_usermods(
         "./xmlchange DATM_YR_END=" + str(end_year) + "\n"
         "./xmlchange START_TOD=" + str(start_tod) + "\n"
         "./xmlchange ATM_NCPL=" + str(atm_ncpl) + "\n"
-        "\n"  # TODO, get working for CTSM5.1:
-        # remove the above line as it's redundant after PLUMBER2SITE is added
-        # Alternatively, we can take this out of default/user_nl_clm
-        # since doing it this way is works fine TODO for 5.2
-        "echo \"fsurdat='/glade/u/home/wwieder/CTSM/tools/site_and_regional/subset_data_single_point/surfdata_1x1_PLUMBER2_"
-        + site
-        + "_hist_16pfts_Irrig_CMIP6_simyr2000_c231005.nc ' \" >> user_nl_clm \n"
+        "\n"
         'echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/'
         + site
         + "/CLM1PT_data/CTSM_DATM_"

From da6e20615435ee4108f9cab6803bf7161afcf6a0 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Tue, 2 Jul 2024 12:05:33 -0600
Subject: [PATCH 0932/1248] fix for plumber file formats

---
 cime_config/buildnml | 44 ++++++++++++++++++++++++++++----------------
 1 file changed, 28 insertions(+), 16 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index acc74868e0..7d3e2b4770 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,7 +182,9 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_path = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -224,16 +226,22 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if ("NEON" in clm_usrdat_name) or ("PLUMBER" in clm_usrdat_name):
-            if clm_force_coldstart == "off":
-                if ("_transient" in clm_nml_use_case) and (
-                    re.fullmatch(r"\w\w\w\w\.transient", casename) is None
-                    or clm_usrdat_name is "NEON.PRISM"
-                ):
-                    logger.warning(
-                        "WARNING: Do you have appropriate initial conditions for this simulation?"
-                        + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
-                    )
+        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
+            if ("_transient" in clm_nml_use_case) and (
+                re.fullmatch(r"\w\w\w\w\.transient", casename) is None
+            ):
+                logger.warning(
+                    "WARNING: Do you have appropriate initial conditions for this simulation?"
+                    + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
+                )
+        if "PLUMBER" in clm_usrdat_name and clm_force_coldstart == "off":
+            if ("_transient" in clm_nml_use_case) and (
+                re.fullmatch(r"\w\w-\w\w\w\.transient", casename) is None
+            ):
+                logger.warning(
+                    "WARNING: Do you have appropriate initial conditions for this simulation?"
+                    + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
+                )
 
     if comp_atm != "datm":
         nomeg = "-no-megan"
@@ -302,7 +310,9 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_file = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
 
     # -----------------------------------------------------
     # Clear out old data
@@ -317,7 +327,6 @@ def buildnml(case, caseroot, compname):
 
     ninst = int(ninst_lnd)
     for inst_counter in range(1, ninst + 1):
-
         # determine instance string
         inst_string = ""
         if ninst > 1:
@@ -365,7 +374,9 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
+                logger.warning(
+                    "WARNING: Could NOT find a start file to use using" + clm_startfile
+                )
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -376,7 +387,9 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
+        create_namelist_infile(
+            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
+        )
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 
@@ -439,7 +452,6 @@ def buildnml(case, caseroot, compname):
 
 ###############################################################################
 def _main_func():
-
     caseroot = parse_input(sys.argv)
     with Case(caseroot) as case:
         compname = case.get_value("COMP_LND")

From 926299cf96270f17175c6649165a9d1985f755f6 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Tue, 2 Jul 2024 12:09:37 -0600
Subject: [PATCH 0933/1248] fix black issue and neon.prism clm_usrdat_name

---
 cime_config/buildnml | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 7d3e2b4770..370291fa70 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,9 +182,7 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml" )
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -229,6 +227,7 @@ def buildnml(case, caseroot, compname):
         if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w\w\w\.transient", casename) is None
+                or clm_usrdat_name is "NEON.PRISM"
             ):
                 logger.warning(
                     "WARNING: Do you have appropriate initial conditions for this simulation?"
@@ -310,9 +309,7 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
 
     # -----------------------------------------------------
     # Clear out old data
@@ -374,9 +371,7 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning(
-                    "WARNING: Could NOT find a start file to use using" + clm_startfile
-                )
+                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -387,9 +382,7 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(
-            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
-        )
+        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From f6a0749845f612b55301ecdc93dc0823d506a929 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Tue, 2 Jul 2024 12:49:50 -0600
Subject: [PATCH 0934/1248] revert everything else to pre-black-fail

---
 cime_config/buildnml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 370291fa70..539be911e6 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -182,7 +182,7 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml" )
+    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -324,6 +324,7 @@ def buildnml(case, caseroot, compname):
 
     ninst = int(ninst_lnd)
     for inst_counter in range(1, ninst + 1):
+
         # determine instance string
         inst_string = ""
         if ninst > 1:
@@ -445,6 +446,7 @@ def buildnml(case, caseroot, compname):
 
 ###############################################################################
 def _main_func():
+
     caseroot = parse_input(sys.argv)
     with Case(caseroot) as case:
         compname = case.get_value("COMP_LND")

From 1548af3bdca0e23de641feffbed59b6094737e37 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Tue, 30 Jul 2024 14:25:11 -0600
Subject: [PATCH 0935/1248] Update buildnml PLUMBER --> PLUMBER2

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 539be911e6..46812602df 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -233,7 +233,7 @@ def buildnml(case, caseroot, compname):
                     "WARNING: Do you have appropriate initial conditions for this simulation?"
                     + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
                 )
-        if "PLUMBER" in clm_usrdat_name and clm_force_coldstart == "off":
+        if "PLUMBER2" in clm_usrdat_name and clm_force_coldstart == "off":
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"\w\w-\w\w\w\.transient", casename) is None
             ):

From e9e7eaf37582cf10dee394f4dbd3a7e1ba592883 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 7 Aug 2024 10:53:15 -0600
Subject: [PATCH 0936/1248] typo fix in config_component.xml

---
 cime_config/config_component.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 1fc7a3a3a1..3951356df9 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -356,7 +356,7 @@
       cold start (finidat will be set to blanks).
       A value of on forces the model to spin up from a cold-start
       (arbitrary initial conditions). Setting this value in the xml file will take
-      precedence over any settings for finidat in the $CASEROOT/user_nl_ctsm file.</desc>
+      precedence over any settings for finidat in the $CASEROOT/user_nl_clm file.</desc>
   </entry>
 
   <entry id="CLM_USER_MODS">

From c8447b8acb8c13472f49d46aae8d07133cc3496f Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Thu, 8 Aug 2024 12:04:49 -0600
Subject: [PATCH 0937/1248] Update plumber2_usermods.py to include new xml var
 and remove additional stream that is now in cdeps

---
 python/ctsm/site_and_regional/plumber2_usermods.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/python/ctsm/site_and_regional/plumber2_usermods.py b/python/ctsm/site_and_regional/plumber2_usermods.py
index 0a083e1dd7..d98899771b 100644
--- a/python/ctsm/site_and_regional/plumber2_usermods.py
+++ b/python/ctsm/site_and_regional/plumber2_usermods.py
@@ -56,18 +56,10 @@ def write_usermods(
         "./xmlchange PTS_LON=" + str(lon) + "\n"
         "./xmlchange PTS_LAT=" + str(lat) + "\n"
         "./xmlchange DATM_YR_END=" + str(end_year) + "\n"
+        "./xmlchange DATM_YR_START_FILENAME=" + str(start_year) + "\n"
         "./xmlchange START_TOD=" + str(start_tod) + "\n"
         "./xmlchange ATM_NCPL=" + str(atm_ncpl) + "\n"
         "\n"
-        'echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/'
-        + site
-        + "/CLM1PT_data/CTSM_DATM_"
-        + site
-        + "_"
-        + str(start_year)
-        + "-"
-        + str(end_year)
-        + '.nc " >> user_nl_datm_streams \n'
         'echo "presaero.SSP3-7.0:year_first=' + str(start_year) + '" >> user_nl_datm_streams \n'
         'echo "presaero.SSP3-7.0:year_last=' + str(end_year) + '" >> user_nl_datm_streams \n'
         'echo "presaero.SSP3-7.0:year_align=' + str(start_year) + '" >> user_nl_datm_streams \n'

From 43f8aeefc0bff8e4cae2ac0a58f510f48fd50bf6 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Thu, 8 Aug 2024 12:05:54 -0600
Subject: [PATCH 0938/1248] fix typo in buildnml

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 46812602df..893f0933c7 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -372,7 +372,7 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile)
+                logger.warning("WARNING: Could NOT find a start file named" + clm_startfile)
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""

From dc6773742b7f0ca30ecf90478fd98e7419d06730 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 8 Aug 2024 12:15:41 -0600
Subject: [PATCH 0939/1248] updated shell commands with new xml var and file
 moved to cdeps

---
 cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands | 2 +-
 cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands | 2 +-
 170 files changed, 170 insertions(+), 170 deletions(-)

diff --git a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
index d7f8707812..f297937768 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-66.459808
 ./xmlchange PTS_LAT=-33.464802
 ./xmlchange DATM_YR_END=2010
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AR-SLu/CLM1PT_data/CTSM_DATM_AR-SLu_2010-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
index dc0750224f..319c52a95d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.3175
 ./xmlchange PTS_LAT=47.116669
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AT-Neu/CLM1PT_data/CTSM_DATM_AT-Neu_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
index f3eae9a24e..afadee1c1e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=133.248993
 ./xmlchange PTS_LAT=-22.283001
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-ASM/CLM1PT_data/CTSM_DATM_AU-ASM_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
index 9e44c8232c..40187f1b46 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=145.427155
 ./xmlchange PTS_LAT=-16.23819
 ./xmlchange DATM_YR_END=2015
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cow/CLM1PT_data/CTSM_DATM_AU-Cow_2010-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
index 114544e9b5..fc3b037ecc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=140.589127
 ./xmlchange PTS_LAT=-34.00206
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cpr/CLM1PT_data/CTSM_DATM_AU-Cpr_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
index 7af2976c83..6710134c78 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=145.446854
 ./xmlchange PTS_LAT=-16.103279
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ctr/CLM1PT_data/CTSM_DATM_AU-Ctr_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
index 8c75b3de45..a2022818c6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=150.722473
 ./xmlchange PTS_LAT=-33.613297
 ./xmlchange DATM_YR_END=2018
+./xmlchange DATM_YR_START_FILENAME=2013
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Cum/CLM1PT_data/CTSM_DATM_AU-Cum_2013-2018.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2018" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
index 44171b3425..28b5b4b446 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=131.3181
 ./xmlchange PTS_LAT=-14.0633
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2009
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaP/CLM1PT_data/CTSM_DATM_AU-DaP_2009-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
index 699b74900a..96acb7b7cf 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=131.388
 ./xmlchange PTS_LAT=-14.159283
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-DaS/CLM1PT_data/CTSM_DATM_AU-DaS_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
index a2a4686230..da520bb88e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=132.370605
 ./xmlchange PTS_LAT=-15.2588
 ./xmlchange DATM_YR_END=2015
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Dry/CLM1PT_data/CTSM_DATM_AU-Dry_2011-2015.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2015" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
index 7d9d557087..a5ccf45884 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=148.474594
 ./xmlchange PTS_LAT=-23.8587
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2012
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Emr/CLM1PT_data/CTSM_DATM_AU-Emr_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
index 26bd398dc1..637c921fae 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=120.654099
 ./xmlchange PTS_LAT=-30.191299
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2013
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-GWW/CLM1PT_data/CTSM_DATM_AU-GWW_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
index 61d3c3eb01..e02f3482ed 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=115.650002
 ./xmlchange PTS_LAT=-31.375
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2012
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Gin/CLM1PT_data/CTSM_DATM_AU-Gin_2012-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
index 7cac687aa3..448f24cc4f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=131.149994
 ./xmlchange PTS_LAT=-12.4952
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-How/CLM1PT_data/CTSM_DATM_AU-How_2003-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
index 7f1a885344..6e69bbc5d2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=130.794495
 ./xmlchange PTS_LAT=-13.17904
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2016
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Lit/CLM1PT_data/CTSM_DATM_AU-Lit_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
index 4016a12e52..c3962c1b33 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=142.816803
 ./xmlchange PTS_LAT=-38.532341
 ./xmlchange DATM_YR_END=2010
+./xmlchange DATM_YR_START_FILENAME=2009
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Otw/CLM1PT_data/CTSM_DATM_AU-Otw_2009-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
index 193f3cc5dd..fc5ecba950 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=145.575897
 ./xmlchange PTS_LAT=-36.649899
 ./xmlchange DATM_YR_END=2016
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rig/CLM1PT_data/CTSM_DATM_AU-Rig_2011-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
index f7f4921746..6e640a50fa 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=145.630096
 ./xmlchange PTS_LAT=-17.1175
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2014
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Rob/CLM1PT_data/CTSM_DATM_AU-Rob_2014-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
index d1dae3a306..1f48d3060f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=152.877808
 ./xmlchange PTS_LAT=-27.3881
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=50400
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Sam/CLM1PT_data/CTSM_DATM_AU-Sam_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
index d0e4cdf638..949257e09f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=133.350204
 ./xmlchange PTS_LAT=-17.1507
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Stp/CLM1PT_data/CTSM_DATM_AU-Stp_2010-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
index 3c878a3ae9..ca7b84c598 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=133.639999
 ./xmlchange PTS_LAT=-22.287001
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2013
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-TTE/CLM1PT_data/CTSM_DATM_AU-TTE_2013-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
index 8e01ca6869..5ad2d9dce2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=148.151703
 ./xmlchange PTS_LAT=-35.656601
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Tum/CLM1PT_data/CTSM_DATM_AU-Tum_2002-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
index 5bde37cdc7..250e8f049e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=145.029404
 ./xmlchange PTS_LAT=-36.673199
 ./xmlchange DATM_YR_END=2016
+./xmlchange DATM_YR_START_FILENAME=2015
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Whr/CLM1PT_data/CTSM_DATM_AU-Whr_2015-2016.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2015" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2015" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
index 76311551ed..c96c57a93f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=146.654495
 ./xmlchange PTS_LAT=-43.09502
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2016
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Wrr/CLM1PT_data/CTSM_DATM_AU-Wrr_2016-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2016" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2016" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
index e7c1c495fc..cc5b8909d7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=146.290695
 ./xmlchange PTS_LAT=-34.9893
 ./xmlchange DATM_YR_END=2017
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/AU-Ync/CLM1PT_data/CTSM_DATM_AU-Ync_2011-2017.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2017" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
index 4cb0c5af5c..93bf56051e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=4.52056
 ./xmlchange PTS_LAT=51.309166
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Bra/CLM1PT_data/CTSM_DATM_BE-Bra_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
index 5ce5a904f5..597961e426 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=4.74613
 ./xmlchange PTS_LAT=50.55159
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Lon/CLM1PT_data/CTSM_DATM_BE-Lon_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
index 0e4e802d91..2a97262b87 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=5.99805
 ./xmlchange PTS_LAT=50.305069
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1997
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BE-Vie/CLM1PT_data/CTSM_DATM_BE-Vie_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1997" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
index 114becfc06..ec8d9bc33a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-54.971436
 ./xmlchange PTS_LAT=-3.018029
 ./xmlchange DATM_YR_END=2003
+./xmlchange DATM_YR_START_FILENAME=2001
 ./xmlchange START_TOD=14400
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BR-Sa3/CLM1PT_data/CTSM_DATM_BR-Sa3_2001-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
index 7d0681f988..64af7dc90f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=23.560329
 ./xmlchange PTS_LAT=-19.9165
 ./xmlchange DATM_YR_END=2000
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/BW-Ma1/CLM1PT_data/CTSM_DATM_BW-Ma1_2000-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
index 47f8762dca..9b4f8d74ec 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-98.483887
 ./xmlchange PTS_LAT=55.8792
 ./xmlchange DATM_YR_END=2003
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS1/CLM1PT_data/CTSM_DATM_CA-NS1_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
index c787c85af0..5563971afc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-98.524689
 ./xmlchange PTS_LAT=55.9058
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS2/CLM1PT_data/CTSM_DATM_CA-NS2_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
index 5e4247d5ee..d6ddd551af 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-98.380615
 ./xmlchange PTS_LAT=55.914398
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS4/CLM1PT_data/CTSM_DATM_CA-NS4_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
index bddbef5bb3..49a320a37d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-98.484985
 ./xmlchange PTS_LAT=55.863098
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS5/CLM1PT_data/CTSM_DATM_CA-NS5_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
index 908a798b98..c5097e87ec 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-98.964417
 ./xmlchange PTS_LAT=55.916698
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS6/CLM1PT_data/CTSM_DATM_CA-NS6_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
index 5734053c2b..583c102ae0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-99.948303
 ./xmlchange PTS_LAT=56.635799
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-NS7/CLM1PT_data/CTSM_DATM_CA-NS7_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
index b68de255cb..892029da56 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-74.03653
 ./xmlchange PTS_LAT=49.267078
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qcu/CLM1PT_data/CTSM_DATM_CA-Qcu_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
index 8829dfb112..3f61fbd901 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-74.342102
 ./xmlchange PTS_LAT=49.692501
 ./xmlchange DATM_YR_END=2010
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-Qfo/CLM1PT_data/CTSM_DATM_CA-Qfo_2004-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
index f227bbb636..49de04986c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-105.817596
 ./xmlchange PTS_LAT=54.485001
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF1/CLM1PT_data/CTSM_DATM_CA-SF1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
index 8083656498..5cc0da8be1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-105.877502
 ./xmlchange PTS_LAT=54.253899
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF2/CLM1PT_data/CTSM_DATM_CA-SF2_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
index 0c48e83347..3f94c02ca9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-106.00531
 ./xmlchange PTS_LAT=54.091599
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CA-SF3/CLM1PT_data/CTSM_DATM_CA-SF3_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
index 8a769f83ff..ca0ad87518 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=8.41044
 ./xmlchange PTS_LAT=47.21022
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2006
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Cha/CLM1PT_data/CTSM_DATM_CH-Cha_2006-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2006" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
index 4a70829314..254c30865a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=9.85592
 ./xmlchange PTS_LAT=46.815334
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1997
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Dav/CLM1PT_data/CTSM_DATM_CH-Dav_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1997" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
index 706c335415..617ed84d7c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=8.53778
 ./xmlchange PTS_LAT=47.115833
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2007
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Fru/CLM1PT_data/CTSM_DATM_CH-Fru_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
index 7dacd7a573..6fb4f3a844 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=7.73194
 ./xmlchange PTS_LAT=47.285831
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CH-Oe1/CLM1PT_data/CTSM_DATM_CH-Oe1_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
index ac02990ed7..f6da50bde1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=128.095795
 ./xmlchange PTS_LAT=42.4025
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cha/CLM1PT_data/CTSM_DATM_CN-Cha_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
index 6e2582d175..648c844408 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=123.509201
 ./xmlchange PTS_LAT=44.593399
 ./xmlchange DATM_YR_END=2009
+./xmlchange DATM_YR_START_FILENAME=2008
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Cng/CLM1PT_data/CTSM_DATM_CN-Cng_2008-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
index 3b9c16a5f4..9616c9d792 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=91.066399
 ./xmlchange PTS_LAT=30.497801
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Dan/CLM1PT_data/CTSM_DATM_CN-Dan_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
index f125b585da..c30e651178 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=112.536102
 ./xmlchange PTS_LAT=23.1733
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Din/CLM1PT_data/CTSM_DATM_CN-Din_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
index ca85d11837..d46dec7f7d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=116.2836
 ./xmlchange PTS_LAT=42.0467
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2007
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Du2/CLM1PT_data/CTSM_DATM_CN-Du2_2007-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
index 8c557f6c07..91d489b75b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=101.18
 ./xmlchange PTS_LAT=37.369999
 ./xmlchange DATM_YR_END=2003
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-HaM/CLM1PT_data/CTSM_DATM_CN-HaM_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
index c0599132ef..484175aa93 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=115.058098
 ./xmlchange PTS_LAT=26.7414
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=57600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CN-Qia/CLM1PT_data/CTSM_DATM_CN-Qia_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
index d0ee8f1b57..7c753c4183 100644
--- a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=14.77035
 ./xmlchange PTS_LAT=49.024651
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2007
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/CZ-wet/CLM1PT_data/CTSM_DATM_CZ-wet_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
index 2a0bb1ed7e..55c14aac5f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.86694
 ./xmlchange PTS_LAT=50.141941
 ./xmlchange DATM_YR_END=1999
+./xmlchange DATM_YR_START_FILENAME=1997
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Bay/CLM1PT_data/CTSM_DATM_DE-Bay_1997-1999.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1997" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
index 9e42e4029f..d57138be71 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=10.9143
 ./xmlchange PTS_LAT=51.100101
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2001
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Geb/CLM1PT_data/CTSM_DATM_DE-Geb_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
index 5ae694eca6..5a27ee5e20 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=13.51253
 ./xmlchange PTS_LAT=50.949471
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Gri/CLM1PT_data/CTSM_DATM_DE-Gri_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
index cfdacd4388..55124b7900 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=10.453
 ./xmlchange PTS_LAT=51.079166
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Hai/CLM1PT_data/CTSM_DATM_DE-Hai_2000-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
index 2b4760861f..860b100586 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=13.52238
 ./xmlchange PTS_LAT=50.893059
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Kli/CLM1PT_data/CTSM_DATM_DE-Kli_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
index ace23c6499..b94a90e206 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=10.65547
 ./xmlchange PTS_LAT=51.275311
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Meh/CLM1PT_data/CTSM_DATM_DE-Meh_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
index 81d983ac51..e633f65987 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=13.72129
 ./xmlchange PTS_LAT=50.786659
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2008
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Obe/CLM1PT_data/CTSM_DATM_DE-Obe_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
index 99b14107c6..c6808b0bf1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=6.44965
 ./xmlchange PTS_LAT=50.870625
 ./xmlchange DATM_YR_END=2010
+./xmlchange DATM_YR_START_FILENAME=2008
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Seh/CLM1PT_data/CTSM_DATM_DE-Seh_2008-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
index 70c6009607..639a2c5195 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.3275
 ./xmlchange PTS_LAT=47.806389
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-SfN/CLM1PT_data/CTSM_DATM_DE-SfN_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
index 33b2870a58..66055b2ee2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=13.56694
 ./xmlchange PTS_LAT=50.963612
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1998
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Tha/CLM1PT_data/CTSM_DATM_DE-Tha_1998-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1998" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1998" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
index 947d965270..de0ad17a95 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.45753
 ./xmlchange PTS_LAT=50.453499
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DE-Wet/CLM1PT_data/CTSM_DATM_DE-Wet_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
index a34d0eb77a..581fd31324 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=9.58722
 ./xmlchange PTS_LAT=56.4842
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Fou/CLM1PT_data/CTSM_DATM_DK-Fou_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
index 06f512c753..b1a1955519 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=12.0833
 ./xmlchange PTS_LAT=55.6833
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Lva/CLM1PT_data/CTSM_DATM_DK-Lva_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
index bb2be42089..86fcb0ba10 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=12.09722
 ./xmlchange PTS_LAT=55.530281
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Ris/CLM1PT_data/CTSM_DATM_DK-Ris_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
index efe8c0ad42..046e9559d2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.64464
 ./xmlchange PTS_LAT=55.48587
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1997
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-Sor/CLM1PT_data/CTSM_DATM_DK-Sor_1997-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1997" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
index cca198c906..234c5e8ba7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-20.550293
 ./xmlchange PTS_LAT=74.473282
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/DK-ZaH/CLM1PT_data/CTSM_DATM_DK-ZaH_2000-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
index 9cc4725f98..9947bb0014 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-0.318817
 ./xmlchange PTS_LAT=39.34597
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=1999
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES1/CLM1PT_data/CTSM_DATM_ES-ES1_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
index 03a6ccf482..235ddfbb32 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-0.315277
 ./xmlchange PTS_LAT=39.275558
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-ES2/CLM1PT_data/CTSM_DATM_ES-ES2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
index f36c6be9fc..c0c83dbbd2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-5.773346
 ./xmlchange PTS_LAT=39.941502
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LMa/CLM1PT_data/CTSM_DATM_ES-LMa_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
index 2a701bb99f..454de1a378 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-2.96582
 ./xmlchange PTS_LAT=37.097935
 ./xmlchange DATM_YR_END=2007
+./xmlchange DATM_YR_START_FILENAME=2007
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-LgS/CLM1PT_data/CTSM_DATM_ES-LgS_2007-2007.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
index e7971529d9..0de3a761a7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=1.4485
 ./xmlchange PTS_LAT=42.15218
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ES-VDA/CLM1PT_data/CTSM_DATM_ES-VDA_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
index 7ac714599a..1861c4a0b6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=24.295
 ./xmlchange PTS_LAT=61.8475
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1996
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Hyy/CLM1PT_data/CTSM_DATM_FI-Hyy_1996-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1996" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
index 339a244afa..9f7b8a0763 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=27.295031
 ./xmlchange PTS_LAT=69.140694
 ./xmlchange DATM_YR_END=2002
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Kaa/CLM1PT_data/CTSM_DATM_FI-Kaa_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
index dea60aca09..14c28c1475 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=24.209181
 ./xmlchange PTS_LAT=67.9972
 ./xmlchange DATM_YR_END=2009
+./xmlchange DATM_YR_START_FILENAME=2007
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Lom/CLM1PT_data/CTSM_DATM_FI-Lom_2007-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
index 08773c8443..7eccb754fb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=26.637831
 ./xmlchange PTS_LAT=67.361862
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2008
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FI-Sod/CLM1PT_data/CTSM_DATM_FI-Sod_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
index 550ce300cd..76a71ab3b2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=2.78014
 ./xmlchange PTS_LAT=48.476398
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Fon/CLM1PT_data/CTSM_DATM_FR-Fon_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
index 169e85a270..5c575b0e97 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=1.95191
 ./xmlchange PTS_LAT=48.844219
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Gri/CLM1PT_data/CTSM_DATM_FR-Gri_2005-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
index 18a9e57b29..1d8ab25532 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=7.06556
 ./xmlchange PTS_LAT=48.67416
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=1997
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Hes/CLM1PT_data/CTSM_DATM_FR-Hes_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1997" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
index ee89868fa1..6b9eb48062 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-0.769287
 ./xmlchange PTS_LAT=44.71711
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-LBr/CLM1PT_data/CTSM_DATM_FR-LBr_2003-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
index c5025aba8b..000fc6d746 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=2.73583
 ./xmlchange PTS_LAT=45.643059
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq1/CLM1PT_data/CTSM_DATM_FR-Lq1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
index 26581437b9..a851919f73 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=2.73703
 ./xmlchange PTS_LAT=45.639191
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Lq2/CLM1PT_data/CTSM_DATM_FR-Lq2_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
index 13fab2f770..1981d675fc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=3.59583
 ./xmlchange PTS_LAT=43.74139
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/FR-Pue/CLM1PT_data/CTSM_DATM_FR-Pue_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
index bafc0737b8..1f10f4a2e1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-52.924866
 ./xmlchange PTS_LAT=5.278772
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=10800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/GF-Guy/CLM1PT_data/CTSM_DATM_GF-Guy_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
index 98e5672dc2..54b635a2a2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=19.601299
 ./xmlchange PTS_LAT=46.691101
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/HU-Bug/CLM1PT_data/CTSM_DATM_HU-Bug_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
index a71ecdf659..13ac0e386f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=114.036392
 ./xmlchange PTS_LAT=-2.345
 ./xmlchange DATM_YR_END=2003
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ID-Pag/CLM1PT_data/CTSM_DATM_ID-Pag_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
index 98d668df9e..2bd80343c3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-6.918152
 ./xmlchange PTS_LAT=52.858791
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Ca1/CLM1PT_data/CTSM_DATM_IE-Ca1_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
index edb036e775..4f27411509 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-8.751801
 ./xmlchange PTS_LAT=51.986691
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IE-Dri/CLM1PT_data/CTSM_DATM_IE-Dri_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
index 3a4195c030..aa7fef51ae 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=13.60516
 ./xmlchange PTS_LAT=41.904099
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Amp/CLM1PT_data/CTSM_DATM_IT-Amp_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
index ada711ab6e..0c620a348c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=14.95744
 ./xmlchange PTS_LAT=40.5238
 ./xmlchange DATM_YR_END=2010
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-BCi/CLM1PT_data/CTSM_DATM_IT-BCi_2005-2010.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
index 9ff3031f4d..831b7897c0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=12.02656
 ./xmlchange PTS_LAT=42.380409
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2012
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA1/CLM1PT_data/CTSM_DATM_IT-CA1_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
index 2041d6983d..dfae27f215 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=12.02604
 ./xmlchange PTS_LAT=42.37722
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2012
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA2/CLM1PT_data/CTSM_DATM_IT-CA2_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
index 50253ccc6b..a3a2ab6c25 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=12.0222
 ./xmlchange PTS_LAT=42.380001
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2012
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-CA3/CLM1PT_data/CTSM_DATM_IT-CA3_2012-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2012" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
index 06e653c0b9..eb817ab43c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=13.58814
 ./xmlchange PTS_LAT=41.849361
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2007
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Col/CLM1PT_data/CTSM_DATM_IT-Col_2007-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2007" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2007" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
index b7b1ae449d..cfad8adb35 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=12.37611
 ./xmlchange PTS_LAT=41.70525
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2001
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Cpz/CLM1PT_data/CTSM_DATM_IT-Cpz_2001-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
index 873293a7aa..125257acd7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=8.63358
 ./xmlchange PTS_LAT=45.812641
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Isp/CLM1PT_data/CTSM_DATM_IT-Isp_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
index b8efb6955e..bca26018b9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=7.58259
 ./xmlchange PTS_LAT=45.15258
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-LMa/CLM1PT_data/CTSM_DATM_IT-LMa_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
index a50e9dc664..87f8e9d947 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.28132
 ./xmlchange PTS_LAT=45.9562
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Lav/CLM1PT_data/CTSM_DATM_IT-Lav_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
index 0c60de60ba..ab42d7a3d8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.04583
 ./xmlchange PTS_LAT=46.014679
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-MBo/CLM1PT_data/CTSM_DATM_IT-MBo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
index 34c3d12aa2..8cf5fdd6d0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.70334
 ./xmlchange PTS_LAT=46.114021
 ./xmlchange DATM_YR_END=2003
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Mal/CLM1PT_data/CTSM_DATM_IT-Mal_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
index bd8d0e486c..8b12cb84db 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=8.15117
 ./xmlchange PTS_LAT=40.606178
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Noe/CLM1PT_data/CTSM_DATM_IT-Noe_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
index 3084a49d8a..c8b4f77f4d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.09109
 ./xmlchange PTS_LAT=44.690189
 ./xmlchange DATM_YR_END=2002
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Non/CLM1PT_data/CTSM_DATM_IT-Non_2002-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
index f82e0b8eb9..629382cea8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=9.06104
 ./xmlchange PTS_LAT=45.200871
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-PT1/CLM1PT_data/CTSM_DATM_IT-PT1_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
index 80927456e8..ebf7cdb500 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.43369
 ./xmlchange PTS_LAT=46.586861
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ren/CLM1PT_data/CTSM_DATM_IT-Ren_2010-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
index 209a0c032d..b400216f9b 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.93001
 ./xmlchange PTS_LAT=42.408119
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro1/CLM1PT_data/CTSM_DATM_IT-Ro1_2002-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
index 55e5f4f128..195c0fdbc9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=11.92093
 ./xmlchange PTS_LAT=42.390259
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-Ro2/CLM1PT_data/CTSM_DATM_IT-Ro2_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
index bd1211a9c7..d981029a77 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=10.29095
 ./xmlchange PTS_LAT=43.732029
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2013
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SR2/CLM1PT_data/CTSM_DATM_IT-SR2_2013-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2013" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
index a0aa3f3aa5..c40b2d8f71 100644
--- a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=10.28444
 ./xmlchange PTS_LAT=43.727859
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/IT-SRo/CLM1PT_data/CTSM_DATM_IT-SRo_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
index 17be0e9534..c93dfef557 100644
--- a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=137.078796
 ./xmlchange PTS_LAT=35.2617
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=54000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/JP-SMF/CLM1PT_data/CTSM_DATM_JP-SMF_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
index fd82f6a049..ccb1290e78 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=4.927
 ./xmlchange PTS_LAT=51.971001
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Ca1/CLM1PT_data/CTSM_DATM_NL-Ca1_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
index e4712093fa..08eb58d8a1 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=5.0713
 ./xmlchange PTS_LAT=52.240349
 ./xmlchange DATM_YR_END=2011
+./xmlchange DATM_YR_START_FILENAME=2008
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Hor/CLM1PT_data/CTSM_DATM_NL-Hor_2008-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
index d825ace2ba..a09cf39408 100644
--- a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=5.74356
 ./xmlchange PTS_LAT=52.16658
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=1997
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/NL-Loo/CLM1PT_data/CTSM_DATM_NL-Loo_1997-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1997" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
index 80bb1b37c5..eb79334eeb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=16.309401
 ./xmlchange PTS_LAT=52.762199
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PL-wet/CLM1PT_data/CTSM_DATM_PL-wet_2004-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
index b56b6968f1..4186dea491 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-8.601807
 ./xmlchange PTS_LAT=38.6394
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Esp/CLM1PT_data/CTSM_DATM_PT-Esp_2002-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
index 2d35f26a06..36a1899bfc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-8.000061
 ./xmlchange PTS_LAT=38.540642
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi1/CLM1PT_data/CTSM_DATM_PT-Mi1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
index b02616ee02..e2986dfac8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-8.024536
 ./xmlchange PTS_LAT=38.476501
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/PT-Mi2/CLM1PT_data/CTSM_DATM_PT-Mi2_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
index dff0478e08..f5172ddb53 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=161.341431
 ./xmlchange PTS_LAT=68.613037
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=46800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Che/CLM1PT_data/CTSM_DATM_RU-Che_2003-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
index d90a4af0bc..69bab319bc 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=32.922081
 ./xmlchange PTS_LAT=56.461529
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Fyo/CLM1PT_data/CTSM_DATM_RU-Fyo_2003-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
index 1d42ea947f..27144db3cb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=89.3508
 ./xmlchange PTS_LAT=60.8008
 ./xmlchange DATM_YR_END=2003
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=61200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/RU-Zot/CLM1PT_data/CTSM_DATM_RU-Zot_2003-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
index 2b471ebc27..6d245703d6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=30.4783
 ./xmlchange PTS_LAT=13.2829
 ./xmlchange DATM_YR_END=2009
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=75600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SD-Dem/CLM1PT_data/CTSM_DATM_SD-Dem_2005-2009.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
index 34a53f5533..0a426dee38 100644
--- a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=19.55669
 ./xmlchange PTS_LAT=64.181969
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=82800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/SE-Deg/CLM1PT_data/CTSM_DATM_SE-Deg_2002-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
index 6cd7cb38f4..c016bf89a7 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-3.798065
 ./xmlchange PTS_LAT=56.60722
 ./xmlchange DATM_YR_END=2001
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Gri/CLM1PT_data/CTSM_DATM_UK-Gri_2000-2001.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
index 6d83e07c57..f92b9a6d69 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-0.858307
 ./xmlchange PTS_LAT=51.15353
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-Ham/CLM1PT_data/CTSM_DATM_UK-Ham_2004-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
index 4237f25d27..10b82dee40 100644
--- a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-1.266663
 ./xmlchange PTS_LAT=51.450001
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=0
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/UK-PL3/CLM1PT_data/CTSM_DATM_UK-PL3_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
index 1f32b6d98c..8b3bb18871 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-99.419983
 ./xmlchange PTS_LAT=36.426701
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR1/CLM1PT_data/CTSM_DATM_US-AR1_2010-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
index 7e436a547c..0eeaef4fe2 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-99.597504
 ./xmlchange PTS_LAT=36.635799
 ./xmlchange DATM_YR_END=2011
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-AR2/CLM1PT_data/CTSM_DATM_US-AR2_2010-2011.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
index 1a0fd06c8b..4045912f3c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-97.4888
 ./xmlchange PTS_LAT=36.605801
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-ARM/CLM1PT_data/CTSM_DATM_US-ARM_2003-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
index 9ab42347b2..043730b19e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-110.509201
 ./xmlchange PTS_LAT=31.5907
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Aud/CLM1PT_data/CTSM_DATM_US-Aud_2003-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
index 81591a2454..4fb0562433 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-71.288086
 ./xmlchange PTS_LAT=44.06464
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bar/CLM1PT_data/CTSM_DATM_US-Bar_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
index 91e1976a9f..a05f46e871 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-96.836182
 ./xmlchange PTS_LAT=44.345291
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bkg/CLM1PT_data/CTSM_DATM_US-Bkg_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
index 5c09021706..fb79abb36e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-120.632751
 ./xmlchange PTS_LAT=38.895302
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Blo/CLM1PT_data/CTSM_DATM_US-Blo_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
index 49c70e98da..b6e243115f 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-88.290405
 ./xmlchange PTS_LAT=40.006199
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=1997
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Bo1/CLM1PT_data/CTSM_DATM_US-Bo1_1997-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1997" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1997" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
index fc6a4841a9..0957a02037 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-109.389999
 ./xmlchange PTS_LAT=38.09
 ./xmlchange DATM_YR_END=2003
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Cop/CLM1PT_data/CTSM_DATM_US-Cop_2002-2003.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
index 2299cbf103..bd5760bfc0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-105.101898
 ./xmlchange PTS_LAT=48.307701
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-FPe/CLM1PT_data/CTSM_DATM_US-FPe_2000-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
index 794d0584a2..fc1b2c4fba 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-106.239899
 ./xmlchange PTS_LAT=41.366501
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2009
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-GLE/CLM1PT_data/CTSM_DATM_US-GLE_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
index 6cc34f40c2..be9ff715aa 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-89.873505
 ./xmlchange PTS_LAT=34.2547
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Goo/CLM1PT_data/CTSM_DATM_US-Goo_2004-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
index a016985d76..bb97980e53 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-72.171509
 ./xmlchange PTS_LAT=42.5378
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=1992
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ha1/CLM1PT_data/CTSM_DATM_US-Ha1_1992-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1992" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1992" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
index c36889758d..803711f8af 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-68.740204
 ./xmlchange PTS_LAT=45.204102
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=1996
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ho1/CLM1PT_data/CTSM_DATM_US-Ho1_1996-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1996" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
index fc3ab78d4f..74ad2113d9 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-80.671539
 ./xmlchange PTS_LAT=28.608578
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2003
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-KS2/CLM1PT_data/CTSM_DATM_US-KS2_2003-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2003" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2003" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
index d0ee0a8b7d..dbc8d3b004 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-89.979187
 ./xmlchange PTS_LAT=46.082699
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Los/CLM1PT_data/CTSM_DATM_US-Los_2000-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
index 12362f6d77..8e8804a887 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-86.413086
 ./xmlchange PTS_LAT=39.3232
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1999
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MMS/CLM1PT_data/CTSM_DATM_US-MMS_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
index a332c04808..223e43a3d6 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-92.200012
 ./xmlchange PTS_LAT=38.74411
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-MOz/CLM1PT_data/CTSM_DATM_US-MOz_2005-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
index 97c8a61316..8555ceb993 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-121.557404
 ./xmlchange PTS_LAT=44.452301
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me2/CLM1PT_data/CTSM_DATM_US-Me2_2002-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
index eef9074dfe..b191f984a5 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-121.622406
 ./xmlchange PTS_LAT=44.499199
 ./xmlchange DATM_YR_END=2000
+./xmlchange DATM_YR_START_FILENAME=1996
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me4/CLM1PT_data/CTSM_DATM_US-Me4_1996-2000.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1996" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1996" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
index 7591643f86..8ffbbe4855 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-121.607803
 ./xmlchange PTS_LAT=44.323299
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Me6/CLM1PT_data/CTSM_DATM_US-Me6_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
index 66e97faf89..2d3103546a 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-121.765106
 ./xmlchange PTS_LAT=38.049801
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Myb/CLM1PT_data/CTSM_DATM_US-Myb_2011-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
index 6ccba5ae4e..cd795160d0 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-105.546402
 ./xmlchange PTS_LAT=40.032902
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1999
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-NR1/CLM1PT_data/CTSM_DATM_US-NR1_1999-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
index 54bbcbe8de..4b205b471d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-96.476593
 ./xmlchange PTS_LAT=41.1651
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne1/CLM1PT_data/CTSM_DATM_US-Ne1_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
index 0587fd1932..beca45f248 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-96.470093
 ./xmlchange PTS_LAT=41.164902
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne2/CLM1PT_data/CTSM_DATM_US-Ne2_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
index 66bcf6d25d..59644ec285 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-96.439697
 ./xmlchange PTS_LAT=41.179699
 ./xmlchange DATM_YR_END=2012
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ne3/CLM1PT_data/CTSM_DATM_US-Ne3_2002-2012.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2012" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
index 76bfb84b9f..979dd2adbe 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-90.272308
 ./xmlchange PTS_LAT=45.9459
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=1995
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-PFa/CLM1PT_data/CTSM_DATM_US-PFa_1995-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1995" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1995" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
index f3c9e49740..34949905d4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-147.487595
 ./xmlchange PTS_LAT=65.123703
 ./xmlchange DATM_YR_END=2013
+./xmlchange DATM_YR_START_FILENAME=2011
 ./xmlchange START_TOD=32400
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Prr/CLM1PT_data/CTSM_DATM_US-Prr_2011-2013.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2011" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2013" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2011" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
index a10cb0956a..07c1611661 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-82.218781
 ./xmlchange PTS_LAT=29.73807
 ./xmlchange DATM_YR_END=2005
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP1/CLM1PT_data/CTSM_DATM_US-SP1_2005-2005.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
index 7b7a589af4..0640843357 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-82.244812
 ./xmlchange PTS_LAT=29.764799
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP2/CLM1PT_data/CTSM_DATM_US-SP2_2000-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
index 882c94c80f..559f2e9282 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-82.163269
 ./xmlchange PTS_LAT=29.75477
 ./xmlchange DATM_YR_END=2004
+./xmlchange DATM_YR_START_FILENAME=1999
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SP3/CLM1PT_data/CTSM_DATM_US-SP3_1999-2004.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
index 7fea8792e6..25269ecc91 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-110.827698
 ./xmlchange PTS_LAT=31.7894
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2009
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRG/CLM1PT_data/CTSM_DATM_US-SRG_2009-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2009" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2009" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
index 3ba018a2b1..97c155f639 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-110.865997
 ./xmlchange PTS_LAT=31.8214
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2004
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-SRM/CLM1PT_data/CTSM_DATM_US-SRM_2004-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2004" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2004" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
index 636e532f38..f78805c4d8 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-89.347717
 ./xmlchange PTS_LAT=46.242001
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2002
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Syv/CLM1PT_data/CTSM_DATM_US-Syv_2002-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2002" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
index 497385372e..81a47579f4 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-120.966003
 ./xmlchange PTS_LAT=38.431599
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2001
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Ton/CLM1PT_data/CTSM_DATM_US-Ton_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
index f212f4bc0f..6a76794659 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-121.641403
 ./xmlchange PTS_LAT=38.103001
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2014
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Tw4/CLM1PT_data/CTSM_DATM_US-Tw4_2014-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2014" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
index 74035ea108..0a36252097 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-121.653107
 ./xmlchange PTS_LAT=38.1087
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2010
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Twt/CLM1PT_data/CTSM_DATM_US-Twt_2010-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2010" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2010" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
index 08f9f17a5a..6587b7967c 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-84.713806
 ./xmlchange PTS_LAT=45.559799
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=18000
 ./xmlchange ATM_NCPL=24
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-UMB/CLM1PT_data/CTSM_DATM_US-UMB_2000-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
index e997931652..ecdf5c95e3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-120.950729
 ./xmlchange PTS_LAT=38.4133
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2001
 ./xmlchange START_TOD=28800
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Var/CLM1PT_data/CTSM_DATM_US-Var_2001-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2001" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2001" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
index 55647b78c0..4f2ca3a65e 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-90.079895
 ./xmlchange PTS_LAT=45.805901
 ./xmlchange DATM_YR_END=2006
+./xmlchange DATM_YR_START_FILENAME=1999
 ./xmlchange START_TOD=21600
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-WCr/CLM1PT_data/CTSM_DATM_US-WCr_1999-2006.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=1999" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2006" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=1999" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
index 51fadcc9f6..458db116f3 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-110.0522
 ./xmlchange PTS_LAT=31.743799
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2008
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Whs/CLM1PT_data/CTSM_DATM_US-Whs_2008-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2008" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
index 5d95ef3e36..0870b9233d 100644
--- a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=-109.941895
 ./xmlchange PTS_LAT=31.7365
 ./xmlchange DATM_YR_END=2014
+./xmlchange DATM_YR_START_FILENAME=2005
 ./xmlchange START_TOD=25200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/US-Wkg/CLM1PT_data/CTSM_DATM_US-Wkg_2005-2014.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2005" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2014" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2005" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
index 6fe9e9c989..8c3463a936 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=31.496901
 ./xmlchange PTS_LAT=-25.019699
 ./xmlchange DATM_YR_END=2002
+./xmlchange DATM_YR_START_FILENAME=2000
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZA-Kru/CLM1PT_data/CTSM_DATM_ZA-Kru_2000-2002.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2000" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2002" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2000" >> user_nl_datm_streams 
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
index ff19816490..448a26c040 100644
--- a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
+++ b/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
@@ -2,10 +2,10 @@
 ./xmlchange PTS_LON=23.252781
 ./xmlchange PTS_LAT=-15.437778
 ./xmlchange DATM_YR_END=2008
+./xmlchange DATM_YR_START_FILENAME=2008
 ./xmlchange START_TOD=79200
 ./xmlchange ATM_NCPL=48
 
-echo "CLM_USRDAT.PLUMBER2:datafiles= \$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/ZM-Mon/CLM1PT_data/CTSM_DATM_ZM-Mon_2008-2008.nc " >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_first=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_last=2008" >> user_nl_datm_streams 
 echo "presaero.SSP3-7.0:year_align=2008" >> user_nl_datm_streams 

From ba1de86775efaed74f9dba24f9be52b230bf3263 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Thu, 8 Aug 2024 12:17:44 -0600
Subject: [PATCH 0940/1248] minor typo fix

---
 tools/site_and_regional/create_PLUMBER2_sites_csv.ncl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/site_and_regional/create_PLUMBER2_sites_csv.ncl b/tools/site_and_regional/create_PLUMBER2_sites_csv.ncl
index 2bcf9915ca..b83e3ef3a7 100644
--- a/tools/site_and_regional/create_PLUMBER2_sites_csv.ncl
+++ b/tools/site_and_regional/create_PLUMBER2_sites_csv.ncl
@@ -163,7 +163,7 @@ begin
 
   fname = "/glade/work/oleson/ctsm_PLUMBERcsv/tools/site_and_regional/PLUMBER2_sites.csv"
   header = (/"#pftX-cth and pftX-cbh are the site=specific canopy top and bottom heights", \
-             "#start_year and end_year will be used to define DATM_YR_ALIGH, DATM_YR_START and DATM_YR_END, and STOP_N in units of nyears.", \
+             "#start_year and end_year will be used to define DATM_YR_ALIGN, DATM_YR_START and DATM_YR_END, and STOP_N in units of nyears.", \
              "#RUN_STARTDATE and START_TOD are specified because we are starting at GMT corresponding to local midnight.", \
              "#ATM_NCPL is specified so that the time step of the model matches the time interval specified by the atm forcing data.", \
              ",Site,Lat,Lon,pft1,pft1-%,pft1-cth,pft1-cbh,pft2,pft2-%,pft2-cth,pft2-cbh,start_year,end_year,RUN_STARTDATE,START_TOD,ATM_NCPL"/)

From 2b265ca9c874ce4e8c25290078d4f1ff19fb8a7d Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Thu, 8 Aug 2024 13:42:18 -0600
Subject: [PATCH 0941/1248] Update buildnml for accurate restart file time of
 day

---
 cime_config/buildnml | 27 +++++++++++++++++++--------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 893f0933c7..06a447e443 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -71,6 +71,7 @@ def buildnml(case, caseroot, compname):
     yr_start = int(yr_start)
     yr_end = int(yr_end)
 
+    clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
     comp_atm = case.get_value("COMP_ATM")
     lnd_grid = case.get_value("LND_GRID")
     ninst_lnd = case.get_value("NINST_LND")
@@ -80,6 +81,7 @@ def buildnml(case, caseroot, compname):
     run_refcase = case.get_value("RUN_REFCASE")
     run_refdate = case.get_value("RUN_REFDATE")
     run_reftod = case.get_value("RUN_REFTOD")
+    start_tod = case.get_value("START_TOD")
     glc_nec = case.get_value("GLC_NEC")
     glc_use_antarctica = case.get_value("GLC_USE_ANTARCTICA")
     mask = case.get_value("MASK_GRID")
@@ -348,13 +350,22 @@ def buildnml(case, caseroot, compname):
         if run_type == "hybrid" or run_type == "branch":
             compnames = ["clm4", "clm5", "clm2"]
             for comp in compnames:
-                clm_startfile = "%s.%s%s.r.%s-%s.nc" % (
-                    run_refcase,
-                    comp,
-                    inst_string,
-                    run_refdate,
-                    run_reftod,
-                )
+                if "PLUMBER2" in clm_usrdat_name:
+                    clm_startfile = "%s.%s%s.r.%s-%s.nc" % (
+                        run_refcase,
+                        comp,
+                        inst_string,
+                        run_refdate,
+                        start_tod,
+                    )
+                else:
+                    clm_startfile = "%s.%s%s.r.%s-%s.nc" % (
+                        run_refcase,
+                        comp,
+                        inst_string,
+                        run_refdate,
+                        run_reftod,
+                    )
                 if os.path.exists(os.path.join(rundir, clm_startfile)):
                     break
                 else:
@@ -372,7 +383,7 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning("WARNING: Could NOT find a start file named" + clm_startfile)
+                logger.warning("WARNING: Could NOT find a start file named " + clm_startfile)
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""

From 5f6d49608409fedb3c22ca1f65076ec175020cf0 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Fri, 16 Aug 2024 16:15:16 -0600
Subject: [PATCH 0942/1248] update cdeps tag in gitmodules for plumber2
 implementation

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index 4e9f5b51fb..80c1640e72 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -92,7 +92,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.34
+fxtag = cdeps1.0.47
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git

From e9b629db2cc57ac52e4ff691b4762968d364e80d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 16 Aug 2024 16:22:53 -0600
Subject: [PATCH 0943/1248] Simplify the validation checking for megan
 specifier as the expressions allowed are much more complex now, this resolves
 #2709

---
 bld/CLMBuildNamelist.pm | 24 ++++--------------------
 1 file changed, 4 insertions(+), 20 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index daf4320c18..e4cc50614c 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -5652,26 +5652,10 @@ sub check_megan_spec {
 
     my $megan_spec      = $nl->get_value('megan_specifier');
     my @megan_spec_list = split( /\s*,\s*/, $megan_spec );
-    foreach $megan_spec ( @megan_spec_list ) {
-       if ( $megan_spec =~ /^['"]+[A-Za-z0-9]+\s*\=\s*([\sA-Za-z0-9+_-]+)["']+$/ ) {
-          my $megan_list = $1;
-          my @megan_cmpds = split( /\s*\+\s*/, $megan_list );
-          my $var = "megan_cmpds";
-          my $warn = 0;
-          foreach my $megan_cmpd ( @megan_cmpds ) {
-             if (  ! $definition->is_valid_value( $var, $megan_cmpd, 'noquotes'=>1 ) ) {
-                $log->warning("megan_compound $megan_cmpd NOT found in list" );
-                $warn++;
-             }
-          }
-          if ( $warn > 0 ) {
-             my @valid_values   = $definition->get_valid_values( $var, 'noquotes'=>1 );
-             $log->warning("list of megan compounds includes:\n" .
-                     "@valid_values\n" .
-                     "Does your megan_factors_file include more compounds?\n" .
-                     "If NOT your simulation will fail." );
-          }
-       } else {
+    foreach my $spec ( @megan_spec_list ) {
+       $megan_spec = remove_leading_and_trailing_quotes($spec);
+       # Do simple validation of the expressions to just check for valid characters
+       if ( ! $megan_spec =~ /[\s=A-Za-z0-9_\+\.\*\(\)-]+/ ) {
           $log->fatal_error("Bad format for megan_specifier = $megan_spec");
        }
     }

From e8b91fe3dd833007a666a6ed5495eb8372ed7bb3 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Fri, 16 Aug 2024 17:04:09 -0600
Subject: [PATCH 0944/1248] Update glacier_region namelist items for new
 GLACIER_REGIONS

We are removing the old second region (in CISM's Greenland domain but
outside Greenland itself). So updating the namelist defaults to align
with this removal.
---
 bld/namelist_files/namelist_defaults_ctsm.xml   | 17 +++++++----------
 cime_config/SystemTests/lvg.py                  |  4 ++--
 .../user_nl_clm                                 |  2 +-
 3 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 97620c770d..cd5e723baa 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -466,30 +466,27 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Default glacier behavior is:
      Mountain glaciers: single_at_atm_topo
-     Greenland - inside CISM grid but outside Greenland itself: virtual
-     Greenland itself: virtual
+     Greenland: virtual
      Antarctica: multiple
 
      If CISM is running over Antarctica, then we change the Antarctica
      behavior to virtual. Note that the Greenland behavior is always
      virtual, even if Greenland isn't included in this run.
 -->
-<glacier_region_behavior glc_use_antarctica="0">'single_at_atm_topo','virtual','virtual','multiple'</glacier_region_behavior>
-<glacier_region_behavior glc_use_antarctica="1">'single_at_atm_topo','virtual','virtual','virtual' </glacier_region_behavior>
+<glacier_region_behavior glc_use_antarctica="0">'single_at_atm_topo','virtual','multiple'</glacier_region_behavior>
+<glacier_region_behavior glc_use_antarctica="1">'single_at_atm_topo','virtual','virtual' </glacier_region_behavior>
 
 <!-- Default glacier melt behavior is:
      Mountain glaciers: remains_in_place
-     Greenland - inside CISM grid but outside Greenland itself: replaced_by_ice
-     Greenland itself: replaced_by_ice
+     Greenland: replaced_by_ice
      Antarctica: replaced_by_ice -->
-<glacier_region_melt_behavior>'remains_in_place','replaced_by_ice','replaced_by_ice','replaced_by_ice'</glacier_region_melt_behavior>
+<glacier_region_melt_behavior>'remains_in_place','replaced_by_ice','replaced_by_ice'</glacier_region_melt_behavior>
 
 <!-- Default glacier ice runoff behavior is:
      Mountain glaciers: melted
-     Greenland - inside CISM grid but outside Greenland itself: melted
-     Greenland itself: remains_ice
+     Greenland: remains_ice
      Antarctica: remains_ice -->
-<glacier_region_ice_runoff_behavior>'melted','melted','remains_ice','remains_ice'</glacier_region_ice_runoff_behavior>
+<glacier_region_ice_runoff_behavior>'melted','remains_ice','remains_ice'</glacier_region_ice_runoff_behavior>
 
 <!-- This parameter is tied (in a scientific sense) to h2osno_max: For large
      values of h2osno_max, glc_snow_persistence_max_days should be 0; for small
diff --git a/cime_config/SystemTests/lvg.py b/cime_config/SystemTests/lvg.py
index 4b990313f5..286712ce0f 100644
--- a/cime_config/SystemTests/lvg.py
+++ b/cime_config/SystemTests/lvg.py
@@ -32,12 +32,12 @@ def _case_one_setup(self):
         append_to_user_nl_files(
             caseroot=self._get_caseroot(),
             component="clm",
-            contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'multiple'",
+            contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'multiple'",
         )
 
     def _case_two_setup(self):
         append_to_user_nl_files(
             caseroot=self._get_caseroot(),
             component="clm",
-            contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'virtual'",
+            contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual'",
         )
diff --git a/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm b/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
index 3486d7abfb..b6c563ed2c 100644
--- a/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
+++ b/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
@@ -5,5 +5,5 @@
 ! This differs from the default in that it turns on virtual columns over Antarctica
 ! This is desired so that we have the output needed to drive a later offline CISM Antarctica simulation
 ! However, this increases the cost of CLM by about 10%
-glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'virtual'
+glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual'
 

From bedff9cb7166472094026e774066706acf48af4c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 20 Aug 2024 13:56:59 -0600
Subject: [PATCH 0945/1248] Whitespace and comment improvements.

---
 .../namelist_definition_ctsm.xml              |  4 +-
 src/biogeochem/CNFireLi2024Mod.F90            | 60 +++++++++----------
 2 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 134f0c41c7..8f39a4e9dd 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -258,8 +258,8 @@ The method type to use for CNFire
 nofire:        Turn fire effects off
 li2014qianfrc: Reference paper Li, et. al.(2014) tuned with QIAN atmospheric forcing
 li2016crufrc:  Reference paper Li, et. al.(2016) tuned with CRU-NCEP atmospheric forcing
-li2021gswpfrc: Reference paper Li, et. al.(2021?) tuned with GSWP3 atmospheric forcing
-li2024gswpfrc: No reference paper yet
+li2021gswpfrc: No reference paper yet, tuned with GSWP3 atmospheric forcing
+li2024gswpfrc: No reference paper yet, tuned with GSWP3 atmospheric forcing
 li2024crujra:  No reference paper yet, tuned with CRU-JRA forcing
 </entry>
 
diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index d749e8000c..b9158d9a17 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -588,36 +588,36 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
               end do
            end if
            fuelc(c) = fuelc(c)/(1._r8-cropf_col(c))
-           fb       = max(0.0_r8,min(1.0_r8,(fuelc(c)-lfuel)/(ufuel-lfuel)))
-              afuel  =min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
-              arh=1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
-              arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
-              if (forc_rh(g) < rh_hgh.and. wtlf(c) > 0._r8 .and. tsoi17(c)> SHR_CONST_TKFRZ)then
-                fire_m   = ((afuel*arh30+(1._r8-afuel)*arh)**1.5_r8) &
-                             *((1._r8-btran_col(c)/wtlf(c))**0.5_r8)
-              else
-                fire_m   = 0._r8
-              end if
-              lh       = pot_hmn_ign_counts_alpha*6.8_r8*hdmlf**(0.43_r8)/30._r8/24._r8
-              fs       = 1._r8-(0.01_r8+0.98_r8*exp(-0.025_r8*hdmlf))
-              if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
-                 ig = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
-                      cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
-                      cnfire_params%ignition_efficiency)*(1._r8-fs)* &
-                      (lfwt(c)**0.5)
-              else
-                 ig = this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
-                      cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
-                      cnfire_params%ignition_efficiency*(1._r8-fs)*  &
-                      (lfwt(c)**0.5)
-              end if
-              nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) !fire counts/km2/sec
-              Lb_lf    = 1._r8+10._r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
-              spread_m = fire_m**0.5_r8
-              fd_col(c)=(lfwt(c)*lgdp1_col(c)*lpop_col(c))**0.5_r8 * fd_col(c)
-              farea_burned(c) = min(1._r8,(cnfire_const%g0*spread_m*fsr_col(c)* &
-                   fd_col(c)/1000._r8)**2*nfire(c)*SHR_CONST_PI*Lb_lf+ &
-                   baf_crop(c)+baf_peatf(c))  ! fraction (0-1) per sec
+           fb = max(0.0_r8,min(1.0_r8,(fuelc(c)-lfuel)/(ufuel-lfuel)))
+           afuel = min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
+           arh = 1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
+           arh30 = 1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
+           if (forc_rh(g) < rh_hgh.and. wtlf(c) > 0._r8 .and. tsoi17(c)> SHR_CONST_TKFRZ)then
+              fire_m = ((afuel*arh30+(1._r8-afuel)*arh)**1.5_r8) &
+                       *((1._r8-btran_col(c)/wtlf(c))**0.5_r8)
+           else
+              fire_m   = 0._r8
+           end if
+           lh = pot_hmn_ign_counts_alpha*6.8_r8*hdmlf**(0.43_r8)/30._r8/24._r8
+           fs = 1._r8-(0.01_r8+0.98_r8*exp(-0.025_r8*hdmlf))
+           if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
+              ig = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
+                   cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
+                   cnfire_params%ignition_efficiency)*(1._r8-fs)* &
+                   (lfwt(c)**0.5)
+           else
+              ig = this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
+                   cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
+                   cnfire_params%ignition_efficiency*(1._r8-fs)*  &
+                   (lfwt(c)**0.5)
+           end if
+           nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) !fire counts/km2/sec
+           Lb_lf    = 1._r8+10._r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
+           spread_m = fire_m**0.5_r8
+           fd_col(c) = (lfwt(c)*lgdp1_col(c)*lpop_col(c))**0.5_r8 * fd_col(c)
+           farea_burned(c) = min(1._r8,(cnfire_const%g0*spread_m*fsr_col(c)* &
+                fd_col(c)/1000._r8)**2*nfire(c)*SHR_CONST_PI*Lb_lf+ &
+                baf_crop(c)+baf_peatf(c))  ! fraction (0-1) per sec
            !
            ! if landuse change data is used, calculate deforestation fires and
            ! add it in the total of burned area fraction

From 861004b3b141102eb35199ee151dfbf13816d445 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 20 Aug 2024 16:05:15 -0600
Subject: [PATCH 0946/1248] Add parameter max_rh30_affecting_fuel.

Value above which 30-day running relative humidity has no effect on fuel combustibility.
---
 bld/CLMBuildNamelist.pm                         | 2 +-
 bld/namelist_files/namelist_defaults_ctsm.xml   | 5 +++++
 bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++
 src/biogeochem/CNFireBaseMod.F90                | 8 +++++++-
 src/biogeochem/CNFireLi2016Mod.F90              | 3 ++-
 src/biogeochem/CNFireLi2021Mod.F90              | 3 ++-
 src/biogeochem/CNFireLi2024Mod.F90              | 3 ++-
 7 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b99be288e7..d09f79afe1 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2266,7 +2266,7 @@ sub setup_logic_cnfire {
 
   my @fire_consts = ( "rh_low", "rh_hgh", "bt_min", "bt_max", "cli_scale", "boreal_peatfire_c", "non_boreal_peatfire_c",
                       "pot_hmn_ign_counts_alpha", "cropfire_a1", "occur_hi_gdp_tree", "lfuel", "ufuel",
-                      "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd" );
+                      "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd", "max_rh30_affecting_fuel" );
   if ( &value_is_true($nl->get_value('use_cn')) ) {
      foreach my $item ( @fire_consts ) {
         if ( ! &value_is_true($nl_flags->{'cnfireson'} ) ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 777b7c4cff..ef797f567a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -244,6 +244,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <fire_method phys="clm5_0" >li2016crufrc</fire_method>
 <fire_method phys="clm4_5" >li2014qianfrc</fire_method>
 
+<max_rh30_affecting_fuel>90.</max_rh30_affecting_fuel>
+
 <rh_low                   fire_method="li2014qianfrc" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2014qianfrc" >80.0d00</rh_hgh>
 <bt_min                   fire_method="li2014qianfrc" >0.3d00</bt_min>
@@ -350,6 +352,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <ufuel                    fire_method="li2021gswpfrc" >1050.d00</ufuel>
 <cmb_cmplt_fact_litter    fire_method="li2021gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2021gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
+<max_rh30_affecting_fuel  fire_method="li2021gswpfrc" >90.</max_rh30_affecting_fuel>
 
 <rh_low                   fire_method="li2024gswpfrc" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2024gswpfrc" >80.0d00</rh_hgh>
@@ -365,6 +368,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <ufuel                    fire_method="li2024gswpfrc" >825.d00</ufuel>
 <cmb_cmplt_fact_litter    fire_method="li2024gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
+<max_rh30_affecting_fuel  fire_method="li2024gswpfrc" >90.</max_rh30_affecting_fuel>
 
 <rh_low                   fire_method="li2024crujra" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2024crujra" >85.0d00</rh_hgh>
@@ -380,6 +384,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <ufuel                    fire_method="li2024crujra" >825.d00</ufuel>
 <cmb_cmplt_fact_litter    fire_method="li2024crujra" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024crujra" >0.28d00</cmb_cmplt_fact_cwd>
+<max_rh30_affecting_fuel  fire_method="li2024crujra" >95.</max_rh30_affecting_fuel>
 
 
 <!-- Canopy fluxes namelist defaults -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 8f39a4e9dd..3e9a0b6b0b 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -333,6 +333,11 @@ Combustion completeness factor for litter (unitless)
 Combustion completeness factor for CWD[Course Woody Debris] (unitless)
 </entry>
 
+<entry id="max_rh30_affecting_fuel" type="real" category="clm_physics"
+       group="lifire_inparm" >
+Value above which 30-day running relative humidity has no effect on fuel combustibility
+</entry>
+
 <entry id="ncrit" type="real" category="clm_physics"
        group="cnprecision_inparm" >
 Critical threshold for truncation of Nitrogen (truncate Nitrogen states to zero below this value)
diff --git a/src/biogeochem/CNFireBaseMod.F90 b/src/biogeochem/CNFireBaseMod.F90
index 7cc7750809..b66e44f8fb 100644
--- a/src/biogeochem/CNFireBaseMod.F90
+++ b/src/biogeochem/CNFireBaseMod.F90
@@ -68,6 +68,7 @@ module CNFireBaseMod
 
       real(r8) :: cmb_cmplt_fact_litter = 0.5_r8       ! combustion completion factor for litter (unitless)
       real(r8) :: cmb_cmplt_fact_cwd    = 0.25_r8      ! combustion completion factor for CWD (unitless)
+      real(r8) :: max_rh30_affecting_fuel = 90._r8     ! Value above which 30-day running relative humidity has no effect on fuel combustibility (%)
   end type
 
   type, public :: params_type
@@ -343,11 +344,13 @@ subroutine FireReadNML( this, NLFilename )
     real(r8) :: non_boreal_peatfire_c, cropfire_a1
     real(r8) :: rh_low, rh_hgh, bt_min, bt_max, occur_hi_gdp_tree
     real(r8) :: lfuel, ufuel, cmb_cmplt_fact_litter, cmb_cmplt_fact_cwd
+    real(r8) :: max_rh30_affecting_fuel
 
     namelist /lifire_inparm/ cli_scale, boreal_peatfire_c, pot_hmn_ign_counts_alpha, &
                              non_boreal_peatfire_c, cropfire_a1,                &
                              rh_low, rh_hgh, bt_min, bt_max, occur_hi_gdp_tree, &
-                             lfuel, ufuel, cmb_cmplt_fact_litter, cmb_cmplt_fact_cwd
+                             lfuel, ufuel, cmb_cmplt_fact_litter, cmb_cmplt_fact_cwd, &
+                             max_rh30_affecting_fuel
 
     if ( this%need_lightning_and_popdens() ) then
        cli_scale                 = cnfire_const%cli_scale
@@ -364,6 +367,7 @@ subroutine FireReadNML( this, NLFilename )
        occur_hi_gdp_tree         = cnfire_const%occur_hi_gdp_tree
        cmb_cmplt_fact_litter     = cnfire_const%cmb_cmplt_fact_litter
        cmb_cmplt_fact_cwd        = cnfire_const%cmb_cmplt_fact_cwd
+       max_rh30_affecting_fuel   = cnfire_const%max_rh30_affecting_fuel
        ! Initialize options to default values, in case they are not specified in
        ! the namelist
 
@@ -397,6 +401,7 @@ subroutine FireReadNML( this, NLFilename )
        call shr_mpi_bcast (occur_hi_gdp_tree       , mpicom)
        call shr_mpi_bcast (cmb_cmplt_fact_litter   , mpicom)
        call shr_mpi_bcast (cmb_cmplt_fact_cwd      , mpicom)
+       call shr_mpi_bcast (max_rh30_affecting_fuel , mpicom)
 
        cnfire_const%cli_scale                 = cli_scale
        cnfire_const%boreal_peatfire_c         = boreal_peatfire_c
@@ -412,6 +417,7 @@ subroutine FireReadNML( this, NLFilename )
        cnfire_const%occur_hi_gdp_tree         = occur_hi_gdp_tree
        cnfire_const%cmb_cmplt_fact_litter     = cmb_cmplt_fact_litter
        cnfire_const%cmb_cmplt_fact_cwd        = cmb_cmplt_fact_cwd
+       cnfire_const%max_rh30_affecting_fuel   = max_rh30_affecting_fuel
 
        if (masterproc) then
           write(iulog,*) ' '
diff --git a/src/biogeochem/CNFireLi2016Mod.F90 b/src/biogeochem/CNFireLi2016Mod.F90
index 955d7fe398..44e33edafc 100644
--- a/src/biogeochem/CNFireLi2016Mod.F90
+++ b/src/biogeochem/CNFireLi2016Mod.F90
@@ -179,6 +179,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          non_boreal_peatfire_c => cnfire_const%non_boreal_peatfire_c           , & ! Input:  [real(r8)         ]  (/hr) c parameter for non-boreal peatland fire
          pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
+         max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -597,7 +598,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
               afuel  =min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
               arh=1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
-              arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
+              arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/max_rh30_affecting_fuel))
               if (forc_rh(g) < rh_hgh.and. wtlf(c) > 0._r8 .and. tsoi17(c)> SHR_CONST_TKFRZ)then
                 fire_m   = ((afuel*arh30+(1._r8-afuel)*arh)**1.5_r8)*((1._r8 -max(0._r8,&
                     min(1._r8,(btran_col(c)/wtlf(c)-bt_min)/(bt_max-bt_min))))**0.5_r8)
diff --git a/src/biogeochem/CNFireLi2021Mod.F90 b/src/biogeochem/CNFireLi2021Mod.F90
index 6d504a1e26..93c384f65a 100644
--- a/src/biogeochem/CNFireLi2021Mod.F90
+++ b/src/biogeochem/CNFireLi2021Mod.F90
@@ -177,6 +177,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          non_boreal_peatfire_c => cnfire_const%non_boreal_peatfire_c           , & ! Input:  [real(r8)         ]  (/hr) c parameter for non-boreal peatland fire
          pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
+         max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -598,7 +599,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            if (trotr1_col(c)+trotr2_col(c)<=0.6_r8) then
               afuel  =min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
               arh=1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
-              arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
+              arh30=1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/max_rh30_affecting_fuel))
               if (forc_rh(g) < rh_hgh.and. wtlf(c) > 0._r8 .and. tsoi17(c)> SHR_CONST_TKFRZ)then
                 fire_m   = ((afuel*arh30+(1._r8-afuel)*arh)**1.5_r8) &
                              *((1._r8-btran_col(c)/wtlf(c))**0.5_r8)
diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index b9158d9a17..8602ff4e46 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -175,6 +175,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          non_boreal_peatfire_c => cnfire_const%non_boreal_peatfire_c           , & ! Input:  [real(r8)         ]  (/hr) c parameter for non-boreal peatland fire
          pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
+         max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -591,7 +592,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            fb = max(0.0_r8,min(1.0_r8,(fuelc(c)-lfuel)/(ufuel-lfuel)))
            afuel = min(1._r8,max(0._r8,(fuelc(c)-2500._r8)/(5000._r8-2500._r8)))
            arh = 1._r8-max(0._r8, min(1._r8,(forc_rh(g)-rh_low)/(rh_hgh-rh_low)))
-           arh30 = 1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/90._r8))
+           arh30 = 1._r8-max(cnfire_params%prh30, min(1._r8,rh30_col(c)/max_rh30_affecting_fuel))
            if (forc_rh(g) < rh_hgh.and. wtlf(c) > 0._r8 .and. tsoi17(c)> SHR_CONST_TKFRZ)then
               fire_m = ((afuel*arh30+(1._r8-afuel)*arh)**1.5_r8) &
                        *((1._r8-btran_col(c)/wtlf(c))**0.5_r8)

From 2d2e093671c922df10222243fde06cee1bf6fbe0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 20 Aug 2024 21:49:20 -0600
Subject: [PATCH 0947/1248] Add parameters for thresholds of precip for
 deforestation fire:

"PFT-dependent thresholds of P60d and P10d" in Li et al. (2013, doi:10.5194/bg-10-2293-2013):
- defo_fire_precip_thresh_bet: Value (mm/d) above which running mean daily precipitation (10 or 60 days) does not allow deforestation fire for a column with broadleaf evergreen tropical trees but no broadleaf deciduous tropical trees.
- defo_fire_precip_thresh_bdt: Vice versa
---
 bld/CLMBuildNamelist.pm                         |  3 ++-
 bld/namelist_files/namelist_defaults_ctsm.xml   |  8 ++++++++
 bld/namelist_files/namelist_definition_ctsm.xml | 10 ++++++++++
 src/biogeochem/CNFireBaseMod.F90                | 12 +++++++++++-
 src/biogeochem/CNFireLi2014Mod.F90              |  8 +++++++-
 src/biogeochem/CNFireLi2016Mod.F90              |  8 +++++++-
 src/biogeochem/CNFireLi2021Mod.F90              |  8 +++++++-
 src/biogeochem/CNFireLi2024Mod.F90              |  8 +++++++-
 8 files changed, 59 insertions(+), 6 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index d09f79afe1..155d4bb4bb 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2266,7 +2266,8 @@ sub setup_logic_cnfire {
 
   my @fire_consts = ( "rh_low", "rh_hgh", "bt_min", "bt_max", "cli_scale", "boreal_peatfire_c", "non_boreal_peatfire_c",
                       "pot_hmn_ign_counts_alpha", "cropfire_a1", "occur_hi_gdp_tree", "lfuel", "ufuel",
-                      "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd", "max_rh30_affecting_fuel" );
+                      "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd", "max_rh30_affecting_fuel",
+                      "defo_fire_precip_thresh_bet", "defo_fire_precip_thresh_bdt" );
   if ( &value_is_true($nl->get_value('use_cn')) ) {
      foreach my $item ( @fire_consts ) {
         if ( ! &value_is_true($nl_flags->{'cnfireson'} ) ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index ef797f567a..246efe04bb 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -245,6 +245,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <fire_method phys="clm4_5" >li2014qianfrc</fire_method>
 
 <max_rh30_affecting_fuel>90.</max_rh30_affecting_fuel>
+<defo_fire_precip_thresh_bet>4.0</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt>1.8</defo_fire_precip_thresh_bdt>
 
 <rh_low                   fire_method="li2014qianfrc" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2014qianfrc" >80.0d00</rh_hgh>
@@ -353,6 +355,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2021gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2021gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
 <max_rh30_affecting_fuel  fire_method="li2021gswpfrc" >90.</max_rh30_affecting_fuel>
+<defo_fire_precip_thresh_bet fire_method="li2021gswpfrc" >4.0</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt fire_method="li2021gswpfrc" >1.8</defo_fire_precip_thresh_bdt>
 
 <rh_low                   fire_method="li2024gswpfrc" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2024gswpfrc" >80.0d00</rh_hgh>
@@ -369,6 +373,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2024gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
 <max_rh30_affecting_fuel  fire_method="li2024gswpfrc" >90.</max_rh30_affecting_fuel>
+<defo_fire_precip_thresh_bet fire_method="li2024gswpfrc" >1.4</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt fire_method="li2024gswpfrc" >0.5</defo_fire_precip_thresh_bdt>
 
 <rh_low                   fire_method="li2024crujra" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2024crujra" >85.0d00</rh_hgh>
@@ -385,6 +391,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2024crujra" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024crujra" >0.28d00</cmb_cmplt_fact_cwd>
 <max_rh30_affecting_fuel  fire_method="li2024crujra" >95.</max_rh30_affecting_fuel>
+<defo_fire_precip_thresh_bet fire_method="li2024crujra" >1.8</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt fire_method="li2024crujra" >0.6</defo_fire_precip_thresh_bdt>
 
 
 <!-- Canopy fluxes namelist defaults -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 3e9a0b6b0b..92a08ab1a7 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -338,6 +338,16 @@ Combustion completeness factor for CWD[Course Woody Debris] (unitless)
 Value above which 30-day running relative humidity has no effect on fuel combustibility
 </entry>
 
+<entry id="defo_fire_precip_thresh_bet" type="real" category="clm_physics"
+       group="lifire_inparm" >
+Value (mm/d) above which running mean daily precipitation (10 or 60 days) does not allow deforestation fire for a column with broadleaf evergreen tropical trees but no broadleaf deciduous tropical trees. "PFT-dependent thresholds of P60d and P10d" in Li et al. (2013, doi:10.5194/bg-10-2293-2013).
+</entry>
+
+<entry id="defo_fire_precip_thresh_bdt" type="real" category="clm_physics"
+       group="lifire_inparm" >
+Value (mm/d) above which running mean daily precipitation (10 or 60 days) does not allow deforestation fire for a column with broadleaf deciduous tropical trees but no broadleaf evergreen tropical trees. "PFT-dependent thresholds of P60d and P10d" in Li et al. (2013, doi:10.5194/bg-10-2293-2013).
+</entry>
+
 <entry id="ncrit" type="real" category="clm_physics"
        group="cnprecision_inparm" >
 Critical threshold for truncation of Nitrogen (truncate Nitrogen states to zero below this value)
diff --git a/src/biogeochem/CNFireBaseMod.F90 b/src/biogeochem/CNFireBaseMod.F90
index b66e44f8fb..4f590ce701 100644
--- a/src/biogeochem/CNFireBaseMod.F90
+++ b/src/biogeochem/CNFireBaseMod.F90
@@ -69,6 +69,8 @@ module CNFireBaseMod
       real(r8) :: cmb_cmplt_fact_litter = 0.5_r8       ! combustion completion factor for litter (unitless)
       real(r8) :: cmb_cmplt_fact_cwd    = 0.25_r8      ! combustion completion factor for CWD (unitless)
       real(r8) :: max_rh30_affecting_fuel = 90._r8     ! Value above which 30-day running relative humidity has no effect on fuel combustibility (%)
+      real(r8) :: defo_fire_precip_thresh_bet = 4.0_r8     ! Max running mean daily precip (mm/d) allowing deforestation fire for broadleaf evergreen trees
+      real(r8) :: defo_fire_precip_thresh_bdt = 1.8_r8     ! Max running mean daily precip (mm/d) allowing deforestation fire for broadleaf deciduous trees
   end type
 
   type, public :: params_type
@@ -345,12 +347,14 @@ subroutine FireReadNML( this, NLFilename )
     real(r8) :: rh_low, rh_hgh, bt_min, bt_max, occur_hi_gdp_tree
     real(r8) :: lfuel, ufuel, cmb_cmplt_fact_litter, cmb_cmplt_fact_cwd
     real(r8) :: max_rh30_affecting_fuel
+    real(r8) :: defo_fire_precip_thresh_bet, defo_fire_precip_thresh_bdt
 
     namelist /lifire_inparm/ cli_scale, boreal_peatfire_c, pot_hmn_ign_counts_alpha, &
                              non_boreal_peatfire_c, cropfire_a1,                &
                              rh_low, rh_hgh, bt_min, bt_max, occur_hi_gdp_tree, &
                              lfuel, ufuel, cmb_cmplt_fact_litter, cmb_cmplt_fact_cwd, &
-                             max_rh30_affecting_fuel
+                             max_rh30_affecting_fuel, &
+                             defo_fire_precip_thresh_bet, defo_fire_precip_thresh_bdt
 
     if ( this%need_lightning_and_popdens() ) then
        cli_scale                 = cnfire_const%cli_scale
@@ -368,6 +372,8 @@ subroutine FireReadNML( this, NLFilename )
        cmb_cmplt_fact_litter     = cnfire_const%cmb_cmplt_fact_litter
        cmb_cmplt_fact_cwd        = cnfire_const%cmb_cmplt_fact_cwd
        max_rh30_affecting_fuel   = cnfire_const%max_rh30_affecting_fuel
+       defo_fire_precip_thresh_bet = cnfire_const%defo_fire_precip_thresh_bet
+       defo_fire_precip_thresh_bdt = cnfire_const%defo_fire_precip_thresh_bdt
        ! Initialize options to default values, in case they are not specified in
        ! the namelist
 
@@ -402,6 +408,8 @@ subroutine FireReadNML( this, NLFilename )
        call shr_mpi_bcast (cmb_cmplt_fact_litter   , mpicom)
        call shr_mpi_bcast (cmb_cmplt_fact_cwd      , mpicom)
        call shr_mpi_bcast (max_rh30_affecting_fuel , mpicom)
+       call shr_mpi_bcast (defo_fire_precip_thresh_bet, mpicom)
+       call shr_mpi_bcast (defo_fire_precip_thresh_bdt, mpicom)
 
        cnfire_const%cli_scale                 = cli_scale
        cnfire_const%boreal_peatfire_c         = boreal_peatfire_c
@@ -418,6 +426,8 @@ subroutine FireReadNML( this, NLFilename )
        cnfire_const%cmb_cmplt_fact_litter     = cmb_cmplt_fact_litter
        cnfire_const%cmb_cmplt_fact_cwd        = cmb_cmplt_fact_cwd
        cnfire_const%max_rh30_affecting_fuel   = max_rh30_affecting_fuel
+       cnfire_const%defo_fire_precip_thresh_bet = defo_fire_precip_thresh_bet
+       cnfire_const%defo_fire_precip_thresh_bdt = defo_fire_precip_thresh_bdt
 
        if (masterproc) then
           write(iulog,*) ' '
diff --git a/src/biogeochem/CNFireLi2014Mod.F90 b/src/biogeochem/CNFireLi2014Mod.F90
index fcd27a7951..11b0e79655 100644
--- a/src/biogeochem/CNFireLi2014Mod.F90
+++ b/src/biogeochem/CNFireLi2014Mod.F90
@@ -172,6 +172,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          non_boreal_peatfire_c => cnfire_const%non_boreal_peatfire_c           , & ! Input:  [real(r8)         ]  (/hr) c parameter for non-boreal peatland fire
          pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
+         defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
+         defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -607,7 +609,11 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                     fbac1(c)        = 0._r8
                     farea_burned(c) = baf_crop(c)+baf_peatf(c)
                  else
-                    cri = (4.0_r8*trotr1_col(c)+1.8_r8*trotr2_col(c))/(trotr1_col(c)+trotr2_col(c))
+                    ! Calculate the precip threshold as the area-weighted mean of that for BET and BDT
+                    cri = (defo_fire_precip_thresh_bet * trotr1_col(c) &
+                         + defo_fire_precip_thresh_bdt * trotr2_col(c)) &
+                         / (trotr1_col(c) + trotr2_col(c))
+
                     cli = (max(0._r8,min(1._r8,(cri-prec60_col(c)*secspday)/cri))**0.5)* &
                          (max(0._r8,min(1._r8,(cri-prec10_col(c)*secspday)/cri))**0.5)* &
                          max(0.0005_r8,min(1._r8,19._r8*dtrotr_col(c)*dayspyr*secspday/dt-0.001_r8))* &
diff --git a/src/biogeochem/CNFireLi2016Mod.F90 b/src/biogeochem/CNFireLi2016Mod.F90
index 44e33edafc..5396158221 100644
--- a/src/biogeochem/CNFireLi2016Mod.F90
+++ b/src/biogeochem/CNFireLi2016Mod.F90
@@ -180,6 +180,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
          max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
+         defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet      , & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
+         defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt      , & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -630,7 +632,11 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                     fbac1(c)        = 0._r8
                     farea_burned(c) = baf_crop(c)+baf_peatf(c)
                  else
-                    cri = (4.0_r8*trotr1_col(c)+1.8_r8*trotr2_col(c))/(trotr1_col(c)+trotr2_col(c))
+                    ! Calculate the precip threshold as the area-weighted mean of that for BET and BDT
+                    cri = (defo_fire_precip_thresh_bet * trotr1_col(c) &
+                         + defo_fire_precip_thresh_bdt * trotr2_col(c)) &
+                         / (trotr1_col(c) + trotr2_col(c))
+
                     cli = (max(0._r8,min(1._r8,(cri-prec60_col(c)*secspday)/cri))**0.5)* &
                          (max(0._r8,min(1._r8,(cri-prec10_col(c)*secspday)/cri))**0.5)* &
                          max(0.0005_r8,min(1._r8,19._r8*dtrotr_col(c)*dayspyr*secspday/dt-0.001_r8))* &
diff --git a/src/biogeochem/CNFireLi2021Mod.F90 b/src/biogeochem/CNFireLi2021Mod.F90
index 93c384f65a..1eecee70d8 100644
--- a/src/biogeochem/CNFireLi2021Mod.F90
+++ b/src/biogeochem/CNFireLi2021Mod.F90
@@ -178,6 +178,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
          max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
+         defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
+         defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -632,7 +634,11 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                     fbac1(c)        = 0._r8
                     farea_burned(c) = baf_crop(c)+baf_peatf(c)
                  else
-                    cri = (4.0_r8*trotr1_col(c)+1.8_r8*trotr2_col(c))/(trotr1_col(c)+trotr2_col(c))
+                    ! Calculate the precip threshold as the area-weighted mean of that for BET and BDT
+                    cri = (defo_fire_precip_thresh_bet * trotr1_col(c) &
+                         + defo_fire_precip_thresh_bdt * trotr2_col(c)) &
+                         / (trotr1_col(c) + trotr2_col(c))
+
                     cli = (max(0._r8,min(1._r8,(cri-prec60_col(c)*secspday)/cri))**0.5)* &
                          (max(0._r8,min(1._r8,(cri-prec10_col(c)*secspday)/cri))**0.5)* &
                          (15._r8*min(0.0016_r8,dtrotr_col(c)/dt*dayspyr*secspday)+0.009_r8)* &
diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 8602ff4e46..7e46a35198 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -176,6 +176,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          pot_hmn_ign_counts_alpha => cnfire_const%pot_hmn_ign_counts_alpha     , & ! Input:  [real(r8)         ]  (/person/month) Potential human ignition counts
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
          max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
+         defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
+         defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -630,7 +632,11 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                     fbac1(c)        = 0._r8
                     farea_burned(c) = baf_crop(c)+baf_peatf(c)
                  else
-                    cri = (1.4_r8*trotr1_col(c)+0.5_r8*trotr2_col(c))/(trotr1_col(c)+trotr2_col(c))
+                    ! Calculate the precip threshold as the area-weighted mean of that for BET and BDT
+                    cri = (defo_fire_precip_thresh_bet * trotr1_col(c) &
+                         + defo_fire_precip_thresh_bdt * trotr2_col(c)) &
+                         / (trotr1_col(c) + trotr2_col(c))
+
                     cli = max(0._r8,min(1._r8,1._r8-prec30_col(c)*secspday/cri))* &
                          (15._r8*min(0.0016_r8,dtrotr_col(c)/dt*dayspyr*secspday)+0.009_r8)* &
                          max(0._r8,min(1._r8,(0.25_r8-(forc_rain(c)+forc_snow(c))*secsphr)/0.25_r8))

From fbb2d89b531d9f1ccf73ba4bf23cf99f456a341d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 21 Aug 2024 08:01:04 -0600
Subject: [PATCH 0948/1248] Add parameters relating to peat fire.

- nonborpeat_fire_precip_denom: Denominator of precipitation in equation relating that to non-boreal peat fire (unitless). Eq. 9 in Li et al. (2013, doi:10.5194/bg-10-2293-2013).
- borpeat_fire_soilmoist_denom: Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless). Eq. 10 in Li et al. (2013, doi:10.5194/bg-10-2293-2013).
---
 bld/CLMBuildNamelist.pm                         |  3 ++-
 bld/namelist_files/namelist_defaults_ctsm.xml   |  5 +++++
 bld/namelist_files/namelist_definition_ctsm.xml | 10 ++++++++++
 src/biogeochem/CNFireBaseMod.F90                | 14 ++++++++++++--
 src/biogeochem/CNFireLi2014Mod.F90              |  7 +++++--
 src/biogeochem/CNFireLi2016Mod.F90              |  6 ++++--
 src/biogeochem/CNFireLi2021Mod.F90              |  6 ++++--
 src/biogeochem/CNFireLi2024Mod.F90              |  6 ++++--
 8 files changed, 46 insertions(+), 11 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 155d4bb4bb..bd710066b6 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2267,7 +2267,8 @@ sub setup_logic_cnfire {
   my @fire_consts = ( "rh_low", "rh_hgh", "bt_min", "bt_max", "cli_scale", "boreal_peatfire_c", "non_boreal_peatfire_c",
                       "pot_hmn_ign_counts_alpha", "cropfire_a1", "occur_hi_gdp_tree", "lfuel", "ufuel",
                       "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd", "max_rh30_affecting_fuel",
-                      "defo_fire_precip_thresh_bet", "defo_fire_precip_thresh_bdt" );
+                      "defo_fire_precip_thresh_bet", "defo_fire_precip_thresh_bdt",
+                      "borpeat_fire_soilmoist_denom", "nonborpeat_fire_precip_denom" );
   if ( &value_is_true($nl->get_value('use_cn')) ) {
      foreach my $item ( @fire_consts ) {
         if ( ! &value_is_true($nl_flags->{'cnfireson'} ) ) {
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 246efe04bb..faf7877302 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -247,6 +247,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <max_rh30_affecting_fuel>90.</max_rh30_affecting_fuel>
 <defo_fire_precip_thresh_bet>4.0</defo_fire_precip_thresh_bet>
 <defo_fire_precip_thresh_bdt>1.8</defo_fire_precip_thresh_bdt>
+<borpeat_fire_soilmoist_denom>0.3</borpeat_fire_soilmoist_denom>
+<nonborpeat_fire_precip_denom>1.0</nonborpeat_fire_precip_denom>
 
 <rh_low                   fire_method="li2014qianfrc" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2014qianfrc" >80.0d00</rh_hgh>
@@ -375,6 +377,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <max_rh30_affecting_fuel  fire_method="li2024gswpfrc" >90.</max_rh30_affecting_fuel>
 <defo_fire_precip_thresh_bet fire_method="li2024gswpfrc" >1.4</defo_fire_precip_thresh_bet>
 <defo_fire_precip_thresh_bdt fire_method="li2024gswpfrc" >0.5</defo_fire_precip_thresh_bdt>
+<nonborpeat_fire_precip_denom fire_method="li2024gswpfrc" >6.0</nonborpeat_fire_precip_denom>
 
 <rh_low                   fire_method="li2024crujra" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2024crujra" >85.0d00</rh_hgh>
@@ -393,6 +396,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <max_rh30_affecting_fuel  fire_method="li2024crujra" >95.</max_rh30_affecting_fuel>
 <defo_fire_precip_thresh_bet fire_method="li2024crujra" >1.8</defo_fire_precip_thresh_bet>
 <defo_fire_precip_thresh_bdt fire_method="li2024crujra" >0.6</defo_fire_precip_thresh_bdt>
+<borpeat_fire_soilmoist_denom fire_method="li2024crujra" > 0.35</borpeat_fire_soilmoist_denom>
+<nonborpeat_fire_precip_denom fire_method="li2024crujra" >6.5</nonborpeat_fire_precip_denom>
 
 
 <!-- Canopy fluxes namelist defaults -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 92a08ab1a7..d2347121c1 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -348,6 +348,16 @@ Value (mm/d) above which running mean daily precipitation (10 or 60 days) does n
 Value (mm/d) above which running mean daily precipitation (10 or 60 days) does not allow deforestation fire for a column with broadleaf deciduous tropical trees but no broadleaf evergreen tropical trees. "PFT-dependent thresholds of P60d and P10d" in Li et al. (2013, doi:10.5194/bg-10-2293-2013).
 </entry>
 
+<entry id="nonborpeat_fire_precip_denom" type="real" category="clm_physics"
+       group="lifire_inparm" >
+Denominator of precipitation in equation relating that to non-boreal peat fire (unitless). Eq. 9 in Li et al. (2013, doi:10.5194/bg-10-2293-2013).
+</entry>
+
+<entry id="borpeat_fire_soilmoist_denom" type="real" category="clm_physics"
+       group="lifire_inparm" >
+Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless). Eq. 10 in Li et al. (2013, doi:10.5194/bg-10-2293-2013).
+</entry>
+
 <entry id="ncrit" type="real" category="clm_physics"
        group="cnprecision_inparm" >
 Critical threshold for truncation of Nitrogen (truncate Nitrogen states to zero below this value)
diff --git a/src/biogeochem/CNFireBaseMod.F90 b/src/biogeochem/CNFireBaseMod.F90
index 4f590ce701..5e4fd2caef 100644
--- a/src/biogeochem/CNFireBaseMod.F90
+++ b/src/biogeochem/CNFireBaseMod.F90
@@ -71,7 +71,9 @@ module CNFireBaseMod
       real(r8) :: max_rh30_affecting_fuel = 90._r8     ! Value above which 30-day running relative humidity has no effect on fuel combustibility (%)
       real(r8) :: defo_fire_precip_thresh_bet = 4.0_r8     ! Max running mean daily precip (mm/d) allowing deforestation fire for broadleaf evergreen trees
       real(r8) :: defo_fire_precip_thresh_bdt = 1.8_r8     ! Max running mean daily precip (mm/d) allowing deforestation fire for broadleaf deciduous trees
-  end type
+      real(r8) :: borpeat_fire_soilmoist_denom = 0.3  ! Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless)
+      real(r8) :: nonborpeat_fire_precip_denom = 1.0  ! Denominator of precipitation in equation relating that to non-boreal peat fire (unitless)
+      end type
 
   type, public :: params_type
      real(r8) :: prh30                ! Factor related to dependence of fuel combustibility on 30-day running mean of relative humidity (unitless)
@@ -348,13 +350,15 @@ subroutine FireReadNML( this, NLFilename )
     real(r8) :: lfuel, ufuel, cmb_cmplt_fact_litter, cmb_cmplt_fact_cwd
     real(r8) :: max_rh30_affecting_fuel
     real(r8) :: defo_fire_precip_thresh_bet, defo_fire_precip_thresh_bdt
+    real(r8) :: borpeat_fire_soilmoist_denom, nonborpeat_fire_precip_denom
 
     namelist /lifire_inparm/ cli_scale, boreal_peatfire_c, pot_hmn_ign_counts_alpha, &
                              non_boreal_peatfire_c, cropfire_a1,                &
                              rh_low, rh_hgh, bt_min, bt_max, occur_hi_gdp_tree, &
                              lfuel, ufuel, cmb_cmplt_fact_litter, cmb_cmplt_fact_cwd, &
                              max_rh30_affecting_fuel, &
-                             defo_fire_precip_thresh_bet, defo_fire_precip_thresh_bdt
+                             defo_fire_precip_thresh_bet, defo_fire_precip_thresh_bdt, &
+                             borpeat_fire_soilmoist_denom, nonborpeat_fire_precip_denom
 
     if ( this%need_lightning_and_popdens() ) then
        cli_scale                 = cnfire_const%cli_scale
@@ -374,6 +378,8 @@ subroutine FireReadNML( this, NLFilename )
        max_rh30_affecting_fuel   = cnfire_const%max_rh30_affecting_fuel
        defo_fire_precip_thresh_bet = cnfire_const%defo_fire_precip_thresh_bet
        defo_fire_precip_thresh_bdt = cnfire_const%defo_fire_precip_thresh_bdt
+       borpeat_fire_soilmoist_denom = cnfire_const%borpeat_fire_soilmoist_denom
+       nonborpeat_fire_precip_denom = cnfire_const%nonborpeat_fire_precip_denom
        ! Initialize options to default values, in case they are not specified in
        ! the namelist
 
@@ -410,6 +416,8 @@ subroutine FireReadNML( this, NLFilename )
        call shr_mpi_bcast (max_rh30_affecting_fuel , mpicom)
        call shr_mpi_bcast (defo_fire_precip_thresh_bet, mpicom)
        call shr_mpi_bcast (defo_fire_precip_thresh_bdt, mpicom)
+       call shr_mpi_bcast (borpeat_fire_soilmoist_denom, mpicom)
+       call shr_mpi_bcast (nonborpeat_fire_precip_denom, mpicom)
 
        cnfire_const%cli_scale                 = cli_scale
        cnfire_const%boreal_peatfire_c         = boreal_peatfire_c
@@ -428,6 +436,8 @@ subroutine FireReadNML( this, NLFilename )
        cnfire_const%max_rh30_affecting_fuel   = max_rh30_affecting_fuel
        cnfire_const%defo_fire_precip_thresh_bet = defo_fire_precip_thresh_bet
        cnfire_const%defo_fire_precip_thresh_bdt = defo_fire_precip_thresh_bdt
+       cnfire_const%borpeat_fire_soilmoist_denom = borpeat_fire_soilmoist_denom
+       cnfire_const%nonborpeat_fire_precip_denom = nonborpeat_fire_precip_denom
 
        if (masterproc) then
           write(iulog,*) ' '
diff --git a/src/biogeochem/CNFireLi2014Mod.F90 b/src/biogeochem/CNFireLi2014Mod.F90
index 11b0e79655..4078da740b 100644
--- a/src/biogeochem/CNFireLi2014Mod.F90
+++ b/src/biogeochem/CNFireLi2014Mod.F90
@@ -174,6 +174,9 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          boreal_peatfire_c  => cnfire_const%boreal_peatfire_c                  , & ! Input:  [real(r8)         ]  (/hr) c parameter for boreal peatland fire
          defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
          defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
+         borpeat_fire_soilmoist_denom  => cnfire_const%borpeat_fire_soilmoist_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless)
+         nonborpeat_fire_precip_denom  => cnfire_const%nonborpeat_fire_precip_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of precipitation in equation relating that to non-boreal peat fire (unitless)
+
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -534,10 +537,10 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         g= col%gridcell(c)
         if(grc%latdeg(g) < cnfire_const%borealat )then
            baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
-                min(1._r8,(4.0_r8-prec60_col(c)*secspday)/ &
+                min(1._r8,(4.0_r8-prec60_col(c)*secspday/nonborpeat_fire_precip_denom)/ &
                 4.0_r8))**2*peatf_lf(c)*(1._r8-fsat(c))
         else
-           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/0.3_r8))* &
+           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/borpeat_fire_soilmoist_denom))* &
                 max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
                 (1._r8-fsat(c))
         end if
diff --git a/src/biogeochem/CNFireLi2016Mod.F90 b/src/biogeochem/CNFireLi2016Mod.F90
index 5396158221..b7c14938f7 100644
--- a/src/biogeochem/CNFireLi2016Mod.F90
+++ b/src/biogeochem/CNFireLi2016Mod.F90
@@ -182,6 +182,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
          defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet      , & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
          defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt      , & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
+         borpeat_fire_soilmoist_denom  => cnfire_const%borpeat_fire_soilmoist_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless)
+         nonborpeat_fire_precip_denom  => cnfire_const%nonborpeat_fire_precip_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of precipitation in equation relating that to non-boreal peat fire (unitless)
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -550,10 +552,10 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         g= col%gridcell(c)
         if(grc%latdeg(g) < cnfire_const%borealat )then
            baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
-                min(1._r8,(4.0_r8-prec60_col(c)*secspday)/ &
+                min(1._r8,(4.0_r8-prec60_col(c)*secspday/nonborpeat_fire_precip_denom)/ &
                 4.0_r8))**2*peatf_lf(c)*(1._r8-fsat(c))
         else
-           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/0.3_r8))* &
+           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/borpeat_fire_soilmoist_denom))* &
                 max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
                 (1._r8-fsat(c))
         end if
diff --git a/src/biogeochem/CNFireLi2021Mod.F90 b/src/biogeochem/CNFireLi2021Mod.F90
index 1eecee70d8..d1fd9338b8 100644
--- a/src/biogeochem/CNFireLi2021Mod.F90
+++ b/src/biogeochem/CNFireLi2021Mod.F90
@@ -180,6 +180,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
          defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
          defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
+         borpeat_fire_soilmoist_denom  => cnfire_const%borpeat_fire_soilmoist_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless)
+         nonborpeat_fire_precip_denom  => cnfire_const%nonborpeat_fire_precip_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of precipitation in equation relating that to non-boreal peat fire (unitless)
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -551,10 +553,10 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         g= col%gridcell(c)
         if(grc%latdeg(g) < cnfire_const%borealat )then
            baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
-                min(1._r8,(4.0_r8-prec60_col(c)*secspday)/ &
+                min(1._r8,(4.0_r8-prec60_col(c)*secspday/nonborpeat_fire_precip_denom)/ &
                 4.0_r8))**2*peatf_lf(c)*(1._r8-fsat(c))
         else
-           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/0.3_r8))* &
+           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/borpeat_fire_soilmoist_denom))* &
                 max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
                 (1._r8-fsat(c))
         end if
diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 7e46a35198..4b7182f252 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -178,6 +178,8 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          max_rh30_affecting_fuel  => cnfire_const%max_rh30_affecting_fuel      , & ! Input:  [real(r8)         ]  (%) Value above which 30-day running relative humidity has no effect on fuel combustibility
          defo_fire_precip_thresh_bet  => cnfire_const%defo_fire_precip_thresh_bet, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf evergreen trees
          defo_fire_precip_thresh_bdt  => cnfire_const%defo_fire_precip_thresh_bdt, & ! Input:  [real(r8)         ]  (mm/day) Max running mean daily precip allowing deforestation fire for broadleaf deciduous trees
+         borpeat_fire_soilmoist_denom  => cnfire_const%borpeat_fire_soilmoist_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless)
+         nonborpeat_fire_precip_denom  => cnfire_const%nonborpeat_fire_precip_denom, & ! Input:  [real(r8)         ]  (unitless) Denominator of precipitation in equation relating that to non-boreal peat fire (unitless)
 
          fsr_pft            => pftcon%fsr_pft                                  , & ! Input:
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
@@ -543,12 +545,12 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         if(grc%latdeg(g) < cnfire_const%borealat )then
             if ((trotr1_col(c)+trotr2_col(c))*col%wtgcell(c)<=0.8_r8.and.trotr1_col(c)+trotr2_col(c)>0.0_r8) then
                baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
-                     min(1._r8,(1._r8-prec30_col(c)*secspday/6._r8)))*peatf_lf(c)
+                     min(1._r8,(1._r8-prec30_col(c)*secspday/nonborpeat_fire_precip_denom)))*peatf_lf(c)
             else
                baf_peatf(c) = 0._r8
             end if
         else
-           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/0.3_r8))* &
+           baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/borpeat_fire_soilmoist_denom))* &
                 max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
                 (1._r8-fsat(c))
         end if

From 0f5819f240a258558b3b2161d7a89676b8a07a91 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 21 Aug 2024 10:56:59 -0600
Subject: [PATCH 0949/1248] black and clarified tod reference

---
 cime_config/buildnml | 50 ++++++++++++++++++++++++++------------------
 1 file changed, 30 insertions(+), 20 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 06a447e443..cbefd4f155 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -184,7 +184,9 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_path = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -291,13 +293,17 @@ def buildnml(case, caseroot, compname):
         if (yr_start != None) and (yr_end != None):
             nyr = yr_end - yr_start + 1
             if (yr_end <= 0) or (yr_start <= 0):
-                logger.error("ERROR: Year start and end are both negative and should not be")
+                logger.error(
+                    "ERROR: Year start and end are both negative and should not be"
+                )
             clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts)
         else:
             logger.warning(
                 "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model"
             )
-            logger.warning("         as it expects regular atmosphere forcing that is cycled over")
+            logger.warning(
+                "         as it expects regular atmosphere forcing that is cycled over"
+            )
 
     infile = os.path.join(ctsmconf, "namelist")
 
@@ -311,7 +317,9 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
+    config_cache_file = os.path.join(
+        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
+    )
 
     # -----------------------------------------------------
     # Clear out old data
@@ -351,21 +359,19 @@ def buildnml(case, caseroot, compname):
             compnames = ["clm4", "clm5", "clm2"]
             for comp in compnames:
                 if "PLUMBER2" in clm_usrdat_name:
-                    clm_startfile = "%s.%s%s.r.%s-%s.nc" % (
-                        run_refcase,
-                        comp,
-                        inst_string,
-                        run_refdate,
-                        start_tod,
-                    )
+                    # start_tod is supplied for PLUMBER cases
+                    tod = start_tod
                 else:
-                    clm_startfile = "%s.%s%s.r.%s-%s.nc" % (
-                        run_refcase,
-                        comp,
-                        inst_string,
-                        run_refdate,
-                        run_reftod,
-                    )
+                    # run_reftod is supplied for other cases
+                    tod = run_reftod
+
+                clm_startfile = "%s.%s%s.r.%s-%s.nc" % (
+                    run_refcase,
+                    comp,
+                    inst_string,
+                    run_refdate,
+                    tod,
+                )
                 if os.path.exists(os.path.join(rundir, clm_startfile)):
                     break
                 else:
@@ -383,7 +389,9 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning("WARNING: Could NOT find a start file named " + clm_startfile)
+                logger.warning(
+                    "WARNING: Could NOT find a start file named " + clm_startfile
+                )
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -394,7 +402,9 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
+        create_namelist_infile(
+            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
+        )
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From b6fc52f6cfdb72c4334b4e035bb9cc0f66774587 Mon Sep 17 00:00:00 2001
From: Teagan King <tking@ucar.edu>
Date: Wed, 21 Aug 2024 11:00:53 -0600
Subject: [PATCH 0950/1248] undo black changes

---
 cime_config/buildnml | 24 ++++++------------------
 1 file changed, 6 insertions(+), 18 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index cbefd4f155..2c4a320046 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -184,9 +184,7 @@ def buildnml(case, caseroot, compname):
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
 
     config_cache_text = _config_cache_template.format(clm_phys=clm_phys)
-    config_cache_path = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
     with open(config_cache_path, "w") as config_cache_file:
         config_cache_file.write(config_cache_text)
 
@@ -293,17 +291,13 @@ def buildnml(case, caseroot, compname):
         if (yr_start != None) and (yr_end != None):
             nyr = yr_end - yr_start + 1
             if (yr_end <= 0) or (yr_start <= 0):
-                logger.error(
-                    "ERROR: Year start and end are both negative and should not be"
-                )
+                logger.error("ERROR: Year start and end are both negative and should not be")
             clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts)
         else:
             logger.warning(
                 "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model"
             )
-            logger.warning(
-                "         as it expects regular atmosphere forcing that is cycled over"
-            )
+            logger.warning("         as it expects regular atmosphere forcing that is cycled over")
 
     infile = os.path.join(ctsmconf, "namelist")
 
@@ -317,9 +311,7 @@ def buildnml(case, caseroot, compname):
         lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file)
         lndfrac_setting = "-lnd_frac " + lndfrac_file
 
-    config_cache_file = os.path.join(
-        caseroot, "Buildconf", compname + "conf", "config_cache.xml"
-    )
+    config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml")
 
     # -----------------------------------------------------
     # Clear out old data
@@ -389,9 +381,7 @@ def buildnml(case, caseroot, compname):
                         break
 
             if not os.path.exists(os.path.join(rundir, clm_startfile)):
-                logger.warning(
-                    "WARNING: Could NOT find a start file named " + clm_startfile
-                )
+                logger.warning("WARNING: Could NOT find a start file named " + clm_startfile)
             clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile)
         else:
             clm_icfile = ""
@@ -402,9 +392,7 @@ def buildnml(case, caseroot, compname):
         user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string)
         namelist_infile = os.path.join(ctsmconf, "namelist")
 
-        create_namelist_infile(
-            case, user_nl_file, namelist_infile, "\n".join(infile_lines)
-        )
+        create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
 
         cmd = os.path.join(lnd_root, "bld", "build-namelist")
 

From a3edb472cff1078bc702b4f9666c33d5d458590b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 21 Aug 2024 11:32:20 -0600
Subject: [PATCH 0951/1248] Ensure new parameters are double-precision.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 30 +++++++++----------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index faf7877302..e18066848e 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -244,11 +244,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <fire_method phys="clm5_0" >li2016crufrc</fire_method>
 <fire_method phys="clm4_5" >li2014qianfrc</fire_method>
 
-<max_rh30_affecting_fuel>90.</max_rh30_affecting_fuel>
-<defo_fire_precip_thresh_bet>4.0</defo_fire_precip_thresh_bet>
-<defo_fire_precip_thresh_bdt>1.8</defo_fire_precip_thresh_bdt>
-<borpeat_fire_soilmoist_denom>0.3</borpeat_fire_soilmoist_denom>
-<nonborpeat_fire_precip_denom>1.0</nonborpeat_fire_precip_denom>
+<max_rh30_affecting_fuel>90.d00</max_rh30_affecting_fuel>
+<defo_fire_precip_thresh_bet>4.0d00</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt>1.8d00</defo_fire_precip_thresh_bdt>
+<borpeat_fire_soilmoist_denom>0.3d00</borpeat_fire_soilmoist_denom>
+<nonborpeat_fire_precip_denom>1.0d00</nonborpeat_fire_precip_denom>
 
 <rh_low                   fire_method="li2014qianfrc" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2014qianfrc" >80.0d00</rh_hgh>
@@ -357,8 +357,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2021gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2021gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
 <max_rh30_affecting_fuel  fire_method="li2021gswpfrc" >90.</max_rh30_affecting_fuel>
-<defo_fire_precip_thresh_bet fire_method="li2021gswpfrc" >4.0</defo_fire_precip_thresh_bet>
-<defo_fire_precip_thresh_bdt fire_method="li2021gswpfrc" >1.8</defo_fire_precip_thresh_bdt>
+<defo_fire_precip_thresh_bet fire_method="li2021gswpfrc" >4.0d00</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt fire_method="li2021gswpfrc" >1.8d00</defo_fire_precip_thresh_bdt>
 
 <rh_low                   fire_method="li2024gswpfrc" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2024gswpfrc" >80.0d00</rh_hgh>
@@ -374,10 +374,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <ufuel                    fire_method="li2024gswpfrc" >825.d00</ufuel>
 <cmb_cmplt_fact_litter    fire_method="li2024gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
-<max_rh30_affecting_fuel  fire_method="li2024gswpfrc" >90.</max_rh30_affecting_fuel>
-<defo_fire_precip_thresh_bet fire_method="li2024gswpfrc" >1.4</defo_fire_precip_thresh_bet>
-<defo_fire_precip_thresh_bdt fire_method="li2024gswpfrc" >0.5</defo_fire_precip_thresh_bdt>
-<nonborpeat_fire_precip_denom fire_method="li2024gswpfrc" >6.0</nonborpeat_fire_precip_denom>
+<max_rh30_affecting_fuel  fire_method="li2024gswpfrc" >90.d00</max_rh30_affecting_fuel>
+<defo_fire_precip_thresh_bet fire_method="li2024gswpfrc" >1.4d00</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt fire_method="li2024gswpfrc" >0.5d00</defo_fire_precip_thresh_bdt>
+<nonborpeat_fire_precip_denom fire_method="li2024gswpfrc" >6.0d00</nonborpeat_fire_precip_denom>
 
 <rh_low                   fire_method="li2024crujra" >30.0d00</rh_low>
 <rh_hgh                   fire_method="li2024crujra" >85.0d00</rh_hgh>
@@ -394,10 +394,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2024crujra" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2024crujra" >0.28d00</cmb_cmplt_fact_cwd>
 <max_rh30_affecting_fuel  fire_method="li2024crujra" >95.</max_rh30_affecting_fuel>
-<defo_fire_precip_thresh_bet fire_method="li2024crujra" >1.8</defo_fire_precip_thresh_bet>
-<defo_fire_precip_thresh_bdt fire_method="li2024crujra" >0.6</defo_fire_precip_thresh_bdt>
-<borpeat_fire_soilmoist_denom fire_method="li2024crujra" > 0.35</borpeat_fire_soilmoist_denom>
-<nonborpeat_fire_precip_denom fire_method="li2024crujra" >6.5</nonborpeat_fire_precip_denom>
+<defo_fire_precip_thresh_bet fire_method="li2024crujra" >1.8d00</defo_fire_precip_thresh_bet>
+<defo_fire_precip_thresh_bdt fire_method="li2024crujra" >0.6d00</defo_fire_precip_thresh_bdt>
+<borpeat_fire_soilmoist_denom fire_method="li2024crujra" > 0.35d00</borpeat_fire_soilmoist_denom>
+<nonborpeat_fire_precip_denom fire_method="li2024crujra" >6.5d00</nonborpeat_fire_precip_denom>
 
 
 <!-- Canopy fluxes namelist defaults -->

From 53a1874b48c82591f45212ba7df5c29254e61a4c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 21 Aug 2024 12:01:57 -0600
Subject: [PATCH 0952/1248] CAM_SETS_DRV_FLDS tests don't need to have
 drv_flds_in settings to be explicit

---
 bld/unit_testers/build-namelist_test.pl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 1b54f29d92..de5a9b0e13 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -454,8 +454,8 @@ sub cat_and_create_namelistinfile {
    $mode = "-phys $phys CAM_SETS_DRV_FLDS";
    &make_config_cache($phys);
    foreach my $options (
-                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam6.0 --infile empty_user_nl_clm",
-                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --no-megan --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam7.0 --infile empty_user_nl_clm",
+                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam6.0 --infile empty_user_nl_clm",
+                      "--res 1.9x2.5 --mask gx1v7 --bgc sp --use_case 20thC_transient --namelist '&a start_ymd=19790101/' --lnd_tuning_mode ${phys}_cam7.0 --infile empty_user_nl_clm",
                      ) {
       &make_env_run( 'LND_SETS_DUST_EMIS_DRV_FLDS'=>"FALSE" );
       eval{ system( "$bldnml --envxml_dir . $options > $tempfile 2>&1 " ); };
@@ -1286,7 +1286,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "bad_megan_spec"            =>{ options=>"-envxml_dir . -bgc bgc -megan",
-                                     namelst=>"megan_specifier='ZZTOP=zztop'",
+                                     namelst=>"megan_specifier='ZZTOP=zztop%'",
                                      phys=>"clm4_5",
                                    },
      "FUN_wo_flexCN"             =>{ options=>"-envxml_dir . -bgc bgc",

From 717f957123f1b10dd2676438f7dcb7b95aa31c59 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 21 Aug 2024 12:10:19 -0600
Subject: [PATCH 0953/1248] Get working with bringing in CAM drv_flds_in

Get it working with bringing in the CAM drv_flds_in file.
And make it not matter on the --megan --drydep --fire_emis options.
Also do dust_emis before the other drv_flds_in namelists,
so the CAM namelist is loaded.
---
 bld/CLMBuildNamelist.pm | 72 ++++++++++++++++++++---------------------
 1 file changed, 36 insertions(+), 36 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index e4cc50614c..1fad577c51 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1449,7 +1449,7 @@ sub setup_cmdl_vichydro {
 
 sub process_namelist_commandline_namelist {
   # Process the commandline '-namelist' arg.
-  my ($opts, $definition, $nl, $envxml_ref) = @_;
+  my ($opts, $definition, $nl, $envxml_ref, %settings) = @_;
 
   if (defined $opts->{'namelist'}) {
     # Parse commandline namelist
@@ -1471,7 +1471,7 @@ sub process_namelist_commandline_namelist {
 }
 
 sub process_namelist_infile {
-   my ($definition, $nl, $envxml_ref, $infile) = @_;
+   my ($definition, $nl, $envxml_ref, $infile, %settings) = @_;
 
    # Make sure a valid file was found
    if (    -f "$infile" ) {
@@ -1493,7 +1493,7 @@ sub process_namelist_infile {
 
    # Merge input values into namelist.  Previously specified values have higher precedence
    # and are not overwritten.
-   $nl->merge_nl($nl_infile_valid);
+   $nl->merge_nl($nl_infile_valid, %settings);
 }
 
 #-------------------------------------------------------------------------------
@@ -1756,6 +1756,12 @@ sub process_namelist_inline_logic {
   ##################################
   setup_logic_lightning_streams($opts,  $nl_flags, $definition, $defaults, $nl);
 
+  ######################################
+  # namelist options for dust emissions
+  ######################################
+  setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
+  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);
+
   #################################
   # namelist group: drydep_inparm #
   #################################
@@ -1766,12 +1772,6 @@ sub process_namelist_inline_logic {
   #################################
   setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl);
 
-  ######################################
-  # namelist options for dust emissions
-  ######################################
-  setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
-  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);
-
   #################################
   # namelist group: megan_emis_nl #
   #################################
@@ -3998,17 +3998,18 @@ sub setup_logic_lightning_streams {
 sub setup_logic_dry_deposition {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
+  my @list = ( "drydep_list", "dep_data_file");
   if ($opts->{'drydep'} ) {
-    if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
-       $log->warning("DryDeposition can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
-                     "   Use the '--no-drydep' option when '-bgc fates' is activated");
-    }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'drydep_list');
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dep_data_file');
-  } else {
-    if ( defined($nl->get_value('drydep_list')) ) {
-      $log->fatal_error("drydep_list defined, but drydep option NOT set");
-    }
+  }
+  if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+     foreach my $var ( @list ) {
+        if ( defined($nl->get_value($var)) ) {
+           $log->warning("DryDeposition $var is being set and can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
+                         "   Use the '--no-drydep' option when '-bgc fates' is activated");
+        }
+     }
   }
 }
 
@@ -4017,20 +4018,20 @@ sub setup_logic_dry_deposition {
 sub setup_logic_fire_emis {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
+  my @list = ( "fire_emis_eleveated", "fire_emis_factors_file", "fire_emis_specifier");
+
   if ($opts->{'fire_emis'} ) {
-     if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
-       $log->warning("Fire emission can NOT be on when FATES is also on.\n" .
-                   "  DON'T use the '-fire_emis' option when '-bgc fates' is activated");
-    }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_factors_file');
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_specifier');
-  } else {
-    if ( defined($nl->get_value('fire_emis_elevated'))     ||
-         defined($nl->get_value('fire_emis_factors_file')) ||
-         defined($nl->get_value('fire_emis_specifier')) ) {
-      $log->fatal_error("fire_emission setting defined: fire_emis_elevated, fire_emis_factors_file, or fire_emis_specifier, but fire_emis option NOT set");
-    }
   }
+  foreach my $var ( @list ) {
+     if ( defined($nl->get_value($var)) ) {
+        if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+          $log->warning("Fire emission option $var can NOT be on when FATES is also on.\n" .
+                      "  DON'T use the '--fire_emis' option when '--bgc fates' is activated");
+       }
+     }
+   }
 }
 
 #-------------------------------------------------------------------------------
@@ -4094,7 +4095,8 @@ sub setup_logic_dust_emis {
       }
       # Now process the CAM drv_flds_in to get the dust settings
       my $infile = $opts->{'envxml_dir'} . "/Buildconf/camconf/drv_flds_in";
-      process_namelist_infile( $definition, $nl, $envxml_ref, $infile );
+      $log->verbose_message("Read in the drv_flds_in file generated by CAM's build-namelist");
+      process_namelist_infile( $definition, $nl, $envxml_ref, $infile, 'die_on_conflict'=>1 );
   }
 }
 
@@ -4115,17 +4117,15 @@ sub setup_logic_megan {
   }
 
   if ($nl_flags->{'megan'} ) {
-    if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
-       $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
-                   "   Use the '-no-megan' option when '-bgc fates' is activated");
-    }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_specifier');
-    check_megan_spec( $opts, $nl, $definition );
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_factors_file');
-  } else {
-    if ( defined($nl->get_value('megan_specifier')) ||
+  }
+  if ( defined($nl->get_value('megan_specifier')) ||
          defined($nl->get_value('megan_factors_file')) ) {
-      $log->fatal_error("megan_specifier or megan_factors_file defined, but megan option NOT set");
+    check_megan_spec( $opts, $nl, $definition );
+    if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+      $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
+                    "   Use the '-no-megan' option when '-bgc fates' is activated");
     }
   }
 }

From 973f5e7bbcf1f6d9ac1867a7c6cc85e352373828 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 21 Aug 2024 13:21:52 -0600
Subject: [PATCH 0954/1248] Make one more constant double-precision.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e18066848e..8aacd3a64d 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -356,7 +356,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <ufuel                    fire_method="li2021gswpfrc" >1050.d00</ufuel>
 <cmb_cmplt_fact_litter    fire_method="li2021gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2021gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
-<max_rh30_affecting_fuel  fire_method="li2021gswpfrc" >90.</max_rh30_affecting_fuel>
+<max_rh30_affecting_fuel  fire_method="li2021gswpfrc" >90.d00</max_rh30_affecting_fuel>
 <defo_fire_precip_thresh_bet fire_method="li2021gswpfrc" >4.0d00</defo_fire_precip_thresh_bet>
 <defo_fire_precip_thresh_bdt fire_method="li2021gswpfrc" >1.8d00</defo_fire_precip_thresh_bdt>
 

From 45eae6057294a73e8a0b05df725615f6525eaaaf Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:24:04 -0600
Subject: [PATCH 0955/1248] Update buildnml to minimize duplication

---
 cime_config/buildnml | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 2c4a320046..e9849a9e50 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -226,23 +226,19 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
+        if ("NEON" in clm_usrdat_name) or ("PLUMBER2" in clm_usrdat_name) and clm_force_coldstart == "off":
+            if "NEON" in clm_usrdat_name:
+                 match = "\w\w\w\w\"
+            if "PLUMBER2" in clm_usrdat_name:
+                 match = "\w\w-\w\w\w\"
             if ("_transient" in clm_nml_use_case) and (
-                re.fullmatch(r"\w\w\w\w\.transient", casename) is None
+                re.fullmatch(r"{}.transient".format(match), casename) is None
                 or clm_usrdat_name is "NEON.PRISM"
             ):
                 logger.warning(
                     "WARNING: Do you have appropriate initial conditions for this simulation?"
                     + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
                 )
-        if "PLUMBER2" in clm_usrdat_name and clm_force_coldstart == "off":
-            if ("_transient" in clm_nml_use_case) and (
-                re.fullmatch(r"\w\w-\w\w\w\.transient", casename) is None
-            ):
-                logger.warning(
-                    "WARNING: Do you have appropriate initial conditions for this simulation?"
-                    + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
-                )
 
     if comp_atm != "datm":
         nomeg = "-no-megan"

From 7cf865d9e9f5ebf2a0966c7d2c2a931acf0b9caf Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:26:32 -0600
Subject: [PATCH 0956/1248] Update match

---
 cime_config/buildnml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index e9849a9e50..19574b0ba6 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -228,9 +228,9 @@ def buildnml(case, caseroot, compname):
         # Write warning about initial condition data
         if ("NEON" in clm_usrdat_name) or ("PLUMBER2" in clm_usrdat_name) and clm_force_coldstart == "off":
             if "NEON" in clm_usrdat_name:
-                 match = "\w\w\w\w\"
+                 match = '\w\w\w\w\'
             if "PLUMBER2" in clm_usrdat_name:
-                 match = "\w\w-\w\w\w\"
+                 match = '\w\w-\w\w\w\'
             if ("_transient" in clm_nml_use_case) and (
                 re.fullmatch(r"{}.transient".format(match), casename) is None
                 or clm_usrdat_name is "NEON.PRISM"

From 82556be443579e6235bda4f39a0009520705e763 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:32:39 -0600
Subject: [PATCH 0957/1248] Update buildnml for fullmatch failure

---
 cime_config/buildnml | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 19574b0ba6..2525624c0e 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -227,14 +227,19 @@ def buildnml(case, caseroot, compname):
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
         if ("NEON" in clm_usrdat_name) or ("PLUMBER2" in clm_usrdat_name) and clm_force_coldstart == "off":
+            warning_init_conditions = False
             if "NEON" in clm_usrdat_name:
-                 match = '\w\w\w\w\'
+                if ("_transient" in clm_nml_use_case) and (
+                    re.fullmatch(r"\w\w\w\w\.transient", casename) is None
+                    or clm_usrdat_name is "NEON.PRISM"
+                ):
+                    warning_init_conditions = True
             if "PLUMBER2" in clm_usrdat_name:
-                 match = '\w\w-\w\w\w\'
-            if ("_transient" in clm_nml_use_case) and (
-                re.fullmatch(r"{}.transient".format(match), casename) is None
-                or clm_usrdat_name is "NEON.PRISM"
-            ):
+                if ("_transient" in clm_nml_use_case) and (
+                    re.fullmatch(r"\w\w-\w\w\w\.transient", casename) is None
+                ):
+                    warning_init_conditions = True
+            if warning_init_conditions == True:
                 logger.warning(
                     "WARNING: Do you have appropriate initial conditions for this simulation?"
                     + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"

From 07f66fde3e2ff5000f7986b600a98bf3eb8f9908 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:37:43 -0600
Subject: [PATCH 0958/1248] Update buildnml - attempt at black fix

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 2525624c0e..11ac16cf9a 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -226,7 +226,7 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if ("NEON" in clm_usrdat_name) or ("PLUMBER2" in clm_usrdat_name) and clm_force_coldstart == "off":
+        if "NEON" in clm_usrdat_name or "PLUMBER2" in clm_usrdat_name and clm_force_coldstart == "off":
             warning_init_conditions = False
             if "NEON" in clm_usrdat_name:
                 if ("_transient" in clm_nml_use_case) and (

From d18b369830dc2f5e6f4945d7a765110a91f5c567 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:44:18 -0600
Subject: [PATCH 0959/1248] Update buildnml based on subset of local black
 changes

---
 cime_config/buildnml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 11ac16cf9a..900f36131d 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -226,7 +226,11 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
-        if "NEON" in clm_usrdat_name or "PLUMBER2" in clm_usrdat_name and clm_force_coldstart == "off":
+        if (
+            "NEON" in clm_usrdat_name
+            or "PLUMBER2" in clm_usrdat_name
+            and clm_force_coldstart == "off":
+        ):
             warning_init_conditions = False
             if "NEON" in clm_usrdat_name:
                 if ("_transient" in clm_nml_use_case) and (

From 8b72bb5f27a971880d8e5bf41bb93a08c31f90e7 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:46:50 -0600
Subject: [PATCH 0960/1248] Update buildnml local black changes remove colon

---
 cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index 900f36131d..e9b7a610cd 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -229,7 +229,7 @@ def buildnml(case, caseroot, compname):
         if (
             "NEON" in clm_usrdat_name
             or "PLUMBER2" in clm_usrdat_name
-            and clm_force_coldstart == "off":
+            and clm_force_coldstart == "off"
         ):
             warning_init_conditions = False
             if "NEON" in clm_usrdat_name:

From 0b5888d61ea83a0895f4b2381383c1d9adf6ca7e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 21 Aug 2024 19:45:35 -0600
Subject: [PATCH 0961/1248] Update abm and peatf rawdata file names in
 gen_mksurfdata_namelist.xml

---
 tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index 3cb168e8fb..f9bb6a3a02 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -162,7 +162,7 @@ version of the raw dataset will probably go away.
 
   <mksrf_fpeat>
     <entry>
-      <data_filename>lnd/clm2/rawdata/mksrf_peatf_0.5x0.5_AVHRR_simyr2000.c130228.nc</data_filename>
+      <data_filename>lnd/clm2/rawdata/mksrf_peatf_0.5x0.5_simyr2000.c240821.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.5x0.5_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
   </mksrf_fpeat>
@@ -176,7 +176,7 @@ version of the raw dataset will probably go away.
 
   <mksrf_fabm>
     <entry>
-      <data_filename>lnd/clm2/rawdata/mksrf_abm_0.5x0.5_AVHRR_simyr2000.c130201.nc</data_filename>
+      <data_filename>lnd/clm2/rawdata/mksrf_abm_0.5x0.5_simyr2000.c240821.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.5x0.5_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
     <entry pft_years="PtVg">

From 822618e669f08af5e4338f4d29e4a9d0ac54a74a Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 15 Aug 2024 13:10:57 -0600
Subject: [PATCH 0962/1248] add test, add warning

---
 bld/CLMBuildNamelist.pm                 | 7 +++++++
 bld/unit_testers/build-namelist_test.pl | 4 ++++
 2 files changed, 11 insertions(+)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b99be288e7..b5e74af000 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2725,6 +2725,13 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
         $log->fatal_error("$useinitvar is being set for you but a $var was not found, so $useinitvar, init_interp_attributes, and finidat must not be set correctly for this configuration in the namelist_default file" );
      }
   }
+
+  # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
+  if ( &value_is_true($nl->get_value($useinitvar)) && value_is_true($nl->get_value("use_hillslope")) ) {
+     $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values" .
+                   " from initial conditions. If you are sure you want this behaviour:")
+  }
+
 } # end initial conditions
 
 #-------------------------------------------------------------------------------
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index c51b0b0cb3..074fdec814 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1284,6 +1284,10 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"fsurdat='build-namelist_test.pl'",
                                      phys=>"clm6_0",
                                    },
+     "hillslope with init_interp"=>{ options=>"-bgc bgc -envxml_dir .",
+                                     namelst=>"use_init_interp=.true.,use_hillslope=.true.",
+                                     phys=>"clm6_0",
+                                   },
                );
 foreach my $key ( keys(%warntest) ) {
    print( "$key\n" );

From e271432f7ea3b01026a5c6edc023ed1665ba92c5 Mon Sep 17 00:00:00 2001
From: mvdebolskiy <nomatdebol@gmail.com>
Date: Thu, 8 Aug 2024 10:33:31 -0600
Subject: [PATCH 0963/1248] add spellcheck in bld-nml-tester

---
 bld/unit_testers/build-namelist_test.pl | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index c51b0b0cb3..a9381d0eae 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1212,6 +1212,13 @@ sub cat_and_create_namelistinfile {
                );
 foreach my $key ( keys(%failtest) ) {
    print( "$key\n" );
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for failtest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($failtest{$key}{"phys"});
    my $options  = $failtest{$key}{"options"};
    my $namelist = $failtest{$key}{"namelst"};
@@ -1287,6 +1294,14 @@ sub cat_and_create_namelistinfile {
                );
 foreach my $key ( keys(%warntest) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for warntest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($warntest{$key}{"phys"});
    my $options  = $warntest{$key}{"options"};
    my $namelist = $warntest{$key}{"namelst"};
@@ -1516,6 +1531,14 @@ sub cat_and_create_namelistinfile {
 
 foreach my $key ( keys(%finidat_files) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "atm_forc", "res", "bgc", "crop", "use_case", "start_ymd", "namelist" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for finidat_file $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    my $phys = $finidat_files{$key}{'phys'};
    print "physics = $phys\n";
    &make_config_cache($phys);

From 89e56cebdb35def494c63334310137b24a38e0cf Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 22 Aug 2024 11:15:29 -0600
Subject: [PATCH 0964/1248] Update ChangeLog/ChangeSum.

---
 doc/ChangeLog | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 68 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 7a6d764c14..42907da404 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,71 @@
 ===============================================================
+Tag name: ctsm5.2.024
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Thu Aug 22 11:07:11 MDT 2024
+One-line Summary: Improve li2024 fire methods
+
+Purpose and description of changes
+----------------------------------
+
+For fire methods li2024gswpfrc and (new) li2024crujra:
+- Improves peat burning dependence on climate
+- Improves dependence of deforestation burning on climate.
+- Allows lightning ignitions in tropical closed forest. (Human ignitions, other than deforestation, still not allowed.)
+- Adds effect of landscape fragmentation on ignitions and fire duration.
+- Recalibrates some parameters.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+- Adds optional fire_method li2024crujra.
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- DIFF
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: Only with optional fire_method li2024gswpfrc
+    - what platforms/compilers: All
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): new climate, probably
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2711: [Fang summer '24 PR 2.1] More improvements to fire model (https://github.com/ESCOMP/CTSM/pull/2711)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.023
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Fri Aug 16 11:00:32 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 176ac066d2..f4b14775b2 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.024 samrabin 08/22/2024 Improve li2024 fire methods
        ctsm5.2.023 samrabin 08/16/2024 Merge b4b-dev
        ctsm5.2.022 samrabin 08/14/2024 Rework crop_calendars suite and cropMonthOutput
        ctsm5.2.021   rgknox 08/13/2024 Adding on-the-fly parameter settings for prescribed N and P in FATES

From 9bcfcffe27bb46c6ee230fb6c29e5bd9c1c6f16d Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Thu, 22 Aug 2024 11:48:48 -0600
Subject: [PATCH 0965/1248] Keep GLACIER_REGION=1 unused

We realized that the renumbering of regions could cause silent wrong
behavior if a user was using an old user_nl_clm file that specified
behaviors for the old 4 regions. So instead, we're keeping the old
numbering for the Greenland and Antarctica regions and keeping
GLACIER_REGION=1 unused for now.
---
 bld/namelist_files/namelist_defaults_ctsm.xml      | 11 +++++++----
 bld/namelist_files/namelist_definition_ctsm.xml    | 14 ++++++++------
 cime_config/SystemTests/lvg.py                     |  4 ++--
 .../cmip6_glaciers_virtual_antarctica/user_nl_clm  |  2 +-
 src/main/glcBehaviorMod.F90                        |  9 ++++++---
 tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml  |  2 +-
 6 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index cd5e723baa..ae40b99d0c 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -466,6 +466,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Default glacier behavior is:
      Mountain glaciers: single_at_atm_topo
+     Currently-unused region 1: UNSET
      Greenland: virtual
      Antarctica: multiple
 
@@ -473,20 +474,22 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
      behavior to virtual. Note that the Greenland behavior is always
      virtual, even if Greenland isn't included in this run.
 -->
-<glacier_region_behavior glc_use_antarctica="0">'single_at_atm_topo','virtual','multiple'</glacier_region_behavior>
-<glacier_region_behavior glc_use_antarctica="1">'single_at_atm_topo','virtual','virtual' </glacier_region_behavior>
+<glacier_region_behavior glc_use_antarctica="0">'single_at_atm_topo','UNSET','virtual','multiple'</glacier_region_behavior>
+<glacier_region_behavior glc_use_antarctica="1">'single_at_atm_topo','UNSET','virtual','virtual' </glacier_region_behavior>
 
 <!-- Default glacier melt behavior is:
      Mountain glaciers: remains_in_place
+     Currently-unused region 1: UNSET
      Greenland: replaced_by_ice
      Antarctica: replaced_by_ice -->
-<glacier_region_melt_behavior>'remains_in_place','replaced_by_ice','replaced_by_ice'</glacier_region_melt_behavior>
+<glacier_region_melt_behavior>'remains_in_place','UNSET','replaced_by_ice','replaced_by_ice'</glacier_region_melt_behavior>
 
 <!-- Default glacier ice runoff behavior is:
      Mountain glaciers: melted
+     Currently-unused region 1: UNSET
      Greenland: remains_ice
      Antarctica: remains_ice -->
-<glacier_region_ice_runoff_behavior>'melted','remains_ice','remains_ice'</glacier_region_ice_runoff_behavior>
+<glacier_region_ice_runoff_behavior>'melted','UNSET','remains_ice','remains_ice'</glacier_region_ice_runoff_behavior>
 
 <!-- This parameter is tied (in a scientific sense) to h2osno_max: For large
      values of h2osno_max, glc_snow_persistence_max_days should be 0; for small
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 0912617872..63525f7ab3 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -550,7 +550,7 @@ Only works when running with a non-stub glacier model.
 
 <entry id="glacier_region_behavior" type="char*32(10)" category="clm_physics"
        group="clm_glacier_behavior"
-       valid_values="multiple,virtual,single_at_atm_topo" >
+       valid_values="multiple,virtual,single_at_atm_topo,UNSET" >
 Behavior of each glacier region (GLACIER_REGION in surface dataset).
 First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
 second to GLACIER_REGION with ID 1, etc.
@@ -563,12 +563,13 @@ Allowed values are:
 'single_at_atm_topo': glacier landunits in these grid cells have a single column,
    whose elevation matches the atmosphere's topographic height (so that there is no
    adjustment due to downscaling)
-Behavior of 'virtual' is required in the region where we have an ice sheet model
+'UNSET': place-holder for non-existent regions
+Behavior of 'virtual' is required in the region(s) where SMB is being sent to an ice sheet model
 </entry>
 
 <entry id="glacier_region_melt_behavior" type="char*32(10)" category="clm_physics"
        group="clm_glacier_behavior"
-       valid_values="replaced_by_ice,remains_in_place" >
+       valid_values="replaced_by_ice,remains_in_place,UNSET" >
 Treatment of ice melt for each glacier region (GLACIER_REGION in surface dataset).
 First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
 second to GLACIER_REGION with ID 1, etc.
@@ -577,17 +578,17 @@ Allowed values are:
    this results in positive liquid runoff and negative ice runoff
 'remains_in_place': any melted ice remains in place as liquid until it refreezes;
    thus, ice melt does not result in any runoff
+'UNSET': place-holder for non-existent regions
 IMPORTANT NOTE: Regions with the 'remains_in_place' behavior also do not
 compute SMB (because negative SMB would be pretty much meaningless in
-those regions). Thus, you cannot use this behavior where GLC is
-operating.
+those regions). Thus, you cannot use this behavior where SMB is being sent to an ice sheet model.
 Regions with the 'replaced_by_ice' behavior also compute SMB for the
 vegetated column.
 </entry>
 
 <entry id="glacier_region_ice_runoff_behavior" type="char*32(10)" category="clm_physics"
        group="clm_glacier_behavior"
-       valid_values="remains_ice,melted" >
+       valid_values="remains_ice,melted,UNSET" >
 Treatment of ice runoff for each glacier region (GLACIER_REGION in surface dataset).
 First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
 second to GLACIER_REGION with ID 1, etc.
@@ -599,6 +600,7 @@ Allowed values are:
    (generating a negative sensible heat flux) and runs off as liquid; this is appropriate in
    regions that have little iceberg calving in reality. This can be important to avoid unrealistic
    cooling of the ocean and consequent runaway sea ice growth.
+'UNSET': place-holder for non-existent regions
 Only applies when melt_non_icesheet_ice_runoff is .true.
 </entry>
 
diff --git a/cime_config/SystemTests/lvg.py b/cime_config/SystemTests/lvg.py
index 286712ce0f..d73f4e707b 100644
--- a/cime_config/SystemTests/lvg.py
+++ b/cime_config/SystemTests/lvg.py
@@ -32,12 +32,12 @@ def _case_one_setup(self):
         append_to_user_nl_files(
             caseroot=self._get_caseroot(),
             component="clm",
-            contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'multiple'",
+            contents="glacier_region_behavior = 'single_at_atm_topo', 'UNSET', 'virtual', 'multiple'",
         )
 
     def _case_two_setup(self):
         append_to_user_nl_files(
             caseroot=self._get_caseroot(),
             component="clm",
-            contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual'",
+            contents="glacier_region_behavior = 'single_at_atm_topo', 'UNSET', 'virtual', 'virtual'",
         )
diff --git a/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm b/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
index b6c563ed2c..9aeba5c9d3 100644
--- a/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
+++ b/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
@@ -5,5 +5,5 @@
 ! This differs from the default in that it turns on virtual columns over Antarctica
 ! This is desired so that we have the output needed to drive a later offline CISM Antarctica simulation
 ! However, this increases the cost of CLM by about 10%
-glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual'
+glacier_region_behavior = 'single_at_atm_topo', 'UNSET', 'virtual', 'virtual'
 
diff --git a/src/main/glcBehaviorMod.F90 b/src/main/glcBehaviorMod.F90
index 0476fe3ecb..d2719a6533 100644
--- a/src/main/glcBehaviorMod.F90
+++ b/src/main/glcBehaviorMod.F90
@@ -405,7 +405,8 @@ subroutine translate_glacier_region_behavior
                glacier_region_behavior(i) = BEHAVIOR_SINGLE_AT_ATM_TOPO
             case (behavior_str_unset)
                write(iulog,*) ' ERROR: glacier_region_behavior not specified for ID ', i
-               write(iulog,*) 'You probably need to extend the glacier_region_behavior namelist array'
+               write(iulog,*) 'You may need to extend the glacier_region_behavior namelist array,'
+               write(iulog,*) 'or you may be running with an old/incompatible surface dataset.'
                call endrun(msg=' ERROR: glacier_region_behavior not specified for ID '// &
                     errMsg(sourcefile, __LINE__))
             case default
@@ -436,7 +437,8 @@ subroutine translate_glacier_region_melt_behavior
                glacier_region_melt_behavior(i) = MELT_BEHAVIOR_REMAINS_IN_PLACE
             case (behavior_str_unset)
                write(iulog,*) ' ERROR: glacier_region_melt_behavior not specified for ID ', i
-               write(iulog,*) 'You probably need to extend the glacier_region_melt_behavior namelist array'
+               write(iulog,*) 'You may need to extend the glacier_region_melt_behavior namelist array,'
+               write(iulog,*) 'or you may be running with an old/incompatible surface dataset.'
                call endrun(msg=' ERROR: glacier_region_melt_behavior not specified for ID '// &
                     errMsg(sourcefile, __LINE__))
             case default
@@ -467,7 +469,8 @@ subroutine translate_glacier_region_ice_runoff_behavior
                glacier_region_ice_runoff_behavior(i) = ICE_RUNOFF_BEHAVIOR_MELTED
             case (behavior_str_unset)
                write(iulog,*) ' ERROR: glacier_region_ice_runoff_behavior not specified for ID ', i
-               write(iulog,*) 'You probably need to extend the glacier_region_ice_runoff_behavior namelist array'
+               write(iulog,*) 'You may need to extend the glacier_region_ice_runoff_behavior namelist array,'
+               write(iulog,*) 'or you may be running with an old/incompatible surface dataset.'
                call endrun(msg=' ERROR: glacier_region_ice_runoff_behavior not specified for ID '// &
                     errMsg(sourcefile, __LINE__))
             case default
diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index f9bb6a3a02..683ea14058 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -140,7 +140,7 @@ version of the raw dataset will probably go away.
 
   <mksrf_fglacierregion>
     <entry>
-      <data_filename>lnd/clm2/rawdata/mksrf_GlacierRegion_10x10min_nomask_cd5_c240815.nc</data_filename>
+      <data_filename>lnd/clm2/rawdata/mksrf_GlacierRegion_10x10min_nomask_cd5_c240822.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_10x10min_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
   </mksrf_fglacierregion>

From 4d808bcb572fd28516e8056f6ebf185ae9d97083 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Thu, 22 Aug 2024 11:50:33 -0600
Subject: [PATCH 0966/1248] Update documentation for new glacier regions

---
 .../tech_note/Glacier/CLM50_Tech_Note_Glacier.rst   | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst
index 3e510561bb..f39777ae6b 100644
--- a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst
+++ b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst
@@ -58,7 +58,7 @@ It is also possible to run CESM with an evolving ice sheet. In this case, CLM re
 Glacier regions and their behaviors
 -----------------------------------
 
-The world's glaciers and ice sheets are broken down into a number of different regions (four by default) that differ in three respects:
+The world's glaciers and ice sheets are broken down into a number of different regions (three by default) that differ in three respects:
 
 #. Whether the gridcell's glacier land unit contains:
 
@@ -80,7 +80,7 @@ The world's glaciers and ice sheets are broken down into a number of different r
 
    b. Ice runoff from snow capping is melted (generating a negative sensible heat flux) and runs off as liquid. This matches the behavior for non-glacier columns. This is appropriate in regions that have little iceberg calving in reality. This can be important to avoid unrealistic cooling of the ocean and consequent runaway sea ice growth.
 
-The default behaviors for the world's glacier and ice sheet regions are described in :numref:`Table Glacier region behaviors`. Note that the standard CISM grid covers Greenland plus enough surrounding area to allow for ice sheet growth and to have a regular rectangular grid. We need to have the "replaced by ice" melt behavior within the CISM domain in order to compute SMB there, and we need virtual elevation classes in that domain in order to compute SMB for all elevation classes and to facilitate glacial advance and retreat in the two-way-coupled case. However, this domain is split into Greenland itself and areas outside Greenland so that ice runoff in the Canadian archipelago (which is inside the CISM domain) is melted before reaching the ocean, to avoid runaway sea ice growth in that region.
+The default behaviors for the world's glacier and ice sheet regions are described in :numref:`Table Glacier region behaviors`. Note that the Greenland region stops at the edge of Greenland as defined by CISM. This means that, by default, SMB is not computed for grid cells outside Greenland but within the CISM domain. (This treatment of the non-Greenland portion of the CISM domain as being the same as the world's mountain glaciers rather than like Greenland itself is mainly for the sake of avoiding unrealistic fluxes from the Canadian archipelago that can potentially result in runaway sea ice growth in that region.)
 
 .. _Table Glacier region behaviors:
 
@@ -93,13 +93,6 @@ The default behaviors for the world's glacier and ice sheet regions are describe
  | Greenland     | Virtual       | Replaced by   | Remains ice   |
  |               |               | ice           |               |
  +---------------+---------------+---------------+---------------+
- | Inside        | Virtual       | Replaced by   | Melted        |
- | standard CISM |               | ice           |               |
- | grid but      |               |               |               |
- | outside       |               |               |               |
- | Greenland     |               |               |               |
- | itself        |               |               |               |
- +---------------+---------------+---------------+---------------+
  | Antarctica    | Multiple      | Replaced by   | Remains ice   |
  |               |               | ice           |               |
  +---------------+---------------+---------------+---------------+
@@ -109,7 +102,7 @@ The default behaviors for the world's glacier and ice sheet regions are describe
 
 .. note::
 
- In regions that have both the ``Glacial melt = Replaced by ice`` and the ``Ice runoff = Melted`` behaviors (by default, this is just the region inside the standard CISM grid but outside Greenland itself): During periods of glacial melt, a negative ice runoff is generated (due to the ``Glacial melt = Replaced by ice`` behavior); this negative ice runoff is converted to a negative liquid runoff plus a positive sensible heat flux (due to the ``Ice runoff = Melted`` behavior). We recommend that you limit the portion of the globe with both of these behaviors combined, in order to avoid having too large of an impact of this non-physical behavior.
+ The combination of the ``Glacial melt = Replaced by ice`` and the ``Ice runoff = Melted`` behaviors results in particularly non-physical behavior: During periods of glacial melt, a negative ice runoff is generated (due to the ``Glacial melt = Replaced by ice`` behavior); this negative ice runoff is converted to a negative liquid runoff plus a positive sensible heat flux (due to the ``Ice runoff = Melted`` behavior). The net result is zero runoff but a positive sensible heat flux generated from glacial melt. Because of how physically unrealistic this is, CLM does not allow this combination of behaviors.
 
 .. _Multiple elevation class scheme:
 

From 23c32ecb99e000ca88b2ea598dbcfd143f8d13b7 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Thu, 22 Aug 2024 14:31:35 -0600
Subject: [PATCH 0967/1248] Add a note in documentation.

---
 doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst
index f39777ae6b..9ed8fe280e 100644
--- a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst
+++ b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst
@@ -100,6 +100,10 @@ The default behaviors for the world's glacier and ice sheet regions are describe
  |               |               | place         |               |
  +---------------+---------------+---------------+---------------+
 
+.. note::
+
+It is possible to have non-virtual, non-SMB-computing areas within the CISM domain (as is the case for the portion of CISM's Greenland domain outside of Greenland itself). However, these areas will send 0 SMB and will not be able to adjust to CISM-dictated changes in glacier area. Therefore, it is best to set up the glacier regions and their behaviors so that as much of the CISM domain as possible is covered by virtual, SMB-computing areas.
+
 .. note::
 
  The combination of the ``Glacial melt = Replaced by ice`` and the ``Ice runoff = Melted`` behaviors results in particularly non-physical behavior: During periods of glacial melt, a negative ice runoff is generated (due to the ``Glacial melt = Replaced by ice`` behavior); this negative ice runoff is converted to a negative liquid runoff plus a positive sensible heat flux (due to the ``Ice runoff = Melted`` behavior). The net result is zero runoff but a positive sensible heat flux generated from glacial melt. Because of how physically unrealistic this is, CLM does not allow this combination of behaviors.

From 406edd4596fe6bba3d3d5095996fe729d0bccbd3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 22 Aug 2024 14:39:14 -0600
Subject: [PATCH 0968/1248] Add some comments about some of this being
 temporary and point to the issue regarding it

---
 bld/CLMBuildNamelist.pm          | 32 +++++++++++++++++++++-----------
 cime_config/config_component.xml |  1 +
 2 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 1fad577c51..52ac4c1d6f 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1756,25 +1756,29 @@ sub process_namelist_inline_logic {
   ##################################
   setup_logic_lightning_streams($opts,  $nl_flags, $definition, $defaults, $nl);
 
-  ######################################
+  ############################################################################################
   # namelist options for dust emissions
-  ######################################
+  # NOTE: This MUST be done before other drv_flds_in settings (megan, drydep, fire_emis etc.)
+  ############################################################################################
   setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
   setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);
 
-  #################################
-  # namelist group: drydep_inparm #
-  #################################
+  #####################################
+  # namelist group: drydep_inparm     #
+  # NOTE: After setup_logic_dust_emis #
+  #####################################
   setup_logic_dry_deposition($opts, $nl_flags, $definition, $defaults, $nl);
 
-  #################################
-  # namelist group: fire_emis_nl  #
-  #################################
+  #####################################
+  # namelist group: fire_emis_nl      #
+  # NOTE: After setup_logic_dust_emis #
+  #####################################
   setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl);
 
-  #################################
-  # namelist group: megan_emis_nl #
-  #################################
+  #####################################
+  # namelist group: megan_emis_nl     #
+  # NOTE: After setup_logic_dust_emis #
+  #####################################
   setup_logic_megan($opts, $nl_flags, $definition, $defaults, $nl);
 
   ##################################
@@ -4041,6 +4045,8 @@ sub setup_logic_dust_emis {
   my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;
 
   # Only set dust emission settings -- if not connected to CAM
+  # Longer term plan is to remove this logic and have CTSM just set it and for CAM to use what CLM decides
+  # See: https://github.com/ESCOMP/CTSM/issues/2713
   my $lnd_sets_dust = logical_to_fortran($envxml_ref->{'LND_SETS_DUST_EMIS_DRV_FLDS'});
   if ( &value_is_true( $lnd_sets_dust)) {
 
@@ -4094,8 +4100,12 @@ sub setup_logic_dust_emis {
          }
       }
       # Now process the CAM drv_flds_in to get the dust settings
+      # This requires that the CAM drv_flds_in namelist be created BEFORE CLM
+      # and that the path below NOT be changed. Hence, there's some fragility here
+      # to future changes.
       my $infile = $opts->{'envxml_dir'} . "/Buildconf/camconf/drv_flds_in";
       $log->verbose_message("Read in the drv_flds_in file generated by CAM's build-namelist");
+      # When merging the CAM namelist in -- die with an error if there's a conflict between CAM and CLM
       process_namelist_infile( $definition, $nl, $envxml_ref, $infile, 'die_on_conflict'=>1 );
   }
 }
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 3c48e16651..e3f559b08a 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -167,6 +167,7 @@
   </entry>
 
   <entry id="LND_SETS_DUST_EMIS_DRV_FLDS">
+    <!-- See https://github.com/ESCOMP/CTSM/issues/2713 we plan to phase this out -->
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>
     <default_value>TRUE</default_value>

From 980bc1649a85c955369c456cd770b54ea1ac3965 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Thu, 22 Aug 2024 14:48:45 -0600
Subject: [PATCH 0969/1248] Improve documentation of glacier region namelist
 options

---
 .../namelist_definition_ctsm.xml              | 28 ++++++++++++++-----
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 63525f7ab3..e6eadaae2c 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -564,7 +564,15 @@ Allowed values are:
    whose elevation matches the atmosphere's topographic height (so that there is no
    adjustment due to downscaling)
 'UNSET': place-holder for non-existent regions
-Behavior of 'virtual' is required in the region(s) where SMB is being sent to an ice sheet model
+Most (if not all) of the region where there is an ice sheet model should have a behavior
+of 'virtual': This behavior is needed to compute surface mass balance (SMB) in all
+elevation classes for the sake of vertical downscaling, and is needed to allow two-way
+feedbacks of glacier areas. You are allowed to have gridcells with non-virtual behavior in
+this domain, but this should be minimized: SMB cannot be computed there, and CLM subgrid
+areas will not remain in sync with the GLC model. (Within the icemask - i.e., the active
+glc domain - you are NOT allowed to have gridcells with non-virtual behavior that also
+have glacier_region_melt_behavior='replaced_by_ice': within the icemask, you're only
+allowed to have non-virtual behavior in places where you are not computing SMB).
 </entry>
 
 <entry id="glacier_region_melt_behavior" type="char*32(10)" category="clm_physics"
@@ -579,11 +587,12 @@ Allowed values are:
 'remains_in_place': any melted ice remains in place as liquid until it refreezes;
    thus, ice melt does not result in any runoff
 'UNSET': place-holder for non-existent regions
-IMPORTANT NOTE: Regions with the 'remains_in_place' behavior also do not
-compute SMB (because negative SMB would be pretty much meaningless in
-those regions). Thus, you cannot use this behavior where SMB is being sent to an ice sheet model.
-Regions with the 'replaced_by_ice' behavior also compute SMB for the
-vegetated column.
+IMPORTANT NOTE: Regions with the 'remains_in_place' behavior also do not compute SMB
+(because negative SMB would be pretty much meaningless in those regions). Thus, most (if
+not all) of the region where there is an ice sheet model should have the 'replaced_by_ice'
+behavior; the SMB sent to the GLC model will be 0 in any gridcells with the
+'remains_in_place' behavior.
+Regions with the 'replaced_by_ice' behavior also compute SMB for the vegetated column.
 </entry>
 
 <entry id="glacier_region_ice_runoff_behavior" type="char*32(10)" category="clm_physics"
@@ -599,7 +608,12 @@ Allowed values are:
 'melted': ice runoff generated by the CLM physics (primarily due to snow capping) is melted
    (generating a negative sensible heat flux) and runs off as liquid; this is appropriate in
    regions that have little iceberg calving in reality. This can be important to avoid unrealistic
-   cooling of the ocean and consequent runaway sea ice growth.
+   cooling of the ocean and consequent runaway sea ice growth. This option cannot be
+   combined with glacier_region_melt_behavior='replaced_by_ice': While there is nothing
+   fundamentally wrong with this combination, it can result in problematic, non-physical
+   fluxes (particularly, a large positive sensible heat flux during glacial melt in
+   regions where the ice sheet is not fully dynamic and two-way-coupled; see
+   https://github.com/ESCOMP/ctsm/issues/423 for details).
 'UNSET': place-holder for non-existent regions
 Only applies when melt_non_icesheet_ice_runoff is .true.
 </entry>

From fa7f8f5928609f67cd710149802db30bf886428b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 22 Aug 2024 15:22:19 -0600
Subject: [PATCH 0970/1248] Fix bug in setting of init_interp_attributes that
 should have been for clm6_0_cam6.0, that came about due to XML code
 duplication

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 167ded8c62..668ea1e05f 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1193,12 +1193,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <!-- If an exact match for these grids and start years -->
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="0.9x1.25" use_cn=".false." maxpft="17"
 >hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
 >hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>

From 796bd834fb575153d681992cc3641ee0636333bd Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 22 Aug 2024 15:35:14 -0600
Subject: [PATCH 0971/1248] Get the megan_spec checker working for identifying
 bad characters in a string

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 52ac4c1d6f..37eedff6e5 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -5665,7 +5665,7 @@ sub check_megan_spec {
     foreach my $spec ( @megan_spec_list ) {
        $megan_spec = remove_leading_and_trailing_quotes($spec);
        # Do simple validation of the expressions to just check for valid characters
-       if ( ! $megan_spec =~ /[\s=A-Za-z0-9_\+\.\*\(\)-]+/ ) {
+       if ( $megan_spec !~ /^([\s=A-Za-z0-9_\+\.\*\(\)-]+)$/ ) {
           $log->fatal_error("Bad format for megan_specifier = $megan_spec");
        }
     }

From 5cf4216f279ad55739b17570a97b8555fa50a8fc Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 22 Aug 2024 16:28:26 -0600
Subject: [PATCH 0972/1248] Turn on explicit AC, Leung_2023, and excess ice by
 default

---
 bld/namelist_files/namelist_defaults_ctsm.xml      | 10 +++++-----
 bld/namelist_files/namelist_defaults_dust_emis.xml |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 8aacd3a64d..70ba56e69b 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -161,7 +161,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <calc_human_stress_indices phys="clm4_5" >NONE</calc_human_stress_indices>
 
 <!-- Explicit, time-varying urban air conditioning adoption rate scheme -->
-<urban_explicit_ac phys="clm6_0" >.false.</urban_explicit_ac>
+<urban_explicit_ac phys="clm6_0" >.true.</urban_explicit_ac>
 <urban_explicit_ac phys="clm5_1" >.false.</urban_explicit_ac>
 <urban_explicit_ac phys="clm5_0" >.false.</urban_explicit_ac>
 <urban_explicit_ac phys="clm4_5" >.false.</urban_explicit_ac>
@@ -2449,15 +2449,15 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_fldfilename_urbantv phys="clm6_0" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_0.9x1.25_simyr1849-2106_c200605.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm6_0"  hgrid="0.9x1.25" urban_explicit_ac=".true."
->/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>lnd/clm2/urbandata/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_1" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_0.9x1.25_simyr1849-2106_c200605.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_1"  hgrid="0.9x1.25" urban_explicit_ac=".true."
->/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>lnd/clm2/urbandata/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".true."
->/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>lnd/clm2/urbandata/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm4_5" hgrid="0.9x1.25"
 >lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 
@@ -2694,7 +2694,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- Defaults for excess ice                    -->
 <!-- =========================================  -->
 
-<use_excess_ice>.false.</use_excess_ice>
+<use_excess_ice>.true.</use_excess_ice>
 <excess_ice_coldstart_temp>-1.0</excess_ice_coldstart_temp>
 <excess_ice_coldstart_depth>0.5</excess_ice_coldstart_depth>
 <excess_ice_coldstart_temp use_excess_ice=".true.">-3.15</excess_ice_coldstart_temp>
diff --git a/bld/namelist_files/namelist_defaults_dust_emis.xml b/bld/namelist_files/namelist_defaults_dust_emis.xml
index 40bf3d9078..319110cc55 100644
--- a/bld/namelist_files/namelist_defaults_dust_emis.xml
+++ b/bld/namelist_files/namelist_defaults_dust_emis.xml
@@ -14,7 +14,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <!-- Defaults for dust_emis_inparm namelist  -->
-<dust_emis_method>Zender_2003</dust_emis_method>
+<dust_emis_method>Leung_2023</dust_emis_method>
 
 <zender_soil_erod_source>atm</zender_soil_erod_source>
 

From e4a3c18c03deaa40df15bbff42f03204a3a93d4b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 22 Aug 2024 16:59:10 -0600
Subject: [PATCH 0973/1248] Add finidat entries for f09/1850/clm6 cases

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 70ba56e69b..e94863b32e 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1345,6 +1345,18 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm60BgcCrop-ciso.1361-01-01.ne30pg3_mg17_c240317.nc
 </finidat>
+<finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+</finidat>
+<finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".true."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+</finidat>
 
 <!--
      Present day IC (if use_init_interp is set and .true. then MUST still interpolate even on an exact match)

From a14758bede89c544c45a63915fe03ed2139bbbd6 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Thu, 22 Aug 2024 17:05:38 -0600
Subject: [PATCH 0974/1248] Change logic to account for new allowed /
 disallowed behavior combos

- Weaken the consistency checks between icemask and glc_behavior: We no
  longer require has_virtual_columns and melt_replaced_by_ice - we now
  only require that we do NOT have (melt_replaced_by_ice_grc
  .and. .not. has_virtual_columns_grc).

- Prevent users from setting the combination of
  glacier_region_melt_behavior = "replaced_by_ice" with
  glacier_region_ice_runoff_behavior = "melted". (While there is nothing
  fundamentally wrong with this combination, it can result in
  problematic, non-physical fluxes - particularly, a large positive
  sensible heat flux during glacial melt in regions where the icesheet
  is not fully dynamic and two-way-coupled; see
  https://github.com/ESCOMP/ctsm/issues/423 for details.)

- Only update glacier areas and topo values where the glacier region
  behavior is 'virtual', because that's the only region where we are
  guaranteed to have all of the elevation classes we need in order to
  remain in sync. (Note that, for conservation purposes, it's important
  that we update areas in all regions where we're fully-two-way-coupled
  to the icesheet and we're computing SMB; this requirement is checked
  in check_glc2lnd_icemask.) This change is needed now that we no longer
  require grid cells within the ice mask to have the 'virtual' behavior.

- Ensure that glc_dyn_runoff_routing is 0 wherever we're not computing
  SMB. This change isn't strictly necessary with the current code,
  because it appears that glc_dyn_runoff_routing is only used within the
  do_smb filter. However, this change makes the code more robust to
  future changes. This change is needed now that we no longer require
  grid cells within the ice mask to have the melt_replaced_by_ice
  behavior.

Also fixes / adds unit tests covering these behavior changes
---
 src/main/glc2lndMod.F90                       | 206 ++++++++++--------
 src/main/glcBehaviorMod.F90                   |  31 ++-
 src/main/lnd2glcMod.F90                       |  20 +-
 .../test/glcBehavior_test/test_glcBehavior.pf |   2 +-
 src/main/test/topo_test/test_topo.pf          |  69 ++++--
 5 files changed, 214 insertions(+), 114 deletions(-)

diff --git a/src/main/glc2lndMod.F90 b/src/main/glc2lndMod.F90
index 2d0dbb5791..c2e6290300 100644
--- a/src/main/glc2lndMod.F90
+++ b/src/main/glc2lndMod.F90
@@ -35,7 +35,7 @@ module glc2lndMod
      ! Public data
      ! ------------------------------------------------------------------------
 
-     ! Where we should do runoff routing that is appropriate for having a dynamic icesheet underneath.
+     ! Where we should do SMB-related runoff routing that is appropriate for having a dynamic icesheet underneath.
      real(r8), pointer :: glc_dyn_runoff_routing_grc (:) => null()
 
      ! ------------------------------------------------------------------------
@@ -383,32 +383,32 @@ subroutine check_glc2lnd_icemask(this, bounds)
 
        if (this%icemask_grc(g) > 0._r8) then
 
-          ! Ensure that icemask is a subset of has_virtual_columns. This is needed because
-          ! we allocated memory based on has_virtual_columns, so it is a problem if the
-          ! ice sheet tries to expand beyond the area defined by has_virtual_columns.
-          if (.not. this%glc_behavior%has_virtual_columns_grc(g)) then
-             write(iulog,'(a)') subname//' ERROR: icemask must be a subset of has_virtual_columns.'
-             write(iulog,'(a)') 'Ensure that the glacier_region_behavior namelist item is set correctly.'
-             write(iulog,'(a)') '(It should specify "virtual" for the region corresponding to the GLC domain.)'
-             write(iulog,'(a)') 'If glacier_region_behavior is set correctly, then you can fix this problem'
-             write(iulog,'(a)') 'by modifying GLACIER_REGION on the surface dataset.'
-             write(iulog,'(a)') '(Expand the region that corresponds to the GLC domain'
-             write(iulog,'(a)') '- i.e., the region specified as "virtual" in glacier_region_behavior.)'
-             call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, msg=errMsg(sourcefile, __LINE__))
-          end if
-
-          ! Ensure that icemask is a subset of melt_replaced_by_ice. This is needed
-          ! because we only compute SMB in the region given by melt_replaced_by_ice
-          ! (according to the logic for building the do_smb filter), and we need SMB
-          ! everywhere inside the icemask.
-          if (.not. this%glc_behavior%melt_replaced_by_ice_grc(g)) then
-             write(iulog,'(a)') subname//' ERROR: icemask must be a subset of melt_replaced_by_ice.'
-             write(iulog,'(a)') 'Ensure that the glacier_region_melt_behavior namelist item is set correctly.'
-             write(iulog,'(a)') '(It should specify "replaced_by_ice" for the region corresponding to the GLC domain.)'
-             write(iulog,'(a)') 'If glacier_region_behavior is set correctly, then you can fix this problem'
-             write(iulog,'(a)') 'by modifying GLACIER_REGION on the surface dataset.'
-             write(iulog,'(a)') '(Expand the region that corresponds to the GLC domain'
-             write(iulog,'(a)') '- i.e., the region specified as "replaced_by_ice" in glacier_region_melt_behavior.)'
+          ! Ensure that, within the icemask, there are no points that have (non-virtual
+          ! and compute-SMB). This is important for two reasons:
+          !
+          ! (1) To ensure that, in grid cells where we're producing SMB, we have SMB for
+          !     all elevation classes, so that the downscaling / vertical interpolation
+          !     can be done correctly.
+          !
+          ! (2) To avoid conservation issues, we want to ensure that, in grid cells where
+          !     we're producing SMB and are dynamically coupled to the ice sheet (if 2-way
+          !     coupling is enabled), glacier areas are remaining in-sync with glc. (Note
+          !     that has_virtual_columns_grc dictates where we're able to keep glacier
+          !     areas in sync with glc.) (In principle, I think this one could check
+          !     icemask_coupled_fluxes rather than icemask; we check icemask because we
+          !     needed to check icemask for the other reason anyway; this is okay because
+          !     icemask_coupled_fluxes is a subset of icemask.)
+          if (this%glc_behavior%melt_replaced_by_ice_grc(g) .and. &
+               .not. this%glc_behavior%has_virtual_columns_grc(g)) then
+             write(iulog,'(a)') subname//' ERROR: Within the icemask, there cannot be any points that have'
+             write(iulog,'(a)') '(non-virtual and compute-SMB).'
+             write(iulog,'(a)') 'Ensure that GLACIER_REGION on the surface dataset and the namelist items,'
+             write(iulog,'(a)') 'glacier_region_behavior and glacier_region_melt_behavior are all set correctly:'
+             write(iulog,'(a)') 'Typically, the region encompassing the active GLC domain should specify'
+             write(iulog,'(a)') 'glacier_region_behavior="virtual" and glacier_region_melt_behavior="replaced_by_ice".'
+             write(iulog,'(a)') '(But it is also okay for part of the GLC domain to have'
+             write(iulog,'(a)') 'glacier_region_melt_behavior="remains_in_place"; this part of the domain can have'
+             write(iulog,'(a)') 'any setting for glacier_region_behavior.)'
              call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, msg=errMsg(sourcefile, __LINE__))
           end if
 
@@ -437,10 +437,12 @@ subroutine check_glc2lnd_icemask_coupled_fluxes(this, bounds)
 
     do g = bounds%begg, bounds%endg
 
-       ! Ensure that icemask_coupled_fluxes is a subset of icemask. Although there
-       ! currently is no code in CLM that depends on this relationship, it seems helpful
-       ! to ensure that this intuitive relationship holds, so that code developed in the
-       ! future can rely on it.
+       ! Ensure that icemask_coupled_fluxes is a subset of icemask. This is helpful to
+       ! ensure that the consistency checks that are done on glc behaviors within the
+       ! icemask (in check_glc2lnd_icemask) also apply within the icemask_coupled_fluxes
+       ! region. Other than that convenience, there currently is no code in CLM that
+       ! depends on this relationship, but it seems helpful to ensure that this intuitive
+       ! relationship holds, so that code developed in the future can rely on it.
        if (this%icemask_coupled_fluxes_grc(g) > 0._r8 .and. this%icemask_grc(g) == 0._r8) then
           write(iulog,*) subname//' ERROR: icemask_coupled_fluxes must be a subset of icemask.'
           call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, msg=errMsg(sourcefile, __LINE__))
@@ -477,70 +479,73 @@ subroutine update_glc2lnd_dyn_runoff_routing(this, bounds)
     ! where CISM is running in diagnostic-only mode and therefore is not sending a calving flux -
     ! we have glc_dyn_runoff_routing = 0, and the snowcap flux goes to the runoff model.
     ! This is needed to conserve water correctly in the absence of a calving flux.
+    !
+    ! In places where we are not computing SMB, we also have glc_dyn_runoff_routing = 0.
+    ! Currently glc_dyn_runoff_routing is only used where we're computing SMB, but if it
+    ! were ever used elsewhere, it seems best to have it set to 0 there: this seems
+    ! consistent with the fact that we zero out the SMB flux sent to GLC in that region.
+    ! (However, it's possible that, once we start actually using glc_dyn_runoff_routing
+    ! for some purpose outside the do_smb filter, we'll discover that this logic should
+    ! be changed.)
 
     do g = bounds%begg, bounds%endg
 
-       ! Set glc_dyn_runoff_routing_grc(g) to a value in the range [0,1].
-       !
-       ! This value gives the grid cell fraction that is deemed to be coupled to the
-       ! dynamic ice sheet model. For this fraction of the grid cell, snowcap fluxes are
-       ! sent to the ice sheet model. The remainder of the grid cell sends snowcap fluxes
-       ! to the runoff model.
-       !
-       ! Note: The coupler (in prep_glc_mod.F90) assumes that the fraction coupled to the
-       !       dynamic ice sheet model is min(lfrac, Sg_icemask_l), where lfrac is the
-       !       "frac" component of fraction_lx, and Sg_icemask_l is obtained by mapping
-       !       Sg_icemask_g from the glc to the land grid. Here, ldomain%frac is
-       !       equivalent to lfrac, and this%icemask_grc is equivalent to Sg_icemask_l.
-       !       However, here we use icemask_coupled_fluxes_grc, so that we route all snow
-       !       capping to runoff in areas where the ice sheet is not generating calving
-       !       fluxes. In addition, here we need to divide by lfrac, because the coupler
-       !       multiplies by it later (and, for example, if lfrac = 0.1 and
-       !       icemask_coupled_fluxes = 1, we want all snow capping to go to the ice
-       !       sheet model, not to the runoff model).
-       !
-       ! Note: In regions where CLM overlaps the CISM domain, this%icemask_grc(g) typically
-       !       is nearly equal to ldomain%frac(g). So an alternative would be to simply set
-       !       glc_dyn_runoff_routing_grc(g) = icemask_grc(g).
-       !       The reason to cap glc_dyn_runoff_routing at lfrac is to avoid sending the
-       !       ice sheet model a greater mass of water (in the form of snowcap fluxes)
-       !       than is allowed to fall on a CLM grid cell that is part ocean.
-
-       ! TODO(wjs, 2017-05-08) Ideally, we wouldn't have this duplication in logic
-       ! between the coupler and CLM. The best solution would be to have the coupler
-       ! itself do the partitioning of the snow capping flux between the ice sheet model
-       ! and the runoff model. A next-best solution would be to have the coupler send a
-       ! field to CLM telling it what fraction of snow capping should go to the runoff
-       ! model in each grid cell.
-
-       if (ldomain%frac(g) == 0._r8) then
-          ! Avoid divide by 0; note that, in this case, the amount going to runoff isn't
-          ! important for system-wide conservation, so we could really choose anything we
-          ! want.
-          this%glc_dyn_runoff_routing_grc(g) = this%icemask_coupled_fluxes_grc(g)
-       else
-          this%glc_dyn_runoff_routing_grc(g) = &
-               min(ldomain%frac(g), this%icemask_coupled_fluxes_grc(g)) / &
-               ldomain%frac(g)
-       end if
-
-       if (this%glc_dyn_runoff_routing_grc(g) > 0.0_r8) then
-
-          ! Ensure that glc_dyn_runoff_routing is a subset of melt_replaced_by_ice. This
-          ! is needed because glacial melt is only sent to the runoff stream in the region
-          ! given by melt_replaced_by_ice (because the latter is used to create the do_smb
-          ! filter, and the do_smb filter controls where glacial melt is computed).
-          if (.not. this%glc_behavior%melt_replaced_by_ice_grc(g)) then
-             write(iulog,'(a)') subname//' ERROR: icemask_coupled_fluxes must be a subset of melt_replaced_by_ice.'
-             write(iulog,'(a)') 'Ensure that the glacier_region_melt_behavior namelist item is set correctly.'
-             write(iulog,'(a)') '(It should specify "replaced_by_ice" for the region corresponding to the GLC domain.)'
-             write(iulog,'(a)') 'If glacier_region_behavior is set correctly, then you can fix this problem'
-             write(iulog,'(a)') 'by modifying GLACIER_REGION on the surface dataset.'
-             write(iulog,'(a)') '(Expand the region that corresponds to the GLC domain'
-             write(iulog,'(a)') '- i.e., the region specified as "replaced_by_ice" in glacier_region_melt_behavior.)'
-             call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, msg=errMsg(sourcefile, __LINE__))
+       if (this%glc_behavior%melt_replaced_by_ice_grc(g)) then
+          ! As noted in the comments at the top of this routine, we only set
+          ! glc_dyn_runoff_routing where we are computing SMB
+
+          ! Set glc_dyn_runoff_routing_grc(g) to a value in the range [0,1].
+          !
+          ! This value gives the grid cell fraction that is deemed to be coupled to the
+          ! dynamic ice sheet model. For this fraction of the grid cell, snowcap fluxes are
+          ! sent to the ice sheet model. The remainder of the grid cell sends snowcap fluxes
+          ! to the runoff model.
+          !
+          ! Note: The coupler (in prep_glc_mod.F90) assumes that the fraction coupled to the
+          !       dynamic ice sheet model is min(lfrac, Sg_icemask_l), where lfrac is the
+          !       "frac" component of fraction_lx, and Sg_icemask_l is obtained by mapping
+          !       Sg_icemask_g from the glc to the land grid. Here, ldomain%frac is
+          !       equivalent to lfrac, and this%icemask_grc is equivalent to Sg_icemask_l.
+          !       However, here we use icemask_coupled_fluxes_grc, so that we route all snow
+          !       capping to runoff in areas where the ice sheet is not generating calving
+          !       fluxes. In addition, here we need to divide by lfrac, because the coupler
+          !       multiplies by it later (and, for example, if lfrac = 0.1 and
+          !       icemask_coupled_fluxes = 1, we want all snow capping to go to the ice
+          !       sheet model, not to the runoff model).
+          !
+          ! Note: In regions where CLM overlaps the CISM domain, this%icemask_grc(g) typically
+          !       is nearly equal to ldomain%frac(g). So an alternative would be to simply set
+          !       glc_dyn_runoff_routing_grc(g) = icemask_grc(g).
+          !       The reason to cap glc_dyn_runoff_routing at lfrac is to avoid sending the
+          !       ice sheet model a greater mass of water (in the form of snowcap fluxes)
+          !       than is allowed to fall on a CLM grid cell that is part ocean.
+
+          ! TODO(wjs, 2017-05-08) Ideally, we wouldn't have this duplication in logic
+          ! between the coupler and CLM. The best solution would be to have the coupler
+          ! itself do the partitioning of the snow capping flux between the ice sheet model
+          ! and the runoff model. A next-best solution would be to have the coupler send a
+          ! field to CLM telling it what fraction of snow capping should go to the runoff
+          ! model in each grid cell.
+
+          if (ldomain%frac(g) == 0._r8) then
+             ! Avoid divide by 0; note that, in this case, the amount going to runoff isn't
+             ! important for system-wide conservation, so we could really choose anything we
+             ! want.
+             this%glc_dyn_runoff_routing_grc(g) = this%icemask_coupled_fluxes_grc(g)
+          else
+             this%glc_dyn_runoff_routing_grc(g) = &
+                  min(ldomain%frac(g), this%icemask_coupled_fluxes_grc(g)) / &
+                  ldomain%frac(g)
           end if
+
+       else  ! .not. this%glc_behavior%melt_replaced_by_ice_grc(g)
+          ! As noted in the comments at the top of this routine, we set
+          ! glc_dyn_runoff_routing to 0 where we are not computing SMB. (This assumes that
+          ! gridcells where we compute SMB are the same as gridcells for which
+          ! melt_replaced_by_ice is true.)
+          this%glc_dyn_runoff_routing_grc(g) = 0._r8
        end if
+          
     end do
 
   end subroutine update_glc2lnd_dyn_runoff_routing
@@ -578,8 +583,15 @@ subroutine update_glc2lnd_fracs(this, bounds)
 
     if (glc_do_dynglacier) then
        do g = bounds%begg, bounds%endg
-          ! Values from GLC are only valid within the icemask, so we only update CLM's areas there
-          if (this%icemask_grc(g) > 0._r8) then
+          ! Values from GLC are only valid within the icemask, so we only update CLM's
+          ! areas there. Also, we only update areas where the glacier region behavior is
+          ! 'virtual', because that's the only region where we are guaranteed to have all
+          ! of the elevation classes we need in order to remain in sync. (Note that, for
+          ! conservation purposes, it's important that we update areas in all regions
+          ! where we're fully-two-way-coupled to the icesheet and we're computing SMB;
+          ! this requirement is checked in check_glc2lnd_icemask.) (This conditional
+          ! should be kept consistent with the conditional in update_glc2lnd_topo.)
+          if (this%icemask_grc(g) > 0._r8 .and. this%glc_behavior%has_virtual_columns_grc(g)) then
 
              ! Set total ice landunit area
              area_ice = sum(this%frac_grc(g, 1:maxpatch_glc))
@@ -623,7 +635,7 @@ subroutine update_glc2lnd_fracs(this, bounds)
                         msg="at least one glc column has non-zero area from cpl but has no slot in memory")
                 end if  ! error
              end if  ! area_ice > 0
-          end if  ! this%icemask_grc(g) > 0
+          end if  ! this%icemask_grc(g) > 0 .and. this%glc_behavior%has_virtual_columns_grc(g)
        end do  ! g
     end if  ! glc_do_dynglacier
 
@@ -667,8 +679,12 @@ subroutine update_glc2lnd_topo(this, bounds, topo_col, needs_downscaling_col)
           l = col%landunit(c)
           g = col%gridcell(c)
 
-          ! Values from GLC are only valid within the icemask, so we only update CLM's topo values there
-          if (this%icemask_grc(g) > 0._r8) then
+          ! Values from GLC are only valid within the icemask, so we only update CLM's
+          ! topo values there. Also, consistently with the conditional in
+          ! update_glc2lnd_fracs, we only update topo values where the glacier region
+          ! behavior is 'virtual': it could be problematic to update topo values in a
+          ! grid cell where we're not updating areas.
+          if (this%icemask_grc(g) > 0._r8 .and. this%glc_behavior%has_virtual_columns_grc(g)) then
              if (lun%itype(l) == istice) then
                 ice_class = col_itype_to_ice_class(col%itype(c))
              else
diff --git a/src/main/glcBehaviorMod.F90 b/src/main/glcBehaviorMod.F90
index d2719a6533..315aa88c67 100644
--- a/src/main/glcBehaviorMod.F90
+++ b/src/main/glcBehaviorMod.F90
@@ -72,9 +72,10 @@ module glcBehaviorMod
      logical, allocatable, public :: allow_multiple_columns_grc(:)
 
      ! If melt_replaced_by_ice_grc(g) is true, then any glacier ice melt in gridcell g
-     ! runs off and is replaced by ice. Note that SMB cannot be computed in gridcell g if
-     ! melt_replaced_by_ice_grc(g) is false, since we can't compute a sensible negative
-     ! smb in that case.
+     ! runs off and is replaced by ice. This flag is also used to determine where we
+     ! compute SMB: We compute SMB in all grid cells for which melt_replaced_by_ice_grc is
+     ! true. (SMB cannot be computed in gridcells where melt_replaced_by_ice_grc is false,
+     ! since we can't compute a sensible negative SMB in that case.)
      logical, allocatable, public :: melt_replaced_by_ice_grc(:)
 
      ! If ice_runoff_melted_grc(g) is true, then ice runoff generated by the
@@ -310,6 +311,7 @@ subroutine InitFromInputs(this, begg, endg, &
     call translate_glacier_region_behavior
     call translate_glacier_region_melt_behavior
     call translate_glacier_region_ice_runoff_behavior
+    call check_behaviors
 
     call this%InitAllocate(begg, endg)
 
@@ -484,7 +486,28 @@ subroutine translate_glacier_region_ice_runoff_behavior
       end do
     end subroutine translate_glacier_region_ice_runoff_behavior
 
-  end subroutine InitFromInputs
+    subroutine check_behaviors
+      ! Check the various behaviors for validity / consistency
+      integer :: i
+
+      do i = min_glacier_region_id, max_glacier_region_id
+         if (glacier_region_melt_behavior(i) == MELT_BEHAVIOR_REPLACED_BY_ICE .and. &
+              glacier_region_ice_runoff_behavior(i) == ICE_RUNOFF_BEHAVIOR_MELTED) then
+            write(iulog,*) ' ERROR: Bad glacier region behavior combination for ID ', i
+            write(iulog,*) 'You cannot combine glacier_region_melt_behavior = "replaced_by_ice"'
+            write(iulog,*) 'with glacier_region_ice_runoff_behavior = "melted".'
+            write(iulog,*) 'While there is nothing fundamentally wrong with this combination,'
+            write(iulog,*) 'it can result in problematic, non-physical fluxes (particularly,'
+            write(iulog,*) 'a large positive sensible heat flux during glacial melt in regions'
+            write(iulog,*) 'where the icesheet is not fully dynamic and two-way-coupled;'
+            write(iulog,*) 'see https://github.com/ESCOMP/ctsm/issues/423 for details).'
+            call endrun(msg=' ERROR: Bad glacier region behavior combination '// &
+                 errMsg(sourcefile, __LINE__))
+         end if
+      end do
+    end subroutine check_behaviors
+
+   end subroutine InitFromInputs
 
 
   !-----------------------------------------------------------------------
diff --git a/src/main/lnd2glcMod.F90 b/src/main/lnd2glcMod.F90
index 27fa7639d7..26359ff261 100644
--- a/src/main/lnd2glcMod.F90
+++ b/src/main/lnd2glcMod.F90
@@ -169,10 +169,28 @@ subroutine update_lnd2glc(this, bounds, num_do_smb_c, filter_do_smb_c, &
     character(len=*), parameter :: subname = 'update_lnd2glc'
     !------------------------------------------------------------------------------
 
-    ! Initialize to reasonable defaults
+    ! Initialize to reasonable defaults. These values will be sent for gridcells /
+    ! columns outside the do_smb filter.
 
+    ! NOTE(wjs, 2018-07-03) qice should be 0 outside the do_smb filter to ensure conservation
     this%qice_grc(bounds%begg : bounds%endg, :) = 0._r8
+
+    ! NOTE(wjs, 2018-07-03) tsrf can be anything outside the do_smb filter; 0 deg C seems
+    ! as reasonable as anything (based on input from Bill Lipscomb and Gunter Leguy)
     this%tsrf_grc(bounds%begg : bounds%endg, :) = tfrz
+
+    ! NOTE(wjs, 2018-07-03) The topo values outside the do_smb filter could matter for
+    ! gridcells where we compute SMB for some but not all elevation classes (possibly
+    ! because we haven't even allocated memory for some elevation classes - i.e., if we're
+    ! not using the 'virtual' behavior in that gridcell). In glc2lndMod, we ensure that
+    ! this cannot occur for gridcells within the icemask (i.e., within the icemask, we
+    ! ensure that there are no points that have (non-virtual and compute-SMB)), so this
+    ! isn't a conservation issue, but it could still be important, e.g., for generating
+    ! appropriate forcings for a later dlnd-driven T compset. I'm not sure what is "right"
+    ! here. We've historically used 0 for this, and maybe that's as good as anything,
+    ! because it may lead to the 0 SMB values being ignored for the sake of vertical
+    ! interpolation, but I'm not sure about this. But maybe it would be better to use
+    ! topo at the center of each elevation class?
     this%topo_grc(bounds%begg : bounds%endg, :) = 0._r8     
   
     ! Fill the lnd->glc data on the clm grid
diff --git a/src/main/test/glcBehavior_test/test_glcBehavior.pf b/src/main/test/glcBehavior_test/test_glcBehavior.pf
index ff104458b1..37271d2f98 100644
--- a/src/main/test/glcBehavior_test/test_glcBehavior.pf
+++ b/src/main/test/glcBehavior_test/test_glcBehavior.pf
@@ -170,7 +170,7 @@ contains
     call glc_behavior%InitFromInputs(bounds%begg, bounds%endg, &
          glacier_region_map = [0], &
          glacier_region_behavior_str = ['single_at_atm_topo'], &
-         glacier_region_melt_behavior_str = ['replaced_by_ice'], &
+         glacier_region_melt_behavior_str = ['remains_in_place'], &
          glacier_region_ice_runoff_behavior_str = ['melted'])
 
     @assertTrue(glc_behavior%ice_runoff_melted_grc(bounds%begg))
diff --git a/src/main/test/topo_test/test_topo.pf b/src/main/test/topo_test/test_topo.pf
index 196ce34763..82c3b2cb90 100644
--- a/src/main/test/topo_test/test_topo.pf
+++ b/src/main/test/topo_test/test_topo.pf
@@ -251,13 +251,33 @@ contains
     expected_filter = col_filter_empty(bounds)
 
     call this%topo%Init(bounds)
-    ! Need icemask 0, because we can't have single_at_atm_topo inside the icemask
-    call this%do_UpdateTopo(glc_behavior, icemask_grc = grc_array(0._r8))
+    call this%do_UpdateTopo(glc_behavior, icemask_grc = grc_array(1._r8))
     filter = this%topo%DownscaleFilterc(bounds)
 
     @assertTrue(filter == expected_filter)
   end subroutine downscaleFilter_afterUpdate_doesNotContain_singleAtAtmTopo
 
+  @Test
+  subroutine downscaleFilter_afterUpdate_contains_vegInsideIcemaskAndVirtual(this)
+    ! We expect the downscaleFilter to contain vegetated points if they are both (1)
+    ! inside the icemask, and (2) in the 'virtual' region - because topo is updated in
+    ! that region.
+    class(TestTopo), intent(inout) :: this
+    type(glc_behavior_type) :: glc_behavior
+    type(filter_col_type) :: filter
+    type(filter_col_type) :: expected_filter
+
+    call setup_single_veg_patch(pft_type = 1)
+    glc_behavior = create_glc_behavior_all_virtual()
+    expected_filter = col_filter_from_index_array(bounds, [bounds%begc])
+
+    call this%topo%Init(bounds)
+    call this%do_UpdateTopo(glc_behavior, icemask_grc = grc_array(1._r8))
+    filter = this%topo%DownscaleFilterc(bounds)
+
+    @assertTrue(filter == expected_filter)
+  end subroutine downscaleFilter_afterUpdate_contains_vegInsideIcemaskAndVirtual
+
   @Test
   subroutine downscaleFilter_afterUpdate_doesNotContain_vegOutsideIcemask(this)
     class(TestTopo), intent(inout) :: this
@@ -266,8 +286,6 @@ contains
     type(filter_col_type) :: expected_filter
 
     call setup_single_veg_patch(pft_type = 1)
-    ! Use 'virtual' behavior, to make sure that we're not accidentally trying to
-    ! downscale vegetation over virtual columns.
     glc_behavior = create_glc_behavior_all_virtual()
     expected_filter = col_filter_empty(bounds)
 
@@ -279,7 +297,10 @@ contains
   end subroutine downscaleFilter_afterUpdate_doesNotContain_vegOutsideIcemask
 
   @Test
-  subroutine downscaleFilter_afterUpdate_contains_vegInsideIcemask(this)
+  subroutine downscaleFilter_afterUpdate_doesNotContain_vegNonVirtual(this)
+    ! Since topo is only updated in the 'virtual' region, we expect the downscale filter
+    ! to NOT include vegetated points outside the 'virtual' region, because topo
+    ! shouldn't be updated for those vegetated points.
     class(TestTopo), intent(inout) :: this
     type(glc_behavior_type) :: glc_behavior
     type(filter_col_type) :: filter
@@ -287,14 +308,36 @@ contains
 
     call setup_single_veg_patch(pft_type = 1)
     glc_behavior = create_glc_behavior_all_multiple()
-    expected_filter = col_filter_from_index_array(bounds, [bounds%begc])
+    expected_filter = col_filter_empty(bounds)
 
     call this%topo%Init(bounds)
     call this%do_UpdateTopo(glc_behavior, icemask_grc = grc_array(1._r8))
     filter = this%topo%DownscaleFilterc(bounds)
 
     @assertTrue(filter == expected_filter)
-  end subroutine downscaleFilter_afterUpdate_contains_vegInsideIcemask
+  end subroutine downscaleFilter_afterUpdate_doesNotContain_vegNonVirtual
+
+  @Test
+  subroutine topo_changes_for_glcmecInsideIcemaskAndVirtual(this)
+    class(TestTopo), intent(inout) :: this
+    type(glc_behavior_type) :: glc_behavior
+    real(r8), parameter :: topo_orig = 7._r8
+    real(r8), parameter :: atm_topo = 23._r8
+
+    ! our column should get set to this:
+    real(r8), parameter :: glc_topo = 27._r8
+
+    call setup_single_ice_column(elev_class = 1)
+    glc_behavior = create_glc_behavior_all_virtual()
+    topo_glc_mec(:,:) = topo_orig
+
+    call this%topo%Init(bounds)
+    call this%do_UpdateTopo(glc_behavior, icemask_grc = grc_array(1._r8), &
+         atm_topo_grc = grc_array(atm_topo), &
+         glc_topo = glc_topo)
+
+    @assertEqual(glc_topo, this%topo%topo_col(bounds%begc))
+  end subroutine topo_changes_for_glcmecInsideIcemaskAndVirtual
 
   @Test
   subroutine topo_noChange_for_glcmecOutsideIcemask(this)
@@ -319,17 +362,17 @@ contains
   end subroutine topo_noChange_for_glcmecOutsideIcemask
 
   @Test
-  subroutine topo_changes_for_glcmecInsideIcemask(this)
+  subroutine topo_noChange_for_glcmecNonVirtual(this)
     class(TestTopo), intent(inout) :: this
     type(glc_behavior_type) :: glc_behavior
     real(r8), parameter :: topo_orig = 7._r8
-    real(r8), parameter :: atm_topo = 23._r8
 
-    ! our column should get set to this:
+    ! our column should NOT get set to either of these:
+    real(r8), parameter :: atm_topo = 23._r8
     real(r8), parameter :: glc_topo = 27._r8
 
     call setup_single_ice_column(elev_class = 1)
-    glc_behavior = create_glc_behavior_all_virtual()
+    glc_behavior = create_glc_behavior_all_multiple()
     topo_glc_mec(:,:) = topo_orig
 
     call this%topo%Init(bounds)
@@ -337,8 +380,8 @@ contains
          atm_topo_grc = grc_array(atm_topo), &
          glc_topo = glc_topo)
 
-    @assertEqual(glc_topo, this%topo%topo_col(bounds%begc))
-  end subroutine topo_changes_for_glcmecInsideIcemask
+    @assertEqual(topo_orig, this%topo%topo_col(bounds%begc))
+  end subroutine topo_noChange_for_glcmecNonVirtual
 
   @Test
   subroutine topo_changes_for_singleAtAtmTopo(this)

From b12cea1d6061450be368138fb12a1eacd9340972 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 22 Aug 2024 17:08:03 -0600
Subject: [PATCH 0975/1248] Revisions so that changes apply to clm6 only

---
 bld/namelist_files/namelist_defaults_ctsm.xml      | 8 ++++----
 bld/namelist_files/namelist_defaults_dust_emis.xml | 3 ++-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e94863b32e..20f6d4702a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -161,10 +161,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <calc_human_stress_indices phys="clm4_5" >NONE</calc_human_stress_indices>
 
 <!-- Explicit, time-varying urban air conditioning adoption rate scheme -->
+<urban_explicit_ac>.false.</urban_explicit_ac>
 <urban_explicit_ac phys="clm6_0" >.true.</urban_explicit_ac>
-<urban_explicit_ac phys="clm5_1" >.false.</urban_explicit_ac>
-<urban_explicit_ac phys="clm5_0" >.false.</urban_explicit_ac>
-<urban_explicit_ac phys="clm4_5" >.false.</urban_explicit_ac>
 
 <!-- Default urban traffic flux -->
 <urban_traffic>.false.</urban_traffic>
@@ -2706,7 +2704,9 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- Defaults for excess ice                    -->
 <!-- =========================================  -->
 
-<use_excess_ice>.true.</use_excess_ice>
+<use_excess_ice>.false.</use_excess_ice>
+<use_excess_ice phys="clm6_0">.true.</use_excess_ice>
+
 <excess_ice_coldstart_temp>-1.0</excess_ice_coldstart_temp>
 <excess_ice_coldstart_depth>0.5</excess_ice_coldstart_depth>
 <excess_ice_coldstart_temp use_excess_ice=".true.">-3.15</excess_ice_coldstart_temp>
diff --git a/bld/namelist_files/namelist_defaults_dust_emis.xml b/bld/namelist_files/namelist_defaults_dust_emis.xml
index 319110cc55..a13a23d14b 100644
--- a/bld/namelist_files/namelist_defaults_dust_emis.xml
+++ b/bld/namelist_files/namelist_defaults_dust_emis.xml
@@ -14,7 +14,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <!-- Defaults for dust_emis_inparm namelist  -->
-<dust_emis_method>Leung_2023</dust_emis_method>
+<dust_emis_method>Zender_2003</dust_emis_method>
+<dust_emis_method phys="clm6_0">Leung_2023</dust_emis_method>
 
 <zender_soil_erod_source>atm</zender_soil_erod_source>
 

From b2d7edf8f629406b01ec0044ea8655de9d670da5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 22 Aug 2024 17:14:44 -0600
Subject: [PATCH 0976/1248] Duplicate a bunch of XML so that the namelist unit
 tester works for all the tests

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 44 ++++++++++++++++++-
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 668ea1e05f..394f72a62e 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1059,12 +1059,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
 >hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
@@ -1144,6 +1144,26 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+                        hgrid="0.9x1.25" use_cn=".false." maxpft="17"
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+                        hgrid="1.9x2.5" use_cn=".false." maxpft="17"
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+                        hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
+>hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+                        hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
+>hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
 <!-- clm5_1 physics -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_cam6.0"
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
@@ -1213,6 +1233,26 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+                        hgrid="0.9x1.25" use_cn=".false." maxpft="17"
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+                        hgrid="1.9x2.5" use_cn=".false." maxpft="17"
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+                        hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
+>hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+                        hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
+>hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+</init_interp_attributes>
+
 <!-- 2003 -->
 <init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"

From be5d1d6b8128bd36e264900f58ccd8a69940f0d9 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 22 Aug 2024 17:15:17 -0600
Subject: [PATCH 0977/1248] Change fatal error to warning for megan_specifier

---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 37eedff6e5..94f6bf7e38 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -5666,7 +5666,7 @@ sub check_megan_spec {
        $megan_spec = remove_leading_and_trailing_quotes($spec);
        # Do simple validation of the expressions to just check for valid characters
        if ( $megan_spec !~ /^([\s=A-Za-z0-9_\+\.\*\(\)-]+)$/ ) {
-          $log->fatal_error("Bad format for megan_specifier = $megan_spec");
+          $log->warning("Bad format for megan_specifier = $megan_spec");
        }
     }
 }

From a5a15ed19bd7517e3abfd9994353c3f42bd49e8d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 22 Aug 2024 17:17:11 -0600
Subject: [PATCH 0978/1248] Correct test number and remove fail tests that are
 now allowed to happen because you can set drv_flds_in settings without using
 the CLM_BLDNML_OPTS options for it

---
 bld/unit_testers/build-namelist_test.pl | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index de5a9b0e13..8b2827b069 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3339;
+my $ntests = 3349;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1999;
+   $ntests += 2007;
 }
 plan( tests=>$ntests );
 
@@ -1093,14 +1093,6 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"use_hydrstress=.true.",
                                      phys=>"clm5_0",
                                    },
-     "specWOfireemis"            =>{ options=>"-envxml_dir . -no-fire_emis",
-                                     namelst=>"fire_emis_specifier='bc_a1 = BC'",
-                                     phys=>"clm5_0",
-                                   },
-     "elevWOfireemis"            =>{ options=>"-envxml_dir . -no-fire_emis",
-                                     namelst=>"fire_emis_elevated=.false.",
-                                     phys=>"clm5_0",
-                                   },
      "noanthro_w_crop"            =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -crop -use_case 1850_noanthro_control",
                                      namelst=>"",
                                      phys=>"clm5_0",

From c61aca3708a8908639a884a3bd5926b23b8b5aa5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 23 Aug 2024 02:07:57 -0600
Subject: [PATCH 0979/1248] Update to use the new ctsm5.3 finidat file for f09
 1850

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 21 +++++++------------
 1 file changed, 8 insertions(+), 13 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 20f6d4702a..8e6b9b5d51 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -928,13 +928,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 1850 for CLM5.1/CLM6.0 -->
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm5_1"
->hgrid=ne30np4.pg3 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm5_1_GSWP3v1
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
->hgrid=ne30np4.pg3 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1
 </init_interp_attributes>
 
+
 <!-- present day -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_GSWP3v1"
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
@@ -1335,23 +1336,17 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
-<!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at ne30pg3_mg17 for all clm5_1/clm6_0 options -->
-<!-- use_init_interp true because even though this is a ctsm5.2 dataset it was with early fsurfdat files -->
-<finidat hgrid="ne30np4.pg3" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm60BgcCrop-ciso.1361-01-01.ne30pg3_mg17_c240317.nc
-</finidat>
+<!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at f09 for all clm5_1/clm6_0 options -->
+<!-- use_init_interp true because the file was created with ctsm5.3 datasets -->
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
+         lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>

From 86a8db9acb0574de9f126b86013ee9f040e3651a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 23 Aug 2024 08:55:29 -0600
Subject: [PATCH 0980/1248] Allow non-agri fire in trop. forests in last
 timestep of month.

---
 src/biogeochem/CNFireLi2024Mod.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 4b7182f252..1332cfb773 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -632,7 +632,6 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                  if(( kmo == 1 .and. kda == 1 .and. mcsec == 0) .or. &
                       dtrotr_col(c) <=0._r8 )then
                     fbac1(c)        = 0._r8
-                    farea_burned(c) = baf_crop(c)+baf_peatf(c)
                  else
                     ! Calculate the precip threshold as the area-weighted mean of that for BET and BDT
                     cri = (defo_fire_precip_thresh_bet * trotr1_col(c) &

From bb08dbf2793cd5ab3f20c9a31d32e36486dfcb9b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 23 Aug 2024 09:00:31 -0600
Subject: [PATCH 0981/1248] li2024 fire now fully obeys cli_scale.

---
 src/biogeochem/CNFireLi2024Mod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index 1332cfb773..e1530c9717 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -642,7 +642,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                          (15._r8*min(0.0016_r8,dtrotr_col(c)/dt*dayspyr*secspday)+0.009_r8)* &
                          max(0._r8,min(1._r8,(0.25_r8-(forc_rain(c)+forc_snow(c))*secsphr)/0.25_r8))
 
-                    farea_burned(c) = farea_burned(c)+fb*cli*(0.01_r8/secspday)
+                    farea_burned(c) = farea_burned(c)+fb*cli*(cli_scale/secspday)
                     ! burned area out of conversion region due to land use fire
                     fbac1(c) = max(0._r8,fb*cli*(cli_scale/secspday) - 2.0_r8*lfc(c)/dt)
                  end if

From 5645313482fc3337325ff537bf8792b285d109db Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 23 Aug 2024 09:09:51 -0600
Subject: [PATCH 0982/1248] Add a comment to guide future refactoring.

---
 src/biogeochem/CNFireLi2024Mod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeochem/CNFireLi2024Mod.F90 b/src/biogeochem/CNFireLi2024Mod.F90
index e1530c9717..5f7c0019f6 100644
--- a/src/biogeochem/CNFireLi2024Mod.F90
+++ b/src/biogeochem/CNFireLi2024Mod.F90
@@ -632,7 +632,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
                  if(( kmo == 1 .and. kda == 1 .and. mcsec == 0) .or. &
                       dtrotr_col(c) <=0._r8 )then
                     fbac1(c)        = 0._r8
-                 else
+                 else  ! SSR: Why are the code blocks above and below this else mutually exclusive?
                     ! Calculate the precip threshold as the area-weighted mean of that for BET and BDT
                     cri = (defo_fire_precip_thresh_bet * trotr1_col(c) &
                          + defo_fire_precip_thresh_bdt * trotr2_col(c)) &

From 00d288b297be5806e7abdbb16f42ba37f4e0d54c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 21 Aug 2024 15:24:09 -0600
Subject: [PATCH 0983/1248] Change CTSM machine default for Derecho to develop
 queue w/ 32 cpus.

---
 python/ctsm/machine_defaults.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/machine_defaults.py b/python/ctsm/machine_defaults.py
index a17f063a4b..f07a313dcb 100644
--- a/python/ctsm/machine_defaults.py
+++ b/python/ctsm/machine_defaults.py
@@ -77,13 +77,13 @@
         create_test_queue=CREATE_TEST_QUEUE_UNSPECIFIED,
         job_launcher_defaults={
             JOB_LAUNCHER_QSUB: QsubDefaults(
-                queue="main",
+                queue="develop",
                 walltime="03:50:00",
                 extra_args="",
                 # The following assumes a single node, with a single mpi proc; we may want
                 # to add more flexibility in the future, making the node / proc counts
                 # individually selectable
-                required_args="-l select=1:ncpus=128:mpiprocs=1 -V -r n -k oed",
+                required_args="-l select=1:ncpus=32:mpiprocs=1 -V -r n -k oed",
             )
         },
     ),

From add600b14f1a7ddaea6b163a501bb61fb824905f Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 23 Aug 2024 09:43:49 -0600
Subject: [PATCH 0984/1248] Change to 16 to match GMAKE_J.

---
 python/ctsm/machine_defaults.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/machine_defaults.py b/python/ctsm/machine_defaults.py
index f07a313dcb..16742da47e 100644
--- a/python/ctsm/machine_defaults.py
+++ b/python/ctsm/machine_defaults.py
@@ -83,7 +83,7 @@
                 # The following assumes a single node, with a single mpi proc; we may want
                 # to add more flexibility in the future, making the node / proc counts
                 # individually selectable
-                required_args="-l select=1:ncpus=32:mpiprocs=1 -V -r n -k oed",
+                required_args="-l select=1:ncpus=16:mpiprocs=1 -V -r n -k oed",
             )
         },
     ),

From d4042ee5074e57bce27d11394264f4c786212ba5 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 23 Aug 2024 10:47:32 -0600
Subject: [PATCH 0985/1248] This may be the finidat fix (based on the aux_clm
 failures on izumi)

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 20f6d4702a..cee86cdbd2 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1341,18 +1341,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm60BgcCrop-ciso.1361-01-01.ne30pg3_mg17_c240317.nc
-</finidat>
-<finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
-</finidat>
-<finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
@@ -1394,7 +1382,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_GSWP3v1"
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm52BgcCrop.2000-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240515.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 

From 585935a94cc16397fb16b7df1ad3d1da43981f31 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Fri, 23 Aug 2024 12:32:17 -0600
Subject: [PATCH 0986/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 62 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 42907da404..f283f8a20c 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,65 @@
 ===============================================================
+Tag name: ctsm5.2.025
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Fri Aug 23 12:27:51 MDT 2024
+One-line Summary: Minor fixes to li2024 fire methods
+
+Purpose and description of changes
+----------------------------------
+
+- Allow non-agricultural fire in tropical closed forests in the last timestep of the month
+- li2024 fire now fully obeys cli_scale (b4b change because default parameter matched the magic number)
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description):
+- Resolves ESCOMP/CTSM#2725: Minor bugs in li2024 fire (https://github.com/ESCOMP/CTSM/issues/2725)
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  Note that some Derecho tests did not complete. However, all the fire tests did, and none
+  of the other tests use the code that was modified here.
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2726: Bug fixes to li2024 fire (https://github.com/ESCOMP/CTSM/pull/2726)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.024
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Thu Aug 22 11:07:11 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index f4b14775b2..ce290045fa 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods
        ctsm5.2.024 samrabin 08/22/2024 Improve li2024 fire methods
        ctsm5.2.023 samrabin 08/16/2024 Merge b4b-dev
        ctsm5.2.022 samrabin 08/14/2024 Rework crop_calendars suite and cropMonthOutput

From 5d6987ed5bce252961f0ca011f9762019ef20dc2 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 23 Aug 2024 12:44:58 -0600
Subject: [PATCH 0987/1248] More finidat changes based on aux_clm failure on
 derecho

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index c6afee6f90..fdaee2bcaa 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1473,7 +1473,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <!-- clm6_0 and cam7.0 -->
@@ -1481,7 +1481,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <!-- clm5_0 and cam7.0 -->
@@ -1545,7 +1545,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1608,7 +1608,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1682,14 +1682,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1753,7 +1753,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1817,7 +1817,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->

From 8594b7d9c2b3e8a07c8d383d4218fc231a0e64ab Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 23 Aug 2024 14:49:09 -0600
Subject: [PATCH 0988/1248] Add comments about the new finidat file

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index fdaee2bcaa..dacf75be02 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1385,6 +1385,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm5_1_GSWP3v1"
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1469,6 +1470,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <!-- clm5_1 and cam7.0 -->
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1477,6 +1479,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- clm6_0 and cam7.0 -->
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1541,6 +1544,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1604,6 +1608,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1678,6 +1683,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1685,6 +1691,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1749,6 +1756,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1813,6 +1821,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
+<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."

From 32637e666916aaa92bb7f8e36efdfddf1991b346 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 23 Aug 2024 14:49:39 -0600
Subject: [PATCH 0989/1248] Draft ChangeLog/ChangeSum

---
 doc/ChangeLog | 84 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 85 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index f283f8a20c..d3fd86e6ac 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,88 @@
 ===============================================================
+Tag name: ctsm5.2.026
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 23 Aug 2024 01:23:43 PM MDT
+One-line Summary: Turn on excess ice, explicit AC, Leung_2023 for clm6
+
+Purpose and description of changes
+----------------------------------
+
+ Turn on excess ice, explicit AC, Leung_2023 for clm6.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[X] clm6_0
+
+[X] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+Fixes #2466 Turn excess ice on by default in CESM3
+Fixes #2568 Turn on explicit AC, Leung_2023, and excess ice by default
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+ Namelist defaults changed to turn on excess ice, explicit AC, Leung_2023
+ in clm6; also to pick up new finidat files for clm6.
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ CLM6 cases need new finidat files. We use 1850 finidat files for
+ all clm6 cases because that's all that we have generated for now.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+ CLM6 cases need new finidat files. We use 1850 finidat files for
+ all clm6 cases because that's all that we have generated for now.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - OK, expected FAIL> <Test Id: 379> <Desc: LeungDust_WO_Prigent
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- IN PROG
+    izumi ------- IN PROG
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: clm6, clm51
+    - what platforms/compilers: all
+    - nature of change: more than roundoff
+
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2724
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.025
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Fri Aug 23 12:27:51 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index ce290045fa..6071278954 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6
        ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods
        ctsm5.2.024 samrabin 08/22/2024 Improve li2024 fire methods
        ctsm5.2.023 samrabin 08/16/2024 Merge b4b-dev

From dd9b1b0ab6bd715ccfb77031a0b8575f446d39d1 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 23 Aug 2024 15:52:29 -0600
Subject: [PATCH 0990/1248] Add use_init_interp to an f19 test using the new
 f09 finidat

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index dacf75be02..df3927fd0e 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1389,7 +1389,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_GSWP3v1"
+         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
 </finidat>
 

From 7f76dc031638b399546d15c07effa25522c52422 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 23 Aug 2024 17:28:15 -0600
Subject: [PATCH 0991/1248] Updated ChangeLog

---
 doc/ChangeLog | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index d3fd86e6ac..96c0d6735b 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.026
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
-Date: Fri 23 Aug 2024 01:23:43 PM MDT
+Date: Fri 23 Aug 2024 05:17:56 PM MDT
 One-line Summary: Turn on excess ice, explicit AC, Leung_2023 for clm6
 
 Purpose and description of changes
@@ -38,17 +38,17 @@ Fixes #2568 Turn on explicit AC, Leung_2023, and excess ice by default
 Notes of particular relevance for users
 ---------------------------------------
 Changes made to namelist defaults (e.g., changed parameter values):
- Namelist defaults changed to turn on excess ice, explicit AC, Leung_2023
- in clm6; also to pick up new finidat files for clm6.
+ Namelist defaults now turn on excess ice, explicit AC, Leung_2023
+ in clm6; they also pick up new finidat files for clm6.
 
 Changes to the datasets (e.g., parameter, surface or initial files):
- CLM6 cases need new finidat files. We use 1850 finidat files for
+ CLM6 cases need new finidat files. We use a f09 1850 finidat for
  all clm6 cases because that's all that we have generated for now.
 
 Notes of particular relevance for developers:
 ---------------------------------------------
 Caveats for developers (e.g., code that is duplicated that requires double maintenance):
- CLM6 cases need new finidat files. We use 1850 finidat files for
+ CLM6 cases need new finidat files. We use a f09 1850 finidat for
  all clm6 cases because that's all that we have generated for now.
 
 Testing summary:
@@ -62,8 +62,8 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho ----- IN PROG
-    izumi ------- IN PROG
+    derecho ----- OK
+    izumi ------- OK
 
 Answer changes
 --------------
@@ -75,6 +75,8 @@ Changes answers relative to baseline: Yes
     - what platforms/compilers: all
     - nature of change: more than roundoff
 
+ Details about the diffs from excess ice and explicit AC may be found in
+ the earlier entries of this ChangeLog for ctsm5.2.018 and ctsm5.2.010.
 
 Other details
 -------------

From 1e803f2619ef3f3486ba5aba90496879f1eeb832 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Sat, 24 Aug 2024 08:24:15 -0600
Subject: [PATCH 0992/1248] Fix regridding of glacier region

We should use the maximum existing index, without regards for the
relative coverage of the different indices.
---
 .../src/mkglacierregionMod.F90                | 24 ++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/tools/mksurfdata_esmf/src/mkglacierregionMod.F90 b/tools/mksurfdata_esmf/src/mkglacierregionMod.F90
index 267e46ddfa..4f6563b753 100644
--- a/tools/mksurfdata_esmf/src/mkglacierregionMod.F90
+++ b/tools/mksurfdata_esmf/src/mkglacierregionMod.F90
@@ -56,7 +56,6 @@ subroutine mkglacierregion(file_mesh_i, file_data_i, mesh_o, pioid_o, rc)
     integer , allocatable  :: glacier_region_i(:) ! glacier region on input grid
     integer , allocatable  :: glacier_region_o(:) ! glacier region on output grid
     integer                :: ier, rcode          ! error status
-    integer                :: max_index(1)
     character(len=*), parameter :: subname = 'mkglacierregion'
     !-----------------------------------------------------------------------
 
@@ -141,10 +140,29 @@ subroutine mkglacierregion(file_mesh_i, file_data_i, mesh_o, pioid_o, rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
     ! Determine glacier_region_o
+    !
+    ! We take the maximum glacier region index that has > 0 coverage in the output grid
+    ! cell. The frequency of occurrence of the different glacier regions is irrelevant.
+    ! For example, if the value 1 appears in 99% of source cells overlapping a given
+    ! destination cell and the value 2 appears in just 1%, we'll put 2 in the destination
+    ! cell because it is the maximum value. (This treatment is important so that we give
+    ! priority to non-zero indices, and more generally allow setting up the glacier region
+    ! indices so that higher values take precedence - i.e., if a CTSM grid cell has any
+    ! overlap with a higher-valued region, we use that region.)
     glacier_region_o(:) = 0
     do no = 1,ns_o
-       max_index = maxloc(data_o(:,no))
-       glacier_region_o(no) = max_index(1) - 1
+       ! Note that we loop starting at the highest index so we give priority to higher
+       ! indices. Also note that we stop looking at index 1 (i.e., we don't explicitly
+       ! look at index 0): if we haven't found a region with greater than 0 coverage from
+       ! looking at the indices greater than 0, then we'll default to assigning this to
+       ! glacier region 0, regardless of the coverage of glacier region 0 (though, in
+       ! practice, glacier region 0 should have 100% coverage in this case).
+       do l = nglacier_regions, 1, -1
+          if (data_o(l,no) > 0._r8) then
+             glacier_region_o(no) = l
+             exit
+          end if
+       end do
     end do
     
     ! Write output data

From 37d0e8f3ab6378d3eb3fc1b41a1ed0164633ff16 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 26 Aug 2024 12:19:26 -0600
Subject: [PATCH 0993/1248] Update clm6 param file to new one from Sam R.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 384785b804..1cc58a30b6 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -551,7 +551,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240814.nc</paramfile>
+<paramfile phys="clm6_0" >/glade/work/samrabin/ctsm_fire-li2024-pr2_paramfiles/ctsm60_params.c240822.li2024crujra.nc</paramfile>
 <paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240814.nc</paramfile>
 <paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240814.nc</paramfile>
 <paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240814.nc</paramfile>

From b35320a2c452dcb99e82a183bffda126c1206eb1 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 8 Dec 2021 13:54:28 -0700
Subject: [PATCH 0994/1248] Also include the mizuRoute expected fails list

---
 parse_cime.cs.status | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/parse_cime.cs.status b/parse_cime.cs.status
index 08bb1bfc86..269878d0bd 100755
--- a/parse_cime.cs.status
+++ b/parse_cime.cs.status
@@ -302,6 +302,7 @@ sub print_categories {
    if ( ! -f $expectedfailfile ) {
       $expectedfailfile = "$scrdir/cime_config/testdefs/ExpectedTestFails.xml";
    }
+   my @failfiles = (  $expectedfailfile, "$scrdir/components/mizuRoute/cime_config/testdefs/ExpectedTestFails.xml" );
    my @passes;
    my @fails;
    my @pendings;
@@ -341,8 +342,10 @@ sub print_categories {
       print( "================================================================================\n" );
       foreach my $key ( @passes ) {
          my $expect = ""; 
-         `grep $key $expectedfailfile > /dev/null`;
-         if ( $? == 0 ) { $expect = "FAILED PREVIOUSLY"; }
+         foreach my $expectedfailfile ( @failfiles ) {
+            `grep $key $expectedfailfile > /dev/null`;
+            if ( $? == 0 ) { $expect = "FAILED PREVIOUSLY"; }
+         }
          print( "$key\t\t\t$expect\n" );
       }
    }
@@ -368,8 +371,10 @@ sub print_categories {
       print( "================================================================================\n" );
       foreach my $key ( @pendings ) {
          my $expect = ""; 
-         `grep $key $expectedfailfile > /dev/null`;
-         if ( $? == 0 ) { $expect = "EXPECTED"; }
+         foreach my $expectedfailfile ( @failfiles ) {
+            `grep $key $expectedfailfile > /dev/null`;
+            if ( $? == 0 ) { $expect = "EXPECTED"; }
+         }
          print( "$key\t\t$expect\n" );
       }
    }
@@ -379,8 +384,10 @@ sub print_categories {
       print( "================================================================================\n" );
       foreach my $key ( @fails ) {
          my $expect = ""; 
-         `grep $key $expectedfailfile > /dev/null`;
-         if ( $? == 0 ) { $expect = "EXPECTED"; }
+         foreach my $expectedfailfile ( @failfiles ) {
+            `grep $key $expectedfailfile > /dev/null`;
+            if ( $? == 0 ) { $expect = "EXPECTED"; }
+         }
          print( "$key\t\t$expect\n" );
       }
    }

From 463e85d8f624fb8f8b64592f4a6824b80683bdd9 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 19 Jan 2022 22:45:47 -0700
Subject: [PATCH 0995/1248] Add bit from SLIM that includes what parts FAIL
 when reporting summary of fails

---
 parse_cime.cs.status | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/parse_cime.cs.status b/parse_cime.cs.status
index 269878d0bd..8ef8ef2bf6 100755
--- a/parse_cime.cs.status
+++ b/parse_cime.cs.status
@@ -384,11 +384,12 @@ sub print_categories {
       print( "================================================================================\n" );
       foreach my $key ( @fails ) {
          my $expect = ""; 
+         my $fails = $csstatus{$key}{'FAIL'};
          foreach my $expectedfailfile ( @failfiles ) {
             `grep $key $expectedfailfile > /dev/null`;
             if ( $? == 0 ) { $expect = "EXPECTED"; }
          }
-         print( "$key\t\t$expect\n" );
+         print( "$key\t$fails\t$expect\n" );
       }
    }
 }

From 8fbfcc009c26459e5c76c03309d1d58c678583c8 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 25 Jan 2022 14:32:09 -0700
Subject: [PATCH 0996/1248] Add an extra tab

---
 parse_cime.cs.status | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parse_cime.cs.status b/parse_cime.cs.status
index 8ef8ef2bf6..fb2d8e4283 100755
--- a/parse_cime.cs.status
+++ b/parse_cime.cs.status
@@ -389,7 +389,7 @@ sub print_categories {
             `grep $key $expectedfailfile > /dev/null`;
             if ( $? == 0 ) { $expect = "EXPECTED"; }
          }
-         print( "$key\t$fails\t$expect\n" );
+         print( "$key\t$fails\t\t$expect\n" );
       }
    }
 }

From 0d1a867beb91d1e8a1aacd57a3165dd297c33a1b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 26 Aug 2024 16:06:00 -0600
Subject: [PATCH 0997/1248] Make a little subroutine to check the expected
 fails

---
 parse_cime.cs.status | 31 ++++++++++++++-----------------
 1 file changed, 14 insertions(+), 17 deletions(-)

diff --git a/parse_cime.cs.status b/parse_cime.cs.status
index fb2d8e4283..885b53c6c4 100755
--- a/parse_cime.cs.status
+++ b/parse_cime.cs.status
@@ -290,7 +290,15 @@ sub print_sumperline {
    }
 }
 
-
+sub expectedFails {
+   my ($key, $message, @failfiles) = @_;
+   my $expect = "";
+   foreach my $expectedfailfile ( @failfiles ) {
+      `grep $key $expectedfailfile > /dev/null`;
+      if ( $? == 0 ) { $expect = $message; }
+   }
+   return( $expect );
+}
 
 sub print_categories {
    # Seperate tests into categories
@@ -341,11 +349,7 @@ sub print_categories {
       print( "These tests passed\n" );
       print( "================================================================================\n" );
       foreach my $key ( @passes ) {
-         my $expect = ""; 
-         foreach my $expectedfailfile ( @failfiles ) {
-            `grep $key $expectedfailfile > /dev/null`;
-            if ( $? == 0 ) { $expect = "FAILED PREVIOUSLY"; }
-         }
+         my $expect = &expectedFails( $key, "FAILED PREVIOUSLY", @failfiles );
          print( "$key\t\t\t$expect\n" );
       }
    }
@@ -370,26 +374,19 @@ sub print_categories {
       print( "These tests are pending (some tests may fail in the pending state)\n" );
       print( "================================================================================\n" );
       foreach my $key ( @pendings ) {
-         my $expect = ""; 
-         foreach my $expectedfailfile ( @failfiles ) {
-            `grep $key $expectedfailfile > /dev/null`;
-            if ( $? == 0 ) { $expect = "EXPECTED"; }
-         }
+         my $expect = &expectedFails( $key, "EXPECTED", @failfiles );
          print( "$key\t\t$expect\n" );
       }
    }
    if ( $#fails >= 0 ) {
       print( "================================================================================\n" );
       print( "These tests failed\n" );
+      print( "Test (what Failed) If expected\n" );
       print( "================================================================================\n" );
       foreach my $key ( @fails ) {
-         my $expect = ""; 
+         my $expect = &expectedFails( $key, "EXPECTED", @failfiles );
          my $fails = $csstatus{$key}{'FAIL'};
-         foreach my $expectedfailfile ( @failfiles ) {
-            `grep $key $expectedfailfile > /dev/null`;
-            if ( $? == 0 ) { $expect = "EXPECTED"; }
-         }
-         print( "$key\t$fails\t\t$expect\n" );
+         print( "$key\t($fails)\t\t$expect\n" );
       }
    }
 }

From cd6a94b3512bf9d4def7b7db1af85e77fb3e1690 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 26 Aug 2024 17:03:09 -0600
Subject: [PATCH 0998/1248] Report on the expected fails for tests

---
 parse_cime.cs.status | 46 +++++++++++++++++++++++++++++++++++---------
 1 file changed, 37 insertions(+), 9 deletions(-)

diff --git a/parse_cime.cs.status b/parse_cime.cs.status
index 885b53c6c4..264ba0708f 100755
--- a/parse_cime.cs.status
+++ b/parse_cime.cs.status
@@ -204,7 +204,11 @@ sub run_csstatus {
          do {
             $newline = shift(@lines);
             if (       $newline =~ /FAIL[ ]+$test ([^ ]+)/ ) {
-               $fails .= " $1";
+               if ( $fails eq "" ) {
+                  $fails = $1;
+               } else {
+                  $fails .= " $1";
+               }
                chomp( $fails );
                if ( $1 eq "BASELINE" ) {
                  if ( $newline =~ /ERROR BFAIL baseline directory/ ) {
@@ -291,13 +295,31 @@ sub print_sumperline {
 }
 
 sub expectedFails {
+   # Query expected fail file for the input testname key
    my ($key, $message, @failfiles) = @_;
    my $expect = "";
+   my $expectedfails = "";
    foreach my $expectedfailfile ( @failfiles ) {
-      `grep $key $expectedfailfile > /dev/null`;
-      if ( $? == 0 ) { $expect = $message; }
+      my $fh = IO::File->new($expectedfailfile, '<') or die "ERROR:: failure opening $expectedfailfile\n";
+      while( my $line = <$fh> ) {
+         if ( $line =~ /$key/ ) {
+            $expect = $message;
+            # Read past the testname until the test end is found...
+            # Keep track of all of the expected fails and return it at the end
+            while( my $testline = <$fh> ) {
+               if ( $testline =~ /phase\s+name\s*=\s*\"([a-zA-Z0-9_]+)/ ) {
+                  if ( $expectedfails eq "" ) {
+                    $expectedfails = $1;
+                  } else {
+                    $expectedfails = "$expectedfails $1";
+                  }
+               }
+               if ( $testline =~ /\<\/test\>/ ) { last; }
+            }
+         }
+      }
    }
-   return( $expect );
+   return( $expect, $expectedfails );
 }
 
 sub print_categories {
@@ -349,7 +371,9 @@ sub print_categories {
       print( "These tests passed\n" );
       print( "================================================================================\n" );
       foreach my $key ( @passes ) {
-         my $expect = &expectedFails( $key, "FAILED PREVIOUSLY", @failfiles );
+         my ($expect, $expectFails) = &expectedFails( $key, "FAILED PREVIOUSLY", @failfiles );
+         if ( $expect ne "" ) { $expect = "$expect ($expectFails)"; }
+         if ($expectFails =~ /BASELINE/ ) { $expect = ""; }
          print( "$key\t\t\t$expect\n" );
       }
    }
@@ -358,7 +382,9 @@ sub print_categories {
       print( "These tests compare different to the baseline\n" );
       print( "================================================================================\n" );
       foreach my $key ( @compares_diff ) {
-         print( "$key\n" );
+         my ($expect, $expectFails) = &expectedFails( $key, "EXPECTED POSSIBILITY", @failfiles );
+         if ($expectFails !~ /BASELINE/ ) { $expect = ""; }
+         print( "$key\t\t$expect\n" );
       }
    }
    if ( $#compares_diff_nobase >= 0 ) {
@@ -374,17 +400,19 @@ sub print_categories {
       print( "These tests are pending (some tests may fail in the pending state)\n" );
       print( "================================================================================\n" );
       foreach my $key ( @pendings ) {
-         my $expect = &expectedFails( $key, "EXPECTED", @failfiles );
+         my ($expect, $expectFails) = &expectedFails( $key, "EXPECTED", @failfiles );
+         if ( $expect ne "" ) { $expect = "$expect ($expectFails)"; }
          print( "$key\t\t$expect\n" );
       }
    }
    if ( $#fails >= 0 ) {
       print( "================================================================================\n" );
       print( "These tests failed\n" );
-      print( "Test (what Failed) If expected\n" );
+      print( "Test (what Failed) EXPECTED (what expected to fail)\n" );
       print( "================================================================================\n" );
       foreach my $key ( @fails ) {
-         my $expect = &expectedFails( $key, "EXPECTED", @failfiles );
+         my ($expect, $expectFails) = &expectedFails( $key, "EXPECTED", @failfiles );
+         if ( $expect ne "" ) { $expect = "$expect ($expectFails)"; }
          my $fails = $csstatus{$key}{'FAIL'};
          print( "$key\t($fails)\t\t$expect\n" );
       }

From c5aeec66333b37050bd426c678ac36f9ec3f0c62 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 26 Aug 2024 21:43:31 -0600
Subject: [PATCH 0999/1248] Add some more notes about -drydep, -fire_emis,
 -no-megan options options that they add testing namelists, but you can always
 add the fields to user_nl_clm even when they are turned off

---
 bld/CLMBuildNamelist.pm | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 94f6bf7e38..15d51ccfcb 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -159,16 +159,20 @@ OPTIONS
                               This turns on the namelist variable: use_crop
      -csmdata "dir"           Root directory of CESM input data.
                               Can also be set by using the CSMDATA environment variable.
-     -drydep                  Produce a drydep_inparm namelist that will go into the
+     -drydep                  Produce a drydep_inparm namelist for testing that will go into the
                               "drv_flds_in" file for the driver to pass dry-deposition to the atm.
+                              This populates the namelist with valid drydep settings for testing.
                               Default: -no-drydep
+                              Note: Can always add drydep fields to user_nl_clm even with --no-drydep
                               (Note: buildnml copies the file for use by the driver)
      -dynamic_vegetation      Toggle for dynamic vegetation model. (default is off)
                               (can ONLY be turned on when BGC type is 'bgc')
                               This turns on the namelist variable: use_cndv
                               (Deprecated, this will be removed)
-     -fire_emis               Produce a fire_emis_nl namelist that will go into the
+     -fire_emis               Produce a fire_emis_nl namelist for testing that will go into the
                               "drv_flds_in" file for the driver to pass fire emissions to the atm.
+                              This populates the namelist with valid fire-emiss settings for testing.
+                              Note: Can always add fire_emis fields to user_nl_clm even with --no-fire_emis
                               (Note: buildnml copies the file for use by the driver)
      -glc_nec <name>          Glacier number of elevation classes [0 | 3 | 5 | 10 | 36]
                               (default is 0) (standard option with land-ice model is 10)
@@ -204,9 +208,11 @@ OPTIONS
      -namelist "namelist"     Specify namelist settings directly on the commandline by supplying
                               a string containing FORTRAN namelist syntax, e.g.,
                                  -namelist "&clm_inparm dt=1800 /"
-     -no-megan                DO NOT PRODUCE a megan_emis_nl namelist that will go into the
+     -no-megan                DO NOT PRODUCE a megan_emis_nl namelist for testing that will go into the
                               "drv_flds_in" file for the driver to pass VOCs to the atm.
                               MEGAN (Model of Emissions of Gases and Aerosols from Nature)
+                              This removes setting default values for testing MEGAN fields
+                              Note: Can always add megan fields to user_nl_clm even with --no-megan
                               (Note: buildnml copies the file for use by the driver)
      -[no-]note               Add note to output namelist  [do NOT add note] about the
                               arguments to build-namelist.

From 46a09d91c08cf39a5352f9b2e78e7622f3376503 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 26 Aug 2024 22:10:27 -0600
Subject: [PATCH 1000/1248] Update some of the documentation around the
 -drydep, -fire_emis and --no-megan build-namelist options

---
 bld/namelist_files/namelist_defaults_drydep.xml     | 6 +++---
 bld/namelist_files/namelist_defaults_fire_emis.xml  | 4 ++--
 bld/namelist_files/namelist_definition_drv_flds.xml | 6 +++++-
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_drydep.xml b/bld/namelist_files/namelist_defaults_drydep.xml
index 08bb5adaef..fb73ab6646 100644
--- a/bld/namelist_files/namelist_defaults_drydep.xml
+++ b/bld/namelist_files/namelist_defaults_drydep.xml
@@ -5,7 +5,7 @@
 <namelist_defaults>
 
 <!--
-Values to use by default for creation of CLM model driver namelists.
+Values to use by default for creation of CLM model driver testing namelists.
 The element names are the same as the corresponding namelist
 variables.  Values that depend on the model configuration use
 attributes to express the dependency.  The recognized attributes
@@ -13,7 +13,7 @@ are: RESOLUTION, defaults, mask, ic_ymd, ic_tod, sim_year and all configuration
 attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
-<!-- Defaults for drydep_inparm namelist  -->
+<!-- Defaults for drydep_inparm namelist namelists to test standalone CTSM with  -->
 
 <drydep_list>'O3','NO2','HNO3','NO','HO2NO2','CH3OOH','CH2O','CO','H2O2','CH3COOOH','PAN','MPAN','C2H5OOH','ONIT','POOH','C3H7OOH','ROOH','CH3COCHO','CH3COCH3','Pb','ONITR','MACROOH','XOOH','ISOPOOH','CH3OH','C2H5OH','CH3CHO','GLYALD','HYAC','HYDRALD','ALKOOH','MEKOOH','TOLOOH','TERPOOH','CH3COOH','CB1','CB2','OC1','OC2','SOA','SO2','SO4','NH3','NH4NO3'
 </drydep_list>
@@ -21,7 +21,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- effective Henry's coef data for wet and dry deposition -->
 <dep_data_file>atm/cam/chem/trop_mozart/dvel/dep_data_c201019.nc</dep_data_file>
 
-<!-- Defaults for megan_emis_nl -->
+<!-- Defaults for megan_emis_nl namelists to test standalone CTSM with -->
 
 <megan_specifier>'ISOP = isoprene', 'C10H16 = pinene_a + carene_3 + thujene_a', 'CH3OH = methanol', 'C2H5OH = ethanol', 'CH2O = formaldehyde', 'CH3CHO = acetaldehyde', 'CH3COOH = acetic_acid', 'CH3COCH3 = acetone'</megan_specifier>
 
diff --git a/bld/namelist_files/namelist_defaults_fire_emis.xml b/bld/namelist_files/namelist_defaults_fire_emis.xml
index b7536ba66b..54e67424d5 100644
--- a/bld/namelist_files/namelist_defaults_fire_emis.xml
+++ b/bld/namelist_files/namelist_defaults_fire_emis.xml
@@ -5,7 +5,7 @@
 <namelist_defaults>
 
 <!--
-Values to use by default for creation of CLM model driver namelists.
+Values to use by default for creation of CLM model driver testing namelists.
 The element names are the same as the corresponding namelist
 variables.  Values that depend on the model configuration use
 attributes to express the dependency.  The recognized attributes
@@ -13,7 +13,7 @@ are: RESOLUTION, defaults, mask, ic_ymd, ic_tod, sim_year and all configuration
 attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
-<!-- Defaults for fire_emis_nl namelist  -->
+<!-- Defaults for fire_emis_nl namelists for testing -->
 
 <fire_emis_specifier>'bc_a1 = BC','pom_a1 = 1.4*OC','SO2 = SO2'</fire_emis_specifier>
 
diff --git a/bld/namelist_files/namelist_definition_drv_flds.xml b/bld/namelist_files/namelist_definition_drv_flds.xml
index 9bb1a3e3b0..f440a9a678 100644
--- a/bld/namelist_files/namelist_definition_drv_flds.xml
+++ b/bld/namelist_files/namelist_definition_drv_flds.xml
@@ -35,10 +35,14 @@
 	 group="megan_emis_nl"
 	 valid_values="" >
     MEGAN specifier. This is in the form of: Chem-compound = megan_compound(s)
-    where megan_compound(s) can be the sum of megan compounds with a "+" between them.
+    where megan_compound(s) can be an equation with megan compounds added or subtracted together with multiplication
     In each equation, the item to the left of the equal sign is a CAM chemistry compound, the
     items to the right are compounds known to the MEGAN model (single or combinations).
+    Long lines for equations can be split into multiple specifiers
     For example: megan_specifier = 'ISOP = isoprene', 'C10H16 = pinene_a + carene_3 + thujene_a'
+    or...        megan_specifier = 'SOAE = 0.5954*isoprene + 5.1004*(carene_3 + pinene_a + thujene_a + bornene +',
+                                   ' terpineol_4 + terpineol_a + terpinyl_ACT_a + myrtenal + sabinene + pinene_b + camphene +',
+    and etcetera...
   </entry>
 
   <entry id="megan_mapped_emisfctrs"

From 9a44188bcd97165cd60de212b890e0123b4b22ad Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 26 Aug 2024 23:11:11 -0600
Subject: [PATCH 1001/1248] Update documentation around the drv_flds_in testing
 namelists and command line options to build-namelist -drydep, -fire_emis and
 -no-megan

---
 .../customizing-the-clm-configuration.rst     | 39 ++++++++++++-------
 1 file changed, 26 insertions(+), 13 deletions(-)

diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index e76a9cc6f0..a1efac897e 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -140,10 +140,17 @@ CLM_BLDNML_OPTS
                               Can also be set by using the CSMDATA environment variable.
      -d "directory"           Directory where output namelist file will be written
                               Default: current working directory.
-     -drydep                  Produce a drydep_inparm namelist that will go into the
+     -drydep                  Produce a drydep_inparm namelist for testing that will go into the
                               "drv_flds_in" file for the driver to pass dry-deposition to the atm.
+                              This populates the namelist with valid drydep settings for testing.
                               Default: -no-drydep
-                              (Note: buildnml.csh copies the file for use by the driver)
+                              Note: Can always add drydep fields to user_nl_clm even with --no-drydep
+                              (Note: buildnml copies the file for use by the driver)
+     -fire_emis               Produce a fire_emis_nl namelist for testing that will go into the
+                              "drv_flds_in" file for the driver to pass fire emissions to the atm.
+                              This populates the namelist with valid fire-emiss settings for testing.
+                              Note: Can always add fire_emis fields to user_nl_clm even with --no-fire_emis
+                              (Note: buildnml copies the file for use by the driver)
      -glc_grid "grid"         Glacier model grid and resolution when glacier model,
                               Only used if glc_nec > 0 for determining fglcmask
                               Default:  gland5UM
@@ -185,10 +192,12 @@ CLM_BLDNML_OPTS
      -namelist "namelist"     Specify namelist settings directly on the commandline by supplying
                               a string containing FORTRAN namelist syntax, e.g.,
                                  -namelist "&clm_inparm dt=1800 /"
-     -no-megan                DO NOT PRODUCE a megan_emis_nl namelist that will go into the
+     -no-megan                DO NOT PRODUCE a megan_emis_nl namelist for testing that will go into the
                               "drv_flds_in" file for the driver to pass VOCs to the atm.
                               MEGAN (Model of Emissions of Gases and Aerosols from Nature)
-                              (Note: buildnml.csh copies the file for use by the driver)
+                              This removes setting default values for testing MEGAN fields
+                              Note: Can always add megan fields to user_nl_clm even with --no-megan
+                              (Note: buildnml copies the file for use by the driver)
      -[no-]note               Add note to output namelist  [do NOT add note] about the
                               arguments to build-namelist.
      -rcp "value"             Representative concentration pathway (rcp) to use for
@@ -258,6 +267,8 @@ The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and ma
 
 #. -drydep
 
+#. -fire_emis
+
 #. -ignore_ic_date
 
 #. -ignore_ic_year
@@ -291,7 +302,7 @@ To see a list of valid variables that you could set do this:
 
 .. note:: Using a 20th-Century transient compset or the ``20thC_transient`` use-case using ``CLM_NML_USE_CASE`` would set this as well, but would also use dynamic nitrogen and aerosol deposition files, so using ``-clm_demand`` would be a way to get *just* dynamic vegetation types and NOT the other files as well.
 
-"-drydep" adds the dry-deposition namelist to the driver. This is a driver namelist, but adding the option here has CLM **build-namelist** create the ``drv_flds_in`` file that the driver will copy over and use. Invoking this option does have an impact on performance even for I compsets and will slow the model down. It's also only useful when running with an active atmosphere model that makes use of this information.
+"-drydep" adds a dry-deposition namelist for testing to the driver. This is a driver namelist, but adding the option here has CLM **build-namelist** create the ``drv_flds_in`` file that the driver will copy over and use. Invoking this option does have an impact on performance even for I compsets and will slow the model down. It's also only useful when running with an active atmosphere model that makes use of this information.
 
 "-ignore_ic_date" ignores the Initial Conditions (IC) date completely for finding initial condition files to startup from. Without this option or the "-ignore_ic_year" option below, the date of the file comes into play.
 
@@ -299,7 +310,7 @@ To see a list of valid variables that you could set do this:
 
 When "-irrig on" is used **build-namelist** will try to find surface datasets that have the irrigation model enabled (when running with Sattellitte Phenology). When running with the prognostic crop model on, "-irrig on" will turn irrigate crops on, while "-irrig off" will manage all crop areas as rain-fed without irrigation.
 
-"no-megan" means do NOT add the MEGAN model Biogenic Volatile Organic Compounds (BVOC) namelist to the driver. This namelist is created by default, so normally this WILL be done. This is a driver namelist, so unless "no-megan" is specified the CLM **build-namelist** will create the ``drv_flds_in`` file that the driver will copy over and use (if you are running with CAM and CAM produces this file as well, it's file will have precedence).
+"no-megan" means do NOT add a MEGAN model Biogenic Volatile Organic Compounds (BVOC) testing namelist to the driver. This namelist is created by default, so normally this WILL be done. This is a driver namelist, so unless "no-megan" is specified the CLM **build-namelist** will create the ``drv_flds_in`` file that the driver will copy over and use (if you are running with CAM and CAM produces this file as well, it's file will have precedence).
 
 "-note" adds a note to the bottom of the namelist file, that gives the details of how **build-namelist** was called, giving the specific command-line options given to it.
 
@@ -363,18 +374,20 @@ Example: user_nl_clm namelist file
    ! Users should add all user specific namelist changes below in the form of
    ! namelist_var = new_namelist_value
    !
-   ! Include namelist variables for drv_flds_in ONLY if -megan and/or -drydep options
-   ! are set in the CLM_NAMELIST_OPTS env variable.
-   !
    ! EXCEPTIONS:
+   ! Set use_cndv           by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting
+   ! Set use_vichydro       by the compset you use and the CLM_BLDNML_OPTS -vichydro           setting
+   ! Set use_cn             by the compset you use and CLM_BLDNML_OPTS -bgc  setting
+   ! Set use_crop           by the compset you use and CLM_BLDNML_OPTS -crop setting
+   ! Set spinup_state       by the CLM_BLDNML_OPTS -bgc_spinup      setting
    ! Set co2_ppmv           with CCSM_CO2_PPMV                      option
-   ! Set dtime              with L_NCPL                             option
    ! Set fatmlndfrc         with LND_DOMAIN_PATH/LND_DOMAIN_FILE    options
    ! Set finidat            with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases
    !                        (includes $inst_string for multi-ensemble cases)
-   ! Set glc_grid           with GLC_GRID                           option
-   ! Set glc_smb            with GLC_SMB                            option
-   ! Set maxpatch_glc    with GLC_NEC                            option
+   !                        or with CLM_FORCE_COLDSTART to do a cold start
+   !                        or set it with an explicit filename here.
+   ! Set maxpatch_glc       with GLC_NEC                            option
+   ! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
    !----------------------------------------------------------------------------------
    hist_fincl2    = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS',
                     'FSR','FSA','FGEV','FSH','FGR','TSOI',

From f1ad74d8ee0e081f1c1448a9c3b19a8710cdbed0 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 27 Aug 2024 10:43:20 -0600
Subject: [PATCH 1002/1248] Update change log for new b4b-dev tag, make
 standard for python testing to be run on derecho

---
 doc/.ChangeLog_template |  2 +-
 doc/ChangeLog           | 86 +++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum           |  1 +
 3 files changed, 88 insertions(+), 1 deletion(-)

diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template
index 60a7f49288..c95ea482e3 100644
--- a/doc/.ChangeLog_template
+++ b/doc/.ChangeLog_template
@@ -98,7 +98,7 @@ infrastructure should be run when appropriate, as described below.
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
-    (any machine) -
+    derecho -
 
     [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python
      code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 96c0d6735b..c77ec2204f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,90 @@
 ===============================================================
+Tag name: ctsm5.2.027
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Tue 27 Aug 2024 10:39:39 AM MDT
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+
+Changes made to namelist defaults (e.g., changed parameter values):
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+
+Changes to documentation:
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing:
+
+
+Testing summary: regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): cdeps
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.026
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Fri 23 Aug 2024 05:17:56 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 6071278954..468cbe0077 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.027     erik 08/27/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6
        ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods
        ctsm5.2.024 samrabin 08/22/2024 Improve li2024 fire methods

From ddec5536cd6ae2e040315f550c71d464302ae09f Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 27 Aug 2024 13:13:51 -0600
Subject: [PATCH 1003/1248] Update change files

---
 doc/ChangeLog | 48 +++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 43 insertions(+), 5 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index c77ec2204f..e481310125 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -7,6 +7,17 @@ One-line Summary: Merge b4b-dev
 Purpose and description of changes
 ----------------------------------
 
+Bring b4b-dev branch to main CTSM development.
+
+- PLUMBER2 for ctsm5.2 datasets
+- Last bit of PPE changes for namelist and parameter file settings
+- Update run_sys_tests on Derecho for compiler jobs to run using 16 tasks
+- Bring in a fix for dust emissions for coupling with CAM
+
+Update cs.status parsing script to make expected BASELINE fails more obvious
+
+Fix some issues with finding IC files for certain lnd_tuning_modes: all for cam7, 
+   clm5_0_cam6.0, and clm6_0_cam6.0
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
@@ -31,27 +42,52 @@ Bugs fixed
 ----------
 
 List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes #2687 -- Error in Prigent streams setting when coupled to CAM
+   Fixes #2709 -- Problem in megan_specifier checking in namelist due to update in CMEPS
+   Fixes #2712 -- Allow user to change drydep, fire_emiss, megan namelists in user_nl_clm
+     even when those CLM_BLDNML_OPTS are off
+   Fixes #2567 -- PPE prep work
+   Fixes #1652 -- c3psn is wrong for some PFT's not currently used
+   Fixes #2484 -- update PLUMBER2 user-mods to ctsm5.2 surface datasets
 
 Notes of particular relevance for users
 ---------------------------------------
 
 Caveats for users (e.g., need to interpolate initial conditions):
+   atm_provides_lightning can be set in drv_flds_in now, but doesn't do anything
 
 Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   Changed behavior for CLM_BLDNML_OPTS command line options: -drydep, -megan, and -fire_emis
+   Turning them on now only adds test namelists to use, you can add custom settings for them 
+   in user_nl_clm with or without them on
 
-Changes made to namelist defaults (e.g., changed parameter values):
+   atm_provides_lightning and atm_ozone_frequency can be set in user_nl_clm for drv_flds_in
+      The first is not active, and the second you should probably have CAM set
 
-Changes to the datasets (e.g., parameter, surface or initial files):
+   New XML variable: PLUMBER2SITE to set the site name for PLUMBER2 cases
 
-Changes to documentation:
+Changes made to namelist defaults (e.g., changed parameter values): PLUMBER2 datasets
+
+   Using PLUMBER2 user-mods now gives you ctsm5.2 surface datasets
+
+Changes to the datasets (e.g., parameter, surface or initial files): parameter files
+   New parameter file with c3psn corrected and ndays_on changed to PFT
+   new parameters: crit_onset_gdd_sf, zbedrock, zbedrock_sf
+
+Changes to documentation: Yes regarding build-namelist command line options listed above
 
 Notes of particular relevance for developers:
 ---------------------------------------------
 
 Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   When LND_SETS_DUST_EMIS_DRV_FLD==FALSE (so coupled to CAM) -- The CAM $CASEDIR/Buildconf/camconf/drv_flds_in namelist is read in to get the CAM drv_flds_in settings. For this to work correctly
+   the drydep, and fire-emiss subroutines need to be after the dust_emis subroutine which reads in
+   the CAM drv_flds_in.
+      See plan to phase out LND_SETS_DUST_EMIS_DRV_FLD here:
+      https://github.com/ESCOMP/CTSM/issues/2713
 
 Changes to tests or testing:
-
+  Updated parameter files for some specific test mods
 
 Testing summary: regular
 ----------------
@@ -59,7 +95,7 @@ Testing summary: regular
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho - PASS
+    derecho - PASS (1005 different because of new parameter files)
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
@@ -79,9 +115,11 @@ Other details
 -------------
 
 List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): cdeps
+   cdeps to cdeps1.0.47
 
 Pull Requests that document the changes (include PR ids):
 (https://github.com/ESCOMP/ctsm/pull)
+   https://github.com/ESCOMP/CTSM/pull/2731 -- merge b4b-dev
 
 ===============================================================
 ===============================================================

From bae5c8c9553d4ea9cb986a98187720478f524281 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 27 Aug 2024 22:10:38 -0600
Subject: [PATCH 1004/1248] Update ChangeLog with more details

---
 doc/ChangeLog | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e481310125..cf160fce82 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.027
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
-Date: Tue 27 Aug 2024 10:39:39 AM MDT
+Date: Tue 27 Aug 2024 10:09:39 PM MDT
 One-line Summary: Merge b4b-dev
 
 Purpose and description of changes
@@ -56,6 +56,13 @@ Notes of particular relevance for users
 Caveats for users (e.g., need to interpolate initial conditions):
    atm_provides_lightning can be set in drv_flds_in now, but doesn't do anything
 
+   When LND_SETS_DUST_EMIS_DRV_FLD==FALSE and you are coupled to CAM
+   and there is a conflict between CAM and CTSM settings, a message like this happens:
+
+   Using clm5_0_cam6.0 for lnd_tuning_mode
+Read in the drv_flds_in file generated by CAM's build-namelist
+Build::Namelist::_merge_nl:ERROR: A variable was already set, so we are terminating on the conflict variable name is =dep_data_file 
+
 Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
    Changed behavior for CLM_BLDNML_OPTS command line options: -drydep, -megan, and -fire_emis
    Turning them on now only adds test namelists to use, you can add custom settings for them 

From 9fd631ac427e4db07244eb88d583bd3ecc0c1821 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 28 Aug 2024 14:33:19 -0600
Subject: [PATCH 1005/1248] Update CDEPS to hopefully resolve the CDEPS build
 issue I ran into

---
 .gitmodules      | 2 +-
 components/cdeps | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 80c1640e72..d16396da55 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -92,7 +92,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.47
+fxtag = cdeps1.0.48
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
diff --git a/components/cdeps b/components/cdeps
index 7476950699..7b0b3a8272 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit 7476950699909813d1938a34bd8d71bf5bfbf1e9
+Subproject commit 7b0b3a827241c53d296ec877cb1f59966bf5e5bf

From 4bc95457011259127b8c509c48c221c6ff19a8f4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 28 Aug 2024 16:30:12 -0600
Subject: [PATCH 1006/1248] Increase wall limit for test

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index de9cd0b1be..d1c3171c98 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -152,7 +152,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:40:00</option>
       <option name="comment">CESM3 development Exact restart test for all startup types at the standard coupled resolution</option>
     </options>
   </test>

From 41c3e092b53a749f2002d7b50b0e0965ca19a19e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 28 Aug 2024 17:08:08 -0600
Subject: [PATCH 1007/1248] Remove tests that now pass from expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 23 +---------------------
 1 file changed, 1 insertion(+), 22 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index d1e0a1a8b8..6f4d9ac2dc 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -8,7 +8,7 @@
 
          <test name="...">
            <phase name="...">
-             <status>...</status>
+             <status>...</stSMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydroatus>
            </phase>
          </test>
 
@@ -52,13 +52,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld10.f10_f10_mg37.I2000Clm50BgcCrop.izumi_intel.clm-tracer_consistency">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2444</issue>
-    </phase>
-  </test>
-
   <test name="PEM_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningMode">
     <phase name="COMPARE_base_modpes">
       <status>FAIL</status>
@@ -113,20 +106,6 @@
     </phase>
   </test>
 
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2373</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2373</issue>
-    </phase>
-  </test>
-
   <test name="FUNITCTSM_P1x1.f10_f10_mg37.I2000Clm50Sp.izumi_intel">
     <phase name="RUN">
       <status>FAIL</status>

From 729b688b262bd305d83a1e6ebee8bd29a2d76646 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 28 Aug 2024 18:52:21 -0600
Subject: [PATCH 1008/1248] Another test no longer failing, and fix accidental
 addition

---
 cime_config/testdefs/ExpectedTestFails.xml | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 6f4d9ac2dc..e18b15a26e 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -8,7 +8,7 @@
 
          <test name="...">
            <phase name="...">
-             <status>...</stSMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydroatus>
+             <status>...</status>
            </phase>
          </test>
 
@@ -165,17 +165,6 @@
     </phase>
   </test>
       
-  <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2373</issue>
-    </phase>
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>FATES#701</issue>
-    </phase>
-  </test>
-
   <test name="ERP_P256x2_Ld30.f45_f45_mg37.I2000Clm60FatesRs.derecho_intel.clm-mimicsFatesCold">
     <phase name="RUN">
       <status>FAIL</status>

From 4a62d0dc1edda9ee96fada2b4280f05f8d4c2b9b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 28 Aug 2024 21:14:20 -0600
Subject: [PATCH 1009/1248] Update date for change files

---
 doc/ChangeLog | 2 +-
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index cf160fce82..3499c7d720 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.027
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
-Date: Tue 27 Aug 2024 10:09:39 PM MDT
+Date: Wed 28 Aug 2024 09:13:22 PM MDT
 One-line Summary: Merge b4b-dev
 
 Purpose and description of changes
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 468cbe0077..fdf253760f 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.027     erik 08/27/2024 Merge b4b-dev
+       ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6
        ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods
        ctsm5.2.024 samrabin 08/22/2024 Improve li2024 fire methods

From 9afb92152bb65d005022db52c0d586c6737f795c Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 29 Aug 2024 09:41:24 -0700
Subject: [PATCH 1010/1248] update fates tag to latest

This brings fates up to the latest tag (fire weather refactor)
---
 .gitmodules | 2 +-
 src/fates   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index d16396da55..7274b9acd2 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.77.2_api.36.0.0
+fxtag = sci.1.78.2_api.36.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
diff --git a/src/fates b/src/fates
index e372f0b6cd..e06e0dfcaf 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit e372f0b6cdf46f76f888ee6ac92d9a3572464e8b
+Subproject commit e06e0dfcaf6347993d47dc29944e952d3e4412f7

From 44a7e34fe24eb1ca658fc1632b56f53801308901 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 29 Aug 2024 11:28:49 -0600
Subject: [PATCH 1011/1248] Update new ctsm60_params file and ./rimport

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 1cc58a30b6..b4bfbfdc26 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -551,7 +551,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >/glade/work/samrabin/ctsm_fire-li2024-pr2_paramfiles/ctsm60_params.c240822.li2024crujra.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240822.nc</paramfile>
 <paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240814.nc</paramfile>
 <paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240814.nc</paramfile>
 <paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240814.nc</paramfile>

From 61fa7179b61bd2afd2d728d5cdd6ccdc354eab83 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 29 Aug 2024 12:51:43 -0600
Subject: [PATCH 1012/1248] Update default fire_emis_factors_file.

---
 bld/namelist_files/namelist_defaults_fire_emis.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_fire_emis.xml b/bld/namelist_files/namelist_defaults_fire_emis.xml
index b7536ba66b..37fc85d721 100644
--- a/bld/namelist_files/namelist_defaults_fire_emis.xml
+++ b/bld/namelist_files/namelist_defaults_fire_emis.xml
@@ -17,6 +17,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <fire_emis_specifier>'bc_a1 = BC','pom_a1 = 1.4*OC','SO2 = SO2'</fire_emis_specifier>
 
-<fire_emis_factors_file>lnd/clm2/firedata/fire_emis_factors_c140116.nc</fire_emis_factors_file>
+<fire_emis_factors_file>lnd/clm2/firedata/fire_emission_factors_78PFTs_c20240624.nc</fire_emis_factors_file>
 
 </namelist_defaults>

From 6be8c556c995352217b54a641c013ca6d6f8ee09 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 29 Aug 2024 14:47:53 -0600
Subject: [PATCH 1013/1248] Add global attribute write of dataset compatability
 as a floating point number to surface datasets

---
 tools/mksurfdata_esmf/src/mkfileMod.F90 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/mksurfdata_esmf/src/mkfileMod.F90 b/tools/mksurfdata_esmf/src/mkfileMod.F90
index e22394e1e1..a3423e0c7b 100644
--- a/tools/mksurfdata_esmf/src/mkfileMod.F90
+++ b/tools/mksurfdata_esmf/src/mkfileMod.F90
@@ -105,6 +105,7 @@ subroutine mkfile_define_atts(pioid, dynlanduse)
     character(len= 10)   :: time               ! temporary
     character(len=  5)   :: zone               ! temporary
     integer              :: rcode
+    real(r4), parameter  :: data_version = 5.3   !  Compatibility version number of the datasets to create
     character(len=*), parameter :: subname = 'mkfile_define_atts'
     !-----------------------------------------------------------------------
 
@@ -126,6 +127,7 @@ subroutine mkfile_define_atts(pioid, dynlanduse)
     str = 'Community Land Model: CLM5'
     rcode = pio_put_att (pioid, pio_global, 'Source', trim(str))
     rcode = pio_put_att (pioid, pio_global, 'Version', trim(gitdescribe))
+    rcode = pio_put_att (pioid, pio_global, 'Dataset_Version', data_version)
     rcode = pio_put_att (pioid, pio_global, 'Logname', trim(logname))
     rcode = pio_put_att (pioid, pio_global, 'Host', trim(hostname))
     rcode = pio_put_att (pioid, pio_global, 'Number-of-tasks', npes)

From 92510bbcbf4e142fdf746a218390cc6372209262 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 29 Aug 2024 16:29:10 -0600
Subject: [PATCH 1014/1248] Update new raw dataset paths to /inputdata

---
 .../gen_mksurfdata_namelist.xml               | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index 683ea14058..e6cbdcf426 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -10,7 +10,7 @@
 
   <mksrf_flai>
     <entry>
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_pftlai_CLIM.c240709.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_pftlai_CLIM.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
     <entry pft_years="2005" hires_pft='on'>
@@ -25,7 +25,7 @@
 
   <mksrf_fsoicol>
     <entry>
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_soilcolor_CLIM.c240709.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_soilcolor_CLIM.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
     <entry pft_years="2005" hires_pft='on'>
@@ -221,28 +221,28 @@ version of the raw dataset will probably go away.
     </entry>
 
     <entry pft_years="1700">
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_1700.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_1700.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_1850.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
     </entry>
 
     <entry pft_years="1850">
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_1850.c240709.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_1850.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_1850.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_1850_cdf5_c20220910.nc</urban_filename>
     </entry>
 
     <entry pft_years="2000">
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_2000.c240709.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_2000.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_2000.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_2000_cdf5_c20220910.nc</urban_filename>
     </entry>
 
     <entry pft_years="2005">
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2023Deg025_240709/mksrf_landuse_ctsm53_histTRENDY2023_2005.c240709.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_2005.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_2005.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_2005_cdf5_c20220910.nc</urban_filename>
@@ -268,7 +268,7 @@ version of the raw dataset will probably go away.
     <!-- Lake data from 2018 to 2023 is copied from 2017 -->
     <!-- Urban data from 2016 to 2023 is copied from 2015 -->
     <entry pft_years="1700-2023" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_%y.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histTRENDY2024Deg025_240728/mksrf_landuse_ctsm53_histTRENDY2024_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_%y_cdf5_c20220910.nc</urban_filename>
@@ -283,7 +283,7 @@ version of the raw dataset will probably go away.
 
     <!-- SSP1-RCP 2.6 -->
     <entry  ssp_rcp="SSP1-2.6" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP126Deg025_240728/mksrf_landuse_ctsm53_TRSSP126_%y.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53TRSSP126Deg025_240728/mksrf_landuse_ctsm53_TRSSP126_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
@@ -296,21 +296,21 @@ version of the raw dataset will probably go away.
     </entry>
     <!-- SSP1-RCP 1.9 -->
     <entry  ssp_rcp="SSP1-1.9" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP119Deg025_240728/mksrf_landuse_ctsm53_TRSSP119_%y.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53TRSSP119Deg025_240728/mksrf_landuse_ctsm53_TRSSP119_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp1/urban_properties_GaoOneil_05deg_ThreeClass_ssp1_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP2-RCP 4.5 -->
     <entry  ssp_rcp="SSP2-4.5" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP245Deg025_240728/mksrf_landuse_ctsm53_TRSSP245_%y.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53TRSSP245Deg025_240728/mksrf_landuse_ctsm53_TRSSP245_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp2/urban_properties_GaoOneil_05deg_ThreeClass_ssp2_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP3-RCP 7.0 -->
     <entry  ssp_rcp="SSP3-7.0" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP370Deg025_240728/mksrf_landuse_ctsm53_TRSSP370_%y.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53TRSSP370Deg025_240728/mksrf_landuse_ctsm53_TRSSP370_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp3/urban_properties_GaoOneil_05deg_ThreeClass_ssp3_%y_cdf5_c20220910.nc</urban_filename>
@@ -324,14 +324,14 @@ version of the raw dataset will probably go away.
     </entry>
     <!-- SSP4-RCP 6.0 -->
     <entry  ssp_rcp="SSP4-6.0" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP460Deg025_240728/mksrf_landuse_ctsm53_TRSSP460_%y.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53TRSSP460Deg025_240728/mksrf_landuse_ctsm53_TRSSP460_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp4/urban_properties_GaoOneil_05deg_ThreeClass_ssp4_%y_cdf5_c20220910.nc</urban_filename>
     </entry>
     <!-- SSP5-RCP 8.5 -->
     <entry  ssp_rcp="SSP5-8.5" pft_years_ssp="2024-2100" >
-      <data_filename>/glade/campaign/cesm/development/lmwg/landuse_source_data/CTSM53RawData/globalctsm53TRSSP585Deg025_240728/mksrf_landuse_ctsm53_TRSSP585_%y.c240728.nc</data_filename>
+      <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53TRSSP585Deg025_240728/mksrf_landuse_ctsm53_TRSSP585_%y.c240728.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_%y.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/ssp5/urban_properties_GaoOneil_05deg_ThreeClass_ssp5_%y_cdf5_c20220910.nc</urban_filename>

From cc86114e31743b33b748cffd82cb1f260bf58f9b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 29 Aug 2024 17:12:29 -0600
Subject: [PATCH 1015/1248] Update user_nl_clm to ctsm60_params_cn30.c240822.nc
 in ...CN30 testmod

---
 .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
index 4bfc0520f8..d51360c82b 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240814.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240822.nc'

From e908083e6e67a2cb777383baaa5c55b388369b7b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 30 Aug 2024 14:19:30 -0600
Subject: [PATCH 1016/1248] Remove --vic option from mksurfdata_esmf and from
 testlist_clm

---
 cime_config/testdefs/testlist_clm.xml         | 41 -------------------
 .../gen_mksurfdata_jobscript_multi.py         |  4 +-
 .../ctsm/toolchain/gen_mksurfdata_namelist.py | 24 +----------
 3 files changed, 3 insertions(+), 66 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index d1c3171c98..1a4f331aa0 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -914,22 +914,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f09_g17" compset="I2000Clm50Vic" testmods="clm/vrtlay">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/vrtlay">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50SpCru" testmods="clm/drydepnomegan">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -1263,22 +1247,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_Ld5" grid="f09_g17" compset="I2000Clm50Vic" testmods="clm/vrtlay">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
-  <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/decStart">
-    <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
@@ -2416,15 +2384,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f19_g17" compset="I2000Clm50Vic" testmods="clm/default">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a production gnu test of VIC for clm5_0</option>
-    </options>
-  </test>
   <test name="SMS_D_Ld1_Mmpi-serial" grid="f45_f45_mg37" compset="I2000Clm50SpRs" testmods="clm/ptsROA">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
diff --git a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
index 6c38efdd0d..0d5ca9c376 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
@@ -243,11 +243,11 @@ def main():
             "5x5_amazon",
         ),
         "crop-global-present": (
-            "--start-year 2000 --end-year 2000 --vic                           --res",
+            "--start-year 2000 --end-year 2000                                 --res",
             "standard_res",
         ),
         "crop-global-present-low-res": (
-            "--start-year 2000 --end-year 2000 --vic                           --res",
+            "--start-year 2000 --end-year 2000                                 --res",
             "low_res",
         ),
         "crop-global-present-ne16": (
diff --git a/python/ctsm/toolchain/gen_mksurfdata_namelist.py b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
index 662e58bc8b..fa16f8ae6a 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_namelist.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
@@ -166,16 +166,6 @@ def get_parser():
         dest="input_path",
         default="/glade/campaign/cesm/cesmdata/inputdata/",
     )
-    parser.add_argument(
-        "--vic",
-        help="""
-            Flag for adding the fields required for the VIC model.
-            [default: %(default)s]
-            """,
-        action="store_true",
-        dest="vic_flag",
-        default=False,
-    )
     parser.add_argument(
         "--inlandwet",
         help="""
@@ -273,7 +263,6 @@ def main():
     input_path = args.input_path
     nocrop_flag = args.crop_flag
     nosurfdata_flag = args.surfdata_flag
-    vic_flag = args.vic_flag
     inlandwet = args.inlandwet
     glc_flag = args.glc_flag
     potveg = args.potveg_flag
@@ -400,7 +389,6 @@ def main():
             force_model_mesh_file,
             force_model_mesh_nx,
             force_model_mesh_ny,
-            vic_flag,
             rawdata_files,
             landuse_fname,
             mksrf_ftopostats_override,
@@ -413,7 +401,6 @@ def main():
         # -------------------
         write_nml_outdata(
             nosurfdata_flag,
-            vic_flag,
             inlandwet,
             glc_flag,
             hostname,
@@ -573,7 +560,6 @@ def determine_pft_years(start_year, end_year, potveg):
 
 def write_nml_outdata(
     nosurfdata_flag,
-    vic_flag,
     inlandwet,
     glc_flag,
     hostname,
@@ -604,7 +590,6 @@ def write_nml_outdata(
     nlfile.write(f"  numpft = {num_pft} \n")
     nlfile.write(f"  no_inlandwet = .{str(not inlandwet).lower()}. \n")
     nlfile.write(f"  outnc_3dglc = .{str(glc_flag).lower()}. \n")
-    nlfile.write(f"  outnc_vic = .{str(vic_flag).lower()}. \n")
     nlfile.write("  outnc_large_files = .false. \n")
     nlfile.write("  outnc_double = .true. \n")
     nlfile.write(f"  logname = '{logname}' \n")
@@ -617,7 +602,6 @@ def write_nml_rawinput(
     force_model_mesh_file,
     force_model_mesh_nx,
     force_model_mesh_ny,
-    vic_flag,
     rawdata_files,
     landuse_fname,
     mksrf_ftopostats_override,
@@ -643,7 +627,7 @@ def write_nml_rawinput(
     for key, value in rawdata_files.items():
         if key == "mksrf_ftopostats" and mksrf_ftopostats_override != "":
             nlfile.write(f"  mksrf_ftopostats_override = '{mksrf_ftopostats_override}' \n")
-        elif "_fvic" not in key and "mksrf_fvegtyp" not in key and "mksrf_fgrid" not in key:
+        elif "mksrf_fvegtyp" not in key and "mksrf_fgrid" not in key:
             # write everything else
             nlfile.write(f"  {key} = '{value}' \n")
 
@@ -692,12 +676,6 @@ def write_nml_rawinput(
     nlfile.write(f"  mksrf_fpctlak = '{mksrf_fpctlak}' \n")
     nlfile.write(f"  mksrf_furban = '{mksrf_furban}' \n")
 
-    if vic_flag:
-        mksrf_fvic = rawdata_files["mksrf_fvic"]
-        nlfile.write(f"  mksrf_fvic = '{mksrf_fvic}' \n")
-        mksrf_fvic_mesh = rawdata_files["mksrf_fvic_mesh"]
-        nlfile.write(f"  mksrf_fvic_mesh = '{mksrf_fvic_mesh}' \n")
-
     nlfile.write(f"  mksrf_fdynuse = '{landuse_fname} ' \n")
     return must_run_download_input_data
 

From 1d87ee5d1b427a24f2a423d596031d96f7bc81b3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 30 Aug 2024 14:28:51 -0600
Subject: [PATCH 1017/1248] Rm the --hires_pft option while the corresponding
 raw data need updating

---
 .../test/test_sys_gen_mksurfdata_namelist.py  |  1 -
 .../gen_mksurfdata_jobscript_multi.py         |  1 -
 .../ctsm/toolchain/gen_mksurfdata_namelist.py | 30 ++-----------------
 .../gen_mksurfdata_namelist.xml               | 15 ----------
 4 files changed, 2 insertions(+), 45 deletions(-)

diff --git a/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py b/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py
index 29745e9d80..db8581ef24 100755
--- a/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py
+++ b/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py
@@ -99,7 +99,6 @@ def test_hires_namelist(self):
                 "mpasa15",
                 "--glc-nec",
                 "10",
-                "--hires_pft",
                 "--hires_soitex",
             ]
         )
diff --git a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
index 0d5ca9c376..1afb9e86cb 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
@@ -267,7 +267,6 @@ def main():
             "mpasa480",
         ),
         "crop-global-present-nldas": (
-            # TODO slevis: --hirespft uses old data for now, so keep out
             "--start-year 2000 --end-year 2000                                 --res",
             "nldas_res",
         ),
diff --git a/python/ctsm/toolchain/gen_mksurfdata_namelist.py b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
index fa16f8ae6a..20bd7f7f44 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_namelist.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
@@ -186,19 +186,6 @@ def get_parser():
         dest="glc_flag",
         default=False,
     )
-    parser.add_argument(
-        "--hires_pft",
-        help="""
-            If you want to use the high-resolution pft dataset rather
-            than the default lower resolution dataset.
-            (Low resolution is at quarter-degree, high resolution at 3-minute)
-            [Note: hires only available for 1850 and 2005.]
-            [default: %(default)s]
-            """,
-        action="store_true",
-        dest="hres_pft",
-        default=False,
-    )
     parser.add_argument(
         "--hires_soitex",
         help="""
@@ -268,7 +255,7 @@ def main():
     potveg = args.potveg_flag
     glc_nec = args.glc_nec
 
-    hires_pft, hires_soitex = process_hires_options(args, start_year, end_year)
+    hires_soitex = process_hires_options(args, start_year, end_year)
 
     if force_model_mesh_file is not None:
         open_mesh_file(force_model_mesh_file, force_model_mesh_nx, force_model_mesh_ny)
@@ -299,7 +286,6 @@ def main():
 
     # create attribute list for parsing xml file
     attribute_list = {
-        "hires_pft": hires_pft,
         "hires_soitex": hires_soitex,
         "pft_years": pft_years,
         "pft_years_ssp": pft_years_ssp,
@@ -427,23 +413,11 @@ def process_hires_options(args, start_year, end_year):
     """
     Process options related to hi-res
     """
-    if args.hres_pft:
-        if (start_year == 1850 and end_year == 1850) or (start_year == 2005 and end_year == 2005):
-            hires_pft = "on"
-        else:
-            error_msg = (
-                "ERROR: for --hires_pft you must set both start-year "
-                "and end-year to 1850 or to 2005"
-            )
-            sys.exit(error_msg)
-    else:
-        hires_pft = "off"
-
     if args.hres_soitex:
         hires_soitex = "on"
     else:
         hires_soitex = "off"
-    return hires_pft, hires_soitex
+    return hires_soitex
 
 
 def check_ssp_years(start_year, end_year):
diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index e6cbdcf426..1e050a295f 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -13,10 +13,6 @@
       <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_pftlai_CLIM.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
-    <entry pft_years="2005" hires_pft='on'>
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_lai_histclm52deg005_earthstatmirca_2005.cdf5.c220228.nc</data_filename>
-      <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_3x3min_nomask_cdf5_c200129.nc</mesh_filename>
-    </entry>
   </mksrf_flai>
 
   <!-- ======================== -->
@@ -28,10 +24,6 @@
       <data_filename>/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/rawdata/CTSM53RawData/globalctsm53histMKSRFDeg025_240709/mksrf_landuse_ctsm53_soilcolor_CLIM.c240709.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
     </entry>
-    <entry pft_years="2005" hires_pft='on'>
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_soilcolor_histclm52deg005_earthstatmirca_2005.cdf5.c220228.nc</data_filename>
-      <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_3x3min_nomask_cdf5_c200129.nc</mesh_filename>
-    </entry>
   </mksrf_fsoicol>
 
   <mksrf_fsoitex>
@@ -248,13 +240,6 @@ version of the raw dataset will probably go away.
       <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_2005_cdf5_c20220910.nc</urban_filename>
     </entry>
 
-    <entry pft_years="2005" hires_pft='on'>
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_landuse_clm52deg005_histLUH2_2005.cdf5.c190119.nc</data_filename>
-      <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_3x3min_nomask_cdf5_c200129.nc</mesh_filename>
-      <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_2005.cdf5.c20220325.nc</lake_filename>
-      <urban_filename>lnd/clm2/rawdata/gao_oneill_urban/historical/urban_properties_GaoOneil_05deg_ThreeClass_2005_cdf5_c20220910.nc</urban_filename>
-    </entry>
-
     <!-- Last millenium Historical period from 0850 to 1849 -->
     <entry pft_years="0850-1849" >
       <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr0850-1850.c20230226/mksrf_landuse_ctsm52_histLUH2_%y.c20230226.nc</data_filename>

From b6a98620203fe59b5cf78b659ee3acd79080ac96 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 30 Aug 2024 14:41:40 -0600
Subject: [PATCH 1018/1248] Updates and cleanup for make all to work

---
 python/ctsm/subset_data.py     | 8 --------
 tools/mksurfdata_esmf/Makefile | 4 ++--
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py
index bc9ce97962..d38aee1308 100644
--- a/python/ctsm/subset_data.py
+++ b/python/ctsm/subset_data.py
@@ -597,10 +597,6 @@ def setup_files(args, defaults, cesmroot):
             clmforcingindir,
             os.path.join(defaults.get("surfdat", "dir")),
         ),
-        "mesh_dir": os.path.join(
-            clmforcingindir,
-            os.path.join(defaults.get("surfdat", "mesh_dir")),
-        ),
         "fluse_dir": os.path.join(
             clmforcingindir,
             os.path.join(defaults.get("landuse", "dir")),
@@ -608,7 +604,6 @@ def setup_files(args, defaults, cesmroot):
         "fsurf_in": fsurf_in,
         "fsurf_out": fsurf_out,
         "fluse_in": fluse_in,
-        "mesh_surf": defaults.get("surfdat", "mesh_surf"),
         "datm_tuple": DatmFiles(
             dir_input_datm,
             dir_output_datm,
@@ -736,9 +731,6 @@ def subset_region(args, file_dict: dict):
             specify_fsurf_out=file_dict["fsurf_out"],
         )
 
-    # if region.create_mesh:
-    #    region.create_mesh_at_reg (file_dict["mesh_dir"], file_dict["mesh_surf"])
-
     # --  Create CTSM transient landuse data file
     if region.create_landuse:
         region.create_landuse_at_reg(
diff --git a/tools/mksurfdata_esmf/Makefile b/tools/mksurfdata_esmf/Makefile
index c344843d06..73da3f240e 100644
--- a/tools/mksurfdata_esmf/Makefile
+++ b/tools/mksurfdata_esmf/Makefile
@@ -164,7 +164,7 @@ crop-tropics-present : FORCE
 	$(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL)
 
 1x1_brazil-transient : FORCE
-	$(SUBSETDATA_POINT_ALLLU) --create-surface --create-landuse $(SUBSETDATA_1X1_BRAZIL) --cfg-file ../site_and_regional/default_data_1850.cfg
+	$(SUBSETDATA_POINT_ALLLU) --create-surface --create-landuse --surf-year 1850 $(SUBSETDATA_1X1_BRAZIL) --cfg-file ../site_and_regional/default_data_1850.cfg
 
 #
 # crop
@@ -255,7 +255,7 @@ crop-global-hist-ne30 : FORCE
 # Note (slevis): The next line makes the landuse.timeseries from 1850 to 2015, so also run
 # modify_smallville.sh to generate three modified landuse.timeseries files needed for testing.
 1x1-smallville-transient : FORCE
-	$(SUBSETDATA_POINT) --create-landuse $(SUBSETDATA_1X1_SMALLTRANSIENT)
+	$(SUBSETDATA_POINT) --create-surface --create-landuse --surf-year 1850 $(SUBSETDATA_1X1_SMALLTRANSIENT)
 	../modify_input_files/modify_smallville.sh
 
 1x1-cidadinho-present : FORCE

From df36ab3bcc17d2f54168aa48ee4eaabaa1ace194 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 30 Aug 2024 15:08:22 -0600
Subject: [PATCH 1019/1248] Small corrections for all python tests to pass

---
 python/ctsm/test/test_sys_gen_mksurfdata_namelist.py | 3 +--
 python/ctsm/toolchain/gen_mksurfdata_namelist.py     | 4 ++--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py b/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py
index db8581ef24..c9741daf5c 100755
--- a/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py
+++ b/python/ctsm/test/test_sys_gen_mksurfdata_namelist.py
@@ -62,7 +62,7 @@ def test_simple_namelist(self):
         main()
         self.assertTrue(os.path.exists(self.outfile), "Output surface dataset file should exist")
 
-    def test_vic_nocrop_inlandwet_glc_namelist(self):
+    def test_nocrop_inlandwet_glc_namelist(self):
         """
         Test a namelist with several options on
         """
@@ -75,7 +75,6 @@ def test_vic_nocrop_inlandwet_glc_namelist(self):
                 "1850",
                 "--res",
                 "1.9x2.5",
-                "--vic",
                 "--nocrop",
                 "--inlandwet",
                 "--glc",
diff --git a/python/ctsm/toolchain/gen_mksurfdata_namelist.py b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
index 20bd7f7f44..da9420871b 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_namelist.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_namelist.py
@@ -255,7 +255,7 @@ def main():
     potveg = args.potveg_flag
     glc_nec = args.glc_nec
 
-    hires_soitex = process_hires_options(args, start_year, end_year)
+    hires_soitex = process_hires_options(args)
 
     if force_model_mesh_file is not None:
         open_mesh_file(force_model_mesh_file, force_model_mesh_nx, force_model_mesh_ny)
@@ -409,7 +409,7 @@ def main():
     print(f"Successfully created input namelist file {nlfname}")
 
 
-def process_hires_options(args, start_year, end_year):
+def process_hires_options(args):
     """
     Process options related to hi-res
     """

From 615dff4a0d27304ba917af40df77b8e286f45408 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 30 Aug 2024 17:41:11 -0600
Subject: [PATCH 1020/1248] Updates to the datasets generated by make all

---
 .../gen_mksurfdata_jobscript_multi.py          | 18 +++++++++++++-----
 tools/mksurfdata_esmf/Makefile                 |  5 +++++
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
index 1afb9e86cb..5de67adb12 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
@@ -42,6 +42,7 @@
     "crop-global-hist-low-res",
     "crop-global-hist-ne16",
     "crop-global-hist-ne30",
+    "crop-global-hist-f09",
     "crop-global-SSP1-1.9-f09",
     "crop-global-SSP1-2.6-f09",
     "crop-global-SSP2-4.5-f09",
@@ -198,6 +199,7 @@ def main():
         "low_res_no_crop": ["4x5", "10x15"],
         "ultra_hi_res_no_crop": ["mpasa15", "mpasa3p75"],
         "standard_res": ["360x720cru", "0.9x1.25", "1.9x2.5", "C96", "mpasa120"],
+        "standard_res_no_f09": ["360x720cru", "1.9x2.5", "C96", "mpasa120"],
         "low_res": ["4x5", "10x15", "ne3np4.pg3"],
         "mpasa480": ["mpasa480"],
         "nldas_res": ["0.125nldas2"],
@@ -209,11 +211,13 @@ def main():
             "ne0np4.ARCTICGRIS.ne30x8",
             "ne0np4.ARCTIC.ne30x4",
             "ne0np4CONUS.ne30x8",
+            "ne0np4.POLARCAP.ne30x4",
         ],
         "ne120": [
             "ne0np4.ARCTICGRIS.ne30x8",
             "ne0np4.ARCTIC.ne30x4",
             "ne0np4CONUS.ne30x8",
+            "ne0np4.POLARCAP.ne30x4",
             "ne120np4.pg3",
         ],
     }
@@ -295,21 +299,25 @@ def main():
             "mpasa480",
         ),
         "crop-global-hist": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
-            "standard_res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
+            "standard_res_no_f09",
         ),
         "crop-global-hist-low-res": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
             "low_res",
         ),
         "crop-global-hist-ne16": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
             "ne16",
         ),
         "crop-global-hist-ne30": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
             "ne30",
         ),
+        "crop-global-hist-f09": (
+            "--start-year 1700 --end-year 2023                                 --res",
+            "f09",
+        ),
         "crop-global-SSP1-1.9-f09": (
             "--start-year 1850 --end-year 2100 --nosurfdata --ssp-rcp SSP1-1.9 --res",
             "f09",
diff --git a/tools/mksurfdata_esmf/Makefile b/tools/mksurfdata_esmf/Makefile
index 73da3f240e..a46ca6850a 100644
--- a/tools/mksurfdata_esmf/Makefile
+++ b/tools/mksurfdata_esmf/Makefile
@@ -92,6 +92,7 @@ CROP = \
 	crop-global-present-ne120 \
 	crop-global-present-mpasa480 \
 	crop-global-present-nldas \
+	crop-global-hist-f09 \
 	crop-global-1850 \
 	crop-global-1850-low-res \
 	crop-global-1850-ne16 \
@@ -227,6 +228,10 @@ crop-global-hist : FORCE
 	$(MKSURFDATA)  --number-of-nodes 72 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
 	$(BATCHJOBS) $@.sh
 
+crop-global-hist-f09 : FORCE
+	$(MKSURFDATA)  --number-of-nodes 9 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
+	$(BATCHJOBS) $@.sh
+
 crop-global-hist-low-res : FORCE
 	$(MKSURFDATA)  --number-of-nodes 14 --tasks-per-node 32 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
 	$(BATCHJOBS) $@.sh

From 7118d709485113294c4c6f90ca64853d7d3b3862 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 31 Aug 2024 14:48:16 -0600
Subject: [PATCH 1021/1248] Add a check for compatibility based on the version
 in the surface dataset

---
 src/main/clm_initializeMod.F90 |  3 +-
 src/main/surfrdMod.F90         | 67 +++++++++++++++++++++++++++++++++-
 2 files changed, 68 insertions(+), 2 deletions(-)

diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index 340a799908..c91090f6cb 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -58,7 +58,7 @@ subroutine initialize1(dtime)
     use clm_varcon           , only: clm_varcon_init
     use landunit_varcon      , only: landunit_varcon_init
     use clm_varctl           , only: fsurdat, version
-    use surfrdMod            , only: surfrd_get_num_patches, surfrd_get_nlevurb
+    use surfrdMod            , only: surfrd_get_num_patches, surfrd_get_nlevurb, surfrd_check_file
     use controlMod           , only: control_init, control_print, NLFilename
     use ncdio_pio            , only: ncd_pio_init
     use initGridCellsMod     , only: initGridCells
@@ -100,6 +100,7 @@ subroutine initialize1(dtime)
 
     call control_init(dtime)
     call ncd_pio_init()
+    call surfrd_check_file(fsurdat)
     call surfrd_get_num_patches(fsurdat, actual_maxsoil_patches, actual_numpft, actual_numcft)
     call surfrd_get_nlevurb(fsurdat, actual_nlevurb)
 
diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index 12212e2160..36399c3905 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -7,7 +7,7 @@ module surfrdMod
   !
   ! !USES:
 #include "shr_assert.h"
-  use shr_kind_mod    , only : r8 => shr_kind_r8
+  use shr_kind_mod    , only : r8 => shr_kind_r8, r4 => shr_kind_r4
   use shr_log_mod     , only : errMsg => shr_log_errMsg
   use abortutils      , only : endrun
   use clm_varpar      , only : nlevsoifl
@@ -27,6 +27,7 @@ module surfrdMod
   save
   !
   ! !PUBLIC MEMBER FUNCTIONS:
+  public :: surfrd_check_file       ! Check that this surface dataset is compatible
   public :: surfrd_get_data         ! Read surface dataset and determine subgrid weights
   public :: surfrd_get_num_patches  ! Read surface dataset to determine maxsoil_patches and numcft
   public :: surfrd_get_nlevurb      ! Read surface dataset to determine nlevurb
@@ -45,6 +46,70 @@ module surfrdMod
 
 contains
 
+  !-----------------------------------------------------------------------
+  subroutine surfrd_check_file ( lfsurdat )
+    !
+    ! !DESCRIPTION:
+    ! Check compatability for this surface dataset and abort with an error if it's not
+    !
+    ! !USES:
+    use ncdio_pio, only : check_att
+    ! !ARGUMENTS:
+    character(len=*), intent(in) :: lfsurdat    ! surface dataset filename
+    ! !LOCAL VARIABLES:
+    type(file_desc_t) :: ncid  ! netcdf id
+    logical :: exists          ! If attribute or variable was found on the file
+    integer :: status          ! Status return code
+    real(r4) :: version        ! Version number on the dataset
+    ! NOTE: Only increment the expected_version when surface datasets are incompatible with the previous version
+    !       If datasets are just updated data and backwards compatble leave the expected version alone
+    real(r4), parameter :: expected_version = 5.3_r4
+    character(len=50) :: description
+    character(len=*), parameter :: version_name = 'Dataset_Version'
+
+    call ncd_pio_openfile (ncid, trim(lfsurdat), 0)
+    call check_att(ncid, pio_global, version_name, exists)
+    if (exists) then
+       status = pio_get_att(ncid, pio_global, version_name, version)
+    else
+       ! For a few previous versions guess on the compatability version based on existence of variables
+       call check_var( ncid, 'PCT_OCEAN', exists)
+       if (exists) then
+         version = 5.2_r4
+       else
+         call check_var( ncid, 'PCT_CFT', exists)
+         if (exists) then
+            version = 5.0_r4
+         else
+            call check_var( ncid, 'PCT_GLC_MEC_GIC', exists)
+            if (exists) then
+               version = 4.5_r4
+            else
+               ! This is a version before the main clm4_5 dataseta so marking it as 0 for unknown
+               version = 0.0_r4
+            end if
+         end if
+       end if
+    end if
+    call ncd_pio_closefile(ncid)
+    if ( (version /= expected_version) )then
+      if ( version < expected_version )then
+         description = 'older'
+         if ( version == 0.0_r4 ) description = trim(description)//' than 4.5'
+      else if ( version > expected_version )then
+         description = 'newer'
+      end if
+      if ( masterproc )then
+         write(iulog,*) 'Input surface dataset is: ', trim(lfsurdat)
+         write(iulog,'(3a)') 'This surface dataset is ', trim(description), ' and incompatable with this version of CTSM'
+         write(iulog,'(a,f3.1,a,f3.1)') 'Dataset version = ', version, ' Version expected = ', expected_version
+         write(iulog,*) errMsg(sourcefile, __LINE__)
+      end if
+      call endrun(msg="ERROR: Incompatble surface dataset")
+    end if
+
+  end subroutine surfrd_check_file
+
   !-----------------------------------------------------------------------
   subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
     !

From 744830efada6699b9ee4975e30b6a73bedd3d283 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 3 Sep 2024 10:50:14 -0600
Subject: [PATCH 1022/1248] Update from ctsm52 to ctsm53 NOANTHRO raw dataset

---
 tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
index 1e050a295f..d617fe1c49 100644
--- a/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
+++ b/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml
@@ -206,7 +206,7 @@ version of the raw dataset will probably go away.
   <mksrf_fvegtyp>
     <!-- Potential Vegetation dataset TODO Peter Lawrence? -->
     <entry pft_years="PtVg" >
-      <data_filename>lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.noanthro.c20230226/mksrf_landuse_ctsm52_noanthroLUH2_1.c20230226.nc</data_filename>
+      <data_filename>lnd/clm2/rawdata/CTSM53RawData/globalctsm53histTRNOANTHRODeg025_240831/mksrf_landuse_ctsm53_histTRNOANTHRO_1.c240831.nc</data_filename>
       <mesh_filename>lnd/clm2/mappingdata/grids/UNSTRUCTgrid_0.25x0.25_nomask_cdf5_c200129.nc</mesh_filename>
       <lake_filename>lnd/clm2/rawdata/lake_area/mksurf_lake_0.05x0.05_hist_clm5_hydrolakes_1850.cdf5.c20220325.nc</lake_filename>
       <urban_filename>lnd/clm2/rawdata/mksrf_urban_0.05x0.05_zerourbanpct.cdf5.c181014.nc</urban_filename>

From 852462c507f1bab5457a80685bfb1f933edc4f4c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 3 Sep 2024 11:52:26 -0600
Subject: [PATCH 1023/1248] Remove obsolete comment from namelist_defaults_ctsm

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 60abb3501e..238f14c893 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1902,10 +1902,6 @@ lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_4x5_hist_2000_16pfts_c240216.nc</fsurd
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa60_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="mpasa15"   sim_year="2000" use_crop=".false.">
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa15_hist_2000_16pfts_c240216.nc</fsurdat>
-<!--
-<fsurdat hgrid="mpasa15-3" sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa15-3_hist_2000_16pfts_c240216.nc</fsurdat>
--->
 <fsurdat hgrid="mpasa3p75" sim_year="2000" use_crop=".false.">
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa3p75_hist_2000_16pfts_c240216.nc</fsurdat>
 

From 4161a020d3d2945ea2d9e6cd1c83b98cca4d20a7 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Wed, 4 Sep 2024 10:54:29 -0600
Subject: [PATCH 1024/1248] update fuel classes

---
 src/fates                           | 2 +-
 src/main/histFileMod.F90            | 2 +-
 src/utils/clmfates_interfaceMod.F90 | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/fates b/src/fates
index e372f0b6cd..2263e6f829 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit e372f0b6cdf46f76f888ee6ac92d9a3572464e8b
+Subproject commit 2263e6f8292792a9a05575023eec1f8265ef7bf2
diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
index 8ae4ace7e3..2461a60c92 100644
--- a/src/main/histFileMod.F90
+++ b/src/main/histFileMod.F90
@@ -28,7 +28,7 @@ module histFileMod
   use FatesInterfaceTypesMod , only : nlevheight
   use FatesInterfaceTypesMod , only : nlevdamage
   use FatesConstantsMod      , only : n_landuse_cats
-  use FatesLitterMod         , only : nfsc
+  use FatesFuelClassesMod    , only : nfsc
   use FatesLitterMod         , only : ncwd
   use PRTGenericMod          , only : num_elements_fates  => num_elements
   use FatesInterfaceTypesMod , only : numpft_fates => numpft
diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index e3e7644b90..c01787217d 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -3648,7 +3648,7 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates)
    use FatesInterfaceTypesMod, only : nlevsclass, nlevage, nlevcoage
    use FatesInterfaceTypesMod, only : nlevheight
    use FatesInterfaceTypesMod, only : nlevdamage
-   use FatesLitterMod,         only : nfsc
+   use FatesFuelClassesMod,    only : nfsc
    use FatesLitterMod,         only : ncwd
    use EDParamsMod,            only : nlevleaf, nclmax
    use FatesInterfaceTypesMod, only : numpft_fates => numpft

From fff23bd2b6c96394cf9a25505c48a2c1d1fee808 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Wed, 4 Sep 2024 11:50:10 -0600
Subject: [PATCH 1025/1248] change parmeter file

---
 cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm | 1 +
 src/fates                                                | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
index 91df3e2e61..a8ffe59412 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -28,3 +28,4 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
 'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
 'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU'
+fates_paramfile = '/glade/work/afoster/CTSM/src/fates/parameter_files/fates_param_fuel.nc'
diff --git a/src/fates b/src/fates
index 2263e6f829..3cfb2b1bd9 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit 2263e6f8292792a9a05575023eec1f8265ef7bf2
+Subproject commit 3cfb2b1bd9bcde627e4b3364cfdf2144feaa7ded

From 90a5cf009906bf12b37472c42b89857b2b28c93e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 4 Sep 2024 16:01:45 -0600
Subject: [PATCH 1026/1248] Remove error about surface datasets

Remove the error messaging that talks about
old/incompatible surface dataset because we
now are checking for the surface dataset compatability.
---
 src/main/glcBehaviorMod.F90 | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/src/main/glcBehaviorMod.F90 b/src/main/glcBehaviorMod.F90
index 315aa88c67..8076f8fcaf 100644
--- a/src/main/glcBehaviorMod.F90
+++ b/src/main/glcBehaviorMod.F90
@@ -407,8 +407,7 @@ subroutine translate_glacier_region_behavior
                glacier_region_behavior(i) = BEHAVIOR_SINGLE_AT_ATM_TOPO
             case (behavior_str_unset)
                write(iulog,*) ' ERROR: glacier_region_behavior not specified for ID ', i
-               write(iulog,*) 'You may need to extend the glacier_region_behavior namelist array,'
-               write(iulog,*) 'or you may be running with an old/incompatible surface dataset.'
+               write(iulog,*) 'You may need to extend the glacier_region_behavior namelist array.'
                call endrun(msg=' ERROR: glacier_region_behavior not specified for ID '// &
                     errMsg(sourcefile, __LINE__))
             case default
@@ -439,8 +438,7 @@ subroutine translate_glacier_region_melt_behavior
                glacier_region_melt_behavior(i) = MELT_BEHAVIOR_REMAINS_IN_PLACE
             case (behavior_str_unset)
                write(iulog,*) ' ERROR: glacier_region_melt_behavior not specified for ID ', i
-               write(iulog,*) 'You may need to extend the glacier_region_melt_behavior namelist array,'
-               write(iulog,*) 'or you may be running with an old/incompatible surface dataset.'
+               write(iulog,*) 'You may need to extend the glacier_region_melt_behavior namelist array.'
                call endrun(msg=' ERROR: glacier_region_melt_behavior not specified for ID '// &
                     errMsg(sourcefile, __LINE__))
             case default
@@ -471,8 +469,7 @@ subroutine translate_glacier_region_ice_runoff_behavior
                glacier_region_ice_runoff_behavior(i) = ICE_RUNOFF_BEHAVIOR_MELTED
             case (behavior_str_unset)
                write(iulog,*) ' ERROR: glacier_region_ice_runoff_behavior not specified for ID ', i
-               write(iulog,*) 'You may need to extend the glacier_region_ice_runoff_behavior namelist array,'
-               write(iulog,*) 'or you may be running with an old/incompatible surface dataset.'
+               write(iulog,*) 'You may need to extend the glacier_region_ice_runoff_behavior namelist array.'
                call endrun(msg=' ERROR: glacier_region_ice_runoff_behavior not specified for ID '// &
                     errMsg(sourcefile, __LINE__))
             case default

From 703c2913ec974bf6f536329eb92a4ec175ea2f2b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 4 Sep 2024 16:19:24 -0600
Subject: [PATCH 1027/1248] Add comments about dataset verison

Add some notes that dataset version is only
updated when the new datasets will NOT be
backwards compatible with the previous
version.
---
 tools/mksurfdata_esmf/src/mkfileMod.F90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tools/mksurfdata_esmf/src/mkfileMod.F90 b/tools/mksurfdata_esmf/src/mkfileMod.F90
index a3423e0c7b..997020292b 100644
--- a/tools/mksurfdata_esmf/src/mkfileMod.F90
+++ b/tools/mksurfdata_esmf/src/mkfileMod.F90
@@ -105,6 +105,10 @@ subroutine mkfile_define_atts(pioid, dynlanduse)
     character(len= 10)   :: time               ! temporary
     character(len=  5)   :: zone               ! temporary
     integer              :: rcode
+    ! Surface dataset version these datasets are compatible with:
+    ! - Only update this when the new surface datasets will be incompatible with the previous verison
+    ! - Since whenever we update surface datasets we update to a new minor version this always corresponds
+    !   to a CTSM minor version: 5.3, i6.1, 6.5 etcetera
     real(r4), parameter  :: data_version = 5.3   !  Compatibility version number of the datasets to create
     character(len=*), parameter :: subname = 'mkfile_define_atts'
     !-----------------------------------------------------------------------

From a0a2dfa450566a005d820679b7dab157530bce76 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 4 Sep 2024 16:43:36 -0600
Subject: [PATCH 1028/1248] Makefile updates in preparation for running make
 all for ctsm5.3

---
 tools/mksurfdata_esmf/Makefile | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tools/mksurfdata_esmf/Makefile b/tools/mksurfdata_esmf/Makefile
index a46ca6850a..0359b7dc72 100644
--- a/tools/mksurfdata_esmf/Makefile
+++ b/tools/mksurfdata_esmf/Makefile
@@ -85,27 +85,27 @@ STANDARD = \
 	global-present-low-res \
 
 CROP = \
+	crop-global-future \
+	crop-global-hist-f09 \
+	crop-global-1850-ne120 \
+	crop-global-present-ne120 \
+	crop-global-present-nldas \
+	crop-global-present-ne30 \
 	crop-global-present \
 	crop-global-present-low-res \
 	crop-global-present-ne16 \
-	crop-global-present-ne30 \
-	crop-global-present-ne120 \
 	crop-global-present-mpasa480 \
-	crop-global-present-nldas \
-	crop-global-hist-f09 \
 	crop-global-1850 \
 	crop-global-1850-low-res \
 	crop-global-1850-ne16 \
 	crop-global-1850-ne30 \
-	crop-global-1850-ne120 \
 	crop-global-1850-mpasa480 \
-	crop-global-future \
 
 # Start all with all-subset because user is bound to forget to first run
 # module load nco
 # Usually, include global-present-ultra-hi-res temporarily while
 # generating datasets for a new release
-all : all-subset standard crop crop-tropics-present
+all : all-subset global-present-ultra-hi-res crop standard crop-tropics-present
 
 # These are all the surface datasets generated by subset_data
 # This runs interactively and does not send jobs to the batch queue

From 46b891ac4ac481fe38ed1d539d61c8d9057b8735 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 4 Sep 2024 18:00:32 -0600
Subject: [PATCH 1029/1248] Update to new finidats from latest ctsm5.3 spin-up

Same list of finidats that I updated in this PR:
https://github.com/ESCOMP/CTSM/pull/2724/files
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 238f14c893..b4df3e008f 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1382,13 +1382,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!--
@@ -1430,7 +1430,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 
@@ -1515,7 +1515,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- clm6_0 and cam7.0 -->
@@ -1524,7 +1524,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- clm5_0 and cam7.0 -->
@@ -1589,7 +1589,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1653,7 +1653,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1728,7 +1728,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
@@ -1736,7 +1736,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1801,7 +1801,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1866,7 +1866,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->

From d59dd24f03791366d3b8f1a87c8cf47c0cbc6ce9 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 4 Sep 2024 19:05:52 -0600
Subject: [PATCH 1030/1248] Add placeholder for making fsurdat files for tower
 sites

---
 tools/mksurfdata_esmf/Makefile | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/tools/mksurfdata_esmf/Makefile b/tools/mksurfdata_esmf/Makefile
index 0359b7dc72..7ad8e1aa77 100644
--- a/tools/mksurfdata_esmf/Makefile
+++ b/tools/mksurfdata_esmf/Makefile
@@ -105,6 +105,9 @@ CROP = \
 # module load nco
 # Usually, include global-present-ultra-hi-res temporarily while
 # generating datasets for a new release
+# Eventually, include tower, when we get the corresponding scripts to
+# use absolute paths for their input files; error message posted here:
+# https://github.com/ESCOMP/CTSM/pull/2500 under "PLUMBER2"
 all : all-subset global-present-ultra-hi-res crop standard crop-tropics-present
 
 # These are all the surface datasets generated by subset_data
@@ -119,6 +122,10 @@ all-subset : \
 	1x1-cidadinho-present \
 	urban
 
+# These are all the tower site surface datasets
+tower : neon plumber2
+
+
 DEBUG:
 	@echo "HOST             := $(HOST)"
 	@echo "PROJECT          := $(PROJECT)"
@@ -364,6 +371,15 @@ crop-global-SSP5-8.5-f09 : FORCE
 	$(MKSURFDATA)  --number-of-nodes 9 --scenario $@ --jobscript-file $@.sh --walltime 12:00:00
 	$(BATCHJOBS) $@.sh
 
+#
+# tower sites: NEON, PLUMBER2
+#
+neon : FORCE
+	../site_and_regional/neon_surf_wrapper
+
+plumber2 : FORCE
+	../site_and_regional/plumber2_surf_wrapper
+
 #
 # urban
 #

From 04d45c77ed8c50a490ee022f058592ef79a94515 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 4 Sep 2024 22:47:39 -0700
Subject: [PATCH 1031/1248] add changelog

---
 doc/ChangeLog | 78 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 79 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 3499c7d720..79526be61c 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,82 @@
 ===============================================================
+Tag name: ctsm5.2.028
+Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Wed Sep  4 23:21:30 MDT 2024
+One-line Summary: FATES history flushing update
+
+Purpose and description of changes
+----------------------------------
+
+This updates the way in which FATES history output is flushed during model initialization
+utilizing a new FATES-side subroutine, flush_all_hvars.  This update also makes corrections
+to a subset of FATES testmods as well as expands the FATES test list by duplicating two
+existing tests to run on different compilers for better coverage.  The FATES submodule tag
+has been updated to the latest scientific tag as well.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+Fixes #2657 Add FATES_TRANSITIONS_MATRIX_LULU to FatesColdLUH2 testmods
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+
+Adds nvhpc and gnu FatesSatColdPhen smoke tests to the fates list to expand compiler
+coverage.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, for FATES tests only
+
+Changes are consistent with differences in FATES_EFFECT_WSPEED due to NGEET/fates#1215
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+
+   FATES: sci.1.77.2_api.36.0.0 -> sci.1.78.2_api.36.0.0
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2594
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.027
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Wed 28 Aug 2024 09:13:22 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index fdf253760f..f8adaa60eb 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.028 glemieux 09/04/2024 FATES history flushing update
        ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6
        ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods

From 9a6cd4417d24ddaf775e0aa5f13481cbe15b4322 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 4 Sep 2024 22:49:32 -0700
Subject: [PATCH 1032/1248] correct changelog and sum author

---
 doc/ChangeLog | 3 ++-
 doc/ChangeSum | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 79526be61c..0e6db9823e 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,6 +1,7 @@
 ===============================================================
 Tag name: ctsm5.2.028
-Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Originator(s): rgknox (Ryan Knox, LBNL, rgknox@lbl.gov)
+               glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
 Date: Wed Sep  4 23:21:30 MDT 2024
 One-line Summary: FATES history flushing update
 
diff --git a/doc/ChangeSum b/doc/ChangeSum
index f8adaa60eb..82c7a2a6ef 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.028 glemieux 09/04/2024 FATES history flushing update
+       ctsm5.2.028   rgknox 09/04/2024 FATES history flushing update
        ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6
        ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods

From 0fd3d41e58f6ec992aa78dac42bef707fea14be5 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 5 Sep 2024 01:40:10 -0600
Subject: [PATCH 1033/1248] Change name of the subroutine for the surface
 dataset compatibility check, fix version guessing inside it, fix spelling
 error, respond to rest of the review conversations

---
 src/main/clm_initializeMod.F90 |  4 ++--
 src/main/surfrdMod.F90         | 14 +++++++-------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index c91090f6cb..bf9a97ae58 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -58,7 +58,7 @@ subroutine initialize1(dtime)
     use clm_varcon           , only: clm_varcon_init
     use landunit_varcon      , only: landunit_varcon_init
     use clm_varctl           , only: fsurdat, version
-    use surfrdMod            , only: surfrd_get_num_patches, surfrd_get_nlevurb, surfrd_check_file
+    use surfrdMod            , only: surfrd_get_num_patches, surfrd_get_nlevurb, surfrd_compat_check
     use controlMod           , only: control_init, control_print, NLFilename
     use ncdio_pio            , only: ncd_pio_init
     use initGridCellsMod     , only: initGridCells
@@ -100,7 +100,7 @@ subroutine initialize1(dtime)
 
     call control_init(dtime)
     call ncd_pio_init()
-    call surfrd_check_file(fsurdat)
+    call surfrd_compat_check(fsurdat)
     call surfrd_get_num_patches(fsurdat, actual_maxsoil_patches, actual_numpft, actual_numcft)
     call surfrd_get_nlevurb(fsurdat, actual_nlevurb)
 
diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index 36399c3905..88d43a09cc 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -27,7 +27,7 @@ module surfrdMod
   save
   !
   ! !PUBLIC MEMBER FUNCTIONS:
-  public :: surfrd_check_file       ! Check that this surface dataset is compatible
+  public :: surfrd_compat_check     ! Check that this surface dataset is compatible
   public :: surfrd_get_data         ! Read surface dataset and determine subgrid weights
   public :: surfrd_get_num_patches  ! Read surface dataset to determine maxsoil_patches and numcft
   public :: surfrd_get_nlevurb      ! Read surface dataset to determine nlevurb
@@ -47,7 +47,7 @@ module surfrdMod
 contains
 
   !-----------------------------------------------------------------------
-  subroutine surfrd_check_file ( lfsurdat )
+  subroutine surfrd_compat_check ( lfsurdat )
     !
     ! !DESCRIPTION:
     ! Check compatability for this surface dataset and abort with an error if it's not
@@ -77,11 +77,11 @@ subroutine surfrd_check_file ( lfsurdat )
        if (exists) then
          version = 5.2_r4
        else
-         call check_var( ncid, 'PCT_CFT', exists)
+         call check_var( ncid, 'CONST_HARVEST_SH1', exists)
          if (exists) then
             version = 5.0_r4
          else
-            call check_var( ncid, 'PCT_GLC_MEC_GIC', exists)
+            call check_var( ncid, 'GLACIER_REGION', exists)
             if (exists) then
                version = 4.5_r4
             else
@@ -101,14 +101,14 @@ subroutine surfrd_check_file ( lfsurdat )
       end if
       if ( masterproc )then
          write(iulog,*) 'Input surface dataset is: ', trim(lfsurdat)
-         write(iulog,'(3a)') 'This surface dataset is ', trim(description), ' and incompatable with this version of CTSM'
+         write(iulog,'(3a)') 'This surface dataset is ', trim(description), ' and incompatible with this version of CTSM'
          write(iulog,'(a,f3.1,a,f3.1)') 'Dataset version = ', version, ' Version expected = ', expected_version
          write(iulog,*) errMsg(sourcefile, __LINE__)
       end if
-      call endrun(msg="ERROR: Incompatble surface dataset")
+      call endrun(msg="ERROR: Incompatible surface dataset")
     end if
 
-  end subroutine surfrd_check_file
+  end subroutine surfrd_compat_check
 
   !-----------------------------------------------------------------------
   subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)

From 249f850f8108ddc5aa05e0069fb60ff4a7db3561 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 5 Sep 2024 14:50:07 -0600
Subject: [PATCH 1034/1248] Update date in change files

---
 doc/ChangeLog | 2 +-
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 0e6db9823e..e553a59730 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -2,7 +2,7 @@
 Tag name: ctsm5.2.028
 Originator(s): rgknox (Ryan Knox, LBNL, rgknox@lbl.gov)
                glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
-Date: Wed Sep  4 23:21:30 MDT 2024
+Date: Thu 05 Sep 2024 02:47:14 PM MDT
 One-line Summary: FATES history flushing update
 
 Purpose and description of changes
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 82c7a2a6ef..45bab07440 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.2.028   rgknox 09/04/2024 FATES history flushing update
+       ctsm5.2.028   rgknox 09/05/2024 FATES history flushing update
        ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6
        ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods

From 10241e7691eee234ac02cc676fb58205155e3779 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Fri, 6 Sep 2024 11:27:38 -0600
Subject: [PATCH 1035/1248] fix issues

---
 cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm | 3 ++-
 src/fates                                                | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
index a8ffe59412..055a0d1530 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -28,4 +28,5 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
 'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
 'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU'
-fates_paramfile = '/glade/work/afoster/CTSM/src/fates/parameter_files/fates_param_fuel.nc'
+
+! fates_paramfile = '/glade/work/afoster/CTSM/src/fates/parameter_files/fates_param_fuel.nc'
diff --git a/src/fates b/src/fates
index 3cfb2b1bd9..e06e0dfcaf 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit 3cfb2b1bd9bcde627e4b3364cfdf2144feaa7ded
+Subproject commit e06e0dfcaf6347993d47dc29944e952d3e4412f7

From 6baba6f96fbb178ef5827d98bd28347fd782ad5a Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 6 Sep 2024 12:05:21 -0600
Subject: [PATCH 1036/1248] Start getting the template for the ctsm5.3.0
 ChangeLog

---
 doc/ChangeLog | 138 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |   1 +
 2 files changed, 139 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e553a59730..fd46741fec 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,142 @@
 ===============================================================
+Tag name: ctsm5.3.0
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Fri 06 Sep 2024 02:21:22 AM MDT
+One-line Summary: Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
+
+Purpose and description of changes
+----------------------------------
+
+Changes to CTSM:
+================
+
+
+New surface datasets:
+=====================
+
+
+New input datasets to mksurfdata_esmf:
+======================================
+
+
+Contributors
+------------
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[X] clm6_0
+
+[X] clm5_1
+
+[X] clm5_0
+
+[X] ctsm5_0-nwp
+
+[X] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+
+Changes made to namelist defaults (e.g., changed parameter values):
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+
+Changes to documentation:
+
+Things being deprecated (which will be removed):
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing:
+
+
+Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_esmf python)
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho -
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho -
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho -----
+    izumi -------
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho -----
+    izumi -------
+
+  any other testing (give details below):
+
+  mksurfdata_esmf
+     derecho ---- run "make all" to create all datasets (completes in XXX hours)
+     (crop-global-SSP2-4.5-ne30 was longest at 6 hr, most completed in XXX hours)
+
+  ctsm_sci
+     derecho ----
+
+  mosart
+     derecho ----
+     izumi ------
+
+  rtm
+     derecho ----
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes! New surface datasets so answers change for ALL simulations!
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: ALL
+    - what platforms/compilers: ALL
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+      new climate
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+       - casename:
+
+   URL for LMWG diagnostics output used to validate new climate:
+
+
+Other details
+-------------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.028
 Originator(s): rgknox (Ryan Knox, LBNL, rgknox@lbl.gov)
                glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 45bab07440..c592a29382 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+         ctsm5.3.0     erik 09/06/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
        ctsm5.2.028   rgknox 09/05/2024 FATES history flushing update
        ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6

From d6b2d8fa0678abd9c89fe4dec76441d245fd9424 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 6 Sep 2024 13:04:10 -0600
Subject: [PATCH 1037/1248] Update datasets to ctsm5.3.0 directory and change
 _c240216 to _c240905

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 178 +++++++++---------
 1 file changed, 89 insertions(+), 89 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index b4df3e008f..5ca3030259 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1891,150 +1891,150 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- fsurdat files with 16 PFTS for use with FATES -->
 <fsurdat hgrid="0.9x1.25"  sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_0.9x1.25_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"   sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1.9x2.5_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="10x15"     sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_10x15_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="4x5"       sim_year="2000" use_crop=".false." >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_4x5_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="mpasa60"   sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa60_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa60_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="mpasa15"   sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa15_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa15_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="mpasa3p75" sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa3p75_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa3p75_hist_2000_16pfts_c240216.nc</fsurdat>
 
 <!-- fsurdat files with 78 PFTS -->
 <!-- The same files can be used with use_vichydro='.true.' or '.false' -->
 <fsurdat hgrid="0.9x1.25"     sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="0.9x1.25"     sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"      sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1.9x2.5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"      sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1.9x2.5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="10x15"        sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_10x15_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="10x15"        sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_10x15_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="4x5"          sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="4x5"          sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="1x1_brazil"    sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_brazil_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_2000_78pfts_c240221.nc</fsurdat>
 <fsurdat hgrid="5x5_amazon"    sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_5x5_amazon_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_5x5_amazon_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <!-- Crop versions of the surface datasets that can be used for both crop on and off -->
 <fsurdat hgrid="ne30np4"     sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne30np4_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg2" sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne30np4.pg2_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg3" sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne30np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne16np4.pg3" sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne16np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="0.125nldas2" sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_0.125nldas2_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.125nldas2_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="64x128"      sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_T42_hist_2000_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_T42_hist_2000_78pfts_c240425.nc</fsurdat>
 <fsurdat hgrid="360x720cru"  sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_360x720cru_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="C96"          sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_C96_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="1x1_numaIA"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240221.nc
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240221.nc
 </fsurdat>
 
 <fsurdat hgrid="mpasa480"  sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa480_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="mpasa120"  sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa120_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="ne3np4.pg3"              sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne3np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne120np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne120np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4CONUS.ne30x8_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <!-- 100% Urban single-point datasets (only for sim-year=2000) -->
 <fsurdat hgrid="1x1_vancouverCAN"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240221.nc</fsurdat>
 <fsurdat hgrid="1x1_mexicocityMEX"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240221.nc</fsurdat>
 <fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240221.nc</fsurdat>
 
 <!-- for pre-industrial simulations - year 1850 -->
 
 <fsurdat hgrid="360x720cru"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_360x720cru_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="0.9x1.25"     sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_0.9x1.25_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"      sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1.9x2.5_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="10x15"        sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_10x15_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="4x5"          sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_4x5_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_1850_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="mpasa480"     sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa480_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="mpasa120"     sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa120_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_1850_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="ne30np4"      sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne30np4_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg2"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne30np4.pg2_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg3"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne3np4.pg3"   sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="C96"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_C96_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240221.nc</fsurdat>
 <fsurdat hgrid="1x1_cidadinhoBR" sim_year="2000" >
 lnd/clm2/surfdata_esmf/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240613.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_brazil_hist_1850_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240221.nc</fsurdat>
 
 <fsurdat hgrid="ne3np4.pg3"               sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne16np4.pg3"              sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne120np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne120np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1979_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1979_78pfts_c240425.nc</fsurdat>
 <fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
 
 <!-- Potential vegetation land use dataset, crop is off, and zeroed, all areas are natural vegetation without human disturbance -->
 <fsurdat hgrid="0.9x1.25" sim_year="PtVg" use_crop=".false."
->lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_0.9x1.25_PtVeg_nourb_1850_16pfts_c240216.nc</fsurdat>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_PtVeg_nourb_1850_16pfts_c240216.nc</fsurdat>
 
 <!-- for NEON sites present day simulations - year 2000 -->
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".true.">
-lnd/clm2/surfdata_esmf/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240206.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false.">
-lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240206.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240905.nc</fsurdat>
 <!-- If there are cases where only a few datasets change - they can be listed here for the particular NEONSITE -->
 <!-- for example to override the above for the TOOL site do something like this...
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false." neonsite="TOOL">
@@ -2051,40 +2051,40 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- Historical 1850-2000 -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <!-- Do we need both use_crop=".false." and ".true." for FATES transient? -->
 <!-- As of 2024/02/02 the Grids Support spreadsheet includes no 16-pft landuse files. -->
 <flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2000"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000" 
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2000" 
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240221.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240221.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4.pg3"   sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 
 <!-- Note that these transient files only go up to year 1855.
      This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
 <flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_c240221.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_c240221.nc</flanduse_timeseries>
 
 <!-- Cidadinho test site has no transient data. -->
 <flanduse_timeseries hgrid="1x1_cidadinhoBR" sim_year_range="1850-2000"></flanduse_timeseries>
@@ -2093,57 +2093,57 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- SSP1-RCP2.6 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP1-2.6"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP1-2.6_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP1-2.6_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <!-- SSP2-RCP4.5 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <!-- Do we need both use_crop=".false." and ".true." for FATES transient? -->
 <!-- As of 2024/02/02 the Grids Support spreadsheet includes no 16-pft landuse files. -->
 <flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240221.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240221.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4.pg3"   sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
 
 <!-- SSP3-RCP7.0 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP3-7.0"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP3-7.0_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP3-7.0_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <!-- SSP4-RCP6.0 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP4-6.0"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP4-6.0_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP4-6.0_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <!-- SSP5-RCP8.5 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP5-8.5"
->lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP5-8.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP5-8.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <!-- SSP1-RCP1.9 - relative to {csmdata}) -->
 <!--- currently empty until needed, we can't test because of lack of ndep files for this SSP -->

From fa3fb4d2ee126cca8c13df09637259a738b5b45c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 6 Sep 2024 13:07:59 -0600
Subject: [PATCH 1038/1248] Update _c240221 to _c240905

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 5ca3030259..e6a6741893 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1925,7 +1925,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurd
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="1x1_brazil"    sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_2000_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="5x5_amazon"    sim_year="2000">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_5x5_amazon_hist_2000_78pfts_c240216.nc</fsurdat>
 
@@ -1950,7 +1950,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_2000_78pfts_c240216.nc
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="1x1_numaIA"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240221.nc
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240905.nc
 </fsurdat>
 
 <fsurdat hgrid="mpasa480"  sim_year="2000">
@@ -1971,11 +1971,11 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_2000_78pfts_c2
 
 <!-- 100% Urban single-point datasets (only for sim-year=2000) -->
 <fsurdat hgrid="1x1_vancouverCAN"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="1x1_mexicocityMEX"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240905.nc</fsurdat>
 
 <!-- for pre-industrial simulations - year 1850 -->
 
@@ -2007,11 +2007,11 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc
 <fsurdat hgrid="C96"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="1x1_cidadinhoBR" sim_year="2000" >
 lnd/clm2/surfdata_esmf/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240613.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240221.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240905.nc</fsurdat>
 
 <fsurdat hgrid="ne3np4.pg3"               sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
@@ -2065,7 +2065,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240221.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240905.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
@@ -2084,7 +2084,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- Note that these transient files only go up to year 1855.
      This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
 <flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_c240221.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_c240905.nc</flanduse_timeseries>
 
 <!-- Cidadinho test site has no transient data. -->
 <flanduse_timeseries hgrid="1x1_cidadinhoBR" sim_year_range="1850-2000"></flanduse_timeseries>
@@ -2111,7 +2111,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240221.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240905.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>

From ffdd332ba446364a5f3ffe04a7cdc470601d553b Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Fri, 6 Sep 2024 11:12:59 -0600
Subject: [PATCH 1039/1248] Fix uninitialized mask values

---
 tools/mksurfdata_esmf/src/mksoiltexMod.F90 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/mksurfdata_esmf/src/mksoiltexMod.F90 b/tools/mksurfdata_esmf/src/mksoiltexMod.F90
index fb8396f344..398bbaf51d 100644
--- a/tools/mksurfdata_esmf/src/mksoiltexMod.F90
+++ b/tools/mksurfdata_esmf/src/mksoiltexMod.F90
@@ -165,6 +165,8 @@ subroutine mksoiltex(file_mesh_i, file_mapunit_i, file_lookup_i, mesh_o, pioid_o
     do ni = 1,ns_i
        if (mapunit_i(ni) == 0.) then
           mask_i(ni) = 0
+       else
+          mask_i(ni) = 1
        end if
     end do
     call ESMF_MeshSet(mesh_i, elementMask=mask_i, rc=rc)

From 10319de7db53b0560f85166ef240d051dc440b6a Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Fri, 6 Sep 2024 13:15:45 -0600
Subject: [PATCH 1040/1248] Get mapunit_value_max across all processors

Resolves ESCOMP/CTSM#2744
---
 tools/mksurfdata_esmf/src/mksoiltexMod.F90 | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tools/mksurfdata_esmf/src/mksoiltexMod.F90 b/tools/mksurfdata_esmf/src/mksoiltexMod.F90
index 398bbaf51d..4d24372729 100644
--- a/tools/mksurfdata_esmf/src/mksoiltexMod.F90
+++ b/tools/mksurfdata_esmf/src/mksoiltexMod.F90
@@ -13,13 +13,15 @@ module mksoiltexMod
   use mkutilsMod       , only : chkerr
   use mkdiagnosticsMod , only : output_diagnostics_index
   use mkfileMod        , only : mkfile_output  
-  use mkvarctl         , only : root_task, ndiag, spval
+  use mkvarctl         , only : root_task, ndiag, spval, mpicom
   use mkvarctl         , only : unsetsoil
   use mkvarpar         , only : nlevsoi
 
   implicit none
   private ! By default make data private
 
+#include <mpif.h>
+
   public :: mksoiltex      ! Set soil texture
 
   integer                :: mapunit_value_max
@@ -61,6 +63,7 @@ subroutine mksoiltex(file_mesh_i, file_mapunit_i, file_lookup_i, mesh_o, pioid_o
     integer                :: k,l,m,n
     integer                :: nlay          ! number of soil layers
     integer                :: n_scid
+    integer                :: mapunit_value_max_local
     integer , allocatable  :: mask_i(:)
     real(r4), pointer      :: dataptr(:)
     integer                :: mapunit       ! temporary igbp soil mapunit
@@ -202,7 +205,8 @@ subroutine mksoiltex(file_mesh_i, file_mapunit_i, file_lookup_i, mesh_o, pioid_o
 
     ! Determine mapunit_value_max (set it as a module variable so that it can be
     ! accessible to gen_dominant_mapunit) - this is needed in the dynamic mask routine
-    mapunit_value_max = maxval(dataptr)
+    mapunit_value_max_local = maxval(dataptr)
+    call mpi_allreduce(mapunit_value_max_local, mapunit_value_max, 1, MPI_INTEGER, MPI_MAX, mpicom, rcode)
 
     ! Determine values in field_o
     call ESMF_FieldGet(field_o, farrayptr=dataptr, rc=rc)

From ec134068506d99b7d34053e29b830c787520d6eb Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 6 Sep 2024 16:09:34 -0600
Subject: [PATCH 1041/1248] Change _c240425 and _c240613 to _c240905

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e6a6741893..06e3008491 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1943,7 +1943,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_2000_78pfts_c240216.n
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.125nldas2_hist_2000_78pfts_c240216.nc</fsurdat>
 
 <fsurdat hgrid="64x128"      sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_T42_hist_2000_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_T42_hist_2000_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="360x720cru"  sim_year="2000">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_2000_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="C96"          sim_year="2000">
@@ -2009,7 +2009,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240216.nc</fsurd
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="1x1_cidadinhoBR" sim_year="2000" >
-lnd/clm2/surfdata_esmf/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240613.nc</fsurdat>
+lnd/clm2/surfdata_esmf/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240905.nc</fsurdat>
 
@@ -2020,11 +2020,11 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240216.n
 <fsurdat hgrid="ne120np4.pg3"             sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne120np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1979_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1979_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1979_78pfts_c240905.nc</fsurdat>
 <fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c240425.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c240905.nc</fsurdat>
 
 <!-- Potential vegetation land use dataset, crop is off, and zeroed, all areas are natural vegetation without human disturbance -->
 <fsurdat hgrid="0.9x1.25" sim_year="PtVg" use_crop=".false."
@@ -2127,11 +2127,11 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240905.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240905.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240425.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240905.nc</flanduse_timeseries>
 
 <!-- SSP3-RCP7.0 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP3-7.0"

From 0c68f2e7307b677270c6d1078562ed691dcd3b78 Mon Sep 17 00:00:00 2001
From: Bill Sacks <sacks@ucar.edu>
Date: Sat, 7 Sep 2024 08:35:21 -0600
Subject: [PATCH 1042/1248] Add a comment

---
 tools/mksurfdata_esmf/src/mksoiltexMod.F90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tools/mksurfdata_esmf/src/mksoiltexMod.F90 b/tools/mksurfdata_esmf/src/mksoiltexMod.F90
index 4d24372729..c7655bbc26 100644
--- a/tools/mksurfdata_esmf/src/mksoiltexMod.F90
+++ b/tools/mksurfdata_esmf/src/mksoiltexMod.F90
@@ -205,6 +205,10 @@ subroutine mksoiltex(file_mesh_i, file_mapunit_i, file_lookup_i, mesh_o, pioid_o
 
     ! Determine mapunit_value_max (set it as a module variable so that it can be
     ! accessible to gen_dominant_mapunit) - this is needed in the dynamic mask routine
+    !
+    ! Note that dataptr (obtained from the input field) contains just a subset of the
+    ! source data, based on the source data decomposition. So we need an mpi_allreduce to
+    ! determine the global maximum value of mapunit.
     mapunit_value_max_local = maxval(dataptr)
     call mpi_allreduce(mapunit_value_max_local, mapunit_value_max, 1, MPI_INTEGER, MPI_MAX, mpicom, rcode)
 

From 724c7c36282480a7ae4d6768752331391499689d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 9 Sep 2024 14:02:30 -0600
Subject: [PATCH 1043/1248] Update fsurdat in Hillslope testmod.

---
 cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
index 4fc6fc2373..6cca61d21d 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
@@ -6,6 +6,6 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240216.synthetic_hillslopes.nc'
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes.nc'
 
 use_ssre = .false.

From df3b6a5df38b845025218f4c03a479317641c21c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 9 Sep 2024 14:39:00 -0600
Subject: [PATCH 1044/1248] Update fsurdat in Hillslope testmod w/
 Dataset_Version.

---
 cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
index 6cca61d21d..7b343f8ec8 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
@@ -6,6 +6,6 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes.nc'
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes2.nc'
 
 use_ssre = .false.

From 7dc1cd9a38e3aa2788c59ab2c2b4071bac50db4a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 9 Sep 2024 15:29:39 -0600
Subject: [PATCH 1045/1248] Update fsurdat in Hillslope testmod w/ real
 fsurdat.

---
 cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
index 7b343f8ec8..9a132d5d6a 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
@@ -6,6 +6,6 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes2.nc'
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes3.nc'
 
 use_ssre = .false.

From 61e98207e691e62084b5f2bc26c95b379cec8bb3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 10 Sep 2024 01:18:36 -0600
Subject: [PATCH 1046/1248] Update surface datasets to latest date, verify that
 the build-namelist unit testter works

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 180 +++++++++---------
 1 file changed, 90 insertions(+), 90 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 06e3008491..3efbe5795f 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1891,150 +1891,150 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- fsurdat files with 16 PFTS for use with FATES -->
 <fsurdat hgrid="0.9x1.25"  sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_16pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"   sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_16pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="10x15"     sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_16pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="4x5"       sim_year="2000" use_crop=".false." >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_16pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="mpasa60"   sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa60_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa60_hist_2000_16pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="mpasa15"   sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa15_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa15_hist_2000_16pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="mpasa3p75" sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa3p75_hist_2000_16pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa3p75_hist_2000_16pfts_c240908.nc</fsurdat>
 
 <!-- fsurdat files with 78 PFTS -->
 <!-- The same files can be used with use_vichydro='.true.' or '.false' -->
 <fsurdat hgrid="0.9x1.25"     sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="0.9x1.25"     sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"      sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"      sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="10x15"        sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="10x15"        sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="4x5"          sim_year="2000" use_crop=".true." use_vichydro=".true.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="4x5"          sim_year="2000" use_crop=".true." use_vichydro=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="1x1_brazil"    sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_2000_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="5x5_amazon"    sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_5x5_amazon_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_5x5_amazon_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <!-- Crop versions of the surface datasets that can be used for both crop on and off -->
 <fsurdat hgrid="ne30np4"     sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg2" sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg3" sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne16np4.pg3" sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="0.125nldas2" sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.125nldas2_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.125nldas2_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="64x128"      sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_T42_hist_2000_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_T42_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="360x720cru"  sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="C96"          sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="1x1_numaIA"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240905.nc
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240908.nc
 </fsurdat>
 
 <fsurdat hgrid="mpasa480"  sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="mpasa120"  sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="ne3np4.pg3"              sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne120np4.pg3_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne120np4.pg3_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_2000_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <!-- 100% Urban single-point datasets (only for sim-year=2000) -->
 <fsurdat hgrid="1x1_vancouverCAN"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1x1_mexicocityMEX"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <!-- for pre-industrial simulations - year 1850 -->
 
 <fsurdat hgrid="360x720cru"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="0.9x1.25"     sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"      sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="10x15"        sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_10x15_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="4x5"          sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_1850_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="mpasa480"     sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="mpasa120"     sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_1850_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="ne30np4"      sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg2"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg3"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne3np4.pg3"   sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="C96"  sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1x1_cidadinhoBR" sim_year="2000" >
-lnd/clm2/surfdata_esmf/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="ne3np4.pg3"               sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne16np4.pg3"              sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne120np4.pg3_hist_1850_78pfts_c240216.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne120np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1979_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_1979_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne0np4.ARCTIC.ne30x4"     sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1979_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4.ARCTIC.ne30x4_hist_1979_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne0np4CONUS.ne30x8"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c240908.nc</fsurdat>
 
 <!-- Potential vegetation land use dataset, crop is off, and zeroed, all areas are natural vegetation without human disturbance -->
 <fsurdat hgrid="0.9x1.25" sim_year="PtVg" use_crop=".false."
->lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_PtVeg_nourb_1850_16pfts_c240216.nc</fsurdat>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_PtVeg_nourb_1850_16pfts_c240908.nc</fsurdat>
 
 <!-- for NEON sites present day simulations - year 2000 -->
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".true.">
-lnd/clm2/surfdata_esmf/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false.">
-lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240905.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240908.nc</fsurdat>
 <!-- If there are cases where only a few datasets change - they can be listed here for the particular NEONSITE -->
 <!-- for example to override the above for the TOOL site do something like this...
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false." neonsite="TOOL">
@@ -2051,40 +2051,40 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- Historical 1850-2000 -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <!-- Do we need both use_crop=".false." and ".true." for FATES transient? -->
 <!-- As of 2024/02/02 the Grids Support spreadsheet includes no 16-pft landuse files. -->
 <flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2000"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000" 
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2000" 
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240905.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4.pg3"   sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 
 <!-- Note that these transient files only go up to year 1855.
      This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
 <flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_c240905.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_1850-1855_78pfts_c240908.nc</flanduse_timeseries>
 
 <!-- Cidadinho test site has no transient data. -->
 <flanduse_timeseries hgrid="1x1_cidadinhoBR" sim_year_range="1850-2000"></flanduse_timeseries>
@@ -2093,57 +2093,57 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 
 <!-- SSP1-RCP2.6 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP1-2.6"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP1-2.6_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP1-2.6_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <!-- SSP2-RCP4.5 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <!-- Do we need both use_crop=".false." and ".true." for FATES transient? -->
 <!-- As of 2024/02/02 the Grids Support spreadsheet includes no 16-pft landuse files. -->
 <flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240905.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4.pg3"   sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240905.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne0np4.ARCTIC.ne30x4" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240905.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP2-4.5_1979-2026_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne0np4CONUS.ne30x8" sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240905.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne0np4CONUS.ne30x8_SSP2-4.5_1979-2026_78pfts_c240908.nc</flanduse_timeseries>
 
 <!-- SSP3-RCP7.0 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP3-7.0"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP3-7.0_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP3-7.0_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <!-- SSP4-RCP6.0 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP4-6.0"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP4-6.0_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP4-6.0_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <!-- SSP5-RCP8.5 - relative to {csmdata}) -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2100" ssp_rcp="SSP5-8.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP5-8.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP5-8.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <!-- SSP1-RCP1.9 - relative to {csmdata}) -->
 <!--- currently empty until needed, we can't test because of lack of ndep files for this SSP -->

From c06e816fbee23fbed1b8f2e4229f159c55b59c0c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 10 Sep 2024 08:34:08 -0600
Subject: [PATCH 1047/1248] Update path to synthetic hillslope fsurdat.

---
 cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
index 9a132d5d6a..d27565d98f 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
@@ -6,6 +6,6 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes3.nc'
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes3.nc'
 
 use_ssre = .false.

From 65dc3ce44b65ed6e62c40ee276db968b9e6de74c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 11 Sep 2024 01:35:25 -0600
Subject: [PATCH 1048/1248] Update NEON datasets, remove double setting of NEON
 sites in namelist defaults and user-mods fixing #2752

---
 bld/CLMBuildNamelist.pm                             | 13 +++++++++++--
 bld/namelist_files/namelist_defaults_ctsm.xml       |  8 ++++----
 .../usermods_dirs/NEON/FATES/defaults/user_nl_clm   |  3 ---
 cime_config/usermods_dirs/NEON/defaults/user_nl_clm |  3 ---
 4 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index a5b19dd62b..c18b72ac15 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2506,8 +2506,9 @@ sub setup_logic_surface_dataset {
   # consistent with it
   # MUST BE AFTER: setup_logic_demand which is where flanduse_timeseries is set
   #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $xmlvar_ref) = @_;
+  my ($opts_in, $nl_flags, $definition, $defaults, $nl, $xmlvar_ref) = @_;
 
+  my $opts = $opts_in;
   $nl_flags->{'flanduse_timeseries'} = "null";
   my $flanduse_timeseries = $nl->get_value('flanduse_timeseries');
   if (defined($flanduse_timeseries)) {
@@ -2523,6 +2524,11 @@ sub setup_logic_surface_dataset {
   if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_cndv'}) ) {
      $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation (use_cndv=.true)." );
   }
+  # Turn test option off for NEON until after XML is interpreted
+  my $test_files = $opts->{'test'};
+  if ( &value_is_true($nl_flags->{'neon'})) {
+     $opts->{'test'} = 0;
+  }
   #
   # Always get the crop version of the datasets now and let the code turn it into the form desired
   # Provided this isn't with FATES on
@@ -2548,7 +2554,7 @@ sub setup_logic_surface_dataset {
                  'use_crop'=>$nl_flags->{'use_crop'} );
   }
   #
-  # Expand the XML variables for NEON cases so that NEONSITE will be used
+  # Expand the XML variables for NEON cases so that NEONSITE will be used and test for existence
   #
   if ( &value_is_true($nl_flags->{'neon'}) ) {
      my $fsurdat = $nl->get_value($var);
@@ -2557,6 +2563,9 @@ sub setup_logic_surface_dataset {
         my $group = $definition->get_group_name($var);
         $nl->set_variable_value($group, $var, $newval);
         $log->verbose_message( "This is a NEON site and the fsurdat file selected is: $newval" );
+        if ( $test_files and ($newval !~ /null|none/) and (! -f remove_leading_and_trailing_quotes($newval) ) ) {
+          $log->fatal_error("file not found: $var = $newval");
+        }
      }
   }
 }
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 3efbe5795f..0188f91faa 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2032,13 +2032,13 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c2
 
 <!-- for NEON sites present day simulations - year 2000 -->
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".true.">
-lnd/clm2/surfdata_esmf/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240910.nc</fsurdat>
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false.">
-lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240908.nc</fsurdat>
 <!-- If there are cases where only a few datasets change - they can be listed here for the particular NEONSITE -->
 <!-- for example to override the above for the TOOL site do something like this...
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false." neonsite="TOOL">
-lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c230699.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c230699.nc</fsurdat>
 -->
 
 <!-- Dynamic PFT surface datasets (relative to {csmdata}) -->
@@ -2046,7 +2046,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- When NEON landuse datasets are available uncomment the following for something like this...
      Also change the setting for clm_demand in the namelist_defaults_overall.xml file
 <flanduse_timeseries hgrid="CLM_USRDAT" neon=".true." sim_year_range="1850-2100">
->lnd/clm2/surfdata_esmf/NEON/landuse.timeseries_NEON_${NEONSITE}_hist_78pfts_simyr2018-2023_c230931.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/landuse.timeseries_NEON_${NEONSITE}_hist_78pfts_simyr2018-2023_c230931.nc</flanduse_timeseries>
 -->
 
 <!-- Historical 1850-2000 -->
diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm
index 1a9847a69b..e49d110d51 100644
--- a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm
+++ b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm
@@ -18,9 +18,6 @@
 ! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
 !----------------------------------------------------------------------------------
 
-flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240206.nc"
-
 ! h1 output stream 
 hist_fincl2 = 'FATES_AUTORESP','FCEV','FCTR','FGEV','FIRA','FSA','FSH','FATES_GPP','FATES_GPP_PF','H2OSOI',
              'SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FATES_NPP','FATES_NPP_PF','FATES_VEGC','FATES_VEGC_PF'
diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm
index b73da1f33e..f0e7142990 100644
--- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm
+++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm
@@ -18,9 +18,6 @@
 ! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
 !----------------------------------------------------------------------------------
 
-flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240206.nc"
-
 ! h1 output stream 
 hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI',
              'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr'

From 42ec043dfe01d86483b147298a58ed19594ec489 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 11 Sep 2024 03:10:49 -0600
Subject: [PATCH 1049/1248] Add tests for the PLUMBER2 sites

---
 bld/unit_testers/build-namelist_test.pl | 60 +++++++++++++++++++++++--
 1 file changed, 57 insertions(+), 3 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 8b2827b069..5ea47ad1fa 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -42,7 +42,7 @@ sub make_env_run {
     my %settings = @_;
 
     # Set default settings
-    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE",  LND_SETS_DUST_EMIS_DRV_FLDS=>"TRUE", NEONSITE=>"" );
+    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE",  LND_SETS_DUST_EMIS_DRV_FLDS=>"TRUE", NEONSITE=>"", PLUMBER2SITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
        $env_vars{$item} = $settings{$item};
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3349;
+my $ntests = 3859;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2007;
+   $ntests += 2347;
 }
 plan( tests=>$ntests );
 
@@ -411,6 +411,60 @@ sub cat_and_create_namelistinfile {
    system( "/bin/rm $namelistfile" );
    &cleanup();
 }
+print "\n===============================================================================\n";
+print "Test the PLUMBER2 sites\n";
+print "=================================================================================\n";
+my $phys = "clm6_0";
+$mode = "-phys $phys";
+&make_config_cache($phys);
+my $plumdir      = "../../cime_config/usermods_dirs/PLUMBER2";
+foreach my $site ( 
+    "AR-SLu",  "AU-Emr",  "AU-TTE",  "CA-NS1",  "CA-SF3",  "CN-HaM",  "DE-Obe",  "ES-ES1",  "FR-Gri",  "IE-Dri",  "IT-LMa",  "IT-SRo",  "RU-Fyo",  "US-Aud",  "US-Ho1",  "US-Ne2",  "US-Syv",  "ZM-Mon",
+    "AT-Neu",  "AU-Gin",  "AU-Tum",  "CA-NS2",  "CH-Cha",  "CN-Qia",  "DE-Seh",  "ES-ES2",  "FR-Hes",  "IT-Amp",  "IT-Mal",  "JP-SMF",  "RU-Zot",  "US-Bar",  "US-KS2",  "US-Ne3",  "US-Ton",
+    "AU-ASM",  "AU-GWW",  "AU-Whr",  "CA-NS4",  "CH-Dav",  "CZ-wet",  "DE-SfN",  "ES-LgS",  "FR-LBr",  "IT-BCi",  "IT-MBo",  "NL-Ca1",  "SD-Dem",  "US-Bkg",  "US-Los",  "US-NR1",  "US-Tw4",
+    "AU-Cow",  "AU-How",  "AU-Wrr",  "CA-NS5",  "CH-Fru",  "DE-Bay",  "DE-Tha",  "ES-LMa",  "FR-Lq1",  "IT-CA1",  "IT-Noe",  "NL-Hor",  "SE-Deg",  "US-Blo",  "US-Me2",  "US-PFa",  "US-Twt",
+    "AU-Cpr",  "AU-Lit",  "AU-Ync",  "CA-NS6",  "CH-Oe1",             "DE-Wet",  "ES-VDA",  "FR-Lq2",  "IT-CA2",  "IT-Non",  "NL-Loo",  "UK-Gri",  "US-Bo1",  "US-Me4",  "US-Prr",  "US-UMB",
+    "AU-Ctr",  "AU-Otw",  "BE-Bra",  "CA-NS7",  "CN-Cha",  "DE-Geb",  "DK-Fou",  "FI-Hyy",  "FR-Pue",  "IT-CA3",  "IT-PT1",  "PL-wet",  "UK-Ham",  "US-Cop",  "US-Me6",  "US-SP1",  "US-Var",
+    "AU-Cum",  "AU-Rig",  "BE-Lon",  "CA-Qcu",  "CN-Cng",  "DE-Gri",  "DK-Lva",  "FI-Kaa",  "GF-Guy",  "IT-Col",  "IT-Ren",  "PT-Esp",  "UK-PL3",  "US-FPe",  "US-MMS",  "US-SP2",  "US-WCr",
+    "AU-DaP",  "AU-Rob",  "BE-Vie",  "CA-Qfo",  "CN-Dan",  "DE-Hai",  "DK-Ris",  "FI-Lom",  "HU-Bug",  "IT-Cpz",  "IT-Ro1",  "PT-Mi1",  "US-AR1",  "US-GLE",  "US-MOz",  "US-SP3",  "US-Whs",
+    "AU-DaS",  "AU-Sam",  "BR-Sa3",  "CA-SF1",  "CN-Din",  "DE-Kli",  "DK-Sor",  "FI-Sod",  "ID-Pag",  "IT-Isp",  "IT-Ro2",  "PT-Mi2",  "US-AR2",  "US-Goo",  "US-Myb",  "US-SRG",  "US-Wkg",
+    "AU-Dry",  "AU-Stp",  "BW-Ma1",  "CA-SF2",  "CN-Du2",  "DE-Meh",  "DK-ZaH",  "FR-Fon",  "IE-Ca1",  "IT-Lav",  "IT-SR2",  "RU-Che",  "US-ARM",  "US-Ha1",  "US-Ne1",  "US-SRM",  "ZA-Kru"
+ ) {
+   &make_env_run( PLUMBER2SITE=>"$site" );
+   #
+   # Concatonate  default usermods and specific sitetogether expanding env variables while doing that
+   #
+   if ( ! -d "$plumdir/$site" ) {
+      print "PLUMBER2 directory is not there: $plumdir/$site\n";
+      die "ERROR:: PLUMBER2 site does not exist: $site\n";
+   }
+   my $plumdefaultfile = "$plumdir/defaults/user_nl_clm";
+   my $plumsitefile = "$plumdir/$site/user_nl_clm";
+   if ( ! -f $plumsitefile )  {
+      $plumsitefile = undef;
+   }
+   $ENV{'PLUMBER2'} = $site;
+   my $namelistfile = "temp.namelistinfile_$site";
+   &cat_and_create_namelistinfile( $plumdefaultfile, $plumsitefile, $namelistfile );
+   #
+   # Now run  the site
+   #
+   my $options = "--res CLM_USRDAT --clm_usr_name PLUMBER2 --no-megan --bgc sp --infile $namelistfile";
+   eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
+   is( $@, '', "options: $options" );
+   $cfiles->checkfilesexist( "$options", $mode );
+   $cfiles->shownmldiff( "default", $mode );
+   if ( defined($opts{'compare'}) ) {
+      $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+      $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
+      $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+   }
+   if ( defined($opts{'generate'}) ) {
+      $cfiles->copyfiles( "$options", $mode );
+   }
+   system( "/bin/rm $namelistfile" );
+   &cleanup();
+}
 
 print "\n===============================================================================\n";
 print "Test some CAM specific setups for special grids \n";

From 9c4e66a519511d30e7508fd6a228249ed8bd2f6c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 11 Sep 2024 10:22:05 -0600
Subject: [PATCH 1050/1248] Update the PLUMBER2 datasets to ctsm5.3.0

---
 cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
index fe23065798..fd719fe8eb 100644
--- a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
+++ b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
@@ -19,6 +19,6 @@
 !----------------------------------------------------------------------------------
 
 flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_${PLUMBER2SITE}_hist_2000_16pfts_c240326.nc"
+fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/ctsm5.3.0/surfdata_1x1_PLUMBER2_${PLUMBER2SITE}_hist_2000_16pfts_c240908.nc"
 
 ! custom namelist changes for each site / case

From 10ffe8ab2d06ea0b64e1256be91594bd7839ed27 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 11 Sep 2024 10:24:34 -0600
Subject: [PATCH 1051/1248] Also run FATES for the NEON sites

---
 bld/unit_testers/build-namelist_test.pl | 34 ++++++++++++++-----------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 5ea47ad1fa..540c83c289 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3859;
+my $ntests = 3994;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2347;
+   $ntests += 2437;
 }
 plan( tests=>$ntests );
 
@@ -393,20 +393,24 @@ sub cat_and_create_namelistinfile {
    my $namelistfile = "temp.namelistinfile_$site";
    &cat_and_create_namelistinfile( $neondefaultfile, $neonsitefile, $namelistfile );
    #
-   # Now run  the site
+   # Now run  the site for both bgc and non-FATES
    #
-   my $options = "--res CLM_USRDAT --clm_usr_name NEON --no-megan --bgc bgc --use_case 2018_control --infile $namelistfile";
-   eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
-   is( $@, '', "options: $options" );
-   $cfiles->checkfilesexist( "$options", $mode );
-   $cfiles->shownmldiff( "default", $mode );
-   if ( defined($opts{'compare'}) ) {
-      $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
-      $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
-   }
-   if ( defined($opts{'generate'}) ) {
-      $cfiles->copyfiles( "$options", $mode );
+   foreach my $bgc ( "bgc", "fates") {
+      if ( ($bgc eq "bgc") or ($site ne "STER" and $site ne "KONA")) {
+         my $options = "--res CLM_USRDAT --clm_usr_name NEON --no-megan --bgc $bgc --use_case 2018_control --infile $namelistfile";
+         eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
+         is( $@, '', "options: $options" );
+         $cfiles->checkfilesexist( "$options", $mode );
+         $cfiles->shownmldiff( "default", $mode );
+         if ( defined($opts{'compare'}) ) {
+            $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+            $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
+            $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+         }
+         if ( defined($opts{'generate'}) ) {
+            $cfiles->copyfiles( "$options", $mode );
+         }
+      }
    }
    system( "/bin/rm $namelistfile" );
    &cleanup();

From aa469b160288dc6aad0bfb795d4456c00adf7478 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 11 Sep 2024 11:07:49 -0600
Subject: [PATCH 1052/1248] More updates, add in another double tag ctsm5.2.029
 to document just the part that changes from ctsm5.2.028

---
 README                 |  22 +++---
 README.md              |   4 +-
 README_GITFLEXIMOD.rst |   4 +-
 bld/README             |  16 ++---
 doc/ChangeLog          | 149 ++++++++++++++++++++++++++++++++---------
 doc/ChangeSum          |   3 +-
 6 files changed, 143 insertions(+), 55 deletions(-)

diff --git a/README b/README
index 8b4e15e557..d3dcbce19f 100644
--- a/README
+++ b/README
@@ -1,6 +1,6 @@
-$CTSMROOT/README                                          04/19/2023
+$CTSMROOT/README                                          09/05/2024
 
-Community Terrestrial Systems Model (CTSM) science version 5.2  series -- source code, tools, 
+Community Terrestrial Systems Model (CTSM) science version 5.3 series -- source code, tools, 
 offline-build and test scripts. This gives you everything you need
 to run CTSM with CESM with the CMEPS driver and CDEPS data models to provide CRU NCEP or GSWP3 forcing data in 
 place of a modeled atmosphere.
@@ -51,7 +51,7 @@ tools ------------- CTSM Offline tools to prepare input datasets and process out
 cime_config ------- Configuration files of cime for compsets and CTSM settings
 bin/git-fleximod -- Script to manage the needed sub-component source directories (handled with git submodule)
 py_env_create ----- Script to setup the python environment for CTSM python tools using conda
-python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts
+python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scripts
 
 Directory structure only for a CTSM checkout:
 
@@ -66,6 +66,8 @@ components/cmeps -------------------- CESM top level driver (for NUOPC driver [w
 components/cdeps -------------------- CESM top level data model shared code (for NUOPC driver).
 components/cism --------------------- CESM Community land Ice Sheet Model.
 components/mosart ------------------- Model for Scale Adaptive River Transport
+components/mizuRoute ---------------- Reached based river transport model for water routing 
+                                      (allows both gridded river and Hydrologic Responce Unit river grids)
 components/rtm ---------------------- CESM River Transport Model.
 
 Top level documentation ($CTSMROOT):
@@ -74,6 +76,7 @@ README ------------------- This file
 README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git
 README.rst --------------- File that displays under the project in github
 README_GITFLEXIMOD.rst --- Information on how to work with git-fleximod for CTSM
+WhatsNewinCTSM5.3.md ----- Overview document of the changes between ctsm5.2.0 and ctsm5.3.0
 CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project
 Copyright ---------------- CESM Copyright file
 doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the
@@ -104,17 +107,16 @@ run_sys_tests --------------- Python script to send the standard CTSM testing of
 parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test
                               (can be used along with run_sys_tests)
 doc/Quickstart.GUIDE -------- Quick guide to using NUOPC scripts.
-doc/IMPORTANT_NOTES --------- Some important notes about this version of 
-                                                 CTSM, configuration modes and namelist items 
-                                                 that are not validated or functional.
+doc/IMPORTANT_NOTES.md ------ Some important notes about this version of 
+                              CTSM, configuration modes and namelist items 
+                              that are not validated or functional.
 doc/ChangeLog --------------- Detailed list of changes for each model version.
 doc/ChangeSum --------------- Summary one-line list of changes for each 
                               model version.
 doc/UsersGuide -------------- CTSM Users Guide
-doc/IMPORTANT_NOTES --------- Some important notes on caveats for some configurations/namelist items
 
 bld/README ------------------ Description of how to use the build-namelist scripts.
-bld/build-namelist ---------- Script to build CTSM namelists.
+bld/build-namelist ---------- Lower level script to build CTSM namelists.
 
 cime_config/buildnml ------------- Build the CTSM namelist for CIME
 cime_config/buildlib ------------- Build the CTSM library
@@ -155,9 +157,9 @@ src/dyn_subgrid --- Dynamic land unit change
 src/init_interp --- Online interpolation
 scr/fates --------- FATES model and sub-directories 
                     Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
-                    Experimental Ecosystem Demography model
+                    Ecosystem Demography model
 src/utils --------- Utility codes
-src/self_tests ---- Internal testing (unit tests run as a part of a CTSM simulation)
+src/self_tests ---- Internal testing (unit tests run as a part of a CTSM system test)
 src/unit_test_shr - Unit test shared modules for unit testing
 src/unit_test_stubs Unit test stubs that replicate CTSM code simpler
 
diff --git a/README.md b/README.md
index 045af9f6a1..5e800a0b77 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@
 
 The Community Terrestrial Systems Model.
 
-This includes the Community Land Model (CLM5.0 and CLM4.5) of the Community Earth System Model.
+This includes the Community Land Model of the Community Earth System Model.
 
 For documentation, quick start, diagnostics, model output and
 references, see
@@ -43,7 +43,7 @@ CTSM code management is provided primarily by:
 Software engineering team:
 - [Erik Kluzek](https://github.com/ekluzek)
 - [Bill Sacks](https://github.com/billsacks)
-- [Sam Levis](https://github.com/slevisconsulting)
+- [Sam Levis](https://github.com/slevis-lmwg)
 - [Adrianna Foster](https://github.com/adrifoster)
 - [Sam Rabin](https://github.com/samsrabin)
 - [Greg Lemieux](https://github.com/glemieux)
diff --git a/README_GITFLEXIMOD.rst b/README_GITFLEXIMOD.rst
index de6bbf392f..d1ab767645 100644
--- a/README_GITFLEXIMOD.rst
+++ b/README_GITFLEXIMOD.rst
@@ -67,10 +67,10 @@ Switching to a different CTSM branch or tag
 
 If you have already checked out a branch or tag and **HAVE NOT MADE ANY
 MODIFICATIONS** it is simple to change your sandbox. Say that you
-checked out ctsm1.0.0 but really wanted to have ctsm1.1.0;
+checked out ctsm5.2.0 but really wanted to have ctsm5.3.0;
 you would simply do the following::
 
-  git checkout ctsm1.1.0
+  git checkout ctsm5.3.0
   ./bin/git-fleximod update
 
 You should **not** use this method if you have made any source code
diff --git a/bld/README b/bld/README
index 1e9517b189..feb0b8495c 100644
--- a/bld/README
+++ b/bld/README
@@ -4,16 +4,16 @@ CLM build and configure directory and scripts. Scripts to help
 you prepare to build CLM as a component within CESM, and setup
 a namelist for it.
 
+This is a lower level script called from with CESM/CIME.
+
 Important files/directories:
 
---------- Configure and build scripts
---------- (These scripts are also used by the cesm/cime scripts)
+--------- Namelist build scripts
 
 config_files/clm_phys_vers.pm ------------- Perl module to handle different CLM versions
-config_files/config_definition_ctsm.xml --- XML file defining all CTSM configuration items
+config_files/config_definition_ctsm.xml --- XML file defining CTSM configuration items (mainly physics version)
 
 --------- Scripts to build the namelists
---------- (These scripts are also used by the cesm/cime scripts)
 build-namelist --- Build the namelists needed
 
 
@@ -26,17 +26,17 @@ unit_testers --- Directory of scripts to test scipts in this directory
 ---------- XML Files describing namelists in namelist_files
 namelist_files/namelist_defaults_ctsm.xml --------- List of default values for the ctsm namelist
 namelist_files/namelist_defaults_overall.xml ------ List of default values for overall settings
-namelist_files/namelist_defaults_usr_files.xml ---- List of default values for the user-files
-namelist_files/namelist_definition_ctsm.xml -------- Definition of all namelist items for ctsm
+namelist_files/namelist_defaults_usr_files.xml ---- List of default values for the user-files (deprecated)
+namelist_files/namelist_definition_ctsm.xml ------- Definition of all namelist items for ctsm
 namelist_files/namelist_definition.xsl ------------ Describes how to view the xml file as html
-namelist_files/namelist_defaults_drydep.xml ------- List of default values for the dry deposition module.
 namelist_files/use_cases -------------------------- Specific configurations that build-namelist uses
 namelist_files/use_cases/README ------------------- File explaining the naming convention for use_cases
 
 ---------- Driver namelist files, duplicated information from cime/driver/cime_config
 namelist_files/namelist_defaults_drv.xml ---------- List of default values for driver namelist defaults
-namelist_files/namelist_defaults_drydep.xml ------- List of default values for dry deposition fields 
+namelist_files/namelist_defaults_drydep.xml ------- List of default values for dry deposition and MEGAN fields 
 namelist_files/namelist_defaults_fire_emis.xml ---- List of default values for fire emission fields
+namelist_files/namelist_defaults_dust_emis.xml ---- List of default values for the dust emissions module.
 namelist_files/namelist_definition_drv.xml -------- Definition of all driver namelist items
 namelist_files/namelist_definition_drv_flds.xml --- Definition of add driver fieldsnamelist items
 
diff --git a/doc/ChangeLog b/doc/ChangeLog
index fd46741fec..c5559f7f12 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -4,8 +4,8 @@ Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri 06 Sep 2024 02:21:22 AM MDT
 One-line Summary: Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
 
-Purpose and description of changes
-----------------------------------
+Purpose and description of changes since ctsm5.2.0
+--------------------------------------------------
 
 Changes to CTSM:
 ================
@@ -23,32 +23,11 @@ Contributors
 ------------
 
 
-Significant changes to scientifically-supported configurations
---------------------------------------------------------------
-
-Does this tag change answers significantly for any of the following physics configurations?
-(Details of any changes will be given in the "Answer changes" section below.)
-
-    [Put an [X] in the box for any configuration with significant answer changes.]
-
-[X] clm6_0
-
-[X] clm5_1
-
-[X] clm5_0
-
-[X] ctsm5_0-nwp
-
-[X] clm4_5
-
+Significant changes to scientifically-supported configurations since ctsm5.2.0
+------------------------------------------------------------------------------
 
-Bugs fixed
-----------
-
-List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
-
-Notes of particular relevance for users
----------------------------------------
+Notes of particular relevance for users for ctsm5.2.0 to ctsm5.3.0
+------------------------------------------------------------------
 
 Caveats for users (e.g., need to interpolate initial conditions):
 
@@ -62,8 +41,8 @@ Changes to documentation:
 
 Things being deprecated (which will be removed):
 
-Notes of particular relevance for developers:
----------------------------------------------
+Notes of particular relevance for developers for ctsm5.2.0 to ctsm5.3.0:
+------------------------------------------------------------------------
 
 Caveats for developers (e.g., code that is duplicated that requires double maintenance):
 
@@ -108,8 +87,8 @@ Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_e
      derecho ----
 
 
-Answer changes
---------------
+Answer changes ctsm5.2.0 to ctsm5.3.0
+-------------------------------------
 
 Changes answers relative to baseline: Yes! New surface datasets so answers change for ALL simulations!
 
@@ -128,12 +107,118 @@ Changes answers relative to baseline: Yes! New surface datasets so answers chang
 
 Other details
 -------------
-[Remove any lines that don't apply. Remove entire section if nothing applies.]
 
 List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
 
+===============================================================
+===============================================================
+Tag name: ctsm5.2.029
+Originator(s): multiple
+Date: 10 Sep 2024
+One-line Summary: Update surface datasets: double tag of ctsm5.3.0
+
+Purpose and description of changes
+----------------------------------
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[X] clm6_0
+
+[X] clm5_1
+
+[X] clm5_0
+
+[X] ctsm5_0-nwp
+
+[X] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes #2723
+   Partly addresses #2720
+   Fixes #2452
+   Fixes #2570
+   Fixes #2618
+   Fixes #423
+   Fixes #2734
+   Fixes #2744
+   Fixes #2502
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   glacier_region_behavior updated so that region ID 1 is UNSET
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+   parameter file updated
+   surface datasets updatd
+   f09 1850 finidat file updated
+   fire emissions factor file updated
+
+Changes to documentation:
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing:
+   VIC tests removed
+
+Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_esmf python)
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes! New surface datasets so answers change for ALL simulations!
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: ALL
+    - what platforms/compilers: ALL
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+      new climate
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+       - casename:
+
+   URL for LMWG diagnostics output used to validate new climate:
+
+
+Other details
+-------------
 Pull Requests that document the changes (include PR ids):
 (https://github.com/ESCOMP/ctsm/pull)
+   #2500 -- ctsm5.3.0: New pft/lai/glc-behavior/soilcolor/fire datasets
 
 ===============================================================
 ===============================================================
diff --git a/doc/ChangeSum b/doc/ChangeSum
index c592a29382..31642a7378 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-         ctsm5.3.0     erik 09/06/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
+         ctsm5.3.0 multiple 09/11/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
+       ctsm5.2.029 multiple 09/11/2024 New surface datasets: double tag of ctsm5.3.0
        ctsm5.2.028   rgknox 09/05/2024 FATES history flushing update
        ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6

From a4d105d1da4248a7988b642799d7330d328fe5b1 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 12 Sep 2024 10:04:01 -0600
Subject: [PATCH 1053/1248] Update README.md about generating NEON and PLUMBER2
 fsurdat files

---
 tools/mksurfdata_esmf/README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tools/mksurfdata_esmf/README.md b/tools/mksurfdata_esmf/README.md
index a9c0b80de6..f49d23fb61 100644
--- a/tools/mksurfdata_esmf/README.md
+++ b/tools/mksurfdata_esmf/README.md
@@ -179,6 +179,10 @@ for example try --res 1.9x2.5 --start-year 1850 --end-year 1850:
  make all-subset
 ```
 
+ As of 2024/9/12 one needs to generate NEON and PLUMBER2 fsurdat files by
+ running ./neon_surf_wrapper and ./plumber2_surf_wrapper manually in the
+ /tools/site_and_regional directory.
+
 <!-- = -->
 ## NOTES
 <!-- = -->

From 2f5bd73c2e1f3a6dba959e38db4f63c11d9f180e Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 12 Sep 2024 15:01:28 -0600
Subject: [PATCH 1054/1248] Finish the ctsm5.2.029 section

---
 doc/ChangeLog | 36 +++++++++++++++++++++++++-----------
 1 file changed, 25 insertions(+), 11 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index c5559f7f12..988fe4f504 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -120,6 +120,10 @@ One-line Summary: Update surface datasets: double tag of ctsm5.3.0
 Purpose and description of changes
 ----------------------------------
 
+New surface datasets because of updates in PFT/LAI/soil-color datasets, as well as two fire datasets (AG fire, pearland and the glacier behavior dataset. Also bring in an updated "PPE informed, hand-tuned" parameter file. And turn on Li2024 fire method. Also updates to allow creating transient landuse timeseries files going back to 1700. Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mkaurfdata_esmf giving identical answers with a change in number of processors. Add in creation of ne0np4.POLARCAP.ne30x4 surface datasets.
+
+Asides: Remove VIC fields from surface datasets and testing. Add version to the surface datasets. Update the fire emissions factor dataset for the fire emissions testing in CTSM. Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it.
+
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
 
@@ -143,22 +147,29 @@ Bugs fixed
 ----------
 
 List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
-   Fixes #2723
-   Partly addresses #2720
-   Fixes #2452
-   Fixes #2570
-   Fixes #2618
-   Fixes #423
-   Fixes #2734
-   Fixes #2744
-   Fixes #2502
+   Fixes #2723 -- Version string on CTSM surface datasets to check for compatability
+   Partly addressed #2752 -- NEON surface datasets are defined in two places -- should just be one in namelist_defaults_ctsm.xml
+   Partly addresses #2720 -- Make polarcap surface datasets in ctsm5.3.0, remove VR 1850 datasets
+   Fixes #2452 -- Run mksurfdata_esmf with the new vegetation raw data
+   Fixes #2570 -- Historical configuration for CLM6
+   Fixes #2618 -- Update fire variables on surface dataset
+   Fixes #423 -- Update fire variables on surface dataset
+   Fixes #2734 -- Update fire emissions factors
+   Fixes #2744 -- Soil level clm surface input data for clm5.2.0 have missing values in large domains
+   Fixes #2502 -- fsurdat: PCT_SAND, PCT_CLAY, ORGANIC differ with different PE layouts on derecho
+   Fixes #2748 -- Update hillslope datasets for 5.3
 
 Notes of particular relevance for users
 ---------------------------------------
 
 Caveats for users (e.g., need to interpolate initial conditions):
+  New surface datasets means initial condition files created without ctsm5.3.0 surface
+  datasets will need to be interpolated
 
 Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+  With new surface datasets the following GLC fields have region "1" set to UNSET:
+     glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
+  For mksurfdata_esmf, the --vic and --hires_pft options were removed
 
 Changes made to namelist defaults (e.g., changed parameter values):
    glacier_region_behavior updated so that region ID 1 is UNSET
@@ -166,15 +177,17 @@ Changes made to namelist defaults (e.g., changed parameter values):
 Changes to the datasets (e.g., parameter, surface or initial files):
    parameter file updated
    surface datasets updatd
-   f09 1850 finidat file updated
+   f09 1850 finidat file updated (also used for 2000)
    fire emissions factor file updated
 
 Changes to documentation:
+   Technical Note documentation on glacier region updated
 
 Notes of particular relevance for developers:
 ---------------------------------------------
 
 Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   Region 1 for glacier region is now undefined on purpose
 
 Changes to tests or testing:
    VIC tests removed
@@ -209,9 +222,10 @@ Changes answers relative to baseline: Yes! New surface datasets so answers chang
 
    If this tag changes climate describe the run(s) done to evaluate the new
    climate (put details of the simulations in the experiment database)
-       - casename:
+       - casename: slevis ctsm52026_f09_pSASU
 
    URL for LMWG diagnostics output used to validate new climate:
+       https://github.com/NCAR/LMWG_dev/issues/65
 
 
 Other details

From dc3317db21998538cfc3862ca274ff6cc3dd1bae Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 12 Sep 2024 15:56:15 -0600
Subject: [PATCH 1055/1248] Replace default fire_method li2021gswpfrc with
 li2024crujra.

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 0188f91faa..e4617c3b94 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -238,7 +238,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <melt_non_icesheet_ice_runoff phys="clm4_5" >.false.</melt_non_icesheet_ice_runoff>
 
 <!-- CN Fire model method defaults -->
-<fire_method               >li2021gswpfrc</fire_method>
+<fire_method               >li2024crujra</fire_method>
 <fire_method phys="clm5_0" >li2016crufrc</fire_method>
 <fire_method phys="clm4_5" >li2014qianfrc</fire_method>
 

From 92b76e78ab654c9e659f894c13fa6a88386f8899 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 12 Sep 2024 15:58:07 -0600
Subject: [PATCH 1056/1248] Remove FireLi2024CruJra test from aux_clm, since
 it's now default.

---
 cime_config/testdefs/testlist_clm.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 57e798b963..5bf3909210 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3562,7 +3562,6 @@
 
   <test name="SMS_D_Ld65" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/FireLi2024CruJra">
     <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="fire"/>
     </machines>
     <options>

From 317dc11d0af402fd77746865112e8c5caebfa004 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 12 Sep 2024 18:07:15 -0600
Subject: [PATCH 1057/1248] Updates from troubleshooting failing tests

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 28 +++++++++----------
 .../smallville_dynlakes_monthly/user_nl_clm   |  2 +-
 .../smallville_dynurban_monthly/user_nl_clm   |  2 +-
 .../PLUMBER2/defaults/user_nl_clm             |  2 +-
 python/ctsm/test/test_unit_subset_data.py     |  2 +-
 python/ctsm/test/testinputs/default_data.cfg  | 12 ++++----
 tools/site_and_regional/default_data_1850.cfg |  8 +++---
 tools/site_and_regional/default_data_2000.cfg | 12 ++++----
 8 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index e4617c3b94..10de83236a 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1925,7 +1925,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240908.nc</fsurd
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="1x1_brazil"    sim_year="2000">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_2000_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_2000_78pfts_c240912.nc</fsurdat>
 <fsurdat hgrid="5x5_amazon"    sim_year="2000">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_5x5_amazon_hist_2000_78pfts_c240908.nc</fsurdat>
 
@@ -1950,7 +1950,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_2000_78pfts_c240908.nc
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_2000_78pfts_c240908.nc</fsurdat>
 
 <fsurdat hgrid="1x1_numaIA"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240908.nc
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_numaIA_hist_2000_78pfts_c240912.nc
 </fsurdat>
 
 <fsurdat hgrid="mpasa480"  sim_year="2000">
@@ -1971,11 +1971,11 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_2000_78pfts_c2
 
 <!-- 100% Urban single-point datasets (only for sim-year=2000) -->
 <fsurdat hgrid="1x1_vancouverCAN"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_vancouverCAN_hist_2000_78pfts_c240912.nc</fsurdat>
 <fsurdat hgrid="1x1_mexicocityMEX"   sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_mexicocityMEX_hist_2000_78pfts_c240912.nc</fsurdat>
 <fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_urbanc_alpha_hist_2000_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_urbanc_alpha_synth_hist_2000_78pfts_c240912.nc</fsurdat>
 
 <!-- for pre-industrial simulations - year 1850 -->
 
@@ -2007,11 +2007,11 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc
 <fsurdat hgrid="C96"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_smallvilleIA_synth_hist_1850_78pfts_c240912.nc</fsurdat>
 <fsurdat hgrid="1x1_cidadinhoBR" sim_year="2000" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_cidadinhoBR_synth_hist_2000_78pfts_c240912.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240912.nc</fsurdat>
 
 <fsurdat hgrid="ne3np4.pg3"               sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
@@ -2032,13 +2032,13 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne0np4CONUS.ne30x8_hist_1979_78pfts_c2
 
 <!-- for NEON sites present day simulations - year 2000 -->
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".true.">
-lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240910.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240912.nc</fsurdat>
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false.">
-lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240912.nc</fsurdat>
 <!-- If there are cases where only a few datasets change - they can be listed here for the particular NEONSITE -->
 <!-- for example to override the above for the TOOL site do something like this...
 <fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false." neonsite="TOOL">
-lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c230699.nc</fsurdat>
+lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c240912.nc</fsurdat>
 -->
 
 <!-- Dynamic PFT surface datasets (relative to {csmdata}) -->
@@ -2065,7 +2065,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_s
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240912.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
@@ -2084,7 +2084,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_s
 <!-- Note that these transient files only go up to year 1855.
      This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
 <flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_1850-1855_78pfts_c240908.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_1850-1855_78pfts_c240912.nc</flanduse_timeseries>
 
 <!-- Cidadinho test site has no transient data. -->
 <flanduse_timeseries hgrid="1x1_cidadinhoBR" sim_year_range="1850-2000"></flanduse_timeseries>
@@ -2111,7 +2111,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_s
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1x1_brazil_SSP2-4.5_1850-2100_78pfts_c240912.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
diff --git a/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm
index c86418dabd..6223cc203f 100644
--- a/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm
@@ -6,7 +6,7 @@ do_transient_lakes = .true.
 ! Key points are that lake area starts as 0, increases after the first year, then decreases after the second year.
 ! PCT_CROP is also changed so that PCT_LAKE + PCT_CROP <= 100. (Here, PCT_CROP increases and decreases at the same time as PCT_LAKE in order to exercise the simultaneous increase or decrease of two landunits, but that isn't a critical part of this test.)
 ! Note that the use of this file means that this testmod can only be used with the 1x1_smallvilleIA grid.
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_dynLakes_c240221.nc'
+flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_SSP2-4.5_1850-1855_78pfts_dynLakes_c240912.nc'
 
 ! NOTE slevis (2024/2/23) Adding option for tests to pass. In the long term
 ! ensure that subset_data generates fsurdat and landuse files consistent with
diff --git a/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm
index a5bdb76ac3..958265cffc 100644
--- a/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm
@@ -7,7 +7,7 @@ do_transient_urban = .true.
 ! Medium density urban is set to zero to test the memory-saving behavior of PCT_URBAN_MAX.
 ! PCT_CROP is also changed so that PCT_URBAN + PCT_CROP <= 100. (Here, PCT_CROP increases and decreases at the same time as PCT_URBAN in order to exercise the simultaneous increase or decrease of two landunits, but that isn't a critical part of this test.)
 ! Note that the use of this file means that this testmod can only be used with the 1x1_smallvilleIA grid.
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_dynUrban_c240221.nc'
+flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_SSP2-4.5_1850-1855_78pfts_dynUrban_c240912.nc'
 
 ! NOTE slevis (2024/2/23) Adding option for tests to pass. In the long term
 ! ensure that subset_data generates fsurdat and landuse files consistent with
diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
index fd719fe8eb..5216afb381 100644
--- a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
+++ b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
@@ -19,6 +19,6 @@
 !----------------------------------------------------------------------------------
 
 flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/ctsm5.3.0/surfdata_1x1_PLUMBER2_${PLUMBER2SITE}_hist_2000_16pfts_c240908.nc"
+fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/ctsm5.3.0/surfdata_1x1_PLUMBER2_${PLUMBER2SITE}_hist_2000_16pfts_c240912.nc"
 
 ! custom namelist changes for each site / case
diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py
index 143b632e8c..a918fb35f0 100755
--- a/python/ctsm/test/test_unit_subset_data.py
+++ b/python/ctsm/test/test_unit_subset_data.py
@@ -48,7 +48,7 @@ def test_inputdata_setup_files_basic(self):
         files = setup_files(self.args, self.defaults, self.cesmroot)
         self.assertEqual(
             files["fsurf_in"],
-            "surfdata_0.9x1.25_hist_2000_16pfts_c240216.nc",
+            "surfdata_0.9x1.25_hist_2000_16pfts_c240908.nc",
             "fsurf_in filename not whats expected",
         )
         self.assertEqual(
diff --git a/python/ctsm/test/testinputs/default_data.cfg b/python/ctsm/test/testinputs/default_data.cfg
index d736f2e933..24aa811fee 100644
--- a/python/ctsm/test/testinputs/default_data.cfg
+++ b/python/ctsm/test/testinputs/default_data.cfg
@@ -15,16 +15,16 @@ precname = CLMGSWP3v1.Precip
 tpqwname = CLMGSWP3v1.TPQW
 
 [surfdat]
-dir = lnd/clm2/surfdata_esmf/ctsm5.2.0
-surfdat_16pft = surfdata_0.9x1.25_hist_2000_16pfts_c240216.nc
-surfdat_78pft = surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc
+dir = lnd/clm2/surfdata_esmf/ctsm5.3.0
+surfdat_16pft = surfdata_0.9x1.25_hist_2000_16pfts_c240908.nc
+surfdat_78pft = surfdata_0.9x1.25_hist_2000_78pfts_c240908.nc
 mesh_dir = share/meshes/
 mesh_surf = fv0.9x1.25_141008_ESMFmesh.nc
 
 [landuse]
-dir = lnd/clm2/surfdata_esmf/ctsm5.2.0
-landuse_16pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc
-landuse_78pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc
+dir = lnd/clm2/surfdata_esmf/ctsm5.3.0
+landuse_16pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc
+landuse_78pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc
 
 [domain]
 file = share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc
diff --git a/tools/site_and_regional/default_data_1850.cfg b/tools/site_and_regional/default_data_1850.cfg
index 47cb71ee87..0f3cdab60f 100644
--- a/tools/site_and_regional/default_data_1850.cfg
+++ b/tools/site_and_regional/default_data_1850.cfg
@@ -15,12 +15,12 @@ precname = CLMGSWP3v1.Precip
 tpqwname = CLMGSWP3v1.TPQW
 
 [surfdat]
-dir = lnd/clm2/surfdata_esmf/ctsm5.2.0
-surfdat_78pft = surfdata_0.9x1.25_hist_1850_78pfts_c240216.nc
+dir = lnd/clm2/surfdata_esmf/ctsm5.3.0
+surfdat_78pft = surfdata_0.9x1.25_hist_1850_78pfts_c240908.nc
 
 [landuse]
-dir = lnd/clm2/surfdata_esmf/ctsm5.2.0
-landuse_78pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc
+dir = lnd/clm2/surfdata_esmf/ctsm5.3.0
+landuse_78pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc
 
 [domain]
 file = share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc
diff --git a/tools/site_and_regional/default_data_2000.cfg b/tools/site_and_regional/default_data_2000.cfg
index d736f2e933..24aa811fee 100644
--- a/tools/site_and_regional/default_data_2000.cfg
+++ b/tools/site_and_regional/default_data_2000.cfg
@@ -15,16 +15,16 @@ precname = CLMGSWP3v1.Precip
 tpqwname = CLMGSWP3v1.TPQW
 
 [surfdat]
-dir = lnd/clm2/surfdata_esmf/ctsm5.2.0
-surfdat_16pft = surfdata_0.9x1.25_hist_2000_16pfts_c240216.nc
-surfdat_78pft = surfdata_0.9x1.25_hist_2000_78pfts_c240216.nc
+dir = lnd/clm2/surfdata_esmf/ctsm5.3.0
+surfdat_16pft = surfdata_0.9x1.25_hist_2000_16pfts_c240908.nc
+surfdat_78pft = surfdata_0.9x1.25_hist_2000_78pfts_c240908.nc
 mesh_dir = share/meshes/
 mesh_surf = fv0.9x1.25_141008_ESMFmesh.nc
 
 [landuse]
-dir = lnd/clm2/surfdata_esmf/ctsm5.2.0
-landuse_16pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc
-landuse_78pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc
+dir = lnd/clm2/surfdata_esmf/ctsm5.3.0
+landuse_16pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc
+landuse_78pft = landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc
 
 [domain]
 file = share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc

From e205e2ef8ed005aa3bb7743ba5ea8061bbd22498 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 13 Sep 2024 11:38:56 -0600
Subject: [PATCH 1058/1248] Ignore warnings in Hillslope tests.

---
 .../testdefs/testmods_dirs/clm/Hillslope/shell_commands        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
index 6f3602d2e6..a2759b51b4 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
@@ -2,3 +2,6 @@
 DIN_LOC_ROOT=$(./xmlquery --value DIN_LOC_ROOT)
 meshfile=$DIN_LOC_ROOT/lnd/clm2/testdata/ESMFmesh_10x15_synthetic_cosphill_1.0.nc
 ./xmlchange ATM_DOMAIN_MESH=${meshfile},LND_DOMAIN_MESH=${meshfile}
+
+# -ignore_warnings is needed as long as we don't allow use_hillslope and use_init_interp together
+./xmlchange --append CLM_BLDNML_OPTS=-ignore_warnings

From 90a5ae904e3a1fde12c53d23f47baf45bf95ab10 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 14 Sep 2024 10:15:09 -0600
Subject: [PATCH 1059/1248] All IC files need to have use_init_interp set to
 TRUE

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index b4df3e008f..705888bd17 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1343,7 +1343,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_0_GSWP3v1"
+         lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
 </finidat>
 
@@ -1351,7 +1351,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_0_CRUv7"
+         lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCropCru-ciso.1526-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
 </finidat>
 
@@ -1400,7 +1400,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm4_5_GSWP3v1"
+         lnd_tuning_mode="clm4_5_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 
@@ -1408,7 +1408,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm4_5_CRUv7"
+         lnd_tuning_mode="clm4_5_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 
@@ -1416,13 +1416,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_0_GSWP3v1"
+         lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_1_GSWP3v1"
+         lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
@@ -1438,7 +1438,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_0_CRUv7"
+         lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 

From 2b0e886d8959745f95a7aa863a2ef683764cdd9c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 14 Sep 2024 10:24:22 -0600
Subject: [PATCH 1060/1248] Remove or update surface datasets that were for
 ctsm5.2.0, and for testmods for Sp compsets turn fire-emissions off by
 pointing to nofireemis testmod

---
 .../clm/ExcessIceStreams/include_user_mods       |  1 +
 .../clm/FatesColdLandUse/shell_commands          |  3 +++
 .../clm/FatesColdLandUse/user_nl_clm             |  1 -
 .../clm/SNICARFRC/include_user_mods              |  1 +
 .../collapse_pfts_78_to_16_decStart_f10/README   | 16 ----------------
 .../user_nl_clm                                  |  2 --
 .../clm/f09_dec1990Start_GU_LULCC/user_nl_clm    |  5 +----
 .../testmods_dirs/clm/nofire/include_user_mods   |  1 +
 .../testmods_dirs/clm/nofire/shell_commands      |  1 -
 .../testmods_dirs/clm/nofireemis/shell_commands  |  3 +++
 .../clm/o3lombardozzi2015/include_user_mods      |  1 +
 .../clm/pauseResume/include_user_mods            |  1 +
 .../clm/prescribed/include_user_mods             |  1 +
 .../testmods_dirs/clm/pts/include_user_mods      |  1 +
 .../clm/smallville_dynlakes_monthly/user_nl_clm  |  2 +-
 .../clm/smallville_dynurban_monthly/user_nl_clm  |  2 +-
 .../clm/waccmx_offline/include_user_mods         |  1 +
 17 files changed, 17 insertions(+), 26 deletions(-)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/nofire/include_user_mods
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/nofireemis/shell_commands

diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods
index fe0e18cf88..1e4ddf5337 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods
@@ -1 +1,2 @@
 ../default
+../nofireemis
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
new file mode 100644
index 0000000000..c97c0dfea7
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./xmlchange CLM_BLDNML_OPTS="-i-clm_demand -flanduse_timeseries" --append
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm
index b27a74031c..f718010b07 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm
@@ -1,2 +1 @@
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_hist_16_CMIP6_1850-2015_c230620.nc'
 fates_harvest_mode = 'landuse_timeseries'
diff --git a/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/include_user_mods
index fe0e18cf88..1e4ddf5337 100644
--- a/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/include_user_mods
@@ -1 +1,2 @@
 ../default
+../nofireemis
diff --git a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README
index dbd0696317..f19dd1893e 100644
--- a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README
+++ b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README
@@ -4,22 +4,6 @@ new combination do_transient_crops = .true. and use_crop = .false. while
 exercising the collapse2gencrop branch ability to collapse the full crop data
 to clm's generic crops.
 
-According to the file
-bld/namelist_files/namelist_defaults_ctsm.xml
-the following two files used in this test
-are default files for the following options:
-
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_10x15_hist_1850_78pfts_c240216.nc'
-hgrid="10x15" sim_year="1850" use_crop=".false." irrigate=".true."
-hgrid="10x15" sim_year="1850" use_crop=".true."
-
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc'
--hgrid="10x15" sim_year_range="1850-2000" use_crop=".true."
--hgrid="10x15" rcp="8.5" sim_year_range="1850-2100" use_crop=".true."
--hgrid="10x15" rcp="6" sim_year_range="1850-2100" use_crop=".true."
--hgrid="10x15" rcp="4.5" sim_year_range="1850-2100" use_crop=".true."
--hgrid="10x15" rcp="2.6" sim_year_range="1850-2100" use_crop=".true."
-
 This test includes the settings of the decStart test so as to also test the
 end-of-year transition since it's an IHist case and transient vegetation gets
 updated every new year.
diff --git a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm
deleted file mode 100644
index d7be01280b..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm
+++ /dev/null
@@ -1,2 +0,0 @@
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_10x15_hist_1850_78pfts_c240216.nc'
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240216.nc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm
index 0dbc0b4942..e9040ca841 100644
--- a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm
@@ -1,5 +1,2 @@
- ! Specify a dataset that has non-zero Gross Unrepresented Land Use change fields on it
- ! And turn it on
- flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240216.nc'
- fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_0.9x1.25_hist_1850_78pfts_c240216.nc'
+ ! Turn on Gross Unrepresented Land Use
  do_grossunrep = .true.
diff --git a/cime_config/testdefs/testmods_dirs/clm/nofire/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/nofire/include_user_mods
new file mode 100644
index 0000000000..dbad2e75e6
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/nofire/include_user_mods
@@ -0,0 +1 @@
+../nofireemis
diff --git a/cime_config/testdefs/testmods_dirs/clm/nofire/shell_commands b/cime_config/testdefs/testmods_dirs/clm/nofire/shell_commands
index fe06fd1042..bbe1216f7d 100644
--- a/cime_config/testdefs/testmods_dirs/clm/nofire/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/nofire/shell_commands
@@ -1,5 +1,4 @@
 
-./xmlchange CLM_BLDNML_OPTS="-no-fire_emis" --append
 ./xmlchange BFBFLAG="TRUE"
 
 
diff --git a/cime_config/testdefs/testmods_dirs/clm/nofireemis/shell_commands b/cime_config/testdefs/testmods_dirs/clm/nofireemis/shell_commands
new file mode 100644
index 0000000000..2cef76cc58
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/nofireemis/shell_commands
@@ -0,0 +1,3 @@
+./xmlchange CLM_BLDNML_OPTS="-no-fire_emis" --append
+
+
diff --git a/cime_config/testdefs/testmods_dirs/clm/o3lombardozzi2015/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/o3lombardozzi2015/include_user_mods
index fe0e18cf88..1e4ddf5337 100644
--- a/cime_config/testdefs/testmods_dirs/clm/o3lombardozzi2015/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/o3lombardozzi2015/include_user_mods
@@ -1 +1,2 @@
 ../default
+../nofireemis
diff --git a/cime_config/testdefs/testmods_dirs/clm/pauseResume/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/pauseResume/include_user_mods
index fe0e18cf88..1e4ddf5337 100644
--- a/cime_config/testdefs/testmods_dirs/clm/pauseResume/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/pauseResume/include_user_mods
@@ -1 +1,2 @@
 ../default
+../nofireemis
diff --git a/cime_config/testdefs/testmods_dirs/clm/prescribed/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/prescribed/include_user_mods
index fe0e18cf88..1e4ddf5337 100644
--- a/cime_config/testdefs/testmods_dirs/clm/prescribed/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/prescribed/include_user_mods
@@ -1 +1,2 @@
 ../default
+../nofireemis
diff --git a/cime_config/testdefs/testmods_dirs/clm/pts/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/pts/include_user_mods
index fe0e18cf88..1e4ddf5337 100644
--- a/cime_config/testdefs/testmods_dirs/clm/pts/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/pts/include_user_mods
@@ -1 +1,2 @@
 ../default
+../nofireemis
diff --git a/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm
index c86418dabd..c2f51e29ab 100644
--- a/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm
@@ -6,7 +6,7 @@ do_transient_lakes = .true.
 ! Key points are that lake area starts as 0, increases after the first year, then decreases after the second year.
 ! PCT_CROP is also changed so that PCT_LAKE + PCT_CROP <= 100. (Here, PCT_CROP increases and decreases at the same time as PCT_LAKE in order to exercise the simultaneous increase or decrease of two landunits, but that isn't a critical part of this test.)
 ! Note that the use of this file means that this testmod can only be used with the 1x1_smallvilleIA grid.
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_dynLakes_c240221.nc'
+flanduse_timeseries = '$DIN_LOC_ROOT//lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_1850-1855_78pfts_dynLakes_c240908.nc'
 
 ! NOTE slevis (2024/2/23) Adding option for tests to pass. In the long term
 ! ensure that subset_data generates fsurdat and landuse files consistent with
diff --git a/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm
index a5bdb76ac3..c4b9709438 100644
--- a/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/user_nl_clm
@@ -7,7 +7,7 @@ do_transient_urban = .true.
 ! Medium density urban is set to zero to test the memory-saving behavior of PCT_URBAN_MAX.
 ! PCT_CROP is also changed so that PCT_URBAN + PCT_CROP <= 100. (Here, PCT_CROP increases and decreases at the same time as PCT_URBAN in order to exercise the simultaneous increase or decrease of two landunits, but that isn't a critical part of this test.)
 ! Note that the use of this file means that this testmod can only be used with the 1x1_smallvilleIA grid.
-flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_dynUrban_c240221.nc'
+flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_1850-1855_78pfts_dynUrban_c240908.nc'
 
 ! NOTE slevis (2024/2/23) Adding option for tests to pass. In the long term
 ! ensure that subset_data generates fsurdat and landuse files consistent with
diff --git a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/include_user_mods
index fe0e18cf88..1e4ddf5337 100644
--- a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/include_user_mods
@@ -1 +1,2 @@
 ../default
+../nofireemis

From 010b10de2e481519e2ca04dee5d496438663984b Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 14 Sep 2024 10:26:19 -0600
Subject: [PATCH 1061/1248] Add --nofireemis to tests with Sp compsets, and
 remove the mpas15-3 resolution tests as we aren't going to do that

---
 cime_config/testdefs/testlist_clm.xml | 117 +++++++++++++++-----------
 1 file changed, 69 insertions(+), 48 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 57e798b963..1a4df42194 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -31,7 +31,7 @@
       <option name="comment"  >Repeat last ERI_D_Ld9...default test with matrixcnOn</option>
     </options>
   </test>
-  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm60SpNoAnthro" testmods="clm/decStart1851_noinitial">
+  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm60SpNoAnthro" testmods="clm/decStart1851_noinitial--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
@@ -40,6 +40,7 @@
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >No anthropogenic compset</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm60BgcNoAnthro" testmods="clm/decStart1851_noinitial--clm/matrixcnOn">
@@ -90,7 +91,7 @@
       <option name="comment">Simple test use soil eroditability in CTSM for CAM4 tuning, at 1-degree</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/clm50cam5LndTuningModeZDustSoilErod">
+  <test name="SMS_Ln9" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/clm50cam5LndTuningModeZDustSoilErod--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
@@ -98,6 +99,7 @@
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment">Simple test use soil eroditability in CTSM for CAM5 tuning</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="ERP_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningModeLDust">
@@ -193,80 +195,76 @@
       <option name="comment"  >CTSM science test list for the half degree grid with latest CLM version for historical</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis"/>
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">We have one C96 test in aux_clm; this is another that uses a different compset. No needn't run this additional C96 test with every tag, but include it in the less frequent ctsm_sci testing.</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I1850Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I1850Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">mpasa low resolution grid, tested in CAM, so do both 1850 and 2000 with latest CLM version and include in the CTSM science test list</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">mpasa low resolution grid, tested in CAM, so do both 1850 and 2000 with latest CLM version and include in the CTSM science test list</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Test that the workhorse mpasa resolution functions for CAM, for both Hist and 2000 with latest CLM version. No need to run this test with every tag, but include it in the less frequent ctsm_sci testing.</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Test that the workhorse mpasa resolution functions for CAM, for both Hist and 2000 with latest CLM version. No need to run this test with every tag, but include it in the less frequent ctsm_sci testing.</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningModeLDust">
+  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningModeLDust--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Higher resolution mpasa grid for CAM with latest CLM version. Include it in the less frequent ctsm_sci testing.</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa15_mpasa15" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="mpasa15_mpasa15" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Higher resolution mpasa grid for CAM with latest CLM version. Include it in the less frequent ctsm_sci testing.</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-<!--
-  <test name="SMS_P36x128_Ln9" grid="mpasa15-3-conus_mpasa15-3-conus" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:60:00</option>
-      <option name="comment">High resolution mpasa grid with refined mesh over CONUS for CAM with latest CLM version. Include it in the less frequent ctsm_sci testing.</option>
-    </options>
-  </test>
--->
   <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/vrtlay">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -349,22 +347,24 @@
       <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f09 with CAM7</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19 with CAM7</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="ERP_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50Sp" testmods="clm/prescribed">
@@ -623,112 +623,124 @@
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="IHistClm60SpRs" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="IHistClm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Low resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Low resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Medium resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, test both 1850 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Medium resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, test both 1850 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Medium resolution SE grid for running with CAM with latest CLM version in the CTSM science test list, test IHist</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30_g17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne30_g17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-   <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode">
+   <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Workhorse SE grid for running with CAM with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS" grid="ne30pg3_ne30pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">Workhorse SE grid for running with CAM and with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">High resolution SE grid for running with CAM and with the latest CLM version in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="ne120pg3_t13" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
       <option name="comment">High resolution SE grid for running with CAM and with the latest CLM version  in the CTSM science test list, tested in CAM, so test all of Hist, SSP5-8.5 and 2000</option>
+      <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <!-- Historical clm5_0 physics BgcCrop science support -->
@@ -914,13 +926,14 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50SpCru" testmods="clm/drydepnomegan">
+  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50SpCru" testmods="clm/drydepnomegan--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm60Sp" testmods="clm/default">
@@ -1546,13 +1559,14 @@
       <option name="comment"  >Repeat ERS_D...reseedresetsnow test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERP_P64x2_D_Ld10" grid="f10_f10_mg37" compset="IHistClm50SpG" testmods="clm/glcMEC_decrease">
+  <test name="ERP_P64x2_D_Ld10" grid="f10_f10_mg37" compset="IHistClm50SpG" testmods="clm/glcMEC_decrease--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >Test transient PFTs (via HIST) in conjunction with changing glacier area. This test also covers the reset_dynbal_baselines option. CISM is not answer preserving across processor changes, but short test length should be OK.</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="SMS_Ln9" grid="C96_C96_mg17" compset="IHistClm60BgcCrop" testmods="clm/clm60cam7LndTuningMode">
@@ -1992,33 +2006,36 @@
       <option name="comment"  >Repeat last SMS_D_Ld1...cplhist test with matrixcnOn"</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_PS" grid="f19_f19_mg17" compset="I2010Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
+  <test name="SMS_D_Ld1_PS" grid="f19_f19_mg17" compset="I2010Clm50Sp" testmods="clm/clm50cam6LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_1979Start">
+  <test name="SMS_Ln9" grid="ne0ARCTICne30x4_ne0ARCTICne30x4_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_1979Start--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >Run ARCTIC for transient case starting in 1979 as for AMIP CAM cases (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_1979Start">
+  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_1979Start--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >Run ARCTICGRIS for transient case starting in 1979 as for AMIP CAM cases (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam7LndTuningMode">
+  <test name="SMS_Ln9" grid="ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12" compset="I1850Clm60BgcCrop" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2027,17 +2044,18 @@
       <option name="comment"  >Run ARCTICGRIS for 1850 case (do not run this expensive test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_2013Start">
+  <test name="SMS_Ln9" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode_2013Start--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >Run CONUS for transient case starting in 2013 as for CAM case (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <!-- Historical science support for clm5_0 workhorse resolutions -->
-  <test name="SMS_Ld5" grid="f09_g17" compset="IHistClm50Sp" testmods="clm/default">
+  <test name="SMS_Ld5" grid="f09_g17" compset="IHistClm50Sp" testmods="clm/nofire">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2046,7 +2064,7 @@
       <option name="comment"  >Science support for historical clm5_0 physics with SP mode at f09</option>
     </options>
   </test>
-  <test name="SMS_Ld5" grid="f19_g17" compset="IHistClm50Sp" testmods="clm/default">
+  <test name="SMS_Ld5" grid="f19_g17" compset="IHistClm50Sp" testmods="clm/nofire">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2056,7 +2074,7 @@
     </options>
   </test>
   <!-- Historical science support for clm6_0 workhorse resolutions -->
-  <test name="SMS_Ld5" grid="f09_g17" compset="IHistClm60Sp" testmods="clm/default">
+  <test name="SMS_Ld5" grid="f09_g17" compset="IHistClm60Sp" testmods="clm/nofire">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2065,7 +2083,7 @@
       <option name="comment"  >Science support for historical clm6_0 physics with SP mode at f09</option>
     </options>
   </test>
-  <test name="SMS_Ld5" grid="f19_g17" compset="IHistClm60Sp" testmods="clm/default">
+  <test name="SMS_Ld5" grid="f19_g17" compset="IHistClm60Sp" testmods="clm/nofire">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -2074,13 +2092,14 @@
       <option name="comment"  >Science support for historical clm6_0 physics with SP mode at f19</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm50Sp" testmods="clm/clm50cam6LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
       <option name="comment"  >Run ne30np4.pg2 to make sure will work for CAM"</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="SMS_Ln9" grid="ne30pg2_ne30pg2_mg17" compset="I2000Clm50BgcCrop" testmods="clm/clm50cam6LndTuningMode">
@@ -2101,13 +2120,14 @@
       <option name="comment"  >Run mpasa480 to make sure will work for CAM"</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
+  <test name="SMS_Ln9" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm50Sp" testmods="clm/clm50cam6LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="comment"  >Run coarse resolution ne3pg3_ne3pg3_mg37 to make sure will work for CAM"</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="SMS_D" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/crop">
@@ -2510,7 +2530,7 @@
       <option name="comment"  >include a relatively long crop test at relatively high resolution</option>
     </options>
   </test>
-  <test name="SMS_Lm37" grid="f10_f10_mg37" compset="I1850Clm50SpG" testmods="clm/glcMEC_long">
+  <test name="SMS_Lm37" grid="f10_f10_mg37" compset="I1850Clm50SpG" testmods="clm/glcMEC_long--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
@@ -2518,6 +2538,7 @@
     <options>
       <option name="wallclock">01:30:00</option>
       <option name="comment"  >Long enough test for SMB to be generated in bare land areas; add a month beyond the 3rd year to allow time for CLM to respond to CISM forcing from the 3rd year. (Note: if we had spun-up initial conditions for an IG compset, we could test this with much shorter test, if it also used the glc override options - much of the need for this long test is to allow the snow pack to spin up.)</option>
+      <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
   <test name="SMS_Ly3_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm60BgcCropQianRs" testmods="clm/monthly">

From d3c692625ed24349b0f17c1f550b550bd03335af Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sat, 14 Sep 2024 17:38:48 -0600
Subject: [PATCH 1062/1248] Correct date for file

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 11e63758ba..31274228f8 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2084,7 +2084,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <!-- Note that these transient files only go up to year 1855.
      This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
 <flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_1850-1855_78pfts_c240912.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/landuse.timeseries_1x1_smallvilleIA_synth_1850-1855_78pfts_c240908.nc</flanduse_timeseries>
 
 <!-- Cidadinho test site has no transient data. -->
 <flanduse_timeseries hgrid="1x1_cidadinhoBR" sim_year_range="1850-2000"></flanduse_timeseries>

From 47178e7db33e49adba0b9560bf69e5683079db32 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Sun, 15 Sep 2024 02:34:29 -0600
Subject: [PATCH 1063/1248] Add handling of excess_ice to the picking of
 initial condition files

---
 bld/CLMBuildNamelist.pm                       |  33 +-
 bld/namelist_files/namelist_defaults_ctsm.xml | 310 +++++++++---------
 2 files changed, 184 insertions(+), 159 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index c18b72ac15..d2974e8f2e 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -1665,6 +1665,7 @@ sub process_namelist_inline_logic {
   setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_surface_dataset($opts,  $nl_flags, $definition, $defaults, $nl, $envxml_ref);
   setup_logic_dynamic_subgrid($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_exice($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) {
     setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   }
@@ -1894,7 +1895,7 @@ sub process_namelist_inline_logic {
   #################################
   # namelist group: exice_streams #
   #################################
-  setup_logic_exice($opts, $nl_flags, $definition, $defaults, $nl, $physv);
+  setup_logic_exice_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv);
 
   ##########################################
   # namelist group: clm_temperature_inparm #
@@ -2580,10 +2581,12 @@ sub setup_logic_initial_conditions {
   #
   # MUST BE AFTER: setup_logic_demand   which is where flanduse_timeseries is set
   #         AFTER: setup_logic_irrigate which is where irrigate is set
+  #         AFTER: setup_logic_exice    which is where use_excess_ice is set
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
   my $var = "finidat";
   my $finidat = $nl->get_value($var);
+  $nl_flags->{'excess_ice_on_finidat'} = "unknown";
   if ( $nl_flags->{'clm_start_type'} =~ /cold/ ) {
     if (defined $finidat ) {
       $log->warning("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incomptable with using a cold start" .
@@ -2632,7 +2635,7 @@ sub setup_logic_initial_conditions {
        $settings{'sim_year'}     = $st_year;
     }
     foreach my $item ( "mask", "maxpft", "irrigate", "glc_nec", "use_crop", "use_cn", "use_cndv",
-                       "use_fates",
+                       "use_fates", "use_excess_ice",
                        "lnd_tuning_mode",
                      ) {
        $settings{$item}    = $nl_flags->{$item};
@@ -2653,6 +2656,7 @@ sub setup_logic_initial_conditions {
     my $done = 2;
     do {
        $try++;
+       $nl_flags->{'excess_ice_on_finidat'} = $settings{'use_excess_ice'};
        add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, %settings );
        # If couldn't find a matching finidat file, check if can turn on interpolation and try to find one again
        $finidat = $nl->get_value($var);
@@ -4966,18 +4970,39 @@ sub setup_logic_cnmatrix {
 #-------------------------------------------------------------------------------
 sub setup_logic_exice {
   #
-  # excess ice streams
+  # excess ice streams, must be set before initial conditions
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); 
   my $use_exice = $nl->get_value( 'use_excess_ice' );
+  # Put use_exice into nl_flags so can be referenced later
+  if ( value_is_true($use_exice) ) {
+     $nl_flags->{'use_excess_ice'} = ".true.";
+  } else {
+     $nl_flags->{'use_excess_ice'} = ".false.";
+  }
+}
+
+#-------------------------------------------------------------------------------
+sub setup_logic_exice_streams {
+  #
+  # excess ice streams
+  # Run after initial conditions found as well as after setup_logic_exice
+  #
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+  my $use_exice = $nl_flags->{'use_excess_ice'};
+  my $excess_ice_on_finidat = $nl_flags->{'excess_ice_on_finidat'};
   my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' );
   my $finidat = $nl->get_value('finidat');
   # If coldstart and use_excess_ice is on:
   if ( ( (not defined($use_exice_streams)) && value_is_true($use_exice) ) && string_is_undef_or_empty($finidat) ) {
      $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.true.');
      $use_exice_streams = '.true.';
-     # if excess ice is turned off
+  # If an finidat file was selected and use_excess_ice is on:
+  } elsif ( (not defined($use_exice_streams)) && value_is_true($use_exice) && (not value_is_true($excess_ice_on_finidat)) ) {
+     $nl->set_variable_value('exice_streams', 'use_excess_ice_streams' , '.true.');
+     $use_exice_streams = '.true.';
+  # if excess ice is turned off
   } elsif ( (not defined($use_exice_streams)) && (not value_is_true($use_exice)) ) {
      $use_exice_streams = '.false.';
   # Checking for cold clm_start_type and not finidat here since finidat can be not set set in branch/hybrid runs and
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 31274228f8..67348d8ca2 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -886,232 +886,232 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_GSWP3v1"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_CRUv7"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam7.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- These two needs to specify use_cn=F/T since there is a version for both, other files just use the BGC version -->
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_GSWP3v1" use_cn=".false."
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_GSWP3v1" use_cn=".true."
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- These first two needs to specify use_cn=F/T since there is a version for both, other files just use the BGC version -->
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7" use_cn=".true."
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7" use_cn=".false."
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- 1850 for CLM5.1/CLM6.0 -->
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm5_1"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm5_1_GSWP3v1
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm5_1_GSWP3v1 use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1 use_excess_ice=.true.
 </init_interp_attributes>
 
 
 <!-- present day -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_GSWP3v1"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_CRUv7"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam7.0"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam6.0"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_GSWP3v1"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_GSWP3v1"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_GSWP3v1"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_GSWP3v1"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 <!-- specific low resolution grids should use the 1-degree file for just CLM5.0 -->
 <!-- matches for clm5_0 physics with CAM7.0 -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="0.9x1.25"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="4x5"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="10x15"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="1.9x2.5"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="ne3np4.pg3"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="ne5np4.pg3"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="ne16np4"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="ne16np4.pg3"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="ne30np4"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="C24"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="C48"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="C96"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- clm5_1 physics -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_cam7.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <!-- clm6_0 physics -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <!-- MPAS -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="mpasa480"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="mpasa240"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="mpasa120"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="mpasa60"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
             hgrid="mpasa30"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
             hgrid="mpasa15"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 
 <!-- Anything else should use the high resolution file, but just for CLM5.0 -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
->hgrid=ne120np4.pg3 maxpft=79 mask=tx0.1v3 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne120np4.pg3 maxpft=79 mask=tx0.1v3 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 
 <!-- If an exact match for these grids and start years -->
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- 2003 -->
 <init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- 2013 IC's - exact match for CONUS grid ... -->
 <init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
 			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
->hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 
@@ -1119,183 +1119,183 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- matches for clm5_0 physics with CAM6.0 -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="0.9x1.25"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="4x5"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="10x15"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="1.9x2.5"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="ne3np4.pg3"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="ne5np4.pg3"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="ne16np4"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="ne16np4.pg3"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="ne30np4"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="C24"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="C48"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="C96"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- clm5_1 physics -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <!-- clm6_0 physics -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <!-- MPAS -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="mpasa480"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="mpasa240"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="mpasa120"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="mpasa60"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
             hgrid="mpasa30"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
             hgrid="mpasa15"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 
 <!-- Anything else should use the high resolution file, but just for CLM5.0 -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
->hgrid=ne120np4.pg3 maxpft=79 mask=tx0.1v3 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne120np4.pg3 maxpft=79 mask=tx0.1v3 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 
 <!-- If an exact match for these grids and start years -->
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="ne0np4.ARCTIC.ne30x4" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17"
->hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- 2003 -->
 <init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- 2013 IC's - exact match for CONUS grid ... -->
 <init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
 			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
->hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false.
+>hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!--
@@ -1304,28 +1304,28 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm4_5_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm45BgcGs.0901-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm4_5_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm45BgcCruGs.1101-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm4_5_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm45BgcGs.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm4_5_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm45BgcGs.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
@@ -1333,7 +1333,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
@@ -1341,7 +1341,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
@@ -1349,28 +1349,28 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCropCru-ciso.1526-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc
 </finidat>
 
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101"  sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
@@ -1379,13 +1379,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at f09 for all clm5_1/clm6_0 options -->
 <!-- use_init_interp true because the file was created with ctsm5.3 datasets -->
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1398,7 +1398,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day crop spinup at 2-degree with irrigation on -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm4_5_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
@@ -1406,7 +1406,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- This is the same file as above but, for a different tuning mode -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm4_5_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
@@ -1414,20 +1414,20 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- This is the same file as above but, for a different tuning mode -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1436,7 +1436,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- This is the same file as above but, for a different tuning mode -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
@@ -1444,7 +1444,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup f09/f19 grid with irrigation on -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm4_5_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
@@ -1452,7 +1452,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup f09/f19 grid with irrigation on -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm4_5_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
@@ -1463,14 +1463,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 <!-- clm5_0 and cam7.0 -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
@@ -1478,7 +1478,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
@@ -1486,7 +1486,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
@@ -1494,7 +1494,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
@@ -1502,7 +1502,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
@@ -1512,7 +1512,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- clm5_1 and cam7.0 -->
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1521,7 +1521,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- clm6_0 and cam7.0 -->
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1530,7 +1530,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- clm5_0 and cam7.0 -->
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
@@ -1539,21 +1539,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm5_1 -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
@@ -1561,7 +1561,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
@@ -1569,7 +1569,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
@@ -1577,7 +1577,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
@@ -1586,7 +1586,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1594,7 +1594,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
@@ -1603,21 +1603,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm6_0 -->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
@@ -1625,7 +1625,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
@@ -1633,7 +1633,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
@@ -1641,7 +1641,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
@@ -1650,7 +1650,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1658,7 +1658,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
@@ -1667,7 +1667,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
@@ -1678,14 +1678,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 <!-- clm5_0 and cam6.0-->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
@@ -1693,7 +1693,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
@@ -1701,7 +1701,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
@@ -1709,7 +1709,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
@@ -1717,7 +1717,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
@@ -1725,7 +1725,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1733,7 +1733,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1741,7 +1741,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
@@ -1750,7 +1750,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
@@ -1758,14 +1758,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Repeat above for clm5_1 -->
 <!-- clm5_1 and cam6.0-->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
@@ -1773,7 +1773,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
@@ -1781,7 +1781,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
@@ -1789,7 +1789,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
@@ -1798,7 +1798,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1806,7 +1806,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
@@ -1815,7 +1815,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
@@ -1823,14 +1823,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Repeat above for clm6_0 -->
 <!-- clm6_0 and cam6.0-->
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
@@ -1838,7 +1838,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc
@@ -1846,7 +1846,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day no crop spinup ARCTICGRIS grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTICGRIS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc
@@ -1854,7 +1854,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day crop spinup at 1/4-degree for high resolution with irrigation on -->
 <finidat hgrid="ne120np4.pg3"    maxpft="79"  mask="tx0.1v3" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="2000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc
@@ -1863,7 +1863,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
@@ -1871,7 +1871,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false."
+         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
@@ -1880,7 +1880,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false."
+         ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc

From 77105148dc35bf0767b8ae717c2fca8a5b4c53d7 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 16 Sep 2024 01:53:20 -0600
Subject: [PATCH 1064/1248] update description

---
 doc/ChangeLog | 30 ++++++++++++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 988fe4f504..695323904a 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -7,8 +7,34 @@ One-line Summary: Update surface datasets, CN Matrix, CLM60: excess ice on, expl
 Purpose and description of changes since ctsm5.2.0
 --------------------------------------------------
 
-Changes to CTSM:
-================
+
+Changes to CTSM Infrastructure:
+===============================
+
+ - manage_externals removed and replaced by git-fleximod
+ - Ability to handle CAM7 in LND_TUNING_MODE
+
+Changes to CTSM Answers:
+========================
+ 
+ Changes to defaults for clm6_0 physics:
+  - Urban explicit A/C turned on
+  - Snow thermal conductivity is now Sturm_1997
+  - New IC file for f09 1850
+  - New crop calendars
+  - Dust emissions is now Leung_2023
+  - Excess ice is turned on
+  - Updates to MEGAN for BVOC's
+  - Updates to BGC fire method
+
+ Changes for all physics versions:
+
+  - Parameter files updated
+  - FATES parameter file updated
+  - Glacier region 1 is now undefined
+  - Update in FATES transient Land use
+  - Pass active glacier (CISM) runoff directly to river model (MOSART)
+  - Add the option for using matrix for Carbon/Nitrogen BGC spinup
 
 
 New surface datasets:

From 32897dc5ccec66e0f0382b570a0bb4af144e3045 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 17 Sep 2024 09:50:09 -0600
Subject: [PATCH 1065/1248] Changes suggested by @samrabin to get 16pft surface
 datasets to work with 78 pft fire emission files in #2759

---
 src/biogeochem/FireEmisFactorsMod.F90 | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/FireEmisFactorsMod.F90 b/src/biogeochem/FireEmisFactorsMod.F90
index e97082c0b8..31aba66fb2 100644
--- a/src/biogeochem/FireEmisFactorsMod.F90
+++ b/src/biogeochem/FireEmisFactorsMod.F90
@@ -11,6 +11,7 @@ module FireEmisFactorsMod
   use shr_kind_mod, only : r8 => shr_kind_r8
   use abortutils,   only : endrun
   use clm_varctl,   only : iulog
+  use clm_varpar,   only : maxveg
 !
   implicit none
   private
@@ -21,7 +22,7 @@ module FireEmisFactorsMod
   public :: fire_emis_factors_get
 
 ! !PRIVATE MEMBERS:
-  integer :: npfts ! number of plant function types
+  integer :: npfts ! number of plant function types on the fire emission factors dataset
 !
   type emis_eff_t
      real(r8), pointer :: eff(:) ! emissions efficiency factor
@@ -73,7 +74,9 @@ subroutine fire_emis_factors_get( comp_name, factors, molecwght )
        call endrun(errmes)
     endif
 
-    factors(:npfts) = comp_factors_table( ndx )%eff(:npfts)
+    factors(:maxveg) = comp_factors_table( ndx )%eff(:maxveg)
+    ! If fire emissions factor file only includes natural PFT's, but this is a crop case
+    ! Copy the generic crop factors to the crop CFT's from generic crop
     if ( size(factors) > npfts )then
        factors(npfts+1:) = comp_factors_table( ndx )%eff(nc3crop)
     end if
@@ -96,7 +99,6 @@ subroutine fire_emis_factors_init( filename )
     use ncdio_pio, only : ncd_pio_openfile,ncd_inqdlen
     use pio, only : pio_inq_varid,pio_get_var,file_desc_t,pio_closefile
     use fileutils   , only : getfil
-    use clm_varpar  , only : mxpft
 !
 ! !ARGUMENTS:
     character(len=*),intent(in) :: filename ! FireEmis factors input file
@@ -127,8 +129,9 @@ subroutine fire_emis_factors_init( filename )
     call ncd_inqdlen( ncid, dimid, n_pfts, name='PFT_Num')
 
     npfts = n_pfts
-    if ( npfts /= mxpft .and. npfts /= 16 )then
-       call endrun('Number of PFTs on fire emissions file is NOT correct. Its neither the total number of PFTS nor 16')
+    if ( npfts < maxveg )then
+       write(iulog,*) ' npfts = ', npfts, ' maxveg = ', maxveg
+       call endrun('Number of PFTs on the fire emissions file is less than the number of PFTs from the surface dataset')
     end if
 
     ierr = pio_inq_varid(ncid,'Comp_EF',  comp_ef_vid)

From 5f91d5c54e46c7ab2d29c6f65db4b5e637a54da2 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 17 Sep 2024 13:26:18 -0600
Subject: [PATCH 1066/1248] Fix syntax error in testlist and corect nofireemis
 testmod

---
 cime_config/testdefs/testlist_clm.xml | 36 +++++++++++++--------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 1dbfb36567..0eb3d5012d 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -31,7 +31,7 @@
       <option name="comment"  >Repeat last ERI_D_Ld9...default test with matrixcnOn</option>
     </options>
   </test>
-  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm60SpNoAnthro" testmods="clm/decStart1851_noinitial--clm/nofireemisemis">
+  <test name="SMS_D_Ld3_PS" grid="f09_g17" compset="I1850Clm60SpNoAnthro" testmods="clm/decStart1851_noinitial--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
@@ -91,7 +91,7 @@
       <option name="comment">Simple test use soil eroditability in CTSM for CAM4 tuning, at 1-degree</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/clm50cam5LndTuningModeZDustSoilErod--clm/nofireemisemis">
+  <test name="SMS_Ln9" grid="f10_f10_mg37" compset="I2000Clm50Sp" testmods="clm/clm50cam5LndTuningModeZDustSoilErod--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
@@ -195,7 +195,7 @@
       <option name="comment"  >CTSM science test list for the half degree grid with latest CLM version for historical</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis"/>
+  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -205,7 +205,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I1850Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I1850Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -215,7 +215,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS_Ln9" grid="mpasa480_mpasa480" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -225,7 +225,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -235,7 +235,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS_Ln9" grid="mpasa120_mpasa120" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -245,7 +245,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningModeLDust--clm/nofireemisemis">
+  <test name="SMS_Ln9" grid="mpasa60_mpasa60" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningModeLDust--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -255,7 +255,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="mpasa15_mpasa15" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS_Ln9" grid="mpasa15_mpasa15" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -347,7 +347,7 @@
       <option name="comment"  >Science support for 1850 with clm6_0 for SP mode at f19</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS_Ld1" grid="f09_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -357,7 +357,7 @@
       <option name="comment"  >Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS_Ld1" grid="f19_g17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -623,7 +623,7 @@
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="IHistClm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="IHistClm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -633,7 +633,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS" grid="ne3pg3_ne3pg3_mg37" compset="I2000Clm60SpRs" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -643,7 +643,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -653,7 +653,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -663,7 +663,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS" grid="ne16pg3_ne16pg3_mg17" compset="IHistClm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -673,7 +673,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30_g17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS" grid="ne30_g17" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
@@ -683,7 +683,7 @@
       <option name="comment">Also --nofireemis because this is a SP compset</option>
     </options>
   </test>
-  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemisemis">
+  <test name="SMS" grid="ne30pg2_ne30pg2_mg17" compset="I1850Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>

From d753457b0fa44784b6ba46734a8a42f0a23f9577 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 17 Sep 2024 16:55:43 -0600
Subject: [PATCH 1067/1248] Remove references to PTCLM/PTCLMmkdata.

Resolves ESCOMP/CTSM#2769.
---
 doc/source/users_guide/index.rst              |   1 -
 .../users_guide/overview/getting-help.rst     |   3 -
 .../users_guide/overview/introduction.rst     |   4 +-
 .../running-PTCLM/adding-ptclm-site-data.rst  |  88 ------------
 .../users_guide/running-PTCLM/index.rst       |  20 ---
 .../running-PTCLM/introduction-to-ptclm.rst   | 135 ------------------
 .../running-PTCLM/ptclm-examples.rst          |  33 -----
 .../users_guide/running-PTCLM/using-ptclm.rst | 114 ---------------
 ...point-and-regional-grid-configurations.rst |  11 +-
 doc/source/users_guide/testing/testing.rst    |  11 --
 .../observational-sites-datasets.rst          |   4 +-
 11 files changed, 5 insertions(+), 419 deletions(-)
 delete mode 100644 doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst
 delete mode 100644 doc/source/users_guide/running-PTCLM/index.rst
 delete mode 100644 doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst
 delete mode 100644 doc/source/users_guide/running-PTCLM/ptclm-examples.rst
 delete mode 100644 doc/source/users_guide/running-PTCLM/using-ptclm.rst

diff --git a/doc/source/users_guide/index.rst b/doc/source/users_guide/index.rst
index 75a2949bec..8c675c79db 100644
--- a/doc/source/users_guide/index.rst
+++ b/doc/source/users_guide/index.rst
@@ -24,7 +24,6 @@
    adding-new-resolutions/index.rst
    running-special-cases/index.rst
    running-single-points/index.rst
-   running-PTCLM/index.rst
    trouble-shooting/index.rst
    testing/index.rst
 
diff --git a/doc/source/users_guide/overview/getting-help.rst b/doc/source/users_guide/overview/getting-help.rst
index 74765d1ad0..7c33071db9 100644
--- a/doc/source/users_guide/overview/getting-help.rst
+++ b/doc/source/users_guide/overview/getting-help.rst
@@ -146,9 +146,6 @@ MOSART
 PFT
   Plant Function Type (PFT). A type of vegetation that CLM parameterizes.
 
-PTCLM
-  PoinT CLM (PTCLM) a python script that operates on top of CLM for |version| to run single point simulations for CLM.
-
 ROF
   River runOff Model to route flow of surface water over land out to the ocean. |cesmrelease| has two components options for this
   the new model MOSART and previous model RTM.
diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst
index bc7c1fd82c..e02fa3e422 100644
--- a/doc/source/users_guide/overview/introduction.rst
+++ b/doc/source/users_guide/overview/introduction.rst
@@ -60,9 +60,7 @@ As a followup to the tools chapter, :ref:`adding-new-resolutions-section` tells
 
 In :ref:`running-special-cases-section`, again for the expert user, we give details on how to do some particularly difficult special cases. For example, we give the protocol for spinning up the |version|-BGC and CLMCN models as well as CLM with dynamic vegetation active (CNDV). We give instructions to do a spinup case from a previous case with Coupler history output for atmospheric forcing. We also give instructions on running both the prognostic crop and irrigation models. Lastly we tell the user how to use the DATM model to send historical CO2 data to CLM.
 
-:ref:`running-single-points` outlines how to do single-point or regional simulations using |version|. This is useful to either compare |version| simulations with point observational stations, such as tower sites (which might include your own atmospheric forcing), or to do quick simulations with CLM for example to test a new parameterization. There are several different ways given on how to perform single-point simulations which range from simple PTS_MODE to more complex where you create all your own datasets, tying into :ref:`using-clm-tools-section` and also :ref:`adding-new-resolutions-section` to add the files into the build-namelist XML database. The PTCLM python script to run single-point simulations was added back in for this release (but it has bugs that don't allow it to work out of the box). CLM4 in CESM1.0.5 has a fully working versions of PTCLM.
-
-Need :ref:`running-PTCLM` blurb...
+:ref:`running-single-points` outlines how to do single-point or regional simulations using |version|. This is useful to either compare |version| simulations with point observational stations, such as tower sites (which might include your own atmospheric forcing), or to do quick simulations with CLM for example to test a new parameterization. There are several different ways given on how to perform single-point simulations which range from simple PTS_MODE to more complex where you create all your own datasets, tying into :ref:`using-clm-tools-section` and also :ref:`adding-new-resolutions-section` to add the files into the build-namelist XML database.
 
 :ref:`troubleshooting-index` gives some guidance on trouble-shooting problems when using |version|. It doesn't cover all possible problems with CLM, but gives you some guidelines for things that can be done for some common problems.
 
diff --git a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst
deleted file mode 100644
index b95831427f..0000000000
--- a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst
+++ /dev/null
@@ -1,88 +0,0 @@
-.. include:: ../substitutions.rst
-
-.. _adding-ptclm-site-data:
-
-============================
-Adding PTCLMmkdata Site Data
-============================
-
-The "sitegroupname" option to PTCLMmkdata looks for groups of sites in the files in the ``PTCLM_sitedata`` directory under the PTCLMmkdata directory. You can add new names available for this option including your own lists of sites, by adding more files in this directory. There are three files for each "sitegroupname": ``$SITEGROUP_sitedata.txt``, ``$SITEGROUP_soildata.txt`` and ``$SITEGROUP_pftdata.txt`` (where ``$SITEGROUP`` is the name that would be entered as "sitegroupname" to PTCLMmkdata). Each file needs to have the same list of sites, but gives different information: site data, PFT data, and soil data respectively. Although the site codes need to be the same between the three files, the files do NOT have to be in the same order. Each file has a one-line header that lists the contents of each column which are separated by commas. The first column for each of the files is the "site_code" which must be consistent between the three files. The site code can be any unique character string, but in general we use the AmeriFlux site code.
-
-Site data file:`` $SITEGROUP_sitedata.txt``): The header for this file is:
-::
-
-   site_code,name,state,lon,lat,elev,startyear,endyear,alignyear
-
-The columns: name, state, and elevation are informational only. Name is a longer descriptive name of the site, and state is the state for U.S. sites or country for non U.S. sites. The columns: lon and lat are the longitude and latitude of the location in decimal degrees. The last three columns are the start and ending year for the data and the align year for an 1850 case for the data. The align year is currently unused.
-
-Soil data file: ``$SITEGROUP_soildata.txt``): The header for this file is:
-::
-
-   site_code,soil_depth,n_layers,layer_depth,layer_sand%,layer_clay%
-
-The first three fields after "site_code" are currently unused. The only two that are used are the percent sand and clay columns to set the soil texture.
-
-PFT data file: ``$SITEGROUP_pftdata.txt```): The header for this file is:
-::
-
-   site_code,pft_f1,pft_c1,pft_f2,pft_c2,pft_f3,pft_c3,pft_f4,pft_c4,pft_f5,pft_c5
-
-This file gives the vegetation coverage for the different vegetation types for the site. The file only supports up to five PFT's at the same time. The columns with "pft_f" are the fractions for each PFT, and the columns with "pft_c" is the integer index of the given PFT. Look at the pft-physiology file to see what the PFT index for each PFT type is.
-
-----------------------------------------------------
-Dynamic Land-Use Change Files for use by PTCLMmkdata
-----------------------------------------------------
-
-There is a mechanism for giving site-specific land-use change in PTCLMmkdata. Adding site specific files to the ``PTCLM_sitedata`` directory under PTCLMmkdata allows you to specify the change in vegetation and change in harvesting (for the CN model) for that site. Files are named: ``$SITE_dynpftdata.txt``. There is a sample file for the US-Ha1 site called: ``US-Ha1_dynpftdata.txt``. The file has a one-line header with the information that the file has, and then one-line for each year with a transition. The header line is as follows:
-::
-
-   trans_year,pft_f1,pft_c1,pft_f2,pft_c2,pft_f3,pft_c3,pft_f4,pft_c4,pft_f5,pft_c5,har_vh1,har_vh2,har_sh1,har_sh2,har_sh3,graze,hold_harv,hold_graze
-
-This file only requires a line for each year where a transition or harvest happens. As in the "pftdata" file above "pft_f" refers to the fraction and "pft_c" refers to the PFT index, and only up to five vegetation types are allowed to co-exist. The last eight columns have to do with harvesting and grazing. The last two columns are whether to hold harvesting and/or grazing constant until the next transition year and will just be either 1 or 0. This file will be converted by the **PTCLM_sitedata/cnvrt_trnsyrs2_pftdyntxtfile.pl** script in the PTCLMmkdata directory to a format that **mksurfdata_esmf** can read that has an entry for each year for the range of years valid for the compset in question.
-
-.. _converting-ameriflux-for-ptclmmkdata:
-
-------------------------------------------------
-Converting AmeriFlux Data for use by PTCLMmkdata
-------------------------------------------------
-
-AmeriFlux data comes in comma separated format and is available from: `http://public.ornl.gov/ameriflux/dataproducts.shtml <http://public.ornl.gov/ameriflux/dataproducts.shtml>`_. Before you download the data you need to agree to the usage terms.
-
-Here is a copy of the usage terms from the web-site on June/13/2011.
-
-"The AmeriFlux data provided on this site are freely available and were furnished by individual AmeriFlux scientists who encourage their use. Please kindly inform the appropriate AmeriFlux scientist(s) of how you are using the data and of any publication plans. Please acknowledge the data source as a citation or in the acknowledgments if the data are not yet published. If the AmeriFlux Principal Investigators (PIs) feel that they should be acknowledged or offered participation as authors, they will let you know and we assume that an agreement on such matters will be reached before publishing and/or use of the data for publication. If your work directly competes with the PI's analysis they may ask that they have the opportunity to submit a manuscript before you submit one that uses unpublished data. In addition, when publishing, please acknowledge the agency that supported the research. Lastly, we kindly request that those publishing papers using AmeriFlux data provide preprints to the PIs providing the data and to the data archive at the Carbon Dioxide Information Analysis Center (CDIAC)."
-
-The above agreement applies to the "US-UMB" dataset imported into our repository as well, and Gil Bohrer is the PI on record for that dataset.
-
-The CESM can NOT handle missing data, so we recommend using the "Level 4" Gap filled datasets. The fields will also need to be renamed. The "WS" column becomes "WIND", "PREC" becomes "PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes "FLDS", "PRESS" becomes "PSRF". "ZBOT" can just be set to the constant of "30" (m). The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the value in ``SHR_CONST_TKFRZ`` in the file ``models/csm_share/shr/shr_const.F90`` of ``273.15``. The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and LONGXY should also be set to the latitude and longitude of the site.
-
------------------------------------------------------------------
-Example: PTCLMmkdata transient example over a shorter time period
------------------------------------------------------------------
-
-This is an example of using PTCLMmkdata for Harvard Forest (AmeriFlux site code US-Ha1) for transient land use 1991-2006. In order to do this we would've needed to have converted the AmeriFlux data into NetCDF format as shown in :ref:`converting-ameriflux-for-ptclmmkdata` section above. Also note that this site has a site-specific dynamic land-use change file for it ``PTCLM_sitedata/US-Ha1_dynpftdata.txt`` in the PTCLMmkdata directory and this file will be used for land-use change and harvesting rather than the global dataset.
-
-::
-
-     > cd $CTSMROOT/tools/PTCLM
-     # We are going to use forcing data over 1991 to 2006, but we need to start with
-     # a transient compset to do so, so we use the 20th Century transient: 1850-2000
-     # Note: When creating the fpftdyn dataset for this site it will use the
-     #     PTCLM_sitedata/US-Ha1_dynpftdata.txt
-     # file for land-use change and harvesting
-     > ./PTCLMmkdata -s US-Ha1 -d $MYCSMDATA --sitegroupname AmeriFlux
-     > mkdir $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1
-     > cd $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1
-     # Copy data in NetCDF format to this directory, filenames should be YYYY-MM.nc
-     # The fieldnames on the file should be:
-     #    FLDS,FSDS,LATIXY,   LONGXY,   PRECTmms,PSRF,RH,TBOT,WIND,ZBOT
-     # With units
-     #    W/m2,W/m2,degrees_N,degrees_E,mm/s,    Pa,  %, K,   m/s, m
-     # The time coordinate units should be: days since YYYY-MM-DD 00:00:00
-     > cd ../../../../../US-Ha1_I20TRCRUCLM45BGC
-     # Now we need to set the start date to 1991, and make sure the align year is for 1991
-     > ./xmlchange RUN_STARTDATE=1991-01-01,DATM_CLMNCEP_YR_ALIGN=1991
-     # Similarly for Nitrogen deposition data we cycle over: 1991 to 2006
-     > cat << EOF >> user_nl_clm
-     model_year_align_ndep=1991,stream_year_first_ndep=1991,stream_year_last_ndep=2006
-     EOF
diff --git a/doc/source/users_guide/running-PTCLM/index.rst b/doc/source/users_guide/running-PTCLM/index.rst
deleted file mode 100644
index 0b44c01b49..0000000000
--- a/doc/source/users_guide/running-PTCLM/index.rst
+++ /dev/null
@@ -1,20 +0,0 @@
-.. on documentation master file, created by
-   sphinx-quickstart on Tue Jan 31 19:46:36 2017.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-.. include:: ../substitutions.rst
-
-.. _running-PTCLM:
-
-#####################################
-Running PTCLM
-#####################################
-
-.. toctree::
-   :maxdepth: 2
-
-   introduction-to-ptclm.rst
-   using-ptclm.rst
-   ptclm-examples.rst
-   adding-ptclm-site-data.rst
diff --git a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst
deleted file mode 100644
index 9ae4186d2c..0000000000
--- a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst
+++ /dev/null
@@ -1,135 +0,0 @@
-.. _introduction-to-ptclm.rst:
-
-.. include:: ../substitutions.rst
-
-.. _what-is-ptclm:
-
-=====================
- What is PTCLMmkdata?
-=====================
-
-PTCLMmkdata (pronounced Pee-Tee Cee-L-M make data is a Python script to help you set up PoinT CLM simulations.
-
-It runs the CLM tools for you to get datasets set up, and copies them to a location you can use them including the changes needed for a case to use the dataset with namelist and XML changes.
-
-Then you run **create_newcase** and point to the directory so that the namelist and XML changes are automatically applied.
-
-PTCLMmkdata has a simple ASCII text file for storing basic information for your sites.
-
-We also have complete lists for AmeriFlux and Fluxnet-Canada sites, although we only have the meteorology data for one site.
-
-For other sites you will need to obtain the meteorology data and translate it to a format that the CESM datm model can use.
-
-But, even without meteorology data PTCLMmkdata is useful to setup datasets to run with standard ``CLM_QIAN`` data.
-
-The original authors of PTCLMmkdata are: Daniel M. Ricciuto, Dali Wang, Peter E. Thornton, Wilfred M. Post all at Environmental Sciences Division, Oak Ridge National Laboratory (ORNL) and R. Quinn Thomas at Cornell University. It was then modified fairly extensively by Erik Kluzek at NCAR. We want to thank all of these individuals for this contribution to the CESM effort. We also want to thank the folks at University of Michigan Biological Stations (US-UMB) who allowed us to use their Fluxnet station data and import it into our inputdata repository, especially Gil Bohrer the PI on record for this site.
-
-.. _details-of-ptclm:
-
-=======================
- Details of PTCLMmkdata
-=======================
-
-To get help on PTCLM2_180611 use the "--help" option as follows.
-::
-
-   > cd $CTSMROOT/tools/PTCLM
-   > ./PTCLMmkdata --help
-
-The output to the above command is as follows:
-::
-
-   Usage: PTCLM.py [options] -d inputdatadir -m machine -s sitename
-
-   Python script to create cases to run single point simulations with tower site data.
-
-   Options:
-      --version             show program's version number and exit
-      -h, --help            show this help message and exit
-
-  Required Options:
-    -d CCSM_INPUT, --csmdata=CCSM_INPUT
-                        Location of CCSM input data
-    -m MYMACHINE, --machine=MYMACHINE
-                        Machine, valid CESM script machine (-m list to list valid
-                        machines)
-    -s MYSITE, --site=MYSITE
-                        Site-code to run, FLUXNET code or CLM1PT name (-s list to list
-                        valid names)
-
-  Configure and Run Options:
-    -c MYCOMPSET, --compset=MYCOMPSET
-                        Compset for CCSM simulation (Must be a valid 'I' compset [other
-                        than IG compsets], use -c list to list valid compsets)
-    --coldstart         Do a coldstart with arbitrary initial conditions
-    --caseidprefix=MYCASEID
-                        Unique identifier to include as a prefix to the case name
-    --cesm_root=BASE_CESM
-                        Root CESM directory (top level directory with models and scripts
-                        subdirs)
-    --debug             Flag to turn on debug mode so won't run, but display what would
-                        happen
-    --finidat=FINIDAT   Name of finidat initial conditions file to start CLM from
-    --list              List all valid: sites, compsets, and machines
-    --namelist=NAMELIST
-                        List of namelist items to add to CLM namelist (example:
-                        --namelist="hist_fincl1='TG',hist_nhtfrq=-1"
-    --QIAN_tower_yrs    Use the QIAN forcing data year that correspond to the tower
-                        years
-    --rmold             Remove the old case directory before starting
-    --run_n=MYRUN_N     Number of time units to run simulation
-    --run_units=MYRUN_UNITS
-                        Time units to run simulation (steps,days,years, etc.)
-    --quiet             Print minimul information on what the script is doing
-    --sitegroupname=SITEGROUP
-                        Name of the group of sites to search for you selected site in
-                        (look for prefix group names in the PTCLM_sitedata directory)
-    --stdurbpt          If you want to setup for standard urban namelist settings
-    --useQIAN           use QIAN input forcing data instead of tower site meterology data
-    --verbose           Print out extra information on what the script is doing
-
-  Input data generation options:
-    These are options having to do with generation of input datasets.  Note: When
-    running for supported CLM1PT single-point datasets you can NOT generate new
-    datasets.  For supported CLM1PT single-point datasets, you MUST run with the
-    following settings: --nopointdata And you must NOT set any of these: --soilgrid
-    --pftgrid --owritesrf
-
-    --nopointdata       Do NOT make point data (use data already created)
-    --owritesrf         Overwrite the existing surface datasets if they exist (normally
-                        do NOT recreate them)
-    --pftgrid           Use pft information from global gridded file (rather than site
-                        data)
-    --soilgrid          Use soil information from global gridded file (rather than site
-                        data)
-
-  Main Script Version Id: $Id: PTCLM.py 47576 2013-05-29 19:11:16Z erik $ Scripts URL: $HeadURL: https://svn-ccsm-models.cgd.ucar.edu/PTCLM/trunk_tags/PTCLM1_130529/PTCLM.py $:
-
-Here we give a simple example of using PTCLMmkdata for a straightforward case of running at the US-UMB Fluxnet site on cheyenne where we already have the meteorology data on the machine. Note, see :ref:`converting-ameriflux-for-ptclmmkdata` for permission information to use this data.
-
-Example 6-1. Example of running PTCLMmkdata for US-UMB on cheyenne
-------------------------------------------------------------------
-::
-
-   > setenv CSMDATA   $CESMDATAROOT/inputdata
-   > setenv MYDATAFILES `pwd`/mydatafiles
-   > setenv SITE      US-UMB
-   > setenv MYCASE    testPTCLM
-
-   # Next build all of the clm tools you will need
-   > cd $CTSMROOT/tools/PTCLM
-   > buildtools
-   # next run PTCLM (NOTE -- MAKE SURE python IS IN YOUR PATH)
-   > cd $CTSMROOT/tools/PTCLM
-   # Here we run it using qcmd so that it will be run on a batch node
-   > qcmd --  ./PTCLMmkdata --site=$SITE --csmdata=$CSMDATA --mydatadir=$MYDATAFILES >& ptclmrun.log &
-   > cd $CIMEROOT/scripts
-   > ./create_newcase --user-mods-dir $MYDATAFILES/1x1pt_$SITE --case $MYCASE --res CLM_USRDAT --compset I1PtClm50SpGs
-   # Next setup, build and run as normal
-   > cd $MYCASE
-   > ./case.setup
-
-PTCLMmkdata includes a README file that gives some extra details and a simple example.
-
-.. include:: ../../../../tools/PTCLM/README
-   :literal:
diff --git a/doc/source/users_guide/running-PTCLM/ptclm-examples.rst b/doc/source/users_guide/running-PTCLM/ptclm-examples.rst
deleted file mode 100644
index 6801c5f3d8..0000000000
--- a/doc/source/users_guide/running-PTCLM/ptclm-examples.rst
+++ /dev/null
@@ -1,33 +0,0 @@
-.. include:: ../substitutions.rst
-
-.. _ptclm-examples:
-
-==============================
- Examples of using PTCLMmkdata
-==============================
-
-Now let's give a few more complex examples using some of the options we have discussed above.
-
-Now, let's demonstrate using a different group list, doing a spinup, running with Qian global forcing data, but using tower years to set the years to run over. This uses the options: sitegroupname, useQIAN, and QIANtower_years.
-
-Example: Running PTCLMmkdata without tower years
-------------------------------------------------
-::
-
-   > cd $CTSMROOT/tools/PTCLM
-   > ./PTCLMmkdata -s US-Ha1 -d $CSMDATA --sitegroupname AmeriFlux --donot_use_tower_yrs
-   > cd ../../../../../US-Ha1_ICRUCLM45BGC_QIAN
-   # Now build and run normally
-   ```
-
-Finally, let's demonstrate using a generic machine (which then requires the scratchroot option), using the global grid for PFT and soil types, and setting the run length to two months.
-
-Example: Running PTCLMmkdata with global PFT and soil types dataset
--------------------------------------------------------------------
-::
-
-   > cd $CTSMROOT/tools/PTCLM
-   # Note, see the the Section called Converting AmeriFlux Data for use by PTCLMmkdata with permission information
-   # to use the US-UMB data.
-   > ./PTCLMmkdata -s US-UMB -d $CSMDATA --pftgrid --soilgrid
-   > cd ../../../../../US-UMB_ICRUCLM45BGC
diff --git a/doc/source/users_guide/running-PTCLM/using-ptclm.rst b/doc/source/users_guide/running-PTCLM/using-ptclm.rst
deleted file mode 100644
index e7be79bee6..0000000000
--- a/doc/source/users_guide/running-PTCLM/using-ptclm.rst
+++ /dev/null
@@ -1,114 +0,0 @@
-.. include:: ../substitutions.rst
-
-.. _using-ptclm.rst:
-
-**************************
-Using PTCLMmkdata
-**************************
-
-There are two types of options to PTCLMmkdata: required and optional. The three required options are the three settings that MUST be specified for PTCLMmkdata to work at all. The other settings have default values that will default to something useful. Most options use a double dash "--" "longname" such as "--list", but the most common options also have a short-name with a single dash.
-
-The required options to PTCLMmkdata are: inputdata directory (-d) and site-name (-s). Inputdata directory is the directory where you have the CESM inputdata files. Finally site-name is the name of the site that you want to run for. Site-name is a Fluxnet site name from the list of sites you are running on (see the --sitegroupname for more information about the site lists).
-
-After PTCLMmkdata is run you can run **create_newcase** to setup a case to use the datasets created. It also creates a ``README.PTCLM`` in that directory that documents the commandline options to PTCLMmkdata that were used to create it.
-
-After "help" the "list" option is one of the most useful options for getting help on using PTCLMmkdata. This option gives you information about some of the other options to PTCLMmkdata. To get a list of the sites that can be used for PTCLMmkdata use the "--list" option as follows.
-::
-
-   > cd $CTSMROOT/tools/PTCLM
-   > ./PTCLMmkdata --list
-
-The output to the above command is as follows:
-::
-
-   /bin/sh: line 1: PTCLMmkdata: command not found
-
-Steps in running PTCLMmkdata
-============================
-
-1. Build the CLM tools Next you need to make sure all the CLM FORTRAN tools are built.
-   ::
-
-      > cd $CTSMROOT/tools/PTCLM
-      > ./buildtools
-      > gmake clean
-
-2. Run PTCLMmkdata Next you actually run PTCLMmkdata which does the different things listed below:
-
-   a. PTCLMmkdata names your output file directory based on your input
-      ::
-
-	 [Prefix_]SiteCode
-
-      Where:
-	 ``Prefix`` is from the caseidprefix option (or blank if not used).
-
-	 ``SiteCode`` is the site name you entered with the -s option.
-
-      For example, the casename for the following will be:
-      ::
-
-	 > cd scripts
-	 > ./PTCLMmkdata -s US-UMB -d $MYCSMDATA
-
-   b. PTCLMmkdata creates datasets for you It will populate $MYCSMDATA with new datasets it creates using the CLM tools.
-
-   c. If a transient compset and PTCLMmkdata finds a _dynpftdata.txt file If you are running a transient compset (such as the "I_1850-2000_CN" compset) AND you there is a file in the PTCLM_sitedata directory under the PTCLMmkdata directory called $SITE_dynpftdata.txt it will use this file for the land-use changes. Otherwise it will leave land-use constant, unless you use the pftgrid option so it uses the global dataset for landuse changes. See the Section called Dynamic Land-Use Change Files for use by PTCLMmkdata for more information on this. There is a sample transient dataset called US-Ha1_dynpftdata.txt. Transient compsets, are compsets that create transient land-use change and forcing conditions such as: 'I_1850-2000', 'I_1850-2000_CN', 'I_RCP8.5_CN', 'I_RCP6.0_CN', 'I_RCP4.5_CN', or 'I_RCP2.6_CN'.
-
-   d. PTCLMmkdata creates a pft-physiology for you PTCLMmkdata will create a local copy of the pft-physiology specific for your site that you could then customize with changes specific for that site.
-
-   e. PTCLMmkdata creates a README.PTCLM for you PTCLMmkdata will create a simple text file with the command line for it in a file called README.PTCLM in the case directory it creates for you.
-
-3. Run create_newcase pointing to the directory created
-
-4. Customize, setup, build and run case as normal You then customize your case as you would normally. See the Chapter 1 chapter for more information on doing this.
-
-PTCLMmkdata options
-=========================
-
-Next we discuss the setup and run-time options, dividing them up into setup, initial condition (IC), and run-time options.
-
-Configure options include:
-
-- --cesm_root=BASE_CESM
-- --sitegroupname=SITEGROUP
-- --donot_use_tower_yrs
-
-``--cesm_root``
-  This option is for running PTCLMmkdata with a different root directory to CESM than the version PTCLMmkdata exists in. Normally you do NOT need to use this option.
-
-``--sitegroupname``
-  In the PTCLMmkdata directory there is a subdirectory "PTCLM_sitedata" that contains files with the site, PFT and soil data information for groups of sites. These site groups are all separate ASCII files with the same prefix followed by a "_*data.txt" name. See :ref:`adding-ptclm-site-data` for more information on these files. By default we have provided three different valid group names:
-
-EXAMPLE
--------
-AmeriFlux
-
-Fluxnet-Canada
-
-The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that is the only site we have data provided for. The other two site groups include the site information for all of both the AmeriFlux and Fluxnet-Canada sites. You can use the "sitegroupname" option to use one of the other lists, or you can create your own lists using the EXAMPLE file as an example. Your list of sites could be real world locations or could be theoretical "virtual" sites given to exercise CLM on differing biomes for example. Note, see :ref:`converting-ameriflux-for-ptclmmkdata` with permission information to use the US-UMB data.
-
-``--donot_use_tower_yrs``
-  This option is used with the "useQIAN" option to set the years to cycle over for the Qian data. In this case Qian atmospheric forcing will be used, but the simulation will run over the same years that tower site is available for this site.
-
-**Run-time options include:**
-
-- --debug
-
-This option tells PTCLMmkdata to echo what it would do if it were run, but NOT actually run anything. So it will show you the dataset creation commands it would use. It does however, run **create_newcase**, but then it only displays the **xmlchange** commands and changes that it would do. Also note that if you give the "--rmold" option it won't delete the case directory beforehand. Primarily this is intended for debugging the operation of PTCLMmkdata.
-
-**The dataset generation options are:**
-
-- --pftgrid
-- --soilgrid
-
-The options that with a "grid" suffix all mean to create datasets using the global gridded information rather than using the site specific point data. By default the site specific point data is used. The "nopointdata" and "owritesrfaer" options have to do with file creation.
-
-Because supported single-point datasets already have the data created for them, you MUST use the "nopointdata" and "ndepgrid" options when you are using a supported single-point site. You must use "ndepgrid" even for a compset without CN. You also can NOT use the options: "soilgrid", "pftgrid", "aerdepgrid", or "owritesrfaer".
-
-``--pftgrid``
-  This option says to use the PFT values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_pftdata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset.
-
-``--soilgrid``
-  This option says to use the soil values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_soildata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset.
-
diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
index 34a199ebe8..ab7e923669 100644
--- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
+++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
@@ -8,7 +8,7 @@ Single and Regional Grid Configurations
 
 CLM allows you to set up and run cases with a single-point or a local region as well as global resolutions. This is often useful for running quick cases for testing, evaluating specific vegetation types, or land-units, or running with observed data for a specific site.
 
-There are three different ways to do this for normal-supported site
+There are two different ways to do this for normal-supported site
 
 ``PTS_MODE``
   runs for a single point using global datasets.
@@ -16,11 +16,6 @@ There are three different ways to do this for normal-supported site
 ``CLM_USRDAT_NAME``
   runs using your own datasets (single-point or regional).
 
-``PTCLMmkdata``
-  easily setup simulations to run for tower sites..
-
-.. note:: ``PTS_MODE`` and ``PTCLMmkdata`` only works for a single point, while the other two options can also work for regional datasets as well.
-
 .. _options-for-single-points:
 
 =========================================
@@ -33,7 +28,5 @@ In general :ref:`pts_mode` is the quick and dirty method that gets you started w
 
 Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see :ref:`running-single-point-datasets`). With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method.
 
-Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. A big advantage to it, is that it's one-stop shopping, it runs tools to create datasets, and runs **create_newcase** and sets the appropriate env variables for you. So you only have to learn how to run one tool, rather than work with many different ones. PTCLMmkdata is described in the next chapter, :ref:`running-PTCLM`.
-
-Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in :ref:`creating-your-own-singlepoint-dataset`. You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use. :ref:`converting-ameriflux-for-ptclmmkdata` tells you how to use AmeriFlux data for atmospheric forcing.
+Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in :ref:`creating-your-own-singlepoint-dataset`. You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use.
 
diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst
index 69ca1f7263..ec959d4b82 100644
--- a/doc/source/users_guide/testing/testing.rst
+++ b/doc/source/users_guide/testing/testing.rst
@@ -36,14 +36,3 @@ If something went wrong, you can find the failing tests like so:
 ::
 
    > grep -E "^[0-9]+/[0-9]+ < [a-zA-Z]+" namelist_test.log | grep -v "PASS"
-
-Testing PTCLM
-=============
-
-.. include:: ../../../../tools/PTCLM/README
-   :literal:
-
-To run on cheyenne, you do the following:
-
-.. include:: ../../../../tools/PTCLM/test/README.run_cheyenne
-   :literal:
diff --git a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst
index 50a7969281..05fe461db2 100644
--- a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst
+++ b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst
@@ -6,6 +6,6 @@
 Observational Sites Datasets
 *******************************
 
-There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to overwrite the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In Table :numref:`reqd-files-table` we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: ``fatmlndfrc``, ``fsurdat``, ``faerdep`` (for DATM), and ``stream_fldfilename_ndep``. Note ``mksurfdata_esmf`` as documented previously has options to overwrite the vegetation and soil types. For more information on this also see :ref:`creating-your-own-singlepoint-dataset`. ``PTCLM`` uses these methods to customize datasets; see Chapter :numref:`running-PTCLM`.
+There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to overwrite the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In Table :numref:`reqd-files-table` we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: ``fatmlndfrc``, ``fsurdat``, ``faerdep`` (for DATM), and ``stream_fldfilename_ndep``. Note ``mksurfdata_esmf`` as documented previously has options to overwrite the vegetation and soil types. For more information on this also see :ref:`creating-your-own-singlepoint-dataset`.
 
-Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets; see :ref:`creating-your-own-singlepoint-dataset` for more information on this. :ref:`converting-ameriflux-for-ptclmmkdata` has information on using the AmeriFlux tower site data as atmospheric forcing.
+Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets; see :ref:`creating-your-own-singlepoint-dataset` for more information on this.

From c26ac543735047be12592e6b683e845563eca78d Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 17 Sep 2024 17:06:27 -0600
Subject: [PATCH 1068/1248] Use double-backticks instead of double-hyphens in
 one instance.

---
 doc/source/users_guide/trouble-shooting/trouble-shooting.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
index e139796f71..93798c3c57 100644
--- a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
+++ b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
@@ -152,7 +152,7 @@ Here are some other suggestions on how to track down a problem encountered while
 Run with a smaller set of processors
 ------------------------------------
 
-One way to simplify the system is to run with a smaller set of processors. You will need to clean the setup and edit the --env_mach_pes.xml--. For example, to run with four processors:
+One way to simplify the system is to run with a smaller set of processors. You will need to clean the setup and edit ``env_mach_pes.xml``. For example, to run with four processors:
 ::
 
    > ./case.setup -clean

From fbce6564046b2f72352d3078a7704ec9d38f6fc0 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@izumi.cgd.ucar.edu>
Date: Tue, 17 Sep 2024 11:10:07 -0600
Subject: [PATCH 1069/1248] Fix comments on urban thermal variables

---
 src/biogeophys/SoilTemperatureMod.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90
index 0dc8876d24..d6c9660b96 100644
--- a/src/biogeophys/SoilTemperatureMod.F90
+++ b/src/biogeophys/SoilTemperatureMod.F90
@@ -671,9 +671,9 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter
          tk_wall      =>    urbanparams_inst%tk_wall	     , & ! Input:  [real(r8) (:,:) ]  thermal conductivity of urban wall    
          tk_roof      =>    urbanparams_inst%tk_roof	     , & ! Input:  [real(r8) (:,:) ]  thermal conductivity of urban roof    
          tk_improad   =>    urbanparams_inst%tk_improad	     , & ! Input:  [real(r8) (:,:) ]  thermal conductivity of urban impervious road
-         cv_wall      =>    urbanparams_inst%cv_wall	     , & ! Input:  [real(r8) (:,:) ]  thermal conductivity of urban wall    
-         cv_roof      =>    urbanparams_inst%cv_roof	     , & ! Input:  [real(r8) (:,:) ]  thermal conductivity of urban roof    
-         cv_improad   =>    urbanparams_inst%cv_improad	     , & ! Input:  [real(r8) (:,:) ]  thermal conductivity of urban impervious road
+         cv_wall      =>    urbanparams_inst%cv_wall	     , & ! Input:  [real(r8) (:,:) ]  heat capacity of urban wall    
+         cv_roof      =>    urbanparams_inst%cv_roof	     , & ! Input:  [real(r8) (:,:) ]  heat capacity of urban roof    
+         cv_improad   =>    urbanparams_inst%cv_improad	     , & ! Input:  [real(r8) (:,:) ]  heat capacity of urban impervious road
          
          t_soisno     =>    temperature_inst%t_soisno_col    , & ! Input:  [real(r8) (:,:) ]  soil temperature [K]             
          

From f25a251e58f06bc39484c4687f9daeeef14ba1c1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 22 Mar 2024 11:24:28 -0600
Subject: [PATCH 1070/1248] Fix two hillslope error messages.

---
 src/biogeophys/HillslopeHydrologyMod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeophys/HillslopeHydrologyMod.F90 b/src/biogeophys/HillslopeHydrologyMod.F90
index b2866df679..1fed9b28bb 100644
--- a/src/biogeophys/HillslopeHydrologyMod.F90
+++ b/src/biogeophys/HillslopeHydrologyMod.F90
@@ -335,7 +335,7 @@ subroutine InitHillslope(bounds,fsurdat)
     enddo
     call ncd_io(ncid=ncid, varname='hillslope_distance', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_length not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_distance not found on surface data set.'//errmsg(sourcefile, __LINE__) )
     end if
 
     do l = bounds%begl,bounds%endl
@@ -354,7 +354,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='hillslope_elevation', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_height not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_elevation not found on surface data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)

From b6dd9f986a212c142a609e04986e6978f901136c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 22 Mar 2024 12:12:58 -0600
Subject: [PATCH 1071/1248] Move hillslope variables from fsurdat to
 hillslope_file.

---
 bld/CLMBuildNamelist.pm                       |  4 ++
 .../namelist_definition_ctsm.xml              |  5 ++
 .../testmods_dirs/clm/Hillslope/user_nl_clm   |  2 +-
 src/biogeophys/HillslopeHydrologyMod.F90      | 52 +++++++++----------
 src/main/clm_initializeMod.F90                |  8 +--
 src/main/clm_instMod.F90                      |  4 +-
 src/main/clm_varctl.F90                       |  1 +
 src/main/controlMod.F90                       |  8 ++-
 src/main/histFileMod.F90                      |  3 ++
 src/main/restFileMod.F90                      |  2 +
 src/main/surfrdMod.F90                        | 26 +++++++---
 11 files changed, 74 insertions(+), 41 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 86b9943f34..dc89e932ca 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -3624,6 +3624,10 @@ sub setup_logic_hillslope {
   if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
       $log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
   }
+  my $hillslope_file = $nl->get_value('hillslope_file');
+  if ( &value_is_true($use_hillslope) && ( ! defined($hillslope_file) ) ) {
+    $log->fatal_error("You must provide hillslope_file if use_hillslope is .true.\n" );
+  }
 }
 
 #-------------------------------------------------------------------------------
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index d2347121c1..d8cb2586cd 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -946,6 +946,11 @@ Full pathname datafile with fates parameters
 Full pathname of surface data file.
 </entry>
 
+<entry id="hillslope_file" type="char*256"     category="datasets"
+       input_pathname="abs" group="clm_inparm" valid_values="" >
+Full pathname of hillslope data file.
+</entry>
+
 <entry id="fsnowoptics" type="char*256" category="datasets" 
        input_pathname="abs" group="clm_inparm" valid_values="" >
 SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name
diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
index 4fc6fc2373..c750400672 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
@@ -6,6 +6,6 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240216.synthetic_hillslopes.nc'
+hillslope_file = '$DIN_LOC_ROOT/lnd/clm2/testdata/synthetic_cosphill_1.3.nc'
 
 use_ssre = .false.
diff --git a/src/biogeophys/HillslopeHydrologyMod.F90 b/src/biogeophys/HillslopeHydrologyMod.F90
index 1fed9b28bb..8fccd762f0 100644
--- a/src/biogeophys/HillslopeHydrologyMod.F90
+++ b/src/biogeophys/HillslopeHydrologyMod.F90
@@ -168,7 +168,7 @@ end subroutine check_aquifer_layer
 
   !-----------------------------------------------------------------------
 
-  subroutine InitHillslope(bounds,fsurdat)
+  subroutine InitHillslope(bounds, hillslope_file)
     !
     ! !DESCRIPTION:
     ! Initialize hillslope geomorphology from input dataset
@@ -187,7 +187,7 @@ subroutine InitHillslope(bounds,fsurdat)
     !
     ! !ARGUMENTS:
     type(bounds_type), intent(in) :: bounds
-    character(len=*) , intent(in) :: fsurdat    ! surface data file name
+    character(len=*) , intent(in) :: hillslope_file    ! hillslope data file name
     integer,  pointer     :: ihillslope_in(:,:) ! read in - integer
     integer,  pointer     :: ncolumns_hillslope_in(:) ! read in number of columns
     integer,  allocatable :: ncolumns_hillslope(:)    ! number of hillslope columns
@@ -224,9 +224,9 @@ subroutine InitHillslope(bounds,fsurdat)
     ! consistency check
     call check_aquifer_layer()
 
-    ! Open surface dataset to read in data below
+    ! Open hillslope dataset to read in data below
 
-    call getfil (fsurdat, locfn, 0)
+    call getfil (hillslope_file, locfn, 0)
     call ncd_pio_openfile (ncid, locfn, 0)
 
     allocate( &
@@ -248,7 +248,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='nhillcolumns', flag='read', data=ncolumns_hillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: nhillcolumns not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: nhillcolumns not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -266,7 +266,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='pct_hillslope', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: pct_hillslope not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: pct_hillslope not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -278,7 +278,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='hillslope_index', flag='read', data=ihillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_index not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_index not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -287,7 +287,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='column_index', flag='read', data=ihillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: column_index not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: column_index not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -296,7 +296,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='downhill_column_index', flag='read', data=ihillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: downhill_column_index not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: downhill_column_index not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -307,7 +307,7 @@ subroutine InitHillslope(bounds,fsurdat)
     allocate(fhillslope_in(bounds%begg:bounds%endg,max_columns_hillslope))
     call ncd_io(ncid=ncid, varname='hillslope_slope', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_slope not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_slope not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
 
     do l = bounds%begl,bounds%endl
@@ -317,7 +317,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='hillslope_aspect', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_aspect not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_aspect not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
 
     do l = bounds%begl,bounds%endl
@@ -327,7 +327,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='hillslope_area', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_area not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_area not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -335,7 +335,7 @@ subroutine InitHillslope(bounds,fsurdat)
     enddo
     call ncd_io(ncid=ncid, varname='hillslope_distance', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_distance not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_distance not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
 
     do l = bounds%begl,bounds%endl
@@ -345,7 +345,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='hillslope_width', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_width not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_width not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -354,7 +354,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
     call ncd_io(ncid=ncid, varname='hillslope_elevation', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
     if (masterproc .and. .not. readvar) then
-       call endrun( 'ERROR:: hillslope_elevation not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+       call endrun( 'ERROR:: hillslope_elevation not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
     end if
     do l = bounds%begl,bounds%endl
        g = lun%gridcell(l)
@@ -380,7 +380,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
        call ncd_io(ncid=ncid, varname='hillslope_stream_depth', flag='read', data=fstream_in, dim1name=grlnd, readvar=readvar)
        if (masterproc .and. .not. readvar) then
-          call endrun( 'ERROR:: hillslope_stream_depth not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+          call endrun( 'ERROR:: hillslope_stream_depth not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
        end if
        do l = bounds%begl,bounds%endl
           g = lun%gridcell(l)
@@ -389,7 +389,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
        call ncd_io(ncid=ncid, varname='hillslope_stream_width', flag='read', data=fstream_in, dim1name=grlnd, readvar=readvar)
        if (masterproc .and. .not. readvar) then
-          call endrun( 'ERROR:: hillslope_stream_width not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+          call endrun( 'ERROR:: hillslope_stream_width not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
        end if
        do l = bounds%begl,bounds%endl
           g = lun%gridcell(l)
@@ -398,7 +398,7 @@ subroutine InitHillslope(bounds,fsurdat)
 
        call ncd_io(ncid=ncid, varname='hillslope_stream_slope', flag='read', data=fstream_in, dim1name=grlnd, readvar=readvar)
        if (masterproc .and. .not. readvar) then
-          call endrun( 'ERROR:: hillslope_stream_slope not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+          call endrun( 'ERROR:: hillslope_stream_slope not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
        end if
        do l = bounds%begl,bounds%endl
           g = lun%gridcell(l)
@@ -504,11 +504,11 @@ subroutine InitHillslope(bounds,fsurdat)
              enddo
           end if
 
-          ! if missing hillslope information on surface dataset,
+          ! if missing hillslope information on dataset,
           ! call endrun
           if (ncolumns_hillslope(l) > 0 .and. sum(hillslope_area) == 0._r8 .and. masterproc) then
              write(iulog,*) 'Problem with input data: nhillcolumns is non-zero, but hillslope area is zero'
-             write(iulog,*) 'Check surface data for gridcell at (lon/lat): ', grc%londeg(g),grc%latdeg(g)
+             write(iulog,*) 'Check hillslope data for gridcell at (lon/lat): ', grc%londeg(g),grc%latdeg(g)
              call endrun( 'ERROR:: sum of hillslope areas is zero.'//errmsg(sourcefile, __LINE__) )
           end if
 
@@ -559,7 +559,7 @@ end subroutine InitHillslope
 
   !-----------------------------------------------------------------------
 
-  subroutine SetHillslopeSoilThickness(bounds,fsurdat,soil_depth_lowland_in,soil_depth_upland_in)
+  subroutine SetHillslopeSoilThickness(bounds, hillslope_file, soil_depth_lowland_in, soil_depth_upland_in)
     !
     ! !DESCRIPTION:
     ! Set hillslope column nbedrock values
@@ -578,7 +578,7 @@ subroutine SetHillslopeSoilThickness(bounds,fsurdat,soil_depth_lowland_in,soil_d
     !
     ! !ARGUMENTS:
     type(bounds_type), intent(in) :: bounds
-    character(len=*) , intent(in) :: fsurdat    ! surface data file name
+    character(len=*) , intent(in) :: hillslope_file    ! hillslope data file name
     real(r8), intent(in), optional  :: soil_depth_lowland_in
     real(r8), intent(in), optional  :: soil_depth_upland_in
     real(r8), pointer     :: fhillslope_in(:,:) ! read in - float
@@ -599,14 +599,14 @@ subroutine SetHillslopeSoilThickness(bounds,fsurdat,soil_depth_lowland_in,soil_d
 
     if (soil_profile_method==soil_profile_from_file) then
 
-       ! Open surface dataset to read in data below
-       call getfil (fsurdat, locfn, 0)
+       ! Open hillslope dataset to read in data below
+       call getfil (hillslope_file, locfn, 0)
        call ncd_pio_openfile (ncid, locfn, 0)
 
        allocate(fhillslope_in(bounds%begg:bounds%endg,max_columns_hillslope))
        call ncd_io(ncid=ncid, varname='hillslope_bedrock_depth', flag='read', data=fhillslope_in, dim1name=grlnd, readvar=readvar)
        if (masterproc .and. .not. readvar) then
-          call endrun( 'ERROR:: soil_profile_method = "FromFile", but hillslope_bedrock not found on surface data set.'//errmsg(sourcefile, __LINE__) )
+          call endrun( 'ERROR:: soil_profile_method = "FromFile", but hillslope_bedrock not found on hillslope data set.'//errmsg(sourcefile, __LINE__) )
        end if
        do l = bounds%begl,bounds%endl
           g = lun%gridcell(l)
@@ -896,7 +896,7 @@ end subroutine HillslopeDominantLowlandPft
   subroutine HillslopePftFromFile(bounds,col_pftndx)
     !
     ! !DESCRIPTION:
-    ! Reassign patch type using indices from surface data file
+    ! Reassign patch type using indices from data file
     ! Assumes one patch per hillslope column
     ! In preparation for this reassignment of patch type, only the
     ! first patch was given a non-zero weight in surfrd_hillslope.
diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index 340a799908..e827419aba 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -135,8 +135,8 @@ subroutine initialize2(ni,nj)
     use clm_varpar                    , only : surfpft_lb, surfpft_ub
     use clm_varpar                    , only : nlevsno
     use clm_varpar                    , only : natpft_size,cft_size
-    use clm_varctl                    , only : fsurdat
-    use clm_varctl                    , only : finidat, finidat_interp_source, finidat_interp_dest, fsurdat
+    use clm_varctl                    , only : fsurdat, hillslope_file
+    use clm_varctl                    , only : finidat, finidat_interp_source, finidat_interp_dest
     use clm_varctl                    , only : use_cn, use_fates, use_fates_luh
     use clm_varctl                    , only : use_crop, ndep_from_cpl, fates_spitfire_mode
     use clm_varctl                    , only : use_hillslope
@@ -253,7 +253,7 @@ subroutine initialize2(ni,nj)
     call pftcon%Init()
 
     ! Read surface dataset and set up subgrid weight arrays
-    call surfrd_get_data(begg, endg, ldomain, fsurdat, actual_numcft)
+    call surfrd_get_data(begg, endg, ldomain, fsurdat, hillslope_file, actual_numcft)
 
     if(use_fates) then
 
@@ -304,7 +304,7 @@ subroutine initialize2(ni,nj)
 
     if (use_hillslope) then
        ! Initialize hillslope properties
-       call InitHillslope(bounds_proc, fsurdat)
+       call InitHillslope(bounds_proc, hillslope_file)
     endif
 
     ! Set filters
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index ae83a1b31f..210cff2c2e 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -188,7 +188,7 @@ subroutine clm_instInit(bounds)
     !
     ! !USES: 
     use clm_varpar                         , only : nlevsno
-    use controlMod                         , only : nlfilename, fsurdat
+    use controlMod                         , only : nlfilename, fsurdat, hillslope_file
     use domainMod                          , only : ldomain
     use SoilBiogeochemDecompCascadeMIMICSMod, only : init_decompcascade_mimics
     use SoilBiogeochemDecompCascadeBGCMod  , only : init_decompcascade_bgc
@@ -280,7 +280,7 @@ subroutine clm_instInit(bounds)
 
     ! Set hillslope column bedrock values
     if (use_hillslope) then
-       call SetHillslopeSoilThickness(bounds,fsurdat, &
+       call SetHillslopeSoilThickness(bounds, hillslope_file, &
             soil_depth_lowland_in=8.5_r8,&
             soil_depth_upland_in =2.0_r8)
        call setSoilLayerClass(bounds)
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index cb7e2e3931..5fa2602e5a 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -109,6 +109,7 @@ module clm_varctl
 
   character(len=fname_len), public :: finidat    = ' '        ! initial conditions file name
   character(len=fname_len), public :: fsurdat    = ' '        ! surface data file name
+  character(len=fname_len), public :: hillslope_file = ' '    ! hillslope data file name
   character(len=fname_len), public :: paramfile  = ' '        ! ASCII data file with PFT physiological constants
   character(len=fname_len), public :: nrevsn     = ' '        ! restart data file name for branch run
   character(len=fname_len), public :: fsnowoptics  = ' '      ! snow optical properties file name
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index f65c8c7f47..eedb678ca3 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -148,7 +148,7 @@ subroutine control_init(dtime)
     ! Input datasets
 
     namelist /clm_inparm/  &
-         fsurdat, &
+         fsurdat, hillslope_file, &
          paramfile, fsnowoptics, fsnowaging
 
     ! History, restart options
@@ -736,6 +736,7 @@ subroutine control_spmd()
     call mpi_bcast (finidat_interp_source, len(finidat_interp_source), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (finidat_interp_dest, len(finidat_interp_dest), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fsurdat, len(fsurdat), MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (hillslope_file, len(hillslope_file), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fatmlndfrc,len(fatmlndfrc),MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (paramfile, len(paramfile) , MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fsnowoptics, len(fsnowoptics),  MPI_CHARACTER, 0, mpicom, ier)
@@ -1021,6 +1022,11 @@ subroutine control_print ()
     else
        write(iulog,*) '   surface data   = ',trim(fsurdat)
     end if
+    if (hillslope_file == ' ') then
+       write(iulog,*) '   hillslope_file, hillslope dataset not set'
+    else
+       write(iulog,*) '   hillslope data   = ',trim(hillslope_file)
+    end if
     if (fatmlndfrc == ' ') then
        write(iulog,*) '   fatmlndfrc not set, setting frac/mask to 1'
     else
diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
index 8ae4ace7e3..b2df9abfab 100644
--- a/src/main/histFileMod.F90
+++ b/src/main/histFileMod.F90
@@ -2328,6 +2328,7 @@ subroutine htape_create (t, histrest)
     use clm_varpar      , only : natpft_size, cft_size, maxpatch_glc, nlevdecomp_full, mxsowings, mxharvests
     use landunit_varcon , only : max_lunit
     use clm_varctl      , only : caseid, ctitle, fsurdat, finidat, paramfile
+    use clm_varctl      , only : hillslope_file
     use clm_varctl      , only : version, hostname, username, conventions, source
     use clm_varctl      , only : use_hillslope,nhillslope,max_columns_hillslope
     use domainMod       , only : ldomain
@@ -2428,6 +2429,8 @@ subroutine htape_create (t, histrest)
     call ncd_putatt(lnfid, ncd_global, 'case_id', trim(caseid))
     str = get_filename(fsurdat)
     call ncd_putatt(lnfid, ncd_global, 'Surface_dataset', trim(str))
+    str = get_filename(hillslope_file)
+    call ncd_putatt(lnfid, ncd_global, 'Hillslope_dataset', trim(str))
     if (finidat == ' ') then
        str = 'arbitrary initialization'
     else
diff --git a/src/main/restFileMod.F90 b/src/main/restFileMod.F90
index 6a574406fd..c7dbf0da72 100644
--- a/src/main/restFileMod.F90
+++ b/src/main/restFileMod.F90
@@ -503,6 +503,7 @@ subroutine restFile_dimset( ncid )
     ! !USES:
     use clm_time_manager     , only : get_nstep
     use clm_varctl           , only : caseid, ctitle, version, username, hostname, fsurdat
+    use clm_varctl           , only : hillslope_file
     use clm_varctl           , only : conventions, source
     use dynSubgridControlMod , only : get_flanduse_timeseries
     use clm_varpar           , only : numrad, nlevlak, nlevsno, nlevgrnd, nlevmaxurbgrnd, nlevcan
@@ -569,6 +570,7 @@ subroutine restFile_dimset( ncid )
     call ncd_putatt(ncid, NCD_GLOBAL, 'case_title'     , trim(ctitle))
     call ncd_putatt(ncid, NCD_GLOBAL, 'case_id'        , trim(caseid))
     call ncd_putatt(ncid, NCD_GLOBAL, 'surface_dataset', trim(fsurdat))
+    call ncd_putatt(ncid, NCD_GLOBAL, 'hillslope_dataset', trim(hillslope_file))
     call ncd_putatt(ncid, NCD_GLOBAL, 'flanduse_timeseries', trim(get_flanduse_timeseries()))
     call ncd_putatt(ncid, NCD_GLOBAL, 'title', 'CLM Restart information')
 
diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index 12212e2160..88a4dbd30b 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -46,7 +46,7 @@ module surfrdMod
 contains
 
   !-----------------------------------------------------------------------
-  subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
+  subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, lhillslope_file, actual_numcft)
     !
     ! !DESCRIPTION:
     ! Read the surface dataset and create subgrid weights.
@@ -73,7 +73,8 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
     use clm_varctl  , only : create_crop_landunit, convert_ocean_to_land, collapse_urban, &
                              toosmall_soil, toosmall_crop, toosmall_glacier, &
                              toosmall_lake, toosmall_wetland, toosmall_urban, &
-                             n_dom_landunits
+                             n_dom_landunits, &
+                             use_hillslope
     use fileutils           , only : getfil
     use domainMod           , only : domain_type, domain_init, domain_clean
     use clm_instur          , only : wt_lunit, topo_glc_mec, pct_urban_max
@@ -87,6 +88,7 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
     integer,          intent(in) :: begg, endg, actual_numcft
     type(domain_type),intent(in) :: ldomain     ! land domain
     character(len=*), intent(in) :: lfsurdat    ! surface dataset filename
+    character(len=*), intent(in) :: lhillslope_file ! hillslope dataset filename
     !
     ! !LOCAL VARIABLES:
     type(domain_type) :: surfdata_domain      ! local domain associated with surface dataset
@@ -97,7 +99,8 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
     character(len=16) :: lon_var, lat_var     ! names of lat/lon on dataset
     logical           :: readvar              ! true => variable is on dataset
     real(r8)          :: rmaxlon,rmaxlat      ! local min/max vars
-    type(file_desc_t) :: ncid                 ! netcdf id
+    type(file_desc_t) :: ncid                 ! netcdf id for lfsurdat
+    type(file_desc_t) :: ncid_hillslope       ! netcdf id for lhillslope_file
     logical           :: istype_domain        ! true => input file is of type domain
     logical           :: isgrid2d             ! true => intut grid is 2d
 
@@ -110,6 +113,10 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
           write(iulog,*)'lfsurdat must be specified'
           call endrun(msg=errMsg(sourcefile, __LINE__))
        endif
+       if (use_hillslope .and. lhillslope_file == ' ') then
+          write(iulog,*)'lhillslope_file must be specified'
+          call endrun(msg=errMsg(sourcefile, __LINE__))
+       endif
     endif
 
     wt_lunit(:,:) = 0._r8
@@ -119,6 +126,10 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
 
     call getfil( lfsurdat, locfn, 0 )
     call ncd_pio_openfile (ncid, trim(locfn), 0)
+    if (use_hillslope) then
+       call getfil( lhillslope_file, locfn, 0 )
+       call ncd_pio_openfile (ncid_hillslope, trim(locfn), 0)
+    end if
 
     ! Cmopare surfdat_domain attributes to ldomain attributes
 
@@ -183,7 +194,7 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, actual_numcft)
 
     ! Obtain vegetated landunit info
 
-    call surfrd_veg_all(begg, endg, ncid, ldomain%ns, actual_numcft)
+    call surfrd_veg_all(begg, endg, ncid, ncid_hillslope, ldomain%ns, actual_numcft)
 
     if (use_cndv) then
        call surfrd_veg_dgvm(begg, endg)
@@ -766,7 +777,7 @@ subroutine surfrd_pftformat( begg, endg, ncid )
   end subroutine surfrd_pftformat
 
 !-----------------------------------------------------------------------
-  subroutine surfrd_veg_all(begg, endg, ncid, ns, actual_numcft)
+  subroutine surfrd_veg_all(begg, endg, ncid, ncid_hillslope, ns, actual_numcft)
     !
     ! !DESCRIPTION:
     ! Determine weight arrays for non-dynamic landuse mode
@@ -783,7 +794,8 @@ subroutine surfrd_veg_all(begg, endg, ncid, ns, actual_numcft)
     ! !ARGUMENTS:
     implicit none
     integer, intent(in) :: begg, endg, actual_numcft
-    type(file_desc_t),intent(inout) :: ncid   ! netcdf id
+    type(file_desc_t),intent(inout) :: ncid   ! netcdf id for fsurdat
+    type(file_desc_t),intent(inout) :: ncid_hillslope ! netcdf id for hillslope_file
     integer          ,intent(in)    :: ns     ! domain size
     !
     ! !LOCAL VARIABLES:
@@ -869,7 +881,7 @@ subroutine surfrd_veg_all(begg, endg, ncid, ns, actual_numcft)
 
     ! Obtain hillslope hydrology information and modify pft weights
     if (use_hillslope) then
-       call surfrd_hillslope(begg, endg, ncid, ns)
+       call surfrd_hillslope(begg, endg, ncid_hillslope, ns)
     endif
 
     ! Convert from percent to fraction

From aa3bda9abd35712a9528afffd7c120769e712d16 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 18 Sep 2024 14:28:43 -0600
Subject: [PATCH 1072/1248] Update bassed on ctsm5.3.0

---
 tools/README.filecopies | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/tools/README.filecopies b/tools/README.filecopies
index a96dff1ab7..44c9ef6918 100644
--- a/tools/README.filecopies
+++ b/tools/README.filecopies
@@ -1,4 +1,4 @@
-tools/README.filecopies			      May/26/2011
+tools/README.filecopies			      Sep/18/2024
 
 There are several files that are copies of the original files from
 either CTSM src/utils or src/main, or share/src.
@@ -8,7 +8,7 @@ directories as well.
 
 I. Files that are IDENTICAL:
 
-   1. csm_share files copied that should be identical to share/src:
+   1. cesm_share files copied that should be identical to share/src:
 
        shr_kind_mod.F90
        shr_const_mod.F90
@@ -17,15 +17,11 @@ I. Files that are IDENTICAL:
        
 II. Files with differences
 
-   1. csm_share files copied with differences:
+   1. cesm_share files copied with differences:
 
        shr_sys_mod.F90 - Remove mpi abort and reference to shr_mpi_mod.F90.
 
-   2. CTSM src/utils files with differences:
-
-       fileutils.F90 --- Remove use of masterproc and spmdMod and endrun in abortutils.
-
-   3. Files in mksurfdata_esmf
+   2. Files in mksurfdata_esmf
 
        mkvarpar.F90
        nanMod.F90

From eb8816e7eed76aa983f415860fc8284c59441cf4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 18 Sep 2024 14:35:48 -0600
Subject: [PATCH 1073/1248] Remove mkprocdata, rename README.filecopies to just
 under mksurfdata_esmf

---
 tools/README.testing                          |  58 --
 tools/mkprocdata_map/README                   | 151 -----
 tools/mkprocdata_map/README.filedescriptions  |  25 -
 tools/mkprocdata_map/mkprocdata_map_all       | 202 -------
 .../mkprocdata_map_functions.bash             |  57 --
 tools/mkprocdata_map/mkprocdata_map_wrap      | 250 ---------
 tools/mkprocdata_map/src/Filepath             |   1 -
 tools/mkprocdata_map/src/Makefile             |  10 -
 tools/mkprocdata_map/src/Makefile.common      | 360 ------------
 tools/mkprocdata_map/src/Mkdepends            | 327 -----------
 tools/mkprocdata_map/src/Srcfiles             |   8 -
 tools/mkprocdata_map/src/constMod.F90         |  11 -
 tools/mkprocdata_map/src/fileutils.F90        | 282 ----------
 tools/mkprocdata_map/src/fmain.F90            |  78 ---
 tools/mkprocdata_map/src/gridmapMod.F90       | 289 ----------
 tools/mkprocdata_map/src/mkprocdata_map.F90   | 525 ------------------
 tools/mkprocdata_map/src/nanMod.F90           |  41 --
 tools/mkprocdata_map/src/shr_file_mod.F90     | 164 ------
 tools/mkprocdata_map/src/shr_kind_mod.F90     |  19 -
 tools/{ => mksurfdata_esmf}/README.filecopies |   0
 20 files changed, 2858 deletions(-)
 delete mode 100644 tools/README.testing
 delete mode 100644 tools/mkprocdata_map/README
 delete mode 100644 tools/mkprocdata_map/README.filedescriptions
 delete mode 100755 tools/mkprocdata_map/mkprocdata_map_all
 delete mode 100644 tools/mkprocdata_map/mkprocdata_map_functions.bash
 delete mode 100755 tools/mkprocdata_map/mkprocdata_map_wrap
 delete mode 100644 tools/mkprocdata_map/src/Filepath
 delete mode 100644 tools/mkprocdata_map/src/Makefile
 delete mode 100644 tools/mkprocdata_map/src/Makefile.common
 delete mode 100755 tools/mkprocdata_map/src/Mkdepends
 delete mode 100644 tools/mkprocdata_map/src/Srcfiles
 delete mode 100644 tools/mkprocdata_map/src/constMod.F90
 delete mode 100644 tools/mkprocdata_map/src/fileutils.F90
 delete mode 100644 tools/mkprocdata_map/src/fmain.F90
 delete mode 100644 tools/mkprocdata_map/src/gridmapMod.F90
 delete mode 100644 tools/mkprocdata_map/src/mkprocdata_map.F90
 delete mode 100644 tools/mkprocdata_map/src/nanMod.F90
 delete mode 100644 tools/mkprocdata_map/src/shr_file_mod.F90
 delete mode 100644 tools/mkprocdata_map/src/shr_kind_mod.F90
 rename tools/{ => mksurfdata_esmf}/README.filecopies (100%)

diff --git a/tools/README.testing b/tools/README.testing
deleted file mode 100644
index 9c386a3b26..0000000000
--- a/tools/README.testing
+++ /dev/null
@@ -1,58 +0,0 @@
-tools/README.testing				May/23/2011
-
-There is automated testing for all of the tools and scripts under this tools directory.
-The tests are in the test/tools directory and are any of the scripts
-that have "tools" in the name. There are several assumptions made in order for the 
-testing to work.
-
-
-1.) Executable name is the same as the directory name
-
-The name of the executable program is the same as the directory name of the tool.
-
-2.) Build works the same for any Fortran tools
-
-The build for any Fortran tools should work the same way, with the same options
-and required files for it. The files: Makefile, Mkdepends, Filepath and Srcfile
-are expected to exist in the tool "src" sub-directory. To make maintaining these files easier
-in general the Makefile and Mkdepends files should be kept identical other than
-default settings for OPT and SMP and the output executable name.
-
-Options to the Makefile:
-
- LIB_NETCDF --- Library directory location of NetCDF. (defaults to /usr/local/lib)
- INC_NETCDF --- Include directory location of NetCDF. (defaults to /usr/local/include)
- MOD_NETCDF --- Module directory location of NetCDF.  (defaults to $LIB_NETCDF)
- USER_FC ------ Allow user to override the default Fortran compiler specified in Makefile.
- USER_FCTYP --- Allow user to override the default type of Fortran compiler 
-                (Linux and USER_FC=ftn only).
- USER_CC ------ Allow user to override the default C compiler specified in Makefile
-                (Linux only).
- USER_LINKER -- Allow user to override the default linker specified in Makefile.
- SMP ---------- Shared memory Multi-processing (TRUE or FALSE) [default is FALSE]
- OPT ---------- Use optimized options. (TRUE or FALSE)
-
-3.) Successful completion of the tool ends with "Successfully ..."
-
-After the tool completes it should have an unique string telling of the 
-successful completion of the file that is searchable in the log file starting
-with "Successfully ". If this string isn't found in the log file, it
-will be assumed by the test setup that the test failed.
-
-4.) NetCDF files are created or modified
-
-It is assumed that NetCDF files are created and/or modified by the process. And if
-NetCDF files are NOT created -- something went wrong. For some scripts that copy files
-to other locations this means an "-nomv" option needs to be invoked (and one provided)
-so that it leaves the files created in the current directory.
-
-5.) Namelist examples exist <toolname>.* namelist files
-
-To specify options for the running of the tool, sample namelist files
-are provided or a sample run options file. These files can EITHER be in the 
-tool directory OR the ../../test/tools/nl_files directory.
-
-6.) Specific tests for run scripts
-
-For tools that have scripts to create namelists and run the tool for you, there
-are customized tests to run these tools.
diff --git a/tools/mkprocdata_map/README b/tools/mkprocdata_map/README
deleted file mode 100644
index 92ffb4856c..0000000000
--- a/tools/mkprocdata_map/README
+++ /dev/null
@@ -1,151 +0,0 @@
-$CTSMROOT/tools/mkprocdata_map/clm/README                Oct 30, 2012
-
-This directory contains scripts for regridding CLM output from an
-unstructured grid (1-d output using the lndgrid dimension) to a 2-d
-(lat/lon) grid. The regridding method is area-conservative.
-
-The following steps provide a method to create the necessary inputs to
-this script, produce an executable, and regrid output:
-
-In the following instructions, the "original" resolution is the
-resolution of the run on an unstructured grid, and the "target"
-resolution is the regular lat/lon resolution to which you will regrid
-the output.
-
-(0) Install prerequisites:
-
-  (a) If you do not already have a mapping file from the original
-      resolution to the target resolution, you will need the
-      ESMF_RegridWeightGen tool installed on your system.
-
-  (b) The wrapper scripts describe below require the netCDF operators
-      (NCO). These nco tools (ncks, ncap2, etc.) must be in your path.
-
-(1) Determine the target resolution. This resolution must be a regular
-    lat/lon resolution. Generally, this should be a resolution close
-    to the resolution of the CLM run. For example, when running CLM at
-    ne30_np4 resolution, a good target resolution is 0.9x1.25 (i.e.,
-    finite volume 1 degree: f09); when running CLM at ne120_np4
-    resolution, a good target resolution is 0.23x0.31 (i.e., finitev
-    volume 1/4 degree: f02).
-
-(2) Perform a short CLM run at the target resolution, producing at
-    least one history file. After this run completes, set the
-    environment variable $TEMPLATE_FILE to point to one of the history
-    files created by this run.
-
-(3) Create a conservative mapping file from the original resolution to
-    the target resolution using the ESMF regrid weight generator. The
-    basic method for doing this is:
-
-    $ESMF_PATH/bin/ESMF_RegridWeightGen -s $INGRID -d $OUTGRID -m conserve -w $MAP_FILE -i
-
-    where $INGRID gives the path to a SCRIP grid file at the original
-    resolution, $OUTGRID gives the path to a SCRIP grid file at the
-    template resolution, and $MAP_FILE gives the name of the mapping
-    file that will be generated.
-
-    However, you may want to wrap this in a job script to run it on
-    multiple processors (using mpirun), and you may have to set other
-    machine-specific environment variables.
-
-(4) Build the mkprocdata_map tool. From the current directory, do the
-    following:
-
-   > cd src
-   > gmake
-   > cd ..
-
-   By default code compiles optimized so it's reasonably fast. If you want
-   to use the debugger, with bounds-checking, and float trapping on do the 
-   following:
-      gmake OPT=FALSE
-   See Also: See the components/clm/tools/README file for notes about setting
-   the path for NetCDF.
-
-   This builds the mkprocdata_map executable. However, you generally
-   will not want to run this executable directly: instead, you should
-   use one of the wrapper scripts described below.
-
-(5) Do the regridding using one of the wrapper scripts in this
-    directory. To determine which script is most appropriate: Do you
-    need to regrid just one or a few output files, or most/all of the
-    output files in a directory?
-
-  (a) If you are regridding just one or a few output files, you can
-      use mkprocdata_map_wrap. Its usage is:
-
-      > mkprocdata_map_wrap -i input_file -o output_file -m $MAP_FILE -t $TEMPLATE_FILE
-
-      where:
-      - input_file is the CLM history file you want to regrid
-      - output_file is the name of the regridded file that will be
-        created
-      - $MAP_FILE is the ESMF conservative mapping file created in
-        step (3)
-      - $TEMPLATE_FILE is a CLM history file at the target resolution,
-        created in step (2)
-
-      You may also specify the '-l' option to this script. This option
-      determines whether to determine landfrac and related variables
-      by regridding the input file (when you don't give the '-l'
-      option), or by copying these variables from the template file
-      (when you give the '-l' option). These variables are important
-      for computing regional and global averages, e.g., as is done in
-      the land diagnostics package. Each method may be reasonable,
-      depending on the purposes of the regridding. For example, if you
-      want regional/global integrals to be as true as possible to the
-      original run, you should run withOUT the '-l' option; but if you
-      want to compare regional/global integrals between the original
-      run and a run at the target resolution, then you may want to run
-      WITH the '-l' option.
-
-      Run 'mkprocdata_map_wrap -h' for full usage
-
-  (b) If you need to regrid most or all of the output files in a
-      directory, you can use the convenience script
-      mkprocdata_map_all. This script runs mkprocdata_map_wrap on all
-      files matching a given pattern within a directory. Its basic
-      usage is the following, done from a directory containing many
-      CLM history files:
-
-      > /path/to/mkprocdata_map_all -p $CASE -m $MAP_FILE -t $TEMPLATE_FILE
-
-      where:
-      - $CASE is the case name of the original run (this -p argument
-        is actually more general: it provides the prefix of files on
-        which mkprocdata_map_wrap should be run; run
-        'mkprocdata_map_all -h' for details)
-      - $MAP_FILE is the ESMF conservative mapping file created in
-        step (3)
-      - $TEMPLATE_FILE is a CLM history file at the target resolution,
-        created in step (2)
-
-      There are a number of additional optional arguments to this
-      script, including the '-l' option described in (a), above. Run
-      'mkprocdata_map_all -h' for full usage.
-    
-
-------------------------------------------------------------------------
-Some miscellaneous notes on the scripts contained here
-------------------------------------------------------------------------
-
-- area vs. area_regridded in the output of mkprocdata_map_wrap and
-  mkprocdata_map_all: The 'area' variable gives the actual grid cell
-  area on the destination grid. The 'area_regridded' variable is the
-  result of performing the regridding procedure on the 'area' variable
-  in the original source data. This seems to be the wrong way to
-  regrid areas (e.g., it leads to global totals that do not make
-  sense). However, area_regridded is left in the regridded files as a
-  diagnostic. BUT PLEASE USE CAUTION IF USING THIS AREA_REGRIDDED
-  VALUE, UNLESS YOU KNOW WHAT IT REALLY REPRESENTS!
- 
-- At least as of this writing (Oct 29, 2012), there is insufficient
-  metadata on the CLM history files to regrid all variables
-  perfectly. In particular, note that many CLM history variables apply
-  only over a subset of the grid cell (e.g., over the non-lake portion
-  of the grid cell). Thus, to regrid these variables appropriately, we
-  would need to weight each grid cell's value by the portion of the
-  grid cell over which the field applies. However, doing this would
-  require metadata about each field that is not currently
-  available.
diff --git a/tools/mkprocdata_map/README.filedescriptions b/tools/mkprocdata_map/README.filedescriptions
deleted file mode 100644
index e657e7c7d9..0000000000
--- a/tools/mkprocdata_map/README.filedescriptions
+++ /dev/null
@@ -1,25 +0,0 @@
-$CTSMROOT/tools/mkprocdata_map/README.filedescriptions                        Erik Kluzek
-                                                                              06/08/2018
-
-mkprocdata_map_all ------------ Script to run over a list of files
-mkprocdata_map_wrap ----------- Main script to actually use
-mkprocdata_map_functions.bash - Bash shell functions to use in other scripts
-README ------------------------ Description and how to run
-src --------------------------- Directory with FORTRAN source code
-
-Also there are some sample files that can be used for testing under inputdata in 
-
-$DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map
-
-See how this is done by looking at the file for testing mkprocdata_map: 
-
-../../test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 
-
-Which does something like the following:
-
-./mkprocdata_map_wrap \
--i $DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map/clm4054_ne30g16_I2000.clm2.h0.2000-01_c170430.nc \
--o ne30output_onf19grid.nc \
--m $DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map/map_ne30np4_nomask_to_fv1.9x2.5_nomask_aave_da_c121107.nc \
--t $DIN_LOC_ROOT/lnd/clm2/test_mkprocdata_map/clm4054_f19g16_I2000.clm2.h0.2000-01_c170430.nc
-
diff --git a/tools/mkprocdata_map/mkprocdata_map_all b/tools/mkprocdata_map/mkprocdata_map_all
deleted file mode 100755
index 73e8abedf1..0000000000
--- a/tools/mkprocdata_map/mkprocdata_map_all
+++ /dev/null
@@ -1,202 +0,0 @@
-#!/bin/bash
-
-# This script runs mkprocdata_map_wrap on all files matching a given
-# pattern within a directory.
-
-# Created by Bill Sacks, 5-26-11
-
-# ----------------------------------------------------------------------
-# LOCAL FUNCTIONS DEFINED HERE
-# ----------------------------------------------------------------------
-
-function Usage {
-    script_name=`basename $0`
-    echo "Usage: $script_name -p prefix -m map_file -t template_file [-d] [-e executable-path] [-h] [-i] [-l] [-o output_suffix] [-r diRectory] [-s suffix]"
-    echo ""
-    echo "This script runs mkprocdata_map_wrap on all files matching a"
-    echo "given pattern within a directory."
-    echo ""
-    echo "'prefix' gives the prefix of the files on which"
-    echo "mkprocdata_map_wrap should be run; 'prefix' should NOT contain"
-    echo "wildcard characters. The prefix is also used to translate"
-    echo "from input to output file names (see examples below)"
-    echo ""
-    echo "'map_file' gives the name (and full path if not in the current"
-    echo "directory) of the mapping file"
-    echo ""
-    echo "'template_file' gives the name (and full path if not in the"
-    echo "current directory) of the template file, from which we read"
-    echo "lats, lons and some other variables"
-    echo ""
-    echo "The following are optional arguments:"
-    echo ""
-    echo "[-d]: Do a test (Dry run): do all error-checking on"
-    echo "      arguments and print commands that would be run, but"
-    echo "      don't actually run commands"
-    echo ""
-    echo "[-e executable-path]: Gives the path of the mkprocdata_map executable."
-    echo "                      If not specified, the path is determined by the"
-    echo "                      default value in mkprocdata_map_wrap."
-    echo ""
-    echo "[-h]: Print this help message and exit"
-    echo ""
-    echo "[-i]: Ignore (skip) existing output files; if this option is"
-    echo "      not specified, then the script dies with an error if"
-    echo "      any of the desired output files already exist"
-    echo ""
-    echo "[-l]: Option passed to mkprocdata_map_wrap: rather than computing"
-    echo "      landfrac and related variables by regridding the input file,"
-    echo "      instead copy these variables directly from the template file."
-    echo ""
-    echo "[-o output_suffix]: suffix to append to the end of the prefix"
-    echo "                    on the output files"
-    echo "                    If not specified, '_2d' is used"
-    echo ""
-    echo "[-r diRectory]: Do the processing in the given directory."
-    echo "                If not specified, processing is done in the"
-    echo "                current working directory."
-    echo ""
-    echo "[-s suffix]: Run mkprocdata_map_wrap on all files matching the"
-    echo "             pattern '\${prefix}\${suffix}'. The suffix can -"
-    echo "             and often will - contain wildcards; but"
-    echo "             remember to enclose 'suffix' in quotes to"
-    echo "             prevent shell expansion."
-    echo "             If not specified, run mkprocdata_map_wrap on all"
-    echo "             files matching '\${prefix}*'"
-    echo ""
-    echo ""
-    echo "Example: $script_name -p Ib14_ne30np4_gx1v6 -m map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc -t Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc"
-    echo "This will run mkprocdata_map_wrap on all files whose names begin"
-    echo "with 'Ib14_ne30np4_gx1v6' in the current directory, using the"
-    echo "mapping file named 'map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc'"
-    echo "and the template file named 'Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc'"
-    echo "For an input file named:"
-    echo "  Ib14_ne30np4_gx1v6.clm2.h0.0001-01-06-00000.nc"
-    echo "The output file will be named:"
-    echo "  Ib14_ne30np4_gx1v6_2d.clm2.h0.0001-01-06-00000.nc"
-    echo ""
-    echo "Example: $script_name -o '_remap' -s '*.h0.0001*.nc' -p Ib14_ne30np4_gx1v6 -m map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc -t Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc"
-    echo "This will run mkprocdata_map_wrap on all files whose names match"
-    echo "the pattern 'Ib14_ne30np4_gx1v6*.h0.0001*.nc', in the"
-    echo "current directory, using the mapping file named"
-    echo "'map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc' and the"
-    echo "template file named Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc"
-    echo "For an input file named:"
-    echo "  Ib14_ne30np4_gx1v6.clm2.h0.0001-01-06-00000.nc"
-    echo "The output file will be named:"
-    echo "  Ib14_ne30np4_gx1v6_remap.clm2.h0.0001-01-06-00000.nc"
-    echo ""
-}
-
-# ----------------------------------------------------------------------
-# BEGIN MAIN SCRIPT
-# ----------------------------------------------------------------------
-
-script_dir=`dirname $0`
-source $script_dir/mkprocdata_map_functions.bash
-
-# ----------------------------------------------------------------------
-# Handle command-line arguments
-# ----------------------------------------------------------------------
-
-# define default values:
-# required arguments:
-prefix=""
-map_file=""
-template_file=""
-# optional arguments:
-directory="."
-ignore_existing=0
-output_suffix="_2d"
-suffix="*"
-dryrun=0
-extra_args=""
-
-while getopts de:hilm:o:p:r:s:t: opt; do
-    case $opt in
-	d) dryrun=1;;
-	e) extra_args="$extra_args -e $OPTARG";;
-	h) Usage; exit;;
-	i) ignore_existing=1;;
-	l) extra_args="$extra_args -l";;
-	m) map_file=$OPTARG;;
-	o) output_suffix=$OPTARG;;
-	p) prefix=$OPTARG;;
-	r) directory=$OPTARG;;
-	s) suffix=$OPTARG;;
-	t) template_file=$OPTARG;;
-	\?) Usage; exit 1
-    esac
-done
-
-# ----------------------------------------------------------------------
-# Error checking on arguments
-# ----------------------------------------------------------------------
-
-if [ -z "$prefix" ]; then
-    echo "Must specify a prefix"
-    Usage
-    exit 1
-fi
-
-check_file_arg "$map_file" "map"
-check_file_arg "$template_file" "template"
-
-# Make sure directory is really a directory
-if [ ! -d $directory ]; then
-    echo "ERROR: $directory is not a directory"
-    echo ""
-    Usage
-    exit 1
-fi
-
-
-# ----------------------------------------------------------------------
-# Change to desired directory
-# ----------------------------------------------------------------------
-
-olddir=`pwd`
-cd $directory
-
-# ----------------------------------------------------------------------
-# Get list of files matching the given pattern; make sure there really
-# are some matching files
-# ----------------------------------------------------------------------
-
-files=`ls ${prefix}${suffix}`
-if [ $? -ne 0 ]; then
-    echo "ERROR trying to find files matching: ${prefix}${suffix}"
-    echo ""
-    Usage
-    exit 1
-fi
-
-# ----------------------------------------------------------------------
-# Loop through files matching the given pattern; run mkprocdata_map_wrap for each
-# ----------------------------------------------------------------------
-
-for infile in $files; do
-    outfile=${infile/$prefix/${prefix}${output_suffix}}
-    if [ -e $outfile ]; then
-	if [ $ignore_existing -eq 0 ]; then
-	    echo ""
-	    echo "ERROR: output file $outfile already exists"
-	    exit 1
-	else
-	    echo ""
-	    echo "WARNING: output file $outfile already exists: skipping"
-	    echo ""
-	fi
-    
-    else  # outfile does not exist
-	echo ""
-	do_cmd "${script_dir}/mkprocdata_map_wrap -i $infile -o $outfile -m $map_file -t $template_file $extra_args" $dryrun
-    fi
-done
-
-# ----------------------------------------------------------------------
-# Clean up
-# ----------------------------------------------------------------------
-
-cd $olddir
-
diff --git a/tools/mkprocdata_map/mkprocdata_map_functions.bash b/tools/mkprocdata_map/mkprocdata_map_functions.bash
deleted file mode 100644
index bbc359fb89..0000000000
--- a/tools/mkprocdata_map/mkprocdata_map_functions.bash
+++ /dev/null
@@ -1,57 +0,0 @@
-#!/bin/bash
-
-# This file contains functions used by other bash scripts in this directory.
-
-# This function echoes the command given by $1 (cmd), then executes it.
-# However, if $2 (dryrun) is non-zero, then it only does the echo, not the execution.
-# Usage: do_cmd cmd dryrun
-# Returns 0 on success, non-zero on failure; if there is an error, the error string is echoed.
-function do_cmd {
-    if [[ $# -ne 2 ]]; then
-	echo "ERROR in do_cmd: wrong number of arguments: expected 2, received $#"
-	exit 1
-    fi
-
-    local cmd=$1
-    local dryrun=$2
-
-    echo $cmd
-    if [ $dryrun -eq 0 ]; then
-	# We use 'eval $cmd' rather than just '$cmd', because the
-	# latter doesn't work right if the command contains any quoted
-	# strings (e.g., svn ci -m "this is my message")
-	eval $cmd
-	if [ $? -ne 0 ]; then
-	    echo "ERROR in do_cmd: error executing command"
-	    exit 2
-	fi
-    fi
-
-    return 0
-}
-
-# make sure that the given file name argument was provided, and that
-# the file exists; exit the script with a usage message if either of
-# these is not true
-# 
-# Usage: check_file_arg filename_arg description
-# (description is echoed if there is an error)
-# Example: check_file_arg "$input_file" "input"
-# (note that $input_file must be in quotes)
-function check_file_arg {
-    local filename=$1
-    local description=$2
-    
-    if [ -z "$filename" ]; then
-	echo "ERROR: Must specify $description file"
-	Usage
-	exit 1
-    fi
-
-    if [ ! -f $filename ]; then
-	echo "ERROR: Can't find $description file: $filename"
-	Usage
-	exit 1
-    fi
-}
-
diff --git a/tools/mkprocdata_map/mkprocdata_map_wrap b/tools/mkprocdata_map/mkprocdata_map_wrap
deleted file mode 100755
index 4744b0eacc..0000000000
--- a/tools/mkprocdata_map/mkprocdata_map_wrap
+++ /dev/null
@@ -1,250 +0,0 @@
-#!/bin/bash
-
-# This script is a wrapper around mkprocdata_map that runs that
-# program and then copies some additional variables from the template
-# file to the output file. It also does some additional pre and
-# post-processing in order to create some additional variables.
-
-# Created by Bill Sacks, 5-25-11
-
-# ----------------------------------------------------------------------
-# SET PARAMETERS HERE
-# ----------------------------------------------------------------------
-
-# comma-delimited list of extra variables to copy directly from
-# template file; note that these variables should not be written out
-# by mkprocdata_map (i.e., everything in this list should be listed in
-# the 'ignore_var' function in mkprocdata_map.F90); however, there may
-# be some variables in the 'ignore_var' function that are not listed
-# here - e.g., variables that we treat specially.
-copy_vars="lon,lat"
-
-# comma-delimited list of extra variables to copy from the template
-# file if the -l option is specified -- this option says to copy
-# landfrac and related variables. Note that some of these variables
-# may be written out by mkprocdata_map, in which case they will be
-# overwritten afterwards (slighly less efficient, but that keeps
-# things simpler).
-landfrac_copy_vars="landfrac,landmask,pftmask"
-
-# name of the executable;
-# expected to be in the same directory as this script unless -e option is given
-executable="mkprocdata_map"
-
-# minimum value for regridded pftmask variable for the output variable to be 1
-pftmask_min="1.e-6"
-
-# fill value for landmask
-landmask_fill=-9999
-
-# ----------------------------------------------------------------------
-# LOCAL FUNCTIONS DEFINED HERE
-# ----------------------------------------------------------------------
-
-function Usage {
-    script_name=`basename $0`
-    echo "Usage: $script_name -i input_file -o output_file -m map_file -t template_file [-e executable-path] [-h] [-l]"
-    echo ""
-    echo "This script runs mkprocdata_map with the given arguments (-i, -o, -m and -t),"
-    echo "then copies some additional variables from the template file"
-    echo "to the output file. It also does some additional pre and"
-    echo "post-processing in order to create some additional variables."
-    echo ""
-    echo "Additional optional arguments:"
-    echo ""
-    echo "[-e executable-path]: Gives the path of the mkprocdata_map executable."
-    echo "                      If not specified, the executable is assumed to be"
-    echo "                      in the same directory as this script."
-    echo ""
-    echo "[-h]: Print this help message and exit"
-    echo ""
-    echo "[-l]: Rather than computing landfrac and related variables"
-    echo "by regridding the input file, instead copy these variables"
-    echo "directly from the template file. The variables this pertains"
-    echo "to are:"
-    echo $landfrac_copy_vars
-}
-
-# This function operates on a single variable in a file, changing all
-# places where that variable is missing to some new (non-missing)
-# value. The _FillValue attribute remains unchanged.
-# Usage: change_missing_to_value varname newval infile outfile
-#   - varname: the name of the variable to change
-#   - newval: all instances of the missing value will be replaced with
-#     this new value
-#   - infile: input file name
-#   - outfile: output file name (can be the same as infile)
-function change_missing_to_value {
-    if [[ $# -ne 4 ]]; then
-	echo "ERROR in change_missing_to_value: wrong number of arguments: expected 2, received $#"
-	exit 1
-    fi
-
-    varname=$1
-    newval=$2
-    infile=$3
-    outfile=$4
-
-    varname_tmp=${varname}_tmp_$$
-
-    cat > cmds.nco.tmp.$$ <<EOF
-*missing=${varname}.get_miss();
-
-/* we need to create a temporary variable because it seems that
-delete_miss can only operate on variables that have been previously
-defined in this script */
-*${varname_tmp}=${varname};
-
-/* we need to delete the missing value in order to replace those
-   values with 0 (needed because ncap2 doesn't let you do operations
-   on points that have the missing value) */
-${varname_tmp}.delete_miss();
-
-where(${varname_tmp}==missing)
-   ${varname_tmp}=${newval};
-
-/* WJS (6-28-11): I could imagine the following line having negative
-   performance implications. However, I think it's best to maintain
-   a _FillValue attribute in case some programs expect it.
-   One alternative may be to use ncatted to restore the _FillValue
-   attribute; I don't know if that would be more or less efficient. */
-${varname_tmp}.set_miss(missing);
-
-${varname}=${varname_tmp};
-EOF
-       
-    do_cmd "ncap2 -O -S cmds.nco.tmp.$$ $infile $outfile" 0
-    rm cmds.nco.tmp.$$
-    
-}
-
-
-# ----------------------------------------------------------------------
-# BEGIN MAIN SCRIPT
-# ----------------------------------------------------------------------
-
-script_dir=`dirname $0`
-source $script_dir/mkprocdata_map_functions.bash
-
-# ----------------------------------------------------------------------
-# Handle command-line arguments, and check for errors
-# ----------------------------------------------------------------------
-
-# define default values:
-input_file=""
-output_file=""
-map_file=""
-template_file=""
-executable_path=$script_dir
-do_landfrac_copies=0
-
-while getopts e:hi:lm:o:t: opt; do
-    case $opt in
-	e) executable_path=$OPTARG;;
-	h) Usage; exit;;
-	i) input_file=$OPTARG;;
-	l) do_landfrac_copies=1;;
-	m) map_file=$OPTARG;;
-	o) output_file=$OPTARG;;
-	t) template_file=$OPTARG;;
-	\?) Usage; exit 1
-    esac
-done
-
-check_file_arg "$input_file" "input"
-check_file_arg "$map_file" "map"
-check_file_arg "$template_file" "template"
-
-if [ -z "$output_file" ]; then
-    echo "Must specify an output file"
-    Usage
-    exit 1
-fi
-
-# ----------------------------------------------------------------------
-# Do some preprocessing
-# ---------------------------------------------------------------------- 
-
-tempfile="$output_file.tmp.$$"
-
-if [ $do_landfrac_copies -eq 0 ]; then
-    # the following things are preprocessing that needs to be done on
-    # variables that are only used when do_landfrac_copies==0
-    echo ""
-
-    # for landfrac to be regridded appropriately, it needs to be set
-    # to 0 over ocean grid cells, rather than having the missing value
-    # there
-    change_missing_to_value landfrac 0 $input_file $tempfile
-
-    # we need a pftmask_float variable because we can't regrid integer
-    # variables properly
-    do_cmd "ncap2 -O -s 'pftmask_float=float(pftmask)' $tempfile $tempfile" 0
-    # pftmask_float should also be 0 over the ocean for the regridding
-    # to work as desired (analogously to what we do for landfrac,
-    # above). However, we don't have to do the following
-    # change_missing_to_value call because pftmask already doesn't
-    # have any missing values in the input file (as of 6-28-11).
-    ### change_missing_to_value pftmask_float 0 $tempfile $tempfile
-else
-    ln -s $input_file $tempfile
-fi
-
-# ----------------------------------------------------------------------
-# Run mkprocdata_map
-# ---------------------------------------------------------------------- 
-
-do_cmd "${executable_path}/${executable} -i $tempfile -o $output_file -m $map_file -t $template_file" 0
-
-rm $tempfile
-
-# ----------------------------------------------------------------------
-# Add extra variables to the output file
-# ---------------------------------------------------------------------- 
-
-if [ $do_landfrac_copies -eq 0 ]; then
-    all_copy_vars=$copy_vars
-else
-    all_copy_vars="${copy_vars},${landfrac_copy_vars}"
-fi
-
-echo ""
-do_cmd "ncks -A -v $all_copy_vars $template_file $output_file" 0
-
-# ----------------------------------------------------------------------
-# Do some post-processing
-# ----------------------------------------------------------------------
-
-# --- Rename area-related variables ---
-do_cmd "ncrename -v area,area_regridded -v gw,area $output_file" 0
-do_cmd "ncatted -a long_name,area_regridded,o,c,'grid cell areas, regridded from the original resolution' $output_file" 0
-
-if [ $do_landfrac_copies -eq 0 ]; then
-    # --- Convert pftmask back to integer ---
-    echo ""
-    do_cmd "ncap2 -O -s 'pftmask = int(pftmask_float >= $pftmask_min)' $output_file $output_file" 0
-    do_cmd "ncks -O -x -v pftmask_float $output_file $output_file" 0
-
-    # --- Calculate landmask from landfrac ---
-    echo ""
-
-    cat > cmds.nco.tmp.$$ <<EOF
-/* we need to make a landmask_float then later convert it to the
-   integer landmask, because we need to change the FillValue to be
-   within the range of an integer before converting landmask to an
-   integer */
-*landmask_float=(landfrac > 0);
-landmask_float.change_miss($landmask_fill);
-landmask=int(landmask_float);
-EOF
-
-    do_cmd "ncap2 -O -S cmds.nco.tmp.$$ $output_file $output_file" 0
-    rm cmds.nco.tmp.$$
-
-    change_missing_to_value landmask 0 $output_file $output_file
-
-    # in the following, note that we need to manually set missing_value, because it doesn't get changed through the .set_miss call in nco:
-    do_cmd "ncatted -a long_name,landmask,o,c,'land/ocean mask (0.=ocean and 1.=land)' -a missing_value,landmask,o,i,$landmask_fill $output_file" 0
-fi
-
-echo "Successfully regridded data"
diff --git a/tools/mkprocdata_map/src/Filepath b/tools/mkprocdata_map/src/Filepath
deleted file mode 100644
index 9c558e357c..0000000000
--- a/tools/mkprocdata_map/src/Filepath
+++ /dev/null
@@ -1 +0,0 @@
-.
diff --git a/tools/mkprocdata_map/src/Makefile b/tools/mkprocdata_map/src/Makefile
deleted file mode 100644
index 42f797b3c2..0000000000
--- a/tools/mkprocdata_map/src/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Makefile for mkprocdata_map
-
-EXENAME = ../mkprocdata_map
-
-# Set optimization on by default
-ifeq ($(OPT),$(null))
-  OPT := TRUE
-endif
-
-include Makefile.common
diff --git a/tools/mkprocdata_map/src/Makefile.common b/tools/mkprocdata_map/src/Makefile.common
deleted file mode 100644
index ab79f94144..0000000000
--- a/tools/mkprocdata_map/src/Makefile.common
+++ /dev/null
@@ -1,360 +0,0 @@
-#-----------------------------------------------------------------------
-# This Makefile is for building clm tools on AIX, Linux (with pgf90 or 
-# lf95 compiler), Darwin or IRIX platforms.
-#
-# These macros can be changed by setting environment variables:
-#
-# LIB_NETCDF --- Library directory location of netcdf. (defaults to /usr/local/lib)
-# INC_NETCDF --- Include directory location of netcdf. (defaults to /usr/local/include)
-# MOD_NETCDF --- Module directory location of netcdf.  (defaults to $LIB_NETCDF)
-# USER_FC ------ Allow user to override the default Fortran compiler specified in Makefile.
-# USER_FCTYP --- Allow user to override the default type of Fortran compiler (linux and USER_FC=ftn only).
-# USER_CC ------ Allow user to override the default C compiler specified in Makefile (linux only).
-# USER_LINKER -- Allow user to override the default linker specified in Makefile.
-# USER_CPPDEFS - Additional CPP defines.
-# USER_CFLAGS -- Additional C compiler flags that the user wishes to set.
-# USER_FFLAGS -- Additional Fortran compiler flags that the user wishes to set.
-# USER_LDLAGS -- Additional load flags that the user wishes to set.
-# SMP ---------- Shared memory Multi-processing (TRUE or FALSE) [default is FALSE]
-# OPT ---------- Use optimized options.
-#
-#------------------------------------------------------------------------
-
-# Set up special characters
-null  :=
-
-# Newer makes set the CURDIR variable.
-CURDIR := $(shell pwd)
-
-RM = rm
-
-# Check for the netcdf library and include directories 
-ifeq ($(LIB_NETCDF),$(null))
-  LIB_NETCDF := /usr/local/lib
-endif
-
-ifeq ($(INC_NETCDF),$(null))
-  INC_NETCDF := /usr/local/include
-endif
-
-ifeq ($(MOD_NETCDF),$(null))
-  MOD_NETCDF := $(LIB_NETCDF)
-endif
-
-# Set user specified Fortran compiler
-ifneq ($(USER_FC),$(null))
-  FC := $(USER_FC)
-endif
-
-# Set user specified C compiler
-ifneq ($(USER_CC),$(null))
-  CC := $(USER_CC)
-endif
-
-# Set if Shared memory multi-processing will be used
-ifeq ($(SMP),$(null))
-  SMP := FALSE
-endif
-
-CPPDEF := $(USER_CPPDEFS)
-
-# Set optimization on by default
-ifeq ($(OPT),$(null))
-  OPT := TRUE
-endif
-
-ifeq ($(OPT),TRUE)
-  CPPDEF := -DOPT
-endif
-
-# Determine platform 
-UNAMES := $(shell uname -s)
-
-# Load dependency search path.
-dirs := . $(shell cat Filepath)
-
-# Set cpp search path, include netcdf
-cpp_dirs := $(dirs) $(INC_NETCDF) $(MOD_NETCDF)
-cpp_path := $(foreach dir,$(cpp_dirs),-I$(dir)) # format for command line
-
-# Expand any tildes in directory names. Change spaces to colons.
-# (the vpath itself is set elsewhere, based on this variable)
-vpath_dirs    := $(foreach dir,$(cpp_dirs),$(wildcard $(dir))) 
-vpath_dirs    := $(subst $(space),:,$(vpath_dirs)) 
-
-#Primary Target: build the tool
-all: $(EXENAME)
-
-# Get list of files and build dependency file for all .o files
-#   using perl scripts mkSrcfiles and mkDepends
-
-SOURCES   := $(shell cat Srcfiles)
-
-OBJS      := $(addsuffix .o, $(basename $(SOURCES)))
-
-# Set path to Mkdepends script; assumes that any Makefile including
-# this file is in a sibling of the src directory, in which Mkdepends
-# resides
-Mkdepends := ../src/Mkdepends
-
-$(CURDIR)/Depends: $(CURDIR)/Srcfiles $(CURDIR)/Filepath
-	$(Mkdepends) Filepath Srcfiles > $@
-
-
-# Architecture-specific flags and rules
-#------------------------------------------------------------------------
-# AIX
-#------------------------------------------------------------------------
-
-ifeq ($(UNAMES),AIX)
-CPPDEF += -DAIX 
-cpre = $(null)-WF,-D$(null)
-FPPFLAGS   := $(patsubst -D%,$(cpre)%,$(CPPDEF))
-FFLAGS  = -c -I$(INC_NETCDF) -q64 -qsuffix=f=f90 -qsuffix=f=f90:cpp=F90 \
-	   $(FPPFLAGS)  -g -qfullpath -qarch=auto -qtune=auto -qsigtrap=xl__trcedump  -qsclk=micro
-
-LDFLAGS = -L$(LIB_NETCDF) -q64 -lnetcdff -lnetcdf
-ifneq ($(OPT),TRUE)
-   FFLAGS  += -qinitauto=7FF7FFFF -qflttrap=ov:zero:inv:en -qspillsize=4000 -C
-else
-   FFLAGS  += -O2 -qmaxmem=-1 -Q
-   LDFLAGS += -Q
-endif
-CFLAGS  := -q64 -g $(CPPDEF) -O2
-FFLAGS += $(cpp_path)
-CFLAGS += $(cpp_path)
-
-ifeq ($(SMP),TRUE)
-  FC       = xlf90_r
-  FFLAGS  += -qsmp=omp
-  LDFLAGS += -qsmp=omp
-else
-  FC       = xlf90
-endif
-
-endif
-
-#------------------------------------------------------------------------
-# Darwin
-#------------------------------------------------------------------------
-
-ifeq ($(UNAMES),Darwin)
-
-# Set the default Fortran compiler
-ifeq ($(USER_FC),$(null))
-  FC := g95
-endif
-ifeq ($(USER_CC),$(null))
-  CC := gcc
-endif
-
-CFLAGS  := -g -O2
-CPPDEF  += -DSYSDARWIN -DDarwin -DLINUX
-LDFLAGS :=
-
-ifeq ($(FC),g95)
-
-   CPPDEF   += -DG95
-   FFLAGS   := -c -fno-second-underscore $(CPPDEF) $(cpp_path) -I$(MOD_NETCDF)
-   ifeq ($(OPT),TRUE)
-     FFLAGS += -O2
-   else
-     FFLAGS += -g -fbounds-check
-   endif
-
-endif
-
-ifeq ($(FC),gfortran)
-
-   CPPDEF   += -DG95
-   FFLAGS   := -c -fno-second-underscore $(CPPDEF) $(cpp_path) -I$(MOD_NETCDF) \
-               -fno-range-check
-   ifeq ($(OPT),TRUE)
-     FFLAGS += -O2
-   else
-     FFLAGS += -g -fbounds-check
-   endif
-
-endif
-
-ifeq ($(FC),ifort)
-
-  CPPDEF  += -DFORTRANUNDERSCORE
-  FFLAGS  += -c -ftz -g -fp-model precise $(CPPDEF) $(cpp_path) \
-             -convert big_endian -assume byterecl -traceback -FR
-  LDFLAGS += -m64
-
-  ifneq ($(OPT),TRUE)
-     FFLAGS    += -CB -O0
-  else
-     FFLAGS    += -O2
-  endif
-  ifeq ($(SMP),TRUE)
-    FFLAGS    += -qopenmp
-    LDFLAGS   += -qopenmp
-  endif
-endif
-
-ifeq ($(FC),pgf90)
-
-  CPPDEF  += -DFORTRANUNDERSCORE
-  FFLAGS  += -c $(CPPDEF) $(cpp_path)
-  ifneq ($(OPT),TRUE)
-    FFLAGS += -g -Ktrap=fp -Mbounds -Kieee
-  else
-    FFLAGS += -fast -Kieee
-  endif
-
-  ifeq ($(SMP),TRUE)
-    FFLAGS   += -mp
-    LDFLAGS  += -mp
-  endif
-
-endif
-
-ifeq ($(CC),icc)
-   CFLAGS     += -m64 -g
-   ifeq ($(SMP),TRUE)
-     CFLAGS    += -qopenmp
-   endif
-endif
-ifeq ($(CC),pgcc)
-  CFLAGS     += -g -fast
-endif
-
-CFLAGS  += $(CPPDEF) $(cpp_path)
-LDFLAGS += -L$(LIB_NETCDF) -lnetcdf -lnetcdff
-
-endif
-
-#------------------------------------------------------------------------
-# Linux
-#------------------------------------------------------------------------
-
-ifeq ($(UNAMES),Linux)
-  ifeq ($(USER_FC),$(null))
-    FC    := ifort
-    FCTYP   := ifort
-  else 
-  ifeq ($(USER_FC),ftn)
-      ifneq ($(USER_FCTYP),$(null))
-         FCTYP := $(USER_FCTYP)
-      else
-         FCTYP := pgf90
-      endif
-    else
-      FCTYP := $(USER_FC)
-    endif
-  endif
-  CPPDEF += -DLINUX -DFORTRANUNDERSCORE
-  CFLAGS := $(CPPDEF)
-  LDFLAGS := $(shell $(LIB_NETCDF)/../bin/nf-config --flibs)
-  FFLAGS =
-
-  ifeq ($(FCTYP),pgf90)
-    CC     := pgcc
-    ifneq ($(OPT),TRUE)
-      FFLAGS += -g -Ktrap=fp -Mbounds -Kieee
-    else
-      FFLAGS += -fast -Kieee
-      CFLAGS += -fast
-    endif
-
-    ifeq ($(SMP),TRUE)
-      FFLAGS   += -mp
-      LDFLAGS  += -mp
-    endif
-
-  endif
-
-  ifeq ($(FCTYP),lf95)
-    ifneq ($(OPT),TRUE)
-      FFLAGS += -g --chk a,e,s,u -O0
-    else
-      FFLAGS += -O
-    endif
-    # Threading only works by putting thread memory on the heap rather than the stack
-    # (--threadheap).
-    # As of lf95 version 6.2 the thread stacksize limits are (still) too small to run
-    # even small
-    # resolution problems (FV at 10x15 res fails).
-    ifeq ($(SMP),TRUE)
-      FFLAGS  += --openmp --threadheap 4096
-      LDFLAGS += --openmp --threadheap 4096
-    endif
-  endif
-  ifeq ($(FCTYP),pathf90)
-    FFLAGS += -extend_source -ftpp -fno-second-underscore
-    ifneq ($(OPT),TRUE)
-      FFLAGS += -g -O0
-    else
-      FFLAGS += -O
-    endif
-    ifeq ($(SMP),TRUE)
-      FFLAGS   += -mp
-      LDFLAGS  += -mp
-    endif
-  endif
-  ifeq ($(FCTYP),ifort)
-
-    FFLAGS      += -ftz -g -fp-model precise -convert big_endian -assume byterecl -traceback -FR
-    CFLAGS      += -m64 -g
-    LDFLAGS   += -m64
-
-    ifneq ($(OPT),TRUE)
-       FFLAGS    += -CB -O0
-    else
-       FFLAGS    += -O2
-    endif
-    ifeq ($(SMP),TRUE)
-      FFLAGS    += -qopenmp
-      CFLAGS    += -qopenmp
-      LDFLAGS   += -qopenmp
-    endif
-  endif
-  FFLAGS += -c -I$(INC_NETCDF) $(CPPDEF) $(cpp_path)
-  CFLAGS += $(cpp_path)
-endif
-
-#------------------------------------------------------------------------
-# Default rules and macros
-#------------------------------------------------------------------------
-
-.SUFFIXES:
-.SUFFIXES: .F90 .c .o
-
-# Set the vpath for all file types EXCEPT .o
-# We do this for individual file types rather than generally using
-# VPATH, because for .o files, we don't want to use files from a
-# different build (e.g., in building the unit tester, we don't want to
-# use .o files from the main build)
-vpath %.F90 $(vpath_dirs)
-vpath %.c $(vpath_dirs)
-vpath %.h $(vpath_dirs)
-
-# Append user defined compiler and load flags to Makefile defaults
-CFLAGS   += $(USER_CFLAGS)
-FFLAGS   += $(USER_FFLAGS)
-LDFLAGS  += $(USER_LDFLAGS)
-
-# Set user specified linker
-ifneq ($(USER_LINKER),$(null))
-  LINKER := $(USER_LINKER)
-else
-  LINKER := $(FC)
-endif
-
-.F90.o:
-	$(FC) $(FFLAGS) $<
-
-.c.o:
-	$(CC) -c $(CFLAGS) $<
-
-
-$(EXENAME): $(OBJS)
-	$(LINKER) -o $@ $(OBJS) $(LDFLAGS)
-
-clean:
-	$(RM) -f $(OBJS) *.mod Depends
-
-include $(CURDIR)/Depends
diff --git a/tools/mkprocdata_map/src/Mkdepends b/tools/mkprocdata_map/src/Mkdepends
deleted file mode 100755
index a75e8fdde0..0000000000
--- a/tools/mkprocdata_map/src/Mkdepends
+++ /dev/null
@@ -1,327 +0,0 @@
-#!/usr/bin/env perl
-
-# Generate dependencies in a form suitable for inclusion into a Makefile.
-# The source filenames are provided in a file, one per line.  Directories
-# to be searched for the source files and for their dependencies are provided
-# in another file, one per line.  Output is written to STDOUT.
-#
-# For CPP type dependencies (lines beginning with #include) the dependency
-# search is recursive.  Only dependencies that are found in the specified
-# directories are included.  So, for example, the standard include file
-# stdio.h would not be included as a dependency unless /usr/include were
-# one of the specified directories to be searched.
-#
-# For Fortran module USE dependencies (lines beginning with a case
-# insensitive "USE", possibly preceded by whitespace) the Fortran compiler
-# must be able to access the .mod file associated with the .o file that
-# contains the module.  In order to correctly generate these dependencies
-# two restrictions must be observed.
-# 1) All modules must be contained in files that have the same base name as
-#    the module, in a case insensitive sense.  This restriction implies that
-#    there can only be one module per file.
-# 2) All modules that are to be contained in the dependency list must be
-#    contained in one of the source files in the list provided on the command
-#    line.
-# The reason for the second restriction is that since the makefile doesn't
-# contain rules to build .mod files the dependency takes the form of the .o
-# file that contains the module.  If a module is being used for which the
-# source code is not available (e.g., a module from a library), then adding
-# a .o dependency for that module is a mistake because make will attempt to
-# build that .o file, and will fail if the source code is not available.
-#
-# Author: B. Eaton
-#         Climate Modelling Section, NCAR
-#         Feb 2001
-
-use Getopt::Std;
-use File::Basename;
-
-# Check for usage request.
-@ARGV >= 2                          or usage();
-
-# Process command line.
-my %opt = ();
-getopts( "t:w", \%opt )           or usage();
-my $filepath_arg = shift()        or usage();
-my $srcfile_arg = shift()         or usage();
-@ARGV == 0                        or usage();  # Check that all args were processed.
-
-my $obj_dir;
-if ( defined $opt{'t'} ) { $obj_dir = $opt{'t'}; }
-
-open(FILEPATH, $filepath_arg) or die "Can't open $filepath_arg: $!\n";
-open(SRCFILES, $srcfile_arg) or die "Can't open $srcfile_arg: $!\n";
-
-# Make list of paths to use when looking for files.
-# Prepend "." so search starts in current directory.  This default is for
-# consistency with the way GNU Make searches for dependencies.
-my @file_paths = <FILEPATH>;
-close(FILEPATH);
-chomp @file_paths;
-unshift(@file_paths,'.');
-foreach $dir (@file_paths) {  # (could check that directories exist here)
-    $dir =~ s!/?\s*$!!;  # remove / and any whitespace at end of directory name
-    ($dir) = glob $dir;  # Expand tildes in path names.
-}
-
-# Make list of files containing source code.
-my @src = <SRCFILES>;
-close(SRCFILES);
-chomp @src;
-
-# For each file that may contain a Fortran module (*.[fF]90 *.[fF]) convert the
-# file's basename to uppercase and use it as a hash key whose value is the file's
-# basename.  This allows fast identification of the files that contain modules.
-# The only restriction is that the file's basename and the module name must match
-# in a case insensitive way.
-my %module_files = ();
-my ($f, $name, $path, $suffix, $mod);
-my @suffixes = ('\.[fF]90', '\.[fF]' );
-foreach $f (@src) {
-    ($name, $path, $suffix) = fileparse($f, @suffixes);
-    ($mod = $name) =~ tr/a-z/A-Z/;
-    $module_files{$mod} = $name;
-}
-
-# Now make a list of .mod files in the file_paths.  If a .o source dependency
-# can't be found based on the module_files list above, then maybe a .mod
-# module dependency can if the mod file is visible.  
-my %trumod_files = ();
-my ($dir);
-my ($f, $name, $path, $suffix, $mod);
-my @suffixes = ('\.mod' );
-foreach $dir (@file_paths) {
-    @filenames = (glob("$dir/*.mod"));
-    foreach $f (@filenames) {
-       ($name, $path, $suffix) = fileparse($f, @suffixes);
-       ($mod = $name) =~ tr/a-z/A-Z/;
-       $trumod_files{$mod} = $name;
-    }
-}
-
-#print STDERR "\%module_files\n";
-#while ( ($k,$v) = each %module_files ) {
-#    print STDERR "$k => $v\n";
-#}
-
-# Find module and include dependencies of the source files.
-my ($file_path, $rmods, $rincs);
-my %file_modules = ();
-my %file_includes = ();
-my @check_includes = ();
-foreach $f ( @src ) {
-
-    # Find the file in the seach path (@file_paths).
-    unless ($file_path = find_file($f)) {
-	if (defined $opt{'w'}) {print STDERR "$f not found\n";}
-	next;
-    }
-
-    # Find the module and include dependencies.
-    ($rmods, $rincs) = find_dependencies( $file_path );
-
-    # Remove redundancies (a file can contain multiple procedures that have
-    # the same dependencies).
-    $file_modules{$f} = rm_duplicates($rmods);
-    $file_includes{$f} = rm_duplicates($rincs);
-
-    # Make a list of all include files.
-    push @check_includes, @{$file_includes{$f}};
-}
-
-#print STDERR "\%file_modules\n";
-#while ( ($k,$v) = each %file_modules ) {
-#    print STDERR "$k => @$v\n";
-#}
-#print STDERR "\%file_includes\n";
-#while ( ($k,$v) = each %file_includes ) {
-#    print STDERR "$k => @$v\n";
-#}
-#print STDERR "\@check_includes\n";
-#print STDERR "@check_includes\n";
-
-# Find include file dependencies.
-my %include_depends = ();
-while (@check_includes) {
-    $f = shift @check_includes;
-    if (defined($include_depends{$f})) { next; }
-
-    # Mark files not in path so they can be removed from the dependency list.
-    unless ($file_path = find_file($f)) {
-	$include_depends{$f} = -1;
-	next;
-    }
-
-    # Find include file dependencies.
-    ($rmods, $include_depends{$f}) = find_dependencies($file_path);
-
-    # Add included include files to the back of the check_includes list so
-    # that their dependencies can be found.
-    push @check_includes, @{$include_depends{$f}};
-
-    # Add included modules to the include_depends list.
-    if ( @$rmods ) { push @{$include_depends{$f}}, @$rmods;  }
-}
-
-#print STDERR "\%include_depends\n";
-#while ( ($k,$v) = each %include_depends ) {
-#    print STDERR (ref $v ? "$k => @$v\n" : "$k => $v\n");
-#}
-
-# Remove include file dependencies that are not in the Filepath.
-my $i, $ii;
-foreach $f (keys %include_depends) {
-
-    unless (ref $include_depends{$f}) { next; }
-    $rincs = $include_depends{$f};
-    unless (@$rincs) { next; }
-    $ii = 0;
-    $num_incs = @$rincs;
-    for ($i = 0; $i < $num_incs; ++$i) {
-    	if ($include_depends{$$rincs[$ii]} == -1) {
-	    splice @$rincs, $ii, 1;
-	    next;
-	}
-    ++$ii;
-    }
-}
-
-# Substitute the include file dependencies into the %file_includes lists.
-foreach $f (keys %file_includes) {
-    my @expand_incs = ();
-
-    # Initialize the expanded %file_includes list.
-    my $i;
-    unless (@{$file_includes{$f}}) { next; }
-    foreach $i (@{$file_includes{$f}}) {
-	push @expand_incs, $i  unless ($include_depends{$i} == -1);
-    }
-    unless (@expand_incs) {
-	$file_includes{$f} = [];
-	next;
-    }
-
-    # Expand
-    for ($i = 0; $i <= $#expand_incs; ++$i) {
-	push @expand_incs, @{ $include_depends{$expand_incs[$i]} };
-    }
-
-    $file_includes{$f} = rm_duplicates(\@expand_incs);
-}
-
-#print STDERR "expanded \%file_includes\n";
-#while ( ($k,$v) = each %file_includes ) {
-#    print STDERR "$k => @$v\n";
-#}
-
-# Print dependencies to STDOUT.
-foreach $f (sort keys %file_modules) {
-    $f =~ /(.+)\./;
-    $target = "$1.o";
-    if ( defined $opt{'t'} ) { $target = "$opt{'t'}/$1.o"; }
-    print "$target : $f @{$file_modules{$f}} @{$file_includes{$f}}\n";
-}
-
-#--------------------------------------------------------------------------------------
-
-sub find_dependencies {
-
-    # Find dependencies of input file.
-    # Use'd Fortran 90 modules are returned in \@mods.
-    # Files that are "#include"d by the cpp preprocessor are returned in \@incs.
-
-    my( $file ) = @_;
-    my( @mods, @incs );
-
-    open(FH, $file)  or die "Can't open $file: $!\n";
-
-    while ( <FH> ) {
-	# Search for "#include" and strip filename when found.
-	if ( /^#include\s+[<"](.*)[>"]/ ) {
-	     push @incs, $1;
-	 } 
-	# Search for Fortran include dependencies.
-	elsif ( /^\s*include\s+['"](.*)['"]/ ) {                   #" for emacs fontlock
-	     push @incs, $1;
-	}
-	# Search for module dependencies.
-	elsif ( /^\s*USE\s+(\w+)/i ) {
-	    ($module = $1) =~ tr/a-z/A-Z/;
-	    # Return dependency in the form of a .o version of the file that contains
-	    # the module.  this is from the source list.
-	    if ( defined $module_files{$module} ) { 
-	        if ( defined $obj_dir ) {
-		    push @mods, "$obj_dir/$module_files{$module}.o";
-	        } else {
-	            push @mods, "$module_files{$module}.o";
-	        }
-	    }
-	    # Return dependency in the form of a .mod version of the file that contains
-	    # the module.  this is from the .mod list.  only if .o version not found
-	    elsif ( defined $trumod_files{$module} ) { 
-	        if ( defined $obj_dir ) {
-		    push @mods, "$obj_dir/$trumod_files{$module}.mod";
-	        } else {
-	            push @mods, "$trumod_files{$module}.mod";
-	        }
-            }
-	}
-    }
-    close( FH );
-    return (\@mods, \@incs);
-}
-
-#--------------------------------------------------------------------------------------
-
-sub find_file {
-
-# Search for the specified file in the list of directories in the global
-# array @file_paths.  Return the first occurance found, or the null string if
-# the file is not found.
-
-    my($file) = @_;
-    my($dir, $fname);
-
-    foreach $dir (@file_paths) {
-	$fname = "$dir/$file";
-	if ( -f  $fname ) { return $fname; }
-    }
-    return '';  # file not found
-}
-
-#--------------------------------------------------------------------------------------
-
-sub rm_duplicates {
-
-# Return a list with duplicates removed.
-
-    my ($in) = @_;       # input arrary reference
-    my @out = ();
-    my $i;
-    my %h = ();
-    foreach $i (@$in) {
-	$h{$i} = '';
-    }
-    @out = keys %h;
-    return \@out;
-}
-
-#--------------------------------------------------------------------------------------
-
-sub usage {
-    ($ProgName = $0) =~ s!.*/!!;            # name of program
-    die <<EOF
-SYNOPSIS
-     $ProgName [-t dir] [-w] Filepath Srcfiles
-OPTIONS
-     -t dir
-          Target directory.  If this option is set the .o files that are
-          targets in the dependency rules have the form dir/file.o.
-     -w   Print warnings to STDERR about files or dependencies not found.
-ARGUMENTS
-     Filepath is the name of a file containing the directories (one per 
-     line) to be searched for dependencies.  Srcfiles is the name of a
-     file containing the names of files (one per line) for which
-     dependencies will be generated.
-EOF
-}
diff --git a/tools/mkprocdata_map/src/Srcfiles b/tools/mkprocdata_map/src/Srcfiles
deleted file mode 100644
index e513374ac0..0000000000
--- a/tools/mkprocdata_map/src/Srcfiles
+++ /dev/null
@@ -1,8 +0,0 @@
-fmain.F90
-mkprocdata_map.F90
-gridmapMod.F90
-fileutils.F90
-shr_kind_mod.F90
-shr_file_mod.F90
-nanMod.F90
-constMod.F90
diff --git a/tools/mkprocdata_map/src/constMod.F90 b/tools/mkprocdata_map/src/constMod.F90
deleted file mode 100644
index 2fd1d39345..0000000000
--- a/tools/mkprocdata_map/src/constMod.F90
+++ /dev/null
@@ -1,11 +0,0 @@
-module constMod
-! Define some constants
-
-   use shr_kind_mod, only : r8 => shr_kind_r8
-   implicit none
-   save
-
-   real(R8),parameter :: SHR_CONST_REARTH  = 6.37122e6_R8   ! radius of earth ~ m
-   real(r8),parameter :: re_km = SHR_CONST_REARTH*0.001        ! radius of earth (km)
-
-end module constMod
diff --git a/tools/mkprocdata_map/src/fileutils.F90 b/tools/mkprocdata_map/src/fileutils.F90
deleted file mode 100644
index e1f8e633da..0000000000
--- a/tools/mkprocdata_map/src/fileutils.F90
+++ /dev/null
@@ -1,282 +0,0 @@
-module fileutils
-
-!-----------------------------------------------------------------------
-!BOP
-!
-! !MODULE: fileutils
-!
-! !DESCRIPTION:
-! Module containing file I/O utilities
-!
-! !USES:
-!
-! !PUBLIC TYPES:
-  implicit none
-  save
-!
-! !PUBLIC MEMBER FUNCTIONS:
-  public :: get_filename  !Returns filename given full pathname
-  public :: opnfil        !Open local unformatted or formatted file
-  public :: getfil        !Obtain local copy of file
-  public :: relavu        !Close and release Fortran unit no longer in use
-  public :: getavu        !Get next available Fortran unit number
-!
-! !REVISION HISTORY:
-! Created by Mariana Vertenstein
-!
-!
-! !PRIVATE MEMBER FUNCTIONS: None
-!EOP
-!-----------------------------------------------------------------------
-
-contains
-
-!-----------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: get_filename
-!
-! !INTERFACE:
-  character(len=256) function get_filename (fulpath)
-!
-! !DESCRIPTION:
-! Returns filename given full pathname
-!
-! !ARGUMENTS:
-    implicit none
-    character(len=*), intent(in)  :: fulpath !full pathname
-!
-! !REVISION HISTORY:
-! Created by Mariana Vertenstein
-!
-!
-! !LOCAL VARIABLES:
-!EOP
-    integer i               !loop index
-    integer klen            !length of fulpath character string
-!------------------------------------------------------------------------
-
-    klen = len_trim(fulpath)
-    do i = klen, 1, -1
-       if (fulpath(i:i) == '/') go to 10
-    end do
-    i = 0
-10  get_filename = fulpath(i+1:klen)
-
-  end function get_filename
-
-!------------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: set_filename
-!
-! !INTERFACE:
-  character(len=256) function set_filename (rem_dir, loc_fn)
-!
-! !DESCRIPTION:
-!
-! !ARGUMENTS:
-!
-    implicit none
-    character(len=*), intent(in)  :: rem_dir !remote directory
-    character(len=*), intent(in)  :: loc_fn  !local full path filename
-!
-! !REVISION HISTORY:
-! Created by Mariana Vertenstein
-!
-!
-! !LOCAL VARIABLES:
-!EOP
-    integer :: i   !integer
-!------------------------------------------------------------------------
-
-    set_filename = ' '
-    do i = len_trim(loc_fn), 1, -1
-       if (loc_fn(i:i)=='/') go to 10
-    end do
-    i = 0
-10  set_filename = trim(rem_dir) // loc_fn(i+1:len_trim(loc_fn))
-
-  end function set_filename
-
-!------------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: getfil
-!
-! !INTERFACE:
-   subroutine getfil (fulpath, locfn, iflag)
-!
-! !DESCRIPTION:
-! Obtain local copy of file
-! First check current working directory
-! Next check full pathname[fulpath] on disk
-! Finally check full pathname[fulpath] on archival system
-! 
-! !USES:
-!
-! !ARGUMENTS:
-     implicit none
-     character(len=*), intent(in)  :: fulpath !Archival or permanent disk full pathname
-     character(len=*), intent(out) :: locfn   !output local file name
-     integer, optional, intent(in) :: iflag   !0=>abort if file not found 1=>do not abort
-!
-! !REVISION HISTORY:
-! Created by Mariana Vertenstein
-!
-!
-! !LOCAL VARIABLES:
-!EOP
-     integer i               !loop index
-     integer klen            !length of fulpath character string
-     integer ierr            !error status
-     logical lexist          !true if local file exists
-     character(len=len(fulpath)+5)  :: fulpath2 !Archival full pathname
-!------------------------------------------------------------------------
-
-     ! get local file name from full name: start at end. look for first "/"
-
-     klen = len_trim(fulpath)
-     do i = klen, 1, -1
-        if (fulpath(i:i).eq.'/') go to 100
-     end do
-     i = 0
-100  locfn = fulpath(i+1:klen)
-     if (len_trim(locfn) == 0) then
-	write(6,*)'(GETFIL): local filename has zero length'
-        stop 1
-     else
-        write(6,*)'(GETFIL): attempting to find local file ',trim(locfn)
-     endif
-
-     ! first check if file is in current working directory.
-
-     inquire (file=locfn,exist=lexist)
-     if (lexist) then
-        write(6,*) '(GETFIL): using ',trim(locfn),' in current working directory'
-        RETURN
-     endif
-
-     ! second check for full pathname on disk
-
-     inquire(file=fulpath, exist=lexist)
-     if (lexist) then
-        locfn = trim(fulpath)
-        write(6,*) '(GETFIL): using ',trim(fulpath)
-        RETURN
-     else
-        write(6,*) 'GETFIL: FAILED to get '//trim(fulpath)
-        stop 1
-     end if
-
-   end subroutine getfil
-
-!------------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: opnfil
-!
-! !INTERFACE:
-   subroutine opnfil (locfn, iun, form)
-!
-! !DESCRIPTION:
-! Open file locfn in unformatted or formatted form on unit iun
-!
-! !ARGUMENTS:
-!
-     implicit none
-     character(len=*), intent(in):: locfn  !file name
-     integer, intent(in):: iun             !fortran unit number
-     character(len=1), intent(in):: form   !file format: u = unformatted,
-                                           !f = formatted
-!
-! !REVISION HISTORY:
-! Created by Mariana Vertenstein
-!
-!
-! !LOCAL VARIABLES:
-!EOP
-     integer ioe             !error return from fortran open
-     character(len=11) ft    !format type: formatted. unformatted
-!------------------------------------------------------------------------
-
-     if (len_trim(locfn) == 0) then
-        write(6,*)'OPNFIL: local filename has zero length'
-        stop 1
-     endif
-     if (form=='u' .or. form=='U') then
-        ft = 'unformatted'
-     else
-        ft = 'formatted  '
-     end if
-     open (unit=iun,file=locfn,status='unknown',form=ft,iostat=ioe)
-     if (ioe /= 0) then
-        write(6,*)'(OPNFIL): failed to open file ',trim(locfn),        &
-             &     ' on unit ',iun,' ierr=',ioe
-        stop 1
-     else
-        write(6,*)'(OPNFIL): Successfully opened file ',trim(locfn),' on unit= ',iun
-     end if
-
-   end subroutine opnfil
-
-!------------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: getavu
-!
-! !INTERFACE:
-  integer function getavu()
-!
-! !DESCRIPTION:
-! Get next available Fortran unit number.
-!
-! !USES:
-   use shr_file_mod, only : shr_file_getUnit
-!
-! !ARGUMENTS:
-    implicit none
-!
-! !REVISION HISTORY:
-! Created by Gordon Bonan
-! Modified for clm2 by Mariana Vertenstein
-!
-!
-! !LOCAL VARIABLES:
-!EOP
-!------------------------------------------------------------------------
-
-    getavu = shr_file_getunit()
-
-  end function getavu
-
-!------------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: relavu
-!
-! !INTERFACE:
-  subroutine relavu (iunit)
-!
-! !DESCRIPTION:
-! Close and release Fortran unit no longer in use!
-!
-! !USES:
-   use shr_file_mod, only : shr_file_freeUnit
-!
-! !ARGUMENTS:
-    implicit none
-    integer, intent(in) :: iunit    !Fortran unit number
-!
-! !REVISION HISTORY:
-! Created by Gordon Bonan
-!
-!EOP
-!------------------------------------------------------------------------
-
-    close(iunit)
-    call shr_file_freeUnit(iunit)
-
-  end subroutine relavu
-
-end module fileutils
diff --git a/tools/mkprocdata_map/src/fmain.F90 b/tools/mkprocdata_map/src/fmain.F90
deleted file mode 100644
index ba9e593c1d..0000000000
--- a/tools/mkprocdata_map/src/fmain.F90
+++ /dev/null
@@ -1,78 +0,0 @@
-program fmain
-
-  use mkprocdata_map, only : mkmap
-  implicit none
-
-  character(len= 256) :: arg
-  integer :: n                   !index 
-  integer :: nargs               !number of arguments  
-  integer, external :: iargc     !number of arguments function
-  character(len=256) :: filei    !input file
-  character(len=256) :: fileo    !output mapped file
-  character(len=256) :: fmap     !maping file
-  character(len=256) :: ftemplate !template file, containing lat & lon arrays desired in output file
-  character(len=256) :: cmdline  !input command line
-  integer, parameter :: inival = -999 !initial value for command-line integers
-  !----------------------------------------------------
-
-  filei = ' '
-  fileo = ' '
-  fmap  = ' '
-  ftemplate = ' '
-
-  cmdline = 'mkprocdata_map'
-  nargs = iargc()
-  n = 1
-  do while (n <= nargs)
-    arg = ' '
-    call getarg (n, arg)
-    n = n + 1
-
-    select case (arg)
-    case ('-i')
-       call getarg (n, arg)
-       n = n + 1
-       filei = trim(arg)
-       cmdline = trim(cmdline) // ' -i ' // trim(arg)
-    case ('-o')
-      call getarg (n, arg)
-      n = n + 1
-      fileo = trim(arg)
-      cmdline = trim(cmdline) // ' -o ' // trim(arg)
-    case ('-m')      
-      call getarg (n, arg)
-      n = n + 1
-      fmap = trim(arg)
-      cmdline = trim(cmdline) // ' -m ' // trim(arg)
-    case ('-t')      
-      call getarg (n, arg)
-      n = n + 1
-      ftemplate = trim(arg)
-      cmdline = trim(cmdline) // ' -t ' // trim(arg)
-    case default
-       write (6,*) 'Argument ', arg,' is not known'
-       call usage_exit (' ')
-       cmdline = trim(cmdline) // ' ' // trim(arg)
-    end select
-  end do
-  
-  if (filei == ' ' .or. fileo == ' ' .or. fmap == ' ' &
-      .or. ftemplate == ' ') then
-    call usage_exit ('Must specify all the following arguments')
-  end if
-
-  call mkmap (filei, fileo, fmap, ftemplate)
-
-end program fmain
-
-
-subroutine usage_exit (arg)
-  implicit none
-  character(len=*) :: arg
-  if (arg /= ' ') write (6,*) arg
-  write (6,*) 'Usage: mkprocdata_map -i <input file>  -o <output file> -m <map file> -t <template file>'
-  write (6,*)
-  write (6,*) "The template file must contain the dimensions 'lat' and 'lon';"
-  write (6,*) "these are used to determine the number of latitudes and longitudes in the output file"
-  stop 1 
-end subroutine
diff --git a/tools/mkprocdata_map/src/gridmapMod.F90 b/tools/mkprocdata_map/src/gridmapMod.F90
deleted file mode 100644
index 376692cf0d..0000000000
--- a/tools/mkprocdata_map/src/gridmapMod.F90
+++ /dev/null
@@ -1,289 +0,0 @@
-module gridmapMod
-
-  use shr_kind_mod, only : r8 => shr_kind_r8
-  use fileutils,    only : getfil
-
-  implicit none
-  private
-  include 'netcdf.inc'
-
-  type gridmap_type
-     character(len=32) :: name
-     integer :: na      ! size of source domain
-     integer :: nb      ! size of destination domain
-     integer :: ni      ! number of row in the matrix
-     integer :: nj      ! number of col in the matrix
-     integer :: ns      ! number of non-zero elements in matrix
-     real(r8), pointer :: yc_src(:) 	! "degrees" 
-     real(r8), pointer :: yc_dst(:) 	! "degrees" 
-     real(r8), pointer :: xc_src(:) 	! "degrees" 
-     real(r8), pointer :: xc_dst(:) 	! "degrees" 
-     integer , pointer :: mask_src(:) 	! "unitless" 
-     integer , pointer :: mask_dst(:) 	! "unitless" 
-     real(R8), pointer :: area_src(:)   ! area of a grid in map (radians)
-     real(R8), pointer :: area_dst(:)   ! area of b grid in map (radians)
-     real(r8), pointer :: frac_src(:) 	! "unitless" 
-     real(r8), pointer :: frac_dst(:) 	! "unitless" 
-     integer , pointer :: src_indx(:)   ! correpsonding column index
-     integer , pointer :: dst_indx(:)   ! correpsonding row    index
-     real(r8), pointer :: wovr(:)       ! wt of overlap input cell
-     real(r8), pointer :: scalepft_i(:) ! PFT wt of overlap input cell
-  end type gridmap_type
-  public :: gridmap_type
-
-  public :: gridmap_mapread
-  public :: gridmap_areaave
-  public :: gridmap_clean
-
-  interface gridmap_areaave
-     module procedure gridmap_areaave_default
-     module procedure gridmap_areaave_mask
-  end interface
-
-  ! questions - how does the reverse mapping occur 
-  ! is mask_dst read in - and what happens if this is very different
-  ! from frac_dst which is calculated by mapping frac_src?
-  ! in frac - isn't grid1_frac always 1 or 0?
-  
-contains
-
-  subroutine gridmap_mapread(gridmap, fileName)
-
-    !--- input/output parameters ---
-    type(gridmap_type), intent(out) :: gridmap   ! mapping data
-    character(len=*)   , intent(in)  :: filename  ! netCDF file to read
-
-
-    !--- local ---
-    integer :: n       ! generic loop indicies
-    integer :: na      ! size of source domain
-    integer :: nb      ! size of destination domain
-    integer :: igrow   ! aVect index for matrix row
-    integer :: igcol   ! aVect index for matrix column
-    integer :: iwgt    ! aVect index for matrix element
-    integer :: iarea   ! aVect index for area
-
-
-    character,allocatable :: str(:)  ! variable length char string
-    character(len=256)    :: attstr  ! netCDF attribute name string
-    integer               :: rcode   ! netCDF routine return code
-    integer               :: fid     ! netCDF file      ID
-    integer               :: vid     ! netCDF variable  ID
-    integer               :: did     ! netCDF dimension ID
-    integer               :: ns      ! size of array
-    character(len=256)    :: locfn
-
-    !--- formats ---
-    character(*),parameter :: subName = '(gridmap_map_read) '
-    character(*),parameter :: F00 = '("(gridmap_map_read) ",4a)'
-    character(*),parameter :: F01 = '("(gridmap_map_read) ",2(a,i7))'
-
-    !-------------------------------------------------------------------------------
-    !
-    !-------------------------------------------------------------------------------
-
-    write(6,F00) "reading mapping matrix data..."
-
-    ! open & read the file
-    write(6,F00) "* file name                  : ",trim(fileName)
-
-    call getfil (trim(filename), locfn, 0)
-    rcode = nf_open(locfn ,NF_NOWRITE, fid)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    !--- allocate memory & get matrix data ----------
-    rcode = nf_inq_dimid (fid, 'n_s', did)  ! size of sparse matrix
-    rcode = nf_inq_dimlen(fid, did  , gridmap%ns)
-    rcode = nf_inq_dimid (fid, 'n_a', did)  ! size of  input vector
-    rcode = nf_inq_dimlen(fid, did  , gridmap%na)
-    rcode = nf_inq_dimid (fid, 'n_b', did)  ! size of output vector
-    rcode = nf_inq_dimlen(fid, did  , gridmap%nb)
-
-    write(6,*) "* matrix dimensions rows x cols :",gridmap%na,' x',gridmap%nb
-    write(6,*) "* number of non-zero elements: ",gridmap%ns
-
-    ns = gridmap%ns
-    na = gridmap%na
-    nb = gridmap%nb
-    allocate(gridmap%wovr(ns)    , &
-             gridmap%src_indx(ns), &
-             gridmap%dst_indx(ns), &
-             gridmap%mask_src(na), &
-             gridmap%area_src(na), &
-             gridmap%frac_src(na), &
-             gridmap%area_dst(nb), &
-             gridmap%frac_dst(nb), &
-             gridmap%mask_dst(nb), &
-             gridmap%xc_src(na),   &
-             gridmap%yc_src(na), stat=rcode)
-    if (rcode /= 0) then
-       write(6,*) SubName//' ERROR: allocate gridmap'
-       stop 1
-    endif
-
-    rcode = nf_inq_varid(fid,'S'  ,vid)
-    rcode = nf_get_var_double(fid,vid  ,gridmap%wovr)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'row',vid)
-    rcode = nf_get_var_int(fid, vid  ,gridmap%dst_indx)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'col',vid)
-    rcode = nf_get_var_int(fid, vid, gridmap%src_indx)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'area_a',vid)
-    rcode = nf_get_var_double(fid, vid, gridmap%area_src)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'area_b',vid)
-    rcode = nf_get_var_double(fid, vid, gridmap%area_dst)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'frac_a',vid)
-    rcode = nf_get_var_double(fid, vid, gridmap%frac_src)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'frac_b',vid)
-    rcode = nf_get_var_double(fid, vid, gridmap%frac_dst)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'mask_a',vid)
-    rcode = nf_get_var_int(fid, vid, gridmap%mask_src)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'mask_b',vid)
-    rcode = nf_get_var_int(fid, vid, gridmap%mask_dst)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'xc_a',vid)
-    rcode = nf_get_var_double(fid, vid, gridmap%xc_src)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_inq_varid(fid,'yc_a',vid)
-    rcode = nf_get_var_double(fid, vid, gridmap%yc_src)
-    if (rcode /= NF_NOERR) write(6,F00) nf_strerror(rcode)
-
-    rcode = nf_close(fid)
-
-  end subroutine gridmap_mapread
-
-!==========================================================================
-
-  subroutine gridmap_areaave_default (gridmap, src_array, dst_array)
-
-    !--- input/output parameters ---
-    type(gridmap_type) , intent(in) :: gridmap   ! gridmap data
-    real(r8), intent(in) :: src_array(:)
-    real(r8), intent(out):: dst_array(:)
-    
-    !--- local ---
-    integer :: n,ns,ni,no
-    real(r8):: wt,frac
-    !----------------------------------------------------------
-
-    dst_array = 0._r8
-    do n = 1,gridmap%ns
-       ni = gridmap%src_indx(n)
-       no = gridmap%dst_indx(n)
-       wt = gridmap%wovr(n)
-       frac = gridmap%frac_dst(no)
-       if (frac > 0.) then  
-          dst_array(no) = dst_array(no) + wt * src_array(ni)/frac
-       end if
-    end do
-
-  end subroutine gridmap_areaave_default
-
-!==========================================================================
-
-  subroutine gridmap_areaave_mask (gridmap, src_array, dst_array, src_mask, &
-       spval)
-
-    !--- input/output parameters ---
-    type(gridmap_type) , intent(in) :: gridmap   ! gridmap data
-    real(r8), intent(in) :: src_array(:)
-    real(r8), intent(out):: dst_array(:)
-    real(r8), intent(in) :: src_mask(:)
-    real(r8), intent(in), optional :: spval
-    
-    !--- local ---
-    integer :: n,ns,ni,no
-    real(r8):: wt
-    real(r8), allocatable :: wtnorm(:)
-    !----------------------------------------------------------
-
-    ns = size(dst_array)
-    allocate(wtnorm(ns)) 
-
-    wtnorm(:) = 0._r8
-    do n = 1,gridmap%ns
-       ni = gridmap%src_indx(n)
-       no = gridmap%dst_indx(n)
-       wt = gridmap%wovr(n)
-       if (src_mask(ni) > 0) then
-          wtnorm(no) = wtnorm(no) + wt*src_mask(ni)
-       end if
-    end do
-
-    do no = 1,ns
-       if (wtnorm(no) > 0) then
-          dst_array(no) = 0._r8
-       else
-          if (present(spval)) then
-             dst_array(no) = spval
-          else
-             dst_array(no) = 1.e36
-          end if
-       end if
-    end do
-
-    do n = 1,gridmap%ns
-       ni = gridmap%src_indx(n)
-       no = gridmap%dst_indx(n)
-       wt = gridmap%wovr(n)
-       if (wtnorm(no) > 0) then 
-          dst_array(no) = dst_array(no) + wt*src_mask(ni)*src_array(ni)/wtnorm(no)
-       end if
-    end do
-
-    deallocate(wtnorm)
-
-  end subroutine gridmap_areaave_mask
-
-!==========================================================================
-
-  subroutine gridmap_clean(gridmap)
-
-    !--- input/output parameters ---
-    implicit none
-    type(gridmap_type), intent(inout)       :: gridmap
-
-
-    !--- local ---
-    character(len=*), parameter :: subName = "gridmap_clean"
-    integer ier    ! error flag
-    !----------------------------------------------------------
-
-    deallocate(gridmap%wovr    , &
-               gridmap%src_indx, &
-               gridmap%dst_indx, &
-               gridmap%mask_src, &
-               gridmap%mask_dst, &
-               gridmap%area_src, &
-               gridmap%area_dst, &
-               gridmap%frac_src, &
-               gridmap%frac_dst, &
-               gridmap%xc_src,   &
-               gridmap%yc_src, stat=ier)
-    if (ier /= 0) then
-       write(6,*) SubName//' ERROR: deallocate gridmap'
-       stop 1
-    endif
-
-  end subroutine gridmap_clean
-
-end module gridmapMod
-
-
diff --git a/tools/mkprocdata_map/src/mkprocdata_map.F90 b/tools/mkprocdata_map/src/mkprocdata_map.F90
deleted file mode 100644
index 1d10671364..0000000000
--- a/tools/mkprocdata_map/src/mkprocdata_map.F90
+++ /dev/null
@@ -1,525 +0,0 @@
-module mkprocdata_map
-
-contains
-
-subroutine mkmap(filei, fileo, fmap, ftemplate)
-
-  use netcdf
-  use shr_kind_mod, only : r8 => shr_kind_r8, r4=>shr_kind_r4
-  use fileutils
-  use gridmapMod
-
-  implicit none
-  character(len=256), intent(in) :: filei   ! input  dataset
-  character(len=256), intent(in) :: fileo   ! output mapped dataset
-  character(len=256), intent(in) :: fmap    ! mapping file
-  character(len=256), intent(in) :: ftemplate ! template file, containing lat & lon arrays desired in output file
-
-
-  integer :: nDimensions    ! number of dimensions defined for this netCDF dataset.
-  integer :: nVariables     ! number of variables defined for this netCDF dataset.
-  integer :: output_n       ! number of variables in the output file that are obtained by
-                            ! regridding variables from the input file
-  integer :: nAttributes    ! number of global attributes defined for this netCDF dataset.
-  integer :: unlimitedDimID ! ID of the unlimited dimension, if there is one
-                            ! If no unlimited length dimension has been defined, 
-                            ! -1 is returned.
-  integer :: ier            ! returned error code
-  integer :: nlen
-  integer :: nlon, nlat
-  integer :: dimid
-  integer :: dimid_lndgrid
-  integer :: dimid_lon, dimid_lat
-  integer :: ncidi, ncido, ncidt
-  integer :: varidi, varido
-  integer :: varid_area
-  integer :: dimlen
-  integer :: xtype
-  integer :: ndimsi,ndimso
-  integer :: dimidsi(4)     ! dimension id array
-  integer :: dimidso(4)     ! dimension id array
-  integer :: nAtts          ! number of variable attributes
-  integer :: n,nv,nt,nd,na  ! indices
-  integer :: attlen
-
-  ! input_ids & output_ids: arrays defining mapping between input & output variables:
-  integer, dimension(:), allocatable :: input_ids
-  integer, dimension(:), allocatable :: output_ids
-
-  character(len=256):: locfn
-  character(len=128):: dimname
-  character(len=128):: varname
-  character(len=128):: attname 
-  character(len=128):: cattvalue
-  real(r8)          :: dattvalue
-  real(r4)          :: fattvalue
-  integer           :: iattvalue
-  type(gridmap_type):: tgridmap
-  logical :: mapvar 
-
-  !--------------------------------------------------------
-  ! Read in mapping file - will have frac in it - and input and output domain
-  !--------------------------------------------------------
-
-  call getfil (fmap, locfn, 0)
-
-  call handle_ncerr(nf90_open(locfn, NF90_NOWRITE, ncidi))
-
-  call get_dimlen(ncidi, 'n_b', nlen)
-
-  call handle_ncerr(nf90_close(ncidi))
-  call gridmap_mapread(tgridmap, locfn)
-
-  !--------------------------------------------------------
-  ! Read in template file to get nlon & nlat
-  !--------------------------------------------------------
-
-  call getfil (ftemplate, locfn, 0)
-
-  call handle_ncerr(nf90_open(locfn, NF90_NOWRITE, ncidt))
-
-  call get_dimlen(ncidt, 'lon', nlon)
-  call get_dimlen(ncidt, 'lat', nlat)
-
-  call handle_ncerr(nf90_close(ncidt))
-
-  write(6,*) 'nlon = ', nlon
-  write(6,*) 'nlat = ', nlat
-
-  if (nlon*nlat /= nlen) then
-     write(6,*) 'must have nlon*nlat == nlen'
-     write(6,*) 'nlon = ', nlon
-     write(6,*) 'nlat = ', nlat
-     write(6,*) 'nlen = ', nlen
-     stop 1
-  end if
-
-  call getfil (filei, locfn, 0)
-
-  !--------------------------------------------------------
-  ! Create output file (put it in define mode)
-  !--------------------------------------------------------
-
-  call handle_ncerr(nf90_create(fileo, NF90_64BIT_OFFSET, ncido))
-
-  !--------------------------------------------------------
-  ! Define output dimensions - creating file puts it in define mode 
-  !--------------------------------------------------------
-
-  call handle_ncerr(nf90_open(locfn, NF90_NOWRITE, ncidi))
-  call handle_ncerr(nf90_inquire(ncidi, nDimensions, nVariables, &
-       nAttributes, unlimitedDimId))
-
-  do nd = 1,nDimensions
-     ! Determine input dimensions
-     call handle_ncerr(nf90_inquire_dimension(ncidi, dimid=nd, name=dimname, len=dimlen))
- 
-     ! Define output variables
-     ! Assume that input dimensions are time, lndgrid
-     ! 2d lon,lat       <=> 1d lndgrid
-     if (dimname == 'time') then
-        call handle_ncerr(nf90_def_dim(ncido, name=dimname, len=nf90_unlimited, dimid=dimid))
-     else
-        if (trim(dimname) == 'lndgrid') then
-           dimid_lndgrid= nd
-           call handle_ncerr(nf90_def_dim(ncido, name='lon', len=nlon, dimid=dimid_lon)) 
-           call handle_ncerr(nf90_def_dim(ncido, name='lat', len=nlat, dimid=dimid_lat)) 
-        else
-           call handle_ncerr(nf90_def_dim(ncido, name=dimname, len=dimlen, dimid=dimid))
-        end if
-     end if
-     write(6,*)'n = ',nd,' dimname= ',trim(dimname)
-  end do
-
-  !--------------------------------------------------------
-  ! Define output variables
-  !--------------------------------------------------------
-
-  allocate(input_ids(nVariables), output_ids(nVariables))
-
-  ! Loop over input variables
-  output_n = 0
-  do nv = 1,nVariables
-
-     ! Determine input variable
-     call handle_ncerr(nf90_Inquire_Variable(ncid=ncidi, varid=nv, natts=natts, &
-          name=varname, ndims=ndimsi, dimids=dimidsi, xtype=xtype)) 
-
-     if (ignore_var(varname)) then
-        write(6,*)'skipping writing out variable ',trim(varname)         
-
-     else
-        output_n = output_n + 1
-        
-        ! Determine output dimension ids
-        if (dimidsi(1) == dimid_lndgrid) then
-           ndimso = ndimsi + 1
-           dimidso(1) = dimid_lon
-           dimidso(2) = dimid_lat
-           do n = 2,ndimsi
-              call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(n), dimname))
-              call handle_ncerr(nf90_inq_dimid(ncido, dimname, dimidso(n+1)))
-           end do
-        else
-           ndimso = ndimsi
-           do n = 1,ndimsi
-              call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(n), dimname))
-              call handle_ncerr(nf90_inq_dimid(ncido, dimname, dimidso(n))) 
-           end do
-        end if
-
-        ! Define output variable and attributes 
-        call handle_ncerr(nf90_def_var(ncido, name=varname, xtype=xtype, &
-             dimids=dimidso(1:ndimso), varid=varido))
-
-        input_ids(output_n) = nv
-        output_ids(output_n) = varido
-
-        do na = 1,natts
-           call handle_ncerr(nf90_inq_attname(ncidi, varid=nv, attnum=na, name=attname))
-           call handle_ncerr(nf90_inquire_attribute(ncidi, varid=nv, name=attname, &
-                len=attlen, xtype=xtype))
-           if (xtype == nf90_char) then
-              call handle_ncerr(nf90_get_att(ncidi, varid=nv, name=attname, values=cattvalue))
-              call handle_ncerr(nf90_put_att(ncido, varid=varido, name=attname, &
-                   values=cattvalue(1:attlen)))
-           else if (xtype == nf90_double) then
-              call handle_ncerr(nf90_get_att(ncidi, varid=nv, name=attname, values=dattvalue))
-              call handle_ncerr(nf90_put_att(ncido, varid=varido, name=attname, values=dattvalue))
-           else if (xtype == nf90_float) then
-              call handle_ncerr(nf90_get_att(ncidi, varid=nv, name=attname, values=fattvalue))
-              call handle_ncerr(nf90_put_att(ncido, varid=varido, name=attname, values=fattvalue))
-           else if (xtype == nf90_int) then
-              call handle_ncerr(nf90_get_att(ncidi, varid=nv, name=attname, values=iattvalue))
-              call handle_ncerr(nf90_put_att(ncido, varid=varido, name=attname, values=iattvalue))
-           end if
-        end do
-
-     end if  ! .not. ignore_var
-  end do
-  ! now output_n is the number of output variables that are regridded from input variables
-
-  call def_area(ncido, dimid_lon, dimid_lat, varid_area)
-
-  ! End define mode
-  call handle_ncerr(nf90_enddef(ncido))  
-
-  !--------------------------------------------------------
-  ! Read in variables and write them out
-  !--------------------------------------------------------
-
-  do nv = 1,output_n
-     call outputvar(input_ids(nv), output_ids(nv), nlon, nlat, ncidi, ncido, tgridmap)
-  end do
-
-  call write_area(ncido, varid_area, tgridmap, nlon, nlat)
-
-  call handle_ncerr(nf90_close(ncidi))
-  call handle_ncerr(nf90_close(ncido))
-
-  deallocate(input_ids, output_ids)
-
-contains
-
-   ! return true if we should ignore this variable, false otherwise
-   ! (this allows us to ignore variables that aren't handled properly in the regridding)
-   logical function ignore_var(varname)
-      character(len=*), intent(in) :: varname
-
-      ! We do NOT exclude 'area' because it may be useful to be able to refer to this in
-      ! the regridded file. See also the 'gw' variable created through def_area /
-      ! write_area for the actual grid cell areas of the output grid.
-      ignore_var = (trim(varname) == 'date_written' .or. &
-                    trim(varname) == 'time_written' .or. &
-                    trim(varname) == 'lon' .or. &
-                    trim(varname) == 'lat' .or. &
-                    trim(varname) == 'landmask' .or. &
-                    trim(varname) == 'pftmask')
-   end function ignore_var
-
-   ! return true if we should weight this variable by landfrac, false otherwise
-   ! note that most variables are weighted by landfrac, so this function just lists those
-   ! variables that are NOT weighted by landfrac
-   logical function weight_by_landfrac(varname)
-      character(len=*), intent(in) :: varname
-
-      weight_by_landfrac = .not. (trim(varname) == 'area' .or. &
-                                  trim(varname) == 'landfrac')
-   end function weight_by_landfrac
-
-   ! Get the length of a dimension from an open netcdf file
-   subroutine get_dimlen(ncid, dimname, len)
-      use netcdf
-
-      implicit none
-
-      ! Subroutine arguments
-      integer, intent(in) :: ncid ! ID of an open netcdf file
-      character(len=*), intent(in) :: dimname ! name of dimension of interest
-      integer, intent(out) :: len ! length of dimension
-
-      ! Local variables
-      integer :: dimid
-      integer :: ier
-
-      call handle_ncerr(nf90_inq_dimid(ncid, dimname, dimid))
-      call handle_ncerr(nf90_inquire_dimension(ncid, dimid, len=len))
-
-   end subroutine get_dimlen
- 
-
-  subroutine outputvar(varidi, varido, nlon, nlat, ncidi, ncido, tgridmap)
-
-    integer, intent(in) :: varidi
-    integer, intent(in) :: varido
-    integer, intent(in) :: nlon
-    integer, intent(in) :: nlat
-    integer, intent(in) :: ncidi
-    integer, intent(in) :: ncido
-    type(gridmap_type), intent(inout) :: tgridmap
-
-    integer :: len1,len2,len3,len4
-    integer :: n1,n2,n3,n4
-    integer :: dimidsi(4)     
-    integer :: dimidso(4)     
-    real(r8), allocatable :: rarrayi(:),rarrayo(:)
-    character(len=128):: dimname
-    character(len=128):: varname
-    character(len=128):: attname 
-    integer :: varid_landfrac
-    logical :: first_time = .true.
-    real(r8), allocatable, save :: landfraci(:) 
-    real(r8), allocatable, save :: src_mask(:)
-    integer :: vid
-    real(r8):: spval = 1.e36 
-
-    ! Allocate landfraci and src_mask; determine landfrac on input file
-    if (first_time) then
-       dimname = 'lndgrid'
-       call handle_ncerr(nf90_inq_dimid(ncidi, dimname, dimidsi(1)))
-       call handle_ncerr(nf90_inquire_dimension(ncidi, dimid=dimidsi(1), len=len1))
-       allocate(landfraci(len1))
-       allocate(src_mask(len1))
-       call handle_ncerr(nf90_inq_varid(ncid=ncidi, name='landfrac', varid=varid_landfrac))
-       call handle_ncerr(nf90_get_var(ncidi, varid_landfrac, landfraci))
-       first_time = .false.
-    end if
-
-    call handle_ncerr(nf90_Inquire_Variable(ncid=ncidi, varid=varidi, &
-         name=varname, ndims=ndimsi, dimids=dimidsi, xtype=xtype))
-    write(6,*)'varidi = ',varidi,' varido = ', varido, ' varname= ',trim(varname),' ndimsi= ',ndimsi 
-    
-    call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(1), &
-         len=len1, name=dimname))
-    allocate(rarrayi(len1))
-    if (trim(dimname)=='lndgrid') then
-       mapvar = .true.
-    else
-       mapvar = .false.
-    end if
-
-    call handle_ncerr(nf90_Inquire_Variable(ncid=ncido, varid=varido, &
-         name=varname, ndims=ndimso, dimids=dimidso, xtype=xtype))
-    if (mapvar) then
-       call handle_ncerr(nf90_inquire_dimension(ncido, dimidso(1), &
-            len=len1, name=dimname))
-       call handle_ncerr(nf90_inquire_dimension(ncido, dimidso(2), &
-            len=len2, name=dimname))
-       allocate(rarrayo(len1*len2))
-    else
-       len1 = size(rarrayi)
-       allocate(rarrayo(len1))
-    end if
-
-    ! src_mask will give the relative weight of each grid cell. i.e., if two source grid
-    ! cells have the same area of overlap with a destination grid cell, then their
-    ! relative weightings are given by their src_mask values.
-    ! For most grid cells, this relative weighting is landfrac, but there are a few
-    ! fields for which we do not want to weight by landfrac.
-    ! Note that, for some fields (fields that are NA over certain landunits) we should
-    ! really also be weighting by an additional factor saying the fraction of land area
-    ! over which that field applies; but more metadata need to be added to the clm
-    ! history files before that will be possible.
-    if (mapvar .and. weight_by_landfrac(varname)) then
-       src_mask(:) = landfraci(:)
-    else
-       ! note that, if we get here because mapvar is false, we currently don't use
-       ! src_mask; but we set it to 1 anyway to be safe
-       src_mask(:) = 1
-    end if
-    
-    if (ndimsi == 1) then
-       call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(1), len=len1))
-       call handle_ncerr(nf90_get_var(ncidi, varidi, rarrayi))
-       if (mapvar) then
-          if (xtype == nf90_int) then
-             where (rarrayi == -9999) src_mask = 0
-             call gridmap_areaave(tgridmap, rarrayi, rarrayo, src_mask, &
-                  spval=-9999._r8)
-          else
-             where (rarrayi == spval) src_mask = 0
-             call gridmap_areaave(tgridmap, rarrayi, rarrayo, src_mask)
-          end if
-          call handle_ncerr(nf90_put_var(ncido, varido, &
-               reshape(rarrayo,(/nlon,nlat/))))
-       else
-          rarrayo(:)= rarrayi(:)
-          call handle_ncerr(nf90_put_var(ncido, varido, rarrayo))
-       end if
-    end if
-    
-    if (ndimsi == 2) then
-       call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(1), len=len1))
-       call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(2), len=len2))
-       do n2 = 1,len2
-          call handle_ncerr(nf90_get_var(ncidi, varidi, rarrayi, &
-               start=(/1,n2/), count=(/len1,1/)))
-          if (mapvar) then
-             if (xtype == nf90_int) then
-                where (rarrayi == -9999) src_mask = 0
-                call gridmap_areaave(tgridmap, rarrayi, rarrayo, src_mask, &
-                     spval=-9999._r8)
-             else
-                where (rarrayi == spval) src_mask = 0
-                call gridmap_areaave(tgridmap, rarrayi, rarrayo, src_mask)
-             end if
-
-             call handle_ncerr(nf90_put_var(ncido, varido, &
-                  reshape(rarrayo,(/nlon,nlat/)), &
-                  start=(/1,1,n2/), count=(/nlon,nlat/)))
-          else
-             rarrayo(:)= rarrayi(:)
-             call handle_ncerr(nf90_put_var(ncido, varido, rarrayo, &
-                  start=(/1,n2/), count=(/len1,1/)))
-           end if
-        end do
-     end if
-     
-     if (ndimsi == 3) then
-        call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(1), len=len1))
-        call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(2), len=len2))
-        call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(3), len=len3))
-        do n2 = 1,len2
-        do n3 = 1,len3           
-           call handle_ncerr(nf90_get_var(ncidi, varidi, rarrayi, &
-                start=(/1,n2,n3/), count=(/len1,1,1/)))
-           if (mapvar) then
-              where (rarrayi == spval) src_mask = 0
-              call gridmap_areaave(tgridmap, rarrayi, rarrayo, src_mask)
-              call handle_ncerr(nf90_put_var(ncido, varido, &
-                   reshape(rarrayo,(/nlon,nlat/)), &
-                   start=(/1,1,n2,n3/), count=(/nlon,nlat/)))
-           else
-              rarrayo(:)= rarrayi(:)
-              call handle_ncerr(nf90_put_var(ncido, varido, rarrayo, &
-                   start=(/1,n2,n3/), count=(/len1,1,1/)))
-           end if
-        end do
-        end do
-     end if
-
-     if (ndimsi == 4) then
-        call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(1), len=len1))
-        call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(2), len=len2))
-        call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(3), len=len3))
-        call handle_ncerr(nf90_inquire_dimension(ncidi, dimidsi(4), len=len4))
-        do n2 = 1,len2
-        do n3 = 1,len3           
-        do n4 = 1,len4           
-           call handle_ncerr(nf90_get_var(ncidi, varidi, rarrayi, &
-                start=(/1,n2,n3,n4/), count=(/len1,1,1,1/)))
-           if (mapvar) then
-              src_mask(:) = 0.
-              where (rarrayi == spval) src_mask = spval
-              call gridmap_areaave(tgridmap, rarrayi, rarrayo)
-              call handle_ncerr(nf90_put_var(ncido, varido, &
-                   reshape(rarrayo,(/nlon,nlat/)), &
-                   start=(/ 1,1,n2,n3,n4 /), count=(/nlon,nlat,1,1,1/)))
-           else
-              rarrayo(:)= rarrayi(:)
-              call handle_ncerr(nf90_put_var(ncido, varido, rarrayo, &
-                   start=(/1,n2,n3,n4/), count=(/len1,1,1,1/)))
-           end if
-        end do
-        end do
-        end do
-     end if
-
-     deallocate(rarrayi)
-     deallocate(rarrayo)
-
-  end subroutine outputvar
-
-
-  ! Define the area variable 'gw' in the output file, return the variable id of this
-  ! variable. This variable will give the actual grid cell areas of the output grid. The
-  ! name ('gw') is consistent with the similar variable in the cam homme regridding
-  ! routine.
-  subroutine def_area(ncido, dimid_lon, dimid_lat, varid)
-     implicit none
-
-     ! Subroutine arguments
-     integer, intent(in) :: ncido      ! netcdf id of output netcdf file, in define mode
-     integer, intent(in) :: dimid_lon  ! id of lon dimension in the file given by ncido
-     integer, intent(in) :: dimid_lat  ! id of lat dimension in the file given by ncido
-     integer, intent(out) :: varid     ! variable id of the newly-created area variable
-     
-     call handle_ncerr(nf90_def_var(ncido, name='gw', xtype=NF90_FLOAT, &
-          dimids=(/dimid_lon,dimid_lat/), varid=varid))
-
-     call handle_ncerr(nf90_put_att(ncido, varid=varid, name='long_name', &
-          values='grid cell areas'))
-
-     call handle_ncerr(nf90_put_att(ncido, varid=varid, name='units', &
-          values='km^2'))
-
-  end subroutine def_area
-
-  ! Write the area variable to the output file. This assumes that def_area has already
-  ! been called, and varid is the variable id returned by that subroutine.
-  subroutine write_area(ncido, varid, tgridmap, nlon, nlat)
-     use constMod, only : re_km  ! radius of earth (km)
-
-     implicit none
-
-     ! Subroutine arguments
-     integer, intent(in) :: ncido   ! netcdf id of output netcdf file, open for writing
-     integer, intent(in) :: varid   ! variable id of the area variable in which we'll put data
-     type(gridmap_type), intent(in) :: tgridmap ! grid information; we're interested in
-                                                ! the area_dst component, assumed to be in
-                                                ! square radians
-     integer, intent(in) :: nlon    ! number of longitudes in the output map
-     integer, intent(in) :: nlat    ! number of latitudes in the output map
-
-     ! Local variables
-     real(r8), dimension(:,:), allocatable :: area_2d  ! grid cell areas, on a 2-d array,
-                                                       ! in km^2
-
-
-     allocate(area_2d(nlon,nlat))
-     area_2d = reshape(tgridmap%area_dst,(/nlon,nlat/)) * re_km**2
-
-     call handle_ncerr(nf90_put_var(ncido, varid, area_2d))
-
-     deallocate(area_2d)
-  end subroutine write_area
-
-  subroutine handle_err(status)
-    integer, intent(in) :: status
-    if (status /= nf90_noerr) then
-       write(6,*)trim(nf90_strerror(status))
-       stop 1
-    end if
-  end subroutine handle_err
-
-  subroutine handle_ncerr(ret)
-     integer         , intent(in) :: ret  ! return code from netCDF library routine
-     if ( ret .ne. NF90_NOERR ) then
-        write(6,*) nf90_strerror( ret )
-        stop 1
-     endif
-   end subroutine handle_ncerr
-
-end subroutine mkmap
-
-end module mkprocdata_map
diff --git a/tools/mkprocdata_map/src/nanMod.F90 b/tools/mkprocdata_map/src/nanMod.F90
deleted file mode 100644
index 0cbeeea112..0000000000
--- a/tools/mkprocdata_map/src/nanMod.F90
+++ /dev/null
@@ -1,41 +0,0 @@
-module nanMod
-
-!-----------------------------------------------------------------------
-!BOP
-!
-! !MODULE: nanMod
-!
-! !DESCRIPTION:
-! Set parameters for the floating point flags "inf" Infinity
-! and "nan" not-a-number. As well as "bigint" the point
-! at which integers start to overflow. These values are used
-! to initialize arrays with as a way to detect if arrays
-! are being used before being set.
-! Note that bigint is the largest possible 32-bit integer.
-!
-! !USES:
-  use shr_kind_mod, only: r8 => shr_kind_r8
-!
-! !PUBLIC TYPES:
-  implicit none
-  save
-#ifdef __PGI
-! quiet nan for portland group compilers
-  real(r8), parameter :: inf = O'0777600000000000000000'
-  real(r8), parameter :: nan = O'0777700000000000000000'
-  integer,  parameter :: bigint = O'17777777777'
-#else
-! signaling nan otherwise
-  real(r8), parameter :: inf = O'0777600000000000000000'
-  real(r8), parameter :: nan = O'0777610000000000000000'
-  integer,  parameter :: bigint = O'17777777777'
-#endif
-!
-! !REVISION HISTORY:
-! Created by Mariana Vertenstein based on cam module created by
-! CCM core group
-!
-!EOP
-!-----------------------------------------------------------------------
-
-end module nanMod
diff --git a/tools/mkprocdata_map/src/shr_file_mod.F90 b/tools/mkprocdata_map/src/shr_file_mod.F90
deleted file mode 100644
index 3279f5ab08..0000000000
--- a/tools/mkprocdata_map/src/shr_file_mod.F90
+++ /dev/null
@@ -1,164 +0,0 @@
-!===============================================================================
-!BOP ===========================================================================
-!
-! !MODULE: shr_file_mod.F90 --- Module to handle various file utilily functions.
-!
-! !DESCRIPTION:
-!
-! Miscilaneous methods to handle file and directory utilities as well as FORTRAN
-! unit control. Also put/get local files into/from archival location
-!
-! !INTERFACE: ------------------------------------------------------------------
-
-MODULE shr_file_mod
-
-! !USES:
-
-   use shr_kind_mod  ! defines kinds
-   
-   IMPLICIT none
-
-   PRIVATE           ! By default everything is private to this module
-   
-! !PUBLIC TYPES:               
-   
-   ! no public types
-
-! !PUBLIC MEMBER FUNCTIONS:
-
-   public :: shr_file_getUnit      ! Get a logical unit for reading or writing
-   public :: shr_file_freeUnit     ! Free a logical unit
-
-! !PUBLIC DATA MEMBERS:
-
-   ! Integer flags for recognized prefixes on file get/put operations
-   !--- unit numbers, users can ask for unit numbers from 0 to min, but getUnit
-   !--- won't give a unit below min, users cannot ask for unit number above max
-   !--- for backward compatability.  
-   !--- eventually, recommend min as hard lower limit (tcraig, 9/2007)
-   integer(SHR_KIND_IN),parameter :: shr_file_minUnit = 10      ! Min unit number to give
-   integer(SHR_KIND_IN),parameter :: shr_file_maxUnit = 99      ! Max unit number to give
-   logical, save :: UnitTag(0:shr_file_maxUnit) = .false. ! Logical units in use
-
-!===============================================================================
-CONTAINS
-!===============================================================================
-
-!===============================================================================
-!BOP ===========================================================================
-!
-! !IROUTINE: shr_file_getUnit -- Get a free FORTRAN unit number
-!
-! !DESCRIPTION: Get the next free FORTRAN unit number.
-!
-! !REVISION HISTORY:
-!     2005-Dec-14 - E. Kluzek - creation
-!
-! !INTERFACE: ------------------------------------------------------------------  
-
-INTEGER FUNCTION shr_file_getUnit ( unit )
-
-   implicit none
-
-! !INPUT/OUTPUT PARAMETERS:
-
-   integer(SHR_KIND_IN),intent(in),optional :: unit ! desired unit number
-
-!EOP
-
-   !----- local -----
-   integer(SHR_KIND_IN)   :: n      ! loop index
-   logical                :: opened ! If unit opened or not
-
-   !----- formats -----
-   character(*),parameter :: subName = '(shr_file_getUnit) '
-   character(*),parameter :: F00   = "('(shr_file_getUnit) ',A,I4,A)"
-
-!-------------------------------------------------------------------------------
-! Notes:
-!-------------------------------------------------------------------------------
-
-   if (present (unit)) then
-      inquire( unit, opened=opened )
-      if (unit < 0 .or. unit > shr_file_maxUnit) then
-         write(6,F00) 'invalid unit number request:', unit
-         write(6,*) 'ERROR: bad input unit number' 
-         stop 1
-      else if (opened .or. UnitTag(unit) .or. unit == 0 .or. unit == 5 &
-               .or. unit == 6) then
-         write(6,F00) 'unit number ', unit, ' is already in use'
-         write(6,*)'ERROR: Input unit number already in use' 
-         stop 1
-      else
-         shr_file_getUnit = unit
-         UnitTag (unit)   = .true.
-         return
-      end if
-
-   else
-      ! --- Choose first available unit other than 0, 5, or 6  ------
-      do n=shr_file_maxUnit, shr_file_minUnit, -1
-         inquire( n, opened=opened )
-         if (n == 5 .or. n == 6 .or. opened) then
-            cycle
-         end if
-         if ( .not. UnitTag(n) ) then
-            shr_file_getUnit = n
-            UnitTag(n)       = .true.
-            return
-         end if
-      end do
-   end if
-
-   write(6,*) trim(subName),': Error: no available units found' 
-   stop 1
-
-END FUNCTION shr_file_getUnit
-
-!===============================================================================
-!BOP ===========================================================================
-!
-! !IROUTINE: shr_file_freeUnit -- Free up a FORTRAN unit number
-!
-! !DESCRIPTION: Free up the given unit number
-!
-! !REVISION HISTORY:
-!     2005-Dec-14 - E. Kluzek - creation
-!
-! !INTERFACE: ------------------------------------------------------------------  
-
-SUBROUTINE shr_file_freeUnit ( unit)
-
-   implicit none
-
-! !INPUT/OUTPUT PARAMETERS:
-
-   integer(SHR_KIND_IN),intent(in) :: unit  ! unit number to be freed
-
-!EOP
-
-   !----- local -----
-
-   !----- formats -----
-   character(*), parameter :: subName = '(shr_file_freeUnit) '
-   character(*), parameter :: F00 =   "('(shr_file_freeUnit) ',A,I4,A)"
-
-!-------------------------------------------------------------------------------
-! Notes:
-!-------------------------------------------------------------------------------
-
-   if (unit < 0 .or. unit > shr_file_maxUnit) then
-      write(6,F00) 'invalid unit number request:', unit
-   else if (unit == 0 .or. unit == 5 .or. unit == 6) then
-      write(6,*) trim(subName),': Error: units 0, 5, and 6 must not be freed' 
-   else if (UnitTag(unit)) then
-      UnitTag (unit) = .false.
-   else
-      write(6,F00) 'unit ', unit, ' was not in use'
-   end if
-
-   return
-
-END SUBROUTINE shr_file_freeUnit
-
-END MODULE shr_file_mod
diff --git a/tools/mkprocdata_map/src/shr_kind_mod.F90 b/tools/mkprocdata_map/src/shr_kind_mod.F90
deleted file mode 100644
index d1219223da..0000000000
--- a/tools/mkprocdata_map/src/shr_kind_mod.F90
+++ /dev/null
@@ -1,19 +0,0 @@
-!===============================================================================
-
-MODULE shr_kind_mod
-
-   !----------------------------------------------------------------------------
-   ! precision/kind constants add data public
-   !----------------------------------------------------------------------------
-   public
-   integer,parameter :: SHR_KIND_R8 = selected_real_kind(12) ! 8 byte real
-   integer,parameter :: SHR_KIND_R4 = selected_real_kind( 6) ! 4 byte real
-   integer,parameter :: SHR_KIND_RN = kind(1.0)              ! native real
-   integer,parameter :: SHR_KIND_I8 = selected_int_kind (13) ! 8 byte integer
-   integer,parameter :: SHR_KIND_I4 = selected_int_kind ( 6) ! 4 byte integer
-   integer,parameter :: SHR_KIND_IN = kind(1)                ! native integer
-   integer,parameter :: SHR_KIND_CS = 80                     ! short char
-   integer,parameter :: SHR_KIND_CL = 256                    ! long char
-   integer,parameter :: SHR_KIND_CX = 512                    ! extra-long char
-
-END MODULE shr_kind_mod
diff --git a/tools/README.filecopies b/tools/mksurfdata_esmf/README.filecopies
similarity index 100%
rename from tools/README.filecopies
rename to tools/mksurfdata_esmf/README.filecopies

From 1f97cb1790963a109bd371ae1620567f9b190828 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 18 Sep 2024 14:36:50 -0600
Subject: [PATCH 1074/1248] Remove mention of mkprocdata_map from README files

---
 .gitignore   |  3 ---
 README       |  2 --
 tools/README | 45 ---------------------------------------------
 3 files changed, 50 deletions(-)

diff --git a/.gitignore b/.gitignore
index 27823e7f54..e24a481063 100644
--- a/.gitignore
+++ b/.gitignore
@@ -85,9 +85,6 @@ ctsm.input_data_list.previous
 # mksurfdata unit tests
 unit_test_build
 
-# Tools executables
-/tools/mkprocdata_map/mkprocdata_map
-
 # run_neon output directories
 /tools/site_and_regional/listing.csv
 /tools/site_and_regional/????/
diff --git a/README b/README
index 8b4e15e557..bde1485450 100644
--- a/README
+++ b/README
@@ -130,8 +130,6 @@ cime_config/usermods_dirs -------- Directories of sets of user-modification subd
 
 tools/mksurfdata_esmf --------- Directory to build program to create surface dataset 
                                 at any resolution.
-tools/mkprocdata_map ---------- Process history data from unstructed grids to a gridded 
-                                format.
 tools/mkmapgrids -------------- NCL script to create a SCRIP grid file for a regular lat/lon grid (deprecated)
 tools/crop_calendars ---------- Tools to process and process and create crop calendar datasets for CTSM
 tools/modify_input_files ------ Script to modify existing CTSM input datasets in standard ways
diff --git a/tools/README b/tools/README
index 568dc1239b..693e793370 100644
--- a/tools/README
+++ b/tools/README
@@ -11,8 +11,6 @@ I.  General directory structure:
         crop_calendars --- Regrid and process GGCMI sowing and harvest date files for use in CTSM.
 
         mkmapgrids ------- Create regular lat/lon SCRIP grid files
-        mkprocdata_map --- Convert output unstructured grids into a 2D format that
-                           can be plotted easily
 
         site_and_regional  Scripts for handling input datasets for site and regional cases.
                            These scripts both help with creation of datasets using the 
@@ -33,49 +31,6 @@ I.  General directory structure:
 
 II. Notes on building/running for each of the above tools:
 
-    mkprocdata_map has the following files to facilitate building the FORTRAN code:
-
-	README ------- Specific help for using the specific tool and help on specific 
-                       files in that directory.
-	src/Filepath ----- List of directories needed to build the tool 
-                           (some files in ../src directories are required).
-	src/Makefile ----- GNU Makefile to build the tool 
-                           (these are identical between tools.
-	src/Macros.custom  Customization of make macros for the particular tool in question
-	src/Srcfiles ----- List of source files that are needed.
-        src/Mkdepends ---- Dependency generator program
-
-    To build:
-
-	cd <directory>
-        setenv INC_NETCDF <path-to-NetCDF-include-files>
-        setenv LIB_NETCDF <path-to-NetCDF-library-files>
-	gmake
-
-    The process will create a file called "Depends" which has the dependencies
-    for the build of each file on other files.
-
-      By default some codes may be compiled non-optimized 
-      so that you can use the debugger, and with bounds-checking, and float trapping on. 
-      To speed up do the following...
-
-   gmake OPT=TRUE
-
-      Also some of the tools allow for OpenMP shared memory parallelism 
-      (such as mksurfdata) with
-
-   gmake SMP=TRUE
-
-    To run a program with a namelist:
-
-        ./program < namelist
-
-    To run a program built with SMP=TRUE:
-
-        setenv OMP_NUM_THREADS=<number_of_threads_to_use>
-
-        run normally as above
-
     mksurfdata_esmf has a cime configure and CMake based build using the following files:
 
         gen_mksurfdata_build ---- Build mksurfdata_esmf

From f04535841632028d01708d7ea4cee509ae6745c4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 18 Sep 2024 14:49:08 -0600
Subject: [PATCH 1075/1248] Remove mention of mkprocdata and the FORTRAN tool
 build from the users guide

---
 .../building-the-clm-tools.rst                | 91 +------------------
 .../what-are-the-clm-tools.rst                | 26 +-----
 2 files changed, 6 insertions(+), 111 deletions(-)

diff --git a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
index 95e0333d6d..a397834c2b 100644
--- a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
@@ -4,96 +4,9 @@
 
 .. include:: ../substitutions.rst
 
-The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools **cprnc** and **gen_domain** use the CIME configure/build system which is described in the next section.
+The tools **cprnc** and **gen_domain** use the CIME configure/build system which is described in the next section.
 
-The Makefiles (for **mksurfdata_esmf** and **mkprocdata_map**) use GNU Make extensions and thus require that you use GNU make to use them. They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. There are also environment variables that can be set to set things that must be customized. All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. Finally the tools allow you to turn optimization on (which is off by default but on for **mksurfdata_esmf**) with the OPT flag so that the tool will run faster.
-
-Options used by all:  **mksurfdata_esmf**
-
-- ``LIB_NETCDF`` -- sets the location of the NetCDF library.
-- ``INC_NETCDF`` -- sets the location of the NetCDF include files.
-- ``USER_FC`` -- sets the name of the FORTRAN compiler.
-
-Options used by: **mkprocdata_map**, and **mksurfdata_esmf**
-
-- ``MOD_NETCDF`` -- sets the location of the NetCDF FORTRAN module.
-- ``USER_LINKER`` -- sets the name of the linker to use.
-- ``USER_CPPDEFS`` -- adds any CPP defines to use.
-- ``USER_CFLAGS`` -- add any "C" compiler flags to use.
-- ``USER_FFLAGS`` -- add any FORTRAN compiler flags to use.
-- ``USER_LDFLAGS`` -- add any linker flags to use.
-- ``USER_CC`` -- sets the name of the "C" compiler to use.
-- ``OPT`` -- set to TRUE to compile the code optimized (TRUE or FALSE)
-- ``SMP`` -- set to TRUE to turn on shared memory parallelism (i.e. OpenMP) (TRUE or FALSE)
-- ``Filepath`` -- list of directories to build source code from.
-- ``Srcfiles`` -- list of source code filenames to build executable from.
-- ``Makefile`` -- customized makefile options for this particular tool.
-- ``mkDepends`` -- figure out dependencies between source files, so make can compile in order..
-- ``Makefile.common`` -- General tool Makefile that should be the same between all tools.
-
-More details on each environment variable.
-
-``LIB_NETCDF``
-  This variable sets the path to the NetCDF library file (``libnetcdf.a``). If not set it defaults to ``/usr/local/lib``. In order to use the tools you need to build the NetCDF library and be able to link to it. In order to build the model with a particular compiler you may have to compile the NetCDF library with the same compiler (or at least a compatible one).
-
-``INC_NETCDF``
-  This variable sets the path to the NetCDF include directory (in order to find the include file ``netcdf.inc``). if not set it defaults to ``/usr/local/include``.
-
-``MOD_NETCDF``
-  This variable sets the path to the NetCDF module directory (in order to find the NetCDF FORTRAN-90 module file when NetCDF is used with a FORTRAN-90 **use statement**. When not set it defaults to the ``LIB_NETCDF`` value.
-
-``USER_FC``
-  This variable sets the command name to the FORTRAN-90 compiler to use when compiling the tool. The default compiler to use depends on the platform. And for example, on the AIX platform this variable is NOT used
-
-``USER_LINKER``
-  This variable sets the command name to the linker to use when linking the object files from the compiler together to build the executable. By default this is set to the value of the FORTRAN-90 compiler used to compile the source code.
-
-``USER_CPPDEFS``
-  This variable adds additional optional values to define for the C preprocessor. Normally, there is no reason to do this as there are very few CPP tokens in the CLM tools. However, if you modify the tools there may be a reason to define new CPP tokens.
-
-``USER_CC``
-  This variable sets the command name to the "C" compiler to use when compiling the tool. The default compiler to use depends on the platform. And for example, on the AIX platform this variable is NOT used
-
-``USER_CFLAGS``
-  This variable adds additional compiler options for the "C" compiler to use when compiling the tool. By default the compiler options are picked according to the platform and compiler that will be used.
-
-``USER_FFLAGS``
-  This variable adds additional compiler options for the FORTRAN-90 compiler to use when compiling the tool. By default the compiler options are picked according to the platform and compiler that will be used.
-
-``USER_LDFLAGS``
-  This variable adds additional options to the linker that will be used when linking the object files into the executable. By default the linker options are picked according to the platform and compiler that is used.
-
-``SMP``
-  This variable flags if shared memory parallelism (using OpenMP) should be used when compiling the tool. It can be set to either TRUE or FALSE, by default it is set to FALSE, so shared memory parallelism is NOT used. When set to TRUE you can set the number of threads by using the OMP_NUM_THREADS environment variable. Normally, the most you would set this to would be to the number of on-node CPU processors. Turning this on should make the tool run much faster.
-
-.. warning:: Note, that depending on the compiler answers may be different when SMP is activated.
-
-``OPT``
-  This variable flags if compiler optimization should be used when compiling the tool. It can be set to either ``TRUE`` or ``FALSE``, by default it is set to for both **mksurfdata_esmf** and **mkprocdata_map**. Turning this on should make the tool run much faster.
-
-.. warning:: Note, you should expect that answers will be different when ``OPT`` is activated.
-
-``Filepath``
-  All of the tools are stand-alone and don't need any outside code to operate. The Filepath is the list of directories needed to compile and hence is always simply "." the current directory. Several tools use copies of code outside their directory that is in the CESM distribution (either ``csm_share`` code or CLM source code).
-
-``Srcfiles``
-  The ``Srcfiles`` lists the filenames of the source code to use when building the tool.
-
-``Makefile``
-  The ``Makefile`` is the custom GNU Makefile for this particular tool. It will customize the ``EXENAME`` and the optimization settings for this particular tool.
-
-``Makefile.common``
-  The ``Makefile.common`` is the copy of the general GNU Makefile for all the CLM tools. This file should be identical between the different tools. This file has different sections of compiler options for different Operating Systems and compilers.
-
-``mkDepends``
-  The ``mkDepends`` is the copy of the perl script used by the ``Makefile.common`` to figure out the dependencies between the source files so that it can compile in the necessary order. This file should be identical between the different tools.
-
-.. note:: There are several files that are copies of the original files. By having copies the tools can all be made stand-alone, but any changes to the originals will have to be put into the tool directories as well.
-
-The *README.filecopies* (which can be found in ``$CTSMROOT/tools``) is repeated here.
-
-.. include:: ../../../../tools/README.filecopies
-   :literal:
+The only CLM FORTRAN tool is mksurfdata_esmf which has it's own build system that takes advantage of the cime build.
 
 ================================================================
  Building the CLM tools that use the CIME configure/build system
diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
index 664e23a220..4778294df9 100644
--- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
@@ -18,15 +18,13 @@ The list of generally important scripts and programs are as follows.
 
 #. *mksurfdata_esmf* to create surface datasets from grid datasets (clm4_0 and |version| versions).
 
-#. *./mkprocdata_map* to interpolate output unstructured grids (such as the CAM HOMME dy-core "ne" grids like ne30np4) into a 2D regular lat/long grid format that can be plotted easily. Can be used by either clm4_0 or |version|.
-
 #. *$CIMEROOT/tools/mapping/gen_domain_files/gen_domain* to create a domain file for datm from a mapping file. The domain file is then used by BOTH datm AND CLM to define the grid and land-mask.
 
 #. *$CIMEROOT/tools/cprnc* to compare two NetCDF files.
 
 In the sections to come we will go into detailed description of how to use each of these tools in turn. First, however we will discuss the common environment variables and options that are used by all of the FORTRAN tools. Second, we go over the outline of the entire file creation process for all input files needed by CLM for a new resolution, then we turn to each tool. In the last section we will discuss how to customize files for particular observational sites.
 
-The FORTRAN tools (mksurfdata_esmf and mkprocdata_map) run, with a namelist (mksurfdata_esmf) to provide options, or with command line arguments (mkprocdata_map).
+The FORTRAN tool (mksurfdata_esmf) runs, with a namelist and has a namelist builder for it.
 
 In the following sections, we will outline how to make these files available for build-namelist so that you can easily create simulations that include them. In the chapter on single-point and regional datasets we also give an alternative way to enter new datasets without having to edit files.
 
@@ -39,29 +37,13 @@ Running FORTRAN tools with namelists
 
    ./program < namelist
 
-There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/mksurfdata_esmf.namleist`` that shows you what the namelist should look like. **mksurfdata_esmf** also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the:
+**mksurfdata_esmf** also has a script that creates the namelist and runs the program for you. The namelist values are also documented along with the other namelists in the:
 ::
 
-   $CTSMROOT/bld/namelist_files/namelist_definition.xml`` file
-        and default values in the:
-   $CTSMROOT/bld/namelist_files/namelist_defaults_clm_tools.xml`` file.
+   $CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` file
 
 -----------------------------------------------
 Running FORTRAN tools with command line options
 -----------------------------------------------
 
-**gen_domain**, mkprocdata_map, and **cprnc** run with command line arguments. The detailed sections below will give you more information on the command line arguments specific to each tool. Also running the tool without any arguments will give you a general synopsis on how to run the tool.
-
------------------------------------------
-Running FORTRAN tools built with SMP=TRUE
------------------------------------------
-
-When you enable ``SMP=TRUE`` on your build of one of the tools that make use of it, you are using OpenMP for shared memory parallelism (SMP). In SMP loops are run in parallel with different threads run on different processors all of which access the same memory (called on-node). Thus you can only usefully run up to the number of processors that are available on a single-node of the machine you are running on. For example, on the NCAR machine cheyenne there are 36 processors per node, so you can use up to 36 processors.
-
-.. _using-ncl:
-
----------
-Using NCL
----------
-
-In the tools directory ``$CTSMROOT/tools/ncl_scripts`` and in a few other locations there are scripts that use NCAR Command Language (NCL). Unlike the FORTRAN tools, you will need to get a copy of NCL in order to use them. You also won't have to build an executable in order to use them, hence no Makefile is provided. NCL is provided for free download as either binaries or source code from: `http://www.ncl.ucar.edu/ <http://www.ncl.ucar.edu/>`_. The NCL web-site also contains documentation on NCL and it's use. These scripts are stand-alone and at most use environment variables to control how to use them. In some cases there are perl scripts with command line arguments that call the NCL scripts to control what they do.
+**gen_domain** and **cprnc** run with command line arguments. The detailed sections below will give you more information on the command line arguments specific to each tool. Also running the tool without any arguments will give you a general synopsis on how to run the tool.

From d6a204710c0b7bc812bea919b46a0c3dafe44f70 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Wed, 18 Sep 2024 15:08:41 -0600
Subject: [PATCH 1076/1248] Move how-to-make-mesh.md to the User's Guide; give
 extension .rst.

Also makes it accessible from table of contents. Not actually changing file contents at this point.
---
 doc/source/users_guide/index.rst                |  1 +
 .../using-mesh-maker/how-to-make-mesh.rst}      |  0
 .../users_guide/using-mesh-maker/index.rst      | 17 +++++++++++++++++
 3 files changed, 18 insertions(+)
 rename doc/source/{how-to-make-mesh.md => users_guide/using-mesh-maker/how-to-make-mesh.rst} (100%)
 create mode 100644 doc/source/users_guide/using-mesh-maker/index.rst

diff --git a/doc/source/users_guide/index.rst b/doc/source/users_guide/index.rst
index 8c675c79db..0bb2dbd75d 100644
--- a/doc/source/users_guide/index.rst
+++ b/doc/source/users_guide/index.rst
@@ -26,5 +26,6 @@
    running-single-points/index.rst
    trouble-shooting/index.rst
    testing/index.rst
+   using-mesh-maker/index.rst
 
 Documentation was built: |today|
diff --git a/doc/source/how-to-make-mesh.md b/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
similarity index 100%
rename from doc/source/how-to-make-mesh.md
rename to doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
diff --git a/doc/source/users_guide/using-mesh-maker/index.rst b/doc/source/users_guide/using-mesh-maker/index.rst
new file mode 100644
index 0000000000..ecc20bab9c
--- /dev/null
+++ b/doc/source/users_guide/using-mesh-maker/index.rst
@@ -0,0 +1,17 @@
+.. on documentation master file, created by
+   sphinx-quickstart on Tue Jan 31 19:46:36 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. include:: ../substitutions.rst
+
+.. _using-mesh-maker-index:
+
+#####################################
+Using mesh_maker
+#####################################
+
+.. toctree::
+   :maxdepth: 2
+
+   how-to-make-mesh.rst

From f84c5b7292453e665c33dd4f6351780d929c29c6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Wed, 18 Sep 2024 15:25:50 -0600
Subject: [PATCH 1077/1248] how-to-make-mesh: Markdown to RestructuredText.

---
 .../using-mesh-maker/how-to-make-mesh.rst     | 139 +++++++++---------
 .../using-mesh-maker/test_mesh_1d_global.png  |   3 +
 .../test_mesh_1d_regional.png                 |   3 +
 .../wrf_domain_regional_plot.png              |   3 +
 4 files changed, 81 insertions(+), 67 deletions(-)
 create mode 100644 doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png
 create mode 100644 doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png
 create mode 100644 doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png

diff --git a/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst b/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
index 0620598e05..9e2bd9ca04 100644
--- a/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
+++ b/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
@@ -1,98 +1,103 @@
-# Creating an ESMF mesh file from a netCDF file
+.. include:: ../substitutions.rst
 
-This gist includes instructions for creating and visualizing a mesh file from a netcdf file with valid 1D or 2D lats and lons coordinates.
+.. _how-to-make-mesh:
+
+===============================================
+ Creating an ESMF mesh file from a netCDF file
+===============================================
 
-* **ESMF Mesh file** aka **Unstructured Grid File Format** is a netcdf file (format) that includes the information about the grids coordinates and their connectivity to each other. 
+This gist includes instructions for creating and visualizing a mesh file from a netcdf file with valid 1D or 2D lats and lons coordinates.
 
-Additional information about ESMF mesh files are available [here](https://earthsystemmodeling.org/docs/release/ESMF_8_0_1/ESMF_refdoc/node3.html#SECTION03028200000000000000).
+.. note:: **ESMF Mesh file** aka **Unstructured Grid File Format** is a netcdf file (format) that includes the information about the grids coordinates and their connectivity to each other. Additional information about ESMF mesh files are available `here <https://earthsystemmodeling.org/docs/release/ESMF_8_0_1/ESMF_refdoc/node3.html#SECTION03028200000000000000>`_.
 
-------
+Example: Making and visualizing a mesh file
+-------------------------------------------
 
-In this example, we will use `./mesh_maker.py` which uses `mesh_type.py` to create a mesh file and visualize it.
+In this example, we will use ``./mesh_maker.py`` which uses ``mesh_type.py`` to create a mesh file and visualize it.
 
 1- First clone my fork and branch that includes these capabilities:
-``` Shell
-git clone https://github.com/negin513/ctsm.git ctsm_mesh
-cd ctsm_mesh
 
-git checkout subset_mesh_dask
-```
+::
+
+   git clone https://github.com/negin513/ctsm.git ctsm_mesh
+   cd ctsm_mesh
+   
+   git checkout subset_mesh_dask
+
 
 2- Next run mesh_maker.py for a netcdf file:
 
-```
-cd tools/site_and_regional
-```
+::
+
+   cd tools/site_and_regional
+
 Check all the avaialble options:
 
-```
-./mesh_maker.py --help
-```
+::
+
+   ./mesh_maker.py --help
+
 
 The output shows all available options for this script:
-```
-|------------------------------------------------------------------|
-|---------------------  Instructions  -----------------------------|
-|------------------------------------------------------------------|
-This script creates ESMF unstructured GRID (mesh file) from a netcdf
-file with valid lats and lons. Provided lats and lons can be 1D or 2D.
-
-For example for running WRF-CTSM cases, the user can create a mesh
-file for their domain :
-    ./mesh_maker.py --input wrfinput_d01 --output my_region
-        --lat XLAT --lon XLONG --verbose
-
-optional arguments:
-  -h, --help        show this help message and exit
-  --input INPUT     Netcdf input file for creating ESMF mesh.
-  --output OUTPUT   Name of the ESMF mesh created.
-  --outdir OUT_DIR  Output directory (only if name of output mesh is not
-                    defined)
-  --lat LAT_NAME    Name of latitude varibale on netcdf input file. If none
-                    given, looks to find variables that include 'lat'.
-  --lon LON_NAME    Name of latitude varibale on netcdf input file. If none
-                    given, looks to find variables that include 'lon'.
-  --mask MASK_NAME  Name of mask varibale on netcdf input file. If none given,
-                    create a fake mask with values of 1.
-  --area AREA_NAME  Name of area variable on netcdf input file. If none given,
-                    ESMF calculates element areas automatically.
-  --overwrite       If meshfile exists, overwrite the meshfile.
-  -v, --verbose     Increase output verbosity
-  
-  ```
-  
+
+::
+
+   |------------------------------------------------------------------|
+   |---------------------  Instructions  -----------------------------|
+   |------------------------------------------------------------------|
+   This script creates ESMF unstructured GRID (mesh file) from a netcdf
+   file with valid lats and lons. Provided lats and lons can be 1D or 2D.
+   
+   For example for running WRF-CTSM cases, the user can create a mesh
+   file for their domain :
+       ./mesh_maker.py --input wrfinput_d01 --output my_region
+           --lat XLAT --lon XLONG --verbose
+   
+   optional arguments:
+     -h, --help        show this help message and exit
+     --input INPUT     Netcdf input file for creating ESMF mesh.
+     --output OUTPUT   Name of the ESMF mesh created.
+     --outdir OUT_DIR  Output directory (only if name of output mesh is not
+                       defined)
+     --lat LAT_NAME    Name of latitude varibale on netcdf input file. If none
+                       given, looks to find variables that include 'lat'.
+     --lon LON_NAME    Name of latitude varibale on netcdf input file. If none
+                       given, looks to find variables that include 'lon'.
+     --mask MASK_NAME  Name of mask varibale on netcdf input file. If none given,
+                       create a fake mask with values of 1.
+     --area AREA_NAME  Name of area variable on netcdf input file. If none given,
+                       ESMF calculates element areas automatically.
+     --overwrite       If meshfile exists, overwrite the meshfile.
+     -v, --verbose     Increase output verbosity
+
 Let's create a mesh file from a netcdf file with 1D lats and lons. On the sample files provided 1D lat and long coordinates are saved on `lsmlat` and `lsmlon` variables. 
 
-```
-./mesh_maker.py --input /glade/scratch/negins/example_files/surfdata_4x5_hist_78pfts_CMIP6_simyr1850_275.0-330.0_-40-15_c220705.nc --output test_mesh_1d.nc --lat lsmlat --lon lsmlon --overwrite
-```
-`--verbose` option also provide additional information for debugging. 
+::
 
-This script will create regional and global mesh plots. For example for the above files, the plos are:
-test_mesh_1d_regional.png
-![image](https://user-images.githubusercontent.com/17344536/200441736-972a8136-5c05-4bc9-9bca-b498d972914a.png)
+   ./mesh_maker.py --input /glade/scratch/negins/example_files/surfdata_4x5_hist_78pfts_CMIP6_simyr1850_275.0-330.0_-40-15_c220705.nc --output test_mesh_1d.nc --lat lsmlat --lon lsmlon --overwrite
 
+``--verbose`` option also provide additional information for debugging. 
 
-test_mesh_1d_global.png
+This script will create regional and global mesh plots. For example for the above files, the plos are:
 
-![image](https://user-images.githubusercontent.com/17344536/200441753-d06e95d1-d85b-4216-9c23-d11ba89a31e4.png)
+.. figure:: test_mesh_1d_regional.png
 
+.. figure:: test_mesh_1d_global.png
 
+Example: Creating Mesh files for a WRF domain
+---------------------------------------------
 
-------
-  ## Creating Mesh files for a WRF domain:
-For running WRF-CTSM cases, we need to create ESMF mesh files for the WRF domain. We can create mesh file from wrfinput (wrf initial condition files). wrfinput has 2D coordinate information on `XLAT` and `XLONG` variable.
+For running WRF-CTSM cases, we need to create ESMF mesh files for the WRF domain. We can create mesh file from wrfinput (wrf initial condition files). wrfinput has 2D coordinate information on ``XLAT`` and ``XLONG`` variable.
 
 For example, let's create a mesh file from a WRF input file for WRF-CTSM run.  
- ```
-./mesh_maker.py --input /glade/scratch/negins/example_files/wrfinput_d01  --output test_mesh_wrf.nc --lat XLAT --lon XLONG --overwrite
-```
 
-This produce mesh files for running for our WRF domain. 
+::
+
+   ./mesh_maker.py --input /glade/scratch/negins/example_files/wrfinput_d01  --output test_mesh_wrf.nc --lat XLAT --lon XLONG --overwrite
 
-Here is how the regional plot looks like for this mesh file:
 
- ![image](https://user-images.githubusercontent.com/17344536/200442002-1ee5595c-9252-4934-a07c-2f6ad86aff1b.png)
+This produce mesh files for running for our WRF domain. 
 
+Here is how the regional plot looks like for this mesh file:
 
- 
\ No newline at end of file
+.. figure:: wrf_domain_regional_plot.png
diff --git a/doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png b/doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png
new file mode 100644
index 0000000000..3245fc621a
--- /dev/null
+++ b/doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a93aa72d564e1533b1217cccb0f34373d0c73b53809a30fc70fa92a464d6f24b
+size 309926
diff --git a/doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png b/doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png
new file mode 100644
index 0000000000..cd033b24f3
--- /dev/null
+++ b/doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e19d289cfb7368c2316ef0619ca70b8c5377b549b01e4811c4c6b78ee0b82a4a
+size 222864
diff --git a/doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png b/doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png
new file mode 100644
index 0000000000..c1c79feca5
--- /dev/null
+++ b/doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:aec6232e209815a6aa99f10d1b740e32407279756516ee394eb2a5c8cd496650
+size 1199433

From 2a6ed6dc90409220da0a179fd3ffa688fd939de7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Wed, 18 Sep 2024 15:46:11 -0600
Subject: [PATCH 1078/1248] Improve mesh_maker instructions.

* The experience of making a mesh from an input with 1d vs. 2d coordinates is identical, so only provide one example.
* In example, use as input file the 5x5_amazon surface dataset included with CTSM.
* Various wording and typo fixes.
---
 .../using-mesh-maker/how-to-make-mesh.rst     | 77 +++++--------------
 1 file changed, 19 insertions(+), 58 deletions(-)

diff --git a/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst b/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
index 9e2bd9ca04..f830413b2f 100644
--- a/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
+++ b/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
@@ -6,98 +6,59 @@
  Creating an ESMF mesh file from a netCDF file
 ===============================================
 
-This gist includes instructions for creating and visualizing a mesh file from a netcdf file with valid 1D or 2D lats and lons coordinates.
+This page includes instructions for using the  ``mesh_maker`` tool to create and visualize a mesh file from a netCDF file with valid 1D or 2D latitude and longitude coordinates.
 
-.. note:: **ESMF Mesh file** aka **Unstructured Grid File Format** is a netcdf file (format) that includes the information about the grids coordinates and their connectivity to each other. Additional information about ESMF mesh files are available `here <https://earthsystemmodeling.org/docs/release/ESMF_8_0_1/ESMF_refdoc/node3.html#SECTION03028200000000000000>`_.
+.. note:: An **ESMF mesh file** is a netCDF file that includes the information about the grid's coordinates and their connectivity to each other in an **Unstructured Grid Format**. Additional information about ESMF mesh files is available `here <https://earthsystemmodeling.org/docs/release/ESMF_8_0_1/ESMF_refdoc/node3.html#SECTION03028200000000000000>`_.
 
-Example: Making and visualizing a mesh file
--------------------------------------------
-
-In this example, we will use ``./mesh_maker.py`` which uses ``mesh_type.py`` to create a mesh file and visualize it.
-
-1- First clone my fork and branch that includes these capabilities:
+You can check out the ``mesh_maker`` options like so:
 
 ::
 
-   git clone https://github.com/negin513/ctsm.git ctsm_mesh
-   cd ctsm_mesh
+   > tools/site_and_regional/mesh_maker --help
    
-   git checkout subset_mesh_dask
-
-
-2- Next run mesh_maker.py for a netcdf file:
-
-::
-
-   cd tools/site_and_regional
-
-Check all the avaialble options:
-
-::
-
-   ./mesh_maker.py --help
-
-
-The output shows all available options for this script:
-
-::
-
    |------------------------------------------------------------------|
    |---------------------  Instructions  -----------------------------|
    |------------------------------------------------------------------|
-   This script creates ESMF unstructured GRID (mesh file) from a netcdf
+   This script creates ESMF unstructured GRID (mesh file) from a netCDF
    file with valid lats and lons. Provided lats and lons can be 1D or 2D.
-   
+
    For example for running WRF-CTSM cases, the user can create a mesh
    file for their domain :
        ./mesh_maker.py --input wrfinput_d01 --output my_region
            --lat XLAT --lon XLONG --verbose
-   
+
    optional arguments:
      -h, --help        show this help message and exit
      --input INPUT     Netcdf input file for creating ESMF mesh.
      --output OUTPUT   Name of the ESMF mesh created.
      --outdir OUT_DIR  Output directory (only if name of output mesh is not
                        defined)
-     --lat LAT_NAME    Name of latitude varibale on netcdf input file. If none
+     --lat LAT_NAME    Name of latitude varibale on netCDF input file. If none
                        given, looks to find variables that include 'lat'.
-     --lon LON_NAME    Name of latitude varibale on netcdf input file. If none
+     --lon LON_NAME    Name of latitude varibale on netCDF input file. If none
                        given, looks to find variables that include 'lon'.
-     --mask MASK_NAME  Name of mask varibale on netcdf input file. If none given,
+     --mask MASK_NAME  Name of mask varibale on netCDF input file. If none given,
                        create a fake mask with values of 1.
-     --area AREA_NAME  Name of area variable on netcdf input file. If none given,
+     --area AREA_NAME  Name of area variable on netCDF input file. If none given,
                        ESMF calculates element areas automatically.
      --overwrite       If meshfile exists, overwrite the meshfile.
      -v, --verbose     Increase output verbosity
 
-Let's create a mesh file from a netcdf file with 1D lats and lons. On the sample files provided 1D lat and long coordinates are saved on `lsmlat` and `lsmlon` variables. 
+Example: Making and visualizing a mesh file
+-------------------------------------------
+
+In this example, we will use ``mesh_maker`` to create a mesh file from a netCDF file with 2D latitudes and longitudes. On the sample input provided, those coordinates are saved on the ``LATIXY`` and ``LONGXY`` variables, respectively.
 
 ::
 
-   ./mesh_maker.py --input /glade/scratch/negins/example_files/surfdata_4x5_hist_78pfts_CMIP6_simyr1850_275.0-330.0_-40-15_c220705.nc --output test_mesh_1d.nc --lat lsmlat --lon lsmlon --overwrite
+   input_file="python/ctsm/test/testinputs/surfdata_5x5_amazon_hist_78pfts_CMIP6_2000_c230517.nc"
+   output_file="meshfile_5x5_amazon.nc"
+   tools/site_and_regional/mesh_maker --input "${input_file}" --output "${output_file}" --lon LONGXY --lat LATIXY
 
 ``--verbose`` option also provide additional information for debugging. 
 
-This script will create regional and global mesh plots. For example for the above files, the plos are:
+This script will create regional and global mesh plots. For example for the above files, the plots are:
 
 .. figure:: test_mesh_1d_regional.png
 
 .. figure:: test_mesh_1d_global.png
-
-Example: Creating Mesh files for a WRF domain
----------------------------------------------
-
-For running WRF-CTSM cases, we need to create ESMF mesh files for the WRF domain. We can create mesh file from wrfinput (wrf initial condition files). wrfinput has 2D coordinate information on ``XLAT`` and ``XLONG`` variable.
-
-For example, let's create a mesh file from a WRF input file for WRF-CTSM run.  
-
-::
-
-   ./mesh_maker.py --input /glade/scratch/negins/example_files/wrfinput_d01  --output test_mesh_wrf.nc --lat XLAT --lon XLONG --overwrite
-
-
-This produce mesh files for running for our WRF domain. 
-
-Here is how the regional plot looks like for this mesh file:
-
-.. figure:: wrf_domain_regional_plot.png

From 1b994352afc87c2ff725341f3db1f8d1cf733190 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 18 Sep 2024 16:40:08 -0600
Subject: [PATCH 1079/1248] Fix typo in mesh_plotter arg description.

---
 python/ctsm/mesh_plotter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/ctsm/mesh_plotter.py b/python/ctsm/mesh_plotter.py
index 7bcbae6fb4..db4a649f6c 100644
--- a/python/ctsm/mesh_plotter.py
+++ b/python/ctsm/mesh_plotter.py
@@ -62,7 +62,7 @@ def get_parser():
 
     parser.add_argument(
         "--overwrite",
-        help="If plots  xists, overwrite them.",
+        help="If plots exist, overwrite them.",
         action="store_true",
         dest="overwrite",
         required=False,

From fc261d4b3204df9caf9ad32afc2b18bc1ad6b783 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 18 Sep 2024 16:40:45 -0600
Subject: [PATCH 1080/1248] mesh_plotter now stops if output file exists w/o
 --overwrite given.

---
 python/ctsm/mesh_plotter.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/python/ctsm/mesh_plotter.py b/python/ctsm/mesh_plotter.py
index db4a649f6c..f26e9bff1f 100644
--- a/python/ctsm/mesh_plotter.py
+++ b/python/ctsm/mesh_plotter.py
@@ -148,8 +148,13 @@ def main():
     this_mesh.read_file(ds)
 
     plot_regional = os.path.splitext(mesh_out)[0] + "_regional" + ".png"
+    file_exists_msg = "File already exists but --overwrite not given: "
+    if os.path.exists(plot_regional) and not args.overwrite:
+        raise FileExistsError(file_exists_msg + plot_regional)
 
     plot_global = os.path.splitext(mesh_out)[0] + "_global" + ".png"
+    if os.path.exists(plot_global) and not args.overwrite:
+        raise FileExistsError(file_exists_msg + plot_global)
 
     this_mesh.make_mesh_plot(plot_regional, plot_global)
 

From 627940aef18f7dc84a79eaef4593f2381356d8d7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 18 Sep 2024 16:41:33 -0600
Subject: [PATCH 1081/1248] Add --dpi option to mesh_plotter.

---
 python/ctsm/mesh_plotter.py                     |  9 ++++++++-
 python/ctsm/site_and_regional/mesh_plot_type.py | 10 +++++-----
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/python/ctsm/mesh_plotter.py b/python/ctsm/mesh_plotter.py
index f26e9bff1f..3ce018e7a7 100644
--- a/python/ctsm/mesh_plotter.py
+++ b/python/ctsm/mesh_plotter.py
@@ -68,6 +68,13 @@ def get_parser():
         required=False,
     )
 
+    default_dpi = 300
+    parser.add_argument(
+        "--dpi",
+        help=f"Dots per square inch in output; default {default_dpi}",
+        type=float,
+    )
+
     add_logging_args(parser)
     return parser
 
@@ -156,7 +163,7 @@ def main():
     if os.path.exists(plot_global) and not args.overwrite:
         raise FileExistsError(file_exists_msg + plot_global)
 
-    this_mesh.make_mesh_plot(plot_regional, plot_global)
+    this_mesh.make_mesh_plot(plot_regional, plot_global, args.dpi)
 
 
 if __name__ == "__main__":
diff --git a/python/ctsm/site_and_regional/mesh_plot_type.py b/python/ctsm/site_and_regional/mesh_plot_type.py
index 872c0e8101..3f52918408 100644
--- a/python/ctsm/site_and_regional/mesh_plot_type.py
+++ b/python/ctsm/site_and_regional/mesh_plot_type.py
@@ -24,7 +24,7 @@ class MeshPlotType(MeshType):
     Extend mesh type with some advanced plotting capability
     """
 
-    def make_mesh_plot(self, plot_regional, plot_global):
+    def make_mesh_plot(self, plot_regional, plot_global, dpi):
         """
         Create plots for the ESMF mesh file
 
@@ -36,10 +36,10 @@ def make_mesh_plot(self, plot_regional, plot_global):
             The path to write the ESMF meshfile global plot
         """
 
-        self.mesh_plot(plot_regional, regional=True)
-        self.mesh_plot(plot_global, regional=False)
+        self.mesh_plot(plot_regional, regional=True, dpi=dpi)
+        self.mesh_plot(plot_global, regional=False, dpi=dpi)
 
-    def mesh_plot(self, plot_file, regional):
+    def mesh_plot(self, plot_file, regional, dpi):
         """Make a plot of a mesh file in either a regional or global grid"""
         # -- regional settings
         if regional:
@@ -131,6 +131,6 @@ def mesh_plot(self, plot_file, regional):
 
             ax.legend(handles, labels)
 
-        plt.savefig(plot_file, bbox_inches="tight")
+        plt.savefig(plot_file, bbox_inches="tight", dpi=dpi)
 
         logger.info("Successfully created %s plots for ESMF Mesh file : %s", plot_type, plot_file)

From 7ad5fd0fcb010fcbb972fe9c0e4bebdbc1d7df37 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 18 Sep 2024 16:41:54 -0600
Subject: [PATCH 1082/1248] More reasonable marker sizes in mesh_plotter.

---
 python/ctsm/site_and_regional/mesh_plot_type.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/ctsm/site_and_regional/mesh_plot_type.py b/python/ctsm/site_and_regional/mesh_plot_type.py
index 3f52918408..8ba13ffa53 100644
--- a/python/ctsm/site_and_regional/mesh_plot_type.py
+++ b/python/ctsm/site_and_regional/mesh_plot_type.py
@@ -49,7 +49,7 @@ def mesh_plot(self, plot_file, regional, dpi):
             plot_type = "regional"
             line_width = 1
             marker = "x"
-            marker_size = 1
+            marker_size = 50
         # global settings
         else:
             fig = plt.figure(num=None, figsize=(15, 10), facecolor="w", edgecolor="k")
@@ -58,7 +58,7 @@ def mesh_plot(self, plot_file, regional, dpi):
             plot_type = "global"
             line_width = 0.5
             marker = "o"
-            marker_size = None
+            marker_size = 0.1
 
         ax.add_feature(cfeature.COASTLINE, edgecolor="black")
         ax.add_feature(cfeature.BORDERS, edgecolor="black")

From 42472940d55d14546a2eb322b7000a3a3850ae45 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 19 Sep 2024 00:46:27 -0600
Subject: [PATCH 1083/1248] Get working for 78 or 16 pft surface datasets, as
 well as 16 or 78 pft fire emission factors datasets

---
 src/biogeochem/FireEmisFactorsMod.F90 | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/biogeochem/FireEmisFactorsMod.F90 b/src/biogeochem/FireEmisFactorsMod.F90
index 31aba66fb2..5ae52ce4af 100644
--- a/src/biogeochem/FireEmisFactorsMod.F90
+++ b/src/biogeochem/FireEmisFactorsMod.F90
@@ -12,6 +12,7 @@ module FireEmisFactorsMod
   use abortutils,   only : endrun
   use clm_varctl,   only : iulog
   use clm_varpar,   only : maxveg
+  use pftconMod,    only : nc3crop
 !
   implicit none
   private
@@ -53,7 +54,6 @@ subroutine fire_emis_factors_get( comp_name, factors, molecwght )
 ! Method for getting FireEmis information for a named compound 
 !
 ! !USES:
-    use pftconMod , only : nc3crop
 ! !ARGUMENTS:
     character(len=*),intent(in)  :: comp_name      ! FireEmis compound name
     real(r8),        intent(out) :: factors(:)     ! vegetation type factors for the compound of interest
@@ -99,6 +99,7 @@ subroutine fire_emis_factors_init( filename )
     use ncdio_pio, only : ncd_pio_openfile,ncd_inqdlen
     use pio, only : pio_inq_varid,pio_get_var,file_desc_t,pio_closefile
     use fileutils   , only : getfil
+    use clm_varpar, only : mxpft
 !
 ! !ARGUMENTS:
     character(len=*),intent(in) :: filename ! FireEmis factors input file
@@ -129,16 +130,20 @@ subroutine fire_emis_factors_init( filename )
     call ncd_inqdlen( ncid, dimid, n_pfts, name='PFT_Num')
 
     npfts = n_pfts
-    if ( npfts < maxveg )then
-       write(iulog,*) ' npfts = ', npfts, ' maxveg = ', maxveg
-       call endrun('Number of PFTs on the fire emissions file is less than the number of PFTs from the surface dataset')
+    if ( (npfts < maxveg) .and. (npfts < nc3crop) )then
+       write(iulog,*) ' npfts = ', npfts, ' maxveg = ', maxveg, ' nat_pft = ', nc3crop
+       call endrun('Number of PFTs on the fire emissions file is less than the number of natural PFTs from the surface dataset')
+    end if
+    if ( npfts > mxpft )then
+       write(iulog,*) ' npfts = ', npfts, ' mxpft = ', mxpft
+       call endrun('Number of PFTs on the fire emissions file is more than the max number of PFTs from the surface dataset with crops')
     end if
 
     ierr = pio_inq_varid(ncid,'Comp_EF',  comp_ef_vid)
     ierr = pio_inq_varid(ncid,'Comp_Name',comp_name_vid)
     ierr = pio_inq_varid(ncid,'Comp_MW',  comp_mw_vid)
 
-    allocate( comp_factors(n_pfts) )
+    allocate( comp_factors(maxveg) )
     allocate( comp_names(n_comps) )
     allocate( comp_molecwghts(n_comps) )
 
@@ -149,7 +154,7 @@ subroutine fire_emis_factors_init( filename )
     call  bld_hash_table_indices( comp_names )
     do i=1,n_comps
        start=(/i,1/)
-       count=(/1,npfts/)
+       count=(/1,min(npfts,maxveg)/)
        ierr = pio_get_var( ncid, comp_ef_vid,  start, count, comp_factors )
 
        call enter_hash_data( trim(comp_names(i)), comp_factors, comp_molecwghts(i)  )

From 23192c619e56f072263947fad0cd6326972bc989 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 19 Sep 2024 07:45:50 -0600
Subject: [PATCH 1084/1248] Apply last suggestion from @samrabin removing the
 npfts module variable and just use the local n_pfts variable that matches the
 name on the dataset

---
 src/biogeochem/FireEmisFactorsMod.F90 | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/src/biogeochem/FireEmisFactorsMod.F90 b/src/biogeochem/FireEmisFactorsMod.F90
index 5ae52ce4af..de4b8280ec 100644
--- a/src/biogeochem/FireEmisFactorsMod.F90
+++ b/src/biogeochem/FireEmisFactorsMod.F90
@@ -23,7 +23,6 @@ module FireEmisFactorsMod
   public :: fire_emis_factors_get
 
 ! !PRIVATE MEMBERS:
-  integer :: npfts ! number of plant function types on the fire emission factors dataset
 !
   type emis_eff_t
      real(r8), pointer :: eff(:) ! emissions efficiency factor
@@ -77,8 +76,8 @@ subroutine fire_emis_factors_get( comp_name, factors, molecwght )
     factors(:maxveg) = comp_factors_table( ndx )%eff(:maxveg)
     ! If fire emissions factor file only includes natural PFT's, but this is a crop case
     ! Copy the generic crop factors to the crop CFT's from generic crop
-    if ( size(factors) > npfts )then
-       factors(npfts+1:) = comp_factors_table( ndx )%eff(nc3crop)
+    if ( size(factors) > nc3crop )then
+       factors(nc3crop+1:) = comp_factors_table( ndx )%eff(nc3crop)
     end if
     molecwght  = comp_factors_table( ndx )%wght
 
@@ -129,13 +128,12 @@ subroutine fire_emis_factors_init( filename )
     call ncd_inqdlen( ncid, dimid, n_comps, name='Comp_Num')
     call ncd_inqdlen( ncid, dimid, n_pfts, name='PFT_Num')
 
-    npfts = n_pfts
-    if ( (npfts < maxveg) .and. (npfts < nc3crop) )then
-       write(iulog,*) ' npfts = ', npfts, ' maxveg = ', maxveg, ' nat_pft = ', nc3crop
+    if ( (n_pfts < maxveg) .and. (n_pfts < nc3crop) )then
+       write(iulog,*) ' n_pfts = ', n_pfts, ' maxveg = ', maxveg, ' nat_pft = ', nc3crop
        call endrun('Number of PFTs on the fire emissions file is less than the number of natural PFTs from the surface dataset')
     end if
-    if ( npfts > mxpft )then
-       write(iulog,*) ' npfts = ', npfts, ' mxpft = ', mxpft
+    if ( n_pfts > mxpft )then
+       write(iulog,*) ' n_pfts = ', n_pfts, ' mxpft = ', mxpft
        call endrun('Number of PFTs on the fire emissions file is more than the max number of PFTs from the surface dataset with crops')
     end if
 
@@ -154,7 +152,7 @@ subroutine fire_emis_factors_init( filename )
     call  bld_hash_table_indices( comp_names )
     do i=1,n_comps
        start=(/i,1/)
-       count=(/1,min(npfts,maxveg)/)
+       count=(/1,min(n_pfts,maxveg)/)
        ierr = pio_get_var( ncid, comp_ef_vid,  start, count, comp_factors )
 
        call enter_hash_data( trim(comp_names(i)), comp_factors, comp_molecwghts(i)  )

From 0eed0336363f964a897f283aa1e88bde48e070c1 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 10:36:01 -0600
Subject: [PATCH 1085/1248] Convert I1850 hillslope 5x5_amazon tests to I2000.

Avoids requiring new fsurdat.
---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 cime_config/testdefs/testlist_clm.xml      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index e18b15a26e..a6ca05446b 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -194,7 +194,7 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld5.5x5_amazon.I1850Clm51Bgc.derecho_gnu.clm-HillslopeC">
+  <test name="SMS_D_Ld5.5x5_amazon.I2000Clm51Bgc.derecho_gnu.clm-HillslopeC">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>#2423</issue>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index d1c3171c98..5750e9a027 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3530,7 +3530,7 @@
     </options>
   </test>
 
-  <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I1850Clm60Bgc" testmods="clm/HillslopeC">
+  <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="hillslope"/>
@@ -3540,7 +3540,7 @@
     </options>
   </test>
 
-  <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I1850Clm60Bgc" testmods="clm/HillslopeC">
+  <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>

From 08d0923c54fc89da2a7ef698722b6282506bf745 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 11:21:39 -0600
Subject: [PATCH 1086/1248] Add non-serial HillslopeC 5x5_amazon test to
 hillslope suite.

---
 cime_config/testdefs/testlist_clm.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 5750e9a027..79cf2efbcd 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3543,6 +3543,7 @@
   <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="hillslope"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>

From 7242a6bfc8029fa4b270fabc3e6327f5d5960b1c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 11:22:35 -0600
Subject: [PATCH 1087/1248] Add issue reference to non-serial HillslopeC
 5x5_amazon test.

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 79cf2efbcd..b92c62be15 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3547,7 +3547,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment">Add a non-FATES test to aux_clm for 5x5_amazon that fails because of the ccs_config issue, can remove once this passes</option>
+      <option name="comment">Add a non-FATES test to aux_clm for 5x5_amazon that fails because of the ccs_config issue (see #2423); can remove once this passes</option>
     </options>
   </test>
 

From 8361f8b4719c63e7e171d900cbd175ca1e7ec716 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 11:34:21 -0600
Subject: [PATCH 1088/1248] Fix HillslopeC test in expected fails list.

---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index a6ca05446b..35c452b88c 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -194,7 +194,7 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld5.5x5_amazon.I2000Clm51Bgc.derecho_gnu.clm-HillslopeC">
+  <test name="SMS_D_Ld5.5x5_amazon.I2000Clm60Bgc.derecho_gnu.clm-HillslopeC">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>#2423</issue>

From edbef5f353cbf37fa3dfbeb1ebad1b0322e3f814 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Wed, 18 Sep 2024 17:14:37 -0600
Subject: [PATCH 1089/1248] Add mesh_plotter instructions.

---
 .../using-mesh-maker/how-to-make-mesh.rst         | 15 +++++++++------
 .../using-mesh-maker/test_c240918_global.png      |  3 +++
 .../using-mesh-maker/test_c240918_regional.png    |  3 +++
 .../using-mesh-maker/test_mesh_1d_global.png      |  3 ---
 .../using-mesh-maker/test_mesh_1d_regional.png    |  3 ---
 .../using-mesh-maker/wrf_domain_regional_plot.png |  3 ---
 python/ctsm/site_and_regional/mesh_plot_type.py   |  4 ++--
 7 files changed, 17 insertions(+), 17 deletions(-)
 create mode 100644 doc/source/users_guide/using-mesh-maker/test_c240918_global.png
 create mode 100644 doc/source/users_guide/using-mesh-maker/test_c240918_regional.png
 delete mode 100644 doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png
 delete mode 100644 doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png
 delete mode 100644 doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png

diff --git a/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst b/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
index f830413b2f..f87394fd89 100644
--- a/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
+++ b/doc/source/users_guide/using-mesh-maker/how-to-make-mesh.rst
@@ -6,7 +6,7 @@
  Creating an ESMF mesh file from a netCDF file
 ===============================================
 
-This page includes instructions for using the  ``mesh_maker`` tool to create and visualize a mesh file from a netCDF file with valid 1D or 2D latitude and longitude coordinates.
+This page includes instructions for using the  ``mesh_maker`` tool to create a mesh file from a netCDF file with valid 1D or 2D latitude and longitude coordinates. It also shows how to use ``mesh_plotter`` to visualize a mesh file.
 
 .. note:: An **ESMF mesh file** is a netCDF file that includes the information about the grid's coordinates and their connectivity to each other in an **Unstructured Grid Format**. Additional information about ESMF mesh files is available `here <https://earthsystemmodeling.org/docs/release/ESMF_8_0_1/ESMF_refdoc/node3.html#SECTION03028200000000000000>`_.
 
@@ -53,12 +53,15 @@ In this example, we will use ``mesh_maker`` to create a mesh file from a netCDF
 
    input_file="python/ctsm/test/testinputs/surfdata_5x5_amazon_hist_78pfts_CMIP6_2000_c230517.nc"
    output_file="meshfile_5x5_amazon.nc"
+   
+   # Create the file. (Add --verbose for additional debugging information.)
    tools/site_and_regional/mesh_maker --input "${input_file}" --output "${output_file}" --lon LONGXY --lat LATIXY
+   
+   # Visualize the meshes
+   tools/site_and_regional/mesh_plotter --input "${output_file}"
 
-``--verbose`` option also provide additional information for debugging. 
-
-This script will create regional and global mesh plots. For example for the above files, the plots are:
+This produces two figures:
 
-.. figure:: test_mesh_1d_regional.png
+.. figure:: test_c240918_regional.png
 
-.. figure:: test_mesh_1d_global.png
+.. figure:: test_c240918_global.png
diff --git a/doc/source/users_guide/using-mesh-maker/test_c240918_global.png b/doc/source/users_guide/using-mesh-maker/test_c240918_global.png
new file mode 100644
index 0000000000..b951c570ab
--- /dev/null
+++ b/doc/source/users_guide/using-mesh-maker/test_c240918_global.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:48f47d585b38798710f59edf4cee8fd6b5cb77c81ec1160749fec706c0b106b4
+size 1031528
diff --git a/doc/source/users_guide/using-mesh-maker/test_c240918_regional.png b/doc/source/users_guide/using-mesh-maker/test_c240918_regional.png
new file mode 100644
index 0000000000..f1b761ba10
--- /dev/null
+++ b/doc/source/users_guide/using-mesh-maker/test_c240918_regional.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1dfaa42056d68629c2c6ba1e847ae5e462fccf7d2175d6f6b4d65d5b3aad7491
+size 642577
diff --git a/doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png b/doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png
deleted file mode 100644
index 3245fc621a..0000000000
--- a/doc/source/users_guide/using-mesh-maker/test_mesh_1d_global.png
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a93aa72d564e1533b1217cccb0f34373d0c73b53809a30fc70fa92a464d6f24b
-size 309926
diff --git a/doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png b/doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png
deleted file mode 100644
index cd033b24f3..0000000000
--- a/doc/source/users_guide/using-mesh-maker/test_mesh_1d_regional.png
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:e19d289cfb7368c2316ef0619ca70b8c5377b549b01e4811c4c6b78ee0b82a4a
-size 222864
diff --git a/doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png b/doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png
deleted file mode 100644
index c1c79feca5..0000000000
--- a/doc/source/users_guide/using-mesh-maker/wrf_domain_regional_plot.png
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:aec6232e209815a6aa99f10d1b740e32407279756516ee394eb2a5c8cd496650
-size 1199433
diff --git a/python/ctsm/site_and_regional/mesh_plot_type.py b/python/ctsm/site_and_regional/mesh_plot_type.py
index 872c0e8101..806e884cbe 100644
--- a/python/ctsm/site_and_regional/mesh_plot_type.py
+++ b/python/ctsm/site_and_regional/mesh_plot_type.py
@@ -49,7 +49,7 @@ def mesh_plot(self, plot_file, regional):
             plot_type = "regional"
             line_width = 1
             marker = "x"
-            marker_size = 1
+            marker_size = None
         # global settings
         else:
             fig = plt.figure(num=None, figsize=(15, 10), facecolor="w", edgecolor="k")
@@ -58,7 +58,7 @@ def mesh_plot(self, plot_file, regional):
             plot_type = "global"
             line_width = 0.5
             marker = "o"
-            marker_size = None
+            marker_size = 0.01
 
         ax.add_feature(cfeature.COASTLINE, edgecolor="black")
         ax.add_feature(cfeature.BORDERS, edgecolor="black")

From 5fb68ac1bf2ff90eddb1e759573ebd31c4bf66e6 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 19 Sep 2024 19:11:56 -0600
Subject: [PATCH 1090/1248] UG: Fix path of example mksurfdata_esmf namelist.

---
 .../users_guide/using-clm-tools/what-are-the-clm-tools.rst      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
index 664e23a220..db5cf10798 100644
--- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
@@ -39,7 +39,7 @@ Running FORTRAN tools with namelists
 
    ./program < namelist
 
-There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/mksurfdata_esmf.namleist`` that shows you what the namelist should look like. **mksurfdata_esmf** also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the:
+There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` that shows you what the namelist should look like. **mksurfdata_esmf** also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the:
 ::
 
    $CTSMROOT/bld/namelist_files/namelist_definition.xml`` file

From 2d39418b6e897a62f77c758e7bdb0a2df44e006e Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 19 Sep 2024 19:41:20 -0600
Subject: [PATCH 1091/1248] Add double backticks in lots of places.

---
 ...w-Files-to-the-build-namelist-Database.rst |  2 +-
 .../Adding-Resolution-Names.rst               |  2 +-
 .../users_guide/overview/introduction.rst     |  2 +-
 .../users_guide/overview/quickstart.rst       |  2 +-
 .../running-pts_mode-configurations.rst       |  2 +-
 .../running-single-point-configurations.rst   |  4 +-
 ...point-and-regional-grid-configurations.rst |  2 +-
 ...transient-historical-CO2-concentration.rst |  2 +-
 .../Running-the-prognostic-crop-model.rst     |  2 +-
 .../Running-with-irrigation.rst               |  2 +-
 ...ning-up-the-biogeochemistry-BGC-spinup.rst |  8 +-
 .../customizing-the-clm-configuration.rst     | 90 +++++++++----------
 .../customizing-the-clm-namelist.rst          | 22 ++---
 doc/source/users_guide/testing/testing.rst    |  4 +-
 .../trouble-shooting/trouble-shooting.rst     | 16 ++--
 .../building-the-clm-tools.rst                | 18 ++--
 .../users_guide/using-clm-tools/cprnc.rst     |  2 +-
 .../using-clm-tools/creating-domain-files.rst |  8 +-
 ...g-input-for-surface-dataset-generation.rst |  2 +-
 .../creating-surface-datasets.rst             | 16 ++--
 .../what-are-the-clm-tools.rst                | 20 ++---
 21 files changed, 114 insertions(+), 114 deletions(-)

diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
index 78edaaf629..fc7b2c0ee3 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
@@ -8,7 +8,7 @@
 
 In the last chapter we gave the details on how to create new files for input into CLM. These files could be either global resolutions, regional-grids or even a single grid point. If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. You can deal with them, just by putting the settings in the ``user_nl_clm namelist`` file, or by using ``CLM_USRDAT_NAME``. Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. This keeps one central database for all your files, rather than having multiple locations to keep track of files. If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above.
 
-There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into **create_newcase** -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
+There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into ``create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
 
 The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file.
 
diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst
index 216de19f54..d89cc13930 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst
@@ -6,7 +6,7 @@
  Adding Resolution Names
 =========================
 
-If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. The list of valid resolutions is in the id="res" entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the id="res" entry. The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. The convention for unstructured HOMME grids is ne<size>np4, where <size> corresponds to the resolution. The higher <size> is the higher the resolution. So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. The only hard requirement is that names be unique for different grid files. Here's what the entry for resolutions looks like in the file:
+If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. The list of valid resolutions is in the ``id="res"`` entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the ``id="res"`` entry. The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. The convention for unstructured HOMME grids is ne<size>np4, where <size> corresponds to the resolution. The higher <size> is the higher the resolution. So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. The only hard requirement is that names be unique for different grid files. Here's what the entry for resolutions looks like in the file:
 ::
 
    <entry id="res" type="char*30" category="default_settings"
diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst
index e02fa3e422..8056e6ab16 100644
--- a/doc/source/users_guide/overview/introduction.rst
+++ b/doc/source/users_guide/overview/introduction.rst
@@ -107,7 +107,7 @@ The README (which can be found in ``$CTSMROOT/doc``) is repeated here.
 A CTSM versus a CESM checkout
 =============================
 
-The directory structure for |version| is different depending on if it's checked out from |release| or |cesmrelease|. If |version| is checked out from |ctsm_gh| the CLM source code is directly under the top level directory. If |cesmrelease| is checkout out from |cesm_gh| then the CLM source directories are under "components/clm" from the top level directory. We will refer to this directory for the CLM source directories in the User's Guide as "$CTSMROOT".
+The directory structure for |version| is different depending on if it's checked out from |release| or |cesmrelease|. If |version| is checked out from |ctsm_gh| the CLM source code is directly under the top level directory. If |cesmrelease| is checkout out from |cesm_gh| then the CLM source directories are under ``components/clm`` from the top-level directory. We will refer to this directory for the CLM source directories in the User's Guide as ``$CTSMROOT``.
 
 .. _how-to-use-this-document:
 
diff --git a/doc/source/users_guide/overview/quickstart.rst b/doc/source/users_guide/overview/quickstart.rst
index 5414963c4d..63f4afea6f 100644
--- a/doc/source/users_guide/overview/quickstart.rst
+++ b/doc/source/users_guide/overview/quickstart.rst
@@ -16,7 +16,7 @@ List of utilities required for CESM in the `Software/OS Prerequisites <https://w
 
 Before working with |version| read the `CESM QuickStart Guide <https://escomp.github.io/CESM/versions/cesm2.2/html/>`_. Once you are familiar with how to setup cases for any type of simulation with CESM you will want to direct your attention to the specifics of using CLM.
 
-For some of the details of setting up cases for |version| read the README and text files available from the "$CTSMROOT/doc" directory (see the "CLM Web pages" section for a link to the list of these files). Here are the important ones that you should be familiar with:
+For some of the details of setting up cases for |version| read the README and text files available from the ``$CTSMROOT/doc`` directory (see the "CLM Web pages" section for a link to the list of these files). Here are the important ones that you should be familiar with:
 
 - :ref:`readme` describing the directory structure.
 - The IMPORTANT_NOTES file talks about important things for users to know about using the model scientifically. It content is given in the next chapter on :ref:`scientific-validiation`.
diff --git a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst
index d3b14e6184..edad4c25ff 100644
--- a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst
+++ b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst
@@ -8,7 +8,7 @@ Running a single point using global data - PTS_MODE
 
 ``PTS_MODE`` enables you to run the model using global datasets, but just picking a single point from those datasets and operating on it. It can be a very quick way to do fast simulations and get a quick turnaround.
 
-To setup a ``PTS_MODE`` simulation you use the "-pts_lat" and "-pts_lon" arguments to **create_newcase** to give the latitude and longitude of the point you want to simulate for (the code will pick the point on the global grid nearest to the point you give. Here's an example to setup a simulation for the nearest point at 2-degree resolution to Boulder Colorado.
+To setup a ``PTS_MODE`` simulation you use the ``-pts_lat`` and ``-pts_lon`` arguments to ``create_newcase`` to give the latitude and longitude of the point you want to simulate for (the code will pick the point on the global grid nearest to the point you give. Here's an example to setup a simulation for the nearest point at 2-degree resolution to Boulder Colorado.
 ::
 
    > cd scripts
diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
index 9d2b68456b..766eca63fd 100644
--- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
+++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
@@ -74,7 +74,7 @@ Supported single-point runs for sites with their own atmospheric forcing
 
 Of the supported single-point datasets we have three that also have atmospheric forcing data that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and ``urbanc_alpha`` (test data for an Urban inter-comparison project). Mexico city and Vancouver also have namelist options in the source code for them to work with modified urban data parameters that are particular to these locations. To turn on the atmospheric forcing for these datasets, you set the ``env_run.xml DATM_MODE`` variable to ``CLM1PT``, and then the atmospheric forcing datasets will be used for the point picked. If you use one of the compsets that has "I1Pt" in the name that will be set automatically.
 
-When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. For the supported data points, these values are in the XML database and you can use the **queryDefaultNamelist.pl** script to query the values and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and urbanc_alpha).
+When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. For the supported data points, these values are in the XML database and you can use the ``queryDefaultNamelist.pl`` script to query the values and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and urbanc_alpha).
 
 Example: Use site-specific atmospheric forcings
 -----------------------------------------------
@@ -199,4 +199,4 @@ Example: Setting up a case from the single-point surface dataset just created
    > ./xmlchange CLM_USRDAT_NAME=$GRIDNAME
    > ./case.setup
 
-.. note:: With this and previous versions of the model we recommended using ``CLM_USRDAT_NAME`` as a way to identify your own datasets without having to enter them into the XML database. This has the down-side that you can't include creation dates in your filenames, which means you can't keep track of different versions by date. It also means you HAVE to rename the files after you created them with **mksurfdata.pl**. Now, since ``user_nl`` files are supported for ALL model components, and the same domain files are read by both CLM and DATM and set using the envxml variables: ``ATM_DOMAIN_PATH``, ``ATM_DOMAIN_FILE``, ``LND_DOMAIN_PATH``, and ``LND_DOMAIN_FILE`` -- you can use this mechanism (``user_nl_clm`` and ``user_nl_datm`` and those envxml variables) to point to your datasets in any location. In the future we will deprecate ``CLM_USRDAT_NAME`` and recommend ``user_nl_clm`` and ``user_nl_datm`` and the ``DOMAIN`` envxml variables.
+.. note:: With this and previous versions of the model we recommended using ``CLM_USRDAT_NAME`` as a way to identify your own datasets without having to enter them into the XML database. This has the down-side that you can't include creation dates in your filenames, which means you can't keep track of different versions by date. It also means you HAVE to rename the files after you created them with ``mksurfdata.pl``. Now, since ``user_nl`` files are supported for ALL model components, and the same domain files are read by both CLM and DATM and set using the envxml variables: ``ATM_DOMAIN_PATH``, ``ATM_DOMAIN_FILE``, ``LND_DOMAIN_PATH``, and ``LND_DOMAIN_FILE`` -- you can use this mechanism (``user_nl_clm`` and ``user_nl_datm`` and those envxml variables) to point to your datasets in any location. In the future we will deprecate ``CLM_USRDAT_NAME`` and recommend ``user_nl_clm`` and ``user_nl_datm`` and the ``DOMAIN`` envxml variables.
diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
index ab7e923669..5e20a303fb 100644
--- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
+++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
@@ -24,7 +24,7 @@ There are two different ways to do this for normal-supported site
 
 Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see :ref:`running-single-point-datasets`). All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. The problem is that there is a very limited set of supported datasets. You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region.
 
-In general :ref:`pts_mode` is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from **create_newcase**. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts.
+In general :ref:`pts_mode` is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from ``create_newcase``. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts.
 
 Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see :ref:`running-single-point-datasets`). With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method.
 
diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
index f93bcca2f0..eedefd8744 100644
--- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
+++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
@@ -6,7 +6,7 @@
  Running with historical CO2 forcing
 =====================================
 
-In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. For this example, we will start with the "I_1850-2000_CN" compset that has transient: land-use, Nitrogen and Aerosol deposition already. You could also use another compset if you didn't want these other features to be transient. In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the user_nl_datm file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file.
+In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. For this example, we will start with the ``I_1850-2000_CN`` compset that has transient land-use, Nitrogen and Aerosol deposition already. You could also use another compset if you didn't want these other features to be transient. In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the ``user_nl_datm`` file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file.
 
 .. note:: Most everything here has to do with changing datm rather than CLM to allow this to happen. As such the user that wishes to do this should first become more familiar with datm and read the `CESM Data Model User's Guide <https://esmci.github.io/cime/versions/cesm2.2/html/data_models/index.html>`_ especially as it pertains to the datm.
 
diff --git a/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst b/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst
index 7e19af8678..cb66ef209f 100644
--- a/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst
@@ -6,7 +6,7 @@
  Running the prognostic crop model
 ===================================
 
-The prognostic crop model is setup to work with CLM4.0, CLM4.5 or |version| with either BGC or CN (with or without DV). In order to use the initial condition file, we need to set the ``RUN_TYPE`` to startup rather than ``hybrid`` since the compset for f19 sets up to use an initial condition file without crop active. To activate the crop model you can choose a compset that has "Crop" in the name such as "I1850Clm50BgcCropCru" or simply add "-crop" to ``CLM_BLDNML_OPTS`` (or for CLM4.0 add "-crop on" to ``CLM_CONFIG_OPTS``).
+The prognostic crop model is setup to work with CLM4.0, CLM4.5 or |version| with either BGC or CN (with or without DV). In order to use the initial condition file, we need to set the ``RUN_TYPE`` to startup rather than ``hybrid`` since the compset for f19 sets up to use an initial condition file without crop active. To activate the crop model you can choose a compset that has "Crop" in the name such as "I1850Clm50BgcCropCru" or simply add ``-crop`` to ``CLM_BLDNML_OPTS`` (or for CLM4.0 add ``-crop on`` to ``CLM_CONFIG_OPTS``).
 
 Example: Crop Simulation
 ------------------------------------
diff --git a/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst b/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
index f19b489731..5702e6d49d 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
@@ -6,7 +6,7 @@
  Running with irrigation
 ===================================
 
-In CLM4.0 irrigation isn't an allowed option. In CLM4.5 irrigation can ONLY be used WITH crop. With CLM5.0 irrigation can be used whether crop is on or not -- **BUT** if crop is off, your surface datasets **HAVE** to have irrigation defined appropriately. Right now *ALL* surface datasets without crop enabled have irrigation hard-wired on. In order to create datasets with irrigation off, you'd need to make changes to ``mksurfdata_esmf`` in order to have all generic crops to be non-irrigated. To turn on irrigation in |version| we simply add "-irrig on" to ``CLM_BLDNML_OPTS``.
+In CLM4.0 irrigation isn't an allowed option. In CLM4.5 irrigation can ONLY be used WITH crop. With CLM5.0 irrigation can be used whether crop is on or not -- **BUT** if crop is off, your surface datasets **HAVE** to have irrigation defined appropriately. Right now *ALL* surface datasets without crop enabled have irrigation hard-wired on. In order to create datasets with irrigation off, you'd need to make changes to ``mksurfdata_esmf`` in order to have all generic crops to be non-irrigated. To turn on irrigation in |version| we simply add ``-irrig on`` to ``CLM_BLDNML_OPTS``.
 
 Example: Irrigation Simulation
 ------------------------------------------
diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
index cc266506a8..089603db09 100644
--- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
+++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
@@ -6,7 +6,7 @@
  Spinup of |version|-BGC-Crop
 =============================
 
-To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM **configure**, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic.
+To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM ``configure``, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic.
 
 .. _Figure BGC AD spinup plot for 1850 GSWP3:
 
@@ -14,7 +14,7 @@ To get the |version|-BGC model to a steady state, you first run it from arbitrar
 
  BGC AD spinup plot for a year 1850 case with GSWP3 atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl.
 
-After this you branch from this mode in the "final spinup" (-bgc_spinup off in CLM **configure**, see example below), and run for several hundred simulation years. :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this criteria depending on their application.
+After this you branch from this mode in the "final spinup" (-bgc_spinup off in CLM ``configure``, see example below), and run for several hundred simulation years. :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this criteria depending on their application.
 
 .. _Figure BGC pAD spinup plot for 1850 GSWP3:
 
@@ -41,7 +41,7 @@ You can also start from a default initial file that is setup as part of the sele
 If you use the default initial file and you signficantly change model behavior or atmospheric forcing, and you are concerned about the carbon equilibrium (e.g., TOTECOSYSC, TOTSOMC, TOTVEGC), particularly at high latitudes, then we recommend you put the model back into AD mode to reach a new equilibrium. In this configuration, this will also automatically reseed "dead" plant functional types in the initial file with a bit of leaf carbon to give those plant functional types another chance to grow under the new atmospheric forcing or model conditions.
 
 **1. |version| accelerated-decomposition (AD) spinup**
-     For the first step of running 200+ years in "-bgc_spinup on" mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. So do the following:
+     For the first step of running 200+ years in ``-bgc_spinup on`` mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. So do the following:
 
 Example:: AD_SPINUP Simulation for |version|-BGC
 --------------------------------------------------------
@@ -67,7 +67,7 @@ Example:: AD_SPINUP Simulation for |version|-BGC
 Afterwards save the last restart file from this simulation to use in the next step.
 
 **2. Final spinup for |version|-BGC**
-     Next save the last restart file from this step and use it as the "finidat" file to use for one more spinup for at least 400+ years in normal mode. So do the following:
+     Next save the last restart file from this step and use it as the ``finidat`` file to use for one more spinup for at least 400+ years in normal mode. So do the following:
 
 .. _eg-final-clmbgc-spinup:
 
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index a1efac897e..0987a32e8e 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -6,17 +6,17 @@
  Customizing CLM's Configuration
 ********************************
 
-The section of the |cesmrelease| Quickstart `CESM Create a Case <https://escomp.github.io/cesm/release-cesm2/quickstart.html#create-a-case>`_ gives instructions on creating a case. Also see a similar section in the CIME User's-Guide `CIME Create a case <http://esmci.github.io/cime/users_guide/create-a-case.html>`_. What is of interest here is how to customize your use of CLM for the case that you created.
+The section of the |cesmrelease| Quickstart `CESM Create a Case <https://escomp.github.io/cesm/release-cesm2/quickstart.html#create-a-case>`_ gives instructions on creating a case. Also see a similar section in the CIME User's Guide `CIME Create a case <http://esmci.github.io/cime/users_guide/create-a-case.html>`_. What is of interest here is how to customize your use of CLM for the case that you created.
 
-For CLM when **preview_namelist**, **case.build**, or **case.run** are called there are two steps that take place:
+For CLM when ``preview_namelist``, ``case.build``, or ``case.run`` are called there are two steps that take place:
 
-1. The CLM "**configure**" script is called to setup the build-time configuration for CLM (see :ref:`more-info-clm-config-script`). The env variables for **configure** are locked after the **case.build** step. So the results of the CLM **configure** are locked after the build has taken place.
+1. The CLM ``configure`` script is called to setup the build-time configuration for CLM (see :ref:`more-info-clm-config-script`). The env variables for ``configure`` are locked after the ``case.build`` step. So the results of the CLM ``configure`` are locked after the build has taken place.
 
-2. The CLM "**build-namelist**" script is called to generate the run-time namelist for CLM (more information on **build-namelist** is given below in :ref:`def-nl-items-and-defaults`).
+2. The CLM ``build-namelist`` script is called to generate the run-time namelist for CLM (more information on ``build-namelist`` is given below in :ref:`def-nl-items-and-defaults`).
 
-When customizing your case at the **case.setup** step you are able to modify the process by effecting either one or both of these steps. The CLM "**configure**" and "**build-namelist**" scripts are both available in the "$CTSMROOT/bld" directory in the distribution. Both of these scripts have a "-help" option that is useful to examine to see what types of options you can give either of them.
+When customizing your case at the ``case.setup`` step you are able to modify the process by effecting either one or both of these steps. The CLM ``configure`` and ``build-namelist`` scripts are both available in the ``$CTSMROOT/bld`` directory in the distribution. Both of these scripts have a ``-help`` option that is useful to examine to see what types of options you can give either of them.
 
-There are five different types of customization for the configuration that we will discuss: |version| in |cesmrelease| build-time options, |version| in |cesmrelease| run-time options, User Namelist, other noteworthy |cesmrelease| configuration items, the CLM **configure** script options, and the CLM **build-namelist** script options.
+There are five different types of customization for the configuration that we will discuss: |version| in |cesmrelease| build-time options, |version| in |cesmrelease| run-time options, User Namelist, other noteworthy |cesmrelease| configuration items, the CLM ``configure`` script options, and the CLM ``build-namelist`` script options.
 
 Information on all of the CLM script, configuration, build and run items is found under ``$CTSMROOT/cime_config/config_component.xml``. See `CLM CASEROOT Variable Definitions <http://www.cesm.ucar.edu/models/cesm2/component_settings/clm4_5_input.html>`_.
 
@@ -38,12 +38,12 @@ Below we list each of the CESM configuration items that are specific to CLM. All
    CLM_USRDAT_NAME
    COMP_LND
 
-For the precedence of the different options to **build-namelist** see the section on precedence below.
+For the precedence of the different options to ``build-namelist`` see the section on precedence below.
 
 The first item ``CLM_CONFIG_OPTS`` has to do with customizing the CLM build-time options for your case, the rest all have to do with generating the namelist.
 
 CLM_CONFIG_OPTS
-  The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM **configure** script. It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. Hence, we recommend using the "-append" option to the xmlchange script. In :ref:`more-info-clm-config-script` below we will go into more details on options that can be customized in the CLM "**configure**" script. It's also important to note that the **$CTSMROOT/cime_config/buildnml** script may already invoke certain CLM **configure** options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). The options to CLM **configure** are given with the "-help" option which is given in :ref:`more-info-clm-config-script`... note:: ``CLM_CONFIG_OPTS`` is locked after the **case.build** script is run. If you want to change something in ``CLM_CONFIG_OPTS`` you'll need to clean the build and rerun **case.build**. The other env variables can be changed at run-time so are never locked.
+  The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM ``configure`` script. It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. Hence, we recommend using the ``-append`` option to the xmlchange script. In :ref:`more-info-clm-config-script` below we will go into more details on options that can be customized in the CLM ``configure`` script. It's also important to note that the ``$CTSMROOT/cime_config/buildnml`` script may already invoke certain CLM ``configure`` options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). The options to CLM ``configure`` are given with the ``-help`` option which is given in :ref:`more-info-clm-config-script`... note:: ``CLM_CONFIG_OPTS`` is locked after the ``case.build`` script is run. If you want to change something in ``CLM_CONFIG_OPTS`` you'll need to clean the build and rerun ``case.build``. The other env variables can be changed at run-time so are never locked.
 
 CLM_NML_USE_CASE
   ``CLM_NML_USE_CASE`` is used to set a particular set of conditions that set multiple namelist items, all centering around a particular usage of the model. (See :ref:`precedence-of-opts` for the precedence of this option relative to the others.) To list the valid options do the following:
@@ -101,7 +101,7 @@ CLM_NML_USE_CASE
      stdurbpt_pd = Standard Urban Point Namelist Settings
 
 CLM_BLDNML_OPTS
-  The option CLM_BLDNML_OPTS is for passing options to the CLM "build-namelist" script. As with the CLM "configure" script the CLM $CTSMROOT/cime_config/buildnml may already invoke certain options and as such those options will NOT be available to be set here. The best way to see what options can be sent to the "build-namelist" script is to do
+  The option CLM_BLDNML_OPTS is for passing options to the CLM ``build-namelist`` script. As with the CLM ``configure`` script the CLM $CTSMROOT/cime_config/buildnml may already invoke certain options and as such those options will NOT be available to be set here. The best way to see what options can be sent to the ``build-namelist`` script is to do
   ::
 
      > cd $CTSMROOT/bld
@@ -256,7 +256,7 @@ CLM_BLDNML_OPTS
              (i.e.  CLM_NML_USE_CASE env_run variable)
       6. values from the namelist defaults file.
 
-The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and mask as well as the CLM **configure** file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. Hence only the following different options can be set:
+The ``$CTSMROOT/cime_config/buildnml`` script already sets the resolution and mask as well as the CLM ``configure`` file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. Hence only the following different options can be set:
 
 1.
 -bgc_spinup
@@ -285,14 +285,14 @@ The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and ma
 
 #. -verbose
 
-"-bgc_spinup" is an option only available for |version| for any configuration when CN is turned on (so either CLMCN or CLMBGC). It can be set to "on" or "off". If "on" the model will go into Accelerated Decomposition mode, while for "off" (the default) it will have standard decomposition rates. If you are starting up from initial condition files the model will check what mode the initial condition file is in and do the appropriate action on the first time-step to change the Carbon pools to the appropriate spinup setting. See :ref:`spinning-up-clm-bgc` for an example using this option.
+``-bgc_spinup`` is an option only available for |version| for any configuration when CN is turned on (so either CLMCN or CLMBGC). It can be set to "on" or "off". If "on" the model will go into Accelerated Decomposition mode, while for "off" (the default) it will have standard decomposition rates. If you are starting up from initial condition files the model will check what mode the initial condition file is in and do the appropriate action on the first time-step to change the Carbon pools to the appropriate spinup setting. See :ref:`spinning-up-clm-bgc` for an example using this option.
 
-"-chk_res" ensures that the resolution chosen is supported by CLM. If the resolution is NOT supported it will cause the CLM **build-namelist** to abort when run. So when either **preview_namelist**, **case.build** or **case.run** is executed it will abort early. Since, the CESM scripts only support certain resolutions anyway, in general this option is NOT needed in the context of running CESM cases.
+``-chk_res`` ensures that the resolution chosen is supported by CLM. If the resolution is NOT supported it will cause the CLM ``build-namelist`` to abort when run. So when either ``preview_namelist``, ``case.build`` or ``case.run`` is executed it will abort early. Since, the CESM scripts only support certain resolutions anyway, in general this option is NOT needed in the context of running CESM cases.
 
-"-clm_demand" asks the **build-namelist** step to require that the list of variables entered be set. Typically, this is used to require that optional filenames be used and ensure they are set before continuing. For example, you may want to require that fpftdyn be set to get dynamically changing vegetation types. To do this you would do the following.
+``-clm_demand`` asks the ``build-namelist`` step to require that the list of variables entered be set. Typically, this is used to require that optional filenames be used and ensure they are set before continuing. For example, you may want to require that fpftdyn be set to get dynamically changing vegetation types. To do this you would do the following.
 ::
 
-   > ./xmlchange CLM_BLDNML_OPTS="-clm_demand fpftdyn"``
+   > ./xmlchange CLM_BLDNML_OPTS="-clm_demand fpftdyn"
 
 To see a list of valid variables that you could set do this:
 ::
@@ -302,25 +302,25 @@ To see a list of valid variables that you could set do this:
 
 .. note:: Using a 20th-Century transient compset or the ``20thC_transient`` use-case using ``CLM_NML_USE_CASE`` would set this as well, but would also use dynamic nitrogen and aerosol deposition files, so using ``-clm_demand`` would be a way to get *just* dynamic vegetation types and NOT the other files as well.
 
-"-drydep" adds a dry-deposition namelist for testing to the driver. This is a driver namelist, but adding the option here has CLM **build-namelist** create the ``drv_flds_in`` file that the driver will copy over and use. Invoking this option does have an impact on performance even for I compsets and will slow the model down. It's also only useful when running with an active atmosphere model that makes use of this information.
+``-drydep`` adds a dry-deposition namelist for testing to the driver. This is a driver namelist, but adding the option here has CLM ``build-namelist`` create the ``drv_flds_in`` file that the driver will copy over and use. Invoking this option does have an impact on performance even for I compsets and will slow the model down. It's also only useful when running with an active atmosphere model that makes use of this information.
 
-"-ignore_ic_date" ignores the Initial Conditions (IC) date completely for finding initial condition files to startup from. Without this option or the "-ignore_ic_year" option below, the date of the file comes into play.
+``-ignore_ic_date`` ignores the Initial Conditions (IC) date completely for finding initial condition files to startup from. Without this option or the ``-ignore_ic_year`` option below, the date of the file comes into play.
 
-"-ignore_ic_year" ignores the Initial Conditions (IC) year for finding initial condition files to startup from. The date is used, but the year is ignored. Without this option or the "-ignore_ic_date" option below, the date and year of the file comes into play.
+``-ignore_ic_year`` ignores the Initial Conditions (IC) year for finding initial condition files to startup from. The date is used, but the year is ignored. Without this option or the ``-ignore_ic_date`` option below, the date and year of the file comes into play.
 
-When "-irrig on" is used **build-namelist** will try to find surface datasets that have the irrigation model enabled (when running with Sattellitte Phenology). When running with the prognostic crop model on, "-irrig on" will turn irrigate crops on, while "-irrig off" will manage all crop areas as rain-fed without irrigation.
+When ``-irrig on`` is used ``build-namelist`` will try to find surface datasets that have the irrigation model enabled (when running with Sattellitte Phenology). When running with the prognostic crop model on, ``-irrig on`` will turn irrigate crops on, while ``-irrig off`` will manage all crop areas as rain-fed without irrigation.
 
-"no-megan" means do NOT add a MEGAN model Biogenic Volatile Organic Compounds (BVOC) testing namelist to the driver. This namelist is created by default, so normally this WILL be done. This is a driver namelist, so unless "no-megan" is specified the CLM **build-namelist** will create the ``drv_flds_in`` file that the driver will copy over and use (if you are running with CAM and CAM produces this file as well, it's file will have precedence).
+``no-megan`` means do NOT add a MEGAN model Biogenic Volatile Organic Compounds (BVOC) testing namelist to the driver. This namelist is created by default, so normally this WILL be done. This is a driver namelist, so unless ``no-megan`` is specified the CLM ``build-namelist`` will create the ``drv_flds_in`` file that the driver will copy over and use (if you are running with CAM and CAM produces this file as well, it's file will have precedence).
 
-"-note" adds a note to the bottom of the namelist file, that gives the details of how **build-namelist** was called, giving the specific command-line options given to it.
+``-note`` adds a note to the bottom of the namelist file, that gives the details of how ``build-namelist`` was called, giving the specific command-line options given to it.
 
-"-rcp" is used to set the representative concentration pathway for the future scenarios you want the data-sets to simulate conditions for, in the input datasets. To list the valid options do the following:
+``-rcp`` is used to set the representative concentration pathway for the future scenarios you want the data-sets to simulate conditions for, in the input datasets. To list the valid options do the following:
 ::
 
    > cd $CTSMROOT/doc
    > ../bld/build-namelist -rcp list
 
-"-sim_year" is used to set the simulation year you want the data-sets to simulate conditions for in the input datasets. The simulation "year" can also be a range of years in order to do simulations with changes in the dataset values as the simulation progresses. To list the valid options do the following:
+``-sim_year`` is used to set the simulation year you want the data-sets to simulate conditions for in the input datasets. The simulation ``year`` can also be a range of years in order to do simulations with changes in the dataset values as the simulation progresses. To list the valid options do the following:
 ::
 
    > cd $CTSMROOT/doc
@@ -347,7 +347,7 @@ When "-irrig on" is used **build-namelist** will try to find surface datasets th
    when set to on, *requires* that your simulation do a cold start from arbitrary initial conditions. If this is NOT set, it will use an initial condition file if it can find an appropriate one, and otherwise do a cold start. ``CLM_FORCE_COLDSTART`` is a good way to ensure that you are doing a cold start if that is what you want to do.
 
 ``CLM_USRDAT_NAME``
-   Provides a way to enter your own datasets into the namelist. The files you create must be named with specific naming conventions outlined in :ref:`creating-your-own-singlepoint-dataset`. To see what the expected names of the files are, use the **queryDefaultNamelist.pl** to see what the names will need to be. For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be:
+   Provides a way to enter your own datasets into the namelist. The files you create must be named with specific naming conventions outlined in :ref:`creating-your-own-singlepoint-dataset`. To see what the expected names of the files are, use the ``queryDefaultNamelist.pl`` to see what the names will need to be. For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be:
    ::
 
       > cd $CTSMROOT/bld
@@ -362,7 +362,7 @@ When "-irrig on" is used **build-namelist** will try to find surface datasets th
  User Namelist
 ===============
 
-``CLM_NAMELIST_OPTS`` as described above allows you to set any extra namelist items you would like to appear in your namelist. However, it only allows you a single line to enter namelist items, and strings must be quoted with &apos; which is a bit awkward. If you have a long list of namelist items you want to set (such as a long list of history fields) a convenient way to do it is to add to the ``user_nl_clm`` that is created after the **case.setup** command runs. The file needs to be in valid FORTRAN namelist format (with the exception that the namelist name &namelist and the end of namelist marker "/" are excluded". The **preview_namelist** or **case.run** step will abort if there are syntax errors. All the variable names must be valid and the values must be valid for the datatype and any restrictions for valid values for that variable. Here's an example ``user_nl_clm`` namelist that sets a bunch of history file related items, to create output history files monthly, daily, every six and 1 hours.
+``CLM_NAMELIST_OPTS`` as described above allows you to set any extra namelist items you would like to appear in your namelist. However, it only allows you a single line to enter namelist items, and strings must be quoted with &apos; which is a bit awkward. If you have a long list of namelist items you want to set (such as a long list of history fields) a convenient way to do it is to add to the ``user_nl_clm`` that is created after the ``case.setup`` command runs. The file needs to be in valid FORTRAN namelist format (with the exception that the namelist name ``&namelist`` and the end of namelist marker ``/`` are excluded. The ``preview_namelist`` or ``case.run`` step will abort if there are syntax errors. All the variable names must be valid and the values must be valid for the datatype and any restrictions for valid values for that variable. Here's an example ``user_nl_clm`` namelist that sets a bunch of history file related items, to create output history files monthly, daily, every six and 1 hours.
 
 ----------------------------------
 Example: user_nl_clm namelist file
@@ -410,9 +410,9 @@ Example: user_nl_clm namelist file
    hist_mfilt  = 1, 30,  28, 24
    hist_nhtfrq = 0, -24, -6, -1
 
-**Note:** The comments at the top are some guidance given in the default user_nl_clm and just give some guidance on how to set variables and use the file.
+**Note:** The comments at the top are some guidance given in the default ``user_nl_clm`` and just give some guidance on how to set variables and use the file.
 
-**Note:** You do NOT need to specify the namelist group that the variables are in because the CLM **build-namelist** knows the namelist that specific variable names belong to, and it puts them there.
+**Note:** You do NOT need to specify the namelist group that the variables are in because the CLM ``build-namelist`` knows the namelist that specific variable names belong to, and it puts them there.
 
 Obviously, all of this would be difficult to put in the CLM_NAMELIST_OPTS variable, especially having to put &apos; around all the character strings. For more information on the namelist variables being set here and what they mean, see the section on CLM namelists below, as well as the namelist definition that gives details on each variable.
 
@@ -422,17 +422,17 @@ Obviously, all of this would be difficult to put in the CLM_NAMELIST_OPTS variab
 Precedence of Options
 ---------------------
 
-Note: The precedence for setting the values of namelist variables with the different env_build.xml, env_run.xml options is (highest to lowest):
+Note: The precedence for setting the values of namelist variables with the different ``env_build.xml``, ``env_run.xml`` options is (highest to lowest):
 
-1. Namelist values set by specific command-line options, like, -d, -sim_year (i.e. CLM_BLDNML_OPTS env_build.xml variable)
+1. Namelist values set by specific command-line options, like, ``-d``, ``-sim_year`` (i.e. ``CLM_BLDNML_OPTS`` ``env_build.xml`` variable)
 
-#. Values set on the command-line using the -namelist option, (i.e. CLM_NAMELIST_OPTS env_run.xml variable)
+#. Values set on the command-line using the ``-namelist`` option, (i.e. ``CLM_NAMELIST_OPTS`` ``env_run.xml`` variable)
 
-#. Values read from the file specified by -infile, (i.e. user_nl_clm file)
+#. Values read from the file specified by ``-infile``, (i.e. ``user_nl_clm`` file)
 
-#. Datasets from the -clm_usr_name option, (i.e. CLM_USRDAT_NAME env_run.xml variable)
+#. Datasets from the ``-clm_usr_name`` option, (i.e. ``CLM_USRDAT_NAME`` ``env_run.xml`` variable)
 
-#. Values set from a use-case scenario, e.g., -use_case (i.e. CLM_NML_USE_CASE env_run.xml variable)
+#. Values set from a use-case scenario, e.g., ``-use_case`` (i.e. ``CLM_NML_USE_CASE`` ``env_run.xml`` variable)
 
 #. Values from the namelist defaults file.
 
@@ -451,7 +451,7 @@ Especially with CLMBGC and CLMCN starting from initial conditions is very import
 - :ref:`providing-finidat-in-usernlclm`
 - :ref:`adding-finidat-to-xml`
 
-  **Note:** Your initial condition file MUST agree with the surface dataset you are using to run the simulation. If the two files do NOT agree you will get a run-time about a mis-match in PFT weights, or in the number of PFT's or columns.  To get around this you'll need to add the "use_init_interp=T" namelist flag in your namelist so that the initial conditions will be interpolated on startup.**
+  **Note:** Your initial condition file MUST agree with the surface dataset you are using to run the simulation. If the two files do NOT agree you will get a run-time about a mis-match in PFT weights, or in the number of PFT's or columns.  To get around this you'll need to add the ``use_init_interp=T`` namelist flag in your namelist so that the initial conditions will be interpolated on startup.**
 
 .. _doing-a-hybrid-sim-for-init-conds:
 
@@ -459,7 +459,7 @@ Especially with CLMBGC and CLMCN starting from initial conditions is very import
 Doing a hybrid simulation to provide initial conditions
 -------------------------------------------------------
 
-The first option is to setup a hybrid simulation and give a ``RUN_REFCASE`` and ``RUN_REFDATE`` to specify the reference case simulation name to use. When you setup coupled cases (assuming a CESM checkout), at the standard resolution of "f09" it will already do this for you. For example, if you run an "B1850" compset at "f09_g17_gl4" resolution the following settings will already be done for you.
+The first option is to setup a hybrid simulation and give a ``RUN_REFCASE`` and ``RUN_REFDATE`` to specify the reference case simulation name to use. When you setup coupled cases (assuming a CESM checkout), at the standard resolution of "f09" it will already do this for you. For example, if you run a "B1850" compset at "f09_g17_gl4" resolution the following settings will already be done for you.
 
 ``./xmlchange RUN_TYPE=hybrid,RUN_REFCASE=b.e20.B1850.f09_g17.pi_control.all.297,RUN_REFDATE=0130-01-01,GET_REFCASE=TRUE``
 
@@ -498,7 +498,7 @@ Like other datasets, if you want to use a given initial condition file to be use
 Other noteworthy configuration items
 ------------------------------------
 
-For running "I" cases there are several other noteworthy configuration items that you may want to work with. Most of these involve settings for the DATM, but one ``CCSM_CO2_PPMV`` applies to all models. The list of DATM settings is `here <http://esmci.github.io/cime/data_models/data-atm.html>`_. If you are running an B, E, or F case that doesn't use the DATM obviously the DATM_* settings will not be used. All of the settings below are in your ``env_build.xml`` and ``env_run.xml`` files
+For running "I" cases there are several other noteworthy configuration items that you may want to work with. Most of these involve settings for the DATM, but one ``CCSM_CO2_PPMV`` applies to all models. The list of DATM settings is `here <http://esmci.github.io/cime/data_models/data-atm.html>`_. If you are running a B, E, or F case that doesn't use the DATM obviously the DATM_* settings will not be used. All of the settings below are in your ``env_build.xml`` and ``env_run.xml`` files
 ::
 
    CCSM_CO2_PPMV
@@ -514,7 +514,7 @@ For running "I" cases there are several other noteworthy configuration items tha
    DATM_CPL_YR_END
 
 ``CCSM_CO2_PPMV``
-   Sets the mixing ratio of CO2 in parts per million by volume for ALL CESM components to use. Note that most compsets already set this value to something reasonable. Also note that some compsets may tell the atmosphere model to override this value with either historic or ramped values. If the CCSM_BGC variable is set to something other than "none" the atmosphere model will determine CO2, and CLM will listen and use what the atmosphere sends it. On the CLM side the namelist item co2_type tells CLM to use the value sent from the atmosphere rather than a value set on it's own namelist.
+   Sets the mixing ratio of CO2 in parts per million by volume for ALL CESM components to use. Note that most compsets already set this value to something reasonable. Also note that some compsets may tell the atmosphere model to override this value with either historic or ramped values. If the ``CCSM_BGC`` variable is set to something other than "none" the atmosphere model will determine CO2, and CLM will listen and use what the atmosphere sends it. On the CLM side the namelist item ``co2_type`` tells CLM to use the value sent from the atmosphere rather than a value set on it's own namelist.
 
 ``DATM_MODE``
    Sets the mode that the DATM model should run in this determines how data is handled as well as what the source of the data will be. Many of the modes are setup specifically to be used for ocean and/or sea-ice modeling. The modes that are designed for use by CLM are (CLM_QIAN, CLMCRUNCEP, CLMCRUNCEPv7, CLMGSWP3v1 and CLM1PT):
@@ -540,7 +540,7 @@ For running "I" cases there are several other noteworthy configuration items tha
    The standard mode for CLM4.0 of using global atmospheric data that was developed by Qian et. al. for CLM using NCEP data from 1948 to 2004. See :ref:`clmqian-and-its-datm` for more information. 
 
 ``CLM1PT``
-   This is for the special cases where we have single-point tower data for particular sites. Right now we only have data for three urban locations: MexicoCity Mexico, Vancouver Canada, and the urban-c alpha site. And we have data for the US-UMB AmeriFlux tower site for University of Michigan Biological Station. See :ref:`clm1pt-and-its-datm` for more information.
+   This is for the special cases where we have single-point tower data for particular sites. Right now we only have data for three urban locations: Mexico City Mexico, Vancouver Canada, and the urban-c alpha site. We also have data for the US-UMB AmeriFlux tower site for University of Michigan Biological Station. See :ref:`clm1pt-and-its-datm` for more information.
 
 ``CPLHISTForcing``
    This is for running with atmospheric forcing from a previous CESM simulation. See :ref:`cplhistforcing` for more information.
@@ -591,7 +591,7 @@ Downloading DATM Forcing Data
 
 In Chapter One of the `CESM User's Guide <link-to-CESM-UG>`_ there is a section on "Downloading input data". The normal process of setting up cases will use the "scripts/ccsm_utils/Tools/check_input_data" script to retrieve data from the CESM subversion inputdata repository. This is true for the standard `CLM_QIAN` forcing as well.
 
-The `CLMCRUNCEP` data is uploaded into the subversion inputdata repository as well -- but as it is 1.1 Terabytes of data downloading it is problematic (*IT WILL TAKE SEVERAL DAYS TO DOWNLOAD THE ENTIRE DATASET USING SUBVERSION*). Because of it's size you may also need to download it onto a separate disk space. We have done that on cheyenne for example where it resides in ``$ENV{CESMROOT}/lmwg`` while the rest of the input data resides in ``$ENV{CESMDATAROOT}/inputdata``. The data is also already available on: janus, franklin, and hopper. If you download the data, we recommend that you break your download into several chunks, by setting up a case and setting the year range for ``DATM_CPL_YR_START`` and ``DATM_CPL_YR_END`` in say 20 year sections over 1901 to 2010, and then use **check_input_data** to export the data.
+The `CLMCRUNCEP` data is uploaded into the subversion inputdata repository as well -- but as it is 1.1 Terabytes of data downloading it is problematic (*IT WILL TAKE SEVERAL DAYS TO DOWNLOAD THE ENTIRE DATASET USING SUBVERSION*). Because of its size you may also need to download it onto a separate disk space. We have done that on cheyenne for example where it resides in ``$ENV{CESMROOT}/lmwg`` while the rest of the input data resides in ``$ENV{CESMDATAROOT}/inputdata``. The data is also already available on: janus, franklin, and hopper. If you download the data, we recommend that you break your download into several chunks, by setting up a case and setting the year range for ``DATM_CPL_YR_START`` and ``DATM_CPL_YR_END`` in say 20 year sections over 1901 to 2010, and then use ``check_input_data`` to export the data.
 
 The ``CPLHISTForcing`` DATM forcing data is unique -- because it is large compared to the rest of the input data, and we only have a disk copy on cheyenne. The DATM assumes the path for the previous NCAR machine cheyenne of ``/glade/p/cesm/shared_outputdata/cases/ccsm4/$DATM_CPLHIST_CASE`` for the data. So you will need to change this path in order to run on any other machine. You can download the data itself from NCAR HPSS from ``/CCSM/csm/$DATM_CPLHIST_CASE``.
 
@@ -599,12 +599,12 @@ The ``CPLHISTForcing`` DATM forcing data is unique -- because it is large compar
 Customizing via the build script files
 --------------------------------------
 
-The final thing that the user may wish to do before **case.setup** is run is to edit the build script files which determine the configuration and namelist. The variables in ``env_build.xml`` or ``env_run.xml`` typically mean you will NOT have to edit build script files. But, there are rare instances where it is useful to do so. The build script files are copied to your case directory and are available under Buildconf. The list of build script files you might wish to edit are:
+The final thing that the user may wish to do before ``case.setup`` is run is to edit the build script files which determine the configuration and namelist. The variables in ``env_build.xml`` or ``env_run.xml`` typically mean you will NOT have to edit build script files. But, there are rare instances where it is useful to do so. The build script files are copied to your case directory and are available under ``Buildconf``. The list of build script files you might wish to edit are:
 
-**clm.buildexe.csh**
-**$CTSMROOT/cime_config/buildnml**
-**datm.buildexe.csh**
-**datm.buildnml.csh**
+``clm.buildexe.csh``
+``$CTSMROOT/cime_config/buildnml``
+``datm.buildexe.csh``
+``datm.buildnml.csh``
 
 .. _more-info-clm-config-script:
 
@@ -617,7 +617,7 @@ The CLM ``configure`` script defines the details of a clm configuration and summ
 Help on CLM configure
 ---------------------
 
-Coupling this with looking at the options to CLM **configure** with "-help" as below will enable you to understand how to set the different options.
+Coupling this with looking at the options to CLM ``configure`` with ``-help`` as below will enable you to understand how to set the different options.
 ::
 
    > cd $CTSMROOT/bld
@@ -694,4 +694,4 @@ The output to the above command is as follows:
                               no-nitrif   Turn the Nitrification/denitrification off
                             [no-vert,no-cent,no-nitrif,no-vert:no-cent]
 
-We've given details on how to use the options in env_build.xml and env_run.xml to interact with the CLM "configure" and "build-namelist" scripts, as well as giving a good understanding of how these scripts work and the options to them. In the next section we give further details on the CLM namelist. You could customize the namelist for these options after "case.setup" is run.
+We've given details on how to use the options in ``env_build.xml`` and ``env_run.xml`` to interact with the CLM ``configure`` and ``build-namelist`` scripts, as well as giving a good understanding of how these scripts work and the options to them. In the next section we give further details on the CLM namelist. You could customize the namelist for these options after ``case.setup`` is run.
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst
index ff76a841c9..2d6f58f317 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst
@@ -6,7 +6,7 @@
  Customizing CLM's namelist
 ============================
 
-Once a case has run **case.setup**, we can then customize the case further, by editing the run-time namelist for CLM. First let's list the definition of each namelist item and their valid values, and then we'll list the default values for them. Next for some of the most used or tricky namelist items we'll give examples of their use, and give you example namelists that highlight these features.
+Once a case has run ``case.setup``, we can then customize the case further, by editing the run-time namelist for CLM. First let's list the definition of each namelist item and their valid values, and then we'll list the default values for them. Next for some of the most used or tricky namelist items we'll give examples of their use, and give you example namelists that highlight these features.
 
 In the following, various examples of namelists are provided that feature the use of different namelist options to customize a case for particular uses. Most the examples revolve around how to customize the output history fields. This should give you a good basis for setting up your own CLM namelist.
 
@@ -138,14 +138,14 @@ Example 1-5. Example user_nl_clm namelist removing all history fields
 Various ways to change history output averaging flags
 -----------------------------------------------------
 
-There are two ways to change the averaging of output history fields. The first is using ``hist_avgflag_pertape`` which gives a default value for each history stream, the second is when you add fields using ``hist_fincl*``, you add an averaging flag to the end of the field name after a colon (for example 'TSOI:X', would output the maximum of TSOI). The types of averaging that can be done are:
+There are two ways to change the averaging of output history fields. The first is using ``hist_avgflag_pertape`` which gives a default value for each history stream, the second is when you add fields using ``hist_fincl*``, you add an averaging flag to the end of the field name after a colon (for example ``TSOI:X`` would output the maximum of ``TSOI``). The types of averaging that can be done are:
 
-- *A* Average, over the output interval.
-- *I* Instantaneous, output the value at the output interval.
-- *X* Maximum, over the output interval.
-- *M* Minimum, over the output interval.
+- ``A`` Average, over the output interval.
+- ``I`` Instantaneous, output the value at the output interval.
+- ``X`` Maximum, over the output interval.
+- ``M`` Minimum, over the output interval.
 
-The default averaging depends on the specific fields, but for most fields is an average. A sample user namelist ``user_nl_clm`` making the monthly output fields all averages (except TSOI for the first two streams and FIRE for the 5th stream), and adding auxiliary file streams for instantaneous (6-hourly), maximum (daily), minimum (daily), and average (daily). For some of the fields we diverge from the per-tape value given and customize to some different type of optimization.
+The default averaging depends on the specific fields, but for most fields is an average. A sample user namelist ``user_nl_clm`` making the monthly output fields all averages (except ``TSOI`` for the first two streams and ``FIRE`` for the 5th stream), and adding auxiliary file streams for instantaneous (6-hourly), maximum (daily), minimum (daily), and average (daily). For some of the fields we diverge from the per-tape value given and customize to some different type of optimization.
 
 Example: user_nl_clm namelist with various ways to average history fields
 -------------------------------------------------------------------------------------
@@ -165,7 +165,7 @@ Example: user_nl_clm namelist with various ways to average history fields
    hist_avgflag_pertape = 'A', 'I', 'X',   'M', 'A'
    hist_nhtfrq = 0, -6, -24, -24, -24
 
-In the example we put the same list of fields on each of the tapes: soil-temperature, ground temperature, vegetation temperature, emitted longwave radiation, reflected solar radiation, sensible heat, total latent-heat, and total water storage. We also modify the soil-temperature for the primary and secondary auxiliary tapes by outputting them for a maximum instead of the prescribed per-tape of average and instantaneous respectively. For the tertiary auxiliary tape we output ground temperature instantaneous instead of as a maximum, and for the fourth auxiliary tape we output vegetation temperature instantaneous instead of as a minimum. Finally, for the fifth auxiliary tapes we output ``FIRE`` instantaneously instead of as an average.
+In the example we put the same list of fields on each of the tapes: soil-temperature, ground temperature, vegetation temperature, emitted longwave radiation, reflected solar radiation, sensible heat, total latent-heat, and total water storage. We also modify the soil temperature for the primary and secondary auxiliary tapes by outputting them for a maximum instead of the prescribed per-tape of average and instantaneous respectively. For the tertiary auxiliary tape we output ground temperature instantaneous instead of as a maximum, and for the fourth auxiliary tape we output vegetation temperature instantaneous instead of as a minimum. Finally, for the fifth auxiliary tapes we output ``FIRE`` instantaneously instead of as an average.
 
 .. note:: We also use ``hist_empty_htapes`` as in the previous example, so we can list ONLY the fields that we want on the primary history tapes.
 
@@ -189,8 +189,8 @@ Example: user_nl_clm namelist outputting some files in 1D Vector format
    hist_type2d_pertape = ' ', 'GRID', 'COLS', ' '
    hist_nhtfrq = 0, -24, -24, -24
 
-.. warning:: LAND and COLS are also options to the pertape averaging, but currently there is a bug with them and they fail to work.
+.. warning:: ``LAND`` and ``COLS`` are also options to the pertape averaging, but currently there is a bug with them and they fail to work.
 
-.. note:: Technically the default for hist_nhtfrq is for primary files output monthly and the other auxiliary tapes for daily, so we don't actually have to include hist_nhtfrq, we could use the default for it. Here we specify it for clarity.
+.. note:: Technically the default for ``hist_nhtfrq`` is for primary files output monthly and the other auxiliary tapes for daily, so we don't actually have to include ``hist_nhtfrq``, we could use the default for it. Here we specify it for clarity.
 
-Visualizing global 1D vector files will take effort. You'll probably want to do some post-processing and possibly just extract out single points of interest to see what is going on. Since, the output is a 1D vector, of only land-points traditional plots won't be helpful. The number of points per grid-cell will also vary for anything, but grid-cell averaging. You'll need to use the output fields pfts1d_ixy, and pfts1d_jxy, to get the mapping of the fields to the global 2D array. pfts1d_itype_veg gives you the PFT number for each PFT. Most likely you'll want to do this analysis in a data processing tool (such as NCL, Matlab, Mathmatica, IDL, etcetera that is able to read and process NetCDF data files).
+Visualizing global 1D vector files will take effort. You'll probably want to do some post-processing and possibly just extract out single points of interest to see what is going on. Since the output is a 1D vector of only land points, traditional plots won't be helpful. The number of points per grid-cell will also vary for anything but grid-cell averaging. You'll need to use the output fields ``pfts1d_ixy``, and ``pfts1d_jxy``, to get the mapping of the fields to the global 2D array. ``pfts1d_itype_veg`` gives you the PFT number for each PFT. Most likely you'll want to do this analysis in a data processing tool (such as NCL, Matlab, Mathmatica, IDL, etc. that is able to read and process NetCDF data files).
diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst
index ec959d4b82..b065cb1392 100644
--- a/doc/source/users_guide/testing/testing.rst
+++ b/doc/source/users_guide/testing/testing.rst
@@ -6,12 +6,12 @@
 Testing
 *******
 
-Technically, you could use the customization we gave in :ref:`customizing_section` to test various configuration and namelist options for CLM. Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. There are two types of testing scripts for CLM. The first are the CESM test scripts, which utilize the **create_newcase** scripts that we shown how to use in this User's Guide. The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods.
+Technically, you could use the customization we gave in :ref:`customizing_section` to test various configuration and namelist options for CLM. Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. There are two types of testing scripts for CLM. The first are the CESM test scripts, which utilize the ``create_newcase`` scripts that we shown how to use in this User's Guide. The second are a set of stand-alone scripts that use the CLM ``configure`` and ``build-namelist`` scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods.
 
 CIME Testing scripts
 ====================
 
-We first introduce the test scripts that work for all CESM components. The CIME script **create_test** runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing <http://esmci.github.io/cime/users_guide/testing.html>`_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also see the `CTSM Wiki on Testing <https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide>`_.
+We first introduce the test scripts that work for all CESM components. The CIME script ``create_test`` runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing <http://esmci.github.io/cime/users_guide/testing.html>`_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also see the `CTSM Wiki on Testing <https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide>`_.
 
 CTSM Fortran Unit Tests
 =======================
diff --git a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
index 93798c3c57..418a4aff37 100644
--- a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
+++ b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
@@ -2,7 +2,7 @@
 
 .. _trouble-shooting:
 
-***************
+*************
 Troubleshooting
 ***************
 
@@ -112,20 +112,20 @@ The second method is to use the local index along with the processor number::
 
 By placing these write statements in the code, one can get a sense of how leafc is evolving toward a negative state and why. This is a very complex example of troubleshooting. To make a long story short, as described `here <https://github.com/ESCOMP/CTSM/issues/1163>`_, the error turned out to be caused by a few lines in the phenology code that weren't handling a 20 minute time step properly, thus an actual bug in the code. This was also a good example of where a much less computationally expensive land-only simulation was able to be used for debugging instead of the orginal expensive fully-coupled simulation.
 
-Another method of troubleshooting is to use the **point_of_interest** module.
+Another method of troubleshooting is to use the ``point_of_interest`` module.
 
 Use the point_of_interest module
 --------------------------------
 
-It is common, when debugging, to want to print the values of various variables for all patches or columns of certain landunit types within a certain grid cell of interest. For example, one might be able to identify a certain grid cell with an erroneous value for a particular history field variable (e.g., GPP) using for example ncview. Once the latitude and longitude of this grid cell has been determined, the point_of_interest module (**src/utils/point_of_interest.F90**) helps create the logical functions needed to do this. This module is compiled into every CTSM build, but is not invoked by default. To use it
+It is common, when debugging, to want to print the values of various variables for all patches or columns of certain landunit types within a certain grid cell of interest. For example, one might be able to identify a certain grid cell with an erroneous value for a particular history field variable (e.g., GPP) using for example ncview. Once the latitude and longitude of this grid cell has been determined, the point_of_interest module (``src/utils/point_of_interest.F90``) helps create the logical functions needed to do this. This module is compiled into every CTSM build, but is not invoked by default. To use it
 
-(1) Enter in the latitude/longitude of the point of interest in the function **at_poi** in **point_of_interest.F90** by setting the variables **poi_lat** and **poi_lon**.
+(1) Enter in the latitude/longitude of the point of interest in the function ``at_poi`` in ``point_of_interest.F90`` by setting the variables ``poi_lat`` and ``poi_lon``.
 
-(2) You may customize the **point_of_interest.F90** code by changing the example function (**poi_c**) and/or adding new functions. Look for comments about "Customize" to see what to customize.
+(2) You may customize the ``point_of_interest.F90`` code by changing the example function (``poi_c``) and/or adding new functions. Look for comments about "Customize" to see what to customize.
 
 (3) Add calls to these functions in the CTSM code
 
-The example function in **point_of_interest.F90** is **poi_c**. It finds columns with a given landunit type (in this case, the natural vegetated landunit). That function can be used in a column-level loop to find columns with that landunit within the grid cell of interest. Its typical use in CTSM code is
+The example function in ``point_of_interest.F90`` is ``poi_c``. It finds columns with a given landunit type (in this case, the natural vegetated landunit). That function can be used in a column-level loop to find columns with that landunit within the grid cell of interest. Its typical use in CTSM code is
 ::
 
    do fc = 1, num_nolakec
@@ -136,7 +136,7 @@ The example function in **point_of_interest.F90** is **poi_c**. It finds columns
       end if
    end do
 
-You will also need a **use** statement in the module from which you are calling poi_c
+You will also need a ``use`` statement in the module from which you are calling poi_c
 ::
 
    use point_of_interest, only : poi_c
@@ -193,5 +193,5 @@ Along the same lines, you might try running a simpler case, trying another comps
 Run with a debugger
 -------------------
 
-Another suggestion is to run the model with a debugger such as: **ddt**, **dbx**, **gdb**, or **totalview**. Often to run with a debugger you will need to reduce the number of processors as outlined above. Some debuggers such as **dbx** will only work with one processor, while more advanced debuggers such as **totalview** can work with both MPI tasks and OMP threads. Even simple debuggers though can be used to query core files, to see where the code was at when it died (for example using the **where** in **dbx** for a core file can be very helpful. For help in running with a debugger you will need to contact your system administrators for the machine you are running on.
+Another suggestion is to run the model with a debugger such as: ``ddt``, ``dbx``, ``gdb``, or ``totalview``. Often to run with a debugger you will need to reduce the number of processors as outlined above. Some debuggers such as ``dbx`` will only work with one processor, while more advanced debuggers such as ``totalview`` can work with both MPI tasks and OMP threads. Even simple debuggers though can be used to query core files, to see where the code was at when it died (for example using the ``where`` in ``dbx`` for a core file can be very helpful. For help in running with a debugger you will need to contact your system administrators for the machine you are running on.
 
diff --git a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
index 95e0333d6d..295dfd9380 100644
--- a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
@@ -4,17 +4,17 @@
 
 .. include:: ../substitutions.rst
 
-The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools **cprnc** and **gen_domain** use the CIME configure/build system which is described in the next section.
+The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools ``cprnc`` and ``gen_domain`` use the CIME configure/build system which is described in the next section.
 
-The Makefiles (for **mksurfdata_esmf** and **mkprocdata_map**) use GNU Make extensions and thus require that you use GNU make to use them. They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. There are also environment variables that can be set to set things that must be customized. All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. Finally the tools allow you to turn optimization on (which is off by default but on for **mksurfdata_esmf**) with the OPT flag so that the tool will run faster.
+The Makefiles (for ``mksurfdata_esmf`` and ``mkprocdata_map``) use GNU Make extensions and thus require that you use GNU make to use them. They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. There are also environment variables that can be set to set things that must be customized. All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. Finally the tools allow you to turn optimization on (which is off by default but on for ``mksurfdata_esmf``) with the OPT flag so that the tool will run faster.
 
-Options used by all:  **mksurfdata_esmf**
+Options used by all:  ``mksurfdata_esmf``
 
 - ``LIB_NETCDF`` -- sets the location of the NetCDF library.
 - ``INC_NETCDF`` -- sets the location of the NetCDF include files.
 - ``USER_FC`` -- sets the name of the FORTRAN compiler.
 
-Options used by: **mkprocdata_map**, and **mksurfdata_esmf**
+Options used by: ``mkprocdata_map``, and ``mksurfdata_esmf``
 
 - ``MOD_NETCDF`` -- sets the location of the NetCDF FORTRAN module.
 - ``USER_LINKER`` -- sets the name of the linker to use.
@@ -40,7 +40,7 @@ More details on each environment variable.
   This variable sets the path to the NetCDF include directory (in order to find the include file ``netcdf.inc``). if not set it defaults to ``/usr/local/include``.
 
 ``MOD_NETCDF``
-  This variable sets the path to the NetCDF module directory (in order to find the NetCDF FORTRAN-90 module file when NetCDF is used with a FORTRAN-90 **use statement**. When not set it defaults to the ``LIB_NETCDF`` value.
+  This variable sets the path to the NetCDF module directory (in order to find the NetCDF FORTRAN-90 module file when NetCDF is used with a FORTRAN-90 ``use statement``. When not set it defaults to the ``LIB_NETCDF`` value.
 
 ``USER_FC``
   This variable sets the command name to the FORTRAN-90 compiler to use when compiling the tool. The default compiler to use depends on the platform. And for example, on the AIX platform this variable is NOT used
@@ -69,7 +69,7 @@ More details on each environment variable.
 .. warning:: Note, that depending on the compiler answers may be different when SMP is activated.
 
 ``OPT``
-  This variable flags if compiler optimization should be used when compiling the tool. It can be set to either ``TRUE`` or ``FALSE``, by default it is set to for both **mksurfdata_esmf** and **mkprocdata_map**. Turning this on should make the tool run much faster.
+  This variable flags if compiler optimization should be used when compiling the tool. It can be set to either ``TRUE`` or ``FALSE``, by default it is set to for both ``mksurfdata_esmf`` and ``mkprocdata_map``. Turning this on should make the tool run much faster.
 
 .. warning:: Note, you should expect that answers will be different when ``OPT`` is activated.
 
@@ -90,7 +90,7 @@ More details on each environment variable.
 
 .. note:: There are several files that are copies of the original files. By having copies the tools can all be made stand-alone, but any changes to the originals will have to be put into the tool directories as well.
 
-The *README.filecopies* (which can be found in ``$CTSMROOT/tools``) is repeated here.
+The ``README.filecopies`` (which can be found in ``$CTSMROOT/tools``) is repeated here.
 
 .. include:: ../../../../tools/README.filecopies
    :literal:
@@ -99,7 +99,7 @@ The *README.filecopies* (which can be found in ``$CTSMROOT/tools``) is repeated
  Building the CLM tools that use the CIME configure/build system
 ================================================================
 
-**cprnc** and *gen_domain** both use the CIME configure/build system rather than the CLM specific version described above.
+``cprnc`` and ``gen_domain`` both use the CIME configure/build system rather than the CLM specific version described above.
 
-See `CIME documentation on adding grids <http://esmci.github.io/cime/users_guide/grids.html?highlight=gen_domain#adding-grids>`_ for more information on adding grids, creating mapping files, and running **gen_domain**. Also see the CIME file: ``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build **gen_domain**.
+See `CIME documentation on adding grids <http://esmci.github.io/cime/users_guide/grids.html?highlight=gen_domain#adding-grids>`_ for more information on adding grids, creating mapping files, and running ``gen_domain``. Also see the CIME file: ``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build ``gen_domain``.
 
diff --git a/doc/source/users_guide/using-clm-tools/cprnc.rst b/doc/source/users_guide/using-clm-tools/cprnc.rst
index 05a2ca8279..81418877c9 100644
--- a/doc/source/users_guide/using-clm-tools/cprnc.rst
+++ b/doc/source/users_guide/using-clm-tools/cprnc.rst
@@ -6,7 +6,7 @@
  Comparing History Files
 =========================
 
-**cprnc** is a tool shared by |cesmrelease| to compare two NetCDF history files. It differences every field that is shared on both files, and reports a summary of the difference. The summary includes the three largest differences, as well as the root mean square (RMS) difference. It also gives some summary information on the field as well. You have to enter at least one file, and up to two files. With one file it gives you summary information on the file, and with two it gives you information on the differences between the two. At the end it will give you a summary of the fields compared and how many fields were different and how many were identical.
+``cprnc`` is a tool shared by |cesmrelease| to compare two NetCDF history files. It differences every field that is shared on both files, and reports a summary of the difference. The summary includes the three largest differences, as well as the root mean square (RMS) difference. It also gives some summary information on the field as well. You have to enter at least one file, and up to two files. With one file it gives you summary information on the file, and with two it gives you information on the differences between the two. At the end it will give you a summary of the fields compared and how many fields were different and how many were identical.
 
 Options:
 
diff --git a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
index d4ebd6c4e7..3673e4ac18 100644
--- a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
+++ b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
@@ -6,7 +6,7 @@
  Creating CLM domain files
 *****************************
 
-*gen_domain* to create a domain file for datm from a mapping file. ``gen_domain`` is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of ``mknoocnmap.pl`` (see :ref:`using-mkocnmap`) to create a regional or single-point map file that is then run through ``gen_domain`` to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the $CIMEROOT/tools/mapping/gen_domain_files/README <https://github.com/ESMCI/cime/blob/master/tools/mapping/gen_domain_files/README>`_ file for more help on ``gen_domain``.
+``gen_domain`` to create a domain file for datm from a mapping file. ``gen_domain`` is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of ``mknoocnmap.pl`` (see :ref:`using-mkocnmap`) to create a regional or single-point map file that is then run through ``gen_domain`` to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the $CIMEROOT/tools/mapping/gen_domain_files/README <https://github.com/ESMCI/cime/blob/master/tools/mapping/gen_domain_files/README>`_ file for more help on ``gen_domain``.
 
 Here we create domain files for a regular global domain.
 
@@ -19,7 +19,7 @@ Global Domain file creation
 
   Global Domain file creation
 
-Starting from SCRIP grid files for both your atmosphere and ocean, you use **$CIMEROOT/tools/mapping/gen_mapping_files/gen_cesm_maps.sh** to create a mapping file between the atmosphere and ocean. That mapping file is then used as input to **gen_domain** to create output domain files for both atmosphere and ocean. The atmosphere domain file is then used by both CLM and DATM for I compsets, while the ocean domain file is ignored. For this process you have to define your SCRIP grid files on your own. For a regional or single-point case that doesn't include ocean see :numref:`Figure mknoocnmap.pl`. (See :numref:`Figure Global-Domain` for the legend for this figure.)
+Starting from SCRIP grid files for both your atmosphere and ocean, you use ``$CIMEROOT/tools/mapping/gen_mapping_files/gen_cesm_maps.sh`` to create a mapping file between the atmosphere and ocean. That mapping file is then used as input to ``gen_domain`` to create output domain files for both atmosphere and ocean. The atmosphere domain file is then used by both CLM and DATM for I compsets, while the ocean domain file is ignored. For this process you have to define your SCRIP grid files on your own. For a regional or single-point case that doesn't include ocean see :numref:`Figure mknoocnmap.pl`. (See :numref:`Figure Global-Domain` for the legend for this figure.)
 
 Note that the SCRIP grid file used to start this process is also used in ``mkmapdata.sh`` (see :ref:`using-mkocnmap`). Next we create domain files for a single-point or regional domain.
 
@@ -32,6 +32,6 @@ Domain file creation using mknoocnmap.pl
 
   Domain file creation using mknoocnmap.pl
 
-For a regular latitude/longitude grid that can be used for regional or single point simulations -- you can use **mknoocnmap.pl**. It creates a SCRIP grid file that can then be used as input to **mkmapdata.sh** as well as a SCRIP mapping file that is then input to **gen_domain**. The output of **gen_domain** is a atmosphere domain file used by both CLM and DATM and a ocean domain file that is ignored. (See :numref:`Figure mknoocnmap.pl` for the legend for this figure.)
+For a regular latitude/longitude grid that can be used for regional or single point simulations -- you can use ``mknoocnmap.pl``. It creates a SCRIP grid file that can then be used as input to ``mkmapdata.sh`` as well as a SCRIP mapping file that is then input to ``gen_domain``. The output of ``gen_domain`` is a atmosphere domain file used by both CLM and DATM and a ocean domain file that is ignored. (See :numref:`Figure mknoocnmap.pl` for the legend for this figure.)
 
-In this case the process creates both SCRIP grid files to be used by **mkmapdata.sh** as well as the domain files that will be used by both CLM and DATM.
+In this case the process creates both SCRIP grid files to be used by ``mkmapdata.sh`` as well as the domain files that will be used by both CLM and DATM.
diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst
index a727631a6c..e923b3bab2 100644
--- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst
+++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst
@@ -18,7 +18,7 @@ SCRIP grid files for all the standard model resolutions and the raw surface data
 Using mknocnmap.pl to create grid and maps for single-point regional grids
 --------------------------------------------------------------------------
 
-If you want to create a regular latitude/longitude single-point or regional grid, we suggest you use **mknoocnmap.pl** in ``$CTSMROOT/tools/mkmapdata`` which will create both the SCRIP grid file you need (using ``$CTSMROOT/tools/mkmapgrids/mkscripgrid.ncl`` AND an identity mapping file assuming there is NO ocean in your grid domain. If you HAVE ocean in your domain you could modify the mask in the SCRIP grid file for ocean, and then use **ESMF_RegridWeightGen** to create the mapping file, and **gen_domain** to create the domain file. Like other tools, ``./mkmapdata/mknoocnmap.pl`` has a help option with the following:
+If you want to create a regular latitude/longitude single-point or regional grid, we suggest you use ``mknoocnmap.pl`` in ``$CTSMROOT/tools/mkmapdata`` which will create both the SCRIP grid file you need (using ``$CTSMROOT/tools/mkmapgrids/mkscripgrid.ncl``) AND an identity mapping file assuming there is NO ocean in your grid domain. If you HAVE ocean in your domain you could modify the mask in the SCRIP grid file for ocean, and then use ``ESMF_RegridWeightGen`` to create the mapping file, and ``gen_domain`` to create the domain file. Like other tools, ``./mkmapdata/mknoocnmap.pl`` has a help option with the following:
 ::
 
    SYNOPSIS
diff --git a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst
index d2e2ef7c89..a59163a910 100644
--- a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst
+++ b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst
@@ -26,29 +26,29 @@ Starting from a SCRIP grid file that describes the grid you will run the model o
 
 Green arrows define the input to a program, while red arrows define the output. Cylinders define files that are either created by a program or used as input for a program. Boxes are programs.
 
-You start with a description of a SCRIP grid file for your output grid file and then create mapping files from the raw datasets to it. Once, the mapping files are created **mksurfdata_esmf** is run to create the surface dataset to run the model.
+You start with a description of a SCRIP grid file for your output grid file and then create mapping files from the raw datasets to it. Once, the mapping files are created ``mksurfdata_esmf`` is run to create the surface dataset to run the model.
 
 Creating a Complete Set of Files for Input to CLM
 -------------------------------------------------
 
 1. Create SCRIP grid datasets (if NOT already done)
 
-   First you need to create a descriptor file for your grid, that includes the locations of cell centers and cell corners. There is also a "mask" field, but in this case the mask is set to one everywhere (i.e. all of the masks for the output model grid are "nomask"). An example SCRIP grid file is: $CSMDATA/lnd/clm2/mappingdata/grids/SCRIPgrid_10x15_nomask_c110308.nc. The mkmapgrids and mkscripgrid.ncl NCL script in the $CTSMROOT/tools/mkmapgrids directory can help you with this. SCRIP grid files for all the standard CLM grids are already created for you. See the Section called Creating an output SCRIP grid file at a resolution to run the model on for more information on this.
+   First you need to create a descriptor file for your grid, that includes the locations of cell centers and cell corners. There is also a "mask" field, but in this case the mask is set to one everywhere (i.e. all of the masks for the output model grid are "nomask"). An example SCRIP grid file is: ``$CSMDATA/lnd/clm2/mappingdata/grids/SCRIPgrid_10x15_nomask_c110308.nc``. The ``mkmapgrids`` and ``mkscripgrid.ncl`` NCL script in the ``$CTSMROOT/tools/mkmapgrids`` directory can help you with this. SCRIP grid files for all the standard CLM grids are already created for you. See the Section called Creating an output SCRIP grid file at a resolution to run the model on for more information on this.
 
 2. Create domain dataset (if NOT already done)
 
-   Next use gen_domain to create a domain file for use by DATM and CLM. This is required, unless a domain file was already created. See the Section called Creating a domain file for CLM and DATM for more information on this.
+   Next use ``gen_domain`` to create a domain file for use by DATM and CLM. This is required, unless a domain file was already created. See the Section called Creating a domain file for CLM and DATM for more information on this.
 
-3. Create mapping files for mksurfdata_esmf (if NOT already done)
+3. Create mapping files for ``mksurfdata_esmf`` (if NOT already done)
 
-   Create mapping files for mksurfdata_esmf with mkmapdata.sh in $CTSMROOT/tools/mkmapdata. See the Section called Creating mapping files that mksurfdata_esmf will use for more information on this.
+   Create mapping files for ``mksurfdata_esmf`` with ``mkmapdata.sh`` in ``$CTSMROOT/tools/mkmapdata``. See the Section called Creating mapping files that ``mksurfdata_esmf`` will use for more information on this.
 
 4. Create surface datasets
 
-   Next use mksurfdata_esmf to create a surface dataset, using the mapping datasets created on the previous step as input. There is a version for either clm4_0 or |version| for this program. See the Section called Using mksurfdata_esmf to create surface datasets from grid datasets for more information on this.
+   Next use ``mksurfdata_esmf`` to create a surface dataset, using the mapping datasets created on the previous step as input. There is a version for either clm4_0 or |version| for this program. See the Section called Using ``mksurfdata_esmf`` to create surface datasets from grid datasets for more information on this.
 
-5. Enter the new datasets into the build-namelist XML database
-   The last optional thing to do is to enter the new datasets into the build-namelist XML database. See Chapter 3 for more information on doing this. This is optional because the user may enter these files into their namelists manually. The advantage of entering them into the database is so that they automatically come up when you create new cases.
+5. Enter the new datasets into the ``build-namelist`` XML database
+   The last optional thing to do is to enter the new datasets into the ``build-namelist`` XML database. See Chapter 3 for more information on doing this. This is optional because the user may enter these files into their namelists manually. The advantage of entering them into the database is so that they automatically come up when you create new cases.
 
 The ``$CTSMROOT/tools/README`` goes through the complete process for creating input files needed to run CLM. We repeat that file here:
 
diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
index db5cf10798..c997f403d2 100644
--- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
@@ -12,21 +12,21 @@ The tools produce files that can be used for CLM4.5 and |version|. They do **NOT
 
 The list of generally important scripts and programs are as follows.
 
-1. *./mkmapgrids* to create SCRIP grid data files from old CLM format grid files that can then be used to create new CLM datasets (deprecated). There is also a NCL script (``./mkmapgrids/mkscripgrid.ncl`` to create SCRIP grid files for regular latitude/longitude grids.
+1. ``./mkmapgrids`` to create SCRIP grid data files from old CLM format grid files that can then be used to create new CLM datasets (deprecated). There is also a NCL script (``./mkmapgrids/mkscripgrid.ncl``) to create SCRIP grid files for regular latitude/longitude grids.
 
-#. *./mkmapdata* to create SCRIP mapping data file from SCRIP grid files (uses ESMF).
+#. ``./mkmapdata`` to create SCRIP mapping data file from SCRIP grid files (uses ESMF).
 
-#. *mksurfdata_esmf* to create surface datasets from grid datasets (clm4_0 and |version| versions).
+#. ``mksurfdata_esmf`` to create surface datasets from grid datasets (clm4_0 and |version| versions).
 
-#. *./mkprocdata_map* to interpolate output unstructured grids (such as the CAM HOMME dy-core "ne" grids like ne30np4) into a 2D regular lat/long grid format that can be plotted easily. Can be used by either clm4_0 or |version|.
+#. ``./mkprocdata_map`` to interpolate output unstructured grids (such as the CAM HOMME dy-core "ne" grids like ne30np4) into a 2D regular lat/long grid format that can be plotted easily. Can be used by either clm4_0 or |version|.
 
-#. *$CIMEROOT/tools/mapping/gen_domain_files/gen_domain* to create a domain file for datm from a mapping file. The domain file is then used by BOTH datm AND CLM to define the grid and land-mask.
+#. ``$CIMEROOT/tools/mapping/gen_domain_files/gen_domain`` to create a domain file for datm from a mapping file. The domain file is then used by BOTH datm AND CLM to define the grid and land-mask.
 
-#. *$CIMEROOT/tools/cprnc* to compare two NetCDF files.
+#. ``$CIMEROOT/tools/cprnc`` to compare two NetCDF files.
 
 In the sections to come we will go into detailed description of how to use each of these tools in turn. First, however we will discuss the common environment variables and options that are used by all of the FORTRAN tools. Second, we go over the outline of the entire file creation process for all input files needed by CLM for a new resolution, then we turn to each tool. In the last section we will discuss how to customize files for particular observational sites.
 
-The FORTRAN tools (mksurfdata_esmf and mkprocdata_map) run, with a namelist (mksurfdata_esmf) to provide options, or with command line arguments (mkprocdata_map).
+The FORTRAN tools (``mksurfdata_esmf`` and ``mkprocdata_map``) run, with a namelist (``mksurfdata_esmf``) to provide options, or with command line arguments (``mkprocdata_map``).
 
 In the following sections, we will outline how to make these files available for build-namelist so that you can easily create simulations that include them. In the chapter on single-point and regional datasets we also give an alternative way to enter new datasets without having to edit files.
 
@@ -34,12 +34,12 @@ In the following sections, we will outline how to make these files available for
 Running FORTRAN tools with namelists
 ------------------------------------
 
-**mksurfdata_esmf** runs with a namelist that is read from standard input. Hence, you create a namelist and then run them by redirecting the namelist file into standard input as follows:
+``mksurfdata_esmf`` runs with a namelist that is read from standard input. Hence, you create a namelist and then run them by redirecting the namelist file into standard input as follows:
 ::
 
    ./program < namelist
 
-There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` that shows you what the namelist should look like. **mksurfdata_esmf** also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the:
+There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` that shows you what the namelist should look like. ``mksurfdata_esmf`` also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the:
 ::
 
    $CTSMROOT/bld/namelist_files/namelist_definition.xml`` file
@@ -50,7 +50,7 @@ There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfda
 Running FORTRAN tools with command line options
 -----------------------------------------------
 
-**gen_domain**, mkprocdata_map, and **cprnc** run with command line arguments. The detailed sections below will give you more information on the command line arguments specific to each tool. Also running the tool without any arguments will give you a general synopsis on how to run the tool.
+``gen_domain``, ``mkprocdata_map``, and ``cprnc`` run with command line arguments. The detailed sections below will give you more information on the command line arguments specific to each tool. Also running the tool without any arguments will give you a general synopsis on how to run the tool.
 
 -----------------------------------------
 Running FORTRAN tools built with SMP=TRUE

From ac01cb3e48e3b6348b51eb1adaa73e8f63cdf3b3 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 19 Sep 2024 20:01:28 -0600
Subject: [PATCH 1092/1248] Add doc todo to replace missing figure.

---
 doc/source/lilac/specific-atm-models/wrf-nesting.rst | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/doc/source/lilac/specific-atm-models/wrf-nesting.rst b/doc/source/lilac/specific-atm-models/wrf-nesting.rst
index f4c4570f2f..347a927a59 100644
--- a/doc/source/lilac/specific-atm-models/wrf-nesting.rst
+++ b/doc/source/lilac/specific-atm-models/wrf-nesting.rst
@@ -50,13 +50,14 @@ A full description of all steps for a WRF-CTSM run are included here.
   Therefore, we are not repeating the steps necessary for building WRF and
   CTSM.
 
-In this example we use a nested domain over the CONUS as shows below:
+In this example we use a nested domain over the CONUS as shown below:
 
 .. _Figure ctsm-ndown:
 
-.. figure:: ndown_ctsm_diagram.svg
-
-    Flowchart for WRF-CTSM one-way nested simulations
+.. todo::
+    Replace missing ndown_ctsm_diagram.svg
+    
+Flowchart for WRF-CTSM one-way nested simulations
 
 Nested Simulations : Pre-processing (geogrid.exe)
 -------------------------------------------------

From 5c3ea513f85f394a09e081b1e56fb69a9c1f9eab Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 19 Sep 2024 20:02:15 -0600
Subject: [PATCH 1093/1248] Fix a title overline.

---
 doc/source/users_guide/trouble-shooting/trouble-shooting.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
index 418a4aff37..8f2387996b 100644
--- a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
+++ b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
@@ -2,7 +2,7 @@
 
 .. _trouble-shooting:
 
-*************
+***************
 Troubleshooting
 ***************
 

From 6fca8291a2a087a75be63b9c16134528b8d4f73f Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 19 Sep 2024 20:13:13 -0600
Subject: [PATCH 1094/1248] More formatting fixes.

---
 ...w-Files-to-the-build-namelist-Database.rst |  2 +-
 .../Adding-or-Changing-Default-Filenames.rst  | 20 ++++++-----
 .../customizing-the-clm-configuration.rst     | 35 +++++++++----------
 .../trouble-shooting/trouble-shooting.rst     | 30 ++++++++++------
 4 files changed, 49 insertions(+), 38 deletions(-)

diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
index fc7b2c0ee3..753ea896ee 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
@@ -6,7 +6,7 @@
  Adding New Resolutions
 ========================
 
-In the last chapter we gave the details on how to create new files for input into CLM. These files could be either global resolutions, regional-grids or even a single grid point. If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. You can deal with them, just by putting the settings in the ``user_nl_clm namelist`` file, or by using ``CLM_USRDAT_NAME``. Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. This keeps one central database for all your files, rather than having multiple locations to keep track of files. If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above.
+In the last chapter we gave the details on how to create new files for input into CLM. These files could be either global resolutions, regional-grids or even a single grid point. If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. You can deal with them, just by putting the settings in the ``user_nl_clm`` namelist file, or by using ``CLM_USRDAT_NAME``. Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. This keeps one central database for all your files, rather than having multiple locations to keep track of files. If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above.
 
 There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into ``create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
 
diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
index a2e7fcfc4e..22af143e72 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
@@ -6,17 +6,18 @@
  Changing Default Filenames
 ============================
 
-To add or change the default filenames you edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` and either change an existing filename or add a new one. Most entries in the default namelist files, include different attributes that describe the different properties that describe the differences in the datasets. Attributes include the: resolution, year to simulation, range of years to simulate for transient datafiles, the land-mask, the representative concentration pathway (rcp) for future scenarios, and the type of biogeochemistry (bgc) model used. For example the fsurdat for the 1.9x2.5 resolution is as follows:
+To add or change the default filenames you edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` and either change an existing filename or add a new one. Most entries in the default namelist files, include different attributes that describe the different properties that describe the differences in the datasets. Attributes include the resolution, year to simulation, range of years to simulate for transient datafiles, the land-mask, the representative concentration pathway (RCP) for future scenarios, and the type of biogeochemistry (BGC) model used. For example the surface dataset (``fsurdat``) for the 1.9x2.5 resolution is as follows:
 
-```
-<fsurdat hgrid="0.9x1.25"  sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_CMIP6_simyr1850_c170824.nc
-</fsurdat>
-```
+::
+  
+  <fsurdat hgrid="0.9x1.25"  sim_year="1850" use_crop=".true." >
+  lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_CMIP6_simyr1850_c170824.nc
+  </fsurdat>
 
-Other ``fsurdat`` files are distinguished from this one by their resolution (hgrid), simulation year (sim_year) and prognostic crop (use_crop) attributes.
 
-To add or change the default filenames for CLM tools edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. Editing this file is similar to the ``namelist_defaults_clm4_5.xml`` talked about above.
+Other ``fsurdat`` files are distinguished from this one by their resolution (``hgrid``), simulation year (``sim_year``) and prognostic crop (``use_crop``) attributes.
+
+To add or change the default filenames for CLM tools, edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. Editing this file is similar to the ``namelist_defaults_clm4_5.xml`` talked about above.
 
 ----------------------------
 What are the required files?
@@ -30,4 +31,5 @@ In the following table we list the different files used by CLM, they are listed
 
 Table 3-1. Required Files for Different Configurations and Simulation Types
 ---------------------------------------------------------------------------
-Insert table 3-1
+.. todo::
+    Insert table 3-1
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index 0987a32e8e..2bece02abd 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -256,34 +256,33 @@ CLM_BLDNML_OPTS
              (i.e.  CLM_NML_USE_CASE env_run variable)
       6. values from the namelist defaults file.
 
-The ``$CTSMROOT/cime_config/buildnml`` script already sets the resolution and mask as well as the CLM ``configure`` file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. Hence only the following different options can be set:
+The ``$CTSMROOT/cime_config/buildnml`` script already sets the resolution and mask as well as the CLM ``configure`` file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the: start-type (from ``RUN_TYPE``); namelist options (from ``CLM_NAMELIST_OPTS``); ``co2_ppmv`` (from ``CCSM_CO2_PPMV``); ``co2_type`` (from ``CLM_CO2_TYPE``); ``lnd_frac`` (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``); ``l_ncpl`` (from ``LND_NCPL``); ``glc_grid``, ``glc_smb``, ``glc_nec`` (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``); and ``clm_usr_name`` (to ``CLM_USRDAT_NAME``). Hence only the following different options can be set:
 
-1.
--bgc_spinup
+#. ``-bgc_spinup``
 
-#. -chk_res
+#. ``-chk_res``
 
-#. -clm_demand
+#. ``-clm_demand``
 
-#. -drydep
+#. ``-drydep``
 
-#. -fire_emis
+#. ``-fire_emis``
 
-#. -ignore_ic_date
+#. ``-ignore_ic_date``
 
-#. -ignore_ic_year
+#. ``-ignore_ic_year``
 
-#. -irrig
+#. ``-irrig``
 
-#. -no-megan
+#. ``-no-megan``
 
-#. -note
+#. ``-note``
 
-#. -rcp
+#. ``-rcp``
 
-#. -sim_year
+#. ``-sim_year``
 
-#. -verbose
+#. ``-verbose``
 
 ``-bgc_spinup`` is an option only available for |version| for any configuration when CN is turned on (so either CLMCN or CLMBGC). It can be set to "on" or "off". If "on" the model will go into Accelerated Decomposition mode, while for "off" (the default) it will have standard decomposition rates. If you are starting up from initial condition files the model will check what mode the initial condition file is in and do the appropriate action on the first time-step to change the Carbon pools to the appropriate spinup setting. See :ref:`spinning-up-clm-bgc` for an example using this option.
 
@@ -308,9 +307,9 @@ To see a list of valid variables that you could set do this:
 
 ``-ignore_ic_year`` ignores the Initial Conditions (IC) year for finding initial condition files to startup from. The date is used, but the year is ignored. Without this option or the ``-ignore_ic_date`` option below, the date and year of the file comes into play.
 
-When ``-irrig on`` is used ``build-namelist`` will try to find surface datasets that have the irrigation model enabled (when running with Sattellitte Phenology). When running with the prognostic crop model on, ``-irrig on`` will turn irrigate crops on, while ``-irrig off`` will manage all crop areas as rain-fed without irrigation.
+When ``-irrig on`` is used ``build-namelist`` will try to find surface datasets that have the irrigation model enabled (when running with Sattellitte Phenology). When running with the prognostic crop model on, ``-irrig on`` will turn crop irrigation on, while ``-irrig off`` will manage all crop areas as rain-fed without irrigation.
 
-``no-megan`` means do NOT add a MEGAN model Biogenic Volatile Organic Compounds (BVOC) testing namelist to the driver. This namelist is created by default, so normally this WILL be done. This is a driver namelist, so unless ``no-megan`` is specified the CLM ``build-namelist`` will create the ``drv_flds_in`` file that the driver will copy over and use (if you are running with CAM and CAM produces this file as well, it's file will have precedence).
+``no-megan`` means do NOT add a MEGAN model Biogenic Volatile Organic Compounds (BVOC) testing namelist to the driver. This namelist is created by default, so normally this WILL be done. This is a driver namelist, so unless ``no-megan`` is specified the CLM ``build-namelist`` will create the ``drv_flds_in`` file that the driver will copy over and use. (If you are running with CAM and CAM produces this file as well, its file will have precedence).
 
 ``-note`` adds a note to the bottom of the namelist file, that gives the details of how ``build-namelist`` was called, giving the specific command-line options given to it.
 
@@ -463,7 +462,7 @@ The first option is to setup a hybrid simulation and give a ``RUN_REFCASE`` and
 
 ``./xmlchange RUN_TYPE=hybrid,RUN_REFCASE=b.e20.B1850.f09_g17.pi_control.all.297,RUN_REFDATE=0130-01-01,GET_REFCASE=TRUE``
 
-Setting the ``GET_REFCASE`` option to ``TRUE means`` it will copy the files from the RUN_REFDIR usually under: ``$DIN_LOC_ROOT/cesm2_init/$RUN_REFCASE/$RUN_REFDATE`` directory. Note, that the ``RUN_REFCASE`` and ``RUN_REFDATE`` variables are expanded to get the directory name above. If you do NOT set ``GET_REFCASE`` to ``TRUE`` then you will need to have placed the file in your run directory yourself. In either case, the file is expected to be named: ``$RUN_REFCASE.clm2.r.$RUN_REFDATE-00000.nc`` with the variables expanded of course.
+Setting the ``GET_REFCASE`` option to ``TRUE`` means it will copy the files from the RUN_REFDIR usually under: ``$DIN_LOC_ROOT/cesm2_init/$RUN_REFCASE/$RUN_REFDATE`` directory. Note, that the ``RUN_REFCASE`` and ``RUN_REFDATE`` variables are expanded to get the directory name above. If you do NOT set ``GET_REFCASE`` to ``TRUE`` then you will need to have placed the file in your run directory yourself. In either case, the file is expected to be named: ``$RUN_REFCASE.clm2.r.$RUN_REFDATE-00000.nc`` with the variables expanded of course.
 
 .. _doing-a-branch-sim-for-init-conds:
 
diff --git a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
index 8f2387996b..a971b7f2cb 100644
--- a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
+++ b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst
@@ -71,20 +71,26 @@ So here we know that it is either leaf nitrogen (leafn) or leaf carbon (leafc) t
 
 At this point it is useful as a next step to identify the particular patch index and perhaps the pft type that is triggering the error. In this case, the endrun call is already written to provide this information: the patch index and pft type causing the error, along with some other information, are printed in the lines beginning with ``iam``. The ``iam`` value gives the CTSM processor number (this can be obtained in the code via the ``iam`` variable defined in ``spmdMod``). The local patch index is the value of ``p`` in the current patch loop; "local" implies that it refers to this processor's indexing. However, this same value of ``p`` may appear on other processors, since the local indexing on each processor starts with 1. So, to get the unique patch causing the problem, you either need to use the processor's ``iam`` index (there is only one patch with local index 482 on processor 362), or use the global indices printed below the local index. The "global" term here refers to the global index space across all processors (there is only one patch with a global index of 163723 across all processors). See below for how to use the ``get_global_index`` function to translate from local to global indices.
 
-If you are writing your own ``endrun`` call, you can get this additional information by specifying the ``subgrid_index`` and ``subgrid_level`` arguments; for example::
+If you are writing your own ``endrun`` call, you can get this additional information by specifying the ``subgrid_index`` and ``subgrid_level`` arguments; for example:
 
+::
+  
   call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__))
 
 (The ``subgrid_level_patch`` constant, and similar constants for the other subgrid levels, are defined in ``decompMod``, so can be accessed via ``use decompMod, only : subgrid_level_patch``.)
 
-You can get this same information without aborting the run via a call to ``write_point_context``, which is also defined in the ``abortutils`` module; e.g.::
+You can get this same information without aborting the run via a call to ``write_point_context``, which is also defined in the ``abortutils`` module; e.g.:
 
-   if (abs(carbon_patch(p)) < ccrit) then
-      call write_point_context(subgrid_index=p, subgrid_level=subgrid_level_patch)
-   end if
+::
+  
+  if (abs(carbon_patch(p)) < ccrit) then
+     call write_point_context(subgrid_index=p, subgrid_level=subgrid_level_patch)
+  end if
 
-Or, if all you want is the global index of ``p`` for the sake of writing extra diagnostic prints like the example below, then you can use the ``get_global_index`` function defined in ``decompMod``, like::
+Or, if all you want is the global index of ``p`` for the sake of writing extra diagnostic prints like the example below, then you can use the ``get_global_index`` function defined in ``decompMod``, like:
 
+::
+   
    if (abs(carbon_patch(p)) < ccrit) then
       write(iulog,*) 'carbon patch significantly negative at local, global p = ', &
            p, get_global_index(subgrid_index=p, subgrid_level=subgrid_level_patch)
@@ -92,8 +98,10 @@ Or, if all you want is the global index of ``p`` for the sake of writing extra d
 
 In all of these cases, the output will appear in either the cesm or lnd log file. In the above example, we see that the local patch index is 482 on processor 362 and the global patch index is 163723. From there, one can use this patch index to write out variables that are used in updating leafc, for example, leafc is updated a number of times in CNCStateUpdate1Mod.F90.
 
-There are two equivalent methods to write a conditional statement to provide more output for the problem patch within a loop over all patches. The first method is to translate the local index to a global index::
+There are two equivalent methods to write a conditional statement to provide more output for the problem patch within a loop over all patches. The first method is to translate the local index to a global index:
 
+::
+   
    use decompMod, only : get_global_index, subgrid_level_patch
    ...
    if (get_global_index(p, subgrid_level_patch) == 163723) then
@@ -101,8 +109,10 @@ There are two equivalent methods to write a conditional statement to provide mor
       write(iulog,*)'CNCStateUpdate1Mod +leafc_xfer_to_leafc: ',cf_veg%leafc_xfer_to_leafc_patch(p)*dt
    end if
 
-The second method is to use the local index along with the processor number::
+The second method is to use the local index along with the processor number:
 
+::
+   
    use spmdMod, only : iam
    ...
    if (p == 482 .and. iam == 362) then
@@ -127,7 +137,7 @@ It is common, when debugging, to want to print the values of various variables f
 
 The example function in ``point_of_interest.F90`` is ``poi_c``. It finds columns with a given landunit type (in this case, the natural vegetated landunit). That function can be used in a column-level loop to find columns with that landunit within the grid cell of interest. Its typical use in CTSM code is
 ::
-
+   
    do fc = 1, num_nolakec
       c = filter_nolakec(fc)
       ! Various code here, maybe setting foo and bar variables
@@ -136,7 +146,7 @@ The example function in ``point_of_interest.F90`` is ``poi_c``. It finds columns
       end if
    end do
 
-You will also need a ``use`` statement in the module from which you are calling poi_c
+You will also need a ``use`` statement in the module from which you are calling ``poi_c``
 ::
 
    use point_of_interest, only : poi_c

From 24354eba65d652e9c67f6f93328a49507a8aeb1d Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 19 Sep 2024 20:43:30 -0600
Subject: [PATCH 1095/1248] Replace some :: with :.

---
 doc/source/lilac/specific-atm-models/wrf-nesting.rst            | 2 +-
 .../Spinning-up-the-biogeochemistry-BGC-spinup.rst              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/lilac/specific-atm-models/wrf-nesting.rst b/doc/source/lilac/specific-atm-models/wrf-nesting.rst
index 347a927a59..2e8b88efd0 100644
--- a/doc/source/lilac/specific-atm-models/wrf-nesting.rst
+++ b/doc/source/lilac/specific-atm-models/wrf-nesting.rst
@@ -79,7 +79,7 @@ If the geogrid step finishes successfully, you should see the following message
     !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 The basic difference here with a non-nested case is the namelist.wps should
-have a column for each domain with `max_dom=2`. For example::
+have a column for each domain with `max_dom=2`. For example:
 
     &share
      wrf_core = 'ARW',
diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
index 089603db09..6b39c2b380 100644
--- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
+++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
@@ -43,7 +43,7 @@ If you use the default initial file and you signficantly change model behavior o
 **1. |version| accelerated-decomposition (AD) spinup**
      For the first step of running 200+ years in ``-bgc_spinup on`` mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. So do the following:
 
-Example:: AD_SPINUP Simulation for |version|-BGC
+Example: AD_SPINUP Simulation for |version|-BGC
 --------------------------------------------------------
 ::
 

From e368dd4b021aac7325d93006be0307ed4beeb893 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Thu, 19 Sep 2024 20:49:54 -0600
Subject: [PATCH 1096/1248] Formatting fixes in wrf-nesting.rst.

---
 .../lilac/specific-atm-models/wrf-nesting.rst | 86 +++++++------------
 1 file changed, 29 insertions(+), 57 deletions(-)

diff --git a/doc/source/lilac/specific-atm-models/wrf-nesting.rst b/doc/source/lilac/specific-atm-models/wrf-nesting.rst
index 2e8b88efd0..81428495f0 100644
--- a/doc/source/lilac/specific-atm-models/wrf-nesting.rst
+++ b/doc/source/lilac/specific-atm-models/wrf-nesting.rst
@@ -6,12 +6,9 @@
  Using CTSM with WRF (Nested Model Runs)
 ========================================
 
-This section includes instructions on how to run WRF coupled with CTSM for a
-nested domain.
+This section includes instructions on how to run WRF coupled with CTSM for a nested domain.
 
-A nested domain is usually used to have a finer-resolution domain within the
-coarser model domain. A nested simulation enables running at a higher
-resolution over a smaller domain
+A nested domain is usually used to have a finer-resolution domain within the coarser model domain. A nested simulation enables running at a higher resolution over a smaller domain.
 
 .. note::
     A nest should cover a portion of the parent domain and is fully contained by
@@ -37,9 +34,7 @@ There are currently two types of nesting available within WRF:
     This example clarifies the workflow for running a nested WRF-CTSM case using one-way nesting with ``ndown.exe``.
 
 The procedure for running a nested simulation for WRF with CTSM is
-similar to the workflow for running WRF real cases, except that it requires
-additional steps to (1) clone the CTSM repository, (2) build
-CTSM and LILAC, and (3) define namelist options reuired for CTSM.
+similar to the workflow for running WRF real cases, except that it requires additional steps to (1) clone the CTSM repository, (2) build CTSM and LILAC, and (3) define namelist options reuired for CTSM.
 
 A full description of all steps for a WRF-CTSM run are included here.
 
@@ -61,16 +56,14 @@ Flowchart for WRF-CTSM one-way nested simulations
 
 Nested Simulations : Pre-processing (geogrid.exe)
 -------------------------------------------------
-In the WPS/ directory, edit `namelist.wps` for a nested simulation over your
-desired domains. Make sure to change `max_dom=2`.
+In the WPS/ directory, edit ``namelist.wps`` for a nested simulation over your
+desired domains. Make sure to change ``max_dom=2``.
 
-First, use geogrid.exe to define the domain and interpolate static geographical data
-to the grids::
+First, use geogrid.exe to define the domain and interpolate static geographical data to the grids::
 
     ./geogrid.exe >& log.geogrid
 
-This step creates two files `geo_em.d01.nc` & `geo_em.d02.nc` which includes
-the domain definition for each domain.
+This step creates two files, ``geo_em.d01.nc`` and ``geo_em.d02.nc``, which include the domain definition for each domain.
 
 If the geogrid step finishes successfully, you should see the following message in the log file::
 
@@ -78,9 +71,10 @@ If the geogrid step finishes successfully, you should see the following message
     !  Successful completion of geogrid.  !
     !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-The basic difference here with a non-nested case is the namelist.wps should
-have a column for each domain with `max_dom=2`. For example:
+The basic difference here with a non-nested case is the namelist.wps should have a column for each domain with ``max_dom=2``. For example:
 
+::
+    
     &share
      wrf_core = 'ARW',
      max_dom = 2,
@@ -102,9 +96,7 @@ Therefore ``geogrid.exe`` creates two files corresponding to each domain.
 
 Nested Simulations : Pre-processing (ungrib.exe)
 -------------------------------------------------
-As mentioned previously, the purpose of the ungrib script is to unpack GRIB
-meteorological data and pack it into an intermediate file format.
-This step is exactly identical to a non-nested simulation.
+As mentioned previously, the purpose of the ungrib script is to unpack GRIB meteorological data and pack it into an intermediate file format. This step is exactly identical to a non-nested simulation.
 
 Run ungrib to get gribbed data into usable format to be ingested by WRF.
 
@@ -112,8 +104,7 @@ To run ungrib.exe, first link the GRIB data files that are going to be used::
 
     ./link_grib.csh $your_GRIB_data_path
 
-Based on your GRIB data type, link or copy the appropriate VTable to your WPS directory.
-WRF has some prepared VTable under ``/ungrib/Variable_tables/`` folder.
+Based on your GRIB data type, link or copy the appropriate VTable to your WPS directory. WRF has some prepared VTable under ``/ungrib/Variable_tables/`` folder.
 
 Extract meteorological fields from GRIB-formatted files::
 
@@ -129,21 +120,17 @@ At this point, you should see ungrib output (intermediate files) in your WPS dir
 
 Nested Simulations : Pre-processing (metgrid.exe)
 -------------------------------------------------
-Ensure that the `start_date` and `end_date` for domain two is set correctly for
-your simulation.
-Next, run ``metgrid.exe``::
+Ensure that the `start_date` and `end_date` for domain two is set correctly for your simulation. Next, run ``metgrid.exe``::
 
     ./metgrid.exe >& log.metgrid
 
-Check the metgrid log for the following message showing successful completion of
-metgrid step::
+Check the metgrid log for the following message showing successful completion of metgrid step::
 
     !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     !  Successful completion of metgrid.  !
     !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-Running metgrid for two domains will create files like
-below::
+Running metgrid for two domains will create files like below::
 
     met_em.d01.*
     met_em.d02.*
@@ -151,25 +138,19 @@ below::
 Nested Simulations : real.exe
 ------------------------------
 
-In this step, run ``real.exe`` to generate initial and boundary conditions for
-both domains.
+In this step, run ``real.exe`` to generate initial and boundary conditions for both domains.
 
 In summary, complete the following steps:
 
 Move or link WPS output files (``met_em.d01*`` and ``met_em.d02`` files) to your WRF test directory.
 
-Edit namelist.input for your WRF domain and desirable configurations.
-This should be the same domain as WPS namelist. Make sure you set ``max_dom =
-2,`` in the namelist.
+Edit namelist.input for your WRF domain and desirable configurations. This should be the same domain as WPS namelist. Make sure you set ``max_dom = 2,`` in the namelist.
 
-To run WRF-CTSM, in your namelist change land-surface option to 6 for both
-domains::
+To run WRF-CTSM, in your namelist change land-surface option to 6 for both domains::
 
     sf_surface_physics = 6, 6,
 
-Run real.exe (if compiled parallel submit a batch job) to generate
-initail and boundary condition files for both domain.
-Make sure the following three files have been created in your directory::
+Run real.exe (if compiled parallel submit a batch job) to generate initial and boundary condition files for both domain. Make sure the following three files have been created in your directory::
 
     wrfinput_d01
     wrfinput_d02
@@ -179,6 +160,8 @@ The boundary condition file is only created for the outer domain.
 
 Check the last line of the real log file for the following message:
 
+.. todo:: What message?
+
 Rename wrfinput_d02
 -------------------
 Next, rename the ``wrfinput_d02`` file to ``wrfndi_d02``::
@@ -187,8 +170,7 @@ Next, rename the ``wrfinput_d02`` file to ``wrfndi_d02``::
 
 Run ndown.exe
 -------------
-In this step, we run ndown.exe to create initial and boundary condition for
-domain 2 based on the domain 1 (outer domain).
+In this step, we run ndown.exe to create initial and boundary condition for domain 2 based on the domain 1 (outer domain).
 
 Add the following into your namelist.input file under ``&time_control``::
 
@@ -198,20 +180,15 @@ Run ndown.exe to create ``wrfinput_d02`` and ``wrfbdy_d02``.
 
 Run WRF for coarser domain
 ---------------------------
-In this step, run WRF for the outer domain.
-Make sure that ``max_dom = 1`` to run only for the coarser domain.
+In this step, run WRF for the outer domain. Make sure that ``max_dom = 1`` to run only for the coarser domain.
 
-This step is exactly identical as the previous example and only creates the
-``wrfout*`` files for the coarser domain.
+This step is exactly identical as the previous example and only creates the ``wrfout*`` files for the coarser domain.
 
-Please make sure to copy ``lnd_in`` , ``lilac_in``, and ``lnd_modelio`` for the
-coarser domain in this directory.
+Please make sure to copy ``lnd_in`` , ``lilac_in``, and ``lnd_modelio`` for the coarser domain in this directory.
 
 Create CTSM runtime files for the fine domain
 ---------------------------------------------
-This step is in addition creating CTSM runtime files for coarser domain which
-was explained here. For succesfully completing the previous step you should
-have already created these files for the coarser domain.
+This step is in addition creating CTSM runtime files for coarser domain which was explained here. For succesfully completing the previous step you should have already created these files for the coarser domain.
 
 .. seealso::
 
@@ -220,8 +197,7 @@ have already created these files for the coarser domain.
     files for the finer domain you should follow the steps in section
     :numref:`setting-ctsm-runtime-options`.
 
-Again, the goal here is to create files that determine CTSM runtime options which
-are defined within these three files:
+Again, the goal here is to create files that determine CTSM runtime options which are defined within these three files:
 
 - ``lnd_in``: This is the main namelist input file for CTSM inner domain
 
@@ -231,13 +207,9 @@ are defined within these three files:
 
 Run WRF for the finer domain
 -----------------------------
-First, save (rename or move) the data from the coarser domain simulation
-(``wrfout_d01_*`` files).
-Next, rename ``wrfinput_d02`` and ``wrfbdy_d02`` to ``wrfinput_d01`` and ``wrfbdy_d01``, respectively.
+First, save (rename or move) the data from the coarser domain simulation (``wrfout_d01_*`` files). Next, rename ``wrfinput_d02`` and ``wrfbdy_d02`` to ``wrfinput_d01`` and ``wrfbdy_d01``, respectively.
 
-Edit namelist.input, moving all of the fine-grid domain data from column 2 to column 1
-so that this run will be for the fine-grid domain only. Make sure you set
-`max_dom=1` and set your `time_step` based on the finer domain.
+Edit namelist.input, moving all of the fine-grid domain data from column 2 to column 1 so that this run will be for the fine-grid domain only. Make sure you set ``max_dom=1`` and set your ``time_step`` based on the finer domain.
 
 .. note::
     It may be beneficial to save namelist.input to something else prior to this step in case you need to repeat this

From d1a4552c3e6bc1860568944560dd2eff8d3e1a21 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 20 Sep 2024 18:24:42 -0600
Subject: [PATCH 1097/1248] Update finidat files picked up by LII* tests from
 namelist_defaults_ctsm

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 67348d8ca2..8593c73927 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1343,8 +1343,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
+         lnd_tuning_mode="clm5_0_GSWP3v1"
+>lnd/clm2/initdata_esmf/ctsm5.3/clmi.interp_from.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
 </finidat>
 
 
@@ -1413,11 +1413,17 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- This is the same file as above but, for a different tuning mode -->
+<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".false."
+>lnd/clm2/initdata_esmf/ctsm5.3/clmi.f19_interp_from.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
+</finidat>
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/clmi.f19_interp_from.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc
 </finidat>
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".false."

From 3cf93a9c0388f33fe774a7c1e6da42317295d662 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 15:00:08 -0600
Subject: [PATCH 1098/1248] Add --no-center-coords option.

---
 python/ctsm/mesh_plotter.py                     |  9 ++++++++-
 python/ctsm/site_and_regional/mesh_plot_type.py | 15 +++++++++------
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/python/ctsm/mesh_plotter.py b/python/ctsm/mesh_plotter.py
index 3ce018e7a7..97ae0f3cfb 100644
--- a/python/ctsm/mesh_plotter.py
+++ b/python/ctsm/mesh_plotter.py
@@ -68,6 +68,13 @@ def get_parser():
         required=False,
     )
 
+    parser.add_argument(
+        "--no-center-coords",
+        help="Do not include red Xs at center of grid cells.",
+        action="store_true",
+        required=False,
+    )
+
     default_dpi = 300
     parser.add_argument(
         "--dpi",
@@ -163,7 +170,7 @@ def main():
     if os.path.exists(plot_global) and not args.overwrite:
         raise FileExistsError(file_exists_msg + plot_global)
 
-    this_mesh.make_mesh_plot(plot_regional, plot_global, args.dpi)
+    this_mesh.make_mesh_plot(plot_regional, plot_global, args)
 
 
 if __name__ == "__main__":
diff --git a/python/ctsm/site_and_regional/mesh_plot_type.py b/python/ctsm/site_and_regional/mesh_plot_type.py
index 8ba13ffa53..08fd1c061c 100644
--- a/python/ctsm/site_and_regional/mesh_plot_type.py
+++ b/python/ctsm/site_and_regional/mesh_plot_type.py
@@ -24,7 +24,7 @@ class MeshPlotType(MeshType):
     Extend mesh type with some advanced plotting capability
     """
 
-    def make_mesh_plot(self, plot_regional, plot_global, dpi):
+    def make_mesh_plot(self, plot_regional, plot_global, args):
         """
         Create plots for the ESMF mesh file
 
@@ -36,10 +36,10 @@ def make_mesh_plot(self, plot_regional, plot_global, dpi):
             The path to write the ESMF meshfile global plot
         """
 
-        self.mesh_plot(plot_regional, regional=True, dpi=dpi)
-        self.mesh_plot(plot_global, regional=False, dpi=dpi)
+        self.mesh_plot(plot_regional, args, regional=True)
+        self.mesh_plot(plot_global, args, regional=False)
 
-    def mesh_plot(self, plot_file, regional, dpi):
+    def mesh_plot(self, plot_file, args, regional):
         """Make a plot of a mesh file in either a regional or global grid"""
         # -- regional settings
         if regional:
@@ -59,6 +59,8 @@ def mesh_plot(self, plot_file, regional, dpi):
             line_width = 0.5
             marker = "o"
             marker_size = 0.1
+        if args.no_center_coords:
+            marker_size = 0
 
         ax.add_feature(cfeature.COASTLINE, edgecolor="black")
         ax.add_feature(cfeature.BORDERS, edgecolor="black")
@@ -129,8 +131,9 @@ def mesh_plot(self, plot_file, regional, dpi):
                 *[(k, mpatches.Rectangle((0, 0), 1, 1, facecolor=v)) for k, v in lc_colors.items()]
             )
 
-            ax.legend(handles, labels)
+            if not args.no_center_coords:
+                ax.legend(handles, labels)
 
-        plt.savefig(plot_file, bbox_inches="tight", dpi=dpi)
+        plt.savefig(plot_file, bbox_inches="tight", dpi=args.dpi)
 
         logger.info("Successfully created %s plots for ESMF Mesh file : %s", plot_type, plot_file)

From 06fdc64027684acb087b3553dd8005a8403446d4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 21:47:21 -0600
Subject: [PATCH 1099/1248] Properly handle --outdir.

---
 python/ctsm/mesh_plotter.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/mesh_plotter.py b/python/ctsm/mesh_plotter.py
index 97ae0f3cfb..0a2af11856 100644
--- a/python/ctsm/mesh_plotter.py
+++ b/python/ctsm/mesh_plotter.py
@@ -112,9 +112,10 @@ def process_and_check_args(args):
 
         today = datetime.today()
         today_string = today.strftime("%y%m%d")
+        input_filename = os.path.basename(args.input)
         args.output = os.path.join(
             args.out_dir,
-            os.path.splitext(args.input)[0] + "_c" + today_string,
+            os.path.splitext(input_filename)[0] + "_c" + today_string,
         )
 
     if not os.path.isfile(args.input):

From 0de1673fa67e853bd0dfdc9e61a263e01addbb87 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 21:48:46 -0600
Subject: [PATCH 1100/1248] Add tests to test_advanced_sys_mesh_plotter.py.

---
 .../test/test_advanced_sys_mesh_plotter.py    | 29 +++++++++++++++++--
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/test/test_advanced_sys_mesh_plotter.py b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
index 090f7806bf..39f3728479 100755
--- a/python/ctsm/test/test_advanced_sys_mesh_plotter.py
+++ b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
@@ -34,6 +34,13 @@ def setUp(self):
         )
         self._tempdir = tempfile.mkdtemp()
         self.mesh_out = self._tempdir + "/mesh_out"
+        self.test_basic_argv = [
+            "mesh_plotter",
+            "--input",
+            self._infile,
+            "--output",
+            self.mesh_out,
+        ]
 
     def tearDown(self):
         """
@@ -43,15 +50,31 @@ def tearDown(self):
 
     def test_basic(self):
         """Do a simple basic test"""
+        sys.argv = self.test_basic_argv
+        main()
+        plotfiles = glob.glob(self._tempdir + "/*.png")
+        if not plotfiles:
+            self.fail("plot files were NOT created as they should have")
+
+    def test_need_overwrite(self):
+        """Ensure failure if output file exists but --overwrite not given"""
+        sys.argv = self.test_basic_argv
+        main()
+        with self.assertRaisesRegex(FileExistsError, "File already exists but --overwrite not given"):
+            main()
+
+    def test_outdir(self):
+        """Test that --outdir option works"""
+        outdir = os.path.join(self._tempdir, "abc123")
         sys.argv = [
             "mesh_plotter",
             "--input",
             self._infile,
-            "--output",
-            self.mesh_out,
+            "--outdir",
+            outdir,
         ]
         main()
-        plotfiles = glob.glob(self._tempdir + "/*.png")
+        plotfiles = glob.glob(os.path.join(outdir, "*.png"))
         if not plotfiles:
             self.fail("plot files were NOT created as they should have")
 

From f0c9f31453e00279996ffddf660763e17d2bb590 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 21:50:41 -0600
Subject: [PATCH 1101/1248] Use os.path.join in
 test_advanced_sys_mesh_plotter.py.

---
 python/ctsm/test/test_advanced_sys_mesh_plotter.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/python/ctsm/test/test_advanced_sys_mesh_plotter.py b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
index 39f3728479..c4f3f078a8 100755
--- a/python/ctsm/test/test_advanced_sys_mesh_plotter.py
+++ b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
@@ -26,14 +26,20 @@ class SysTestMeshMaker(unittest.TestCase):
 
     def setUp(self):
         """Setup for all tests"""
-        testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs")
+        testinputs_path = os.path.join(
+            path_to_ctsm_root(),
+            "python",
+            "ctsm",
+            "test",
+            "testinputs",
+        )
         self._testinputs_path = testinputs_path
         self._infile = os.path.join(
             testinputs_path,
             "ESMF_mesh_5x5pt_amazon_from_domain_c230308.nc",
         )
         self._tempdir = tempfile.mkdtemp()
-        self.mesh_out = self._tempdir + "/mesh_out"
+        self.mesh_out = os.path.join(self._tempdir, "mesh_out")
         self.test_basic_argv = [
             "mesh_plotter",
             "--input",
@@ -52,7 +58,7 @@ def test_basic(self):
         """Do a simple basic test"""
         sys.argv = self.test_basic_argv
         main()
-        plotfiles = glob.glob(self._tempdir + "/*.png")
+        plotfiles = glob.glob(os.path.join(self._tempdir, "*.png"))
         if not plotfiles:
             self.fail("plot files were NOT created as they should have")
 

From badbc50369c4ff363ab2e06c31aeacb82181343d Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 21:55:36 -0600
Subject: [PATCH 1102/1248] Add dpi test to test_advanced_sys_mesh_plotter.py.

---
 python/ctsm/test/test_advanced_sys_mesh_plotter.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/python/ctsm/test/test_advanced_sys_mesh_plotter.py b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
index c4f3f078a8..1c17a314ed 100755
--- a/python/ctsm/test/test_advanced_sys_mesh_plotter.py
+++ b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
@@ -62,6 +62,17 @@ def test_basic(self):
         if not plotfiles:
             self.fail("plot files were NOT created as they should have")
 
+    def test_dpi(self):
+        """Test setting dpi"""
+        sys.argv = self.test_basic_argv + [
+            "--dpi",
+            "198.7",
+        ]
+        main()
+        plotfiles = glob.glob(os.path.join(self._tempdir, "*.png"))
+        if not plotfiles:
+            self.fail("plot files were NOT created as they should have")
+
     def test_need_overwrite(self):
         """Ensure failure if output file exists but --overwrite not given"""
         sys.argv = self.test_basic_argv

From 6d3bf8ca468f5b6eb55c2f662cec377cedcf6024 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 21:56:27 -0600
Subject: [PATCH 1103/1248] Format with black.

---
 python/ctsm/test/test_advanced_sys_mesh_plotter.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/test/test_advanced_sys_mesh_plotter.py b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
index 1c17a314ed..4a7c63ecf6 100755
--- a/python/ctsm/test/test_advanced_sys_mesh_plotter.py
+++ b/python/ctsm/test/test_advanced_sys_mesh_plotter.py
@@ -77,7 +77,9 @@ def test_need_overwrite(self):
         """Ensure failure if output file exists but --overwrite not given"""
         sys.argv = self.test_basic_argv
         main()
-        with self.assertRaisesRegex(FileExistsError, "File already exists but --overwrite not given"):
+        with self.assertRaisesRegex(
+            FileExistsError, "File already exists but --overwrite not given"
+        ):
             main()
 
     def test_outdir(self):

From e7257591db5cc530e55b62bbe40c5793d3111b8b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 19 Sep 2024 21:57:08 -0600
Subject: [PATCH 1104/1248] Add previous commit to .git-blame-ignore-revs.

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index b0bf2c5a0c..fca4a8315b 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -51,3 +51,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
 753fda3ff0147837231a73c9c728dd9ce47b5997
+f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c

From 92078e33b8049e0bf165f901365f926310a121fc Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 23 Sep 2024 13:36:45 -0600
Subject: [PATCH 1105/1248] Fixes to finidat settings

Fix some issues in finidat settings.

For clm6_0 use phys rather than lnd_tuning_mode for 1850 and 2000.
Pointing to the spunup f09 1850 for f09/f19 1850 and 2000.

Some lines for 2003 and 2013 were incorrect in the surrounding code block.
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 64 ++++++-------------
 1 file changed, 20 insertions(+), 44 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 67348d8ca2..cac69edf02 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -956,21 +956,17 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_GSWP3v1"
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_GSWP3v1"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." phys="clm5_1"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm5_1_GSWP3v1 use_excess_ice=.true.
 </init_interp_attributes>
-
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." phys="clm6_0"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1 use_excess_ice=.true.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_GSWP3v1"
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7"
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_GSWP3v1"
->hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
-</init_interp_attributes>
 <!-- specific low resolution grids should use the 1-degree file for just CLM5.0 -->
 <!-- matches for clm5_0 physics with CAM7.0 -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
@@ -1033,16 +1029,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<!-- clm5_1 physics -->
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_cam7.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
-</init_interp_attributes>
-
-<!-- clm6_0 physics -->
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
-</init_interp_attributes>
-
 <!-- MPAS -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="mpasa480"
@@ -1109,7 +1095,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </init_interp_attributes>
 
 <!-- 2013 IC's - exact match for CONUS grid ... -->
-<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam7.0"
 			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
 >hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
@@ -1197,16 +1183,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<!-- clm5_1 physics -->
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_1_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
-</init_interp_attributes>
-
-<!-- clm6_0 physics -->
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
-</init_interp_attributes>
-
 <!-- MPAS -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="mpasa480"
@@ -1287,13 +1263,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </init_interp_attributes>
 
 <!-- 2003 -->
-<init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+<init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
 >hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- 2013 IC's - exact match for CONUS grid ... -->
-<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
+<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
 			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
 >hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
@@ -1381,13 +1357,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
+         phys="clm5_1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
+         phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1425,11 +1401,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
+<!-- NB: This pSASU finidat is from an f09 1850 (rather than f19 2000) spin-up -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
+         phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1514,7 +1490,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+         phys="clm5_1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1523,7 +1499,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+         phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1588,7 +1564,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
+         phys="clm5_1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1652,7 +1628,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+         phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1727,7 +1703,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
+         phys="clm5_1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1735,7 +1711,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
+         phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1800,7 +1776,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
+         phys="clm5_1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
@@ -1865,7 +1841,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
+         phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 

From 6bdaef9793ee4de04843a8d1bb91e14440c699ef Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 24 Sep 2024 00:31:13 -0600
Subject: [PATCH 1106/1248] Adjust the failing test to include nofireemis

---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index e18b15a26e..d73e167629 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -29,7 +29,7 @@
 
 
   <!-- ctsm_sci test suite failures -->
-  <test name="SMS_Ld12_Mmpi-serial.1x1_urbanc_alpha.I1PtClm60SpRs.derecho_intel.clm-output_sp_highfreq">
+  <test name="SMS_Ld12_Mmpi-serial.1x1_urbanc_alpha.I1PtClm60SpRs.derecho_intel.clm-output_sp_highfreq--clm-nofireemis">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>CDEPS/#243</issue>

From 21de9a2f444faff1549de0260a6e9d90faddd778 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 24 Sep 2024 01:00:13 -0600
Subject: [PATCH 1107/1248] Adjust init_interp_attributes for 1979 for f09 and
 f19 for clm6_0_cam6.0 and clm6_0_cam7.0, unit tests work, there's likely some
 tests that would have failed without this

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index a984b538c2..650b21cb8d 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1224,12 +1224,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- If an exact match for these grids and start years -->
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
+>hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
@@ -1244,7 +1244,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"

From 318a3129b3be3c3fcc6e883533d72b8ebf60b79b Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:33:57 -0600
Subject: [PATCH 1108/1248] Update namelist_defaults_clm4_5.xml references.

To namelist_definition_ctsm.xml
---
 ...esolutions-or-New-Files-to-the-build-namelist-Database.rst | 2 +-
 .../adding-new-resolutions/Adding-Resolution-Names.rst        | 2 +-
 .../Adding-or-Changing-Default-Filenames.rst                  | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
index 753ea896ee..b2cf742a2c 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
@@ -10,5 +10,5 @@ In the last chapter we gave the details on how to create new files for input int
 
 There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into ``create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
 
-The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file.
+The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file.
 
diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst
index d89cc13930..ea10a3c409 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst
@@ -6,7 +6,7 @@
  Adding Resolution Names
 =========================
 
-If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. The list of valid resolutions is in the ``id="res"`` entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the ``id="res"`` entry. The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. The convention for unstructured HOMME grids is ne<size>np4, where <size> corresponds to the resolution. The higher <size> is the higher the resolution. So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. The only hard requirement is that names be unique for different grid files. Here's what the entry for resolutions looks like in the file:
+If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. The list of valid resolutions is in the ``id="res"`` entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file. You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the ``id="res"`` entry. The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. The convention for unstructured HOMME grids is ne<size>np4, where <size> corresponds to the resolution. The higher <size> is the higher the resolution. So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. The only hard requirement is that names be unique for different grid files. Here's what the entry for resolutions looks like in the file:
 ::
 
    <entry id="res" type="char*30" category="default_settings"
diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
index 22af143e72..4b9a92a542 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
@@ -6,7 +6,7 @@
  Changing Default Filenames
 ============================
 
-To add or change the default filenames you edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` and either change an existing filename or add a new one. Most entries in the default namelist files, include different attributes that describe the different properties that describe the differences in the datasets. Attributes include the resolution, year to simulation, range of years to simulate for transient datafiles, the land-mask, the representative concentration pathway (RCP) for future scenarios, and the type of biogeochemistry (BGC) model used. For example the surface dataset (``fsurdat``) for the 1.9x2.5 resolution is as follows:
+To add or change the default filenames you edit the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` and either change an existing filename or add a new one. Most entries in the default namelist files, include different attributes that describe the different properties that describe the differences in the datasets. Attributes include the resolution, year to simulation, range of years to simulate for transient datafiles, the land-mask, the representative concentration pathway (RCP) for future scenarios, and the type of biogeochemistry (BGC) model used. For example the surface dataset (``fsurdat``) for the 1.9x2.5 resolution is as follows:
 
 ::
   
@@ -17,7 +17,7 @@ To add or change the default filenames you edit the ``$CTSMROOT/bld/namelist_fil
 
 Other ``fsurdat`` files are distinguished from this one by their resolution (``hgrid``), simulation year (``sim_year``) and prognostic crop (``use_crop``) attributes.
 
-To add or change the default filenames for CLM tools, edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. Editing this file is similar to the ``namelist_defaults_clm4_5.xml`` talked about above.
+To add or change the default filenames for CLM tools, edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. Editing this file is similar to the ``namelist_definition_ctsm.xml`` talked about above.
 
 ----------------------------
 What are the required files?

From 260c3c9b5074201fcaaf43f43d0bbe606ff46018 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:36:17 -0600
Subject: [PATCH 1109/1248] namelist_defaults_|version|_tools.xml files no
 longer exist.

---
 ...lutions-or-New-Files-to-the-build-namelist-Database.rst | 2 +-
 .../Adding-or-Changing-Default-Filenames.rst               | 2 --
 .../users_guide/using-clm-tools/what-are-the-clm-tools.rst | 7 +------
 3 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
index b2cf742a2c..9309f2efae 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
@@ -10,5 +10,5 @@ In the last chapter we gave the details on how to create new files for input int
 
 There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into ``create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
 
-The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file.
+The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file. If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file.
 
diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
index 4b9a92a542..a39ffa9426 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst
@@ -17,8 +17,6 @@ To add or change the default filenames you edit the ``$CTSMROOT/bld/namelist_fil
 
 Other ``fsurdat`` files are distinguished from this one by their resolution (``hgrid``), simulation year (``sim_year``) and prognostic crop (``use_crop``) attributes.
 
-To add or change the default filenames for CLM tools, edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. Editing this file is similar to the ``namelist_definition_ctsm.xml`` talked about above.
-
 ----------------------------
 What are the required files?
 ----------------------------
diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
index c997f403d2..7a1325884c 100644
--- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
@@ -39,12 +39,7 @@ Running FORTRAN tools with namelists
 
    ./program < namelist
 
-There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` that shows you what the namelist should look like. ``mksurfdata_esmf`` also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the:
-::
-
-   $CTSMROOT/bld/namelist_files/namelist_definition.xml`` file
-        and default values in the:
-   $CTSMROOT/bld/namelist_files/namelist_defaults_clm_tools.xml`` file.
+There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` that shows you what the namelist should look like. ``mksurfdata_esmf`` also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the ``$CTSMROOT/bld/namelist_files/namelist_definition.xml`` file,
 
 -----------------------------------------------
 Running FORTRAN tools with command line options

From 5d2ebe14af08d4aee3e56383a32215b4027a8213 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:39:16 -0600
Subject: [PATCH 1110/1248] Fix namelist XML refs in
 what-are-the-clm-tools.rst.

---
 .../users_guide/using-clm-tools/what-are-the-clm-tools.rst      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
index 7a1325884c..fa80ffa61e 100644
--- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
@@ -39,7 +39,7 @@ Running FORTRAN tools with namelists
 
    ./program < namelist
 
-There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` that shows you what the namelist should look like. ``mksurfdata_esmf`` also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the ``$CTSMROOT/bld/namelist_files/namelist_definition.xml`` file,
+There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfdata_namelist.xml`` that shows you what the namelist should look like. ``mksurfdata_esmf`` also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file, with default values in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_ctsm.xml`` file.
 
 -----------------------------------------------
 Running FORTRAN tools with command line options

From 9ed3cca9f3bb9aa58eb77f40b078414ed114436b Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:47:09 -0600
Subject: [PATCH 1111/1248] Specify path to create_newcase.

---
 ...or-New-Files-to-the-build-namelist-Database.rst |  2 +-
 .../running-pts_mode-configurations.rst            |  4 ++--
 .../running-single-point-configurations.rst        | 14 +++++++++-----
 ...ngle-point-and-regional-grid-configurations.rst |  2 +-
 ...with-transient-historical-CO2-concentration.rst |  2 +-
 .../Running-the-prognostic-crop-model.rst          |  2 +-
 ...-as-atmospheric-forcing-to-spinup-the-model.rst |  2 +-
 .../Running-with-irrigation.rst                    |  2 +-
 ...-as-atmospheric-forcing-to-spinup-the-model.rst |  4 ++--
 .../Spinning-up-the-biogeochemistry-BGC-spinup.rst |  4 ++--
 doc/source/users_guide/testing/testing.rst         |  5 ++++-
 11 files changed, 25 insertions(+), 18 deletions(-)

diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
index 9309f2efae..6a12fa4b1d 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
@@ -8,7 +8,7 @@
 
 In the last chapter we gave the details on how to create new files for input into CLM. These files could be either global resolutions, regional-grids or even a single grid point. If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. You can deal with them, just by putting the settings in the ``user_nl_clm`` namelist file, or by using ``CLM_USRDAT_NAME``. Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. This keeps one central database for all your files, rather than having multiple locations to keep track of files. If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above.
 
-There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into ``create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
+There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution to ``$CTSMROOT/cime/scripts/create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
 
 The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file. If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file.
 
diff --git a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst
index edad4c25ff..53cae1bdf4 100644
--- a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst
+++ b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst
@@ -8,10 +8,10 @@ Running a single point using global data - PTS_MODE
 
 ``PTS_MODE`` enables you to run the model using global datasets, but just picking a single point from those datasets and operating on it. It can be a very quick way to do fast simulations and get a quick turnaround.
 
-To setup a ``PTS_MODE`` simulation you use the ``-pts_lat`` and ``-pts_lon`` arguments to ``create_newcase`` to give the latitude and longitude of the point you want to simulate for (the code will pick the point on the global grid nearest to the point you give. Here's an example to setup a simulation for the nearest point at 2-degree resolution to Boulder Colorado.
+To setup a ``PTS_MODE`` simulation you use the ``-pts_lat`` and ``-pts_lon`` arguments to ``cime/scripts/create_newcase`` to give the latitude and longitude of the point you want to simulate for (the code will pick the point on the global grid nearest to the point you give. Here's an example to setup a simulation for the nearest point at 2-degree resolution to Boulder Colorado.
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case testPTS_MODE -res f19_g17_gl4 -compset I1850Clm50BgcCropCru -pts_lat 40.0 -pts_lon -105
    > cd testPTS_MODE
 
diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
index 766eca63fd..b601040742 100644
--- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
+++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
@@ -45,7 +45,7 @@ Example: Use global forcings at a site without its own special forcings
 This example uses the single-point site in Brazil.
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > set SITE=1x1_brazil
    > ./create_newcase -case testSPDATASET -res $SITE -compset I2000Clm50SpGs
    > cd testSPDATASET
@@ -59,7 +59,7 @@ The urban Mexico City test site has its own atmosphere forcing data (see Sect. :
 
 ::
 
-   > cd scripts
+   > cd cime/scripts
    # Set a variable to the site you want to use (as it's used several times below)
    > set SITE=1x1_mexicocityMEX
    > ./create_newcase -case testSPDATASET -res $SITE -compset I1PtClm50SpGs
@@ -81,7 +81,7 @@ Example: Use site-specific atmospheric forcings
 In this example, we show how to use the atmospheric forcings specific to the Vancouver, Canada point.
 ::
 
-   > cd scripts
+   > cd cime/scripts
 
    # Set a variable to the site you want to use (as it's used several times below)
    > set SITE=1x1_vancouverCAN
@@ -121,7 +121,7 @@ Example: Using CLM_USRDAT_NAME to run a simulation using user datasets for a spe
 -----------------------------------------------------------------------------------------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case my_userdataset_test -res CLM_USRDAT -compset I2000Clm50BgcCruGs
    > cd my_userdataset_test/
    > set GRIDNAME=13x12pt_f19_alaskaUSA
@@ -176,6 +176,10 @@ The next step is to create a case that points to the files you created above. We
 
 Example: Setting up a case from the single-point surface dataset just created
 --------------------------------------------------------------------------------------------
+
+.. todo::
+    Change this to provide instructions for a CTSM checkout instead of a CESM one.
+
 ::
 
    # First setup an environment variable that points to the top of the CESM directory.
@@ -188,7 +192,7 @@ Example: Setting up a case from the single-point surface dataset just created
    # naming convention (leave off the creation date)
    > cp $CESMROOT/$CTSMROOT/tools/mksurfdata_esmf/surfdata_${GRIDNAME}_simyr1850_$CDATE.nc \
    $MYCSMDATA/lnd/clm2/surfdata_map/surfdata_${GRIDNAME}_simyr1850.nc
-   > cd $CESMROOT/scripts
+   > cd $CESMROOT/cime/scripts
    > ./create_newcase -case my_usernldatasets_test -res CLM_USRDAT -compset I1850Clm50BgcCropCru \
    -mach cheyenne_intel
    > cd my_usernldatasets_test
diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
index 5e20a303fb..61e1f25de8 100644
--- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
+++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst
@@ -24,7 +24,7 @@ There are two different ways to do this for normal-supported site
 
 Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see :ref:`running-single-point-datasets`). All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. The problem is that there is a very limited set of supported datasets. You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region.
 
-In general :ref:`pts_mode` is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from ``create_newcase``. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts.
+In general :ref:`pts_mode` is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from ``cime/scripts/create_newcase``. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts.
 
 Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see :ref:`running-single-point-datasets`). With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method.
 
diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
index eedefd8744..60ef7658d0 100644
--- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
+++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
@@ -22,7 +22,7 @@ Example: Transient Simulation with Historical CO2
 --------------------------------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case DATM_CO2_TSERIES -res f19_g17_gl4 -compset IHistClm50BgcCrop
    > cd DATM_CO2_TSERIES
 
diff --git a/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst b/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst
index cb66ef209f..56620b2fde 100644
--- a/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-the-prognostic-crop-model.rst
@@ -12,7 +12,7 @@ Example: Crop Simulation
 ------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case CROP -res f19_g17_gl4 -compset I1850Clm50BgcCropCru
    > cd CROP
 
diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
index dbe01c497c..769755937d 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
@@ -14,7 +14,7 @@ Example: Simulation with MOAR Data on cheyenne
 -------------------------------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case MOARforce1850 -res f19_g17_gl4 -compset I1850Clm50BgcSpinup
    > cd MOARforce1850
    # The following sets the casename to point to for atm forcing (you could also use an editor)
diff --git a/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst b/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
index 5702e6d49d..88bc9729ec 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
@@ -13,7 +13,7 @@ Example: Irrigation Simulation
 ::
 
    # Note here we do a CLMSP simulation as that is what has been validated
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case IRRIG -res f19_g17_gl4 -compset I1850Clm50BgcCrop
    > cd IRRIG
 
diff --git a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst
index ff05836f6e..2a55cbed1e 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst
@@ -14,7 +14,7 @@ Example: Fully Coupled Simulation to Create Data to Force Next Example Simulatio
 ----------------------------------------------------------------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case myB1850 -res f09_g17_gl4 -compset B1850
    > cd myB1850
    > ./case.setup
@@ -44,7 +44,7 @@ Example: Simulation Forced with Data from the Previous Simulation
 ------------------------------------------------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case frcwmyB1850 -res f09_g17_gl4 -compset I1850Clm50BgcSpinup
    > cd frcWmyB1850
    # The following sets the casename to point to for atm forcing (you could also use an editor)
diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
index 6b39c2b380..87049e6f1b 100644
--- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
+++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
@@ -47,7 +47,7 @@ Example: AD_SPINUP Simulation for |version|-BGC
 --------------------------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case BGC_spinup -res f19_g17_gl4 -compset I1850Clm50BgcCropCru
    > cd BGC_spinup
    # Change accelerated spinup mode
@@ -75,7 +75,7 @@ Example: Final CLMBGC Spinup Simulation for |version|-BGC
 ------------------------------------------------------------------
 ::
 
-   > cd scripts
+   > cd cime/scripts
    > ./create_newcase -case BGC_finalspinup -res f19_g17_gl4 -compset I1850Clm50BgcCropCru
    > cd BGC_finalspinup
    # Now, Copy the last CLM restart file from the earlier case into your run directory
diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst
index b065cb1392..a9b0be0462 100644
--- a/doc/source/users_guide/testing/testing.rst
+++ b/doc/source/users_guide/testing/testing.rst
@@ -6,7 +6,10 @@
 Testing
 *******
 
-Technically, you could use the customization we gave in :ref:`customizing_section` to test various configuration and namelist options for CLM. Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. There are two types of testing scripts for CLM. The first are the CESM test scripts, which utilize the ``create_newcase`` scripts that we shown how to use in this User's Guide. The second are a set of stand-alone scripts that use the CLM ``configure`` and ``build-namelist`` scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods.
+Technically, you could use the customization we gave in :ref:`customizing_section` to test various configuration and namelist options for CLM. Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. There are two types of testing scripts for CLM. The first are the CESM test scripts, which utilize the ``cime/scripts/create_newcase`` scripts that we shown how to use in this User's Guide. The second are a set of stand-alone scripts that use the CLM ``configure`` and ``bld/build-namelist`` scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods.
+
+.. todo::
+    Does ``configure`` script still exist?
 
 CIME Testing scripts
 ====================

From f22f22775ebc4ef9f9b478eecb85a9e3418d6010 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:48:57 -0600
Subject: [PATCH 1112/1248] Add TODOs to update refs to
 queryDefaultNamelist.pl.

---
 .../running-single-point-configurations.rst                    | 3 +++
 .../customizing-the-clm-configuration.rst                      | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
index b601040742..5977dc7be0 100644
--- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
+++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
@@ -74,6 +74,9 @@ Supported single-point runs for sites with their own atmospheric forcing
 
 Of the supported single-point datasets we have three that also have atmospheric forcing data that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and ``urbanc_alpha`` (test data for an Urban inter-comparison project). Mexico city and Vancouver also have namelist options in the source code for them to work with modified urban data parameters that are particular to these locations. To turn on the atmospheric forcing for these datasets, you set the ``env_run.xml DATM_MODE`` variable to ``CLM1PT``, and then the atmospheric forcing datasets will be used for the point picked. If you use one of the compsets that has "I1Pt" in the name that will be set automatically.
 
+.. todo::
+    Update the below, as ``queryDefaultNamelist.pl`` no longer exists.
+
 When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. For the supported data points, these values are in the XML database and you can use the ``queryDefaultNamelist.pl`` script to query the values and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and urbanc_alpha).
 
 Example: Use site-specific atmospheric forcings
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index 2bece02abd..7f03784f98 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -345,6 +345,9 @@ When ``-irrig on`` is used ``build-namelist`` will try to find surface datasets
 ``CLM_FORCE_COLDSTART``
    when set to on, *requires* that your simulation do a cold start from arbitrary initial conditions. If this is NOT set, it will use an initial condition file if it can find an appropriate one, and otherwise do a cold start. ``CLM_FORCE_COLDSTART`` is a good way to ensure that you are doing a cold start if that is what you want to do.
 
+.. todo::
+    Update the below, as ``queryDefaultNamelist.pl`` no longer exists.
+
 ``CLM_USRDAT_NAME``
    Provides a way to enter your own datasets into the namelist. The files you create must be named with specific naming conventions outlined in :ref:`creating-your-own-singlepoint-dataset`. To see what the expected names of the files are, use the ``queryDefaultNamelist.pl`` to see what the names will need to be. For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be:
    ::

From 8304414e9f6065da2fc36d57eba9060c10656a2f Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:51:57 -0600
Subject: [PATCH 1113/1248] Add TODOs to update refs to mksurfdata.pl.

---
 doc/source/lilac/specific-atm-models/wrf-tools.rst             | 3 +++
 .../running-single-point-configurations.rst                    | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/doc/source/lilac/specific-atm-models/wrf-tools.rst b/doc/source/lilac/specific-atm-models/wrf-tools.rst
index f67a05ea0a..720f7ad4fa 100644
--- a/doc/source/lilac/specific-atm-models/wrf-tools.rst
+++ b/doc/source/lilac/specific-atm-models/wrf-tools.rst
@@ -52,6 +52,9 @@ is described in here.
 
      ./gen_domain -m /glade/work/$USER/ctsm/nldas_grid/scrip/wrf2clm_mapping_noneg.nc -o wrf2clm_ocn_noneg -l wrf2clm_lnd_noneg
 
+.. todo::
+    Update the below, as ``mksurfdata.pl`` no longer exists.
+
 6. Create surface datasets in ``tools/mksurfdata_esmf``::
 
      ./mksurfdata.pl -res usrspec -usr_gname "nldas" -usr_gdate "190124" -usr_mapdir "/glade/work/$USER/ctsm/nldas_grid/map" -y 2000 -exedir "/glade/u/home/$USER/src/ctsm/ctsm_surfdata/tools/mksurfdata_esmf" -no-crop
diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
index 5977dc7be0..34e930b7cf 100644
--- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
+++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
@@ -145,6 +145,9 @@ The first step is to create the domain and surface datasets using the process ou
 
 Example: Creating a surface dataset for a single point
 ---------------------------------------------------------------------
+.. todo::
+    Update the below, as ``mksurfdata.pl`` no longer exists.
+
 ::
 
    # set the GRIDNAME and creation date that will be used later

From 962a0901c388ac3bccb7b9a696428c2669f1ebb8 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:55:14 -0600
Subject: [PATCH 1114/1248] Fix compset and add TODO to "Running with
 historical CO2 forcing."

---
 ...alone-CLM-with-transient-historical-CO2-concentration.rst | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
index 60ef7658d0..f2f4c6cdd9 100644
--- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
+++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
@@ -6,7 +6,10 @@
  Running with historical CO2 forcing
 =====================================
 
-In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. For this example, we will start with the ``I_1850-2000_CN`` compset that has transient land-use, Nitrogen and Aerosol deposition already. You could also use another compset if you didn't want these other features to be transient. In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the ``user_nl_datm`` file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file.
+In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. For this example, we will start with the ``IHistClm50BgcCrop`` compset that has transient land-use, Nitrogen and Aerosol deposition already. You could also use another compset if you didn't want these other features to be transient. In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the ``user_nl_datm`` file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file.
+
+.. todo::
+    ``user_nl_datm`` or ``user_nl_datm_streams``?
 
 .. note:: Most everything here has to do with changing datm rather than CLM to allow this to happen. As such the user that wishes to do this should first become more familiar with datm and read the `CESM Data Model User's Guide <https://esmci.github.io/cime/versions/cesm2.2/html/data_models/index.html>`_ especially as it pertains to the datm.
 

From 8a3107762669a7a755ff8ae838b648f16feb8ab2 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:56:23 -0600
Subject: [PATCH 1115/1248] TODO added in "Running with irrigation".

---
 .../running-special-cases/Running-with-irrigation.rst          | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst b/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
index 88bc9729ec..5e9adb4b6a 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-irrigation.rst
@@ -6,6 +6,9 @@
  Running with irrigation
 ===================================
 
+.. todo::
+    Remove refs to pre-5.0 behavior?
+
 In CLM4.0 irrigation isn't an allowed option. In CLM4.5 irrigation can ONLY be used WITH crop. With CLM5.0 irrigation can be used whether crop is on or not -- **BUT** if crop is off, your surface datasets **HAVE** to have irrigation defined appropriately. Right now *ALL* surface datasets without crop enabled have irrigation hard-wired on. In order to create datasets with irrigation off, you'd need to make changes to ``mksurfdata_esmf`` in order to have all generic crops to be non-irrigated. To turn on irrigation in |version| we simply add ``-irrig on`` to ``CLM_BLDNML_OPTS``.
 
 Example: Irrigation Simulation

From 42ff69c713521459b900f4189b8b51060fd49eef Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:58:10 -0600
Subject: [PATCH 1116/1248] Add TODO about -bgc_spinup.

---
 .../customizing-the-clm-configuration.rst                      | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index 7f03784f98..a33c5e5a2d 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -286,6 +286,9 @@ The ``$CTSMROOT/cime_config/buildnml`` script already sets the resolution and ma
 
 ``-bgc_spinup`` is an option only available for |version| for any configuration when CN is turned on (so either CLMCN or CLMBGC). It can be set to "on" or "off". If "on" the model will go into Accelerated Decomposition mode, while for "off" (the default) it will have standard decomposition rates. If you are starting up from initial condition files the model will check what mode the initial condition file is in and do the appropriate action on the first time-step to change the Carbon pools to the appropriate spinup setting. See :ref:`spinning-up-clm-bgc` for an example using this option.
 
+.. todo::
+    Update the above.
+
 ``-chk_res`` ensures that the resolution chosen is supported by CLM. If the resolution is NOT supported it will cause the CLM ``build-namelist`` to abort when run. So when either ``preview_namelist``, ``case.build`` or ``case.run`` is executed it will abort early. Since, the CESM scripts only support certain resolutions anyway, in general this option is NOT needed in the context of running CESM cases.
 
 ``-clm_demand`` asks the ``build-namelist`` step to require that the list of variables entered be set. Typically, this is used to require that optional filenames be used and ensure they are set before continuing. For example, you may want to require that fpftdyn be set to get dynamically changing vegetation types. To do this you would do the following.

From 2bf912f4d8a2189220ea3f67d823d36e78fc84fb Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 10:59:58 -0600
Subject: [PATCH 1117/1248] Add TODOs about mkprocdata_map.

---
 .../users_guide/using-clm-tools/building-the-clm-tools.rst  | 6 ++++++
 .../users_guide/using-clm-tools/what-are-the-clm-tools.rst  | 6 ++++++
 2 files changed, 12 insertions(+)

diff --git a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
index 295dfd9380..3d2664bcec 100644
--- a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
@@ -6,6 +6,9 @@
 
 The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools ``cprnc`` and ``gen_domain`` use the CIME configure/build system which is described in the next section.
 
+.. todo::
+    Remove references to mkprocdata_map?
+
 The Makefiles (for ``mksurfdata_esmf`` and ``mkprocdata_map``) use GNU Make extensions and thus require that you use GNU make to use them. They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. There are also environment variables that can be set to set things that must be customized. All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. Finally the tools allow you to turn optimization on (which is off by default but on for ``mksurfdata_esmf``) with the OPT flag so that the tool will run faster.
 
 Options used by all:  ``mksurfdata_esmf``
@@ -71,6 +74,9 @@ More details on each environment variable.
 ``OPT``
   This variable flags if compiler optimization should be used when compiling the tool. It can be set to either ``TRUE`` or ``FALSE``, by default it is set to for both ``mksurfdata_esmf`` and ``mkprocdata_map``. Turning this on should make the tool run much faster.
 
+.. todo::
+    Remove reference to mkprocdata_map above?
+
 .. warning:: Note, you should expect that answers will be different when ``OPT`` is activated.
 
 ``Filepath``
diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
index fa80ffa61e..29eccf6b2e 100644
--- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
@@ -6,6 +6,9 @@
  What are the CLM tools
 ========================
 
+.. todo::
+    Remove references to mkprocdata_map?
+
 There are several tools provided with CLM that allow you to create your own input datasets at resolutions you choose, or to interpolate initial conditions to a different resolution, or used to compare CLM history files between different cases. The tools are all available in the ``$CTSMROOT/tools`` directory. Most of the tools are FORTRAN stand-alone programs in their own directory, but there is also a suite of NCL scripts in the ``$CTSMROOT/tools//ncl_scripts`` directory, and some of the tools are scripts that may also call the ESMF regridding program. Some of the NCL scripts are very specialized and not meant for general use, and we won't document them here. They still contain documentation in the script itself and the README file in the tools directory.
 
 The tools produce files that can be used for CLM4.5 and |version|. They do **NOT** produce files that can be used for CLM4.0. If you need files for CLM4.0, you'll need to use a previous version of CLM.
@@ -45,6 +48,9 @@ There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_esmf/gen_mksurfda
 Running FORTRAN tools with command line options
 -----------------------------------------------
 
+.. todo::
+    Remove reference to mkprocdata_map?
+
 ``gen_domain``, ``mkprocdata_map``, and ``cprnc`` run with command line arguments. The detailed sections below will give you more information on the command line arguments specific to each tool. Also running the tool without any arguments will give you a general synopsis on how to run the tool.
 
 -----------------------------------------

From 6ac23b250edbaf7c1789dd123da6c690d52fa3df Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 11:04:06 -0600
Subject: [PATCH 1118/1248] Add TODOs about domain files not being needed in
 nuopc.

---
 doc/source/lilac/specific-atm-models/wrf-tools.rst          | 3 +++
 .../running-single-point-configurations.rst                 | 5 ++++-
 .../users_guide/using-clm-tools/building-the-clm-tools.rst  | 6 ++++++
 .../users_guide/using-clm-tools/creating-domain-files.rst   | 3 +++
 .../creating-input-for-surface-dataset-generation.rst       | 3 +++
 .../using-clm-tools/creating-surface-datasets.rst           | 3 +++
 .../users_guide/using-clm-tools/what-are-the-clm-tools.rst  | 6 ++++++
 7 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/doc/source/lilac/specific-atm-models/wrf-tools.rst b/doc/source/lilac/specific-atm-models/wrf-tools.rst
index 720f7ad4fa..1222a16f10 100644
--- a/doc/source/lilac/specific-atm-models/wrf-tools.rst
+++ b/doc/source/lilac/specific-atm-models/wrf-tools.rst
@@ -48,6 +48,9 @@ is described in here.
 
      ../../../configure --macros-format Makefile --mpilib mpi-serial
 
+.. todo::
+    Update the below, as domain files aren't needed with nuopc.
+
 5. Generate CTSM domain files using ``get_domain`` tool::
 
      ./gen_domain -m /glade/work/$USER/ctsm/nldas_grid/scrip/wrf2clm_mapping_noneg.nc -o wrf2clm_ocn_noneg -l wrf2clm_lnd_noneg
diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
index 34e930b7cf..0e7f1262e2 100644
--- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
+++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst
@@ -146,7 +146,7 @@ The first step is to create the domain and surface datasets using the process ou
 Example: Creating a surface dataset for a single point
 ---------------------------------------------------------------------
 .. todo::
-    Update the below, as ``mksurfdata.pl`` no longer exists.
+    Update the below, as ``mksurfdata.pl`` no longer exists and domain files aren't needed with nuopc.
 
 ::
 
@@ -186,6 +186,9 @@ Example: Setting up a case from the single-point surface dataset just created
 .. todo::
     Change this to provide instructions for a CTSM checkout instead of a CESM one.
 
+.. todo::
+    Update the below, as domain files aren't needed with nuopc.
+
 ::
 
    # First setup an environment variable that points to the top of the CESM directory.
diff --git a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
index 3d2664bcec..013af36a1c 100644
--- a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst
@@ -4,6 +4,9 @@
 
 .. include:: ../substitutions.rst
 
+.. todo::
+  Update the below, as domain files aren't needed with nuopc.
+
 The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools ``cprnc`` and ``gen_domain`` use the CIME configure/build system which is described in the next section.
 
 .. todo::
@@ -105,6 +108,9 @@ The ``README.filecopies`` (which can be found in ``$CTSMROOT/tools``) is repeate
  Building the CLM tools that use the CIME configure/build system
 ================================================================
 
+.. todo::
+    Update the below, as domain files aren't needed with nuopc.
+
 ``cprnc`` and ``gen_domain`` both use the CIME configure/build system rather than the CLM specific version described above.
 
 See `CIME documentation on adding grids <http://esmci.github.io/cime/users_guide/grids.html?highlight=gen_domain#adding-grids>`_ for more information on adding grids, creating mapping files, and running ``gen_domain``. Also see the CIME file: ``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build ``gen_domain``.
diff --git a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
index 3673e4ac18..3c920a449e 100644
--- a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
+++ b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
@@ -2,6 +2,9 @@
 
 .. _creating-domain-files:
 
+.. todo::
+    Delete this page? Domain files aren't needed with nuopc.
+
 *****************************
  Creating CLM domain files
 *****************************
diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst
index e923b3bab2..66a65adbde 100644
--- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst
+++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst
@@ -18,6 +18,9 @@ SCRIP grid files for all the standard model resolutions and the raw surface data
 Using mknocnmap.pl to create grid and maps for single-point regional grids
 --------------------------------------------------------------------------
 
+.. todo::
+    Update the below, as domain files aren't needed with nuopc.
+
 If you want to create a regular latitude/longitude single-point or regional grid, we suggest you use ``mknoocnmap.pl`` in ``$CTSMROOT/tools/mkmapdata`` which will create both the SCRIP grid file you need (using ``$CTSMROOT/tools/mkmapgrids/mkscripgrid.ncl``) AND an identity mapping file assuming there is NO ocean in your grid domain. If you HAVE ocean in your domain you could modify the mask in the SCRIP grid file for ocean, and then use ``ESMF_RegridWeightGen`` to create the mapping file, and ``gen_domain`` to create the domain file. Like other tools, ``./mkmapdata/mknoocnmap.pl`` has a help option with the following:
 ::
 
diff --git a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst
index a59163a910..8394f17b3f 100644
--- a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst
+++ b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst
@@ -35,6 +35,9 @@ Creating a Complete Set of Files for Input to CLM
 
    First you need to create a descriptor file for your grid, that includes the locations of cell centers and cell corners. There is also a "mask" field, but in this case the mask is set to one everywhere (i.e. all of the masks for the output model grid are "nomask"). An example SCRIP grid file is: ``$CSMDATA/lnd/clm2/mappingdata/grids/SCRIPgrid_10x15_nomask_c110308.nc``. The ``mkmapgrids`` and ``mkscripgrid.ncl`` NCL script in the ``$CTSMROOT/tools/mkmapgrids`` directory can help you with this. SCRIP grid files for all the standard CLM grids are already created for you. See the Section called Creating an output SCRIP grid file at a resolution to run the model on for more information on this.
 
+.. todo::
+    Update the below, as domain files aren't needed with nuopc.
+
 2. Create domain dataset (if NOT already done)
 
    Next use ``gen_domain`` to create a domain file for use by DATM and CLM. This is required, unless a domain file was already created. See the Section called Creating a domain file for CLM and DATM for more information on this.
diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
index 29eccf6b2e..b77893222b 100644
--- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
+++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst
@@ -23,6 +23,9 @@ The list of generally important scripts and programs are as follows.
 
 #. ``./mkprocdata_map`` to interpolate output unstructured grids (such as the CAM HOMME dy-core "ne" grids like ne30np4) into a 2D regular lat/long grid format that can be plotted easily. Can be used by either clm4_0 or |version|.
 
+.. todo::
+    Update the below, as domain files aren't needed with nuopc.
+
 #. ``$CIMEROOT/tools/mapping/gen_domain_files/gen_domain`` to create a domain file for datm from a mapping file. The domain file is then used by BOTH datm AND CLM to define the grid and land-mask.
 
 #. ``$CIMEROOT/tools/cprnc`` to compare two NetCDF files.
@@ -51,6 +54,9 @@ Running FORTRAN tools with command line options
 .. todo::
     Remove reference to mkprocdata_map?
 
+.. todo::
+    Update the below, as domain files aren't needed with nuopc.
+
 ``gen_domain``, ``mkprocdata_map``, and ``cprnc`` run with command line arguments. The detailed sections below will give you more information on the command line arguments specific to each tool. Also running the tool without any arguments will give you a general synopsis on how to run the tool.
 
 -----------------------------------------

From 5e75f2eef913391bfeee03505250a809bef4312a Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 11:06:44 -0600
Subject: [PATCH 1119/1248] Add TODO about updating "Observational Sites
 Datasets".

---
 .../using-clm-tools/observational-sites-datasets.rst           | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst
index 05fe461db2..82169e8238 100644
--- a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst
+++ b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst
@@ -6,6 +6,9 @@
 Observational Sites Datasets
 *******************************
 
+.. todo::
+    Update this.
+
 There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to overwrite the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In Table :numref:`reqd-files-table` we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: ``fatmlndfrc``, ``fsurdat``, ``faerdep`` (for DATM), and ``stream_fldfilename_ndep``. Note ``mksurfdata_esmf`` as documented previously has options to overwrite the vegetation and soil types. For more information on this also see :ref:`creating-your-own-singlepoint-dataset`.
 
 Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets; see :ref:`creating-your-own-singlepoint-dataset` for more information on this.

From 38598dad1bbac0ffcabbcde9a2fae38c6689a1c9 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 11:18:57 -0600
Subject: [PATCH 1120/1248] Fix another namelist_definition_clm4_5.xml
 reference.

---
 ...-Resolutions-or-New-Files-to-the-build-namelist-Database.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
index 6a12fa4b1d..5b22f8a706 100644
--- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
+++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst
@@ -8,7 +8,7 @@
 
 In the last chapter we gave the details on how to create new files for input into CLM. These files could be either global resolutions, regional-grids or even a single grid point. If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. You can deal with them, just by putting the settings in the ``user_nl_clm`` namelist file, or by using ``CLM_USRDAT_NAME``. Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. This keeps one central database for all your files, rather than having multiple locations to keep track of files. If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above.
 
-There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution to ``$CTSMROOT/cime/scripts/create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
+There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution to ``$CTSMROOT/cime/scripts/create_newcase`` -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file.
 
 The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml`` file. If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file.
 

From a2515820dbfb05b05b64ba3e54f930039edf2085 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 11:23:26 -0600
Subject: [PATCH 1121/1248] More double-backticks in "Spinup of
 |version|-BGC-Crop".

---
 .../Spinning-up-the-biogeochemistry-BGC-spinup.rst            | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
index 87049e6f1b..8376c280b1 100644
--- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
+++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
@@ -6,7 +6,7 @@
  Spinup of |version|-BGC-Crop
 =============================
 
-To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM ``configure``, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic.
+To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (``-bgc_spinup on`` in CLM ``configure``, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic.
 
 .. _Figure BGC AD spinup plot for 1850 GSWP3:
 
@@ -14,7 +14,7 @@ To get the |version|-BGC model to a steady state, you first run it from arbitrar
 
  BGC AD spinup plot for a year 1850 case with GSWP3 atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl.
 
-After this you branch from this mode in the "final spinup" (-bgc_spinup off in CLM ``configure``, see example below), and run for several hundred simulation years. :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this criteria depending on their application.
+After this you branch from this mode in the "final spinup" (``-bgc_spinup off`` in CLM ``configure``, see example below), and run for several hundred simulation years. :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this criteria depending on their application.
 
 .. _Figure BGC pAD spinup plot for 1850 GSWP3:
 

From b5a82cc14ecf9fb39d092ecdda0bccf0ebbf967e Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 11:40:59 -0600
Subject: [PATCH 1122/1248] Remove User's Guide section about running w/
 transient hist CO2.

---
 ...transient-historical-CO2-concentration.rst | 42 -------------------
 .../running-special-cases/index.rst           |  1 -
 .../customizing-the-clm-configuration.rst     |  2 +-
 3 files changed, 1 insertion(+), 44 deletions(-)
 delete mode 100644 doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst

diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
deleted file mode 100644
index f2f4c6cdd9..0000000000
--- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
+++ /dev/null
@@ -1,42 +0,0 @@
-.. include:: ../substitutions.rst
-
-.. _running-with-historical-co2-forcing:
-
-=====================================
- Running with historical CO2 forcing
-=====================================
-
-In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. For this example, we will start with the ``IHistClm50BgcCrop`` compset that has transient land-use, Nitrogen and Aerosol deposition already. You could also use another compset if you didn't want these other features to be transient. In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the ``user_nl_datm`` file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file.
-
-.. todo::
-    ``user_nl_datm`` or ``user_nl_datm_streams``?
-
-.. note:: Most everything here has to do with changing datm rather than CLM to allow this to happen. As such the user that wishes to do this should first become more familiar with datm and read the `CESM Data Model User's Guide <https://esmci.github.io/cime/versions/cesm2.2/html/data_models/index.html>`_ especially as it pertains to the datm.
-
-.. warning:: This section documents the process for doing something that is non-standard. There may be errors with the documentation and process, and you may have to do some work before all of this works for you. If that is the case, we recommend that you do further research into understanding the process and the files, as well as understanding the datm and how it works. You may have to read documentation found in the code for datm as well as "csm_share".
-
-The datm has "streams" files that have rough XML-like syntax and specify the location and file to get data from, as well as information on the variable names and the data locations of the grid points. The datm expects specific variable names and the datm "maps" the expected variable names from the file to the names expected by datm. The file we are working with here is a file with a single-point, that covers the entire globe (so the vertices go from -90 to 90 degrees in latitude and 0 to 360 degrees in longitude). Since it's a single point it's a little easier to work with than datasets that may be at a given horizontal resolution. The datm also expects that variables will be in certain units, and only expects a limited number of variables so arbitrary fields can NOT be exchanged this way. However, the process would be similar for datasets that do contain more than one point.
-
-The three things that are needed: a domain file, a data file, and a streams text file. The domain file is a CF-compliant NetCDF file that has information on the grid points (latitudes and longitudes for cell-centers and vertices, mask, fraction, and areas). The datafile is a CF-compliant NetCDF file with the data that will be mapped. The streams text file is the XML-like file that tells datm how to find the files and how to map the variables datm knows about to the variable names on the NetCDF files. Note, that in our case the domain file and the data file are the same file. In other cases, the domain file may be separate from the data file.
-
-First we are going to create a case, and we will edit the ``user_nl_datm`` so that we add a CO2 data stream in. There is a streams text file available in ``$CTSMROOT/doc/UsersGuide/co2_streams.txt``, that includes file with a CO2 time-series from 1765 to 2007.
-
-Example: Transient Simulation with Historical CO2
---------------------------------------------------------------
-::
-
-   > cd cime/scripts
-   > ./create_newcase -case DATM_CO2_TSERIES -res f19_g17_gl4 -compset IHistClm50BgcCrop
-   > cd DATM_CO2_TSERIES
-
-   # Historical CO2 will already be setup correctly for this compset
-   # to check that look at the variables: CCSM_BGC,CLM_CO2_TYPE, and DATM_CO2_TSERIES
-   > ./xmlquery CCSM_BGC,CLM_CO2_TYPE,DATM_CO2_TSERIES
-   # Expect: CCSM_BGC=CO2A,CLM_CO2_TYPE=diagnostic,DATM_CO2_TSERIES=20tr
-   > ./case.setup
-
-   # Run preview namelist so we have the namelist in CaseDocs
-   > ./preview_namelists
-
-Once, you've done that you can build and run your case normally.
-
diff --git a/doc/source/users_guide/running-special-cases/index.rst b/doc/source/users_guide/running-special-cases/index.rst
index 9173825d04..31d5a3b148 100644
--- a/doc/source/users_guide/running-special-cases/index.rst
+++ b/doc/source/users_guide/running-special-cases/index.rst
@@ -24,5 +24,4 @@ Running Special Cases
    Running-with-excess-ground-ice.rst
    Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
    Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst
-   Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst
    Running-with-anomaly-forcing.rst
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index a33c5e5a2d..7cd8ce9c9c 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -361,7 +361,7 @@ When ``-irrig on`` is used ``build-namelist`` will try to find surface datasets
    An example of using ``CLM_USRDAT_NAME`` for a simulation is given in Example :numref:`creating-your-own-singlepoint-dataset`.
 
 ``CLM_CO2_TYPE``
-   sets the type of input CO2 for either "constant", "diagnostic" or prognostic". If "constant" the value from ``CCSM_CO2_PPMV`` will be used. If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model. See :ref:`running-with-historical-co2-forcing` for more information on how to send CO2 from the data atmosphere model.
+   sets the type of input CO2 for either "constant", "diagnostic" or prognostic". If "constant" the value from ``CCSM_CO2_PPMV`` will be used. If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model.
 
 ===============
  User Namelist

From edefa3c596eb5d7750595afd9c9b180badd60031 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 24 Sep 2024 11:47:15 -0600
Subject: [PATCH 1123/1248] Resolve a docs build warning.

---
 .../users_guide/using-clm-tools/creating-domain-files.rst   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
index 3c920a449e..90814e1927 100644
--- a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
+++ b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst
@@ -2,13 +2,13 @@
 
 .. _creating-domain-files:
 
-.. todo::
-    Delete this page? Domain files aren't needed with nuopc.
-
 *****************************
  Creating CLM domain files
 *****************************
 
+.. todo::
+    Delete this page? Domain files aren't needed with nuopc.
+
 ``gen_domain`` to create a domain file for datm from a mapping file. ``gen_domain`` is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of ``mknoocnmap.pl`` (see :ref:`using-mkocnmap`) to create a regional or single-point map file that is then run through ``gen_domain`` to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the $CIMEROOT/tools/mapping/gen_domain_files/README <https://github.com/ESMCI/cime/blob/master/tools/mapping/gen_domain_files/README>`_ file for more help on ``gen_domain``.
 
 Here we create domain files for a regular global domain.

From 482d78617a84a6db46419d36d20118edcf8ed932 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 24 Sep 2024 18:52:14 -0600
Subject: [PATCH 1124/1248] Fix typo in test in ExpectedTestFails.xml

---
 cime_config/testdefs/ExpectedTestFails.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index d73e167629..36245661c0 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -144,7 +144,7 @@
 
   <!-- fates test suite failures -->
 
-  <test name="ERS_D_Ld3.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLUH2">
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLUH2">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>#2653</issue>

From a25bf74bff9a698df0b73915cbb698c7c5979266 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <ekluzek@users.noreply.github.com>
Date: Tue, 24 Sep 2024 19:40:48 -0600
Subject: [PATCH 1125/1248] Update doc/ChangeLog

Description of changes to surface datasets...

Co-authored-by: Samuel Levis <slevis@ucar.edu>
---
 doc/ChangeLog | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 695323904a..a104795230 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -40,7 +40,15 @@ Changes to CTSM Answers:
 New surface datasets:
 =====================
 
-
+- New surface datasets because of updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset. 
+- With new surface datasets the following GLC fields have region "1" set to UNSET:
+     glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
+- Updates to allow creating transient landuse timeseries files going back to 1700. 
+- Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mksurfdata_esmf now giving identical answers with a change in number of processors, as it should. 
+- Add in creation of ne0np4.POLARCAP.ne30x4 surface datasets.
+- Add version to the surface datasets. 
+- Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it.
+- Remove VIC fields from surface datasets.
 New input datasets to mksurfdata_esmf:
 ======================================
 

From 1e75db08fc30a250433b54942fc0ced7b4a045b3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 24 Sep 2024 20:05:47 -0600
Subject: [PATCH 1126/1248] A few updates

---
 doc/ChangeLog | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 695323904a..03f58ccc1d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -4,8 +4,8 @@ Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri 06 Sep 2024 02:21:22 AM MDT
 One-line Summary: Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
 
-Purpose and description of changes since ctsm5.2.0
---------------------------------------------------
+Purpose and description of changes since ctsm5.2.005
+----------------------------------------------------
 
 
 Changes to CTSM Infrastructure:
@@ -48,6 +48,8 @@ New input datasets to mksurfdata_esmf:
 Contributors
 ------------
 
+    @slevis-lmwg @ekluzek @lawrencepj1 @wwieder @adrifoster @samsrabin @billsacks @lifang0209 @linniahawkins @olyson
+
 
 Significant changes to scientifically-supported configurations since ctsm5.2.0
 ------------------------------------------------------------------------------
@@ -139,7 +141,7 @@ List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
 ===============================================================
 ===============================================================
 Tag name: ctsm5.2.029
-Originator(s): multiple
+Originator(s): multiple (see contributors below)
 Date: 10 Sep 2024
 One-line Summary: Update surface datasets: double tag of ctsm5.3.0
 
@@ -148,7 +150,7 @@ Purpose and description of changes
 
 New surface datasets because of updates in PFT/LAI/soil-color datasets, as well as two fire datasets (AG fire, pearland and the glacier behavior dataset. Also bring in an updated "PPE informed, hand-tuned" parameter file. And turn on Li2024 fire method. Also updates to allow creating transient landuse timeseries files going back to 1700. Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mkaurfdata_esmf giving identical answers with a change in number of processors. Add in creation of ne0np4.POLARCAP.ne30x4 surface datasets.
 
-Asides: Remove VIC fields from surface datasets and testing. Add version to the surface datasets. Update the fire emissions factor dataset for the fire emissions testing in CTSM. Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it.
+Asides: Remove VIC fields from surface datasets and testing. Add version to the surface datasets. Update the fire emissions factor dataset for the fire emissions testing in CTSM. Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it. Also delete mkprocdata_map.
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
@@ -175,7 +177,8 @@ Bugs fixed
 List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
    Fixes #2723 -- Version string on CTSM surface datasets to check for compatability
    Partly addressed #2752 -- NEON surface datasets are defined in two places -- should just be one in namelist_defaults_ctsm.xml
-   Partly addresses #2720 -- Make polarcap surface datasets in ctsm5.3.0, remove VR 1850 datasets
+   Partly addressed #2672 -- Excess ice testing
+   Fixes #2720 -- Make polarcap surface datasets in ctsm5.3.0, remove VR 1850 datasets
    Fixes #2452 -- Run mksurfdata_esmf with the new vegetation raw data
    Fixes #2570 -- Historical configuration for CLM6
    Fixes #2618 -- Update fire variables on surface dataset
@@ -184,6 +187,11 @@ List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
    Fixes #2744 -- Soil level clm surface input data for clm5.2.0 have missing values in large domains
    Fixes #2502 -- fsurdat: PCT_SAND, PCT_CLAY, ORGANIC differ with different PE layouts on derecho
    Fixes #2748 -- Update hillslope datasets for 5.3
+   Fixes #2773 -- Deprecate and remove mkprocdata_map
+
+Contributors
+------------
+    @slevis-lmwg @ekluzek @lawrencepj1 @wwieder @adrifoster @samsrabin @billsacks @lifang0209 @linniahawkins @olyson
 
 Notes of particular relevance for users
 ---------------------------------------

From f120fcd3d145f63025bbfd9d125e28c6e741aa01 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 24 Sep 2024 21:36:30 -0600
Subject: [PATCH 1127/1248] Update contributors and more in the change files

---
 doc/ChangeLog | 71 +++++++++++++++++++++++++++++++++++----------------
 1 file changed, 49 insertions(+), 22 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 822486c0b6..8c79e548b8 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,12 +1,16 @@
 ===============================================================
 Tag name: ctsm5.3.0
-Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Originator(s): multiple (see below)
 Date: Fri 06 Sep 2024 02:21:22 AM MDT
 One-line Summary: Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
 
 Purpose and description of changes since ctsm5.2.005
 ----------------------------------------------------
 
+Bring in updates needed for the CESM3.0 science capability/functionality "chill". Most importantly bringing
+in: CN Matrix to speed up spinup for the BGC model, updated surface datasets, updated Leung 2023 dust emissions,
+explicit Air Conditioning for the Urban model, updates to crop calendars. For clm6_0 physics these options are now
+default turned on in addition to Sturm snow, and excess ice.
 
 Changes to CTSM Infrastructure:
 ===============================
@@ -16,7 +20,7 @@ Changes to CTSM Infrastructure:
 
 Changes to CTSM Answers:
 ========================
- 
+
  Changes to defaults for clm6_0 physics:
   - Urban explicit A/C turned on
   - Snow thermal conductivity is now Sturm_1997
@@ -36,28 +40,51 @@ Changes to CTSM Answers:
   - Pass active glacier (CISM) runoff directly to river model (MOSART)
   - Add the option for using matrix for Carbon/Nitrogen BGC spinup
 
-
 New surface datasets:
 =====================
 
-- New surface datasets because of updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset. 
+- New surface datasets because of updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset.
 - With new surface datasets the following GLC fields have region "1" set to UNSET:
      glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
-- Updates to allow creating transient landuse timeseries files going back to 1700. 
-- Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mksurfdata_esmf now giving identical answers with a change in number of processors, as it should. 
+- Updates to allow creating transient landuse timeseries files going back to 1700.
+- Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mksurfdata_esmf now giving identical answers with a change in number of processors, as it should.
 - Add in creation of ne0np4.POLARCAP.ne30x4 surface datasets.
-- Add version to the surface datasets. 
+- Add version to the surface datasets.
 - Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it.
 - Remove VIC fields from surface datasets.
+
 New input datasets to mksurfdata_esmf:
 ======================================
 
 
-Contributors
+Contributors (alphabetical order by github handle)
 ------------
 
-    @slevis-lmwg @ekluzek @lawrencepj1 @wwieder @adrifoster @samsrabin @billsacks @lifang0209 @linniahawkins @olyson
-
+    @adrifoster
+    @billsacks
+    @cathyxinchangli
+    @chrislxj
+    @dmleung
+    @ekluzek
+    @Face2sea
+    @fang-bowen
+    @glemieux
+    @HuiWangWanderInGitHub
+    @jedwards
+    @jenniferholm
+    @jfkok
+    @KateC
+    @keerzhang1
+    @lawrencepj1
+    @lifang0209
+    @linniahawkins
+    @mvdebolskiy
+    @mvertens
+    @olyson
+    @rgknox
+    @samsrabin
+    @slevis-lmwg
+    @wwieder
 
 Significant changes to scientifically-supported configurations since ctsm5.2.0
 ------------------------------------------------------------------------------
@@ -91,20 +118,20 @@ Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_e
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho -
+    derecho - PASS
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
-    derecho -
+    derecho - PASS
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho -----
-    izumi -------
+    derecho ----- OK
+    izumi ------- OK
 
   fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
-    derecho -----
-    izumi -------
+    derecho ----- OK
+    izumi ------- OK
 
   any other testing (give details below):
 
@@ -113,14 +140,14 @@ Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_e
      (crop-global-SSP2-4.5-ne30 was longest at 6 hr, most completed in XXX hours)
 
   ctsm_sci
-     derecho ----
+     derecho ---- OK
 
   mosart
-     derecho ----
-     izumi ------
+     derecho ---- OK
+     izumi ------ PASS
 
   rtm
-     derecho ----
+     derecho ---- OK
 
 
 Answer changes ctsm5.2.0 to ctsm5.3.0
@@ -240,7 +267,7 @@ Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_e
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho - PASS
+    derecho - PASS (1433 namelists differ compared to ctsm5.2.028)
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
@@ -374,7 +401,7 @@ Bring b4b-dev branch to main CTSM development.
 
 Update cs.status parsing script to make expected BASELINE fails more obvious
 
-Fix some issues with finding IC files for certain lnd_tuning_modes: all for cam7, 
+Fix some issues with finding IC files for certain lnd_tuning_modes: all for cam7,
    clm5_0_cam6.0, and clm6_0_cam6.0
 
 Significant changes to scientifically-supported configurations

From e86c33a38a25ce1f39e09ef6a480d25fa3bfe439 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 24 Sep 2024 23:37:47 -0600
Subject: [PATCH 1128/1248] Finish descriptions on updates in the Change files

---
 doc/ChangeLog | 138 ++++++++++++++++++++++++++++++++++++--------------
 doc/ChangeSum |   4 +-
 2 files changed, 103 insertions(+), 39 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8c79e548b8..675545633d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.3.0
 Originator(s): multiple (see below)
-Date: Fri 06 Sep 2024 02:21:22 AM MDT
+Date: Tue 24 Sep 2024 11:34:58 PM MDT
 One-line Summary: Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
 
 Purpose and description of changes since ctsm5.2.005
@@ -43,7 +43,6 @@ Changes to CTSM Answers:
 New surface datasets:
 =====================
 
-- New surface datasets because of updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset.
 - With new surface datasets the following GLC fields have region "1" set to UNSET:
      glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
 - Updates to allow creating transient landuse timeseries files going back to 1700.
@@ -56,6 +55,7 @@ New surface datasets:
 New input datasets to mksurfdata_esmf:
 ======================================
 
+- Updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset.
 
 Contributors (alphabetical order by github handle)
 ------------
@@ -84,33 +84,98 @@ Contributors (alphabetical order by github handle)
     @rgknox
     @samsrabin
     @slevis-lmwg
+    @TeaganKing
     @wwieder
 
-Significant changes to scientifically-supported configurations since ctsm5.2.0
-------------------------------------------------------------------------------
+Significant changes to scientifically-supported configurations since ctsm5.2.005
+--------------------------------------------------------------------------------
 
-Notes of particular relevance for users for ctsm5.2.0 to ctsm5.3.0
-------------------------------------------------------------------
+glacier_behavior namelist items changed for clm4_5 and clm5_0 physics
+parameter and surface datasets updated for all physics options
+
+Notes of particular relevance for users for ctsm5.2.005 to ctsm5.3.0
+--------------------------------------------------------------------
 
 Caveats for users (e.g., need to interpolate initial conditions):
+   With the updated surface datasets all finidat files being used will need to
+   be run with use_init_interp = TRUE
 
 Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   New namelist items or options:
+     fire_method -- new options: li2024gswpfrc,li2024crujra
+
+      new fire options:
+        max_rh30_affecting_fuel
+        defo_fire_precip_thresh_bet
+        defo_fire_precip_thresh_bdt
+        nonborpeat_fire_precip_denom
+        borpeat_fire_soilmoist_denom
+
+      new fates options:
+        fates_harvest_mode
+        use_fates_lupft
+        use_fates_potentialveg
+        flandusepftdat
+
+      new physics options:
+        hillslope_fsat_equals_zero
+        urban_explicit_ac
+        use_prigent_roughness
+        stream_fldfilename_prigentroughness
+        stream_meshfile_prigentroughness
+        excess_ice_coldstart_temp
+        excess_ice_coldstart_depth
+
+      new cropcal options:
+        stream_year_last_cropcal_swindows
+        model_year_align_cropcal_swindows
+        stream_year_first_cropcal_cultivar_gdds
+        stream_year_last_cropcal_cultivar_gdds
+        model_year_align_cropcal_cultivar_gdds
+        stream_fldFileName_gdd20_baseline
+        stream_gdd20_seasons
+        flush_gdd20
+        allow_invalid_gdd20_season_inputs
+        stream_fldFileName_gdd20_season_start
+        stream_fldFileName_gdd20_season_end
+
+      cropcal options with names changed:
+        stream_year_first_cropcal => cropcals_rx
+        stream_year_last_cropcal => cropcals_rx_adapt
+        model_year_align_cropcal => stream_year_first_cropcal_swindows
+
+      new CN matrix options:
+        use_matrixcn
+        use_soil_matrixcn
+        hist_wrt_matrixcn_diag
+        spinup_matrixcn
+        nyr_forcing
+        nyr_sasu
+        iloop_avg
+
+   Namelist items removed:
+     use_fates_logging
+     use_dynroot
+
+   Changes to XML options:
+
+   LND_TUNING_MODE:             New forcing options for cam4.0, cam5.0, and cam7.0
+   CLM_BLDNML_OPTS:             "-bgc cn" option removed
+   CLM_ACCELERATED_SPINUP:      sasu option added
+   LND_SETS_DUST_EMIS_DRV_FLDS: New option to determine if CAM or CTSM set dust emission options
+   PLUMBER2SITE:                New option to run for PLUMBER2 tower site locations
 
 Changes made to namelist defaults (e.g., changed parameter values):
 
 Changes to the datasets (e.g., parameter, surface or initial files):
-
-Changes to documentation:
+   parameter files updated
+   surface datasets updated
+   many finidat files updated
 
 Things being deprecated (which will be removed):
-
-Notes of particular relevance for developers for ctsm5.2.0 to ctsm5.3.0:
-------------------------------------------------------------------------
-
-Caveats for developers (e.g., code that is duplicated that requires double maintenance):
-
-Changes to tests or testing:
-
+   Running with VIC hydrology being deprecated with testing removed
+   mkprocdata_map was removed
+   test/tools testing framework was removed
 
 Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_esmf python)
 ----------------
@@ -118,7 +183,7 @@ Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_e
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho - PASS
+    derecho - PASS (1710 namelists differ from ctsm5.2.005)
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
@@ -136,8 +201,8 @@ Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_e
   any other testing (give details below):
 
   mksurfdata_esmf
-     derecho ---- run "make all" to create all datasets (completes in XXX hours)
-     (crop-global-SSP2-4.5-ne30 was longest at 6 hr, most completed in XXX hours)
+     derecho ---- run "make all" to create all datasets (completes in 6 hours)
+     (crop-global-SSP2-4.5-ne30 was longest at 6 hr)
 
   ctsm_sci
      derecho ---- OK
@@ -150,34 +215,33 @@ Testing summary: release testing (regular ctsm_sci fates mosart rtm mksurfdata_e
      derecho ---- OK
 
 
-Answer changes ctsm5.2.0 to ctsm5.3.0
--------------------------------------
-
-Changes answers relative to baseline: Yes! New surface datasets so answers change for ALL simulations!
-
-  Summarize any changes to answers, i.e.,
-    - what code configurations: ALL
-    - what platforms/compilers: ALL
-    - nature of change (roundoff; larger than roundoff/same climate; new climate):
-      new climate
-
-   If this tag changes climate describe the run(s) done to evaluate the new
-   climate (put details of the simulations in the experiment database)
-       - casename:
-
-   URL for LMWG diagnostics output used to validate new climate:
+Simulations to go with ctsm5.3.0:
+---------------------------------
 
+   https://github.com/NCAR/LMWG_dev/issues/69
+   https://github.com/NCAR/LMWG_dev/issues/65
 
 Other details
 -------------
 
-List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+List git submodules:
+
+fates      = sci.1.78.2_api.36.0.0
+cism       = cismwrap_2_2_002
+rtm        = rtm1_0_80
+mosart     = mosart1.1.02
+mizuRoute  = cesm-coupling.n02_v2.1.2
+ccs_config = ccs_config_cesm1.0.0
+cime       = cime6.0.246
+cmeps      = cmeps0.14.77
+cdeps      = cdeps1.0.48
+share      = share1.0.19
 
 ===============================================================
 ===============================================================
 Tag name: ctsm5.2.029
 Originator(s): multiple (see contributors below)
-Date: 10 Sep 2024
+Date: Tue 24 Sep 2024 11:34:58 PM MDT
 One-line Summary: Update surface datasets: double tag of ctsm5.3.0
 
 Purpose and description of changes
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 31642a7378..ebbab3ce01 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,7 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-         ctsm5.3.0 multiple 09/11/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
-       ctsm5.2.029 multiple 09/11/2024 New surface datasets: double tag of ctsm5.3.0
+         ctsm5.3.0 multiple 09/24/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
+       ctsm5.2.029 multiple 09/24/2024 New surface datasets: double tag of ctsm5.3.0
        ctsm5.2.028   rgknox 09/05/2024 FATES history flushing update
        ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6

From 508a96676db91a734a4890ae7f06a7ae2227bd64 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 24 Sep 2024 23:59:54 -0600
Subject: [PATCH 1129/1248] Add the WhatsNew markdown file

---
 README                                        |  2 +-
 WhatsNewInCTSM5.3.md                          | 53 +++++++++++++++++++
 .../README.NUOPC_driver.md                    |  0
 3 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 WhatsNewInCTSM5.3.md
 rename README.NUOPC_driver.md => doc/README.NUOPC_driver.md (100%)

diff --git a/README b/README
index 0e3464583e..c5c06daae7 100644
--- a/README
+++ b/README
@@ -76,7 +76,7 @@ README ------------------- This file
 README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git
 README.rst --------------- File that displays under the project in github
 README_GITFLEXIMOD.rst --- Information on how to work with git-fleximod for CTSM
-WhatsNewinCTSM5.3.md ----- Overview document of the changes between ctsm5.2.0 and ctsm5.3.0
+WhatsNewInCTSM5.3.md ----- Overview document of the changes between ctsm5.2.0 and ctsm5.3.0
 CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project
 Copyright ---------------- CESM Copyright file
 doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the
diff --git a/WhatsNewInCTSM5.3.md b/WhatsNewInCTSM5.3.md
new file mode 100644
index 0000000000..b1f753081b
--- /dev/null
+++ b/WhatsNewInCTSM5.3.md
@@ -0,0 +1,53 @@
+Purpose and description of changes since ctsm5.2.005
+----------------------------------------------------
+
+Bring in updates needed for the CESM3.0 science capability/functionality "chill". Most importantly bringing
+in: CN Matrix to speed up spinup for the BGC model, updated surface datasets, updated Leung 2023 dust emissions,
+explicit Air Conditioning for the Urban model, updates to crop calendars. For clm6_0 physics these options are now
+default turned on in addition to Sturm snow, and excess ice.
+
+Changes to CTSM Infrastructure:
+===============================
+
+ - manage_externals removed and replaced by git-fleximod
+ - Ability to handle CAM7 in LND_TUNING_MODE
+
+Changes to CTSM Answers:
+========================
+
+ Changes to defaults for clm6_0 physics:
+  - Urban explicit A/C turned on
+  - Snow thermal conductivity is now Sturm_1997
+  - New IC file for f09 1850
+  - New crop calendars
+  - Dust emissions is now Leung_2023
+  - Excess ice is turned on
+  - Updates to MEGAN for BVOC's
+  - Updates to BGC fire method
+
+ Changes for all physics versions:
+
+  - Parameter files updated
+  - FATES parameter file updated
+  - Glacier region 1 is now undefined
+  - Update in FATES transient Land use
+  - Pass active glacier (CISM) runoff directly to river model (MOSART)
+  - Add the option for using matrix for Carbon/Nitrogen BGC spinup
+
+New surface datasets:
+=====================
+
+- With new surface datasets the following GLC fields have region "1" set to UNSET:
+     glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
+- Updates to allow creating transient landuse timeseries files going back to 1700.
+- Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mksurfdata_esmf now giving identical answers with a change in number of processors, as it should.
+- Add in creation of ne0np4.POLARCAP.ne30x4 surface datasets.
+- Add version to the surface datasets.
+- Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it.
+- Remove VIC fields from surface datasets.
+
+New input datasets to mksurfdata_esmf:
+======================================
+
+- Updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset.
+
diff --git a/README.NUOPC_driver.md b/doc/README.NUOPC_driver.md
similarity index 100%
rename from README.NUOPC_driver.md
rename to doc/README.NUOPC_driver.md

From cc34cc4f8d79dadaec080a312f3924442dd322e4 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 25 Sep 2024 01:22:35 -0600
Subject: [PATCH 1130/1248] Update changelog date

---
 doc/ChangeLog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 675545633d..d11efad6b3 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.3.0
 Originator(s): multiple (see below)
-Date: Tue 24 Sep 2024 11:34:58 PM MDT
+Date: Wed 25 Sep 2024 01:22:06 AM MDT
 One-line Summary: Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
 
 Purpose and description of changes since ctsm5.2.005
@@ -241,7 +241,7 @@ share      = share1.0.19
 ===============================================================
 Tag name: ctsm5.2.029
 Originator(s): multiple (see contributors below)
-Date: Tue 24 Sep 2024 11:34:58 PM MDT
+Date: Wed 25 Sep 2024 01:22:06 AM MDT
 One-line Summary: Update surface datasets: double tag of ctsm5.3.0
 
 Purpose and description of changes

From c20866f9eb85f53468f5413db1cd37ae9b3fd461 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 25 Sep 2024 08:35:38 -0600
Subject: [PATCH 1131/1248] remove old version

---
 .../git-fleximod/.github/workflows/pre-commit |  13 -
 .../.github/workflows/pytest.yaml             |  77 --
 .lib/git-fleximod/.pre-commit-config.yaml     |  18 -
 .lib/git-fleximod/License                     |  20 -
 .lib/git-fleximod/README.md                   | 108 ---
 .lib/git-fleximod/doc/Makefile                |  20 -
 .lib/git-fleximod/doc/conf.py                 |  26 -
 .lib/git-fleximod/doc/index.rst               |  24 -
 .lib/git-fleximod/doc/make.bat                |  35 -
 .lib/git-fleximod/escomp_install              |  25 -
 .lib/git-fleximod/git_fleximod/__init__.py    |   0
 .lib/git-fleximod/git_fleximod/cli.py         | 129 ----
 .../git-fleximod/git_fleximod/git_fleximod.py | 624 ----------------
 .../git-fleximod/git_fleximod/gitinterface.py |  79 --
 .lib/git-fleximod/git_fleximod/gitmodules.py  |  97 ---
 .../git-fleximod/git_fleximod/lstripreader.py |  43 --
 .lib/git-fleximod/git_fleximod/metoflexi.py   | 236 ------
 .lib/git-fleximod/git_fleximod/utils.py       | 365 ---------
 .lib/git-fleximod/poetry.lock                 | 693 ------------------
 .lib/git-fleximod/pyproject.toml              |  41 --
 .lib/git-fleximod/tbump.toml                  |  43 --
 .lib/git-fleximod/tests/__init__.py           |   3 -
 .lib/git-fleximod/tests/conftest.py           | 138 ----
 .lib/git-fleximod/tests/test_a_import.py      |   8 -
 .lib/git-fleximod/tests/test_b_update.py      |  26 -
 .lib/git-fleximod/tests/test_c_required.py    |  30 -
 .lib/git-fleximod/tests/test_d_complex.py     |  66 --
 27 files changed, 2987 deletions(-)
 delete mode 100644 .lib/git-fleximod/.github/workflows/pre-commit
 delete mode 100644 .lib/git-fleximod/.github/workflows/pytest.yaml
 delete mode 100644 .lib/git-fleximod/.pre-commit-config.yaml
 delete mode 100644 .lib/git-fleximod/License
 delete mode 100644 .lib/git-fleximod/README.md
 delete mode 100644 .lib/git-fleximod/doc/Makefile
 delete mode 100644 .lib/git-fleximod/doc/conf.py
 delete mode 100644 .lib/git-fleximod/doc/index.rst
 delete mode 100644 .lib/git-fleximod/doc/make.bat
 delete mode 100644 .lib/git-fleximod/escomp_install
 delete mode 100644 .lib/git-fleximod/git_fleximod/__init__.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/cli.py
 delete mode 100755 .lib/git-fleximod/git_fleximod/git_fleximod.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/gitinterface.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/gitmodules.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/lstripreader.py
 delete mode 100755 .lib/git-fleximod/git_fleximod/metoflexi.py
 delete mode 100644 .lib/git-fleximod/git_fleximod/utils.py
 delete mode 100644 .lib/git-fleximod/poetry.lock
 delete mode 100644 .lib/git-fleximod/pyproject.toml
 delete mode 100644 .lib/git-fleximod/tbump.toml
 delete mode 100644 .lib/git-fleximod/tests/__init__.py
 delete mode 100644 .lib/git-fleximod/tests/conftest.py
 delete mode 100644 .lib/git-fleximod/tests/test_a_import.py
 delete mode 100644 .lib/git-fleximod/tests/test_b_update.py
 delete mode 100644 .lib/git-fleximod/tests/test_c_required.py
 delete mode 100644 .lib/git-fleximod/tests/test_d_complex.py

diff --git a/.lib/git-fleximod/.github/workflows/pre-commit b/.lib/git-fleximod/.github/workflows/pre-commit
deleted file mode 100644
index 1a6ad0082a..0000000000
--- a/.lib/git-fleximod/.github/workflows/pre-commit
+++ /dev/null
@@ -1,13 +0,0 @@
-name: pre-commit
-on:
-  pull_request:
-  push:
-    branches: [main]
-
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: pre-commit/action@v3.0.0
diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml
deleted file mode 100644
index 0868dd9a33..0000000000
--- a/.lib/git-fleximod/.github/workflows/pytest.yaml
+++ /dev/null
@@ -1,77 +0,0 @@
-# Run this job on pushes to `main`, and for pull requests. If you don't specify
-# `branches: [main], then this actions runs _twice_ on pull requests, which is
-# annoying.
-
-on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
-      # reference the matrixe python version here.
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
-
-      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
-      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
-      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
-      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
-      # mildly cleaner by using an environment variable, but I don't really care.
-      - name: cache poetry install
-        uses: actions/cache@v4
-        with:
-          path: ~/.local
-          key: poetry-1.7.1
-
-      # Install Poetry. You could do this manually, or there are several actions that do this.
-      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
-      # Poetry's default install script, which feels correct. I pin the Poetry version here
-      # because Poetry does occasionally change APIs between versions and I don't want my
-      # actions to break if it does.
-      #
-      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
-      # venv as a `.venv` in your testing directory, which allows the next step to easily
-      # cache it.
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.7.1
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
-      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
-      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v4
-        with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-
-      # Install dependencies. `--no-root` means "install all dependencies but not the project
-      # itself", which is what you want to avoid caching _your_ code. The `if` statement
-      # ensures this only runs on a cache miss.
-      - run: poetry install --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-
-      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
-      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
-      # pyproject.toml and makes that if you add things like console-scripts at some point that
-      # they'll be installed and working.
-      - run: poetry install --no-interaction
-
-      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
-      # so this line is super-simple. But it could be as complex as you need.
-      - run: |
-          git config --global user.name "${GITHUB_ACTOR}"
-          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-          poetry run pytest
-
diff --git a/.lib/git-fleximod/.pre-commit-config.yaml b/.lib/git-fleximod/.pre-commit-config.yaml
deleted file mode 100644
index 2f6089da72..0000000000
--- a/.lib/git-fleximod/.pre-commit-config.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-exclude: ^utils/.*$
-
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
-    hooks:
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/pylint
-    rev: v2.11.1
-    hooks:
-      - id: pylint
-        args:
-          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/.lib/git-fleximod/License b/.lib/git-fleximod/License
deleted file mode 100644
index 88bc22515e..0000000000
--- a/.lib/git-fleximod/License
+++ /dev/null
@@ -1,20 +0,0 @@
-Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR)
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-“Software”), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/.lib/git-fleximod/README.md b/.lib/git-fleximod/README.md
deleted file mode 100644
index 53917da400..0000000000
--- a/.lib/git-fleximod/README.md
+++ /dev/null
@@ -1,108 +0,0 @@
-# git-fleximod
-
-Flexible, Enhanced Submodule Management for Git
-
-## Overview
-
-Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
-
-## Installation
-
-  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
-
-## Usage
-
-    Basic Usage:
-        git fleximod <command> [options]
-    Available Commands:
-        status: Display the status of submodules.
-        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
-        test: Make sure that fxtags and submodule hashes are consistant,
-              make sure that official urls (as defined by fxDONOTUSEurl) are set
-              make sure that fxtags are defined for all submodules
-    Additional Options:
-        See git fleximod --help for more details.
-
-## Supported .gitmodules Variables
-
-    fxtag: Specify a specific tag or branch to checkout for a submodule.
-    fxrequired: Mark a submodule's checkout behavior, with allowed values:
-      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
-      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
-      - AlwaysRequired:       Always required (always checked out).
-      - AlwaysOptional:       Always optional (checked out with --optional flag).
-    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
-    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
-           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
-           changed by users.  Use the url variable to change to a fork if desired.
-
-## Sparse Checkouts
-
-    To enable sparse checkout for a submodule, set the fxsparse variable
-    in the .gitmodules file to the path of a file containing the desired
-    sparse checkout paths. Git-fleximod will automatically configure
-    sparse checkout based on this file when applicable commands are run.
-    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
-    for details on the format of this file.
-
-## Tests
-
-   The git fleximod test action is designed to be used by, for example, github workflows
-   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
-
-## Examples
-
-Here are some common usage examples:
-
-Update all submodules, including optional ones:
-```bash
-  git fleximod update --optional
-```
-
-Updating a specific submodule to the fxtag indicated in .gitmodules:
-
-```bash
-    git fleximod update submodule-name
-```
-Example .gitmodules entry:
-```ini, toml
-    [submodule "cosp2"]
-        path = src/physics/cosp2/src
-        url = https://github.com/CFMIP/COSPv2.0
-        fxsparse = ../.cosp_sparse_checkout
-        fxrequired = AlwaysRequired
-        fxtag = v2.1.4cesm
-```
-Explanation:
-
-This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
-should be checked out into the directory src/physics/cosp2/src
-relative to the .gitmodules directory.  It should be checked out from
-the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
-described in the file ../.cosp_sparse_checkout relative to the path
-directory.  It should be checked out anytime this .gitmodules entry is
-read.
-
-Additional example:
-```ini, toml
-    [submodule "cime"]
-        path = cime
-        url = https://github.com/jedwards4b/cime
-        fxrequired = ToplevelRequired
-        fxtag = cime6.0.198_rme01
-```
-
-Explanation:
-
-This entry indicates that the submodule cime should be checked out
-into a directory named cime at tag cime6.0.198_rme01 from the URL
-https://github.com/jedwards4b/cime.  This should only be done if
-the .gitmodules file is at the top level of the repository clone.
-
-## Contributing
-
-We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
-
-## License
-
-Git-fleximod is released under the MIT License.
diff --git a/.lib/git-fleximod/doc/Makefile b/.lib/git-fleximod/doc/Makefile
deleted file mode 100644
index d4bb2cbb9e..0000000000
--- a/.lib/git-fleximod/doc/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/.lib/git-fleximod/doc/conf.py b/.lib/git-fleximod/doc/conf.py
deleted file mode 100644
index 423099eec9..0000000000
--- a/.lib/git-fleximod/doc/conf.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
-project = "git-fleximod"
-author = "Jim Edwards <jedwards@ucar.edu>"
-release = "0.4.0"
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
-extensions = ["sphinx_argparse_cli"]
-
-templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
-
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = "alabaster"
-html_static_path = ["_static"]
diff --git a/.lib/git-fleximod/doc/index.rst b/.lib/git-fleximod/doc/index.rst
deleted file mode 100644
index 0f9c1a7f7e..0000000000
--- a/.lib/git-fleximod/doc/index.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-.. git-fleximod documentation master file, created by
-   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to git-fleximod's documentation!
-========================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-.. module:: sphinxcontrib.autoprogram
-.. sphinx_argparse_cli::
-   :module: git_fleximod.cli
-   :func: get_parser
-   :prog: git-fleximod
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/.lib/git-fleximod/doc/make.bat b/.lib/git-fleximod/doc/make.bat
deleted file mode 100644
index 32bb24529f..0000000000
--- a/.lib/git-fleximod/doc/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/.lib/git-fleximod/escomp_install b/.lib/git-fleximod/escomp_install
deleted file mode 100644
index ae782e72a4..0000000000
--- a/.lib/git-fleximod/escomp_install
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python
-# updates git-fleximod in an ESCOMP model
-# this script should be run from the model root directory, it expects
-# git-fleximod to already be installed with the script in bin
-# and the classes in lib/python/site-packages
-import sys
-import shutil
-import os
-
-from glob import iglob
-
-fleximod_root = sys.argv[1]
-fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
-if os.path.isfile(fleximod_path):
-   with open(fleximod_path,"r") as f:
-        fleximod = f.readlines()
-   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
-        for line in fleximod:
-            f.write(line)
-            if "import argparse" in line:
-               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
-
-   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
-       shutil.copy(file,
-        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/.lib/git-fleximod/git_fleximod/__init__.py b/.lib/git-fleximod/git_fleximod/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
deleted file mode 100644
index a15a226de4..0000000000
--- a/.lib/git-fleximod/git_fleximod/cli.py
+++ /dev/null
@@ -1,129 +0,0 @@
-from pathlib import Path
-import argparse
-from git_fleximod import utils
-
-__version__ = "0.7.8"
-
-def find_root_dir(filename=".gitmodules"):
-    """ finds the highest directory in tree
-    which contains a file called filename """
-    d = Path.cwd()
-    root = Path(d.root)
-    dirlist = []
-    dl = d
-    while dl != root:
-        dirlist.append(dl)
-        dl = dl.parent
-    dirlist.append(root)
-    dirlist.reverse()
-
-    for dl in dirlist:
-        attempt = dl / filename
-        if attempt.is_file():
-            return str(dl)
-    return None
-
-
-def get_parser():
-    description = """
-    %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models
-    """
-    parser = argparse.ArgumentParser(
-        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-    )
-
-    #
-    # user options
-    #
-    choices = ["update", "status", "test"]
-    parser.add_argument(
-        "action",
-        choices=choices,
-        default="update",
-        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
-    )
-
-    parser.add_argument(
-        "components",
-        nargs="*",
-        help="Specific component(s) to checkout. By default, "
-        "all required submodules are checked out.",
-    )
-
-    parser.add_argument(
-        "-C",
-        "--path",
-        default=find_root_dir(),
-        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
-    )
-
-    parser.add_argument(
-        "-g",
-        "--gitmodules",
-        nargs="?",
-        default=".gitmodules",
-        help="The submodule description filename. " "Default: %(default)s.",
-    )
-
-    parser.add_argument(
-        "-x",
-        "--exclude",
-        nargs="*",
-        help="Component(s) listed in the gitmodules file which should be ignored.",
-    )
-    parser.add_argument(
-        "-f",
-        "--force",
-        action="store_true",
-        default=False,
-        help="Override cautions and update or checkout over locally modified repository.",
-    )
-
-    parser.add_argument(
-        "-o",
-        "--optional",
-        action="store_true",
-        default=False,
-        help="By default only the required submodules "
-        "are checked out. This flag will also checkout the "
-        "optional submodules relative to the toplevel directory.",
-    )
-
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        action="count",
-        default=0,
-        help="Output additional information to "
-        "the screen and log file. This flag can be "
-        "used up to two times, increasing the "
-        "verbosity level each time.",
-    )
-
-    parser.add_argument(
-        "-V",
-        "--version",
-        action="version",
-        version=f"%(prog)s {__version__}",
-        help="Print version and exit.",
-    )
-
-    #
-    # developer options
-    #
-    parser.add_argument(
-        "--backtrace",
-        action="store_true",
-        help="DEVELOPER: show exception backtraces as extra " "debugging output",
-    )
-
-    parser.add_argument(
-        "-d",
-        "--debug",
-        action="store_true",
-        default=False,
-        help="DEVELOPER: output additional debugging "
-        "information to the screen and log file.",
-    )
-
-    return parser
diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
deleted file mode 100755
index e1b8f484a5..0000000000
--- a/.lib/git-fleximod/git_fleximod/git_fleximod.py
+++ /dev/null
@@ -1,624 +0,0 @@
-#!/usr/bin/env python
-import sys
-
-MIN_PYTHON = (3, 7)
-if sys.version_info < MIN_PYTHON:
-    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
-
-import os
-import shutil
-import logging
-import textwrap
-from git_fleximod import utils
-from git_fleximod import cli
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-from configparser import NoOptionError
-
-# logger variable is global
-logger = None
-
-
-def fxrequired_allowed_values():
-    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"]
-
-
-def commandline_arguments(args=None):
-    parser = cli.get_parser()
-
-    if args:
-        options = parser.parse_args(args)
-    else:
-        options = parser.parse_args()
-
-    # explicitly listing a component overrides the optional flag
-    if options.optional or options.components:
-        fxrequired = [
-            "ToplevelRequired",
-            "ToplevelOptional",
-            "AlwaysRequired",
-            "AlwaysOptional",
-        ]
-    else:
-        fxrequired = ["ToplevelRequired", "AlwaysRequired"]
-
-    action = options.action
-    if not action:
-        action = "update"
-    handlers = [logging.StreamHandler()]
-
-    if options.debug:
-        try:
-            open("fleximod.log", "w")
-        except PermissionError:
-            sys.exit("ABORT: Could not write file fleximod.log")
-        level = logging.DEBUG
-        handlers.append(logging.FileHandler("fleximod.log"))
-    elif options.verbose:
-        level = logging.INFO
-    else:
-        level = logging.WARNING
-    # Configure the root logger
-    logging.basicConfig(
-        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
-    )
-
-    if hasattr(options, "version"):
-        exit()
-
-    return (
-        options.path,
-        options.gitmodules,
-        fxrequired,
-        options.components,
-        options.exclude,
-        options.force,
-        action,
-    )
-
-
-def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
-    """
-    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
-    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
-    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
-    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
-    and disk space consuming.
-
-    Parameters:
-    root_dir (str): The root directory for the git operation.
-    name (str): The name of the submodule.
-    url (str): The URL of the submodule.
-    path (str): The path to the submodule.
-    sparsefile (str): The sparse file for the submodule.
-    tag (str, optional): The tag to checkout. Defaults to "master".
-
-    Returns:
-    None
-    """
-    logger.info("Called sparse_checkout for {}".format(name))
-    rgit = GitInterface(root_dir, logger)
-    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
-    if superroot:
-        gitroot = superroot.strip()
-    else:
-        gitroot = root_dir.strip()
-    assert os.path.isdir(os.path.join(gitroot, ".git"))
-    # first create the module directory
-    if not os.path.isdir(os.path.join(root_dir, path)):
-        os.makedirs(os.path.join(root_dir, path))
-
-    # initialize a new git repo and set the sparse checkout flag
-    sprep_repo = os.path.join(root_dir, path)
-    sprepo_git = GitInterface(sprep_repo, logger)
-    if os.path.exists(os.path.join(sprep_repo, ".git")):
-        try:
-            logger.info("Submodule {} found".format(name))
-            chk = sprepo_git.config_get_value("core", "sparseCheckout")
-            if chk == "true":
-                logger.info("Sparse submodule {} already checked out".format(name))
-                return
-        except NoOptionError:
-            logger.debug("Sparse submodule {} not present".format(name))
-        except Exception as e:
-            utils.fatal_error("Unexpected error {} occured.".format(e))
-
-    sprepo_git.config_set_value("core", "sparseCheckout", "true")
-
-    # set the repository remote
-
-    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
-    status = sprepo_git.git_operation("remote", "-v")
-    if url not in status:
-        sprepo_git.git_operation("remote", "add", "origin", url)
-
-    topgit = os.path.join(gitroot, ".git")
-
-    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
-        with open(os.path.join(root_dir, ".git")) as f:
-            gitpath = os.path.relpath(
-                os.path.join(root_dir, f.read().split()[1]),
-                start=os.path.join(root_dir, path),
-            )
-        topgit = os.path.join(gitpath, "modules")
-    else:
-        topgit = os.path.relpath(
-            os.path.join(root_dir, ".git", "modules"),
-            start=os.path.join(root_dir, path),
-        )
-
-    with utils.pushd(sprep_repo):
-        if not os.path.isdir(topgit):
-            os.makedirs(topgit)
-    topgit += os.sep + name
-
-    if os.path.isdir(os.path.join(root_dir, path, ".git")):
-        with utils.pushd(sprep_repo):
-            shutil.move(".git", topgit)
-            with open(".git", "w") as f:
-                f.write("gitdir: " + os.path.relpath(topgit))
-            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
-            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
-        if os.path.isfile(gitsparse):
-            logger.warning(
-                "submodule {} is already initialized {}".format(name, topgit)
-            )
-            return
-
-        with utils.pushd(sprep_repo):
-            shutil.copy(sparsefile, gitsparse)
-
-    # Finally checkout the repo
-    sprepo_git.git_operation("fetch", "origin", "--tags")
-    sprepo_git.git_operation("checkout", tag)
-
-    print(f"Successfully checked out {name:>20} at {tag}")
-    rgit.config_set_value(f'submodule "{name}"', "active", "true")
-    rgit.config_set_value(f'submodule "{name}"', "url", url)
-
-
-def single_submodule_checkout(
-    root, name, path, url=None, tag=None, force=False, optional=False
-):
-    """
-    This function checks out a single git submodule.
-
-    Parameters:
-    root (str): The root directory for the git operation.
-    name (str): The name of the submodule.
-    path (str): The path to the submodule.
-    url (str, optional): The URL of the submodule. Defaults to None.
-    tag (str, optional): The tag to checkout. Defaults to None.
-    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
-    optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False.
-
-    Returns:
-    None
-    """
-    # function implementation...
-    git = GitInterface(root, logger)
-    repodir = os.path.join(root, path)
-    logger.info("Checkout {} into {}/{}".format(name, root, path))
-    # if url is provided update to the new url
-    tmpurl = None
-    repo_exists = False
-    if os.path.exists(os.path.join(repodir, ".git")):
-        logger.info("Submodule {} already checked out".format(name))
-        repo_exists = True
-    # Look for a .gitmodules file in the newly checkedout repo
-    if not repo_exists and url:
-        # ssh urls cause problems for those who dont have git accounts with ssh keys defined
-        # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
-        # opened with a GitModules object we don't need to worry about restoring the file here
-        # it will be done by the GitModules class
-        if url.startswith("git@"):
-            tmpurl = url
-            url = url.replace("git@github.com:", "https://github.com/")
-            git.git_operation("clone", url, path)
-            smgit = GitInterface(repodir, logger)
-            if not tag:
-                tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
-            smgit.git_operation("checkout", tag)
-            # Now need to move the .git dir to the submodule location
-            rootdotgit = os.path.join(root, ".git")
-            if os.path.isfile(rootdotgit):
-                with open(rootdotgit) as f:
-                    line = f.readline()
-                    if line.startswith("gitdir: "):
-                        rootdotgit = line[8:].rstrip()
-
-            newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name))
-            if os.path.exists(newpath):
-                shutil.rmtree(os.path.join(repodir, ".git"))
-            else:
-                shutil.move(os.path.join(repodir, ".git"), newpath)
-
-            with open(os.path.join(repodir, ".git"), "w") as f:
-                f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
-                
-    if not os.path.exists(repodir):
-        parent = os.path.dirname(repodir)
-        if not os.path.isdir(parent):
-            os.makedirs(parent)
-        git.git_operation("submodule", "add", "--name", name, "--", url, path) 
-
-    if not repo_exists or not tmpurl:
-        git.git_operation("submodule", "update", "--init", "--", path)
-            
-    if os.path.exists(os.path.join(repodir, ".gitmodules")):
-        # recursively handle this checkout
-        print(f"Recursively checking out submodules of {name}")
-        gitmodules = GitModules(logger, confpath=repodir)
-        requiredlist = ["AlwaysRequired"]
-        if optional:
-            requiredlist.append("AlwaysOptional")
-        submodules_checkout(gitmodules, repodir, requiredlist, force=force)
-    if not os.path.exists(os.path.join(repodir, ".git")):
-        utils.fatal_error(
-            f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}"
-        )
-
-    if tmpurl:
-        print(git.git_operation("restore", ".gitmodules"))
-
-    return
-
-def add_remote(git, url):
-    remotes = git.git_operation("remote", "-v")
-    newremote = "newremote.00"
-    if url in remotes:
-        for line in remotes:
-            if url in line and "fetch" in line:
-                newremote = line.split()[0]
-                break
-    else:
-        i = 0
-        while "newremote" in remotes:
-            i = i + 1
-            newremote = f"newremote.{i:02d}"
-        git.git_operation("remote", "add", newremote, url)
-    return newremote
-
-def submodules_status(gitmodules, root_dir, toplevel=False):
-    testfails = 0
-    localmods = 0
-    needsupdate = 0
-    for name in gitmodules.sections():
-        path = gitmodules.get(name, "path")
-        tag = gitmodules.get(name, "fxtag")
-        url = gitmodules.get(name, "url")
-        required = gitmodules.get(name, "fxrequired")
-        level = required and "Toplevel" in required
-        if not path:
-            utils.fatal_error("No path found in .gitmodules for {}".format(name))
-        newpath = os.path.join(root_dir, path)
-        logger.debug("newpath is {}".format(newpath))
-        if not os.path.exists(os.path.join(newpath, ".git")):
-            rootgit = GitInterface(root_dir, logger)
-            # submodule commands use path, not name
-            url = url.replace("git@github.com:", "https://github.com/")
-            tags = rootgit.git_operation("ls-remote", "--tags", url)
-            result = rootgit.git_operation("submodule","status",newpath).split()
-            ahash = None
-            if result:
-                ahash = result[0][1:]
-            hhash = None
-            atag = None
-            
-            needsupdate += 1
-            if not toplevel and level:
-                continue
-            for htag in tags.split("\n"):
-                if htag.endswith('^{}'):
-                    htag = htag[:-3]
-                if ahash and not atag and ahash in htag:
-                    atag = (htag.split()[1])[10:]
-                if tag and not hhash and htag.endswith(tag):
-                    hhash = htag.split()[0]
-                if hhash and atag:
-                    break
-            optional = " (optional)" if required and "Optional" in required else ""
-            if tag and (ahash == hhash or atag == tag):
-                print(f"e {name:>20} not checked out, aligned at tag {tag}{optional}")
-            elif tag:
-                ahash = rootgit.git_operation(
-                    "submodule", "status", "{}".format(path)
-                ).rstrip()
-                ahash = ahash[1 : len(tag) + 1]
-                if tag == ahash:
-                    print(f"e {name:>20} not checked out, aligned at hash {ahash}{optional}")
-                else:
-                    print(
-                        f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}{optional}"
-                    )
-                    testfails += 1
-            else:
-                print(f"e {name:>20} has no fxtag defined in .gitmodules{optional}")
-                testfails += 1
-        else:
-            with utils.pushd(newpath):
-                git = GitInterface(newpath, logger)
-                atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                ahash =  git.git_operation("rev-list", "HEAD").partition("\n")[0]
-                rurl = git.git_operation("ls-remote","--get-url").rstrip()
-                if rurl != url:
-                    remote = add_remote(git, url)
-                    git.git_operation("fetch", remote)
-                if tag and atag == tag:
-                    print(f"  {name:>20} at tag {tag}")
-                elif tag and ahash[: len(tag)] == tag:
-                    print(f"  {name:>20} at hash {ahash}")
-                elif atag == ahash:
-                    print(f"  {name:>20} at hash {ahash}")
-                elif tag:
-                    print(
-                        f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}"
-                    )
-                    testfails += 1
-                    needsupdate += 1
-                else:
-                    print(
-                        f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}"
-                    )
-                    testfails += 1
-
-                status = git.git_operation("status", "--ignore-submodules", "-uno")
-                if "nothing to commit" not in status:
-                    localmods = localmods + 1
-                    print("M" + textwrap.indent(status, "                      "))
-
-    return testfails, localmods, needsupdate
-
-
-def submodules_update(gitmodules, root_dir, requiredlist, force):
-    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-
-    if localmods and not force:
-        local_mods_output()
-        return
-    if needsupdate == 0:
-        return
-
-    for name in gitmodules.sections():
-        fxtag = gitmodules.get(name, "fxtag")
-        path = gitmodules.get(name, "path")
-        url = gitmodules.get(name, "url")
-        logger.info(
-            "name={} path={} url={} fxtag={} requiredlist={} ".format(
-                name, os.path.join(root_dir, path), url, fxtag, requiredlist
-            )
-        )
-
-        fxrequired = gitmodules.get(name, "fxrequired")
-        assert fxrequired in fxrequired_allowed_values()
-        rgit = GitInterface(root_dir, logger)
-        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
-
-        fxsparse = gitmodules.get(name, "fxsparse")
-
-        if (
-            fxrequired
-            and (superroot and "Toplevel" in fxrequired)
-            or fxrequired not in requiredlist
-        ):
-            if "ToplevelOptional" == fxrequired:
-                print("Skipping optional component {}".format(name))
-            continue
-        if fxsparse:
-            logger.debug(
-                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
-                    root_dir, name, url, path, fxsparse, fxtag
-                )
-            )
-            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
-        else:
-            logger.info(
-                "Calling submodule_checkout({},{},{},{})".format(
-                    root_dir, name, path, url
-                )
-            )
-
-            single_submodule_checkout(
-                root_dir,
-                name,
-                path,
-                url=url,
-                tag=fxtag,
-                force=force,
-                optional=("AlwaysOptional" in requiredlist),
-            )
-
-        if os.path.exists(os.path.join(path, ".git")):
-            submoddir = os.path.join(root_dir, path)
-            with utils.pushd(submoddir):
-                git = GitInterface(submoddir, logger)
-                # first make sure the url is correct
-                upstream = git.git_operation("ls-remote", "--get-url").rstrip()
-                newremote = "origin"
-                if upstream != url:
-                    add_remote(git, url)
-
-                tags = git.git_operation("tag", "-l")
-                if fxtag and fxtag not in tags:
-                    git.git_operation("fetch", newremote, "--tags")
-                atag = git.git_operation("describe", "--tags", "--always").rstrip()
-                if fxtag and fxtag != atag:
-                    try:
-                        git.git_operation("checkout", fxtag)
-                        print(f"{name:>20} updated to {fxtag}")
-                    except Exception as error:
-                        print(error)
-                elif not fxtag:
-                    print(f"No fxtag found for submodule {name:>20}")
-                else:
-                    print(f"{name:>20} up to date.")
-
-
-
-
-def local_mods_output():
-    text = """\
-    The submodules labeled with 'M' above are not in a clean state.
-    The following are options for how to proceed:
-    (1) Go into each submodule which is not in a clean state and issue a 'git status'
-        Either revert or commit your changes so that the submodule is in a clean state.
-    (2) use the --force option to git-fleximod
-    (3) you can name the particular submodules to update using the git-fleximod command line
-    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
-        then rerun git-fleximod update.
-"""
-    print(text)
-
-
-# checkout is done by update if required so this function may be depricated
-def submodules_checkout(gitmodules, root_dir, requiredlist, force=False):
-    """
-    This function checks out all git submodules based on the provided parameters.
-
-    Parameters:
-    gitmodules (ConfigParser): The gitmodules configuration.
-    root_dir (str): The root directory for the git operation.
-    requiredlist (list): The list of required modules.
-    force (bool, optional): If set to True, forces the checkout operation. Defaults to False.
-
-    Returns:
-    None
-    """
-    # function implementation...
-    print("")
-    _, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-    if localmods and not force:
-        local_mods_output()
-        return
-    if not needsupdate:
-        return
-    for name in gitmodules.sections():
-        fxrequired = gitmodules.get(name, "fxrequired")
-        fxsparse = gitmodules.get(name, "fxsparse")
-        fxtag = gitmodules.get(name, "fxtag")
-        path = gitmodules.get(name, "path")
-        url = gitmodules.get(name, "url")
-        if fxrequired and fxrequired not in requiredlist:
-            if "Optional" in fxrequired:
-                print("Skipping optional component {}".format(name))
-            continue
-
-        if fxsparse:
-            logger.debug(
-                "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format(
-                    root_dir, name, url, path, fxsparse, fxtag
-                )
-            )
-            submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag)
-        else:
-            logger.debug(
-                "Calling submodule_checkout({},{},{})".format(root_dir, name, path)
-            )
-            single_submodule_checkout(
-                root_dir,
-                name,
-                path,
-                url=url,
-                tag=fxtag,
-                force=force,
-                optional="AlwaysOptional" in requiredlist,
-            )
-
-
-def submodules_test(gitmodules, root_dir):
-    """
-    This function tests the git submodules based on the provided parameters.
-
-    It first checks that fxtags are present and in sync with submodule hashes.
-    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
-    and that sparse checkout files exist.
-
-    Parameters:
-    gitmodules (ConfigParser): The gitmodules configuration.
-    root_dir (str): The root directory for the git operation.
-
-    Returns:
-    int: The number of test failures.
-    """
-    # First check that fxtags are present and in sync with submodule hashes
-    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
-    print("")
-    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
-    # and that sparse checkout files exist
-    for name in gitmodules.sections():
-        url = gitmodules.get(name, "url")
-        fxurl = gitmodules.get(name, "fxDONOTMODIFYurl")
-        fxsparse = gitmodules.get(name, "fxsparse")
-        path = gitmodules.get(name, "path")
-        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
-        url = url[:-4] if url.endswith(".git") else url
-        if not fxurl or url.lower() != fxurl.lower():
-            print(f"{name:>20} url {url} not in sync with required {fxurl}")
-            testfails += 1
-        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
-            print(f"{name:>20} sparse checkout file {fxsparse} not found")
-            testfails += 1
-    return testfails + localmods + needsupdate
-
-
-def main():
-    (
-        root_dir,
-        file_name,
-        fxrequired,
-        includelist,
-        excludelist,
-        force,
-        action,
-    ) = commandline_arguments()
-    # Get a logger for the package
-    global logger
-    logger = logging.getLogger(__name__)
-
-    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
-    
-    if not root_dir or not os.path.isfile(os.path.join(root_dir, file_name)):
-        if root_dir:
-            file_path = utils.find_upwards(root_dir, file_name)
-
-        if root_dir is None or file_path is None:
-            root_dir = "."
-            utils.fatal_error(
-                "No {} found in {} or any of it's parents".format(file_name, root_dir)
-            )
-
-        root_dir = os.path.dirname(file_path)
-    logger.info(
-        "root_dir is {} includelist={} excludelist={}".format(
-            root_dir, includelist, excludelist
-        )
-    )
-    gitmodules = GitModules(
-        logger,
-        confpath=root_dir,
-        conffile=file_name,
-        includelist=includelist,
-        excludelist=excludelist,
-    )
-    if not gitmodules.sections():
-        sys.exit("No submodule components found")
-    retval = 0
-    if action == "update":
-        submodules_update(gitmodules, root_dir, fxrequired, force)
-    elif action == "status":
-        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
-        if tfails + lmods + updates > 0:
-            print(
-                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
-            )
-            if lmods > 0:
-                local_mods_output()
-    elif action == "test":
-        retval = submodules_test(gitmodules, root_dir)
-    else:
-        utils.fatal_error(f"unrecognized action request {action}")
-    return retval
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py
deleted file mode 100644
index 93ae38ecde..0000000000
--- a/.lib/git-fleximod/git_fleximod/gitinterface.py
+++ /dev/null
@@ -1,79 +0,0 @@
-import os
-import sys
-from . import utils
-from pathlib import Path
-
-class GitInterface:
-    def __init__(self, repo_path, logger):
-        logger.debug("Initialize GitInterface for {}".format(repo_path))
-        if isinstance(repo_path, str):
-            self.repo_path = Path(repo_path).resolve()
-        elif isinstance(repo_path, Path):
-            self.repo_path = repo_path.resolve()
-        else:
-            raise TypeError("repo_path must be a str or Path object")
-        self.logger = logger
-        try:
-            import git
-
-            self._use_module = True
-            try:
-                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
-            except git.exc.InvalidGitRepositoryError:
-                self.git = git
-                self._init_git_repo()
-            msg = "Using GitPython interface to git"
-        except ImportError:
-            self._use_module = False
-            if not (self.repo_path / ".git").exists():
-                self._init_git_repo()
-            msg = "Using shell interface to git"
-        self.logger.info(msg)
-
-    def _git_command(self, operation, *args):
-        self.logger.info(operation)
-        if self._use_module and operation != "submodule":
-            try:
-                return getattr(self.repo.git, operation)(*args)
-            except Exception as e:
-                sys.exit(e)
-        else:
-            return ["git", "-C", str(self.repo_path), operation] + list(args)
-
-    def _init_git_repo(self):
-        if self._use_module:
-            self.repo = self.git.Repo.init(str(self.repo_path))
-        else:
-            command = ("git", "-C", str(self.repo_path), "init")
-            utils.execute_subprocess(command)
-
-    # pylint: disable=unused-argument
-    def git_operation(self, operation, *args, **kwargs):
-        command = self._git_command(operation, *args)
-        self.logger.info(command)
-        if isinstance(command, list):
-            try:
-                return utils.execute_subprocess(command, output_to_caller=True)
-            except Exception as e:
-                sys.exit(e)
-        else:
-            return command
-
-    def config_get_value(self, section, name):
-        if self._use_module:
-            config = self.repo.config_reader()
-            return config.get_value(section, name)
-        else:
-            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
-            output = utils.execute_subprocess(cmd, output_to_caller=True)
-            return output.strip()
-
-    def config_set_value(self, section, name, value):
-        if self._use_module:
-            with self.repo.config_writer() as writer:
-                writer.set_value(section, name, value)
-            writer.release()  # Ensure changes are saved
-        else:
-            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
-            self.logger.info(cmd)
-            utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/.lib/git-fleximod/git_fleximod/gitmodules.py b/.lib/git-fleximod/git_fleximod/gitmodules.py
deleted file mode 100644
index 7e4e05394a..0000000000
--- a/.lib/git-fleximod/git_fleximod/gitmodules.py
+++ /dev/null
@@ -1,97 +0,0 @@
-import shutil
-from pathlib import Path
-from configparser import RawConfigParser, ConfigParser
-from .lstripreader import LstripReader
-
-
-class GitModules(RawConfigParser):
-    def __init__(
-        self,
-        logger,
-        confpath=Path.cwd(),
-        conffile=".gitmodules",
-        includelist=None,
-        excludelist=None,
-    ):
-        """
-        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
-        conffile: Name of the configuration file (defaults to .gitmodules).
-        includelist: Optional list of submodules to include.
-        excludelist: Optional list of submodules to exclude.
-        """
-        self.logger = logger
-        self.logger.debug(
-            "Creating a GitModules object {} {} {} {}".format(
-                confpath, conffile, includelist, excludelist
-            )
-        )
-        super().__init__()
-        self.conf_file = (Path(confpath) / Path(conffile))
-        if self.conf_file.exists():
-            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
-        self.includelist = includelist
-        self.excludelist = excludelist
-        self.isdirty = False
-        
-    def reload(self):
-        self.clear()
-        if self.conf_file.exists():
-            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
-
-        
-    def set(self, name, option, value):
-        """
-        Sets a configuration value for a specific submodule:
-        Ensures the appropriate section exists for the submodule.
-        Calls the parent class's set method to store the value.
-        """
-        self.isdirty = True
-        self.logger.debug("set called {} {} {}".format(name, option, value))
-        section = f'submodule "{name}"'
-        if not self.has_section(section):
-            self.add_section(section)
-        super().set(section, option, str(value))
-
-    # pylint: disable=redefined-builtin, arguments-differ
-    def get(self, name, option, raw=False, vars=None, fallback=None):
-        """
-        Retrieves a configuration value for a specific submodule:
-        Uses the parent class's get method to access the value.
-        Handles potential errors if the section or option doesn't exist.
-        """
-        self.logger.debug("git get called {} {}".format(name, option))
-        section = f'submodule "{name}"'
-        try:
-            return ConfigParser.get(
-                self, section, option, raw=raw, vars=vars, fallback=fallback
-            )
-        except ConfigParser.NoOptionError:
-            return None
-
-    def save(self):
-        if self.isdirty:
-            self.logger.info("Writing {}".format(self.conf_file))
-            with open(self.conf_file, "w") as fd:
-                self.write(fd)
-        self.isdirty = False
-        
-    def __del__(self):
-        self.save()
-
-    def sections(self):
-        """Strip the submodule part out of section and just use the name"""
-        self.logger.debug("calling GitModules sections iterator")
-        names = []
-        for section in ConfigParser.sections(self):
-            name = section[11:-1]
-            if self.includelist and name not in self.includelist:
-                continue
-            if self.excludelist and name in self.excludelist:
-                continue
-            names.append(name)
-        return names
-
-    def items(self, name, raw=False, vars=None):
-        self.logger.debug("calling GitModules items for {}".format(name))
-        section = f'submodule "{name}"'
-        return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/.lib/git-fleximod/git_fleximod/lstripreader.py b/.lib/git-fleximod/git_fleximod/lstripreader.py
deleted file mode 100644
index 01d5580ee8..0000000000
--- a/.lib/git-fleximod/git_fleximod/lstripreader.py
+++ /dev/null
@@ -1,43 +0,0 @@
-class LstripReader(object):
-    "LstripReader formats .gitmodules files to be acceptable for configparser"
-
-    def __init__(self, filename):
-        with open(filename, "r") as infile:
-            lines = infile.readlines()
-        self._lines = list()
-        self._num_lines = len(lines)
-        self._index = 0
-        for line in lines:
-            self._lines.append(line.lstrip())
-
-    def readlines(self):
-        """Return all the lines from this object's file"""
-        return self._lines
-
-    def readline(self, size=-1):
-        """Format and return the next line or raise StopIteration"""
-        try:
-            line = self.next()
-        except StopIteration:
-            line = ""
-
-        if (size > 0) and (len(line) < size):
-            return line[0:size]
-
-        return line
-
-    def __iter__(self):
-        """Begin an iteration"""
-        self._index = 0
-        return self
-
-    def next(self):
-        """Return the next line or raise StopIteration"""
-        if self._index >= self._num_lines:
-            raise StopIteration
-
-        self._index = self._index + 1
-        return self._lines[self._index - 1]
-
-    def __next__(self):
-        return self.next()
diff --git a/.lib/git-fleximod/git_fleximod/metoflexi.py b/.lib/git-fleximod/git_fleximod/metoflexi.py
deleted file mode 100755
index cc347db2dd..0000000000
--- a/.lib/git-fleximod/git_fleximod/metoflexi.py
+++ /dev/null
@@ -1,236 +0,0 @@
-#!/usr/bin/env python
-from configparser import ConfigParser
-import sys
-import shutil
-from pathlib import Path
-import argparse
-import logging
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-from git_fleximod import utils
-
-logger = None
-
-def find_root_dir(filename=".git"):
-    d = Path.cwd()
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.is_dir():
-            return d
-        d = d.parent
-    return None
-
-
-def get_parser():
-    description = """
-    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
-    """
-    parser = argparse.ArgumentParser(
-        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-    )
-
-    parser.add_argument('-e', '--externals', nargs='?',
-                        default='Externals.cfg',
-                        help='The externals description filename. '
-                        'Default: %(default)s.')
-
-    parser.add_argument(
-        "-C",
-        "--path",
-        default=find_root_dir(),
-        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
-    )
-
-    parser.add_argument(
-        "-g",
-        "--gitmodules",
-        nargs="?",
-        default=".gitmodules",
-        help="The submodule description filename. " "Default: %(default)s.",
-    )
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        action="count",
-        default=0,
-        help="Output additional information to "
-        "the screen and log file. This flag can be "
-        "used up to two times, increasing the "
-        "verbosity level each time.",
-    )
-    parser.add_argument(
-        "-d",
-        "--debug",
-        action="store_true",
-        default=False,
-        help="DEVELOPER: output additional debugging "
-        "information to the screen and log file.",
-    )
-
-    return parser
-
-def commandline_arguments(args=None):
-    parser = get_parser()
-
-    options = parser.parse_args(args)
-    handlers = [logging.StreamHandler()]
-
-    if options.debug:
-        try:
-            open("fleximod.log", "w")
-        except PermissionError:
-            sys.exit("ABORT: Could not write file fleximod.log")
-        level = logging.DEBUG
-        handlers.append(logging.FileHandler("fleximod.log"))
-    elif options.verbose:
-        level = logging.INFO
-    else:
-        level = logging.WARNING
-    # Configure the root logger
-    logging.basicConfig(
-        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
-    )
-
-    return(
-        options.path,
-        options.gitmodules,
-        options.externals
-        )
-
-class ExternalRepoTranslator:
-    """
-    Translates external repositories configured in an INI-style externals file.
-    """
-
-    def __init__(self, rootpath, gitmodules, externals):
-        self.rootpath = rootpath
-        if gitmodules:
-            self.gitmodules = GitModules(logger, confpath=rootpath)
-        self.externals = (rootpath / Path(externals)).resolve()
-        print(f"Translating {self.externals}")
-        self.git = GitInterface(rootpath, logger)
-        
-#    def __del__(self):
-#        if (self.rootpath / "save.gitignore"):
-            
-
-    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
-        """
-        Translates a single repository based on configuration details.
-
-        Args:
-            rootpath (str): Root path of the main repository.
-            gitmodules (str): Path to the .gitmodules file.
-            tag (str): The tag to use for the external repository.
-            url (str): The URL of the external repository.
-            path (str): The relative path within the main repository for the external repository.
-            efile (str): The external file or file containing submodules.
-            hash_ (str): The commit hash to checkout (if applicable).
-            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
-            protocol (str): The protocol to use (e.g., 'git', 'http').
-        """
-        assert protocol != "svn", "SVN protocol is not currently supported"
-        print(f"Translating repository {section}")
-        if efile:
-            file_path = Path(path) / Path(efile)
-            newroot = (self.rootpath / file_path).parent.resolve()
-            if not newroot.exists():
-                newroot.mkdir(parents=True)
-            logger.info("Newroot is {}".format(newroot))
-            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
-            newt.translate_repo()
-        if protocol == "externals_only":
-            if tag:
-                self.gitmodules.set(section, "fxtag", tag)
-            if hash_:
-                self.gitmodules.set(section, "fxtag", hash_)
-            
-            self.gitmodules.set(section, "fxDONOTUSEurl", url)
-            if sparse:
-                self.gitmodules.set(section, "fxsparse", sparse)
-            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-        else:
-            newpath = (self.rootpath / Path(path))
-            if newpath.exists():
-                shutil.rmtree(newpath)
-                logger.info("Creating directory {}".format(newpath))
-            newpath.mkdir(parents=True)
-            if tag:
-                logger.info("cloning {}".format(section))
-                try:
-                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
-                except:
-                    self.git.git_operation("clone", url, path)
-                    with utils.pushd(newpath):
-                        ngit = GitInterface(newpath, logger)
-                        ngit.git_operation("checkout", tag)
-            if hash_:
-                self.git.git_operation("clone", url, path)
-                git = GitInterface(newpath, logger)
-                git.git_operation("fetch", "origin")
-                git.git_operation("checkout", hash_)
-            if sparse:
-                print("setting as sparse submodule {}".format(section))
-                sparsefile = (newpath / Path(sparse))
-                newfile = (newpath / ".git" / "info" / "sparse-checkout")
-                print(f"sparsefile {sparsefile} newfile {newfile}")
-                shutil.copy(sparsefile, newfile)
-        
-            logger.info("adding submodule {}".format(section))        
-            self.gitmodules.save()
-            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
-            self.git.git_operation("submodule","absorbgitdirs")
-            self.gitmodules.reload()
-            if tag:
-                self.gitmodules.set(section, "fxtag", tag)
-            if hash_:
-                self.gitmodules.set(section, "fxtag", hash_)
-            
-            self.gitmodules.set(section, "fxDONOTUSEurl", url)
-            if sparse:
-                self.gitmodules.set(section, "fxsparse", sparse)
-            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-    
-        
-    def translate_repo(self):
-        """
-        Translates external repositories defined within an external file.
-
-        Args:
-            rootpath (str): Root path of the main repository.
-            gitmodules (str): Path to the .gitmodules file.
-            external_file (str): The path to the external file containing repository definitions.
-        """
-        econfig = ConfigParser()
-        econfig.read((self.rootpath / Path(self.externals)))
-
-        for section in econfig.sections():
-            if section == "externals_description":
-                logger.info("skipping section {}".format(section))
-                return
-            logger.info("Translating section {}".format(section))
-            tag = econfig.get(section, "tag", raw=False, fallback=None)
-            url = econfig.get(section, "repo_url", raw=False, fallback=None)
-            path = econfig.get(section, "local_path", raw=False, fallback=None)
-            efile = econfig.get(section, "externals", raw=False, fallback=None)
-            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
-            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
-            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
-
-            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
-
-
-
-def _main():
-    rootpath, gitmodules, externals = commandline_arguments()
-    global logger
-    logger = logging.getLogger(__name__)
-    with utils.pushd(rootpath):
-        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
-        logger.info("Translating {}".format(rootpath))
-        t.translate_repo()
-
-        
-if __name__ == "__main__":
-    sys.exit(_main())
diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
deleted file mode 100644
index 1a2d5ccf2f..0000000000
--- a/.lib/git-fleximod/git_fleximod/utils.py
+++ /dev/null
@@ -1,365 +0,0 @@
-#!/usr/bin/env python3
-"""
-Common public utilities for manic package
-
-"""
-
-import logging
-import os
-import subprocess
-import sys
-from threading import Timer
-from pathlib import Path
-
-LOCAL_PATH_INDICATOR = "."
-# ---------------------------------------------------------------------
-#
-# functions to massage text for output and other useful utilities
-#
-# ---------------------------------------------------------------------
-from contextlib import contextmanager
-
-
-@contextmanager
-def pushd(new_dir):
-    """context for chdir. usage: with pushd(new_dir)"""
-    previous_dir = os.getcwd()
-    os.chdir(new_dir)
-    try:
-        yield
-    finally:
-        os.chdir(previous_dir)
-
-
-def log_process_output(output):
-    """Log each line of process output at debug level so it can be
-    filtered if necessary. By default, output is a single string, and
-    logging.debug(output) will only put log info heading on the first
-    line. This makes it hard to filter with grep.
-
-    """
-    output = output.split("\n")
-    for line in output:
-        logging.debug(line)
-
-
-def printlog(msg, **kwargs):
-    """Wrapper script around print to ensure that everything printed to
-    the screen also gets logged.
-
-    """
-    logging.info(msg)
-    if kwargs:
-        print(msg, **kwargs)
-    else:
-        print(msg)
-    sys.stdout.flush()
-
-
-def find_upwards(root_dir, filename):
-    """Find a file in root dir or any of it's parents"""
-    d = Path(root_dir)
-    root = Path(d.root)
-    while d != root:
-        attempt = d / filename
-        if attempt.exists():
-            return attempt
-        d = d.parent
-    return None
-
-
-def last_n_lines(the_string, n_lines, truncation_message=None):
-    """Returns the last n lines of the given string
-
-    Args:
-        the_string: str
-        n_lines: int
-        truncation_message: str, optional
-
-    Returns a string containing the last n lines of the_string
-
-    If truncation_message is provided, the returned string begins with
-    the given message if and only if the string is greater than n lines
-    to begin with.
-    """
-
-    lines = the_string.splitlines(True)
-    if len(lines) <= n_lines:
-        return_val = the_string
-    else:
-        lines_subset = lines[-n_lines:]
-        str_truncated = "".join(lines_subset)
-        if truncation_message:
-            str_truncated = truncation_message + "\n" + str_truncated
-        return_val = str_truncated
-
-    return return_val
-
-
-def indent_string(the_string, indent_level):
-    """Indents the given string by a given number of spaces
-
-    Args:
-       the_string: str
-       indent_level: int
-
-    Returns a new string that is the same as the_string, except that
-    each line is indented by 'indent_level' spaces.
-
-    In python3, this can be done with textwrap.indent.
-    """
-
-    lines = the_string.splitlines(True)
-    padding = " " * indent_level
-    lines_indented = [padding + line for line in lines]
-    return "".join(lines_indented)
-
-
-# ---------------------------------------------------------------------
-#
-# error handling
-#
-# ---------------------------------------------------------------------
-
-
-def fatal_error(message):
-    """
-    Error output function
-    """
-    logging.error(message)
-    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
-
-
-# ---------------------------------------------------------------------
-#
-# Data conversion / manipulation
-#
-# ---------------------------------------------------------------------
-def str_to_bool(bool_str):
-    """Convert a sting representation of as boolean into a true boolean.
-
-    Conversion should be case insensitive.
-    """
-    value = None
-    str_lower = bool_str.lower()
-    if str_lower in ("true", "t"):
-        value = True
-    elif str_lower in ("false", "f"):
-        value = False
-    if value is None:
-        msg = (
-            'ERROR: invalid boolean string value "{0}". '
-            'Must be "true" or "false"'.format(bool_str)
-        )
-        fatal_error(msg)
-    return value
-
-
-REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
-
-
-def is_remote_url(url):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    """
-    remote_url = False
-    for prefix in REMOTE_PREFIXES:
-        if url.startswith(prefix):
-            remote_url = True
-    return remote_url
-
-
-def split_remote_url(url):
-    """check if the user provided a local file path or a
-    remote. If remote, try to strip off protocol info.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        return url
-
-    for prefix in REMOTE_PREFIXES:
-        url = url.replace(prefix, "")
-
-    if "@" in url:
-        url = url.split("@")[1]
-
-    if ":" in url:
-        url = url.split(":")[1]
-
-    return url
-
-
-def expand_local_url(url, field):
-    """check if the user provided a local file path instead of a
-    remote. If so, it must be expanded to an absolute
-    path.
-
-    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
-    represent local copy only, don't work with the remotes.
-
-    """
-    remote_url = is_remote_url(url)
-    if not remote_url:
-        if url.strip() == LOCAL_PATH_INDICATOR:
-            pass
-        else:
-            url = os.path.expandvars(url)
-            url = os.path.expanduser(url)
-            if not os.path.isabs(url):
-                msg = (
-                    'WARNING: Externals description for "{0}" contains a '
-                    "url that is not remote and does not expand to an "
-                    "absolute path. Version control operations may "
-                    "fail.\n\nurl={1}".format(field, url)
-                )
-                printlog(msg)
-            else:
-                url = os.path.normpath(url)
-    return url
-
-
-# ---------------------------------------------------------------------
-#
-# subprocess
-#
-# ---------------------------------------------------------------------
-
-# Give the user a helpful message if we detect that a command seems to
-# be hanging.
-_HANGING_SEC = 300
-
-
-def _hanging_msg(working_directory, command):
-    print(
-        """
-
-Command '{command}'
-from directory {working_directory}
-has taken {hanging_sec} seconds. It may be hanging.
-
-The command will continue to run, but you may want to abort
-git-fleximod with ^C and investigate. A possible cause of hangs is git
-requires authentication to access a private repository. On some
-systems, git requests for authentication information will not
-be displayed to the user. In this case, the program will appear to
-hang. Ensure you can run git manually and access all
-repositories without entering your authentication information.
-
-""".format(
-            command=command,
-            working_directory=working_directory,
-            hanging_sec=_HANGING_SEC,
-        )
-    )
-
-
-def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
-    """Wrapper around subprocess.check_output to handle common
-    exceptions.
-
-    check_output runs a command with arguments and waits
-    for it to complete.
-
-    check_output raises an exception on a nonzero return code.  if
-    status_to_caller is true, execute_subprocess returns the subprocess
-    return code, otherwise execute_subprocess treats non-zero return
-    status as an error and raises an exception.
-
-    """
-    cwd = os.getcwd()
-    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
-    logging.info(msg)
-    commands_str = " ".join(str(element) for element in commands)
-    logging.info(commands_str)
-    return_to_caller = status_to_caller or output_to_caller
-    status = -1
-    output = ""
-    hanging_timer = Timer(
-        _HANGING_SEC,
-        _hanging_msg,
-        kwargs={"working_directory": cwd, "command": commands_str},
-    )
-    hanging_timer.start()
-    try:
-        output = subprocess.check_output(
-            commands, stderr=subprocess.STDOUT, universal_newlines=True
-        )
-        log_process_output(output)
-        status = 0
-    except OSError as error:
-        msg = failed_command_msg(
-            "Command execution failed. Does the executable exist?", commands
-        )
-        logging.error(error)
-        fatal_error(msg)
-    except ValueError as error:
-        msg = failed_command_msg(
-            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
-        )
-        logging.error(error)
-        fatal_error(msg)
-    except subprocess.CalledProcessError as error:
-        # Only report the error if we are NOT returning to the
-        # caller. If we are returning to the caller, then it may be a
-        # simple status check. If returning, it is the callers
-        # responsibility determine if an error occurred and handle it
-        # appropriately.
-        if not return_to_caller:
-            msg_context = (
-                "Process did not run successfully; "
-                "returned status {0}".format(error.returncode)
-            )
-            msg = failed_command_msg(msg_context, commands, output=error.output)
-            logging.error(error)
-            logging.error(msg)
-            log_process_output(error.output)
-            fatal_error(msg)
-        status = error.returncode
-    finally:
-        hanging_timer.cancel()
-
-    if status_to_caller and output_to_caller:
-        ret_value = (status, output)
-    elif status_to_caller:
-        ret_value = status
-    elif output_to_caller:
-        ret_value = output
-    else:
-        ret_value = None
-
-    return ret_value
-
-
-def failed_command_msg(msg_context, command, output=None):
-    """Template for consistent error messages from subprocess calls.
-
-    If 'output' is given, it should provide the output from the failed
-    command
-    """
-
-    if output:
-        output_truncated = last_n_lines(
-            output, 20, truncation_message="[... Output truncated for brevity ...]"
-        )
-        errmsg = (
-            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
-        )
-    else:
-        errmsg = ""
-
-    command_str = " ".join(command)
-    errmsg += """In directory
-    {cwd}
-{context}:
-    {command}
-""".format(
-        cwd=os.getcwd(), context=msg_context, command=command_str
-    )
-
-    if output:
-        errmsg += "See above for output from failed command.\n"
-
-    return errmsg
diff --git a/.lib/git-fleximod/poetry.lock b/.lib/git-fleximod/poetry.lock
deleted file mode 100644
index b59ed3942c..0000000000
--- a/.lib/git-fleximod/poetry.lock
+++ /dev/null
@@ -1,693 +0,0 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
-
-[[package]]
-name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
-]
-
-[[package]]
-name = "babel"
-version = "2.14.0"
-description = "Internationalization utilities"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
-    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
-]
-
-[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
-
-[package.extras]
-dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
-
-[[package]]
-name = "certifi"
-version = "2024.2.2"
-description = "Python package for providing Mozilla's CA Bundle."
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
-    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
-]
-
-[[package]]
-name = "charset-normalizer"
-version = "3.3.2"
-description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-optional = false
-python-versions = ">=3.7.0"
-files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9063e24fdb1e498ab71cb7419e24622516c4a04476b17a2dab57e8baa30d6e03"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6897af51655e3691ff853668779c7bad41579facacf5fd7253b0133308cf000d"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1d3193f4a680c64b4b6a9115943538edb896edc190f0b222e73761716519268e"},
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-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a9a8e9031d613fd2009c182b69c7b2c1ef8239a0efb1df3f7c8da66d5dd3d537"},
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-    {file = "charset_normalizer-3.3.2-cp310-cp310-win32.whl", hash = "sha256:3d47fa203a7bd9c5b6cee4736ee84ca03b8ef23193c0d1ca99b5089f72645c73"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-win_amd64.whl", hash = "sha256:10955842570876604d404661fbccbc9c7e684caf432c09c715ec38fbae45ae09"},
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-    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
-]
-
-[[package]]
-name = "requests"
-version = "2.31.0"
-description = "Python HTTP for Humans."
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
-    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
-]
-
-[package.dependencies]
-certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<4"
-idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<3"
-
-[package.extras]
-socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
-
-[[package]]
-name = "smmap"
-version = "5.0.1"
-description = "A pure Python implementation of a sliding window memory map manager"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "smmap-5.0.1-py3-none-any.whl", hash = "sha256:e6d8668fa5f93e706934a62d7b4db19c8d9eb8cf2adbb75ef1b675aa332b69da"},
-    {file = "smmap-5.0.1.tar.gz", hash = "sha256:dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62"},
-]
-
-[[package]]
-name = "snowballstemmer"
-version = "2.2.0"
-description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-optional = false
-python-versions = "*"
-files = [
-    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
-    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
-]
-
-[[package]]
-name = "sphinx"
-version = "5.3.0"
-description = "Python documentation generator"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "Sphinx-5.3.0.tar.gz", hash = "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"},
-    {file = "sphinx-5.3.0-py3-none-any.whl", hash = "sha256:060ca5c9f7ba57a08a1219e547b269fadf125ae25b06b9fa7f66768efb652d6d"},
-]
-
-[package.dependencies]
-alabaster = ">=0.7,<0.8"
-babel = ">=2.9"
-colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.14,<0.20"
-imagesize = ">=1.3"
-importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
-Jinja2 = ">=3.0"
-packaging = ">=21.0"
-Pygments = ">=2.12"
-requests = ">=2.5.0"
-snowballstemmer = ">=2.0"
-sphinxcontrib-applehelp = "*"
-sphinxcontrib-devhelp = "*"
-sphinxcontrib-htmlhelp = ">=2.0.0"
-sphinxcontrib-jsmath = "*"
-sphinxcontrib-qthelp = "*"
-sphinxcontrib-serializinghtml = ">=1.1.5"
-
-[package.extras]
-docs = ["sphinxcontrib-websupport"]
-lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
-test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
-
-[[package]]
-name = "sphinxcontrib-applehelp"
-version = "1.0.4"
-description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
-    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "sphinxcontrib-devhelp"
-version = "1.0.2"
-description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
-    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "sphinxcontrib-htmlhelp"
-version = "2.0.1"
-description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
-    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["html5lib", "pytest"]
-
-[[package]]
-name = "sphinxcontrib-jsmath"
-version = "1.0.1"
-description = "A sphinx extension which renders display math in HTML via JavaScript"
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
-    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
-]
-
-[package.extras]
-test = ["flake8", "mypy", "pytest"]
-
-[[package]]
-name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
-    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
-    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
-]
-
-[package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
-
-[[package]]
-name = "tomli"
-version = "2.0.1"
-description = "A lil' TOML parser"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
-]
-
-[[package]]
-name = "urllib3"
-version = "2.2.0"
-description = "HTTP library with thread-safe connection pooling, file post, and more."
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "urllib3-2.2.0-py3-none-any.whl", hash = "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"},
-    {file = "urllib3-2.2.0.tar.gz", hash = "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20"},
-]
-
-[package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
-h2 = ["h2 (>=4,<5)"]
-socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-zstd = ["zstandard (>=0.18.0)"]
-
-[[package]]
-name = "wheel"
-version = "0.42.0"
-description = "A built-package format for Python"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "wheel-0.42.0-py3-none-any.whl", hash = "sha256:177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d"},
-    {file = "wheel-0.42.0.tar.gz", hash = "sha256:c45be39f7882c9d34243236f2d63cbd58039e360f85d0913425fbd7ceea617a8"},
-]
-
-[package.extras]
-test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
-
-[[package]]
-name = "zipp"
-version = "3.17.0"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
-
-[metadata]
-lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
deleted file mode 100644
index 5b1332549c..0000000000
--- a/.lib/git-fleximod/pyproject.toml
+++ /dev/null
@@ -1,41 +0,0 @@
-[tool.poetry]
-name = "git-fleximod"
-version = "0.7.8"
-description = "Extended support for git-submodule and git-sparse-checkout"
-authors = ["Jim Edwards <jedwards@ucar.edu>"]
-maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
-license = "MIT"
-readme = "README.md"
-homepage = "https://github.com/jedwards4b/git-fleximod"
-keywords = ["git", "submodule", "sparse-checkout"]
-packages = [
-{ include = "git_fleximod"},
-{ include = "doc"},
-]
-
-[tool.poetry.scripts]
-git-fleximod = "git_fleximod.git_fleximod:main"
-me2flexi = "git_fleximod.metoflexi:_main"
-fsspec = "fsspec.fuse:main"
-
-[tool.poetry.dependencies]
-python = "^3.8"
-GitPython = "^3.1.0"
-sphinx = "^5.0.0"
-fsspec = "^2023.12.2"
-wheel = "^0.42.0"
-pytest = "^8.0.0"
-pyfakefs = "^5.3.5"
-
-[tool.poetry.urls]
-"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
-
-[tool.pytest.ini_options]
-markers = [
-        "skip_after_first: only run on first iteration"
-]
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
deleted file mode 100644
index c4f7ac96ea..0000000000
--- a/.lib/git-fleximod/tbump.toml
+++ /dev/null
@@ -1,43 +0,0 @@
-# Uncomment this if your project is hosted on GitHub:
-github_url = "https://github.com/jedwards4b/git-fleximod/"
-
-[version]
-current = "0.7.8"
-
-# Example of a semver regexp.
-# Make sure this matches current_version before
-# using tbump
-regex = '''
-  (?P<major>\d+)
-  \.
-  (?P<minor>\d+)
-  \.
-  (?P<patch>\d+)
-  '''
-
-[git]
-message_template = "Bump to {new_version}"
-tag_template = "v{new_version}"
-
-# For each file to patch, add a [[file]] config
-# section containing the path of the file, relative to the
-# tbump.toml location.
-[[file]]
-src = "git_fleximod/cli.py"
-
-[[file]]
-src = "pyproject.toml"
-
-# You can specify a list of commands to
-# run after the files have been patched
-# and before the git commit is made
-
-#  [[before_commit]]
-#  name = "check changelog"
-#  cmd = "grep -q {new_version} Changelog.rst"
-
-# Or run some commands after the git tag and the branch
-# have been pushed:
-#  [[after_push]]
-#  name = "publish"
-#  cmd = "./publish.sh"
diff --git a/.lib/git-fleximod/tests/__init__.py b/.lib/git-fleximod/tests/__init__.py
deleted file mode 100644
index 4d4c66c78e..0000000000
--- a/.lib/git-fleximod/tests/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-import sys, os
-
-sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py
deleted file mode 100644
index 65ee85d23d..0000000000
--- a/.lib/git-fleximod/tests/conftest.py
+++ /dev/null
@@ -1,138 +0,0 @@
-import pytest 
-from git_fleximod.gitinterface import GitInterface
-import os
-import subprocess
-import logging
-from pathlib import Path
-
-@pytest.fixture(scope='session')
-def logger():
-    logging.basicConfig(
-        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
-    )
-    logger = logging.getLogger(__name__)
-    return logger
-
-all_repos=[
-    {"subrepo_path": "modules/test",
-     "submodule_name": "test_submodule",
-     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_submodule at tag MPIserial_2.4.0",
-     "status3" : "test_submodule at tag MPIserial_2.4.0",
-     "status4" : "test_submodule at tag MPIserial_2.4.0",
-     "gitmodules_content" : """
-    [submodule "test_submodule"]
-    path = modules/test
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.4.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelRequired
-"""},
-    {"subrepo_path": "modules/test_optional",
-     "submodule_name": "test_optional",
-     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0 (optional)",
-     "status4" : "test_optional at tag MPIserial_2.4.0",
-     "gitmodules_content": """
-     [submodule "test_optional"]
-    path = modules/test_optional
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.4.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = ToplevelOptional
-"""},
-    {"subrepo_path": "modules/test_alwaysoptional",
-     "submodule_name": "test_alwaysoptional",
-     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
-     "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "out of sync at tag None, expected tag is e5cf35c",
-     "status4" : "test_alwaysoptional at hash e5cf35c",
-     "gitmodules_content": """
-    [submodule "test_alwaysoptional"]
-    path = modules/test_alwaysoptional
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = e5cf35c
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = AlwaysOptional
-"""},    
-    {"subrepo_path": "modules/test_sparse",
-     "submodule_name": "test_sparse",
-     "status1" : "test_sparse at tag MPIserial_2.5.0",
-     "status2" : "test_sparse at tag MPIserial_2.5.0",
-     "status3" : "test_sparse at tag MPIserial_2.5.0",
-     "status4" : "test_sparse at tag MPIserial_2.5.0",
-     "gitmodules_content": """
-    [submodule "test_sparse"]
-    path = modules/test_sparse
-    url = https://github.com/ESMCI/mpi-serial.git
-    fxtag = MPIserial_2.5.0
-    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
-    fxrequired = AlwaysRequired
-    fxsparse = ../.sparse_file_list
-"""},
-]
-@pytest.fixture(params=all_repos)
-
-def shared_repos(request):
-    return request.param
-
-@pytest.fixture
-def get_all_repos():
-    return all_repos
-
-def write_sparse_checkout_file(fp):
-    sparse_content = """m4
-"""
-    fp.write_text(sparse_content)
-
-@pytest.fixture
-def test_repo(shared_repos, tmp_path, logger):
-    subrepo_path = shared_repos["subrepo_path"]
-    submodule_name = shared_repos["submodule_name"]
-    test_dir = tmp_path / "testrepo"
-    test_dir.mkdir()
-    str_path = str(test_dir)
-    gitp = GitInterface(str_path, logger)
-    assert test_dir.joinpath(".git").is_dir()
-    (test_dir / "modules").mkdir()
-    if "sparse" in submodule_name:
-        (test_dir / subrepo_path).mkdir()
-        # Add the sparse checkout file
-        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
-        gitp.git_operation("add","modules/.sparse_file_list")
-    else:
-        gitp = GitInterface(str(test_dir), logger)
-        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
-        assert test_dir.joinpath(".gitmodules").is_file()
-        gitp.git_operation("add",subrepo_path)
-    gitp.git_operation("commit","-a","-m","\"add submod\"")
-    test_dir2 = tmp_path / "testrepo2"
-    gitp.git_operation("clone",test_dir,test_dir2)
-    return test_dir2    
-
-
-@pytest.fixture
-def complex_repo(tmp_path, logger):
-    test_dir = tmp_path / "testcomplex"
-    test_dir.mkdir()
-    str_path = str(test_dir)
-    gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
-    gitp.git_operation("fetch", "origin", "main")
-    gitp.git_operation("checkout", "main")
-    return test_dir
-    
-@pytest.fixture
-def git_fleximod():
-    def _run_fleximod(path, args, input=None):
-        cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=path, input=input, 
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
-                                text=True)
-        if result.returncode:
-            print(result.stdout)
-            print(result.stderr)
-        return result
-    return _run_fleximod
-
diff --git a/.lib/git-fleximod/tests/test_a_import.py b/.lib/git-fleximod/tests/test_a_import.py
deleted file mode 100644
index d5ca878de5..0000000000
--- a/.lib/git-fleximod/tests/test_a_import.py
+++ /dev/null
@@ -1,8 +0,0 @@
-# pylint: disable=unused-import
-from git_fleximod import cli
-from git_fleximod import utils
-from git_fleximod.gitinterface import GitInterface
-from git_fleximod.gitmodules import GitModules
-
-def test_import():
-    print("here")
diff --git a/.lib/git-fleximod/tests/test_b_update.py b/.lib/git-fleximod/tests/test_b_update.py
deleted file mode 100644
index 159f1cfae0..0000000000
--- a/.lib/git-fleximod/tests/test_b_update.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import pytest
-from pathlib import Path
-                
-def test_basic_checkout(git_fleximod, test_repo, shared_repos):
-    # Prepare a simple .gitmodules
-    gm = shared_repos['gitmodules_content']
-    file_path = (test_repo / ".gitmodules")
-    repo_name = shared_repos["submodule_name"]
-    repo_path = shared_repos["subrepo_path"]
-
-    file_path.write_text(gm)
-    
-    # Run the command
-    result = git_fleximod(test_repo, f"update {repo_name}")
-
-    # Assertions
-    assert result.returncode == 0 
-    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
-    if "sparse" in repo_name:
-        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
-        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
-    
-    status = git_fleximod(test_repo, f"status {repo_name}")
-        
-    assert shared_repos["status2"] in status.stdout
-        
diff --git a/.lib/git-fleximod/tests/test_c_required.py b/.lib/git-fleximod/tests/test_c_required.py
deleted file mode 100644
index 89ab8d294d..0000000000
--- a/.lib/git-fleximod/tests/test_c_required.py
+++ /dev/null
@@ -1,30 +0,0 @@
-import pytest
-from pathlib import Path
-                
-def test_required(git_fleximod, test_repo, shared_repos):
-    file_path = (test_repo / ".gitmodules")
-    gm = shared_repos["gitmodules_content"]
-    repo_name = shared_repos["submodule_name"]
-    if file_path.exists():
-        with file_path.open("r") as f:
-            gitmodules_content = f.read()
-            # add the entry if it does not exist
-            if repo_name not in gitmodules_content:
-                file_path.write_text(gitmodules_content+gm)
-            # or if it is incomplete
-            elif gm not in gitmodules_content:
-                file_path.write_text(gm)
-    else:
-        file_path.write_text(gm)
-    result = git_fleximod(test_repo, "update")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status3"] in status.stdout
-    status = git_fleximod(test_repo, f"update --optional")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
-    status = git_fleximod(test_repo, f"update {repo_name}")
-    assert result.returncode == 0
-    status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
diff --git a/.lib/git-fleximod/tests/test_d_complex.py b/.lib/git-fleximod/tests/test_d_complex.py
deleted file mode 100644
index edde7d816d..0000000000
--- a/.lib/git-fleximod/tests/test_d_complex.py
+++ /dev/null
@@ -1,66 +0,0 @@
-import pytest
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
-
-def test_complex_checkout(git_fleximod, complex_repo, logger):
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, aligned at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
-    
-    # This should checkout and update test_submodule and complex_sub
-    result = git_fleximod(complex_repo, "update")    
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
-
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex")
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
-    # update a single optional submodule
-
-    result = git_fleximod(complex_repo, "update ToplevelOptional")
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
-
-    # Finally update optional
-    result = git_fleximod(complex_repo, "update --optional")
-    assert result.returncode == 0
-
-    status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
-    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
-    
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex" )
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
-

From 14043a8c5aa7b0d3c163dcf3d5c32043087234c9 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 25 Sep 2024 09:04:04 -0600
Subject: [PATCH 1132/1248] Squashed '.lib/git-fleximod/' content from commit
 02e859950

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 02e859950fd79064ad5b64565ce1073bea5d3ffa
---
 .github/workflows/pre-commit   |  13 +
 .github/workflows/pytest.yaml  |  80 ++++
 .pre-commit-config.yaml        |  18 +
 CODE_OF_CONDUCT.md             | 107 +++++
 License                        |  20 +
 README.md                      | 108 +++++
 doc/Makefile                   |  20 +
 doc/conf.py                    |  26 ++
 doc/index.rst                  |  24 ++
 doc/make.bat                   |  35 ++
 escomp_install                 |  25 ++
 git_fleximod/__init__.py       |   0
 git_fleximod/cli.py            | 129 ++++++
 git_fleximod/git_fleximod.py   | 365 +++++++++++++++++
 git_fleximod/gitinterface.py   |  92 +++++
 git_fleximod/gitmodules.py     |  97 +++++
 git_fleximod/lstripreader.py   |  43 ++
 git_fleximod/metoflexi.py      | 236 +++++++++++
 git_fleximod/submodule.py      | 427 ++++++++++++++++++++
 git_fleximod/utils.py          | 365 +++++++++++++++++
 poetry.lock                    | 693 +++++++++++++++++++++++++++++++++
 pyproject.toml                 |  41 ++
 tbump.toml                     |  43 ++
 tests/__init__.py              |   3 +
 tests/conftest.py              | 150 +++++++
 tests/test_a_import.py         |   8 +
 tests/test_b_update.py         |  26 ++
 tests/test_c_required.py       |  30 ++
 tests/test_d_complex.py        |  66 ++++
 tests/test_e_complex_update.py |  69 ++++
 30 files changed, 3359 insertions(+)
 create mode 100644 .github/workflows/pre-commit
 create mode 100644 .github/workflows/pytest.yaml
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 CODE_OF_CONDUCT.md
 create mode 100644 License
 create mode 100644 README.md
 create mode 100644 doc/Makefile
 create mode 100644 doc/conf.py
 create mode 100644 doc/index.rst
 create mode 100644 doc/make.bat
 create mode 100644 escomp_install
 create mode 100644 git_fleximod/__init__.py
 create mode 100644 git_fleximod/cli.py
 create mode 100755 git_fleximod/git_fleximod.py
 create mode 100644 git_fleximod/gitinterface.py
 create mode 100644 git_fleximod/gitmodules.py
 create mode 100644 git_fleximod/lstripreader.py
 create mode 100755 git_fleximod/metoflexi.py
 create mode 100644 git_fleximod/submodule.py
 create mode 100644 git_fleximod/utils.py
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 create mode 100644 tbump.toml
 create mode 100644 tests/__init__.py
 create mode 100644 tests/conftest.py
 create mode 100644 tests/test_a_import.py
 create mode 100644 tests/test_b_update.py
 create mode 100644 tests/test_c_required.py
 create mode 100644 tests/test_d_complex.py
 create mode 100644 tests/test_e_complex_update.py

diff --git a/.github/workflows/pre-commit b/.github/workflows/pre-commit
new file mode 100644
index 0000000000..1a6ad0082a
--- /dev/null
+++ b/.github/workflows/pre-commit
@@ -0,0 +1,13 @@
+name: pre-commit
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
new file mode 100644
index 0000000000..6cb8102b94
--- /dev/null
+++ b/.github/workflows/pytest.yaml
@@ -0,0 +1,80 @@
+# Run this job on pushes to `main`, and for pull requests. If you don't specify
+# `branches: [main], then this actions runs _twice_ on pull requests, which is
+# annoying.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
+      # reference the matrixe python version here.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
+      # from installing Poetry every time, which can be slow. Note the use of the Poetry version
+      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
+      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
+      # mildly cleaner by using an environment variable, but I don't really care.
+      - name: cache poetry install
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: poetry-1.8.2
+
+      # Install Poetry. You could do this manually, or there are several actions that do this.
+      # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
+      # Poetry's default install script, which feels correct. I pin the Poetry version here
+      # because Poetry does occasionally change APIs between versions and I don't want my
+      # actions to break if it does.
+      #
+      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
+      # venv as a `.venv` in your testing directory, which allows the next step to easily
+      # cache it.
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.8.2
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
+      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
+      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
+      - name: cache deps
+        id: cache-deps
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+
+      # Install dependencies. `--no-root` means "install all dependencies but not the project
+      # itself", which is what you want to avoid caching _your_ code. The `if` statement
+      # ensures this only runs on a cache miss.
+      - run: poetry install --no-interaction --no-root
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+
+      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
+      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
+      # pyproject.toml and makes that if you add things like console-scripts at some point that
+      # they'll be installed and working.
+      - run: poetry install --no-interaction
+
+      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
+      # so this line is super-simple. But it could be as complex as you need.
+      - run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+          poetry run pytest
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
+
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000..2f6089da72
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+exclude: ^utils/.*$
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/pylint
+    rev: v2.11.1
+    hooks:
+      - id: pylint
+        args:
+          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
new file mode 100644
index 0000000000..84f2925bba
--- /dev/null
+++ b/CODE_OF_CONDUCT.md
@@ -0,0 +1,107 @@
+# Contributor Code of Conduct
+_The Contributor Code of Conduct is for participants in our software projects and community._
+
+## Our Pledge
+We, as contributors, creators, stewards, and maintainers (participants), of **git-fleximod** pledge to make participation in
+our software, system or hardware project and community a safe, productive, welcoming and inclusive experience for everyone.
+All participants are required to abide by this Code of Conduct.
+This includes respectful treatment of everyone regardless of age, body size, disability, ethnicity, gender identity or expression,
+level of experience, nationality, political affiliation, veteran status, pregnancy, genetic information, physical appearance, race,
+religion, or sexual orientation, as well as any other characteristic protected under applicable US federal or state law.
+
+## Our Standards
+Examples of behaviors that contribute to a positive environment include:
+
+* All participants are treated with respect and consideration, valuing a diversity of views and opinions
+* Be considerate, respectful, and collaborative
+* Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism
+* Acknowledging the contributions of others
+* Avoid personal attacks directed toward other participants
+* Be mindful of your surroundings and of your fellow participants 
+* Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress
+* Respect the rules and policies of the project and venue
+
+Examples of unacceptable behavior include, but are not limited to:
+
+* Harassment, intimidation, or discrimination in any form
+* Physical, verbal, or written abuse by anyone to anyone, including repeated use of pronouns other than those requested
+* Unwelcome sexual attention or advances
+* Personal attacks directed at other guests, members, participants, etc.
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Alarming, intimidating, threatening, or hostile comments or conduct
+* Inappropriate use of nudity and/or sexual images 
+* Threatening or stalking anyone, including a participant
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Scope
+This Code of Conduct applies to all spaces managed by the Project whether they be physical, online or face-to-face.
+This includes project code, code repository, associated web pages, documentation, mailing lists, project websites and wiki pages,
+issue tracker, meetings, telecons, events, project social media accounts, and any other forums created by the project team which the
+community uses for communication.
+In addition, violations of this Code of Conduct outside these spaces may affect a person's ability to participate within them.
+Representation of a project may be further defined and clarified by project maintainers.
+
+## Community Responsibilities
+Everyone in the community is empowered to respond to people who are showing unacceptable behavior.
+They can talk to them privately or publicly.
+Anyone requested to stop unacceptable behavior is expected to comply immediately.
+If the behavior continues concerns may be brought to the project administrators or to any other party listed in the
+[Reporting](#reporting) section below.
+
+## Project Administrator Responsibilities
+Project administrators are responsible for clarifying the standards of acceptable behavior and are encouraged to model appropriate
+behavior and provide support when people in the community point out inappropriate behavior.
+Project administrator(s) are normally the ones that would be tasked to carry out the actions in the [Consequences](#consequences)
+section below.
+
+Project administrators are also expected to keep this Code of Conduct updated with the main one housed at UCAR, as listed below in
+the [Attribution](#attribution) section.
+
+## Reporting
+Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as
+outlined in the [Consequences](#consequences) section below.
+However, making a report to a project administrator is not considered an 'official report' to UCAR. 
+
+Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint
+Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's
+EthicsPoint Hotline](https://www2.fin.ucar.edu/ethics/anonymous-reporting).
+
+Complaints received by UCAR will be handled pursuant to the procedures outlined in UCAR's Harassment Reporting and Complaint
+Procedure.
+Complaints to UCAR will be held as confidential as practicable under the circumstances, and retaliation against a person who
+initiates a complaint or an inquiry about inappropriate behavior will not be tolerated.
+
+Any Contributor can use these reporting methods even if they are not directly affiliated with UCAR.
+The Frequently Asked Questions (FAQ) page for reporting is [here](https://www2.fin.ucar.edu/procedures/hr/reporting-faqs).
+
+## Consequences
+Upon receipt of a complaint, the project administrator(s) may take any action deemed necessary and appropriate under the
+circumstances.
+Such action can include things such as: removing, editing, or rejecting comments, commits, code, wiki edits, email, issues, and
+other contributions that are not aligned to this Code of Conduct, or banning temporarily or permanently any contributor for other
+behaviors that are deemed inappropriate, threatening, offensive, or harmful.
+Project administrators also have the right to report violations to UCAR HR and/or UCAR's Office of Diversity, Equity and Inclusion
+(ODEI), as well as a participant's home institution and/or law enforcement.
+In the event an incident is reported to UCAR, UCAR will follow its Harassment Reporting and Complaint Procedure.
+
+## Process for Changes
+All UCAR managed projects are required to adopt this Contributor Code of Conduct.
+Adoption is assumed even if not expressly stated in the repository.
+Projects should fill in sections where prompted with project-specific information, including, project name and adoption date.
+
+Projects that adopt this Code of Conduct need to stay up to date with UCAR's Contributor Code of Conduct, linked with a DOI in the
+[Attribution](#attribution) section below.
+Projects can make limited substantive changes to the Code of Conduct, however, the changes must be limited in scope and may not
+contradict the UCAR Contributor Code of Conduct.
+
+## Attribution
+This Code of Conduct was originally adapted from the [Contributor Covenant](http://contributor-covenant.org/version/1/4), version
+1.4.
+We then aligned it with the UCAR Participant Code of Conduct, which also borrows from the American Geophysical Union (AGU) Code of
+Conduct.
+The UCAR Participant Code of Conduct applies to both UCAR employees as well as participants in activities run by UCAR.
+The original version of this for all software projects that have strong management from UCAR or UCAR staff is available on the UCAR
+website at https://doi.org/10.5065/6w2c-a132.
+The date that it was adopted by this project was **Feb/13/2018**.
+When responding to complaints, UCAR HR and ODEI will do so based on the latest published version.
+Therefore, any project-specific changes should follow the [Process for Changes](#process-for-changes) section above.
diff --git a/License b/License
new file mode 100644
index 0000000000..88bc22515e
--- /dev/null
+++ b/License
@@ -0,0 +1,20 @@
+Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+“Software”), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000..53917da400
--- /dev/null
+++ b/README.md
@@ -0,0 +1,108 @@
+# git-fleximod
+
+Flexible, Enhanced Submodule Management for Git
+
+## Overview
+
+Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way.
+
+## Installation
+
+  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
+
+## Usage
+
+    Basic Usage:
+        git fleximod <command> [options]
+    Available Commands:
+        status: Display the status of submodules.
+        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
+        test: Make sure that fxtags and submodule hashes are consistant,
+              make sure that official urls (as defined by fxDONOTUSEurl) are set
+              make sure that fxtags are defined for all submodules
+    Additional Options:
+        See git fleximod --help for more details.
+
+## Supported .gitmodules Variables
+
+    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxrequired: Mark a submodule's checkout behavior, with allowed values:
+      - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
+      - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - AlwaysRequired:       Always required (always checked out).
+      - AlwaysOptional:       Always optional (checked out with --optional flag).
+    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
+    fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
+           **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be
+           changed by users.  Use the url variable to change to a fork if desired.
+
+## Sparse Checkouts
+
+    To enable sparse checkout for a submodule, set the fxsparse variable
+    in the .gitmodules file to the path of a file containing the desired
+    sparse checkout paths. Git-fleximod will automatically configure
+    sparse checkout based on this file when applicable commands are run.
+    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
+    for details on the format of this file.
+
+## Tests
+
+   The git fleximod test action is designed to be used by, for example, github workflows
+   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
+
+## Examples
+
+Here are some common usage examples:
+
+Update all submodules, including optional ones:
+```bash
+  git fleximod update --optional
+```
+
+Updating a specific submodule to the fxtag indicated in .gitmodules:
+
+```bash
+    git fleximod update submodule-name
+```
+Example .gitmodules entry:
+```ini, toml
+    [submodule "cosp2"]
+        path = src/physics/cosp2/src
+        url = https://github.com/CFMIP/COSPv2.0
+        fxsparse = ../.cosp_sparse_checkout
+        fxrequired = AlwaysRequired
+        fxtag = v2.1.4cesm
+```
+Explanation:
+
+This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
+should be checked out into the directory src/physics/cosp2/src
+relative to the .gitmodules directory.  It should be checked out from
+the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
+described in the file ../.cosp_sparse_checkout relative to the path
+directory.  It should be checked out anytime this .gitmodules entry is
+read.
+
+Additional example:
+```ini, toml
+    [submodule "cime"]
+        path = cime
+        url = https://github.com/jedwards4b/cime
+        fxrequired = ToplevelRequired
+        fxtag = cime6.0.198_rme01
+```
+
+Explanation:
+
+This entry indicates that the submodule cime should be checked out
+into a directory named cime at tag cime6.0.198_rme01 from the URL
+https://github.com/jedwards4b/cime.  This should only be done if
+the .gitmodules file is at the top level of the repository clone.
+
+## Contributing
+
+We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
+
+## License
+
+Git-fleximod is released under the MIT License.
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000000..d4bb2cbb9e
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000000..423099eec9
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,26 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "git-fleximod"
+author = "Jim Edwards <jedwards@ucar.edu>"
+release = "0.4.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx_argparse_cli"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000000..0f9c1a7f7e
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,24 @@
+.. git-fleximod documentation master file, created by
+   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to git-fleximod's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+.. module:: sphinxcontrib.autoprogram
+.. sphinx_argparse_cli::
+   :module: git_fleximod.cli
+   :func: get_parser
+   :prog: git-fleximod
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/doc/make.bat b/doc/make.bat
new file mode 100644
index 0000000000..32bb24529f
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/escomp_install b/escomp_install
new file mode 100644
index 0000000000..ae782e72a4
--- /dev/null
+++ b/escomp_install
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# updates git-fleximod in an ESCOMP model
+# this script should be run from the model root directory, it expects
+# git-fleximod to already be installed with the script in bin
+# and the classes in lib/python/site-packages
+import sys
+import shutil
+import os
+
+from glob import iglob
+
+fleximod_root = sys.argv[1]
+fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
+if os.path.isfile(fleximod_path):
+   with open(fleximod_path,"r") as f:
+        fleximod = f.readlines()
+   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
+        for line in fleximod:
+            f.write(line)
+            if "import argparse" in line:
+               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
+
+   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
+       shutil.copy(file,
+        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))
diff --git a/git_fleximod/__init__.py b/git_fleximod/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
new file mode 100644
index 0000000000..208bc04684
--- /dev/null
+++ b/git_fleximod/cli.py
@@ -0,0 +1,129 @@
+from pathlib import Path
+import argparse
+from git_fleximod import utils
+
+__version__ = "0.9.2"
+
+def find_root_dir(filename=".gitmodules"):
+    """ finds the highest directory in tree
+    which contains a file called filename """
+    d = Path.cwd()
+    root = Path(d.root)
+    dirlist = []
+    dl = d
+    while dl != root:
+        dirlist.append(dl)
+        dl = dl.parent
+    dirlist.append(root)
+    dirlist.reverse()
+
+    for dl in dirlist:
+        attempt = dl / filename
+        if attempt.is_file():
+            return str(dl)
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    #
+    # user options
+    #
+    choices = ["update", "status", "test"]
+    parser.add_argument(
+        "action",
+        choices=choices,
+        default="update",
+        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
+    )
+
+    parser.add_argument(
+        "components",
+        nargs="*",
+        help="Specific component(s) to checkout. By default, "
+        "all required submodules are checked out.",
+    )
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--exclude",
+        nargs="*",
+        help="Component(s) listed in the gitmodules file which should be ignored.",
+    )
+    parser.add_argument(
+        "-f",
+        "--force",
+        action="store_true",
+        default=False,
+        help="Override cautions and update or checkout over locally modified repository.",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--optional",
+        action="store_true",
+        default=False,
+        help="By default only the required submodules "
+        "are checked out. This flag will also checkout the "
+        "optional submodules relative to the toplevel directory.",
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+
+    parser.add_argument(
+        "-V",
+        "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Print version and exit.",
+    )
+
+    #
+    # developer options
+    #
+    parser.add_argument(
+        "--backtrace",
+        action="store_true",
+        help="DEVELOPER: show exception backtraces as extra " "debugging output",
+    )
+
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
new file mode 100755
index 0000000000..0851e9d095
--- /dev/null
+++ b/git_fleximod/git_fleximod.py
@@ -0,0 +1,365 @@
+#!/usr/bin/env python
+import sys
+
+MIN_PYTHON = (3, 7)
+if sys.version_info < MIN_PYTHON:
+    sys.exit("Python %s.%s or later is required." % MIN_PYTHON)
+
+import os
+import shutil
+import logging
+import textwrap
+from git_fleximod import utils
+from git_fleximod import cli
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from git_fleximod.submodule import Submodule
+
+# logger variable is global
+logger = None
+
+
+def fxrequired_allowed_values():
+    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional", "TopLevelRequired", "TopLevelOptional"]
+
+
+def commandline_arguments(args=None):
+    parser = cli.get_parser()
+
+    if args:
+        options = parser.parse_args(args)
+    else:
+        options = parser.parse_args()
+
+    # explicitly listing a component overrides the optional flag
+    if options.optional or options.components:
+        fxrequired = fxrequired_allowed_values()
+    else:
+        fxrequired = ["ToplevelRequired", "AlwaysRequired", "TopLevelRequired"]
+
+    action = options.action
+    if not action:
+        action = "update"
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    if hasattr(options, "version"):
+        exit()
+
+    return (
+        options.path,
+        options.gitmodules,
+        fxrequired,
+        options.components,
+        options.exclude,
+        options.force,
+        action,
+    )
+
+
+def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"):
+    """
+    This function performs a sparse checkout of a git submodule.  It does so by first creating the .git/info/sparse-checkout fileq
+    in the submodule and then checking out the desired tag.  If the submodule is already checked out, it will not be checked out again.
+    Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed.  This is important
+    because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time
+    and disk space consuming.
+
+    Parameters:
+    root_dir (str): The root directory for the git operation.
+    name (str): The name of the submodule.
+    url (str): The URL of the submodule.
+    path (str): The path to the submodule.
+    sparsefile (str): The sparse file for the submodule.
+    tag (str, optional): The tag to checkout. Defaults to "master".
+
+    Returns:
+    None
+    """
+    logger.info("Called sparse_checkout for {}".format(name))
+    rgit = GitInterface(root_dir, logger)
+    superroot = git_toplevelroot(root_dir, logger)
+
+    if superroot:
+        gitroot = superroot.strip()
+    else:
+        gitroot = root_dir.strip()
+    assert os.path.isdir(os.path.join(gitroot, ".git"))
+    # first create the module directory
+    if not os.path.isdir(os.path.join(root_dir, path)):
+        os.makedirs(os.path.join(root_dir, path))
+
+    # initialize a new git repo and set the sparse checkout flag
+    sprep_repo = os.path.join(root_dir, path)
+    sprepo_git = GitInterface(sprep_repo, logger)
+    if os.path.exists(os.path.join(sprep_repo, ".git")):
+        try:
+            logger.info("Submodule {} found".format(name))
+            chk = sprepo_git.config_get_value("core", "sparseCheckout")
+            if chk == "true":
+                logger.info("Sparse submodule {} already checked out".format(name))
+                return
+        except NoOptionError:
+            logger.debug("Sparse submodule {} not present".format(name))
+        except Exception as e:
+            utils.fatal_error("Unexpected error {} occured.".format(e))
+
+    sprepo_git.config_set_value("core", "sparseCheckout", "true")
+
+    # set the repository remote
+
+    logger.info("Setting remote origin in {}/{}".format(root_dir, path))
+    _, remotelist = sprepo_git.git_operation("remote", "-v")
+    if url not in remotelist:
+        sprepo_git.git_operation("remote", "add", "origin", url)
+
+    topgit = os.path.join(gitroot, ".git")
+
+    if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")):
+        with open(os.path.join(root_dir, ".git")) as f:
+            gitpath = os.path.relpath(
+                os.path.join(root_dir, f.read().split()[1]),
+                start=os.path.join(root_dir, path),
+            )
+        topgit = os.path.join(gitpath, "modules")
+    else:
+        topgit = os.path.relpath(
+            os.path.join(root_dir, ".git", "modules"),
+            start=os.path.join(root_dir, path),
+        )
+
+    with utils.pushd(sprep_repo):
+        if not os.path.isdir(topgit):
+            os.makedirs(topgit)
+    topgit += os.sep + name
+
+    if os.path.isdir(os.path.join(root_dir, path, ".git")):
+        with utils.pushd(sprep_repo):
+            if os.path.isdir(os.path.join(topgit,".git")):
+                shutil.rmtree(os.path.join(topgit,".git"))
+            shutil.move(".git", topgit)
+            with open(".git", "w") as f:
+                f.write("gitdir: " + os.path.relpath(topgit))
+            #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
+            gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
+        if os.path.isfile(gitsparse):
+            logger.warning(
+                "submodule {} is already initialized {}".format(name, topgit)
+            )
+            return
+
+        with utils.pushd(sprep_repo):
+            if os.path.isfile(sparsefile):
+                shutil.copy(sparsefile, gitsparse)
+                
+
+    # Finally checkout the repo
+    sprepo_git.git_operation("fetch", "origin", "--tags")
+    sprepo_git.git_operation("checkout", tag)
+
+    print(f"Successfully checked out {name:>20} at {tag}")
+    rgit.config_set_value(f'submodule "{name}"', "active", "true")
+    rgit.config_set_value(f'submodule "{name}"', "url", url)
+
+def init_submodule_from_gitmodules(gitmodules, name, root_dir, logger):
+    path = gitmodules.get(name, "path")
+    url = gitmodules.get(name, "url")
+    assert path and url, f"Malformed .gitmodules file {path} {url}"
+    tag = gitmodules.get(name, "fxtag")
+    fxurl = gitmodules.get(name, "fxDONOTUSEurl")
+    fxsparse = gitmodules.get(name, "fxsparse")
+    fxrequired = gitmodules.get(name, "fxrequired")
+    return Submodule(root_dir, name, path, url, fxtag=tag, fxurl=fxurl, fxsparse=fxsparse, fxrequired=fxrequired, logger=logger)
+
+def submodules_status(gitmodules, root_dir, toplevel=False, depth=0):
+    testfails = 0
+    localmods = 0
+    needsupdate = 0
+    wrapper = textwrap.TextWrapper(initial_indent=' '*(depth*10), width=120,subsequent_indent=' '*(depth*20))
+    for name in gitmodules.sections():
+        submod = init_submodule_from_gitmodules(gitmodules, name, root_dir, logger)
+            
+        result,n,l,t = submod.status()
+        if toplevel or not submod.toplevel():
+            print(wrapper.fill(result))
+            testfails += t
+            localmods += l
+            needsupdate += n
+        subdir = os.path.join(root_dir, submod.path)
+        if os.path.exists(os.path.join(subdir, ".gitmodules")):
+            gsubmod = GitModules(logger, confpath=subdir)
+            t,l,n = submodules_status(gsubmod, subdir, depth=depth+1)
+            if toplevel or not submod.toplevel():
+                testfails += t
+                localmods += l
+                needsupdate += n
+            
+    return testfails, localmods, needsupdate
+
+def git_toplevelroot(root_dir, logger):
+    rgit = GitInterface(root_dir, logger)
+    _, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+    return superroot
+
+def submodules_update(gitmodules, root_dir, requiredlist, force):
+    for name in gitmodules.sections():
+        submod = init_submodule_from_gitmodules(gitmodules, name, root_dir, logger)
+    
+        _, needsupdate, localmods, testfails = submod.status()
+        if not submod.fxrequired:
+            submod.fxrequired = "AlwaysRequired"
+        fxrequired = submod.fxrequired    
+        allowedvalues = fxrequired_allowed_values()
+        assert fxrequired in allowedvalues
+
+        superroot = git_toplevelroot(root_dir, logger)
+                                     
+        if (
+            fxrequired
+            and ((superroot and "Toplevel" in fxrequired)
+            or fxrequired not in requiredlist)
+        ):
+            if "Optional" in fxrequired and "Optional" not in requiredlist:
+                if fxrequired.startswith("Always"):
+                    print(f"Skipping optional component {name:>20}")
+                continue
+        optional = "AlwaysOptional" in requiredlist
+
+        if fxrequired in requiredlist:
+            submod.update()
+            repodir = os.path.join(root_dir, submod.path)
+            if os.path.exists(os.path.join(repodir, ".gitmodules")):
+                # recursively handle this checkout
+                print(f"Recursively checking out submodules of {name}")
+                gitsubmodules = GitModules(submod.logger, confpath=repodir)
+                newrequiredlist = ["AlwaysRequired"]
+                if optional:
+                    newrequiredlist.append("AlwaysOptional")
+
+                submodules_update(gitsubmodules, repodir, newrequiredlist, force=force)
+
+def local_mods_output():
+    text = """\
+    The submodules labeled with 'M' above are not in a clean state.
+    The following are options for how to proceed:
+    (1) Go into each submodule which is not in a clean state and issue a 'git status'
+        Either revert or commit your changes so that the submodule is in a clean state.
+    (2) use the --force option to git-fleximod
+    (3) you can name the particular submodules to update using the git-fleximod command line
+    (4) As a last resort you can remove the submodule (via 'rm -fr [directory]')
+        then rerun git-fleximod update.
+"""
+    print(text)
+
+def submodules_test(gitmodules, root_dir):
+    """
+    This function tests the git submodules based on the provided parameters.
+
+    It first checks that fxtags are present and in sync with submodule hashes.
+    Then it ensures that urls are consistent with fxurls (not forks and not ssh)
+    and that sparse checkout files exist.
+
+    Parameters:
+    gitmodules (ConfigParser): The gitmodules configuration.
+    root_dir (str): The root directory for the git operation.
+
+    Returns:
+    int: The number of test failures.
+    """
+    # First check that fxtags are present and in sync with submodule hashes
+    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    print("")
+    # Then make sure that urls are consistant with fxurls (not forks and not ssh)
+    # and that sparse checkout files exist
+    for name in gitmodules.sections():
+        url = gitmodules.get(name, "url")
+        fxurl = gitmodules.get(name, "fxDONOTUSEurl")
+        fxsparse = gitmodules.get(name, "fxsparse")
+        path = gitmodules.get(name, "path")
+        fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl
+        url = url[:-4] if url.endswith(".git") else url
+        if not fxurl or url.lower() != fxurl.lower():
+            print(f"{name:>20} url {url} not in sync with required {fxurl}")
+            testfails += 1
+        if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)):
+            print(f"{name:>20} sparse checkout file {fxsparse} not found")
+            testfails += 1
+    return testfails + localmods + needsupdate
+
+
+def main():
+    (
+        root_dir,
+        file_name,
+        fxrequired,
+        includelist,
+        excludelist,
+        force,
+        action,
+    ) = commandline_arguments()
+    # Get a logger for the package
+    global logger
+    logger = logging.getLogger(__name__)
+
+    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
+    
+    if not root_dir or not os.path.isfile(os.path.join(root_dir, file_name)):
+        if root_dir:
+            file_path = utils.find_upwards(root_dir, file_name)
+
+        if root_dir is None or file_path is None:
+            root_dir = "."
+            utils.fatal_error(
+                "No {} found in {} or any of it's parents".format(file_name, root_dir)
+            )
+
+        root_dir = os.path.dirname(file_path)
+    logger.info(
+        "root_dir is {} includelist={} excludelist={}".format(
+            root_dir, includelist, excludelist
+        )
+    )
+    gitmodules = GitModules(
+        logger,
+        confpath=root_dir,
+        conffile=file_name,
+        includelist=includelist,
+        excludelist=excludelist,
+    )
+    if not gitmodules.sections():
+        sys.exit("No submodule components found")
+    retval = 0
+    if action == "update":
+        submodules_update(gitmodules, root_dir, fxrequired, force)
+    elif action == "status":
+        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
+        if tfails + lmods + updates > 0:
+            print(
+                f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
+            )
+            if lmods > 0:
+                local_mods_output()
+    elif action == "test":
+        retval = submodules_test(gitmodules, root_dir)
+    else:
+        utils.fatal_error(f"unrecognized action request {action}")
+    return retval
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py
new file mode 100644
index 0000000000..fb20883cd0
--- /dev/null
+++ b/git_fleximod/gitinterface.py
@@ -0,0 +1,92 @@
+import os
+import sys
+from . import utils
+from pathlib import Path
+
+class GitInterface:
+    def __init__(self, repo_path, logger):
+        logger.debug("Initialize GitInterface for {}".format(repo_path))
+        if isinstance(repo_path, str):
+            self.repo_path = Path(repo_path).resolve()
+        elif isinstance(repo_path, Path):
+            self.repo_path = repo_path.resolve()
+        else:
+            raise TypeError("repo_path must be a str or Path object")
+        self.logger = logger
+        try:
+            import git
+
+            self._use_module = True
+            try:
+                self.repo = git.Repo(str(self.repo_path))  # Initialize GitPython repo
+            except git.exc.InvalidGitRepositoryError:
+                self.git = git
+                self._init_git_repo()
+            msg = "Using GitPython interface to git"
+        except ImportError:
+            self._use_module = False
+            if not (self.repo_path / ".git").exists():
+                self._init_git_repo()
+            msg = "Using shell interface to git"
+        self.logger.info(msg)
+
+    def _git_command(self, operation, *args):
+        self.logger.info(operation)
+        if self._use_module and operation != "submodule":
+            try:
+                return getattr(self.repo.git, operation)(*args)
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return ["git", "-C", str(self.repo_path), operation] + list(args)
+
+    def _init_git_repo(self):
+        if self._use_module:
+            self.repo = self.git.Repo.init(str(self.repo_path))
+        else:
+            command = ("git", "-C", str(self.repo_path), "init")
+            utils.execute_subprocess(command)
+
+    # pylint: disable=unused-argument
+    def git_operation(self, operation, *args, **kwargs):
+        newargs = []
+        for a in args:
+            # Do not use ssh interface
+            if isinstance(a, str):
+                a = a.replace("git@github.com:", "https://github.com/")
+            newargs.append(a)
+
+        command = self._git_command(operation, *newargs)
+        if isinstance(command, list):
+            try:
+                status, output = utils.execute_subprocess(command, status_to_caller=True, output_to_caller=True)
+                return status, output.rstrip()
+            except Exception as e:
+                sys.exit(e)
+        else:
+            return 0, command
+
+    def config_get_value(self, section, name):
+        if self._use_module:
+            config = self.repo.config_reader()
+            try:
+                val = config.get_value(section, name)
+            except:
+                val = None
+            return val
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
+            output = utils.execute_subprocess(cmd, output_to_caller=True)
+            return output.strip()
+
+    def config_set_value(self, section, name, value):
+        if self._use_module:
+            with self.repo.config_writer() as writer:
+                if "." in section:  
+                    section = section.replace("."," \"")+'"'           
+                writer.set_value(section, name, value)
+            writer.release()  # Ensure changes are saved
+        else:
+            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
+            self.logger.info(cmd)
+            utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py
new file mode 100644
index 0000000000..cf8b350dd6
--- /dev/null
+++ b/git_fleximod/gitmodules.py
@@ -0,0 +1,97 @@
+import shutil, os
+from pathlib import Path
+from configparser import RawConfigParser, ConfigParser
+from .lstripreader import LstripReader
+
+
+class GitModules(RawConfigParser):
+    def __init__(
+        self,
+        logger,
+        confpath=Path.cwd(),
+        conffile=".gitmodules",
+        includelist=None,
+        excludelist=None,
+    ):
+        """
+        confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory).
+        conffile: Name of the configuration file (defaults to .gitmodules).
+        includelist: Optional list of submodules to include.
+        excludelist: Optional list of submodules to exclude.
+        """
+        self.logger = logger
+        self.logger.debug(
+            "Creating a GitModules object {} {} {} {}".format(
+                confpath, conffile, includelist, excludelist
+            )
+        )
+        super().__init__()
+        self.conf_file = (Path(confpath) / Path(conffile))
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=conffile)
+        self.includelist = includelist
+        self.excludelist = excludelist
+        self.isdirty = False
+        
+    def reload(self):
+        self.clear()
+        if self.conf_file.exists():
+            self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
+
+        
+    def set(self, name, option, value):
+        """
+        Sets a configuration value for a specific submodule:
+        Ensures the appropriate section exists for the submodule.
+        Calls the parent class's set method to store the value.
+        """
+        self.isdirty = True
+        self.logger.debug("set called {} {} {}".format(name, option, value))
+        section = f'submodule "{name}"'
+        if not self.has_section(section):
+            self.add_section(section)
+        super().set(section, option, str(value))
+
+    # pylint: disable=redefined-builtin, arguments-differ
+    def get(self, name, option, raw=False, vars=None, fallback=None):
+        """
+        Retrieves a configuration value for a specific submodule:
+        Uses the parent class's get method to access the value.
+        Handles potential errors if the section or option doesn't exist.
+        """
+        self.logger.debug("git get called {} {}".format(name, option))
+        section = f'submodule "{name}"'
+        try:
+            return ConfigParser.get(
+                self, section, option, raw=raw, vars=vars, fallback=fallback
+            )
+        except ConfigParser.NoOptionError:
+            return None
+
+    def save(self):
+        if self.isdirty:
+            self.logger.info("Writing {}".format(self.conf_file))
+            with open(self.conf_file, "w") as fd:
+                self.write(fd)
+        self.isdirty = False
+        
+    def __del__(self):
+        self.save()
+
+    def sections(self):
+        """Strip the submodule part out of section and just use the name"""
+        self.logger.debug("calling GitModules sections iterator")
+        names = []
+        for section in ConfigParser.sections(self):
+            name = section[11:-1]
+            if self.includelist and name not in self.includelist:
+                continue
+            if self.excludelist and name in self.excludelist:
+                continue
+            names.append(name)
+        return names
+
+    def items(self, name, raw=False, vars=None):
+        self.logger.debug("calling GitModules items for {}".format(name))
+        section = f'submodule "{name}"'
+        return ConfigParser.items(section, raw=raw, vars=vars)
diff --git a/git_fleximod/lstripreader.py b/git_fleximod/lstripreader.py
new file mode 100644
index 0000000000..01d5580ee8
--- /dev/null
+++ b/git_fleximod/lstripreader.py
@@ -0,0 +1,43 @@
+class LstripReader(object):
+    "LstripReader formats .gitmodules files to be acceptable for configparser"
+
+    def __init__(self, filename):
+        with open(filename, "r") as infile:
+            lines = infile.readlines()
+        self._lines = list()
+        self._num_lines = len(lines)
+        self._index = 0
+        for line in lines:
+            self._lines.append(line.lstrip())
+
+    def readlines(self):
+        """Return all the lines from this object's file"""
+        return self._lines
+
+    def readline(self, size=-1):
+        """Format and return the next line or raise StopIteration"""
+        try:
+            line = self.next()
+        except StopIteration:
+            line = ""
+
+        if (size > 0) and (len(line) < size):
+            return line[0:size]
+
+        return line
+
+    def __iter__(self):
+        """Begin an iteration"""
+        self._index = 0
+        return self
+
+    def next(self):
+        """Return the next line or raise StopIteration"""
+        if self._index >= self._num_lines:
+            raise StopIteration
+
+        self._index = self._index + 1
+        return self._lines[self._index - 1]
+
+    def __next__(self):
+        return self.next()
diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
new file mode 100755
index 0000000000..cc347db2dd
--- /dev/null
+++ b/git_fleximod/metoflexi.py
@@ -0,0 +1,236 @@
+#!/usr/bin/env python
+from configparser import ConfigParser
+import sys
+import shutil
+from pathlib import Path
+import argparse
+import logging
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+from git_fleximod import utils
+
+logger = None
+
+def find_root_dir(filename=".git"):
+    d = Path.cwd()
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.is_dir():
+            return d
+        d = d.parent
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    parser.add_argument('-e', '--externals', nargs='?',
+                        default='Externals.cfg',
+                        help='The externals description filename. '
+                        'Default: %(default)s.')
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser
+
+def commandline_arguments(args=None):
+    parser = get_parser()
+
+    options = parser.parse_args(args)
+    handlers = [logging.StreamHandler()]
+
+    if options.debug:
+        try:
+            open("fleximod.log", "w")
+        except PermissionError:
+            sys.exit("ABORT: Could not write file fleximod.log")
+        level = logging.DEBUG
+        handlers.append(logging.FileHandler("fleximod.log"))
+    elif options.verbose:
+        level = logging.INFO
+    else:
+        level = logging.WARNING
+    # Configure the root logger
+    logging.basicConfig(
+        level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
+    )
+
+    return(
+        options.path,
+        options.gitmodules,
+        options.externals
+        )
+
+class ExternalRepoTranslator:
+    """
+    Translates external repositories configured in an INI-style externals file.
+    """
+
+    def __init__(self, rootpath, gitmodules, externals):
+        self.rootpath = rootpath
+        if gitmodules:
+            self.gitmodules = GitModules(logger, confpath=rootpath)
+        self.externals = (rootpath / Path(externals)).resolve()
+        print(f"Translating {self.externals}")
+        self.git = GitInterface(rootpath, logger)
+        
+#    def __del__(self):
+#        if (self.rootpath / "save.gitignore"):
+            
+
+    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
+        """
+        Translates a single repository based on configuration details.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            tag (str): The tag to use for the external repository.
+            url (str): The URL of the external repository.
+            path (str): The relative path within the main repository for the external repository.
+            efile (str): The external file or file containing submodules.
+            hash_ (str): The commit hash to checkout (if applicable).
+            sparse (str):  Boolean indicating whether to use sparse checkout (if applicable).
+            protocol (str): The protocol to use (e.g., 'git', 'http').
+        """
+        assert protocol != "svn", "SVN protocol is not currently supported"
+        print(f"Translating repository {section}")
+        if efile:
+            file_path = Path(path) / Path(efile)
+            newroot = (self.rootpath / file_path).parent.resolve()
+            if not newroot.exists():
+                newroot.mkdir(parents=True)
+            logger.info("Newroot is {}".format(newroot))
+            newt = ExternalRepoTranslator(newroot, ".gitmodules", efile)
+            newt.translate_repo()
+        if protocol == "externals_only":
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+        else:
+            newpath = (self.rootpath / Path(path))
+            if newpath.exists():
+                shutil.rmtree(newpath)
+                logger.info("Creating directory {}".format(newpath))
+            newpath.mkdir(parents=True)
+            if tag:
+                logger.info("cloning {}".format(section))
+                try:
+                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+                except:
+                    self.git.git_operation("clone", url, path)
+                    with utils.pushd(newpath):
+                        ngit = GitInterface(newpath, logger)
+                        ngit.git_operation("checkout", tag)
+            if hash_:
+                self.git.git_operation("clone", url, path)
+                git = GitInterface(newpath, logger)
+                git.git_operation("fetch", "origin")
+                git.git_operation("checkout", hash_)
+            if sparse:
+                print("setting as sparse submodule {}".format(section))
+                sparsefile = (newpath / Path(sparse))
+                newfile = (newpath / ".git" / "info" / "sparse-checkout")
+                print(f"sparsefile {sparsefile} newfile {newfile}")
+                shutil.copy(sparsefile, newfile)
+        
+            logger.info("adding submodule {}".format(section))        
+            self.gitmodules.save()
+            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
+            self.git.git_operation("submodule","absorbgitdirs")
+            self.gitmodules.reload()
+            if tag:
+                self.gitmodules.set(section, "fxtag", tag)
+            if hash_:
+                self.gitmodules.set(section, "fxtag", hash_)
+            
+            self.gitmodules.set(section, "fxDONOTUSEurl", url)
+            if sparse:
+                self.gitmodules.set(section, "fxsparse", sparse)
+            self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
+    
+        
+    def translate_repo(self):
+        """
+        Translates external repositories defined within an external file.
+
+        Args:
+            rootpath (str): Root path of the main repository.
+            gitmodules (str): Path to the .gitmodules file.
+            external_file (str): The path to the external file containing repository definitions.
+        """
+        econfig = ConfigParser()
+        econfig.read((self.rootpath / Path(self.externals)))
+
+        for section in econfig.sections():
+            if section == "externals_description":
+                logger.info("skipping section {}".format(section))
+                return
+            logger.info("Translating section {}".format(section))
+            tag = econfig.get(section, "tag", raw=False, fallback=None)
+            url = econfig.get(section, "repo_url", raw=False, fallback=None)
+            path = econfig.get(section, "local_path", raw=False, fallback=None)
+            efile = econfig.get(section, "externals", raw=False, fallback=None)
+            hash_ = econfig.get(section, "hash", raw=False, fallback=None)
+            sparse = econfig.get(section, "sparse", raw=False, fallback=None)
+            protocol = econfig.get(section, "protocol", raw=False, fallback=None)
+
+            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
+
+
+
+def _main():
+    rootpath, gitmodules, externals = commandline_arguments()
+    global logger
+    logger = logging.getLogger(__name__)
+    with utils.pushd(rootpath):
+        t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals)
+        logger.info("Translating {}".format(rootpath))
+        t.translate_repo()
+
+        
+if __name__ == "__main__":
+    sys.exit(_main())
diff --git a/git_fleximod/submodule.py b/git_fleximod/submodule.py
new file mode 100644
index 0000000000..c939d54bc9
--- /dev/null
+++ b/git_fleximod/submodule.py
@@ -0,0 +1,427 @@
+import os
+import textwrap
+import shutil
+import string
+from configparser import NoOptionError
+from git_fleximod import utils
+from git_fleximod.gitinterface import GitInterface
+
+class Submodule():
+    """
+    Represents a Git submodule with enhanced features for flexible management.
+
+    Attributes:
+        name (str): The name of the submodule.
+        root_dir (str): The root directory of the main project.
+        path (str): The relative path from the root directory to the submodule.
+        url (str): The URL of the submodule repository.
+        fxurl (str): The URL for flexible submodule management (optional).
+        fxtag (str): The tag for flexible submodule management (optional).
+        fxsparse (str): Path to the sparse checkout file relative to the submodule path, see git-sparse-checkout for details (optional).
+        fxrequired (str): Indicates if the submodule is optional or required (optional).
+        logger (logging.Logger): Logger instance for logging (optional).
+    """
+    def __init__(self, root_dir, name, path, url, fxtag=None, fxurl=None, fxsparse=None, fxrequired=None, logger=None):
+        """
+        Initializes a new Submodule instance with the provided attributes.
+        """
+        self.name = name
+        self.root_dir = root_dir
+        self.path = path 
+        self.url = url
+        self.fxurl = fxurl
+        self.fxtag = fxtag
+        self.fxsparse = fxsparse
+        if fxrequired:
+            self.fxrequired = fxrequired
+        else:
+            self.fxrequired = "AlwaysRequired"
+        self.logger = logger
+       
+    def status(self):
+        """
+        Checks the status of the submodule and returns 4 parameters:
+        - result (str): The status of the submodule.
+        - needsupdate (bool): An indicator if the submodule needs to be updated.
+        - localmods (bool): An indicator if the submodule has local modifications.
+        - testfails (bool): An indicator if the submodule has failed a test, this is used for testing purposes.        
+        """
+
+        smpath = os.path.join(self.root_dir, self.path)
+        testfails = False
+        localmods = False
+        needsupdate = False
+        ahash = None
+        optional = ""
+        if "Optional" in self.fxrequired:
+            optional = " (optional)" 
+        required = None
+        level = None
+        if not os.path.exists(os.path.join(smpath, ".git")):
+            rootgit = GitInterface(self.root_dir, self.logger)
+            # submodule commands use path, not name
+            status, tags = rootgit.git_operation("ls-remote", "--tags", self.url)
+            status, result = rootgit.git_operation("submodule","status",smpath)
+            result = result.split()
+            
+            if result:
+                ahash = result[0][1:]
+            hhash = None
+            atag = None
+            for htag in tags.split("\n"):
+                if htag.endswith('^{}'):
+                    htag = htag[:-3]
+                if ahash and not atag and ahash in htag:
+                    atag = (htag.split()[1])[10:]
+                if self.fxtag and not hhash and htag.endswith(self.fxtag):
+                    hhash = htag.split()[0]
+                if hhash and atag:
+                    break
+            if self.fxtag and (ahash == hhash or atag == self.fxtag):
+                result = f"e {self.name:>20} not checked out, aligned at tag {self.fxtag}{optional}"
+                needsupdate = True
+            elif self.fxtag:
+                status, ahash = rootgit.git_operation(
+                    "submodule", "status", "{}".format(self.path)
+                )
+                ahash = ahash[1 : len(self.fxtag) + 1]
+                if self.fxtag == ahash:
+                    result = f"e {self.name:>20} not checked out, aligned at hash {ahash}{optional}"
+                else:
+                    result = f"e {self.name:>20} not checked out, out of sync at tag {atag}, expected tag is {self.fxtag}{optional}"
+                    testfails = True
+                needsupdate = True
+            else:
+                result = f"e {self.name:>20} has no fxtag defined in .gitmodules{optional}"
+                testfails = False
+        else:
+            with utils.pushd(smpath):
+                git = GitInterface(smpath, self.logger)
+                status, remote = git.git_operation("remote")
+                if remote == '':
+                    result = f"e {self.name:>20} has no associated remote"
+                    testfails = True
+                    needsupdate = True
+                    return result, needsupdate, localmods, testfails                    
+                status, rurl = git.git_operation("ls-remote","--get-url")
+                status, lines = git.git_operation("log", "--pretty=format:\"%h %d\"")
+                line = lines.partition('\n')[0]
+                parts = line.split()
+                ahash = parts[0][1:]
+                atag = None
+                if len(parts) > 3:
+                    idx = 0
+                    while idx < len(parts)-1:
+                        idx = idx+1
+                        if parts[idx] == 'tag:':
+                            atag = parts[idx+1]
+                            while atag.endswith(')') or atag.endswith(',') or atag.endswith("\""):
+                                atag = atag[:-1]
+                            if atag == self.fxtag:
+                                break
+
+                
+                #print(f"line is {line} ahash is {ahash} atag is {atag} {parts}")
+                #                atag = git.git_operation("describe", "--tags", "--always")
+                # ahash =  git.git_operation("rev-list", "HEAD").partition("\n")[0]
+                    
+                recurse = False
+                if rurl != self.url:
+                    remote = self._add_remote(git)
+                    git.git_operation("fetch", remote)
+                if self.fxtag and atag == self.fxtag:
+                    result = f"  {self.name:>20} at tag {self.fxtag}"
+                    recurse = True
+                    testfails = False
+                elif self.fxtag and (ahash[: len(self.fxtag)] == self.fxtag or (self.fxtag.find(ahash)==0)):
+                    result = f"  {self.name:>20} at hash {ahash}"
+                    recurse = True
+                    testfails = False
+                elif atag == ahash:
+                    result = f"  {self.name:>20} at hash {ahash}"
+                    recurse = True
+                elif self.fxtag:
+                    result = f"s {self.name:>20} {atag} {ahash} is out of sync with .gitmodules {self.fxtag}"
+                    testfails = True
+                    needsupdate = True
+                else:
+                    if atag:
+                        result = f"e {self.name:>20} has no fxtag defined in .gitmodules, module at {atag}"
+                    else:
+                        result = f"e {self.name:>20} has no fxtag defined in .gitmodules, module at {ahash}"
+                    testfails = False
+                    
+                status, output = git.git_operation("status", "--ignore-submodules", "-uno")
+                if "nothing to commit" not in output:
+                    localmods = True
+                    result = "M" + textwrap.indent(output, "                      ")
+#        print(f"result {result} needsupdate {needsupdate} localmods {localmods} testfails {testfails}")
+        return result, needsupdate, localmods, testfails
+
+    
+    def _add_remote(self, git):
+        """
+        Adds a new remote to the submodule if it does not already exist.
+
+        This method checks the existing remotes of the submodule. If the submodule's URL is not already listed as a remote,
+        it attempts to add a new remote. The name for the new remote is generated dynamically to avoid conflicts. If no
+        remotes exist, it defaults to naming the new remote 'origin'.
+
+        Args:
+            git (GitInterface): An instance of GitInterface to perform git operations.
+
+        Returns:
+            str: The name of the new remote if added, or the name of the existing remote that matches the submodule's URL.
+        """ 
+        status, remotes = git.git_operation("remote", "-v")
+        remotes = remotes.splitlines()
+        upstream = None
+        if remotes:
+            status, upstream = git.git_operation("ls-remote", "--get-url")
+            newremote = "newremote.00"
+            tmpurl = self.url.replace("git@github.com:", "https://github.com/")
+            line = next((s for s in remotes if self.url in s or tmpurl in s), None)
+            if line:
+                newremote = line.split()[0]
+                return newremote
+            else:
+                i = 0
+                while newremote in remotes:
+                    i = i + 1
+                    newremote = f"newremote.{i:02d}"
+        else:
+            newremote = "origin"
+        git.git_operation("remote", "add", newremote, self.url)
+        return newremote
+
+    def toplevel(self):
+        """
+        Returns True if the submodule is Toplevel (either Required or Optional)
+        """
+        return True if "Top" in self.fxrequired else False
+
+    def sparse_checkout(self):
+        """
+        Performs a sparse checkout of the submodule.
+
+        This method optimizes the checkout process by only checking out files specified in the submodule's sparse-checkout configuration,
+        rather than the entire submodule content. It achieves this by first ensuring the `.git/info/sparse-checkout` file is created and
+        configured in the submodule's directory. Then, it proceeds to checkout the desired tag. If the submodule has already been checked out,
+        this method will not perform the checkout again.
+
+        This approach is particularly beneficial for submodules with a large number of files, as it significantly reduces the time and disk space
+        required for the checkout process by avoiding the unnecessary checkout and subsequent removal of unneeded files.
+
+        Returns:
+            None
+        """ 
+        self.logger.info("Called sparse_checkout for {}".format(self.name))
+        rgit = GitInterface(self.root_dir, self.logger)
+        status, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+        if superroot:
+            gitroot = superroot.strip()
+        else:
+            gitroot = self.root_dir.strip()
+        # Now need to move the .git dir to the submodule location
+        rootdotgit = os.path.join(self.root_dir, ".git")
+        while os.path.isfile(rootdotgit):
+            with open(rootdotgit) as f:
+                line = f.readline().rstrip()
+                if line.startswith("gitdir: "):
+                    rootdotgit = os.path.abspath(os.path.join(self.root_dir,line[8:]))
+        assert os.path.isdir(rootdotgit)
+        # first create the module directory
+        if not os.path.isdir(os.path.join(self.root_dir, self.path)):
+            os.makedirs(os.path.join(self.root_dir, self.path))
+
+        # initialize a new git repo and set the sparse checkout flag
+        sprep_repo = os.path.join(self.root_dir, self.path)
+        sprepo_git = GitInterface(sprep_repo, self.logger)
+        if os.path.exists(os.path.join(sprep_repo, ".git")):
+            try:
+                self.logger.info("Submodule {} found".format(self.name))
+                chk = sprepo_git.config_get_value("core", "sparseCheckout")
+                if chk == "true":
+                    self.logger.info("Sparse submodule {} already checked out".format(self.name))
+                    return
+            except (NoOptionError):
+                self.logger.debug("Sparse submodule {} not present".format(self.name))
+            except Exception as e:
+                utils.fatal_error("Unexpected error {} occured.".format(e))
+
+        sprepo_git.config_set_value("core", "sparseCheckout", "true")
+
+        # set the repository remote
+        
+        self.logger.info("Setting remote origin in {}/{}".format(self.root_dir, self.path))
+        status, remotes = sprepo_git.git_operation("remote", "-v")
+        if self.url not in remotes:
+            sprepo_git.git_operation("remote", "add", "origin", self.url)
+
+        topgit = os.path.join(gitroot, ".git")
+
+        if gitroot != self.root_dir and os.path.isfile(os.path.join(self.root_dir, ".git")):
+            with open(os.path.join(self.root_dir, ".git")) as f:
+                gitpath = os.path.relpath(
+                    os.path.join(self.root_dir, f.read().split()[1]),
+                    start=os.path.join(self.root_dir, self.path),
+                )
+                rootdotgit = os.path.join(gitpath, "modules", self.name)
+        else:
+            rootdotgit = os.path.relpath(
+                os.path.join(self.root_dir, ".git", "modules", self.name),
+                start=os.path.join(self.root_dir, self.path),
+            )
+
+        if os.path.isdir(os.path.join(self.root_dir, self.path, ".git")):
+            with utils.pushd(sprep_repo):
+                if os.path.isdir(os.path.join(rootdotgit,".git")):
+                    shutil.rmtree(os.path.join(rootdotgit,".git"))
+                shutil.move(".git", rootdotgit)
+                with open(".git", "w") as f:
+                    f.write("gitdir: " + os.path.relpath(rootdotgit))
+                infodir = os.path.join(rootdotgit, "info")
+                if not os.path.isdir(infodir):
+                    os.makedirs(infodir)
+                gitsparse = os.path.abspath(os.path.join(infodir, "sparse-checkout"))
+            if os.path.isfile(gitsparse):
+                self.logger.warning(
+                    "submodule {} is already initialized {}".format(self.name, rootdotgit)
+                )
+                return
+
+            with utils.pushd(sprep_repo):
+                if os.path.isfile(self.fxsparse):
+                    
+                    shutil.copy(self.fxsparse, gitsparse)
+                
+
+        # Finally checkout the repo
+        sprepo_git.git_operation("fetch", "origin", "--tags")
+        status,_ = sprepo_git.git_operation("checkout", self.fxtag)
+        if status:
+            print(f"Error checking out {self.name:>20} at {self.fxtag}")
+        else:
+            print(f"Successfully checked out {self.name:>20} at {self.fxtag}")
+        rgit.config_set_value('submodule.' + self.name, "active", "true")
+        rgit.config_set_value('submodule.' + self.name, "url", self.url)
+        rgit.config_set_value('submodule.' + self.name, "path", self.path)
+
+    def update(self):
+        """
+        Updates the submodule to the latest or specified version.
+
+        This method handles the update process of the submodule, including checking out the submodule into the specified path,
+        handling sparse checkouts if configured, and updating the submodule's URL if necessary. It supports both SSH and HTTPS URLs,
+        automatically converting SSH URLs to HTTPS to avoid issues for users without SSH keys.
+
+        The update process involves the following steps:
+        1. If the submodule is configured for sparse checkout, it performs a sparse checkout.
+        2. If the submodule is not already checked out, it clones the submodule using the provided URL.
+        3. If a specific tag or hash is provided, it checks out that tag; otherwise, it checks out the latest version.
+        4. If the root `.git` is a file (indicating a submodule or a worktree), additional steps are taken to integrate the submodule properly.
+
+        Args:
+           None
+        Note:
+            - SSH URLs are automatically converted to HTTPS to accommodate users without SSH keys.
+
+        Returns:
+            None
+        """
+        git = GitInterface(self.root_dir, self.logger)
+        repodir = os.path.join(self.root_dir, self.path)
+        self.logger.info("Checkout {} into {}/{}".format(self.name, self.root_dir, self.path))
+        # if url is provided update to the new url
+        tag = None
+        repo_exists = False
+        if os.path.exists(os.path.join(repodir, ".git")):
+            self.logger.info("Submodule {} already checked out".format(self.name))
+            repo_exists = True
+        # Look for a .gitmodules file in the newly checkedout repo
+        if self.fxsparse:
+            print(f"Sparse checkout {self.name} fxsparse {self.fxsparse}")
+            self.sparse_checkout()
+        else:
+            if not repo_exists and self.url:
+                # ssh urls cause problems for those who dont have git accounts with ssh keys defined
+                # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was
+                # opened with a GitModules object we don't need to worry about restoring the file here
+                # it will be done by the GitModules class
+                if self.url.startswith("git@"):
+                    git.git_operation("clone", self.url, self.path)
+                    smgit = GitInterface(repodir, self.logger)
+                    if not tag:
+                        status, tag = smgit.git_operation("describe", "--tags", "--always")
+                    smgit.git_operation("checkout", tag)
+                    # Now need to move the .git dir to the submodule location
+                    rootdotgit = os.path.join(self.root_dir, ".git")
+                    if os.path.isfile(rootdotgit):
+                        with open(rootdotgit) as f:
+                            line = f.readline()
+                            if line.startswith("gitdir: "):
+                                rootdotgit = line[8:]
+
+                    newpath = os.path.abspath(os.path.join(self.root_dir, rootdotgit, "modules", self.name))
+                    if os.path.exists(newpath):
+                        shutil.rmtree(os.path.join(repodir, ".git"))
+                    else:
+                        shutil.move(os.path.join(repodir, ".git"), newpath)
+                    
+                    with open(os.path.join(repodir, ".git"), "w") as f:
+                        f.write("gitdir: " + os.path.relpath(newpath, start=repodir))
+
+            if not os.path.exists(repodir):
+                parent = os.path.dirname(repodir)
+                if not os.path.isdir(parent):
+                    os.makedirs(parent)
+                git.git_operation("submodule", "add", "--name", self.name, "--", self.url, self.path) 
+
+            if not repo_exists:
+                git.git_operation("submodule", "update", "--init", "--", self.path)
+
+            if self.fxtag:        
+                smgit = GitInterface(repodir, self.logger)
+                newremote = self._add_remote(smgit)
+                # Trying to distingush a tag from a hash
+                allowed = set(string.digits + 'abcdef') 
+                if not set(self.fxtag) <= allowed:
+                    # This is a tag
+                    tag = f"refs/tags/{self.fxtag}:refs/tags/{self.fxtag}"
+                    smgit.git_operation("fetch", newremote, tag)
+                smgit.git_operation("checkout", self.fxtag)
+
+            if not os.path.exists(os.path.join(repodir, ".git")):
+                utils.fatal_error(
+                    f"Failed to checkout {self.name} {repo_exists} {repodir} {self.path}"
+                )
+                
+
+        if os.path.exists(os.path.join(self.path, ".git")):
+            submoddir = os.path.join(self.root_dir, self.path)
+            with utils.pushd(submoddir):
+                git = GitInterface(submoddir, self.logger)
+                # first make sure the url is correct
+                newremote = self._add_remote(git)
+                status, tags = git.git_operation("tag", "-l")
+                fxtag = self.fxtag
+                if fxtag and fxtag not in tags:
+                    git.git_operation("fetch", newremote, "--tags")
+                status, atag = git.git_operation("describe", "--tags", "--always")
+                if fxtag and fxtag != atag:
+                    try:
+                        status, _ = git.git_operation("checkout", fxtag)
+                        if not status:
+                            print(f"{self.name:>20} updated to {fxtag}")
+                    except Exception as error:
+                        print(error)
+                    
+
+                elif not fxtag:
+                    print(f"No fxtag found for submodule {self.name:>20}")
+                else:
+                    print(f"{self.name:>20} up to date.")
+
+
+                
+        return
diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py
new file mode 100644
index 0000000000..c4f43d5238
--- /dev/null
+++ b/git_fleximod/utils.py
@@ -0,0 +1,365 @@
+#!/usr/bin/env python3
+"""
+Common public utilities for manic package
+
+"""
+
+import logging
+import os
+import subprocess
+import sys
+from threading import Timer
+from pathlib import Path
+
+LOCAL_PATH_INDICATOR = "."
+# ---------------------------------------------------------------------
+#
+# functions to massage text for output and other useful utilities
+#
+# ---------------------------------------------------------------------
+from contextlib import contextmanager
+
+
+@contextmanager
+def pushd(new_dir):
+    """context for chdir. usage: with pushd(new_dir)"""
+    previous_dir = os.getcwd()
+    os.chdir(new_dir)
+    try:
+        yield
+    finally:
+        os.chdir(previous_dir)
+
+
+def log_process_output(output):
+    """Log each line of process output at debug level so it can be
+    filtered if necessary. By default, output is a single string, and
+    logging.debug(output) will only put log info heading on the first
+    line. This makes it hard to filter with grep.
+
+    """
+    output = output.split("\n")
+    for line in output:
+        logging.debug(line)
+
+
+def printlog(msg, **kwargs):
+    """Wrapper script around print to ensure that everything printed to
+    the screen also gets logged.
+
+    """
+    logging.info(msg)
+    if kwargs:
+        print(msg, **kwargs)
+    else:
+        print(msg)
+    sys.stdout.flush()
+
+
+def find_upwards(root_dir, filename):
+    """Find a file in root dir or any of it's parents"""
+    d = Path(root_dir)
+    root = Path(d.root)
+    while d != root:
+        attempt = d / filename
+        if attempt.exists():
+            return attempt
+        d = d.parent
+    return None
+
+
+def last_n_lines(the_string, n_lines, truncation_message=None):
+    """Returns the last n lines of the given string
+
+    Args:
+        the_string: str
+        n_lines: int
+        truncation_message: str, optional
+
+    Returns a string containing the last n lines of the_string
+
+    If truncation_message is provided, the returned string begins with
+    the given message if and only if the string is greater than n lines
+    to begin with.
+    """
+
+    lines = the_string.splitlines(True)
+    if len(lines) <= n_lines:
+        return_val = the_string
+    else:
+        lines_subset = lines[-n_lines:]
+        str_truncated = "".join(lines_subset)
+        if truncation_message:
+            str_truncated = truncation_message + "\n" + str_truncated
+        return_val = str_truncated
+
+    return return_val
+
+
+def indent_string(the_string, indent_level):
+    """Indents the given string by a given number of spaces
+
+    Args:
+       the_string: str
+       indent_level: int
+
+    Returns a new string that is the same as the_string, except that
+    each line is indented by 'indent_level' spaces.
+
+    In python3, this can be done with textwrap.indent.
+    """
+
+    lines = the_string.splitlines(True)
+    padding = " " * indent_level
+    lines_indented = [padding + line for line in lines]
+    return "".join(lines_indented)
+
+
+# ---------------------------------------------------------------------
+#
+# error handling
+#
+# ---------------------------------------------------------------------
+
+
+def fatal_error(message):
+    """
+    Error output function
+    """
+    logging.error(message)
+    raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message))
+
+
+# ---------------------------------------------------------------------
+#
+# Data conversion / manipulation
+#
+# ---------------------------------------------------------------------
+def str_to_bool(bool_str):
+    """Convert a sting representation of as boolean into a true boolean.
+
+    Conversion should be case insensitive.
+    """
+    value = None
+    str_lower = bool_str.lower()
+    if str_lower in ("true", "t"):
+        value = True
+    elif str_lower in ("false", "f"):
+        value = False
+    if value is None:
+        msg = (
+            'ERROR: invalid boolean string value "{0}". '
+            'Must be "true" or "false"'.format(bool_str)
+        )
+        fatal_error(msg)
+    return value
+
+
+REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"]
+
+
+def is_remote_url(url):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    """
+    remote_url = False
+    for prefix in REMOTE_PREFIXES:
+        if url.startswith(prefix):
+            remote_url = True
+    return remote_url
+
+
+def split_remote_url(url):
+    """check if the user provided a local file path or a
+    remote. If remote, try to strip off protocol info.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        return url
+
+    for prefix in REMOTE_PREFIXES:
+        url = url.replace(prefix, "")
+
+    if "@" in url:
+        url = url.split("@")[1]
+
+    if ":" in url:
+        url = url.split(":")[1]
+
+    return url
+
+
+def expand_local_url(url, field):
+    """check if the user provided a local file path instead of a
+    remote. If so, it must be expanded to an absolute
+    path.
+
+    Note: local paths of LOCAL_PATH_INDICATOR have special meaning and
+    represent local copy only, don't work with the remotes.
+
+    """
+    remote_url = is_remote_url(url)
+    if not remote_url:
+        if url.strip() == LOCAL_PATH_INDICATOR:
+            pass
+        else:
+            url = os.path.expandvars(url)
+            url = os.path.expanduser(url)
+            if not os.path.isabs(url):
+                msg = (
+                    'WARNING: Externals description for "{0}" contains a '
+                    "url that is not remote and does not expand to an "
+                    "absolute path. Version control operations may "
+                    "fail.\n\nurl={1}".format(field, url)
+                )
+                printlog(msg)
+            else:
+                url = os.path.normpath(url)
+    return url
+
+
+# ---------------------------------------------------------------------
+#
+# subprocess
+#
+# ---------------------------------------------------------------------
+
+# Give the user a helpful message if we detect that a command seems to
+# be hanging.
+_HANGING_SEC = 300
+
+
+def _hanging_msg(working_directory, command):
+    print(
+        """
+
+Command '{command}'
+from directory {working_directory}
+has taken {hanging_sec} seconds. It may be hanging.
+
+The command will continue to run, but you may want to abort
+git-fleximod with ^C and investigate. A possible cause of hangs is git
+requires authentication to access a private repository. On some
+systems, git requests for authentication information will not
+be displayed to the user. In this case, the program will appear to
+hang. Ensure you can run git manually and access all
+repositories without entering your authentication information.
+
+""".format(
+            command=command,
+            working_directory=working_directory,
+            hanging_sec=_HANGING_SEC,
+        )
+    )
+
+
+def execute_subprocess(commands, status_to_caller=False, output_to_caller=False):
+    """Wrapper around subprocess.check_output to handle common
+    exceptions.
+
+    check_output runs a command with arguments and waits
+    for it to complete.
+
+    check_output raises an exception on a nonzero return code.  if
+    status_to_caller is true, execute_subprocess returns the subprocess
+    return code, otherwise execute_subprocess treats non-zero return
+    status as an error and raises an exception.
+
+    """
+    cwd = os.getcwd()
+    msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd)
+    logging.info(msg)
+    commands_str = " ".join(str(element) for element in commands)
+    logging.info(commands_str)
+    return_to_caller = status_to_caller or output_to_caller
+    status = -1
+    output = ""
+    hanging_timer = Timer(
+        _HANGING_SEC,
+        _hanging_msg,
+        kwargs={"working_directory": cwd, "command": commands_str},
+    )
+    hanging_timer.start()
+    try:
+        output = subprocess.check_output(
+            commands, stderr=subprocess.STDOUT, universal_newlines=True
+        )
+        log_process_output(output)
+        status = 0
+    except OSError as error:
+        msg = failed_command_msg(
+            "Command execution failed. Does the executable exist?", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except ValueError as error:
+        msg = failed_command_msg(
+            "DEV_ERROR: Invalid arguments trying to run subprocess", commands
+        )
+        logging.error(error)
+        fatal_error(msg)
+    except subprocess.CalledProcessError as error:
+        # Only report the error if we are NOT returning to the
+        # caller. If we are returning to the caller, then it may be a
+        # simple status check. If returning, it is the callers
+        # responsibility determine if an error occurred and handle it
+        # appropriately.
+        msg_context = (
+            "Process did not run successfully; "
+            "returned status {0}".format(error.returncode)
+        )
+        msg = failed_command_msg(msg_context, commands, output=error.output)
+        if not return_to_caller:
+            logging.error(error)
+            logging.error(msg)
+            log_process_output(error.output)
+            fatal_error(msg)
+        status = error.returncode
+    finally:
+        hanging_timer.cancel()
+
+    if status_to_caller and output_to_caller:
+        ret_value = (status, output)
+    elif status_to_caller:
+        ret_value = status
+    elif output_to_caller:
+        ret_value = output
+    else:
+        ret_value = None
+
+    return ret_value
+
+
+def failed_command_msg(msg_context, command, output=None):
+    """Template for consistent error messages from subprocess calls.
+
+    If 'output' is given, it should provide the output from the failed
+    command
+    """
+
+    if output:
+        output_truncated = last_n_lines(
+            output, 20, truncation_message="[... Output truncated for brevity ...]"
+        )
+        errmsg = (
+            "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: "
+        )
+    else:
+        errmsg = ""
+
+    command_str = " ".join(command)
+    errmsg += """In directory
+    {cwd}
+{context}:
+    {command}
+""".format(
+        cwd=os.getcwd(), context=msg_context, command=command_str
+    )
+
+    if output:
+        errmsg += "See above for output from failed command.\n"
+
+    return errmsg
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000000..3a74effcd1
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,693 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "babel"
+version = "2.15.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
+    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+]
+
+[package.dependencies]
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.6.2"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
+[[package]]
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+version = "3.3.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
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diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000..619cdabe3b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,41 @@
+[tool.poetry]
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+description = "Extended support for git-submodule and git-sparse-checkout"
+authors = ["Jim Edwards <jedwards@ucar.edu>"]
+maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/jedwards4b/git-fleximod"
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+git-fleximod = "git_fleximod.git_fleximod:main"
+me2flexi = "git_fleximod.metoflexi:_main"
+fsspec = "fsspec.fuse:main"
+
+[tool.poetry.dependencies]
+python = "^3.8"
+GitPython = "^3.1.0"
+sphinx = "^5.0.0"
+fsspec = "^2023.12.2"
+wheel = "^0.42.0"
+pytest = "^8.0.0"
+pyfakefs = "^5.3.5"
+
+[tool.poetry.urls]
+"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
+
+[tool.pytest.ini_options]
+markers = [
+        "skip_after_first: only run on first iteration"
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
diff --git a/tbump.toml b/tbump.toml
new file mode 100644
index 0000000000..920ff0591c
--- /dev/null
+++ b/tbump.toml
@@ -0,0 +1,43 @@
+# Uncomment this if your project is hosted on GitHub:
+github_url = "https://github.com/jedwards4b/git-fleximod/"
+
+[version]
+current = "0.9.2"
+
+# Example of a semver regexp.
+# Make sure this matches current_version before
+# using tbump
+regex = '''
+  (?P<major>\d+)
+  \.
+  (?P<minor>\d+)
+  \.
+  (?P<patch>\d+)
+  '''
+
+[git]
+message_template = "Bump to {new_version}"
+tag_template = "v{new_version}"
+
+# For each file to patch, add a [[file]] config
+# section containing the path of the file, relative to the
+# tbump.toml location.
+[[file]]
+src = "git_fleximod/cli.py"
+
+[[file]]
+src = "pyproject.toml"
+
+# You can specify a list of commands to
+# run after the files have been patched
+# and before the git commit is made
+
+#  [[before_commit]]
+#  name = "check changelog"
+#  cmd = "grep -q {new_version} Changelog.rst"
+
+# Or run some commands after the git tag and the branch
+# have been pushed:
+#  [[after_push]]
+#  name = "publish"
+#  cmd = "./publish.sh"
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000000..4d4c66c78e
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1,3 @@
+import sys, os
+
+sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src"))
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000000..81edbe713e
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,150 @@
+import pytest 
+from git_fleximod.gitinterface import GitInterface
+import os
+import subprocess
+import logging
+from pathlib import Path
+
+@pytest.fixture(scope='session')
+def logger():
+    logging.basicConfig(
+        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
+    )
+    logger = logging.getLogger(__name__)
+    return logger
+
+all_repos=[
+    {"subrepo_path": "modules/test",
+     "submodule_name": "test_submodule",
+     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_submodule at tag MPIserial_2.4.0",
+     "status3" : "test_submodule at tag MPIserial_2.4.0",
+     "status4" : "test_submodule at tag MPIserial_2.4.0",
+     "gitmodules_content" : """
+    [submodule "test_submodule"]
+    path = modules/test
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelRequired
+"""},
+    {"subrepo_path": "modules/test_optional",
+     "submodule_name": "test_optional",
+     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+     "status2" : "test_optional at tag MPIserial_2.4.0",
+     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0 (optional)",
+     "status4" : "test_optional at tag MPIserial_2.4.0",
+     "gitmodules_content": """
+     [submodule "test_optional"]
+    path = modules/test_optional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.4.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = ToplevelOptional
+"""},
+    {"subrepo_path": "modules/test_alwaysoptional",
+     "submodule_name": "test_alwaysoptional",
+     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
+     "status2" : "test_alwaysoptional at hash e5cf35c",
+     "status3" : "out of sync at tag None, expected tag is e5cf35c",
+     "status4" : "test_alwaysoptional at hash e5cf35c",
+     "gitmodules_content": """
+    [submodule "test_alwaysoptional"]
+    path = modules/test_alwaysoptional
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = e5cf35c
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysOptional
+"""},    
+    {"subrepo_path": "modules/test_sparse",
+     "submodule_name": "test_sparse",
+     "status1" : "test_sparse at tag MPIserial_2.5.0",
+     "status2" : "test_sparse at tag MPIserial_2.5.0",
+     "status3" : "test_sparse at tag MPIserial_2.5.0",
+     "status4" : "test_sparse at tag MPIserial_2.5.0",
+     "gitmodules_content": """
+    [submodule "test_sparse"]
+    path = modules/test_sparse
+    url = https://github.com/ESMCI/mpi-serial.git
+    fxtag = MPIserial_2.5.0
+    fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
+    fxrequired = AlwaysRequired
+    fxsparse = ../.sparse_file_list
+"""},
+]
+@pytest.fixture(params=all_repos)
+
+def shared_repos(request):
+    return request.param
+
+@pytest.fixture
+def get_all_repos():
+    return all_repos
+
+def write_sparse_checkout_file(fp):
+    sparse_content = """m4
+"""
+    fp.write_text(sparse_content)
+
+@pytest.fixture
+def test_repo(shared_repos, tmp_path, logger):
+    subrepo_path = shared_repos["subrepo_path"]
+    submodule_name = shared_repos["submodule_name"]
+    test_dir = tmp_path / "testrepo"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    assert test_dir.joinpath(".git").is_dir()
+    (test_dir / "modules").mkdir()
+    if "sparse" in submodule_name:
+        (test_dir / subrepo_path).mkdir()
+        # Add the sparse checkout file
+        write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
+        gitp.git_operation("add","modules/.sparse_file_list")
+    else:
+        gitp = GitInterface(str(test_dir), logger)
+        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+        assert test_dir.joinpath(".gitmodules").is_file()
+        gitp.git_operation("add",subrepo_path)
+    gitp.git_operation("commit","-a","-m","\"add submod\"")
+    test_dir2 = tmp_path / "testrepo2"
+    gitp.git_operation("clone",test_dir,test_dir2)
+    return test_dir2    
+
+
+@pytest.fixture
+def complex_repo(tmp_path, logger):
+    test_dir = tmp_path / "testcomplex"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation("fetch", "origin")
+    gitp.git_operation("checkout", "v0.0.1")
+    return test_dir
+
+@pytest.fixture
+def complex_update(tmp_path, logger):
+    test_dir = tmp_path / "testcomplex"
+    test_dir.mkdir()
+    str_path = str(test_dir)
+    gitp = GitInterface(str_path, logger)
+    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation("fetch", "origin")
+    gitp.git_operation("checkout", "v0.0.2")
+    
+    return test_dir
+    
+@pytest.fixture
+def git_fleximod():
+    def _run_fleximod(path, args, input=None):
+        cmd = ["git", "fleximod"] + args.split()
+        result = subprocess.run(cmd, cwd=path, input=input, 
+                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
+                                text=True)
+        if result.returncode:
+            print(result.stdout)
+            print(result.stderr)
+        return result
+    return _run_fleximod
+
diff --git a/tests/test_a_import.py b/tests/test_a_import.py
new file mode 100644
index 0000000000..d5ca878de5
--- /dev/null
+++ b/tests/test_a_import.py
@@ -0,0 +1,8 @@
+# pylint: disable=unused-import
+from git_fleximod import cli
+from git_fleximod import utils
+from git_fleximod.gitinterface import GitInterface
+from git_fleximod.gitmodules import GitModules
+
+def test_import():
+    print("here")
diff --git a/tests/test_b_update.py b/tests/test_b_update.py
new file mode 100644
index 0000000000..159f1cfae0
--- /dev/null
+++ b/tests/test_b_update.py
@@ -0,0 +1,26 @@
+import pytest
+from pathlib import Path
+                
+def test_basic_checkout(git_fleximod, test_repo, shared_repos):
+    # Prepare a simple .gitmodules
+    gm = shared_repos['gitmodules_content']
+    file_path = (test_repo / ".gitmodules")
+    repo_name = shared_repos["submodule_name"]
+    repo_path = shared_repos["subrepo_path"]
+
+    file_path.write_text(gm)
+    
+    # Run the command
+    result = git_fleximod(test_repo, f"update {repo_name}")
+
+    # Assertions
+    assert result.returncode == 0 
+    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
+    if "sparse" in repo_name:
+        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
+        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
+    
+    status = git_fleximod(test_repo, f"status {repo_name}")
+        
+    assert shared_repos["status2"] in status.stdout
+        
diff --git a/tests/test_c_required.py b/tests/test_c_required.py
new file mode 100644
index 0000000000..89ab8d294d
--- /dev/null
+++ b/tests/test_c_required.py
@@ -0,0 +1,30 @@
+import pytest
+from pathlib import Path
+                
+def test_required(git_fleximod, test_repo, shared_repos):
+    file_path = (test_repo / ".gitmodules")
+    gm = shared_repos["gitmodules_content"]
+    repo_name = shared_repos["submodule_name"]
+    if file_path.exists():
+        with file_path.open("r") as f:
+            gitmodules_content = f.read()
+            # add the entry if it does not exist
+            if repo_name not in gitmodules_content:
+                file_path.write_text(gitmodules_content+gm)
+            # or if it is incomplete
+            elif gm not in gitmodules_content:
+                file_path.write_text(gm)
+    else:
+        file_path.write_text(gm)
+    result = git_fleximod(test_repo, "update")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status3"] in status.stdout
+    status = git_fleximod(test_repo, f"update --optional")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
+    status = git_fleximod(test_repo, f"update {repo_name}")
+    assert result.returncode == 0
+    status = git_fleximod(test_repo, f"status {repo_name}")
+    assert shared_repos["status4"] in status.stdout
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
new file mode 100644
index 0000000000..edde7d816d
--- /dev/null
+++ b/tests/test_d_complex.py
@@ -0,0 +1,66 @@
+import pytest
+from pathlib import Path
+from git_fleximod.gitinterface import GitInterface
+
+def test_complex_checkout(git_fleximod, complex_repo, logger):
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex not checked out, aligned at tag testtag02" in status.stdout)
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+    
+    # This should checkout and update test_submodule and complex_sub
+    result = git_fleximod(complex_repo, "update")    
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
+
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex")
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+    # update a single optional submodule
+
+    result = git_fleximod(complex_repo, "update ToplevelOptional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+
+    # Finally update optional
+    result = git_fleximod(complex_repo, "update --optional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_repo, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag02" in status.stdout)
+    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
+    
+    # now check the complex_sub
+    root = (complex_repo / "modules" / "complex" )
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+
diff --git a/tests/test_e_complex_update.py b/tests/test_e_complex_update.py
new file mode 100644
index 0000000000..0c3ab4c6a6
--- /dev/null
+++ b/tests/test_e_complex_update.py
@@ -0,0 +1,69 @@
+import pytest
+from pathlib import Path
+from git_fleximod.gitinterface import GitInterface
+
+def test_complex_update(git_fleximod, complex_update, logger):
+    status = git_fleximod(complex_update, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex not checked out, out of sync at tag testtag02, expected tag is testtag3" in status.stdout)
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+    
+    # This should checkout and update test_submodule and complex_sub
+    result = git_fleximod(complex_update, "update")    
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_update, "status")
+    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag3" in status.stdout)
+
+    # now check the complex_sub
+    root = (complex_update / "modules" / "complex")
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serialAR" / ".git").exists())
+    assert((root / "modules" / "mpi-serialSAR" / ".git").exists())
+    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+    # update a single optional submodule
+
+    result = git_fleximod(complex_update, "update ToplevelOptional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_update, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag3" in status.stdout)
+    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+
+    # Finally update optional
+    result = git_fleximod(complex_update, "update --optional")
+    assert result.returncode == 0
+
+    status = git_fleximod(complex_update, "status")
+    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
+    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
+    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
+    assert("Complex at tag testtag3" in status.stdout)
+    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
+    
+    # now check the complex_sub
+    root = (complex_update / "modules" / "complex" )
+    assert(not (root / "libraries" / "gptl" / ".git").exists())
+    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
+    assert(not (root / "modules" / "mpi-serial" / ".git").exists())
+    assert((root / "modules" / "mpi-serialAR" / ".git").exists())
+    assert((root / "modules" / "mpi-serialSAR" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / ".git").exists())
+    assert((root / "modules" / "mpi-serial2" / ".git").exists())
+    assert((root / "modules" / "mpi-sparse" / "m4").exists())
+    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+
+

From 6c7ecf62ddb7e742a4b993ec9f351d6cd7025a93 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Wed, 25 Sep 2024 11:19:25 -0600
Subject: [PATCH 1133/1248] PPE change to sa_leaf

---
 src/biogeophys/CanopyFluxesMod.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90
index a969dc0583..0c5431728d 100644
--- a/src/biogeophys/CanopyFluxesMod.F90
+++ b/src/biogeophys/CanopyFluxesMod.F90
@@ -753,6 +753,7 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
                  .or. dbh(p) < min_stem_diameter) then
                frac_rad_abs_by_stem(p) = 0.0_r8
                sa_stem(p) = 0.0_r8
+               sa_leaf(p) = sa_leaf(p) + esai(p)
             endif
 
             ! if using Satellite Phenology mode, calculate leaf and stem biomass

From a9cd52f0191feaa387b6d3f1fc5c245a4d29b4f0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 20 Sep 2024 09:15:54 -0600
Subject: [PATCH 1134/1248] Error in Hillslope/shell_commands if running on
 grid w/o a hillslope_file.

---
 .../testmods_dirs/clm/Hillslope/shell_commands       | 12 ++++++++++++
 .../testdefs/testmods_dirs/clm/Hillslope/user_nl_clm |  2 --
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
index a2759b51b4..9b50ed6fe5 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
@@ -1,5 +1,17 @@
 ./xmlchange CLM_BLDNML_OPTS="-bgc sp"
 DIN_LOC_ROOT=$(./xmlquery --value DIN_LOC_ROOT)
+
+# Set hillslope_file. Needed for any grids without default hillslope_file already set by CTSM.
+lnd_grid=$(./xmlquery --value LND_GRID)
+if [[ ${lnd_grid} == "10x15" ]]; then
+    hillslope_file='$DIN_LOC_ROOT/lnd/clm2/testdata/synthetic_cosphill_1.3.nc'
+else
+    echo "ERROR: Hillslope file not found for LND_GRID=${lnd_grid}" >&2
+    exit 1
+fi
+echo -e "hillslope_file = '${hillslope_file}'\n" >> user_nl_clm
+
+# Set mesh file
 meshfile=$DIN_LOC_ROOT/lnd/clm2/testdata/ESMFmesh_10x15_synthetic_cosphill_1.0.nc
 ./xmlchange ATM_DOMAIN_MESH=${meshfile},LND_DOMAIN_MESH=${meshfile}
 
diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
index c750400672..e108e93d91 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
@@ -6,6 +6,4 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-hillslope_file = '$DIN_LOC_ROOT/lnd/clm2/testdata/synthetic_cosphill_1.3.nc'
-
 use_ssre = .false.

From d837838470375f1ce191cf193025530d327b1681 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Wed, 25 Sep 2024 16:30:48 -0600
Subject: [PATCH 1135/1248] Hillslope testmod: Add hillslope_file for
 5x5_amazon.

---
 cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
index 9b50ed6fe5..06576c405f 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
@@ -5,6 +5,8 @@ DIN_LOC_ROOT=$(./xmlquery --value DIN_LOC_ROOT)
 lnd_grid=$(./xmlquery --value LND_GRID)
 if [[ ${lnd_grid} == "10x15" ]]; then
     hillslope_file='$DIN_LOC_ROOT/lnd/clm2/testdata/synthetic_cosphill_1.3.nc'
+elif [[ ${lnd_grid} == "5x5_amazon" ]]; then
+    hillslope_file='/glade/derecho/scratch/samrabin/hillslopes_5x5_amazon/hand_analysis_global/combined/hilldata_5x5_amazon_hist_2000_78pfts_c240216.nc'
 else
     echo "ERROR: Hillslope file not found for LND_GRID=${lnd_grid}" >&2
     exit 1

From 615224a87a7a20fcb180312e26ec9fbd8aa2c5c9 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 26 Sep 2024 14:43:43 -0600
Subject: [PATCH 1136/1248] Updated number of tests

---
 bld/unit_testers/build-namelist_test.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 3480243371..06c9bcc361 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3994;
+my $ntests = 3997;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2437;

From cb7e9223d7d773fe2d066906c5621a0b39937dfd Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Thu, 26 Sep 2024 12:48:48 -0600
Subject: [PATCH 1137/1248] Don't manually set meshfile in Hillslope tests.

---
 .../testdefs/testmods_dirs/clm/Hillslope/shell_commands       | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
index 06576c405f..33504f51f4 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
@@ -13,9 +13,5 @@ else
 fi
 echo -e "hillslope_file = '${hillslope_file}'\n" >> user_nl_clm
 
-# Set mesh file
-meshfile=$DIN_LOC_ROOT/lnd/clm2/testdata/ESMFmesh_10x15_synthetic_cosphill_1.0.nc
-./xmlchange ATM_DOMAIN_MESH=${meshfile},LND_DOMAIN_MESH=${meshfile}
-
 # -ignore_warnings is needed as long as we don't allow use_hillslope and use_init_interp together
 ./xmlchange --append CLM_BLDNML_OPTS=-ignore_warnings

From ed5d17bb2176c410b15f52721cd951f0a8f0fcc5 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 26 Sep 2024 15:40:34 -0600
Subject: [PATCH 1138/1248] First draft ChangeLog/ChangeSum

---
 doc/ChangeLog | 85 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 86 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index d11efad6b3..ded12c54f8 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,89 @@
 ===============================================================
+Tag name: ctsm5.3.001
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 26 Sep 2024 03:10:40 PM MDT
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+- Keith fixed comments on urban thermal variables.
+- Sam R removed references to PTCLM*.
+- Sam R made updates to the documentation.
+- Sam R made improvements to mesh_plotter.
+- Matvey and Sam R worked on hillslope hydrology warnings.
+- Matvey added a test and a warning.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+PR #2770 documentation fixes and improvements
+PR #2772 mesh_plotter improvements
+PR #2765 fix comments on urban thermal variables
+PR #2703 add a namelist warning
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to documentation:
+ Yes, see "bugs fixed" above.
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ Test(s) added to bld/unit_testers/build-namelist_test.pl
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+Changes answers relative to baseline: No
+
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2792
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.0
 Originator(s): multiple (see below)
 Date: Wed 25 Sep 2024 01:22:06 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index ebbab3ce01..1014612b40 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.001 multiple 09/26/2024 Merge b4b-dev
          ctsm5.3.0 multiple 09/24/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
        ctsm5.2.029 multiple 09/24/2024 New surface datasets: double tag of ctsm5.3.0
        ctsm5.2.028   rgknox 09/05/2024 FATES history flushing update

From 830e675efe30851e7f5701231302b5117a34ce8c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 26 Sep 2024 16:57:01 -0600
Subject: [PATCH 1139/1248] Updated EXPECTED FAILUREs (I should have done this
 in ctsm5.3.0)

---
 cime_config/testdefs/ExpectedTestFails.xml | 44 ++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 36245661c0..8acaf71eab 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -37,6 +37,50 @@
   </test>
 
   <!-- aux_clm test suite failures -->
+  <test name="SMS_Ld2_D_PS.f09_g17.I1850Clm50BgcCropCmip6.derecho_intel.clm-basic_interp">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2787</issue>
+      <comment>The issue shows how to fix it.</comment>
+    </phase>
+  </test>
+  <test name="ERS_Ly3.f10_f10_mg37.I1850Clm50BgcCropCmip6.derecho_intel.clm-basic">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2787</issue>
+      <comment>The issue shows how to fix it.</comment>
+    </phase>
+  </test>
+  <test name="SMS_Lm1.f10_f10_mg37.I1850Clm50BgcCropCmip6waccm.derecho_gnu.clm-basic">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2787</issue>
+      <comment>The issue shows how to fix it.</comment>
+    </phase>
+  </test>
+
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV--clm-matrixcnOn">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2780</issue>
+      <comment>Crashes in the matrix solver.</comment>
+    </phase>
+  </test>
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-default--clm-NEON-HARV--clm-matrixcnOn">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2780</issue>
+      <comment>Crashes in the matrix solver.</comment>
+    </phase>
+  </test>
+  <test name="SMS_D.1x1_brazil.I1850Clm60BgcCrop.derecho_gnu.clm-mimics_matrixcn">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2780</issue>
+      <comment>Crashes in the matrix solver.</comment>
+    </phase>
+  </test>
+
   <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
     <phase name="BASELINE">
       <status>FAIL</status>

From c393123b48f148041c713d0478da4f6d6d5d237a Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 26 Sep 2024 22:10:19 -0700
Subject: [PATCH 1140/1248] correct clm_demand option typo

---
 .../testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
index c97c0dfea7..d88457df12 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-./xmlchange CLM_BLDNML_OPTS="-i-clm_demand -flanduse_timeseries" --append
+./xmlchange CLM_BLDNML_OPTS="--clm_demand -flanduse_timeseries" --append

From e591a1a677e9576382be2d6d2025ebc9b5760a24 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 27 Sep 2024 12:12:35 -0600
Subject: [PATCH 1141/1248] Remove parallel 5x5_amazon test from expected
 fails.

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 35c452b88c..c4f4ac0fc7 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -194,13 +194,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld5.5x5_amazon.I2000Clm60Bgc.derecho_gnu.clm-HillslopeC">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2423</issue>
-    </phase>
-  </test>
-
   <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>

From 4f2129fb4a70120e6e0163a66a77073d653579bf Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 27 Sep 2024 12:28:08 -0600
Subject: [PATCH 1142/1248] Rename 10x15 synthetic hillslope_file to include
 10x15.

---
 cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
index 33504f51f4..7bec6fd7f6 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
@@ -4,7 +4,7 @@ DIN_LOC_ROOT=$(./xmlquery --value DIN_LOC_ROOT)
 # Set hillslope_file. Needed for any grids without default hillslope_file already set by CTSM.
 lnd_grid=$(./xmlquery --value LND_GRID)
 if [[ ${lnd_grid} == "10x15" ]]; then
-    hillslope_file='$DIN_LOC_ROOT/lnd/clm2/testdata/synthetic_cosphill_1.3.nc'
+    hillslope_file='$DIN_LOC_ROOT/lnd/clm2/testdata/synthetic_cosphill_10x15_1.3.nc'
 elif [[ ${lnd_grid} == "5x5_amazon" ]]; then
     hillslope_file='/glade/derecho/scratch/samrabin/hillslopes_5x5_amazon/hand_analysis_global/combined/hilldata_5x5_amazon_hist_2000_78pfts_c240216.nc'
 else

From ad0ab606eb7b1dbda164979a531c64581f4a4a06 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 27 Sep 2024 12:33:38 -0600
Subject: [PATCH 1143/1248] Add/edit comments about 5x5_amazon hillslope tests.

---
 cime_config/testdefs/testlist_clm.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index b92c62be15..d27d1d0ec9 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3537,6 +3537,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment">Serial test of 5x5_amazon hillslopes</option>
     </options>
   </test>
 
@@ -3547,7 +3548,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment">Add a non-FATES test to aux_clm for 5x5_amazon that fails because of the ccs_config issue (see #2423); can remove once this passes</option>
+      <option name="comment">Parallel test of 5x5_amazon hillslopes</option>
     </options>
   </test>
 

From 061b1c90bc2391fea6a13a162b007b3bf0857158 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 27 Sep 2024 12:36:12 -0600
Subject: [PATCH 1144/1248] Remove parallel 5x5_amazon hillslope test from
 aux_clm.

---
 cime_config/testdefs/testlist_clm.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index d27d1d0ec9..c27cd3eda2 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3543,7 +3543,6 @@
 
   <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="hillslope"/>
     </machines>
     <options>

From 792abd1342121126dae3929bd04d6f03242aed8a Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 27 Sep 2024 14:24:51 -0600
Subject: [PATCH 1145/1248] Adding one more EXPECTED FAILURE

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 8acaf71eab..30b19ce862 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -95,6 +95,13 @@
       <comment>This failure relates to the preceding ERP failure.</comment>
     </phase>
   </test>
+  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
+    <phase name="BASELINE">
+      <status>FAIL</status>
+      <issue>#2619</issue>
+      <comment>This failure relates to the preceding ERP failure.</comment>
+    </phase>
+  </test>
 
   <test name="PEM_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningMode">
     <phase name="COMPARE_base_modpes">

From adecc67a7f31922b3ecf4077282c954656e60a5b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 27 Sep 2024 14:13:19 -0700
Subject: [PATCH 1146/1248] Revert "Merge tag 'ctsm5.3.001' into b4b-dev"


From 039626c391e5e25761fc6200796c7a13f2a24f87 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 27 Sep 2024 16:03:16 -0600
Subject: [PATCH 1147/1248] Fix clm-basic tests

---
 cime_config/config_component.xml | 10 +++++-----
 cime_config/config_compsets.xml  |  8 ++++----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 3fb682ccf0..ec78008477 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -14,7 +14,7 @@
   <!-- Descriptions of all the different valid configurations for different model versions -->
   <description modifier_mode="1">
     <desc lnd="CLM45[%SP][%SP-VIC][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP]"                  >clm4.5:</desc>
-    <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm5.0:</desc>
+    <desc lnd="CLM60[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc lnd="CLM51[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm5.1:</desc>
     <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc option="SP"              >Satellite phenology:</desc>
@@ -367,10 +367,10 @@
     <values match="last">
       <value                  compset="_CLM60%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
       <value                  compset="_CLM51%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
-      <value                  compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
-      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
-      <value                  compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
-      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
     </values>
     <group>run_component_ctsm</group>
     <file>env_case.xml</file>
diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
index 538329e523..7618c51c98 100644
--- a/cime_config/config_compsets.xml
+++ b/cime_config/config_compsets.xml
@@ -197,15 +197,15 @@
   <!-- Primarily for testing the CMIP6DECK compset option -->
   <!-- Use the CMIP6 version (clm5_0) -->
   <compset>
-    <alias>I1850Clm50BgcCropCmip6</alias>
-    <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+    <alias>I1850Clm60BgcCropCmip6</alias>
+    <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
   </compset>
 
   <!-- Primarily for testing the CMIP6WACCMDECK compset option -->
   <!-- Use the CMIP6 version (clm5_0) -->
   <compset>
-    <alias>I1850Clm50BgcCropCmip6waccm</alias>
-    <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+    <alias>I1850Clm60BgcCropCmip6waccm</alias>
+    <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
   </compset>
 
   <!-- clm5_0 (CMIP6) version with BGC-Crop and CRU forcing -->

From 70c9f8b5a825b9271cf0c268f72876f0834f687e Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 27 Sep 2024 18:08:39 -0600
Subject: [PATCH 1148/1248] Updates for my fix to take effect correctly

---
 cime_config/config_component.xml      | 8 ++++++--
 cime_config/config_compsets.xml       | 8 ++++++++
 cime_config/testdefs/testlist_clm.xml | 6 +++---
 3 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index ec78008477..454e95826e 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -14,9 +14,9 @@
   <!-- Descriptions of all the different valid configurations for different model versions -->
   <description modifier_mode="1">
     <desc lnd="CLM45[%SP][%SP-VIC][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP]"                  >clm4.5:</desc>
-    <desc lnd="CLM60[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
+    <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc lnd="CLM51[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm5.1:</desc>
-    <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
+    <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc option="SP"              >Satellite phenology:</desc>
 
     <desc option="SP-VIC"          >Satellite phenology with VIC hydrology:</desc>
@@ -367,6 +367,10 @@
     <values match="last">
       <value                  compset="_CLM60%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
       <value                  compset="_CLM51%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
+      <value                  compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
+      <value                  compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
       <value                  compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
       <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
       <value                  compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
index 7618c51c98..e5d716384a 100644
--- a/cime_config/config_compsets.xml
+++ b/cime_config/config_compsets.xml
@@ -196,6 +196,10 @@
 
   <!-- Primarily for testing the CMIP6DECK compset option -->
   <!-- Use the CMIP6 version (clm5_0) -->
+  <compset>
+    <alias>I1850Clm50BgcCropCmip6</alias>
+    <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
   <compset>
     <alias>I1850Clm60BgcCropCmip6</alias>
     <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
@@ -203,6 +207,10 @@
 
   <!-- Primarily for testing the CMIP6WACCMDECK compset option -->
   <!-- Use the CMIP6 version (clm5_0) -->
+  <compset>
+    <alias>I1850Clm50BgcCropCmip6waccm</alias>
+    <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
   <compset>
     <alias>I1850Clm60BgcCropCmip6waccm</alias>
     <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 0eb3d5012d..f0c089f3a4 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1732,7 +1732,7 @@
       <option name="comment"       >Repeat ERS_Ly20_Mmpi-serial...cropMonthlyNoinitial test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic">
+  <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm60BgcCropCmip6" testmods="clm/basic">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -2431,7 +2431,7 @@
       <option name="comment"  >include a production intel test of Clm45</option>
     </options>
   </test>
-  <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic_interp">
+  <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm60BgcCropCmip6" testmods="clm/basic_interp">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -3262,7 +3262,7 @@
       <option name="comment">12 month exact restart FATES single site debug test covering anthropogenic fire ignition mode.</option>
     </options>
   </test>
-  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6waccm" testmods="clm/basic">
+  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm60BgcCropCmip6waccm" testmods="clm/basic">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prealpha"/>

From 698902d003d582babbc08dcf993fc7ac752d2637 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 27 Sep 2024 18:15:09 -0600
Subject: [PATCH 1149/1248] Small important correction

---
 cime_config/config_component.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index 454e95826e..540d285a85 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -14,7 +14,7 @@
   <!-- Descriptions of all the different valid configurations for different model versions -->
   <description modifier_mode="1">
     <desc lnd="CLM45[%SP][%SP-VIC][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP]"                  >clm4.5:</desc>
-    <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
+    <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm5.0:</desc>
     <desc lnd="CLM51[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm5.1:</desc>
     <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc option="SP"              >Satellite phenology:</desc>

From bcbc46295766fc4e2ce1421fdf6876bc50040360 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 30 Sep 2024 12:19:57 -0600
Subject: [PATCH 1150/1248] Change testlist_clm ne30pg3_t061 tests to
 ne30pg3_t232

---
 cime_config/testdefs/testlist_clm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 0eb3d5012d..34a9caffb5 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1987,7 +1987,7 @@
       <option name="comment"  >Simple test to make sure the basic Fates-SP compset works"</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t232" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -1996,7 +1996,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t232" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>

From f312b8add316daca532a9be6ba6a96c695a654a0 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 30 Sep 2024 13:36:55 -0600
Subject: [PATCH 1151/1248] First commit for CESM3 tuning of the dust emission
 module by dmleung. 30 Sep 2024

---
 src/biogeochem/DustEmisLeung2023.F90         | 10 ++++++----
 src/biogeophys/SoilStateInitTimeConstMod.F90 |  4 +++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 869c18c0dc..b77dcae9dc 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -384,14 +384,16 @@ subroutine DustEmission (this, bounds, &
     real(r8) :: wnd_frc_thr_slt_it  ! [m/s] created for impact threshold friction velocity
     real(r8) :: wnd_frc_thr_slt     ! [m/s] used for wet fluid threshold friction velocity
     real(r8) :: K_length            ! [dimless] normalized mean interobstacle distance, or called gap length (Okin, 2008)
+    ! dmleung has these variables and will change them into pointers and prepare for their history outputs. 30 Sep 2024
     real(r8) :: bare_frc            ! LUH2 bare soil land cover fraction
-    real(r8) :: veg_frc             ! LUH2 natural vegetation + crop land cover fraction
+    real(r8) :: natveg_frc          ! LUH2 natural vegetation cover fraction
+    real(r8) :: crop_frc            ! LUH2 crop cover fraction.
     !
     ! constants
     !
     real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
     real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
-    real(r8), parameter :: vai_mbl_thr = 1.0_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests 1, and Zender's scheme uses 0.3
+    real(r8), parameter :: vai_mbl_thr = 0.5_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests something between 0.6 and 1 for tuning. Zender's scheme uses 0.3. Simone Tilmes might want this as a namelist variable for easier CESM tuning. dmleung 30 Sep 2024.
 
     real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient
     real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent
@@ -407,7 +409,7 @@ subroutine DustEmission (this, bounds, &
     real(r8), parameter :: D_p = 130e-6_r8             ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2023). dmleung 16 Feb 2024
     real(r8), parameter :: gamma_Shao = 1.65e-4_r8     ! [kg s-2] interparticle cohesion: fitting parameter in Shao and Lu (2000) (S&L00). dmleung 16 Feb 2024
     real(r8), parameter :: A_Shao = 0.0123_r8          ! [dimless] coefficient for aerodynamic force: fitting parameter in Shao and Lu (2000). dmleung 16 Feb 2024
-    real(r8), parameter :: frag_expt_thr = 5.0_r8      ! [dimless] threshold for fragmentation exponent defined in Leung et al. (2023), somewhere within 3 to 5. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024
+    real(r8), parameter :: frag_expt_thr = 2.5_r8      ! [dimless] Maximum value or threshold for fragmentation exponent defined in Leung et al. (2023). Danny M. Leung suggested it to be somewhere between 3 and 5 for tuning. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024. Update: Simone Tilmes might want this as a namelist variable for easier CESM tuning. 30 Sep 2024.
     real(r8), parameter :: z0a_glob = 1e-4_r8          ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
     real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
     real(r8), parameter :: vai0_Okin = 0.1_r8          ! [m2/m2] minimum VAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
@@ -886,4 +888,4 @@ end subroutine SetDragPartition
 
  !==============================================================================
 
-end module DustEmisLeung2023
\ No newline at end of file
+end module DustEmisLeung2023
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index e6fcca0f27..fc542075fe 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -765,12 +765,14 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
   !------------------------------------------------------------------------------
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
+      real(r8), parameter :: a = 0.5_r8   ! Tuning factor for the soil moisture effect. This parameter could also be added into ThresholdSoilMoistKok2014. Simone Tilmes suggested to change this parameter into a namelist variable for easier CESM tuning. dmleung 30 Sep 2024.
+
       if ( clay < 0.0_r8 .or. clay > 100.0_r8 )then
          ThresholdSoilMoistZender2003 = nan
          call endrun( 'Clay fraction is out of bounds (0 to 100)')
          return
       end if
-      ThresholdSoilMoistZender2003 = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
+      ThresholdSoilMoistZender2003 = a * ( 0.17_r8 + 0.14_r8 * (clay*0.01_r8) )
   end function ThresholdSoilMoistZender2003
 
   !------------------------------------------------------------------------------

From d3d4e2ee89246654d02b22f286c4365ef63de92b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 30 Sep 2024 17:08:32 -0600
Subject: [PATCH 1152/1248] Allocate elevclass_o before use in mkglcmecMod.F90

---
 tools/mksurfdata_esmf/src/mkglcmecMod.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/mksurfdata_esmf/src/mkglcmecMod.F90 b/tools/mksurfdata_esmf/src/mkglcmecMod.F90
index 25fa4a8edc..4bc3d83e06 100644
--- a/tools/mksurfdata_esmf/src/mkglcmecMod.F90
+++ b/tools/mksurfdata_esmf/src/mkglcmecMod.F90
@@ -100,6 +100,7 @@ subroutine mkglcmecInit( pioid_o )
        call shr_sys_abort()
     end if
 
+    allocate(elevclass_o(size(elevclass)))
     elevclass_o(:) = elevclass(:)
 
     if (root_task)  write(ndiag, '(a)') trim(subname)//" writing out GLC_MEC"

From f40ee1a4174c318d3580d7c0810098e4ff5627c3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 30 Sep 2024 17:30:16 -0600
Subject: [PATCH 1153/1248] Change testlist_clm C96_t061 test to C96_t232

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 34a9caffb5..25bedadb76 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -195,7 +195,7 @@
       <option name="comment"  >CTSM science test list for the half degree grid with latest CLM version for historical</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
+  <test name="SMS_Ln9" grid="C96_t232" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>

From b15640f6d35ecc95bdeb6157561e8f8cee741e07 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 30 Sep 2024 18:16:33 -0600
Subject: [PATCH 1154/1248] Remove elevclass_o altogether because it is NOT
 used

---
 tools/mksurfdata_esmf/src/mkglcmecMod.F90 | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tools/mksurfdata_esmf/src/mkglcmecMod.F90 b/tools/mksurfdata_esmf/src/mkglcmecMod.F90
index 4bc3d83e06..6dc363ecac 100644
--- a/tools/mksurfdata_esmf/src/mkglcmecMod.F90
+++ b/tools/mksurfdata_esmf/src/mkglcmecMod.F90
@@ -49,7 +49,6 @@ subroutine mkglcmecInit( pioid_o )
     ! local variables:
     type(var_desc_t)      :: pio_varid
     type(io_desc_t)       :: pio_iodesc
-    real(r8), allocatable :: elevclass_o(:)          ! elevation classes
     integer               :: rcode
     character(len=*), parameter :: subname = 'mkglcmecInit'
     !-----------------------------------------------------------------------
@@ -100,9 +99,6 @@ subroutine mkglcmecInit( pioid_o )
        call shr_sys_abort()
     end if
 
-    allocate(elevclass_o(size(elevclass)))
-    elevclass_o(:) = elevclass(:)
-
     if (root_task)  write(ndiag, '(a)') trim(subname)//" writing out GLC_MEC"
     rcode = pio_inq_varid(pioid_o, 'GLC_MEC', pio_varid)
     rcode = pio_put_var(pioid_o, pio_varid, elevclass)

From 191a399fe12f92dc93edfcf6169d9ebd1808b353 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Mon, 30 Sep 2024 18:20:10 -0600
Subject: [PATCH 1155/1248] dmleung deleted a few unused parameters and
 variables. 30 Sep 2024

---
 src/biogeochem/DustEmisLeung2023.F90 | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index b77dcae9dc..31f827faaf 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -358,10 +358,6 @@ subroutine DustEmission (this, bounds, &
     ! !LOCAL VARIABLES
     integer  :: fp,p,c,l,g,m,n      ! indices
     real(r8) :: liqfrac             ! fraction of total water that is liquid
-    real(r8) :: wnd_frc_rat         ! [frc] Wind friction threshold over wind friction
-    real(r8) :: wnd_frc_slt_dlt     ! [m s-1] Friction velocity increase from saltatn
-    real(r8) :: wnd_rfr_dlt         ! [m s-1] Reference windspeed excess over threshld
-    real(r8) :: dst_slt_flx_rat_ttl
     real(r8) :: flx_mss_hrz_slt_ttl
     real(r8) :: flx_mss_vrt_dst_ttl(bounds%begp:bounds%endp)
     real(r8) :: frc_thr_wet_fct
@@ -391,8 +387,6 @@ subroutine DustEmission (this, bounds, &
     !
     ! constants
     !
-    real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
-    real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
     real(r8), parameter :: vai_mbl_thr = 0.5_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests something between 0.6 and 1 for tuning. Zender's scheme uses 0.3. Simone Tilmes might want this as a namelist variable for easier CESM tuning. dmleung 30 Sep 2024.
 
     real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient

From efbeafc636410a0361054453cc7084f56af73bed Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 30 Sep 2024 18:33:21 -0600
Subject: [PATCH 1156/1248] Revert change to C96 test; will do later, when
 ccs_config gets updated

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 25bedadb76..34a9caffb5 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -195,7 +195,7 @@
       <option name="comment"  >CTSM science test list for the half degree grid with latest CLM version for historical</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="C96_t232" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
+  <test name="SMS_Ln9" grid="C96_t061" compset="I2000Clm60Sp" testmods="clm/clm60cam7LndTuningMode--clm/nofireemis">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>

From 79811dd9e5af7892aad6f1bac6d3c241c5f23491 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 30 Sep 2024 17:02:50 -0600
Subject: [PATCH 1157/1248] Add domain check for hillslope file.

---
 src/main/surfrdMod.F90 | 140 ++++++++++++++++++++++++-----------------
 1 file changed, 81 insertions(+), 59 deletions(-)

diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index 88a4dbd30b..af92aea48d 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -45,6 +45,82 @@ module surfrdMod
 
 contains
 
+  subroutine check_domain_attributes(ncid, begg, endg, ldomain, info)
+    ! !DESCRIPTION:
+    ! Checks for mismatches between the land domain and a surface or similar dataset's domain.
+    !
+    ! !USES:
+    use domainMod, only : domain_type, domain_init
+    !
+    ! !ARGUMENTS
+    type(file_desc_t), intent(inout) :: ncid ! netcdf id for input file
+    integer, intent(in) :: begg, endg
+    type(domain_type), intent(in) :: ldomain  ! land domain
+    character(len=*), intent(in) :: info  ! information to include in messages
+    !
+    ! !LOCAL VARIABLES
+    type(domain_type) :: surfdata_domain  ! local domain associated with dataset
+    logical :: readvar  ! true => variable is on dataset
+    logical :: istype_domain  ! true => input file is of type domain
+    character(len=16) :: lon_var, lat_var  ! names of lat/lon on dataset
+    logical :: isgrid2d  ! true => input grid is 2d
+    integer :: ni, nj, ns  ! domain sizes
+    integer :: n
+    real(r8) :: rmaxlon, rmaxlat  ! local min/max vars
+
+   character(len=32) :: subname = 'check_domain_attributes'  ! subroutine name
+
+    call check_var(ncid=ncid, varname='xc', readvar=readvar)
+    if (readvar) then
+       istype_domain = .true.
+    else
+       call check_var(ncid=ncid, varname='LONGXY', readvar=readvar)
+       if (readvar) then
+          istype_domain = .false.
+       else
+          call endrun( msg=' ERROR: unknown '//info//' domain type---'//errMsg(sourcefile, __LINE__))
+       end if
+    end if
+    if (istype_domain) then
+       lon_var  = 'xc'
+       lat_var  = 'yc'
+    else
+       lon_var  = 'LONGXY'
+       lat_var  = 'LATIXY'
+    end if
+    if ( masterproc )then
+       write(iulog,*) trim(subname),' ',info,' lon_var = ',trim(lon_var),' lat_var =',trim(lat_var)
+    end if
+
+    call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
+    call domain_init(surfdata_domain, isgrid2d, ni, nj, begg, endg, subgrid_level=grlnd)
+
+    call ncd_io(ncid=ncid, varname=lon_var, flag='read', data=surfdata_domain%lonc, &
+         dim1name=grlnd, readvar=readvar)
+    if (.not. readvar) call endrun( msg=' ERROR: lon var NOT on '//info//' dataset---'//errMsg(sourcefile, __LINE__))
+
+    call ncd_io(ncid=ncid, varname=lat_var, flag='read', data=surfdata_domain%latc, &
+         dim1name=grlnd, readvar=readvar)
+    if (.not. readvar) call endrun( msg=' ERROR: lat var NOT on '//info//' dataset---'//errMsg(sourcefile, __LINE__))
+
+    rmaxlon = 0.0_r8
+    rmaxlat = 0.0_r8
+    do n = begg,endg
+       if (ldomain%lonc(n)-surfdata_domain%lonc(n) > 300.) then
+          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)-360._r8))
+       elseif (ldomain%lonc(n)-surfdata_domain%lonc(n) < -300.) then
+          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)+360._r8))
+       else
+          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)))
+       endif
+       rmaxlat = max(rmaxlat,abs(ldomain%latc(n)-surfdata_domain%latc(n)))
+    enddo
+    if (rmaxlon > 0.001_r8 .or. rmaxlat > 0.001_r8) then
+       write(iulog,*)' ERROR: '//info//' dataset vs. land domain lon/lat mismatch error', rmaxlon,rmaxlat
+       call endrun(msg=errMsg(sourcefile, __LINE__))
+    end if
+  end subroutine check_domain_attributes
+
   !-----------------------------------------------------------------------
   subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, lhillslope_file, actual_numcft)
     !
@@ -76,7 +152,7 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, lhillslope_file, actu
                              n_dom_landunits, &
                              use_hillslope
     use fileutils           , only : getfil
-    use domainMod           , only : domain_type, domain_init, domain_clean
+    use domainMod           , only : domain_type
     use clm_instur          , only : wt_lunit, topo_glc_mec, pct_urban_max
     use landunit_varcon     , only : max_lunit, istsoil, isturb_MIN, isturb_MAX
     use dynSubgridControlMod, only : get_flanduse_timeseries
@@ -91,18 +167,10 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, lhillslope_file, actu
     character(len=*), intent(in) :: lhillslope_file ! hillslope dataset filename
     !
     ! !LOCAL VARIABLES:
-    type(domain_type) :: surfdata_domain      ! local domain associated with surface dataset
     character(len=256):: locfn                ! local file name
     integer, parameter :: n_dom_urban = 1     ! # of dominant urban landunits
-    integer           :: n                    ! loop indices
-    integer           :: ni,nj,ns             ! domain sizes
-    character(len=16) :: lon_var, lat_var     ! names of lat/lon on dataset
-    logical           :: readvar              ! true => variable is on dataset
-    real(r8)          :: rmaxlon,rmaxlat      ! local min/max vars
     type(file_desc_t) :: ncid                 ! netcdf id for lfsurdat
     type(file_desc_t) :: ncid_hillslope       ! netcdf id for lhillslope_file
-    logical           :: istype_domain        ! true => input file is of type domain
-    logical           :: isgrid2d             ! true => intut grid is 2d
 
     character(len=32) :: subname = 'surfrd_get_data'    ! subroutine name
     !-----------------------------------------------------------------------
@@ -131,56 +199,10 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, lhillslope_file, actu
        call ncd_pio_openfile (ncid_hillslope, trim(locfn), 0)
     end if
 
-    ! Cmopare surfdat_domain attributes to ldomain attributes
-
-    call check_var(ncid=ncid, varname='xc', readvar=readvar)
-    if (readvar) then
-       istype_domain = .true.
-    else
-       call check_var(ncid=ncid, varname='LONGXY', readvar=readvar)
-       if (readvar) then
-          istype_domain = .false.
-       else
-          call endrun( msg=' ERROR: unknown domain type'//errMsg(sourcefile, __LINE__))
-       end if
-    end if
-    if (istype_domain) then
-       lon_var  = 'xc'
-       lat_var  = 'yc'
-    else
-       lon_var  = 'LONGXY'
-       lat_var  = 'LATIXY'
-    end if
-    if ( masterproc )then
-       write(iulog,*) trim(subname),' lon_var = ',trim(lon_var),' lat_var =',trim(lat_var)
-    end if
-
-    call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
-    call domain_init(surfdata_domain, isgrid2d, ni, nj, begg, endg, subgrid_level=grlnd)
-
-    call ncd_io(ncid=ncid, varname=lon_var, flag='read', data=surfdata_domain%lonc, &
-         dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) call endrun( msg=' ERROR: lon var NOT on surface dataset'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io(ncid=ncid, varname=lat_var, flag='read', data=surfdata_domain%latc, &
-         dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) call endrun( msg=' ERROR: lat var NOT on surface dataset'//errMsg(sourcefile, __LINE__))
-
-    rmaxlon = 0.0_r8
-    rmaxlat = 0.0_r8
-    do n = begg,endg
-       if (ldomain%lonc(n)-surfdata_domain%lonc(n) > 300.) then
-          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)-360._r8))
-       elseif (ldomain%lonc(n)-surfdata_domain%lonc(n) < -300.) then
-          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)+360._r8))
-       else
-          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)))
-       endif
-       rmaxlat = max(rmaxlat,abs(ldomain%latc(n)-surfdata_domain%latc(n)))
-    enddo
-    if (rmaxlon > 0.001_r8 .or. rmaxlat > 0.001_r8) then
-       write(iulog,*)' ERROR: surfdata_domain/ldomain lon/lat mismatch error', rmaxlon,rmaxlat
-       call endrun(msg=errMsg(sourcefile, __LINE__))
+    ! Compare dataset domain attributes to ldomain attributes
+    call check_domain_attributes(ncid, begg, endg, ldomain, 'surface')
+    if (use_hillslope) then
+       call check_domain_attributes(ncid_hillslope, begg, endg, ldomain, 'hillslope')
     end if
 
     !~! TODO(SPM, 022015) - if we deallocate and clean ldomain here, then you

From ea9228c7d8f4259bdf59cda611308989083f3371 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 1 Oct 2024 09:40:56 -0600
Subject: [PATCH 1158/1248] Update 10x15 hillslope_file (now has
 LATIXY/LONGXY).

---
 .../testdefs/testmods_dirs/clm/Hillslope/shell_commands       | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
index 7bec6fd7f6..9cef7eb66f 100644
--- a/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands
@@ -4,8 +4,10 @@ DIN_LOC_ROOT=$(./xmlquery --value DIN_LOC_ROOT)
 # Set hillslope_file. Needed for any grids without default hillslope_file already set by CTSM.
 lnd_grid=$(./xmlquery --value LND_GRID)
 if [[ ${lnd_grid} == "10x15" ]]; then
-    hillslope_file='$DIN_LOC_ROOT/lnd/clm2/testdata/synthetic_cosphill_10x15_1.3.nc'
+    # Synthetic data
+    hillslope_file='$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_1850_78pfts_c240216.synth_hillslopes_241001.nc'
 elif [[ ${lnd_grid} == "5x5_amazon" ]]; then
+    # Real data
     hillslope_file='/glade/derecho/scratch/samrabin/hillslopes_5x5_amazon/hand_analysis_global/combined/hilldata_5x5_amazon_hist_2000_78pfts_c240216.nc'
 else
     echo "ERROR: Hillslope file not found for LND_GRID=${lnd_grid}" >&2

From 4b032be5b4a279723ed840b4be851829cd37ec9c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 1 Oct 2024 09:59:52 -0600
Subject: [PATCH 1159/1248] Improve use_init_interp+use_hillslope namelist
 warning.

---
 bld/CLMBuildNamelist.pm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index dc89e932ca..e9a4ff4d56 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2746,8 +2746,7 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
 
   # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
   if ( &value_is_true($nl->get_value($useinitvar)) && value_is_true($nl->get_value("use_hillslope")) ) {
-     $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values" .
-                   " from initial conditions. If you are sure you want this behaviour:")
+     $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values from initial conditions, even if the initial conditions (finidat) file has hillslope information. If you are sure you want this behaviour, add -ignore_warnings to CLM_BLDNML_OPTS.")
   }
 
 } # end initial conditions

From 5c74ff44cb78427c458f429a4c255405e2eb69a9 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 1 Oct 2024 11:19:07 -0600
Subject: [PATCH 1160/1248] Call domain_clean() at end of
 check_domain_attributes().

Resolves nag error in hillslope call of check_domain_attributes()---somehow, surfdata_domain was marked as "set" but was uninitialized, causing error in domain_init().
---
 src/main/surfrdMod.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index 1404ee03f2..bb2a90022c 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -51,7 +51,7 @@ subroutine check_domain_attributes(ncid, begg, endg, ldomain, info)
     ! Checks for mismatches between the land domain and a surface or similar dataset's domain.
     !
     ! !USES:
-    use domainMod, only : domain_type, domain_init
+    use domainMod, only : domain_type, domain_init, domain_clean
     !
     ! !ARGUMENTS
     type(file_desc_t), intent(inout) :: ncid ! netcdf id for input file
@@ -120,6 +120,7 @@ subroutine check_domain_attributes(ncid, begg, endg, ldomain, info)
        write(iulog,*)' ERROR: '//info//' dataset vs. land domain lon/lat mismatch error', rmaxlon,rmaxlat
        call endrun(msg=errMsg(sourcefile, __LINE__))
     end if
+    call domain_clean(surfdata_domain)
   end subroutine check_domain_attributes
 
   !-----------------------------------------------------------------------

From 1a93690347ba7c1a3c38ccdfc0e77154c94a535b Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 1 Oct 2024 11:21:24 -0600
Subject: [PATCH 1161/1248] Remove outdated comment/TODO.

---
 src/main/surfrdMod.F90 | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index bb2a90022c..59094ac1f3 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -271,11 +271,6 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat, lhillslope_file, actu
        call check_domain_attributes(ncid_hillslope, begg, endg, ldomain, 'hillslope')
     end if
 
-    !~! TODO(SPM, 022015) - if we deallocate and clean ldomain here, then you
-    !~! get errors in htape_timeconst where the information is needed to write
-    !~! the *.h0* file
-    !~!call domain_clean(surfdata_domain)
-
     ! Obtain special landunit info
 
     call surfrd_special(begg, endg, ncid, ldomain%ns)

From 5e71b7d92588d345ec8016e76f6d24f4b3271664 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 1 Oct 2024 11:22:20 -0600
Subject: [PATCH 1162/1248] Rename surfdata_domain to inputdata_domain.

More general to reflect that it's not necessarily the surface dataset's domain.
---
 src/main/surfrdMod.F90 | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index 59094ac1f3..4005ec7845 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -60,7 +60,7 @@ subroutine check_domain_attributes(ncid, begg, endg, ldomain, info)
     character(len=*), intent(in) :: info  ! information to include in messages
     !
     ! !LOCAL VARIABLES
-    type(domain_type) :: surfdata_domain  ! local domain associated with dataset
+    type(domain_type) :: inputdata_domain  ! local domain associated with input dataset
     logical :: readvar  ! true => variable is on dataset
     logical :: istype_domain  ! true => input file is of type domain
     character(len=16) :: lon_var, lat_var  ! names of lat/lon on dataset
@@ -94,33 +94,33 @@ subroutine check_domain_attributes(ncid, begg, endg, ldomain, info)
     end if
 
     call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
-    call domain_init(surfdata_domain, isgrid2d, ni, nj, begg, endg, subgrid_level=grlnd)
+    call domain_init(inputdata_domain, isgrid2d, ni, nj, begg, endg, subgrid_level=grlnd)
 
-    call ncd_io(ncid=ncid, varname=lon_var, flag='read', data=surfdata_domain%lonc, &
+    call ncd_io(ncid=ncid, varname=lon_var, flag='read', data=inputdata_domain%lonc, &
          dim1name=grlnd, readvar=readvar)
     if (.not. readvar) call endrun( msg=' ERROR: lon var NOT on '//info//' dataset---'//errMsg(sourcefile, __LINE__))
 
-    call ncd_io(ncid=ncid, varname=lat_var, flag='read', data=surfdata_domain%latc, &
+    call ncd_io(ncid=ncid, varname=lat_var, flag='read', data=inputdata_domain%latc, &
          dim1name=grlnd, readvar=readvar)
     if (.not. readvar) call endrun( msg=' ERROR: lat var NOT on '//info//' dataset---'//errMsg(sourcefile, __LINE__))
 
     rmaxlon = 0.0_r8
     rmaxlat = 0.0_r8
     do n = begg,endg
-       if (ldomain%lonc(n)-surfdata_domain%lonc(n) > 300.) then
-          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)-360._r8))
-       elseif (ldomain%lonc(n)-surfdata_domain%lonc(n) < -300.) then
-          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)+360._r8))
+       if (ldomain%lonc(n)-inputdata_domain%lonc(n) > 300.) then
+          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-inputdata_domain%lonc(n)-360._r8))
+       elseif (ldomain%lonc(n)-inputdata_domain%lonc(n) < -300.) then
+          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-inputdata_domain%lonc(n)+360._r8))
        else
-          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-surfdata_domain%lonc(n)))
+          rmaxlon = max(rmaxlon,abs(ldomain%lonc(n)-inputdata_domain%lonc(n)))
        endif
-       rmaxlat = max(rmaxlat,abs(ldomain%latc(n)-surfdata_domain%latc(n)))
+       rmaxlat = max(rmaxlat,abs(ldomain%latc(n)-inputdata_domain%latc(n)))
     enddo
     if (rmaxlon > 0.001_r8 .or. rmaxlat > 0.001_r8) then
        write(iulog,*)' ERROR: '//info//' dataset vs. land domain lon/lat mismatch error', rmaxlon,rmaxlat
        call endrun(msg=errMsg(sourcefile, __LINE__))
     end if
-    call domain_clean(surfdata_domain)
+    call domain_clean(inputdata_domain)
   end subroutine check_domain_attributes
 
   !-----------------------------------------------------------------------

From 3295adb9ac0e40f48b20a5c6c9d0b9c02d58351d Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 1 Oct 2024 14:42:06 -0600
Subject: [PATCH 1163/1248] Correct the name of the hash to use in the checks
 that hash values are all set in fail, warn, and finidat tests

---
 bld/unit_testers/build-namelist_test.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 421bf81b5e..096409065f 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1376,7 +1376,7 @@ sub cat_and_create_namelistinfile {
 
    my $var;
    foreach $var ( "phys" , "options", "namelst" ) {
-      if ( not exists $failtest{$key}{$var} ) {
+      if ( not exists $warntest{$key}{$var} ) {
          die  "ERROR: Subkey $var does not exist for warntest $key\nERROR:Check if you spelled $var correctly\n"
       }
    }
@@ -1613,7 +1613,7 @@ sub cat_and_create_namelistinfile {
 
    my $var;
    foreach $var ( "phys" , "atm_forc", "res", "bgc", "crop", "use_case", "start_ymd", "namelist" ) {
-      if ( not exists $failtest{$key}{$var} ) {
+      if ( not exists $finidat_files{$key}{$var} ) {
          die  "ERROR: Subkey $var does not exist for finidat_file $key\nERROR:Check if you spelled $var correctly\n"
       }
    }

From 6c352166d3e7a4f0909ba24d8f338a55ecf98622 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 1 Oct 2024 16:51:00 -0600
Subject: [PATCH 1164/1248] dmleung changed the values of the tuning parameters
 and added a new tuning factor for vegetation drag partition effect. Also a
 first attempt to modify the code for soil moisture effect on dust to avoid
 having a factor that changes the answer of Zender's dust emissions.

---
 src/biogeochem/DustEmisLeung2023.F90         |  9 +++++----
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 19 ++++++++++++++-----
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 31f827faaf..3b250aa003 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -387,7 +387,7 @@ subroutine DustEmission (this, bounds, &
     !
     ! constants
     !
-    real(r8), parameter :: vai_mbl_thr = 0.5_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests something between 0.6 and 1 for tuning. Zender's scheme uses 0.3. Simone Tilmes might want this as a namelist variable for easier CESM tuning. dmleung 30 Sep 2024.
+    real(r8), parameter :: vai_mbl_thr = 0.6_r8        ! [m2 m-2] new VAI threshold; Danny M. Leung suggests something between 0.6 and 1 for tuning. Zender's scheme uses 0.3. Simone Tilmes might want this as a namelist variable for easier CESM tuning. dmleung 30 Sep 2024.
 
     real(r8), parameter :: Cd0 = 4.4e-5_r8             ! [dimless] proportionality constant in calculation of dust emission coefficient
     real(r8), parameter :: Ca = 2.7_r8                 ! [dimless] proportionality constant in scaling of dust emission exponent
@@ -403,11 +403,12 @@ subroutine DustEmission (this, bounds, &
     real(r8), parameter :: D_p = 130e-6_r8             ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2023). dmleung 16 Feb 2024
     real(r8), parameter :: gamma_Shao = 1.65e-4_r8     ! [kg s-2] interparticle cohesion: fitting parameter in Shao and Lu (2000) (S&L00). dmleung 16 Feb 2024
     real(r8), parameter :: A_Shao = 0.0123_r8          ! [dimless] coefficient for aerodynamic force: fitting parameter in Shao and Lu (2000). dmleung 16 Feb 2024
-    real(r8), parameter :: frag_expt_thr = 2.5_r8      ! [dimless] Maximum value or threshold for fragmentation exponent defined in Leung et al. (2023). Danny M. Leung suggested it to be somewhere between 3 and 5 for tuning. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024. Update: Simone Tilmes might want this as a namelist variable for easier CESM tuning. 30 Sep 2024.
+    real(r8), parameter :: frag_expt_thr = 3.0_r8      ! [dimless] Maximum value or threshold for fragmentation exponent defined in Leung et al. (2023). Danny M. Leung suggested it to be somewhere between 3 and 5 for tuning. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024. Update: Simone Tilmes might want this as a namelist variable for easier CESM tuning. 30 Sep 2024.
     real(r8), parameter :: z0a_glob = 1e-4_r8          ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
     real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
     real(r8), parameter :: vai0_Okin = 0.1_r8          ! [m2/m2] minimum VAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
     real(r8), parameter :: zii = 1000.0_r8             ! [m] convective boundary layer height added by dmleung 20 Feb 2024, following other CTSM modules (e.g., CanopyFluxesMod). Should we transfer PBL height (PBLH) from CAM?
+    real(r8), parameter :: dust_veg_part_fact = 0.7_r8 ! [dimless] dmleung added a tuning factor for Greg Okin's vegetation drag partition effect. dmleung suggested a smaller vegetation drag partition effect given an increase in vegetation roughness after CTSM switched from using ZengWang2007 to Meier2022. This is simply because the drag partition effect should decrease with increasing roughness, but Okin's scheme is only a function of LAI. One might want to change this factor to 1_r8 when using ZengWang2007. dmleung 30 Sep 2024
     real(r8) :: numer                                  ! Numerator term for threshold crossing rate
     real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     !------------------------------------------------------------------------
@@ -646,8 +647,8 @@ subroutine DustEmission (this, bounds, &
 
 
             ! calculate Okin's shear stress ratio (SSR, which is vegetation drag partition factor) using Pierre's equation
-            K_length = 2.0_r8 * (1.0_r8/vai_Okin(p) - 1.0_r8)   ! Here LAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
-            ssr(p) = (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023). This line is Pierre's formulation.
+            K_length = 2.0_r8 * (1.0_r8/vai_Okin(p) - 1.0_r8)   ! Here VAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
+            ssr(p) = dust_veg_part_fact * (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023). This line is Pierre's formulation. dmleung added a tuning factor for Okin's vegetation drag partition effect (SSR) on 30 Sep 2024.
 
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index fc542075fe..3bd280761f 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -220,6 +220,7 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     real(r8)           :: perturbed_sand                ! temporary for paramfile implementation of +/- sand percentage
     real(r8)           :: residual_clay_frac            ! temporary for paramfile implementation of +/- residual clay percentage
     real(r8)           :: perturbed_residual_clay_frac  ! temporary for paramfile implementation of +/- residual clay percentage
+    real(r8)           :: dust_moist_fact               ! tuning factor for soil moisture effect on limiting dust emissions, used by Charlie Zender. Simone Tilmes suggested to change this parameter into a namelist variable for easier CESM tuning. dmleung added 30 Sep 2024
     integer            :: dimid                         ! dimension id
     logical            :: readvar 
     type(file_desc_t)  :: ncid                          ! netcdf id
@@ -708,16 +709,24 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
     ! Initialize threshold soil moisture, and mass fraction of clay as
     ! scaling coefficient of dust emission flux (kg/m2/s) in each DustEmisType
     ! module. See the comments in each function.
+    ! Zender suggested that threshold soil moisture is tunable (see comment
+    ! inside ThresholdSoilMoistZender2003). dmleung further add dust_moist_fact
+    ! ofr modelers to tune the threshold soil moisture. The resulting tuning 
+    ! factor is thus a = dust_moist_fact / (clay3d). dmleung 30 Sep 2024
     ! --------------------------------------------------------------------
 
     do c = begc,endc
        g = col%gridcell(c)
 
-       soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay3d(g,1) )
+       !soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay3d(g,1) )
        if ( is_dust_emis_leung() )then
           soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClayLeung2023( clay3d(g,1) )
+          dust_moist_fact = 0.9_r8   ! change this into a namelist variable later.
+          soilstate_inst%gwc_thr_col(c) = dust_moist_fact * ThresholdSoilMoistZender2003( clay3d(g,1) )
        else
           soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay3d(g,1) )
+          dust_moist_fact = 1.0_r8
+          soilstate_inst%gwc_thr_col(c) = dust_moist_fact * ThresholdSoilMoistZender2003( clay3d(g,1) )
        end if
 
     end do
@@ -739,9 +748,11 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
   ! Calculate the threshold gravimetric water content needed for dust emission, based on clay content
   ! This was the original equation with a = 1 / (%clay) being the tuning factor for soil
   ! moisture effect in Zender's 2003 dust emission scheme (only for top layer).
+  ! dmleung further added dust_moist_fact for more flexibility in tuning, so the tuning factor here
+  ! is a = dust_moist_fact / (%clay). dmleung added dust_moist_fact on 30 Sep 2024.
   !
   ! 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to
-  ! convert surface clay fraction from percentage to fraction.
+  ! convert surface clay from percentage to fraction.
   ! The equation comes from Eq. 14 of Fecan et al. (1999; https://doi.org/10.1007/s00585-999-0149-7).
   !
   ! NOTE: dmleung 19 Feb 2024.
@@ -765,14 +776,12 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
   !------------------------------------------------------------------------------
       real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%)
 
-      real(r8), parameter :: a = 0.5_r8   ! Tuning factor for the soil moisture effect. This parameter could also be added into ThresholdSoilMoistKok2014. Simone Tilmes suggested to change this parameter into a namelist variable for easier CESM tuning. dmleung 30 Sep 2024.
-
       if ( clay < 0.0_r8 .or. clay > 100.0_r8 )then
          ThresholdSoilMoistZender2003 = nan
          call endrun( 'Clay fraction is out of bounds (0 to 100)')
          return
       end if
-      ThresholdSoilMoistZender2003 = a * ( 0.17_r8 + 0.14_r8 * (clay*0.01_r8) )
+      ThresholdSoilMoistZender2003 = 0.17_r8 + 0.14_r8 * (clay*0.01_r8) 
   end function ThresholdSoilMoistZender2003
 
   !------------------------------------------------------------------------------

From f2f75351febd4a413b0788dae256443fe5734510 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 1 Oct 2024 15:53:22 -0700
Subject: [PATCH 1165/1248] add shell call to generate fates hydro parameter
 file on the fly

This is a temporary update to avoid NGEET/fates#1254 and should be
removed once a fix comes in on the fates-side.
---
 .../testmods_dirs/clm/FatesColdHydro/shell_commands       | 8 ++++++++
 .../testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm | 1 +
 2 files changed, 9 insertions(+)
 create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands
new file mode 100644
index 0000000000..e629e7ca34
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands
@@ -0,0 +1,8 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates
+FATESPARAMFILE=$CASEDIR/fates_params_hydrograsstempfix.nc
+
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
+
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_allom_smode --val 1 --allpfts
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
index f0bdb388eb..15dcf6de1a 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
@@ -2,6 +2,7 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_planthydro= .true.
+fates_paramfile = '$CASEROOT/fates_params_hydrograsstempfix.n'
 hist_fincl1       = 'FATES_ERRH2O_SZPF', 'FATES_TRAN_SZPF',
 'FATES_SAPFLOW_SZPF', 'FATES_ITERH1_SZPF','FATES_ABSROOT_H2O_SZPF',
 'FATES_TRANSROOT_H2O_SZPF','FATES_STEM_H2O_SZPF','FATES_LEAF_H2O_SZPF',

From 52e5801fd9ffe8dfa309c63edd695c08d7630e31 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Tue, 1 Oct 2024 17:10:57 -0600
Subject: [PATCH 1166/1248] dmleung renamed the tuning parameter for Okin's
 vegetation drag partition factor to dust_veg_drag_fact from
 dust_veg_part_fact. 1 Oct 2024

---
 src/biogeochem/DustEmisLeung2023.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 3b250aa003..0fee001e64 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -408,7 +408,7 @@ subroutine DustEmission (this, bounds, &
     real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
     real(r8), parameter :: vai0_Okin = 0.1_r8          ! [m2/m2] minimum VAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
     real(r8), parameter :: zii = 1000.0_r8             ! [m] convective boundary layer height added by dmleung 20 Feb 2024, following other CTSM modules (e.g., CanopyFluxesMod). Should we transfer PBL height (PBLH) from CAM?
-    real(r8), parameter :: dust_veg_part_fact = 0.7_r8 ! [dimless] dmleung added a tuning factor for Greg Okin's vegetation drag partition effect. dmleung suggested a smaller vegetation drag partition effect given an increase in vegetation roughness after CTSM switched from using ZengWang2007 to Meier2022. This is simply because the drag partition effect should decrease with increasing roughness, but Okin's scheme is only a function of LAI. One might want to change this factor to 1_r8 when using ZengWang2007. dmleung 30 Sep 2024
+    real(r8), parameter :: dust_veg_drag_fact = 0.7_r8 ! [dimless] dmleung added a tuning factor for Greg Okin's vegetation drag partition effect. dmleung suggested a smaller vegetation drag partition effect given an increase in vegetation roughness after CTSM switched from using ZengWang2007 to Meier2022. This is simply because the drag partition effect should decrease with increasing roughness, but Okin's scheme is only a function of LAI. One might want to change this factor to 1_r8 when using ZengWang2007. dmleung 30 Sep 2024
     real(r8) :: numer                                  ! Numerator term for threshold crossing rate
     real(r8) :: denom                                  ! Denominator term for threshold crossing rate
     !------------------------------------------------------------------------
@@ -648,7 +648,7 @@ subroutine DustEmission (this, bounds, &
 
             ! calculate Okin's shear stress ratio (SSR, which is vegetation drag partition factor) using Pierre's equation
             K_length = 2.0_r8 * (1.0_r8/vai_Okin(p) - 1.0_r8)   ! Here VAI has to be non-zero to avoid blowup, and < 1 to avoid -ve K_length. See this equation in Leung et al. (2023). This line is Okin's formulation
-            ssr(p) = dust_veg_part_fact * (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023). This line is Pierre's formulation. dmleung added a tuning factor for Okin's vegetation drag partition effect (SSR) on 30 Sep 2024.
+            ssr(p) = dust_veg_drag_fact * (K_length+f_0*c_e)/(K_length+c_e) ! see this equation in Caroline Pierre et al. (2014) or Leung et al. (2023). This line is Pierre's formulation. dmleung added a tuning factor for Okin's vegetation drag partition effect (SSR) on 30 Sep 2024.
 
             ! calculation of the hybrid/total drag partition effect considering both rock and vegetation drag partitioning using LUH2 bare and veg fractions within a grid
             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then

From 97d1657754c75fedd6482d4d71b773859029be5d Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 1 Oct 2024 16:11:33 -0700
Subject: [PATCH 1167/1248] fix typo in fates hydro user_nl_clm

---
 .../testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
index 15dcf6de1a..318a34dfec 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
@@ -2,7 +2,7 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_planthydro= .true.
-fates_paramfile = '$CASEROOT/fates_params_hydrograsstempfix.n'
+fates_paramfile = '$CASEROOT/fates_params_hydrograsstempfix.nc'
 hist_fincl1       = 'FATES_ERRH2O_SZPF', 'FATES_TRAN_SZPF',
 'FATES_SAPFLOW_SZPF', 'FATES_ITERH1_SZPF','FATES_ABSROOT_H2O_SZPF',
 'FATES_TRANSROOT_H2O_SZPF','FATES_STEM_H2O_SZPF','FATES_LEAF_H2O_SZPF',

From 52389c01d69b6943ffec8d547dfe2379c71188d5 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 2 Oct 2024 14:12:45 -0700
Subject: [PATCH 1168/1248] correct call typo to clm_demand for fateslanduse
 test mod

---
 .../testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
index d88457df12..6152f0bd0c 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-./xmlchange CLM_BLDNML_OPTS="--clm_demand -flanduse_timeseries" --append
+./xmlchange CLM_BLDNML_OPTS="-clm_demand flanduse_timeseries" --append

From 69b815b3885f8ff9d5932d072713f143774b4ecd Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 2 Oct 2024 16:13:44 -0700
Subject: [PATCH 1169/1248] update default fates parameter files

This update incorporates multiple parameter file updates per NGEET/fates#1255
---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index bc4a93ec4a..63b4ee9576 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -560,7 +560,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_12pft_c240814.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241002.nc</fates_paramfile>
 
 
 <!-- ================================================================== -->

From 4e0197bd3e4911413745feb6aec6e889f294834a Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Wed, 2 Oct 2024 16:21:36 -0700
Subject: [PATCH 1170/1248] update the gitmodules tag for fates

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index 7274b9acd2..1f6da08484 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.2_api.36.0.0
+fxtag = sci.1.78.3_api.36.1.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release

From 1f851c46371256fb38a0247ccde8981fb77e6ea6 Mon Sep 17 00:00:00 2001
From: "Danny M. Leung" <dannymleung@ucla.edu>
Date: Wed, 2 Oct 2024 18:07:11 -0600
Subject: [PATCH 1171/1248] Getting a new set of tuning parameters for dust.
 dmleung 2 Oct 2024

---
 src/biogeochem/DustEmisLeung2023.F90         | 2 +-
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/biogeochem/DustEmisLeung2023.F90 b/src/biogeochem/DustEmisLeung2023.F90
index 0fee001e64..e9306029be 100644
--- a/src/biogeochem/DustEmisLeung2023.F90
+++ b/src/biogeochem/DustEmisLeung2023.F90
@@ -403,7 +403,7 @@ subroutine DustEmission (this, bounds, &
     real(r8), parameter :: D_p = 130e-6_r8             ! [m] Medium soil particle diameter, assuming a global constant of ~130 um following Leung et al. (2023). dmleung 16 Feb 2024
     real(r8), parameter :: gamma_Shao = 1.65e-4_r8     ! [kg s-2] interparticle cohesion: fitting parameter in Shao and Lu (2000) (S&L00). dmleung 16 Feb 2024
     real(r8), parameter :: A_Shao = 0.0123_r8          ! [dimless] coefficient for aerodynamic force: fitting parameter in Shao and Lu (2000). dmleung 16 Feb 2024
-    real(r8), parameter :: frag_expt_thr = 3.0_r8      ! [dimless] Maximum value or threshold for fragmentation exponent defined in Leung et al. (2023). Danny M. Leung suggested it to be somewhere between 3 and 5 for tuning. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024. Update: Simone Tilmes might want this as a namelist variable for easier CESM tuning. 30 Sep 2024.
+    real(r8), parameter :: frag_expt_thr = 2.5_r8      ! [dimless] Maximum value or threshold for fragmentation exponent defined in Leung et al. (2023). Danny M. Leung suggested it to be somewhere between 3 and 5 for tuning. It is used to prevent a local AOD blowup (over Patagonia, Argentina), but one can test larger values and relax the threshold if wanted. dmleung 16 Feb 2024. Update: Simone Tilmes might want this as a namelist variable for easier CESM tuning. 30 Sep 2024.
     real(r8), parameter :: z0a_glob = 1e-4_r8          ! [m] assumed globally constant aeolian roughness length value in Leung et al. (2023), for the log law of the wall for Comola et al. (2019) intermittency scheme. dmleung 20 Feb 2024
     real(r8), parameter :: hgt_sal = 0.1_r8            ! [m] saltation height used by Comola et al. (2019) intermittency scheme for the log law of the wall. dmleung 20 Feb 2024
     real(r8), parameter :: vai0_Okin = 0.1_r8          ! [m2/m2] minimum VAI needed for Okin-Pierre's vegetation drag partition equation. lai=0 in the equation will lead to infinity, so a small value is added into this lai dmleung defined.
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 3bd280761f..38076d8327 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -721,7 +721,8 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
        !soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay3d(g,1) )
        if ( is_dust_emis_leung() )then
           soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClayLeung2023( clay3d(g,1) )
-          dust_moist_fact = 0.9_r8   ! change this into a namelist variable later.
+          !dust_moist_fact = 0.9_r8   ! change this into a namelist variable later.
+          dust_moist_fact = 1.0_r8   ! change this into a namelist variable later.
           soilstate_inst%gwc_thr_col(c) = dust_moist_fact * ThresholdSoilMoistZender2003( clay3d(g,1) )
        else
           soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay3d(g,1) )

From 65d26e68b9121ed3205e8012ea44098815acce79 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 3 Oct 2024 09:02:07 -0700
Subject: [PATCH 1172/1248] add expected failure for FatesColdLandUse test mod

This is due to needing a new 16 pft historical flanduse_timeseries file.
See #2810.  Note this is the older fates harvest mode, not the newer raw
LUH2 driven modes.
---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 30b19ce862..7b17d5743b 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -280,6 +280,13 @@
     </phase>
   </test>
 
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLandUse">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2810</issue>
+    </phase>
+  </test>
+
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 
   <test name="SMS_Lh3.f10_f10_mg37.I2000Clm51Sp.derecho_intel.mosart-clmAccelSpinupIgnoreWarn">

From 1045e1ba7492381186bb1c7092c13a1c04cefdd3 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 3 Oct 2024 09:50:53 -0700
Subject: [PATCH 1173/1248] add new changelog entry

---
 doc/ChangeLog | 87 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  2 ++
 2 files changed, 89 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index ded12c54f8..99611540cb 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,91 @@
 ===============================================================
+Tag name: ctsm5.3.003
+Originator(s): rgknox (Ryan Knox, LBNL, rgknox@lbl.gov)
+               glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Thu Oct  3 10:20:00 MDT 2024
+One-line Summary: FATES default parameter file update
+
+Purpose and description of changes
+----------------------------------
+
+This tag updates the default parameter file for FATES bringing in a number of updates:
+	- adds two new arctic shrub pfts
+	- updates the default sapwood allometry mode for grass pfts
+	- updates understory leaf turnover specifications for longer turnover rates
+	- changes the default behavior of nutrient uptake
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes #2783 -- Error in FatescoldLandUse testmod
+   Fixes FATES#1211 -- Switching the default fates_cnp_prescribed_* parameters from 1 to 0
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+   FatesColdLandUse build has been added to the list of expected failures due to #2810
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi -------
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi -------
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: FATES mode
+    - what platforms/compilers: ALL
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   fates: sci.1.78.2_api.36.0.0 -> sci.1.78.3_api.36.1.0
+
+Pull Requests that document the changes (include PR ids):
+   https://github.com/ESCOMP/CTSM/pull/2700
+   https://github.com/NGEET/fates/pull/1255
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.002
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 26 Sep 2024 03:10:40 PM MDT
+One-line Summary: Duplicate tag of ctsm5.3.001
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.001
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu 26 Sep 2024 03:10:40 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 1014612b40..14c8b10465 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.003 multiple 10/03/2024 FATES default parameter file update
+       ctsm5.3.002 multiple 09/26/2024 Duplicate tag (same as 5.3.001)
        ctsm5.3.001 multiple 09/26/2024 Merge b4b-dev
          ctsm5.3.0 multiple 09/24/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
        ctsm5.2.029 multiple 09/24/2024 New surface datasets: double tag of ctsm5.3.0

From 9abbb70d24d421e21f24b092fcac90e663e65ade Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 3 Oct 2024 13:20:11 -0700
Subject: [PATCH 1174/1248] minor changelog update

---
 doc/ChangeLog | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 99611540cb..7c84572c58 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -2,17 +2,17 @@
 Tag name: ctsm5.3.003
 Originator(s): rgknox (Ryan Knox, LBNL, rgknox@lbl.gov)
                glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
-Date: Thu Oct  3 10:20:00 MDT 2024
+Date: Thu Oct 03 10:20:00 MDT 2024
 One-line Summary: FATES default parameter file update
 
 Purpose and description of changes
 ----------------------------------
 
 This tag updates the default parameter file for FATES bringing in a number of updates:
-	- adds two new arctic shrub pfts
-	- updates the default sapwood allometry mode for grass pfts
-	- updates understory leaf turnover specifications for longer turnover rates
-	- changes the default behavior of nutrient uptake
+   - adds two new arctic shrub pfts
+   - updates the default sapwood allometry mode for grass pfts
+   - updates understory leaf turnover specifications for longer turnover rates
+   - changes the default behavior of nutrient uptake
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------

From b12f6ff78df69f864f4611f56de27db05c55a674 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 3 Oct 2024 13:20:46 -0700
Subject: [PATCH 1175/1248] update filename

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 63b4ee9576..34910ec900 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -560,7 +560,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241002.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241003.nc</fates_paramfile>
 
 
 <!-- ================================================================== -->

From b9fde417b86b083a38500061e1275a2749cff395 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Fri, 4 Oct 2024 15:02:25 -0700
Subject: [PATCH 1176/1248] update fates tag to api36.1

---
 src/fates | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fates b/src/fates
index e06e0dfcaf..825579d0b4 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit e06e0dfcaf6347993d47dc29944e952d3e4412f7
+Subproject commit 825579d0b406fe99344591b5ed8356e5c7aeebec

From c3ddc480785d513d05390f655df3ec587c3642d4 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 7 Oct 2024 09:31:43 -0700
Subject: [PATCH 1177/1248] update testing results for ctsm5.3.003

---
 doc/ChangeLog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 7c84572c58..d8b2290f38 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -52,11 +52,11 @@ Testing summary:
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
     derecho ----- OK
-    izumi -------
+    izumi ------- OK
 
   fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
     derecho ----- OK
-    izumi -------
+    izumi ------- OK
 
 Answer changes
 --------------

From 29f9ac85b258c0731b4361e8d8ebced17db8b345 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Mon, 7 Oct 2024 09:34:27 -0700
Subject: [PATCH 1178/1248] update changelog and changesum date/time for
 ctsm5.3.003

---
 doc/ChangeLog | 2 +-
 doc/ChangeSum | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index d8b2290f38..8e76002a92 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -2,7 +2,7 @@
 Tag name: ctsm5.3.003
 Originator(s): rgknox (Ryan Knox, LBNL, rgknox@lbl.gov)
                glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
-Date: Thu Oct 03 10:20:00 MDT 2024
+Date: Mon Oct 07 10:33:14 AM MDT 2024
 One-line Summary: FATES default parameter file update
 
 Purpose and description of changes
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 14c8b10465..c16940615b 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.3.003 multiple 10/03/2024 FATES default parameter file update
+       ctsm5.3.003 multiple 10/07/2024 FATES default parameter file update
        ctsm5.3.002 multiple 09/26/2024 Duplicate tag (same as 5.3.001)
        ctsm5.3.001 multiple 09/26/2024 Merge b4b-dev
          ctsm5.3.0 multiple 09/24/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data

From 1fbe88ab0bf5da4112f9927b3248c30ecaf8bb62 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Mon, 7 Oct 2024 14:01:28 -0600
Subject: [PATCH 1179/1248] Revert this change as it changed answers for
 SMS_Ln9.ne30pg2_ne30pg2_mg17.I1850Clm50Sp.derecho_intel.clm-clm50cam6LndTuningMode--clm-nofireemis,
 unit tests and some other tests went back to identical, but at least this one
 changed

---
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 3bd280761f..07423fcc4d 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -781,7 +781,7 @@ real(r8) function ThresholdSoilMoistZender2003( clay )
          call endrun( 'Clay fraction is out of bounds (0 to 100)')
          return
       end if
-      ThresholdSoilMoistZender2003 = 0.17_r8 + 0.14_r8 * (clay*0.01_r8) 
+      ThresholdSoilMoistZender2003 = 0.17_r8 + 0.14_r8 * clay * 0.01_r8
   end function ThresholdSoilMoistZender2003
 
   !------------------------------------------------------------------------------

From 3f5aa0f5421cf3ade4d3761ccac4289d4a0a4d5c Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 7 Oct 2024 15:30:23 -0600
Subject: [PATCH 1180/1248] Bump up wallclock time for one test.

ERS_Ly5_P128x1.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-cropMonthOutput--clm-matrixcnOn_ignore_warnings
See ESCOMP/CTSM#2814 (https://github.com/ESCOMP/CTSM/issues/2814)
---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index ab1755bb77..2b6a35f9eb 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1773,7 +1773,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">01:40:00</option>
+      <option name="wallclock">02:30:00</option>
       <option name="comment"  >Repeat ERS_Ly5_P128x1...cropMonthOutput test with matrixcnOn</option>
     </options>
   </test>

From 3ec9215c09004385621f6523ca68c8eb2a55bd48 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 7 Oct 2024 15:51:49 -0600
Subject: [PATCH 1181/1248] Remove include_user_mods from matrixcnOn testmod.

Should avoid unnecessary levels of history writing.
Resolves ESCOMP/CTSM#2814.
---
 cime_config/testdefs/testlist_clm.xml                           | 2 +-
 .../testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods     | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)
 delete mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 0eb3d5012d..7943b5c55e 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3332,7 +3332,7 @@
       <option name="tput_tolerance">0.1</option>
     </options>
   </test>
-  <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/matrixcnOn">
+  <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods
deleted file mode 100644
index fe0e18cf88..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../default

From ae6b18844d186c10a369f62aa749b940d40714c0 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 7 Oct 2024 20:59:31 -0600
Subject: [PATCH 1182/1248] Change a test wallclock time to ensure it's what we
 want.

---
 cime_config/testdefs/testlist_clm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 7943b5c55e..cdb00db524 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1333,7 +1333,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">01:40:00</option>
+      <option name="wallclock">01:40:01</option>
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
     </options>
   </test>

From 6ae37190e2ac05253c7027fcb2c1928564f596ad Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Mon, 7 Oct 2024 21:29:34 -0600
Subject: [PATCH 1183/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 54 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8e76002a92..49f0a48a54 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,57 @@
 ===============================================================
+Tag name: ctsm5.3.004
+Originator(s): samrabin (Sam Rabin)
+Date: Mon Oct  7 21:25:20 MDT 2024
+One-line Summary: Move hillslope data off surface datasets
+
+Purpose and description of changes
+----------------------------------
+
+Moves hillslope data off surface datasets onto its own separate hillslope_file. This makes it so we don't need to generate new surface datasets specifically for hillslope testing whenever the surface datasets are updated.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Not in real runs, only our testing.
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2434 (https://github.com/ESCOMP/CTSM/pull/2434)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.003
 Originator(s): rgknox (Ryan Knox, LBNL, rgknox@lbl.gov)
                glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
diff --git a/doc/ChangeSum b/doc/ChangeSum
index c16940615b..ad552e320e 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.004 samrabin 10/07/2024 Move hillslope data off surface datasets
        ctsm5.3.003 multiple 10/07/2024 FATES default parameter file update
        ctsm5.3.002 multiple 09/26/2024 Duplicate tag (same as 5.3.001)
        ctsm5.3.001 multiple 09/26/2024 Merge b4b-dev

From 4c9631bd797b770084a946fcc0415cf669517f9c Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 8 Oct 2024 01:39:18 -0600
Subject: [PATCH 1184/1248] Make dust_moist_fact different for Leung and
 Zender, even though both are 1.0, and then have the duplicated line outside
 of the if statement

---
 src/biogeophys/SoilStateInitTimeConstMod.F90 | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
index 9f4a458dda..a730417315 100644
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ b/src/biogeophys/SoilStateInitTimeConstMod.F90
@@ -721,14 +721,12 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename)
        !soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay3d(g,1) )
        if ( is_dust_emis_leung() )then
           soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClayLeung2023( clay3d(g,1) )
-          !dust_moist_fact = 0.9_r8   ! change this into a namelist variable later.
-          dust_moist_fact = 1.0_r8   ! change this into a namelist variable later.
-          soilstate_inst%gwc_thr_col(c) = dust_moist_fact * ThresholdSoilMoistZender2003( clay3d(g,1) )
+          dust_moist_fact = 1.0_r8   ! change this into a namelist variable later., currrently not used but could be in the future
        else
           soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay3d(g,1) )
           dust_moist_fact = 1.0_r8
-          soilstate_inst%gwc_thr_col(c) = dust_moist_fact * ThresholdSoilMoistZender2003( clay3d(g,1) )
        end if
+       soilstate_inst%gwc_thr_col(c) = dust_moist_fact * ThresholdSoilMoistZender2003( clay3d(g,1) )
 
     end do
 

From 146dba46b7ebba8be78bf88021c8d65ecf15ca88 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Wed, 2 Oct 2024 08:18:22 -0600
Subject: [PATCH 1185/1248] Fix issue #2793

---
 src/biogeophys/EnergyFluxType.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/EnergyFluxType.F90 b/src/biogeophys/EnergyFluxType.F90
index 16929d9708..6a31293fa3 100644
--- a/src/biogeophys/EnergyFluxType.F90
+++ b/src/biogeophys/EnergyFluxType.F90
@@ -579,7 +579,7 @@ subroutine InitHistory(this, bounds, is_simple_buildtemp, is_prog_buildtemp)
             avgflag='A', long_name='urban heating flux', &
             ptr_col=this%eflx_urban_heat_col, set_nourb=0._r8, c2l_scale_type='urbanf')
     else
-       this%eflx_urban_ac_lun(begl:endl) = spval
+       this%eflx_building_lun(begl:endl) = spval
        call hist_addfld1d (fname='EFLXBUILD', units='W/m^2',  &
             avgflag='A', long_name='building heat flux from change in interior building air temperature', &
             ptr_lunit=this%eflx_building_lun, set_nourb=0._r8, l2g_scale_type='unity')

From c1fe2580ccabaad8ebe334e581876196a9a7e1cf Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 8 Oct 2024 16:56:09 -0600
Subject: [PATCH 1186/1248] Clm60 finidat updates for ne30, f09, f19 grids

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 102 ++++++++----------
 1 file changed, 43 insertions(+), 59 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 34910ec900..1356e0c222 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1354,18 +1354,32 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at f09 for all clm5_1/clm6_0 options -->
-<!-- use_init_interp true because the file was created with ctsm5.3 datasets -->
+<!-- TODO slevis VALID COMMENT? use_init_interp true because the file was created with ctsm5.3 datasets -->
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          phys="clm5_1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc
+</finidat>
+<!-- Corresponding ne30 -->
+<finidat hgrid="ne30np4" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+         phys="clm6_0" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_pSASU.clm2.r.0121-01-01-00000.nc
+</finidat>
+<!-- Corresponding f19 -->
+<finidat hgrid="1.9x2.5" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+         phys="clm6_0" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm530_f19_PPE_pSASU.clm2.r.0161-01-01-00000.nc
 </finidat>
 
 <!--
@@ -1408,12 +1422,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
-<!-- NB: This pSASU finidat is from an f09 1850 (rather than f19 2000) spin-up -->
+<!-- NB: This pSASU finidat is from an f09 2000 spin-up -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.2000-01-01-00000.nc
 </finidat>
 
 
@@ -1493,21 +1507,25 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <!-- clm5_1 and cam7.0 -->
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm5_1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.2000-01-01-00000.nc
 </finidat>
 
 <!-- clm6_0 and cam7.0 -->
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.2000-01-01-00000.nc
+</finidat>
+<finidat hgrid="ne30np4"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         phys="clm6_0" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.2000-01-01-00000.nc
 </finidat>
 
 <!-- clm5_0 and cam7.0 -->
@@ -1532,7 +1550,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+>lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1567,13 +1585,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
-<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm5_1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
-</finidat>
 
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1596,7 +1607,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+>lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
+</finidat>
+<finidat hgrid="ne30np4"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1631,13 +1648,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
-<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
-</finidat>
 
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1706,22 +1716,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc
 </finidat>
 
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
-<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm5_1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
-</finidat>
-
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
-<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
-</finidat>
-
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
@@ -1744,7 +1738,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+>lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1779,14 +1773,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
-<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm5_1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
-</finidat>
-
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
@@ -1809,7 +1795,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc
+>lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
+</finidat>
+<finidat hgrid="ne30np4"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
+>lnd/clm2/initdata_map/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1844,14 +1836,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
-<!-- NB: This pSASU finidat is from an 1850 spin-up -->
-<finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
-</finidat>
-
 <!-- 2003 -->
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."

From 058320d2467b0f1b3ce5258698aa32bd185510c7 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Wed, 9 Oct 2024 12:41:39 -0600
Subject: [PATCH 1187/1248] Fix hillslope with use_init_interp warning test, by
 specifying the hillslope_file this fixes #2826

---
 bld/unit_testers/build-namelist_test.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 06c9bcc361..5fb7b4f39b 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1359,8 +1359,8 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"fsurdat='build-namelist_test.pl'",
                                      phys=>"clm6_0",
                                    },
-     "hillslope with init_interp"=>{ options=>"-bgc bgc -envxml_dir .",
-                                     namelst=>"use_init_interp=.true.,use_hillslope=.true.",
+     "hillslope with init_interp"=>{ options=>"--res 10x15 --bgc bgc --envxml_dir .",
+                                     namelst=>"use_init_interp=.true.,use_hillslope=.true.,hillslope_file='/dev/null'",
                                      phys=>"clm6_0",
                                    },
                );

From 081427459cb67da29e3927664764f04b5e564a16 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 9 Oct 2024 16:43:15 -0600
Subject: [PATCH 1188/1248] ne30 updates in response to Keith Oleson's review

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 31 ++++++++++---------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 1356e0c222..6708e5ba8f 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -936,6 +936,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1 use_excess_ice=.true.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
+			hgrid="ne30np4.pg3"
+>hgrid=ne30np4.pg3 mask=t232
+</init_interp_attributes>
 
 <!-- present day -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_GSWP3v1"
@@ -1148,6 +1152,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 			hgrid="ne30np4"
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." phys="clm6_0"
+			hgrid="ne30np4.pg3"
+>hgrid=ne30np4.pg3 maxpft=79 mask=t232 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
+</init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="C24"
@@ -1263,6 +1271,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
+			hgrid="ne30np4.pg3"
+>hgrid=ne30np4.pg3 mask=t232
+</init_interp_attributes>
+
 <!-- 2003 -->
 <init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
@@ -1368,9 +1381,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc
 </finidat>
 <!-- Corresponding ne30 -->
-<finidat hgrid="ne30np4" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+<finidat hgrid="ne30np4.pg3" mask="t232" sim_year="1850"
          phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_pSASU.clm2.r.0121-01-01-00000.nc
 </finidat>
@@ -1521,7 +1532,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.2000-01-01-00000.nc
 </finidat>
-<finidat hgrid="ne30np4"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+<finidat hgrid="ne30np4.pg3"    maxpft="79"  mask="t232" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm6_0" use_init_interp=".true."
@@ -1609,10 +1620,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
-<finidat hgrid="ne30np4"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+<finidat hgrid="ne30np4.pg3"  mask="t232" sim_year="1979"
+         phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_map/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
@@ -1797,12 +1806,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
-<finidat hgrid="ne30np4"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.1979-01-01-00000.nc
-</finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."

From e47ffab57edb549d721e665aacdcf98f143998c8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 9 Oct 2024 16:43:55 -0600
Subject: [PATCH 1189/1248] f19 updates for test to pick up the correct finidat

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 6708e5ba8f..296feb03ba 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -936,6 +936,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1 use_excess_ice=.true.
 </init_interp_attributes>
 
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
+			hgrid="1.9x2.5"
+>hgrid=1.9x2.5 mask=gx1v7
+</init_interp_attributes>
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
 			hgrid="ne30np4.pg3"
 >hgrid=ne30np4.pg3 mask=t232
@@ -1386,9 +1390,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_pSASU.clm2.r.0121-01-01-00000.nc
 </finidat>
 <!-- Corresponding f19 -->
-<finidat hgrid="1.9x2.5" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+<finidat hgrid="1.9x2.5" mask="gx1v7" sim_year="1850"
          phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm530_f19_PPE_pSASU.clm2.r.0161-01-01-00000.nc
 </finidat>

From 10ff40411a43b6a214700b14bc0edd197e036832 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 10 Oct 2024 02:19:46 -0600
Subject: [PATCH 1190/1248] Add more expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 3b80016f82..7049e9672b 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -135,6 +135,17 @@
     </phase>
   </test>
   
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2310</issue>
+    </phase>
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2310</issue>
+    </phase>
+  </test>
+  
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
@@ -171,6 +182,13 @@
     </phase>
   </test>
 
+  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
+    <phase name="CREATE_NEWCASE">
+      <status>FAIL</status>
+      <issue>#2454</issue>
+    </phase>
+  </test>
+
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>

From 87778795589cd919b98df068ec90147fa85bed80 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 10 Oct 2024 03:17:38 -0600
Subject: [PATCH 1191/1248] Update change files

---
 doc/ChangeLog | 91 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 92 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 49f0a48a54..8f5b81d52b 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,95 @@
 ===============================================================
+Tag name: ctsm5.3.005
+Originator(s): dmleung (Danny Leung)
+Date: Thu 10 Oct 2024 03:15:52 AM MDT
+One-line Summary: Hardcoded tuning adjustments for Leung_2024 dust emissions
+
+Purpose and description of changes
+----------------------------------
+
+Changes to dust emissions when Leung_2024 method is being used.
+
+Tuning was needed since we saw some high biases in dust over semiarid regions given all the updates in CTSM and CAM. The biggest
+changes in CTSM that affects dust is an increase in friction velocity (ustar; fv in CTSM) over vegetated, semiarid regions, mainly
+due to a switch in the roughness scheme from 'ZengWang2007' to 'Meier2022'. Since dust emission is very sensitive to ustar, the dust
+emission scheme magnifies this increase and caused strong high biases over semiarid regions, including Australia and Patagonia (see
+plots in issue #2732). To enhance the robustness of Leung_2023 and reduce the likelihood to see huge changes in answers in the
+future, we tried to limit the sensitivity of dust emissions to ustar. We also tried different methods (see specific notes below) to
+reduce dust emissions from semiarid regions given the high biases over there.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[x] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+
+   Start of work on tuning for #2732
+   Fixes #2826 -- Fix failing warning test
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   Dust tuning parameters are hardcoded in FORTRAN and need to be moved to namelists
+
+Testing summary: Regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes for clm6_0
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: clm6_0
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+        Just updates dust emissions when Leung_2024 method is used
+
+    Only the dust emission fields are changed all other fields are untouched
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+   https://github.com/ESCOMP/CTSM/pull/2803 -- Tuning Leung_2023 dust emissions for clm6_0_cam7.0
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.004
 Originator(s): samrabin (Sam Rabin)
 Date: Mon Oct  7 21:25:20 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index ad552e320e..358fb8060e 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.005     erik 10/10/2024 Hardcoded tuning adjustments for Leung_2024 dust emissions
        ctsm5.3.004 samrabin 10/07/2024 Move hillslope data off surface datasets
        ctsm5.3.003 multiple 10/07/2024 FATES default parameter file update
        ctsm5.3.002 multiple 09/26/2024 Duplicate tag (same as 5.3.001)

From 33c8d55740e6d0100d2ef22a2d8019e34d45e928 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 10 Oct 2024 17:03:40 -0600
Subject: [PATCH 1192/1248] Updates after Erik's reviewr; ne30 1979 does not
 work, yet

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 54 ++++++++++---------
 1 file changed, 29 insertions(+), 25 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 296feb03ba..44951814a4 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -938,11 +938,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
 			hgrid="1.9x2.5"
->hgrid=1.9x2.5 mask=gx1v7
+>mask=gx1v7 use_cn=.true. do_transient_pfts=.false. use_excess_ice=.true. use_crop=.false. irrigate=.false.
 </init_interp_attributes>
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
 			hgrid="ne30np4.pg3"
->hgrid=ne30np4.pg3 mask=t232
+>mask=t232 use_cn=.true. do_transient_pfts=.false. use_excess_ice=.true. use_crop=.true. irrigate=.false.
 </init_interp_attributes>
 
 <!-- present day -->
@@ -1275,9 +1275,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
-			hgrid="ne30np4.pg3"
->hgrid=ne30np4.pg3 mask=t232
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
+                        hgrid="ne30np4.pg3" use_cn=".false." maxpft="17"
+>hgrid=ne30np4.pg3 maxpft=17 mask=t232 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
 <!-- 2003 -->
@@ -1371,27 +1371,30 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at f09 for all clm5_1/clm6_0 options -->
-<!-- TODO slevis VALID COMMENT? use_init_interp true because the file was created with ctsm5.3 datasets -->
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         phys="clm5_1" use_init_interp=".true."
+         phys="clm5_1"
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
-         phys="clm6_0" use_init_interp=".true."
+         phys="clm6_0"
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc
 </finidat>
 <!-- Corresponding ne30 -->
-<finidat hgrid="ne30np4.pg3" mask="t232" sim_year="1850"
-         phys="clm6_0" use_init_interp=".true."
+<finidat hgrid="ne30np4.pg3" mask="t232" use_cn=".true." use_cndv=".false." use_fates=".false."
+         sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
+         use_crop=".true." irrigate=".false."
+         phys="clm6_0"
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_pSASU.clm2.r.0121-01-01-00000.nc
 </finidat>
 <!-- Corresponding f19 -->
-<finidat hgrid="1.9x2.5" mask="gx1v7" sim_year="1850"
-         phys="clm6_0" use_init_interp=".true."
+<finidat hgrid="1.9x2.5" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
+         use_crop=".false." irrigate=".false."
+         phys="clm6_0"
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm530_f19_PPE_pSASU.clm2.r.0161-01-01-00000.nc
 </finidat>
 
@@ -1435,7 +1438,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
-<!-- NB: This pSASU finidat is from an f09 2000 spin-up -->
 <finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
@@ -1537,7 +1539,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="ne30np4.pg3"    maxpft="79"  mask="t232" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm6_0" use_init_interp=".true."
+         phys="clm6_0"
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.2000-01-01-00000.nc
 </finidat>
 
@@ -1562,8 +1564,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
+         lnd_tuning_mode="clm5_1_cam7.0"
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1619,12 +1621,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
+         lnd_tuning_mode="clm6_0_cam7.0"
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
-<finidat hgrid="ne30np4.pg3"  mask="t232" sim_year="1979"
-         phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_map/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.1979-01-01-00000.nc
+<finidat hgrid="ne30np4.pg3"  maxpft="17"  mask="t232" use_cn=".false." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1748,8 +1752,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
+         lnd_tuning_mode="clm5_1_cam6.0"
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1805,8 +1809,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
+         lnd_tuning_mode="clm6_0_cam6.0"
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."

From ab9bdf9e1674d61a85a35cda0ad81b9ed3ba3e5c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Thu, 10 Oct 2024 17:07:38 -0600
Subject: [PATCH 1193/1248] Draft ChangeLog/Sum

---
 doc/ChangeLog | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 doc/ChangeSum |  2 ++
 2 files changed, 93 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8f5b81d52b..8be750f8a7 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,87 @@
 ===============================================================
+Tag name: ctsm5.3.007
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 10 Oct 2024 10:12:18 AM MDT
+One-line Summary: Clm60 finidat updates for ne30, f09, f19 grids
+
+Purpose and description of changes
+----------------------------------
+ Updates appear in namelist_defaults_ctsm.xml.
+ As before, I updated clm51, too, to keep it same as clm60 (and clm51 will go away soon).
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[X] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Relates to (fixes?) #2403; needs more work to close?
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+ Clm60 and clm51 finidat updates for ne30, f09, f19 grids.
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ Clm60 and clm51 finidat updates for ne30, f09, f19 grids.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - TODO
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - TODO
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- TODO
+    izumi ------- TODO
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes.
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: clm60 (and clm51 which goes away very soon)
+    - what platforms/compilers: all
+    - nature of change: larger than roundoff/same climate
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2821
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.006
+===============================================================
+===============================================================
 Tag name: ctsm5.3.005
 Originator(s): dmleung (Danny Leung)
 Date: Thu 10 Oct 2024 03:15:52 AM MDT
@@ -132,7 +215,14 @@ Testing summary:
 Answer changes
 --------------
 
-Changes answers relative to baseline: Not in real runs, only our testing.
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: Hillslope (tests only)
+    - what platforms/compilers: Tests on Izumi and Derecho
+    - nature of change: Larger than roundoff
+
+   Only our tests are affected because I had to make changes to the test setup for compatibility; this included changing mesh file and hillslope data for some tests/testmods.
 
 
 Other details
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 358fb8060e..293e0fc9ce 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.007   slevis 10/11/2024 Clm60 finidat updates for ne30, f09, f19 grids
+       ctsm5.3.006
        ctsm5.3.005     erik 10/10/2024 Hardcoded tuning adjustments for Leung_2024 dust emissions
        ctsm5.3.004 samrabin 10/07/2024 Move hillslope data off surface datasets
        ctsm5.3.003 multiple 10/07/2024 FATES default parameter file update

From cfcd041b9455a41d122cc58fa335e6bc86c9b2d7 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Fri, 11 Oct 2024 07:18:52 -0600
Subject: [PATCH 1194/1248] Update ChangeLog/ChangeSum.

---
 doc/ChangeLog | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 doc/ChangeSum |  1 +
 2 files changed, 70 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8f5b81d52b..737bec2b97 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,72 @@
 ===============================================================
+Tag name: ctsm5.3.006
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Fri Oct 11 07:01:09 MDT 2024
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+- Fix clm-basic tests (resolves ESCOMP/CTSM#2787)
+- Change testlist_clm ne30pg3_t061 tests to ne30pg3_t232 (resolves ESCOMP/CTSM#2702)
+- Remove unused variable elevclass_o in mkglcmecMod.F90 (resolves ESCOMP/CTSM#2802)
+- Add a check in failtest, warntest, finidat_files, so when a new test or finidat file are added and one of the subkeys is misspelled you will get an error and tester will die (resolves ESCOMP/CTSM#2673)
+- Move from deprecated shr_file to shr_log
+- Set eflx_building_lun to spval properly (resolves ESCOMP/CTSM#2793)
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed:
+- ESCOMP/CTSM#2787 (aux_clm "clm-basic" tests fail as of ctsm5.3.0 because they need c13 in finidat; https://github.com/ESCOMP/CTSM/issues/2787)
+- ESCOMP/CTSM#2702 (Tests failing in ctsm5.2.019 for CESM alpha testing; https://github.com/ESCOMP/CTSM/issues/2702)
+- ESCOMP/CTSM#2802 (Array elevclass_o in mksurfdata_esmf/src/mkglcmecMod.F90 is not allocated before use; https://github.com/ESCOMP/CTSM/issues/2802)
+- ESCOMP/CTSM#2673 (Catch use of namelist attribute in failure testing in perl build-namelist tester; https://github.com/ESCOMP/CTSM/issues/2673)
+- ESCOMP/CTSM#2793 (Potential typo/bug in EnergyFluxType.F90; https://github.com/ESCOMP/CTSM/issues/2793)
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Other details
+-------------
+
+Pull Requests that document the changes:
+- ESCOMP/CTSM#2798: Fix clm-basic tests (https://github.com/ESCOMP/CTSM/pull/2798)
+- ESCOMP/CTSM#2799: Change testlist_clm ne30pg3_t061 tests to ne30pg3_t232 (https://github.com/ESCOMP/CTSM/pull/2799)
+- ESCOMP/CTSM#2804: Remove unused variable elevclass_o in mkglcmecMod.F90 (https://github.com/ESCOMP/CTSM/pull/2804)
+- ESCOMP/CTSM#2678: Add check in build-namelist_test.pl (https://github.com/ESCOMP/CTSM/pull/2678)
+- ESCOMP/CTSM#2627: move from depricated shr_file to shr_log (https://github.com/ESCOMP/CTSM/pull/2627)
+- ESCOMP/CTSM#2806: Set eflx_building_lun to spval properly (https://github.com/ESCOMP/CTSM/pull/2806)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.005
 Originator(s): dmleung (Danny Leung)
 Date: Thu 10 Oct 2024 03:15:52 AM MDT
@@ -91,7 +159,7 @@ Pull Requests that document the changes (include PR ids):
 ===============================================================
 ===============================================================
 Tag name: ctsm5.3.004
-Originator(s): samrabin (Sam Rabin)
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Mon Oct  7 21:25:20 MDT 2024
 One-line Summary: Move hillslope data off surface datasets
 
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 358fb8060e..f74348094c 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.006 samrabin 10/11/2024 Merge b4b-dev
        ctsm5.3.005     erik 10/10/2024 Hardcoded tuning adjustments for Leung_2024 dust emissions
        ctsm5.3.004 samrabin 10/07/2024 Move hillslope data off surface datasets
        ctsm5.3.003 multiple 10/07/2024 FATES default parameter file update

From bb97fb3bd5831f0a08b768df61ee6c013e9b2cc0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Fri, 11 Oct 2024 13:59:05 -0600
Subject: [PATCH 1195/1248] Updates from review with Erik and subsequent
 testing

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 132 +++++++-----------
 1 file changed, 51 insertions(+), 81 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 44951814a4..11a7d68e71 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -942,7 +942,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </init_interp_attributes>
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
 			hgrid="ne30np4.pg3"
->mask=t232 use_cn=.true. do_transient_pfts=.false. use_excess_ice=.true. use_crop=.true. irrigate=.false.
+>mask=tx2_3v2 use_cn=.true. do_transient_pfts=.false. use_excess_ice=.true. use_crop=.true. irrigate=.false.
 </init_interp_attributes>
 
 <!-- present day -->
@@ -965,11 +965,16 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_GSWP3v1"
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
+
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." phys="clm5_1"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm5_1_GSWP3v1 use_excess_ice=.true.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nex=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." phys="clm6_0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1 use_excess_ice=.true.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nex=10 do_transient_pfts=.false. use_excess_ice=.true.
+</init_interp_attributes>
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." phys="clm6_0"
+			hgrid="ne30np4.pg3"
+>hgrid=ne30np4.pg3 maxpft=79 mask=tx2_3v2 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7"
@@ -1156,10 +1161,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 			hgrid="ne30np4"
 >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." phys="clm6_0"
-			hgrid="ne30np4.pg3"
->hgrid=ne30np4.pg3 maxpft=79 mask=t232 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.true.
-</init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="C24"
@@ -1255,14 +1256,17 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
-                        hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
+                        hgrid="0.9x1.25"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
 </init_interp_attributes>
-
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
-                        hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
+                        hgrid="1.9x2.5"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
+</init_interp_attributes>
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
+			hgrid="ne30np4.pg3"
+>hgrid=ne30np4.pg3 maxpft=79 mask=tx2_3v2 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
@@ -1275,11 +1279,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
-                        hgrid="ne30np4.pg3" use_cn=".false." maxpft="17"
->hgrid=ne30np4.pg3 maxpft=17 mask=t232 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
-</init_interp_attributes>
-
 <!-- 2003 -->
 <init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
                         hgrid="1.9x2.5" use_cn=".false." maxpft="17"
@@ -1375,27 +1374,27 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          phys="clm5_1"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_pSASU.clm60.r.0161-01-01.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          phys="clm6_0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_pSASU.clm60.r.0161-01-01.nc
 </finidat>
 <!-- Corresponding ne30 -->
-<finidat hgrid="ne30np4.pg3" mask="t232" use_cn=".true." use_cndv=".false." use_fates=".false."
+<finidat hgrid="ne30np4.pg3" mask="tx2_3v2" use_cn=".true." use_cndv=".false." use_fates=".false."
          sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          use_crop=".true." irrigate=".false."
          phys="clm6_0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_pSASU.clm2.r.0121-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_BgcCrop_exice_pSASU.clm60.r.0121-01-01.nc
 </finidat>
 <!-- Corresponding f19 -->
 <finidat hgrid="1.9x2.5" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          use_crop=".false." irrigate=".false."
          phys="clm6_0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm530_f19_PPE_pSASU.clm2.r.0161-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm530_f19_g17_Bgc_exice_pSASU.clm60.r.0161-01-01.nc
 </finidat>
 
 <!--
@@ -1438,12 +1437,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
 </finidat>
-<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.2000-01-01-00000.nc
-</finidat>
 
 
 <!-- This is the same file as above but, for a different tuning mode -->
@@ -1523,24 +1516,26 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- clm5_1 and cam7.0 -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
+         ic_ymd="20000101" sim_year="2000" use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm5_1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.2000-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_hist.clm60.r.2000-01-01.nc
 </finidat>
 
 <!-- clm6_0 and cam7.0 -->
+<!-- slevis-lmwg, ekluzek 2024/10/11: do_transient_pfts was removed here to bypass a bug that doesn't allow
+           do_transient_pfts=.true. when use_init_interp=.false. -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
+         ic_ymd="20000101" sim_year="2000" use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.2000-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_hist.clm60.r.2000-01-01.nc
 </finidat>
-<finidat hgrid="ne30np4.pg3"    maxpft="79"  mask="t232" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false." use_excess_ice=".true."
+<finidat hgrid="ne30np4.pg3"    maxpft="79"  mask="tx2_3v2" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="20000101" sim_year="2000" use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
-         phys="clm6_0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.2000-01-01-00000.nc
+         phys="clm6_0" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_BgcCrop_exice_hist.clm60.r.2000-01-01.nc
 </finidat>
 
 <!-- clm5_0 and cam7.0 -->
@@ -1560,12 +1555,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          lnd_tuning_mode="clm5_0_cam7.0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
-<!-- Repeat above for clm5_1 -->
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam7.0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
+<!-- Repeat for clm5_1 -->
+<finidat hgrid="0.9x1.25" maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" use_excess_ice=".true."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         phys="clm5_1" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_hist.clm60.r.1979-01-01.nc
 </finidat>
 
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1618,24 +1613,19 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm6_0 -->
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
-</finidat>
-<finidat hgrid="ne30np4.pg3"  maxpft="17"  mask="t232" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_hist.clm2.r.1979-01-01-00000.nc
+<!-- slevis-lmwg, ekluzek 2024/10/11: do_transient_pfts was removed here to bypass a bug that doesn't allow
+           do_transient_pfts=.true. when use_init_interp=.false. -->
+<finidat hgrid="0.9x1.25" maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" use_excess_ice=".true."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         phys="clm6_0" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_hist.clm60.r.1979-01-01.nc
 </finidat>
-
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
+<finidat hgrid="ne30np4.pg3" maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+         ic_ymd="19790101"  sim_year="1979" use_excess_ice=".true."
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+         phys="clm6_0" use_init_interp=".true."
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_ne30pg3t232_BgcCrop_exice_hist.clm60.r.1979-01-01.nc
 </finidat>
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
@@ -1749,13 +1739,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 <!-- Repeat above for clm5_1 -->
 <!-- clm5_1 and cam6.0-->
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
-</finidat>
-
 <finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
          ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
@@ -1806,19 +1789,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 <!-- Repeat above for clm6_0 -->
 <!-- clm6_0 and cam6.0-->
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_hist.clm2.r.1979-01-01-00000.nc
-</finidat>
-
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
-</finidat>
 
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."

From 38e6fb1a77cccaa58e07eca402a66e3729325d26 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 11 Oct 2024 17:37:53 -0600
Subject: [PATCH 1196/1248] Correct mask for ne30pg3 1979 finidat file

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 11a7d68e71..ad02f86de7 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1621,7 +1621,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          phys="clm6_0" use_init_interp=".true."
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_hist.clm60.r.1979-01-01.nc
 </finidat>
-<finidat hgrid="ne30np4.pg3" maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
+<finidat hgrid="ne30np4.pg3" maxpft="79"  mask="tx2_3v2" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm6_0" use_init_interp=".true."

From 78745213e0ab3cb82ebffcc825a90f7a282e06a3 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Fri, 11 Oct 2024 23:28:54 -0600
Subject: [PATCH 1197/1248] Remove 2003 finidat settings for clm5_1/clm6_0 so
 will use 2000 files, handle 1979 finidat settings consistently for f09, f19,
 and ne30pg3

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 120 +++---------------
 1 file changed, 18 insertions(+), 102 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index ad02f86de7..d03a840fd3 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -756,18 +756,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!--
      clm5_1 physics with CAM7.0 grids...
 -->
-<!-- These first five are for SP mode and CLM5.1 only -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="0.9x1.25"            >.true.</use_init_interp>
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"             >.true.</use_init_interp>
+<!-- These next two are for SP mode and CLM5.1 only -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam7.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTICGRIS.ne30x8">.true.</use_init_interp>
-<!-- 2003 -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2003" lnd_tuning_mode="clm5_1_cam7.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"                 >.true.</use_init_interp>
 
 <!-- 2013 -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm5_1_cam7.0"
@@ -776,18 +769,18 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!--
      clm6_0 physics with CAM7.0 grids...
 -->
-<!-- These first five are for SP mode and CLM6.0 only -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="0.9x1.25"            >.true.</use_init_interp>
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"             >.true.</use_init_interp>
+<!-- These are for 1979 for f09 and f19 for any atmospheric forcing -->
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" phys="clm6_0"
+                  hgrid="0.9x1.25"            >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" phys="clm6_0"
+                  hgrid="1.9x2.5"            >.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" phys="clm6_0"
+                  hgrid="1.9x2.5"            >.true.</use_init_interp>
+<!-- These next two are for SP mode and CLM6.0 with CAM7.0 only -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTICGRIS.ne30x8">.true.</use_init_interp>
-<!-- 2003 -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2003" lnd_tuning_mode="clm6_0_cam7.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"                 >.true.</use_init_interp>
 
 <!-- 2013 -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm6_0_cam7.0"
@@ -815,18 +808,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!--
      clm5_1 physics with CAM6.0 grids (duplicates above)
 -->
-<!-- These first five are for SP mode and CLM5.1 only -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam6.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="0.9x1.25"            >.true.</use_init_interp>
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam6.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"             >.true.</use_init_interp>
+<!-- These next two are for SP mode and CLM5.1 only -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam6.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm5_1_cam6.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTICGRIS.ne30x8">.true.</use_init_interp>
-<!-- 2003 -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2003" lnd_tuning_mode="clm5_1_cam6.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"                 >.true.</use_init_interp>
 
 <!-- 2013 -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm5_1_cam6.0"
@@ -835,18 +821,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!--
      clm6_0 physics with CAM6.0 grids...
 -->
-<!-- These first five are for SP mode and CLM6.0 only -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam6.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="0.9x1.25"            >.true.</use_init_interp>
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam6.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"             >.true.</use_init_interp>
+<!-- These first two are for SP mode and CLM6.0 only -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam6.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam6.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTICGRIS.ne30x8">.true.</use_init_interp>
-<!-- 2003 -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2003" lnd_tuning_mode="clm6_0_cam6.0"
-                  maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="1.9x2.5"                 >.true.</use_init_interp>
 
 <!-- 2013 -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2013" lnd_tuning_mode="clm6_0_cam6.0"
@@ -1236,14 +1215,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 
 <!-- If an exact match for these grids and start years -->
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
-                        hgrid="0.9x1.25" use_cn=".false." maxpft="17"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
+                        hgrid="0.9x1.25"
+>maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
-                        hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
+<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
+                        hgrid="1.9x2.5"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam6.0"
@@ -1256,17 +1235,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
-                        hgrid="0.9x1.25"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
-</init_interp_attributes>
-<init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
-                        hgrid="1.9x2.5"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
-</init_interp_attributes>
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." phys="clm6_0"
 			hgrid="ne30np4.pg3"
->hgrid=ne30np4.pg3 maxpft=79 mask=tx2_3v2 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
+>maxpft=79 mask=tx2_3v2 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1979" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
@@ -1279,12 +1250,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
-<!-- 2003 -->
-<init_interp_attributes sim_year="2003" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
-                        hgrid="1.9x2.5" use_cn=".false." maxpft="17"
->hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
-</init_interp_attributes>
-
 <!-- 2013 IC's - exact match for CONUS grid ... -->
 <init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_cam7.0"
 			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
@@ -1563,13 +1528,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_esmf/ctsm5.3/ctsm53n04ctsm52028_f09_g17_BgcCrop_exice_hist.clm60.r.1979-01-01.nc
 </finidat>
 
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
-</finidat>
-
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
@@ -1596,15 +1554,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 
-<!-- 2003 -->
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
-</finidat>
-
-
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
@@ -1654,15 +1603,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
 
-<!-- 2003 -->
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
-</finidat>
-
-
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="20130101"  sim_year="2013" do_transient_pfts=".false." use_excess_ice=".false."
@@ -1738,14 +1678,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc
 </finidat>
 <!-- Repeat above for clm5_1 -->
-<!-- clm5_1 and cam6.0-->
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc
-</finidat>
-
 <!-- Present day no crop spinup ARCTIC grid with irrigation on -->
 <finidat hgrid="ne0np4.ARCTIC.ne30x4"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
          ic_ymd="19790101"  sim_year="1979" do_transient_pfts=".false." use_excess_ice=".false."
@@ -1771,14 +1703,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
-<!-- 2003 -->
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
-</finidat>
-
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."
@@ -1815,14 +1739,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </finidat>
 
 <!-- Present day for coupled cases at 1-degree or lower resolutions  -->
-<!-- 2003 -->
-<finidat hgrid="1.9x2.5"   maxpft="17"  mask="gx1v7" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="20030101"  sim_year="2003" do_transient_pfts=".false." use_excess_ice=".false."
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
-         lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc
-</finidat>
-
 
 <!-- 2013 -->
 <finidat hgrid="ne0np4CONUS.ne30x8"    maxpft="17"  mask="tx0.1v2" use_cn=".false." use_cndv=".false." use_fates=".false."

From 29023fbc5756104f2172a6a595622ebf6ddfdae8 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Sun, 13 Oct 2024 15:48:40 -0600
Subject: [PATCH 1198/1248] Updated ChangeLog/Sum

---
 doc/ChangeLog | 20 ++++++++++++--------
 doc/ChangeSum |  2 +-
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 191cd7753a..867d23c5c5 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,13 +1,17 @@
 ===============================================================
 Tag name: ctsm5.3.007
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
-Date: Thu 10 Oct 2024 10:12:18 AM MDT
+Date: Mon 13 Oct 2024 10:12:18 AM MDT
 One-line Summary: Clm60 finidat updates for ne30, f09, f19 grids
 
 Purpose and description of changes
 ----------------------------------
  Updates appear in namelist_defaults_ctsm.xml.
- As before, I updated clm51, too, to keep it same as clm60 (and clm51 will go away soon).
+ For the most part I updated clm51, too, to keep it same as clm60, knowing
+ that clm51 will go away soon.
+ I had significant help from Erik Kluzek in disentangling the .xml settings
+ so that cases would pick up the correct finidat settings and other namelist
+ settings.
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
@@ -31,7 +35,7 @@ Does this tag change answers significantly for any of the following physics conf
 Bugs fixed
 ----------
 List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
- Relates to (fixes?) #2403; needs more work to close?
+ Relates to #2403; needs more work to close?
 
 Notes of particular relevance for users
 ---------------------------------------
@@ -48,16 +52,16 @@ Testing summary:
 
   build-namelist tests (if CLMBuildNamelist.pm has changed):
 
-    derecho - TODO
+    derecho - PASS
 
   python testing (if python code has changed; see instructions in python/README.md; document testing done):
 
-    derecho - TODO
+    derecho - PASS
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho ----- TODO
-    izumi ------- TODO
+    derecho ----- OK
+    izumi ------- OK
 
 
 Answer changes
@@ -66,7 +70,7 @@ Answer changes
 Changes answers relative to baseline: Yes.
 
   Summarize any changes to answers, i.e.,
-    - what code configurations: clm60 (and clm51 which goes away very soon)
+    - what code configurations: clm60 and clm51; the latter goes away soon
     - what platforms/compilers: all
     - nature of change: larger than roundoff/same climate
 
diff --git a/doc/ChangeSum b/doc/ChangeSum
index caf03f27da..7d01340622 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,6 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
-       ctsm5.3.007   slevis 10/11/2024 Clm60 finidat updates for ne30, f09, f19 grids
+       ctsm5.3.007   slevis 10/14/2024 Clm60 finidat updates for ne30, f09, f19 grids
        ctsm5.3.006 samrabin 10/11/2024 Merge b4b-dev
        ctsm5.3.005     erik 10/10/2024 Hardcoded tuning adjustments for Leung_2024 dust emissions
        ctsm5.3.004 samrabin 10/07/2024 Move hillslope data off surface datasets

From 941ec71a216ce58dd5cab2d41baa21174e915628 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Sun, 13 Oct 2024 16:06:36 -0600
Subject: [PATCH 1199/1248] Remove redundant lines

---
 bld/namelist_files/namelist_defaults_ctsm.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index d03a840fd3..d7dc104183 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -774,8 +774,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
                   hgrid="0.9x1.25"            >.true.</use_init_interp>
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" phys="clm6_0"
                   hgrid="1.9x2.5"            >.true.</use_init_interp>
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" phys="clm6_0"
-                  hgrid="1.9x2.5"            >.true.</use_init_interp>
 <!-- These next two are for SP mode and CLM6.0 with CAM7.0 only -->
 <use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1979" lnd_tuning_mode="clm6_0_cam7.0"
                   maxpft="17"        use_cn=".false."    use_crop=".false." hgrid="ne0np4.ARCTIC.ne30x4"    >.true.</use_init_interp>

From 5f9d597bef097fdd746a626d2e8a8d2e1e400e52 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 14 Oct 2024 10:50:09 -0600
Subject: [PATCH 1200/1248] Add matrixcn test suite.

---
 cime_config/testdefs/testlist_clm.xml | 51 +++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index cdb00db524..146a7abe6e 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -11,6 +11,7 @@
         aux_cime_baselines: CESM cime baselines (subset of aux_clm tests)
         hillslope: Experimental test list used for the hillslope option of the model
         rxcropmaturity: Short tests to be run during development related to prescribed crop calendars
+        matrixcn: Tests exercising the matrix-CN capability
 -->
 <testlist version="2.0">
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/default">
@@ -25,6 +26,7 @@
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -47,6 +49,7 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -276,6 +279,7 @@
   <test name="ERI_D_Ld9" grid="ne30_g17" compset="I2000Clm50BgcCru" testmods="clm/vrtlay--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:60:00</option>
@@ -482,6 +486,7 @@
   <test name="ERI_Ld9" grid="f45_g37" compset="I2000Clm50BgcCru" testmods="clm/nofire--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -517,6 +522,7 @@
   <test name="ERS_Ld3" grid="f10_f10_mg37" compset="I2000Clm60Bgc" testmods="clm/ciso_cwd_hr--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -544,6 +550,7 @@
   <test name="ERP_D" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/decStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -802,6 +809,7 @@
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/allActive--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -820,6 +828,7 @@
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/anoxia--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -837,6 +846,7 @@
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/ciso_flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -846,7 +856,9 @@
   <test name="SMS_D" grid="f10_f10_mg37" compset="I1850Clm60BgcCrop" testmods="clm/ciso_soil_matrixcn_only">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">01:20:00</option>
@@ -866,6 +878,7 @@
   <test name="ERS_D" grid="f19_g17" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">01:20:00</option>
@@ -875,6 +888,7 @@
   <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="izumi"    compiler="nag" category="aux_clm"/>
+      <machine name="izumi"    compiler="nag" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">01:20:00</option>
@@ -884,6 +898,7 @@
   <test name="ERS_Lm54_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -893,6 +908,7 @@
   <test name="LCISO_Lm13" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -985,6 +1001,7 @@
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/ciso--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1003,6 +1020,7 @@
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/ciso_decStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -1022,6 +1040,7 @@
   <test name="ERP_D_Ld10_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -1040,6 +1059,7 @@
   <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -1077,6 +1097,7 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="clm_short"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1094,6 +1115,7 @@
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/coldStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1103,6 +1125,7 @@
   <test name="SMS_D" grid="1x1_brazil" compset="I1850Clm60BgcCrop" testmods="clm/mimics_matrixcn">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1147,6 +1170,7 @@
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1164,6 +1188,7 @@
   <test name="ERP_D_P64x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1237,6 +1262,7 @@
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
       <machine name="izumi" compiler="nag" category="prealpha"/>
+      <machine name="izumi" compiler="nag" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1297,6 +1323,7 @@
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1314,6 +1341,7 @@
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/noFUN_flexCN--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1340,6 +1368,7 @@
   <test name="ERP_Ly3_P64x2" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -1376,6 +1405,7 @@
   <test name="ERP_P64x2_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1421,6 +1451,7 @@
   <test name="ERP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1431,6 +1462,7 @@
   <test name="REP_P64x2_Lm13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1441,6 +1473,7 @@
   <test name="REP_P64x2_Ld13" grid="f10_f10_mg37" compset="IHistClm60Bgc" testmods="clm/monthly--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1553,6 +1586,7 @@
   <test name="ERS_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/reseedresetsnow--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1688,6 +1722,7 @@
   <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1725,6 +1760,7 @@
   <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock"     >04:00:00</option>
@@ -1771,6 +1807,7 @@
   <test name="ERS_Ly5_P128x1" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -1827,6 +1864,7 @@
   <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1857,6 +1895,7 @@
   <test name="LII_D_Ld3_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1875,6 +1914,7 @@
   <test name="LII2FINIDATAREAS_D_P256x2_Ld1" grid="f09_g17" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1904,6 +1944,7 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prebeta"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">01:30:00</option>
@@ -1941,6 +1982,7 @@
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="intel" category="prebeta"/>
+      <machine name="izumi" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1960,6 +2002,7 @@
   <test name="PET_P64x2_D" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2000,6 +2043,7 @@
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2205,6 +2249,7 @@
       <machine name="derecho" compiler="intel" category="clm_short"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
       <machine name="derecho" compiler="intel" category="aux_cime_baselines"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2273,7 +2318,9 @@
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/HARV--clm/matrixcnOn">
     <machines>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
+      <machine name="derecho"  compiler="gnu" category="matrixcn"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2354,6 +2401,7 @@
   <test name="ERS_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50BgcQian" testmods="clm/ciso_bombspike1963DecStart--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2515,6 +2563,7 @@
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/nlevgrnd_small--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">0:20:00</option>
@@ -2562,6 +2611,7 @@
   <test name="SSPMATRIXCN_Ly5_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/ciso_monthly">
     <machines>
       <machine name="izumi"    compiler="intel" category="aux_clm"/>
+      <machine name="izumi"    compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -3335,6 +3385,7 @@
   <test name="PFS_Ld10_PS" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/default--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>

From 4797fd22795103464c1e9291ddd3f69483ba514c Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 14 Oct 2024 11:11:04 -0600
Subject: [PATCH 1201/1248] Final update to ChangeLog

---
 doc/ChangeLog | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 867d23c5c5..e6804811d2 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,17 +1,15 @@
 ===============================================================
 Tag name: ctsm5.3.007
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
-Date: Mon 13 Oct 2024 10:12:18 AM MDT
+Date: Mon 13 Oct 2024 11:04:18 AM MDT
 One-line Summary: Clm60 finidat updates for ne30, f09, f19 grids
 
 Purpose and description of changes
 ----------------------------------
  Updates appear in namelist_defaults_ctsm.xml.
- For the most part I updated clm51, too, to keep it same as clm60, knowing
- that clm51 will go away soon.
+ For the most part I updated clm51 to match clm60, though clm51 will go away soon.
  I had significant help from Erik Kluzek in disentangling the .xml settings
- so that cases would pick up the correct finidat settings and other namelist
- settings.
+ so that cases would pick up the correct finidat and other namelist settings.
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
@@ -35,7 +33,7 @@ Does this tag change answers significantly for any of the following physics conf
 Bugs fixed
 ----------
 List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
- Relates to #2403; needs more work to close?
+ Relates to #2403 but may need more work to close the issue
 
 Notes of particular relevance for users
 ---------------------------------------
@@ -76,8 +74,6 @@ Changes answers relative to baseline: Yes.
 
 Other details
 -------------
-List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
-
 Pull Requests that document the changes (include PR ids):
  https://github.com/ESCOMP/ctsm/pull/2821
 

From 9f4844cbf5d55db7768e13086786eab13d08f03b Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 14 Oct 2024 12:07:57 -0600
Subject: [PATCH 1202/1248] Draft ChangeLog/Sum

---
 doc/ChangeLog | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 69 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index e6804811d2..02f7fa763f 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,72 @@
 ===============================================================
+Tag name: ctsm5.3.008
+Originator(s): olyson (Keith Oleson,UCAR/TSS)
+Date: Mon 14 Oct 2024 11:56:12 AM MDT
+One-line Summary: PPE change to sa_leaf in CanopyFluxesMod.F90
+
+Purpose and description of changes
+----------------------------------
+
+ Add change to sa_leaf that was in PPE branch but did not get on master.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[X] clm6_0
+
+[X] clm5_1
+
+[X] clm5_0
+
+[X] ctsm5_0-nwp
+
+[X] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2777
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho -----
+    izumi -------
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: All
+    - what platforms/compilers: All
+    - nature of change: larger than roundoff/same climate)
+
+ The changes in answers are explained in this post:
+ https://github.com/ESCOMP/CTSM/issues/2777#issuecomment-2371697380
+
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2788
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.007
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Mon 13 Oct 2024 11:04:18 AM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 7d01340622..5698b8654f 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.008   olyson 10/14/2024 PPE change to sa_leaf in CanopyFluxesMod.F90
        ctsm5.3.007   slevis 10/14/2024 Clm60 finidat updates for ne30, f09, f19 grids
        ctsm5.3.006 samrabin 10/11/2024 Merge b4b-dev
        ctsm5.3.005     erik 10/10/2024 Hardcoded tuning adjustments for Leung_2024 dust emissions

From 77fdb8d07e6a0dfb674e0da5d11939cdf20e74c3 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 14 Oct 2024 13:14:09 -0600
Subject: [PATCH 1203/1248] Updated ChangeLog from Keith Oleson's review

---
 doc/ChangeLog | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 02f7fa763f..986f58973d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.3.008
 Originator(s): olyson (Keith Oleson,UCAR/TSS)
-Date: Mon 14 Oct 2024 11:56:12 AM MDT
+Date: Mon 14 Oct 2024 01:08:47 PM MDT
 One-line Summary: PPE change to sa_leaf in CanopyFluxesMod.F90
 
 Purpose and description of changes
@@ -18,15 +18,15 @@ Does this tag change answers significantly for any of the following physics conf
 
     [Put an [X] in the box for any configuration with significant answer changes.]
 
-[X] clm6_0
+[ ] clm6_0
 
-[X] clm5_1
+[ ] clm5_1
 
-[X] clm5_0
+[ ] clm5_0
 
-[X] ctsm5_0-nwp
+[ ] ctsm5_0-nwp
 
-[X] clm4_5
+[ ] clm4_5
 
 
 Bugs fixed
@@ -56,8 +56,10 @@ Changes answers relative to baseline: Yes
     - what platforms/compilers: All
     - nature of change: larger than roundoff/same climate)
 
- The changes in answers are explained in this post:
+ The changes in answers are explained in this post
  https://github.com/ESCOMP/CTSM/issues/2777#issuecomment-2371697380
+ and the diagnostics are here
+ https://webext.cgd.ucar.edu/I2000/ctsm53n04ctsm52028_f09_saleaf/lnd/ctsm53n04ctsm52028_f09_saleaf_2000_2001_2004-ctsm53n04ctsm52028_f09_2000_2001_2004/setsIndex.html
 
 
 Other details

From ea0dadda04ed84814c8c40e9364e7165566d6ebb Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Mon, 14 Oct 2024 16:05:22 -0600
Subject: [PATCH 1204/1248] Final ChangeLog

---
 doc/ChangeLog | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 986f58973d..bfaa2e71f7 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
 Tag name: ctsm5.3.008
 Originator(s): olyson (Keith Oleson,UCAR/TSS)
-Date: Mon 14 Oct 2024 01:08:47 PM MDT
+Date: Mon 14 Oct 2024 04:03:26 PM MDT
 One-line Summary: PPE change to sa_leaf in CanopyFluxesMod.F90
 
 Purpose and description of changes
@@ -42,8 +42,8 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho -----
-    izumi -------
+    derecho ----- OK
+    izumi ------- OK
 
 
 Answer changes

From b846e2b1926a94af73342650fe5dfd22d4db46b4 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 15 Oct 2024 09:38:19 -0600
Subject: [PATCH 1205/1248] Roll back change of one cnmatrix test length.

---
 cime_config/testdefs/testlist_clm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 9e0235a6ab..4654f53c45 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -1361,7 +1361,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">01:40:01</option>
+      <option name="wallclock">01:40:00</option>
       <option name="comment"  >Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test</option>
     </options>
   </test>
@@ -1810,7 +1810,7 @@
       <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
-      <option name="wallclock">02:30:00</option>
+      <option name="wallclock">01:40:00</option>
       <option name="comment"  >Repeat ERS_Ly5_P128x1...cropMonthOutput test with matrixcnOn</option>
     </options>
   </test>

From 82a0952fc6bcee3540dc5ca7e82d674fc52dca70 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Tue, 15 Oct 2024 17:46:01 -0600
Subject: [PATCH 1206/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 73 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index bfaa2e71f7..3620cd8c15 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,76 @@
 ===============================================================
+Tag name: ctsm5.3.009
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Tue Oct 15 17:35:40 MDT 2024
+One-line Summary: Reduce outputs from matrixcnOn tests
+
+Purpose and description of changes
+----------------------------------
+
+Reduces size and runtime of our tests of the CN Matrix capability. See "Notes of particular relevance for developers" for more details.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description):
+- Resolves ESCOMP/CTSM#2814: Remove include_user_mods from matrixcnOn testmod (https://github.com/ESCOMP/CTSM/pull/2815)
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+- Removing the include_user_mods file from the matrixcnOn test (and thus also matrixcnOn_ignore_warnings) means that the default outputs no longer overwrite outputs specified by earlier test mods. For example, in LCISO_Lm13.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-ciso_monthly--clm-matrixcnOn_ignore_warnings, it should have been saving monthly (the ciso_monthly test mod) but was actually being saved at much higher frequency (because matrixcnOn_ignore_warnings was after ciso_monthly in the test name). That test goes from 30 to 3 GB after this change.
+- Adds matrixcn test suite, which can be used during Matrix CN development. All tests in this suite are also still run in aux_clm.
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- DIFF
+    izumi ------- DIFF
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: aux_clm tests only
+    - what platforms/compilers: all
+    - nature of change: larger than roundoff
+
+  Changes are due to changed history field lists (and some other settings) due to the removal of include_user_mods from the matrixcnOn test mod. No answer changes occurred in any test other than those using matrixcnOn(_ignore_warnings); no answer changes will occur for any non-test run.
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- PR ESCOMP/CTSM#2815: Remove include_user_mods from matrixcnOn testmod (https://github.com/ESCOMP/CTSM/pull/2815)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.008
 Originator(s): olyson (Keith Oleson,UCAR/TSS)
 Date: Mon 14 Oct 2024 04:03:26 PM MDT
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 5698b8654f..af6e1675b4 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.009 samrabin 10/15/2024 Reduce outputs from matrixcnOn tests
        ctsm5.3.008   olyson 10/14/2024 PPE change to sa_leaf in CanopyFluxesMod.F90
        ctsm5.3.007   slevis 10/14/2024 Clm60 finidat updates for ne30, f09, f19 grids
        ctsm5.3.006 samrabin 10/11/2024 Merge b4b-dev

From 694333f8f49aab356a41df18b0d69515c9e3ef83 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Sun, 20 Oct 2024 10:09:49 -0600
Subject: [PATCH 1207/1248] Transfer the following parameters from namelist to
 parameter file: Jmaxb1 (now called jmaxb1 and pft-dependent)
 upplim_destruct_metamorph maximum_leaf_wetted_fraction interception_fraction

---
 bld/CLMBuildNamelist.pm                       | 14 ----
 bld/namelist_files/namelist_defaults_ctsm.xml | 18 +----
 .../namelist_definition_ctsm.xml              | 20 -----
 bld/unit_testers/build-namelist_test.pl       |  4 -
 src/biogeophys/CanopyHydrologyMod.F90         | 18 ++---
 src/biogeophys/LunaMod.F90                    | 80 +++----------------
 src/biogeophys/SnowHydrologyMod.F90           | 11 +--
 src/main/controlMod.F90                       |  2 -
 src/main/pftconMod.F90                        |  6 ++
 9 files changed, 36 insertions(+), 137 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index b881cdbfac..4d8ad454ba 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -3603,17 +3603,6 @@ sub setup_logic_luna {
   if ( &value_is_true($nl->get_value('lnc_opt') ) && not &value_is_true( $nl_flags->{'use_cn'}) ) {
      $log->fatal_error("Cannot turn lnc_opt to true when bgc=sp" );
   }
-  my $var = "jmaxb1";
-  if ( &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                 'use_luna'=>$nl_flags->{'use_luna'} );
-  }
-  my $val = $nl->get_value($var);
-  if ( ! &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     if ( defined($val) ) {
-        $log->fatal_error("Cannot set $var when use_luna is NOT on" );
-     }
-  }
 }
 
 #-------------------------------------------------------------------------------
@@ -4523,8 +4512,6 @@ sub setup_logic_canopyhydrology {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' );
 }
 
@@ -4543,7 +4530,6 @@ sub setup_logic_snowpack {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela');
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 650b21cb8d..8eb8e2cccb 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -413,11 +413,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Canopy hydrology namelist defaults -->
 <use_clm5_fpi                               >.true.</use_clm5_fpi>
-<interception_fraction                      >1.0</interception_fraction>
-<maximum_leaf_wetted_fraction               >0.05</maximum_leaf_wetted_fraction>
 <use_clm5_fpi                 phys="clm4_5" >.false.</use_clm5_fpi>
-<interception_fraction        phys="clm4_5" >0.25</interception_fraction>
-<maximum_leaf_wetted_fraction phys="clm4_5" >1.0</maximum_leaf_wetted_fraction>
 
 <!-- Soilwater movement namelist defaults -->
 <soilwater_movement_method               >1</soilwater_movement_method>
@@ -493,9 +489,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <lotmp_snowdensity_method               >'Slater2017'</lotmp_snowdensity_method>
 <lotmp_snowdensity_method phys="clm4_5" >'TruncatedAnderson1976'</lotmp_snowdensity_method>
 
-<upplim_destruct_metamorph                 >175.d00</upplim_destruct_metamorph>
-<upplim_destruct_metamorph   phys="clm4_5" >100.d00</upplim_destruct_metamorph>
-
 <overburden_compress_tfactor>0.08d00</overburden_compress_tfactor>
 
 <reset_snow>.false.</reset_snow>
@@ -551,10 +544,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240822.nc</paramfile>
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240814.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240814.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240814.nc</paramfile>
+<paramfile phys="clm6_0" >/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm60_params.c241017.nc</paramfile>
+<paramfile phys="clm5_1" >/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm51_params.c241017.nc</paramfile>
+<paramfile phys="clm5_0" >/glade/campaign/cgd/tss/people/oleson/modify_param/clm50_params.c241017.nc</paramfile>
+<paramfile phys="clm4_5" >/glade/campaign/cgd/tss/people/oleson/modify_param/clm45_params.c241017.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -605,9 +598,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_fertilizer                   >.false.</use_fertilizer>
 <use_fertilizer use_crop=".true." >.true.</use_fertilizer>
 
-<!-- Could depend on physics version -->
-<jmaxb1 use_luna=".true." >0.17</jmaxb1>
-
 <!-- o3_veg_stress_method-->
 <o3_veg_stress_method>unset</o3_veg_stress_method>
 
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 417444914e..01fc6587ec 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -404,21 +404,11 @@ Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the
 <default>Default: 40</default>
 </entry>
 
-<entry id="interception_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Fraction of intercepted precipitation
-</entry>
-
 <entry id="use_clm5_fpi" type="logical" category="clm_physics"
        group="clm_canopyhydrology_inparm" valid_values="" >
 If TRUE use clm5 equation for fraction of intercepted precipitation
 </entry>
 
-<entry id="maximum_leaf_wetted_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Maximum fraction of leaf that may be wet prior to drip occuring
-</entry>
-
 <entry id="baseflow_scalar" type="real" category="clm_physics"
        group="soilhydrology_inparm" valid_values="" >
 Scalar multiplier for base flow rate
@@ -712,11 +702,6 @@ Scalar of leaf respiration to vcmax
 The maximum value to use for zeta under stable conditions
 </entry>
 
-<entry id="Jmaxb1" type="real" category="clm_physics"
-       group="luna" >
-baseline proportion of nitrogen allocated for electron transport (J)
-</entry>
-
 <entry id="use_fates" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the FATES model
@@ -2839,11 +2824,6 @@ TruncatedAnderson1976 -- Truncate the Anderson-1976 equation at the value for -1
 Slater2017 ------------- Use equation from Slater that increases snow density for very cold temperatures  (Arctic, Antarctic)
 </entry>
 
-<entry id="upplim_destruct_metamorph" type="real" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-Upper Limit on Destructive Metamorphism Compaction [kg/m3]
-</entry>
-
 <entry id="overburden_compress_Tfactor" type="real" category="clm_physics"
        group="clm_snowhydrology_inparm"   >
 Snow compaction overburden exponential factor (1/K)
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 096409065f..64126ab347 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1235,10 +1235,6 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"use_luna=.true., lnc_opt=.true.",
                                      phys=>"clm5_0",
                                    },
-     "NOlunabutsetJmaxb1"        =>{ options=>"-envxml_dir . -bgc sp",
-                                     namelst=>"use_luna=.false., jmaxb1=1.0",
-                                     phys=>"clm5_0",
-                                   },
      "envxml_not_dir"            =>{ options=>"-envxml_dir myuser_nl_clm",
                                      namelst=>"",
                                      phys=>"clm5_0",
diff --git a/src/biogeophys/CanopyHydrologyMod.F90 b/src/biogeophys/CanopyHydrologyMod.F90
index 9ce9995ce6..166aa6d53d 100644
--- a/src/biogeophys/CanopyHydrologyMod.F90
+++ b/src/biogeophys/CanopyHydrologyMod.F90
@@ -49,6 +49,8 @@ module CanopyHydrologyMod
      real(r8) :: snow_canopy_storage_scalar ! Canopy-storage-of-snow parameter (kg/m2)
      real(r8) :: snowcan_unload_temp_fact   ! Temperature canopy snow unload scaling (C2 in Eq. 14, Roesch et al. 2001) (K*s)
      real(r8) :: snowcan_unload_wind_fact   ! Wind canopy snow unload scaling (modifies 1.56e5, where 1.56e5 is C3 in Eq. 15, Roesch et al. 2001) (-)
+     real(r8) :: interception_fraction      ! Fraction of intercepted precipitation (-)
+     real(r8) :: maximum_leaf_wetted_fraction ! Maximum fraction of leaf that may be wet (-)
   end type params_type
   type(params_type), private ::  params_inst
   !
@@ -67,8 +69,6 @@ module CanopyHydrologyMod
   private :: BulkDiag_FracWet                            ! Determine fraction of vegetated surface that is wet
   !
   ! !PRIVATE DATA MEMBERS:
-  real(r8) :: interception_fraction ! Fraction of intercepted precipitation
-  real(r8) :: maximum_leaf_wetted_fraction ! Maximum fraction of leaf that may be wet
   logical, private :: use_clm5_fpi    = .false. ! use clm5 fpi equation
 
   character(len=*), parameter, private :: sourcefile = &
@@ -99,8 +99,6 @@ subroutine CanopyHydrology_readnl( NLFilename )
     character(len=32) :: subname = 'CanopyHydrology_readnl'  ! subroutine name
     !-----------------------------------------------------------------------
     namelist /clm_canopyhydrology_inparm/ &
-         interception_fraction, &
-         maximum_leaf_wetted_fraction, &
          use_clm5_fpi
 
     ! ----------------------------------------------------------------------
@@ -125,15 +123,11 @@ subroutine CanopyHydrology_readnl( NLFilename )
     end if
 
     ! Broadcast namelist variables read in
-    call shr_mpi_bcast(interception_fraction, mpicom)
-    call shr_mpi_bcast(maximum_leaf_wetted_fraction, mpicom)
     call shr_mpi_bcast(use_clm5_fpi, mpicom)
 
     if (masterproc) then
        write(iulog,*) ' '
        write(iulog,*) 'canopyhydrology settings:'
-       write(iulog,*) '  interception_fraction        = ',interception_fraction
-       write(iulog,*) '  maximum_leaf_wetted_fraction = ',maximum_leaf_wetted_fraction
        write(iulog,*) '  use_clm5_fpi                 = ',use_clm5_fpi
     endif
 
@@ -162,6 +156,10 @@ subroutine readParams( ncid )
     call readNcdioScalar(ncid, 'snowcan_unload_temp_fact', subname, params_inst%snowcan_unload_temp_fact)
     ! Wind canopy snow unload scaling (modifies 1.56e5, where 1.56e5 is C3 in Eq. 15, Roesch et al. 2001) (-)
     call readNcdioScalar(ncid, 'snowcan_unload_wind_fact', subname, params_inst%snowcan_unload_wind_fact)
+    ! Fraction of intercepted precipitation (-)
+    call readNcdioScalar(ncid, 'interception_fraction', subname, params_inst%interception_fraction)
+    ! Maximum fraction of leaf that may be wet (-)
+    call readNcdioScalar(ncid, 'maximum_leaf_wetted_fraction', subname, params_inst%maximum_leaf_wetted_fraction)
 
    end subroutine readParams
 
@@ -535,7 +533,7 @@ subroutine BulkFlux_CanopyInterceptionAndThroughfall(bounds, num_nolakep, filter
         if (check_point_for_interception_and_excess(p)) then
            ! Coefficient of interception
            if (use_clm5_fpi) then
-              fpiliq = interception_fraction * tanh(elai(p) + esai(p))
+              fpiliq = params_inst%interception_fraction * tanh(elai(p) + esai(p))
            else
               fpiliq = 0.25_r8*(1._r8 - exp(-0.5_r8*(elai(p) + esai(p))))
            end if
@@ -1170,7 +1168,7 @@ subroutine BulkDiag_FracWet(bounds, num_soilp, filter_soilp, &
            if (h2ocan > 0._r8) then
               vegt    = frac_veg_nosno(p)*(elai(p) + esai(p))
               fwet(p) = (h2ocan / (vegt * params_inst%liq_canopy_storage_scalar))**0.666666666666_r8
-              fwet(p) = min (fwet(p),maximum_leaf_wetted_fraction)   ! Check for maximum limit of fwet
+              fwet(p) = min (fwet(p),params_inst%maximum_leaf_wetted_fraction)   ! Check for maximum limit of fwet
               if (snocan(p) > 0._r8) then
                  fcansno(p) = (snocan(p) / (vegt * params_inst%snow_canopy_storage_scalar))**0.15_r8 ! must match snocanmx 
                  fcansno(p) = min (fcansno(p),1.0_r8)
diff --git a/src/biogeophys/LunaMod.F90 b/src/biogeophys/LunaMod.F90
index dbd39daedf..3f5f7d0e3c 100644
--- a/src/biogeophys/LunaMod.F90
+++ b/src/biogeophys/LunaMod.F90
@@ -12,7 +12,7 @@ module LunaMod
   use clm_varcon            , only : rgas, tfrz,spval
   use abortutils            , only : endrun
   use clm_varctl            , only : iulog
-  use clm_varpar            , only : nlevcan
+  use clm_varpar            , only : nlevcan, mxpft
   use decompMod             , only : bounds_type, subgrid_level_patch
   use pftconMod             , only : pftcon
   use FrictionvelocityMod   , only : frictionvel_type 
@@ -33,7 +33,6 @@ module LunaMod
 
   !------------------------------------------------------------------------------
   ! PUBLIC MEMBER FUNCTIONS:
-  public  :: LunaReadNML                                   !subroutine to read in the Luna namelist
   public  :: Update_Photosynthesis_Capacity                !subroutine to update the canopy nitrogen profile
   public  :: Acc24_Climate_LUNA                            !subroutine to accumulate 24 hr climates
   public  :: Acc240_Climate_LUNA                           !subroutine to accumulate 10 day climates
@@ -78,7 +77,6 @@ module LunaMod
   real(r8), parameter :: CO2ref = 380.0_r8                   ! reference CO2 concentration for calculation of reference NUE. 
   real(r8), parameter :: forc_pbot_ref = 101325.0_r8       ! reference air pressure for calculation of reference NUE
   real(r8), parameter :: Q10Enz = 2.0_r8                   ! Q10 value for enzyme decay rate
-  real(r8)            :: Jmaxb1 = 0.1_r8                   ! the baseline proportion of nitrogen allocated for electron transport (J)    
   real(r8), parameter :: NMCp25 = 0.715_r8                 ! estimated by assuming 80% maintenance respiration is used for photosynthesis enzyme maintenance
   real(r8), parameter :: Trange1 = 5.0_r8                  ! lower temperature limit (oC) for nitrogen optimization  
   real(r8), parameter :: Trange2 = 42.0_r8                 ! upper temperature limit (oC) for nitrogen optimization
@@ -92,70 +90,11 @@ module LunaMod
   
   contains
 
-  !********************************************************************************************************************************************************************** 
-  ! Read in LUNA namelist
-  subroutine LunaReadNML( NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Read the namelist for LUNA
-    !
-    ! !USES:
-    use fileutils      , only : getavu, relavu, opnfil
-    use shr_nl_mod     , only : shr_nl_find_group_name
-    use spmdMod        , only : masterproc, mpicom
-    use shr_mpi_mod    , only : shr_mpi_bcast
-    use clm_varctl     , only : iulog
-    use shr_log_mod    , only : errMsg => shr_log_errMsg
-    use abortutils     , only : endrun
-    !
-    ! !ARGUMENTS:
-    character(len=*), intent(in) :: NLFilename ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-
-    character(len=*), parameter :: subname = 'lunaReadNML'
-    character(len=*), parameter :: nmlname = 'luna'
-    !-----------------------------------------------------------------------
-    namelist /luna/ Jmaxb1
-
-    ! Initialize options to default values, in case they are not specified in
-    ! the namelist
-
-
-    if (masterproc) then
-       unitn = getavu()
-       write(iulog,*) 'Read in '//nmlname//'  namelist'
-       call opnfil (NLFilename, unitn, 'F')
-       call shr_nl_find_group_name(unitn, nmlname, status=ierr)
-       if (ierr == 0) then
-          read(unitn, nml=luna, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(__FILE__, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR could NOT find "//nmlname//"namelist"//errmsg(__FILE__, __LINE__))
-       end if
-       call relavu( unitn )
-    end if
-
-    call shr_mpi_bcast (Jmaxb1, mpicom)
-
-    if (masterproc) then
-       write(iulog,*) ' '
-       write(iulog,*) nmlname//' settings:'
-       write(iulog,nml=luna)
-       write(iulog,*) ' '
-    end if
-
-  end subroutine lunaReadNML
-
 !----------------------------------------------------------------------------
   subroutine readParams( ncid )
     !
     ! !USES:
-    use ncdio_pio, only: file_desc_t
+    use ncdio_pio, only: file_desc_t,ncd_io
     use paramUtilMod, only: readNcdioScalar
     !
     ! !ARGUMENTS:
@@ -164,6 +103,10 @@ subroutine readParams( ncid )
     !
     ! !LOCAL VARIABLES:
     character(len=*), parameter :: subname = 'readParams_Luna'
+    character(len=100) :: errCode = '-Error reading in parameters file:'
+    logical            :: readv ! has variable been read in or not
+    real(r8)           :: temp1d(0:mxpft) ! temporary to read in parameter
+    character(len=100) :: tString ! temp. var for reading
     !--------------------------------------------------------------------
 
     ! CO2 compensation point at 25°C at present day O2 levels
@@ -314,6 +257,7 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
     c3psn         => pftcon%c3psn                                     , & ! photosynthetic pathway: 0.  =  c4, 1.  =  c3
     slatop        => pftcon%slatop                                    , & ! specific leaf area at top of canopy, projected area basis [m^2/gC]
     leafcn        => pftcon%leafcn                                    , & ! leaf C:N (gC/gN)        
+    jmaxb1        => pftcon%jmaxb1                                    , & ! Coefficient determining the response of electron transport rate to light availability (-)
     forc_pbot10   => atm2lnd_inst%forc_pbot240_downscaled_patch       , & ! Input:  [real(r8) (:)   ] 10 day mean atmospheric pressure(Pa)  
     CO2_p240      => atm2lnd_inst%forc_pco2_240_patch                 , & ! Input:  [real(r8) (:)   ] 10-day mean CO2 partial pressure (Pa)
     O2_p240       => atm2lnd_inst%forc_po2_240_patch                  , & ! Input:  [real(r8) (:)   ] 10-day mean O2 partial pressure (Pa)    
@@ -439,8 +383,8 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
                          PNcbold   = 0.0_r8                                     
                          call NitrogenAllocation(FNCa,forc_pbot10(p), relh10, CO2a10, O2a10, PARi10, PARimx10, rb10v, hourpd, &
                               tair10, tleafd10, tleafn10, &
-                              Jmaxb1, PNlcold, PNetold, PNrespold, PNcbold, dayl_factor(p), o3coefjmax(p), &
-                              PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
+                              jmaxb1(ft), PNlcold, PNetold, PNrespold, PNcbold, dayl_factor(p), &
+                              o3coefjmax(p), PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
                          vcmx25_opt= PNcbopt * FNCa * Fc25
                          jmx25_opt= PNetopt * FNCa * Fj25
                           
@@ -825,7 +769,7 @@ end subroutine Clear24_Climate_LUNA
 !************************************************************************************************************************************************
 !Use the LUNA model to calculate the Nitrogen partioning 
 subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PARimx10,rb10, hourpd, tair10, tleafd10, tleafn10, &
-     Jmaxb1, PNlcold, PNetold, PNrespold, PNcbold, dayl_factor,o3coefjmax, &
+     jmaxb1, PNlcold, PNetold, PNrespold, PNcbold, dayl_factor,o3coefjmax, &
      PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
   implicit none
   real(r8), intent (in) :: FNCa                       !Area based functional nitrogen content (g N/m2 leaf)
@@ -840,7 +784,7 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
   real(r8), intent (in) :: tair10                     !10-day running mean of the 2m temperature (oC)
   real(r8), intent (in) :: tleafd10                   !10-day running mean of daytime leaf temperature (oC) 
   real(r8), intent (in) :: tleafn10                   !10-day running mean of nighttime leaf temperature (oC) 
-  real(r8), intent (in) :: Jmaxb1                     !coefficient determining the response of electron transport rate to light availability (unitless) 
+  real(r8), intent (in) :: jmaxb1                     !coefficient determining the response of electron transport rate to light availability (unitless) 
   real(r8), intent (in) :: PNlcold                    !old value of the proportion of nitrogen allocated to light capture (unitless)
   real(r8), intent (in) :: PNetold                    !old value of the proportion of nitrogen allocated to electron transport (unitless)
   real(r8), intent (in) :: PNrespold                  !old value of the proportion of nitrogen allocated to respiration (unitless)
@@ -928,7 +872,7 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
   tleafd10c = min(max(tleafd10, Trange1), Trange2)    !constrain the physiological range
   tleafn10c = min(max(tleafn10, Trange1), Trange2)    !constrain the physiological range
   ci = 0.7_r8 * CO2a10 
-  JmaxCoef = Jmaxb1 * dayl_factor * (1.0_r8 - exp(-params_inst%relhExp * max(relh10 - &
+  JmaxCoef = jmaxb1 * dayl_factor * (1.0_r8 - exp(-params_inst%relhExp * max(relh10 - &
       params_inst%minrelh, 0.0_r8) / (1.0_r8 - params_inst%minrelh)))
   do while (PNlcoldi .NE. PNlc .and. jj < 100)      
      Fc = VcmxTKattge(tair10, tleafd10c) * Fc25
diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90
index 9fb1a52dbc..57e9088ece 100644
--- a/src/biogeophys/SnowHydrologyMod.F90
+++ b/src/biogeophys/SnowHydrologyMod.F90
@@ -87,6 +87,7 @@ module SnowHydrologyMod
       real(r8) :: scvng_fct_mlt_dst4    ! scavenging factor for dust species 4 inclusion in meltwater  [frc]
       real(r8) :: ceta                  ! Overburden compaction constant (kg/m3)
       real(r8) :: snw_rds_min  ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns]
+      real(r8) :: upplim_destruct_metamorph ! Upper limit on destructive metamorphism compaction
   end type params_type
   type(params_type), private ::  params_inst
 
@@ -151,7 +152,6 @@ module SnowHydrologyMod
 
   integer  :: overburden_compaction_method = -1
   integer  :: new_snow_density            = LoTmpDnsSlater2017 ! Snow density type
-  real(r8) :: upplim_destruct_metamorph   = 100.0_r8           ! Upper Limit on Destructive Metamorphism Compaction [kg/m3]
   real(r8) :: overburden_compress_Tfactor = 0.08_r8            ! snow compaction overburden exponential factor (1/K)
 
   ! ------------------------------------------------------------------------
@@ -211,8 +211,7 @@ subroutine SnowHydrology_readnl( NLFilename)
 
     namelist /clm_snowhydrology_inparm/ &
          wind_dependent_snow_density, snow_overburden_compaction_method, &
-         lotmp_snowdensity_method, upplim_destruct_metamorph, &
-         overburden_compress_Tfactor, &
+         lotmp_snowdensity_method, overburden_compress_Tfactor, &
          reset_snow, reset_snow_glc, reset_snow_glc_ela, &
          snow_dzmin_1, snow_dzmax_l_1, snow_dzmax_u_1, &
          snow_dzmin_2, snow_dzmax_l_2, snow_dzmax_u_2
@@ -246,7 +245,6 @@ subroutine SnowHydrology_readnl( NLFilename)
     call shr_mpi_bcast (wind_dependent_snow_density, mpicom)
     call shr_mpi_bcast (snow_overburden_compaction_method, mpicom)
     call shr_mpi_bcast (lotmp_snowdensity_method   , mpicom)
-    call shr_mpi_bcast (upplim_destruct_metamorph  , mpicom)
     call shr_mpi_bcast (overburden_compress_Tfactor, mpicom)
     call shr_mpi_bcast (reset_snow                 , mpicom)
     call shr_mpi_bcast (reset_snow_glc             , mpicom)
@@ -333,6 +331,8 @@ subroutine readParams( ncid )
     call readNcdioScalar(ncid, 'ceta', subname, params_inst%ceta)
     ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns]
     call readNcdioScalar(ncid, 'snw_rds_min', subname, params_inst%snw_rds_min)
+    ! Upper limit on destructive metamorphism compaction (kg/m3)
+    call readNcdioScalar(ncid, 'upplim_destruct_metamorph', subname, params_inst%upplim_destruct_metamorph)
 
   end subroutine readParams
 
@@ -1972,7 +1972,8 @@ subroutine SnowCompaction(bounds, num_snowc, filter_snowc, &
                 ! Settling as a result of destructive metamorphism
 
                 ddz1 = -c3*dexpf
-                if (bi > upplim_destruct_metamorph) ddz1 = ddz1*exp(-46.0e-3_r8*(bi-upplim_destruct_metamorph))
+                if (bi > params_inst%upplim_destruct_metamorph) ddz1 = &
+                        ddz1*exp(-46.0e-3_r8*(bi-params_inst%upplim_destruct_metamorph))
 
                 ! Liquid water term
 
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index f65c8c7f47..3b2409344d 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -119,7 +119,6 @@ subroutine control_init(dtime)
     !
     ! !USES:
     use CNMRespMod                       , only : CNMRespReadNML
-    use LunaMod                          , only : LunaReadNML
     use CNNDynamicsMod                   , only : CNNDynamicsReadNML
     use CNPhenologyMod                   , only : CNPhenologyReadNML
     use landunit_varcon                  , only : max_lunit
@@ -584,7 +583,6 @@ subroutine control_init(dtime)
     call SnowHydrology_readnl   ( NLFilename )
     call UrbanReadNML           ( NLFilename )
     call HumanIndexReadNML      ( NLFilename )
-    call LunaReadNML            ( NLFilename )
 
     ! ----------------------------------------------------------------------
     ! Broadcast all control information if appropriate
diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90
index b987879c03..4f8a7f16fc 100644
--- a/src/main/pftconMod.F90
+++ b/src/main/pftconMod.F90
@@ -164,6 +164,7 @@ module pftconMod
      real(r8), allocatable :: wood_density  (:)   ! wood density (kg/m3)
      real(r8), allocatable :: crit_onset_gdd_sf(:)! scale factor for crit_onset_gdd
      real(r8), allocatable :: ndays_on(:)         ! number of days to complete leaf onset
+     real(r8), allocatable :: jmaxb1(:)           ! Coefficient determining the response of electron transport rate to light availability
 
      !  crop
 
@@ -506,6 +507,7 @@ subroutine InitAllocate (this)
     allocate( this%wood_density  (0:mxpft) )
     allocate( this%crit_onset_gdd_sf (0:mxpft) )
     allocate( this%ndays_on      (0:mxpft) )
+    allocate( this%jmaxb1        (0:mxpft) )
  
   end subroutine InitAllocate
 
@@ -1017,6 +1019,9 @@ subroutine InitRead(this)
     call ncd_io('medlynintercept', this%medlynintercept, 'read', ncid, readvar=readv)  
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
+    call ncd_io('jmaxb1', this%jmaxb1, 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
     call ncd_io('mxmat', this%mxmat, 'read', ncid, readvar=readv)  
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
@@ -1596,6 +1601,7 @@ subroutine Clean(this)
     deallocate( this%taper)
     deallocate( this%crit_onset_gdd_sf)
     deallocate( this%ndays_on)
+    deallocate( this%jmaxb1)
   end subroutine Clean
 
 end module pftconMod

From 77b8e8017c80af86dd85b1bc819af053fbe70ebb Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Tue, 22 Oct 2024 08:47:59 -0600
Subject: [PATCH 1208/1248] Make jmaxb0, wc2wjb0, r_mort pft-dimensioned

---
 src/biogeochem/CNGapMortalityMod.F90 | 13 +++----------
 src/biogeophys/LunaMod.F90           | 28 ++++++++++++++--------------
 src/main/pftconMod.F90               | 18 ++++++++++++++++++
 3 files changed, 35 insertions(+), 24 deletions(-)

diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90
index 8979b1eebd..70709bce8b 100644
--- a/src/biogeochem/CNGapMortalityMod.F90
+++ b/src/biogeochem/CNGapMortalityMod.F90
@@ -34,7 +34,6 @@ module CNGapMortalityMod
   public :: CNGapMortality
 
   type, private :: params_type
-     real(r8):: am     ! mortality rate based on annual rate, fractional mortality (1/yr)
      real(r8):: k_mort ! coeff. of growth efficiency in mortality equation
   end type params_type
   !
@@ -70,11 +69,6 @@ subroutine readParams ( ncid )
     character(len=100) :: tString ! temp. var for reading
     !-----------------------------------------------------------------------
 
-    tString='r_mort'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%am=tempr
-
     tString='k_mort'
     call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
     if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
@@ -140,6 +134,7 @@ subroutine CNGapMortality (bounds, num_soilp, filter_soilp, &
          
          leafcn                   => pftcon%leafcn               , & ! Input:  [real(r8) (:)]  leaf C:N (gC/gN)                        
          livewdcn                 => pftcon%livewdcn             , & ! Input:  [real(r8) (:)]  live wood (phloem and ray parenchyma) C:N (gC/gN) 
+         r_mort                   => pftcon%r_mort               , & ! Input:  [real(r8) (:)]  Mortality rate (1/year)
          laisun                   => canopystate_inst%laisun_patch  , & ! Input:  [real(r8) (:)   ]  sunlit projected leaf area index      
          laisha                   => canopystate_inst%laisha_patch  , & ! Input:  [real(r8) (:)   ]  shaded projected leaf area index   
          nind                     => dgvs_inst%nind_patch                           , & ! Output:[real(r8)(:)] number of individuals (#/m2) added by F. Li and S. Levis
@@ -183,8 +178,6 @@ subroutine CNGapMortality (bounds, num_soilp, filter_soilp, &
          )
 
       dt = real( get_step_size(), r8 )
-      ! set the mortality rate based on annual rate
-      am = params_inst%am
       ! set coeff of growth efficiency in mortality equation 
       k_mort = params_inst%k_mort
 
@@ -216,12 +209,12 @@ subroutine CNGapMortality (bounds, num_soilp, filter_soilp, &
                am = min(1._r8, am + heatstress(p))
             else ! lpj didn't set this for grasses; cn does
                ! set the mortality rate based on annual rate
-               am = params_inst%am
+               am = r_mort(ivt(p))
             end if
 
          end if
 
-         m  = am/(get_average_days_per_year() * secspday)
+         m  = r_mort(ivt(p))/(get_average_days_per_year() * secspday)
 
          !------------------------------------------------------
          ! patch-level gap mortality carbon fluxes
diff --git a/src/biogeophys/LunaMod.F90 b/src/biogeophys/LunaMod.F90
index 3f5f7d0e3c..04bcf8256e 100644
--- a/src/biogeophys/LunaMod.F90
+++ b/src/biogeophys/LunaMod.F90
@@ -46,8 +46,6 @@ module LunaMod
       real(r8) :: kc25_coef     ! Michaelis-Menten const. at 25°C for CO2 (unitless)
       real(r8) :: ko25_coef     ! Michaelis-Menten const. at 25°C for O2 (unitless)
       real(r8) :: luna_theta_cj ! LUNA empirical curvature parameter for ac, aj photosynthesis co-limitation (unitless)
-      real(r8) :: jmaxb0        ! The baseline proportion of nitrogen allocated for electron transport (J)
-      real(r8) :: wc2wjb0       ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (unitless)
       real(r8) :: enzyme_turnover_daily ! The daily turnover rate for photosynthetic enzyme at 25oC in view of ~7 days of half-life time for Rubisco (Suzuki et al. 2001) (unitless)
       real(r8) :: relhExp       ! Specifies the impact of relative humidity on electron transport rate (unitless)
       real(r8) :: minrelh       ! Minimum relative humidity for nitrogen optimization (fraction)
@@ -120,10 +118,6 @@ subroutine readParams( ncid )
     params_inst%kc25_coef = params_inst%kc25_coef * 1.e5_r8  ! from mol/mol to Luna units
     ! LUNA empirical curvature parameter for ac, aj photosynthesis co-limitation
     call readNcdioScalar(ncid, 'luna_theta_cj', subname, params_inst%luna_theta_cj)
-    ! The baseline proportion of nitrogen allocated for electron transport (J)
-    call readNcdioScalar(ncid, 'jmaxb0', subname, params_inst%jmaxb0)
-    ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (unitless)
-    call readNcdioScalar(ncid, 'wc2wjb0', subname, params_inst%wc2wjb0)
     ! The daily turnover rate for photosynthetic enzyme at 25oC in view of ~7 days of half-life time for Rubisco (Suzuki et al. 2001) (unitless)
     call readNcdioScalar(ncid, 'enzyme_turnover_daily', subname, params_inst%enzyme_turnover_daily)
     ! Specifies the impact of relative humidity on electron transport rate (unitless)
@@ -257,7 +251,9 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
     c3psn         => pftcon%c3psn                                     , & ! photosynthetic pathway: 0.  =  c4, 1.  =  c3
     slatop        => pftcon%slatop                                    , & ! specific leaf area at top of canopy, projected area basis [m^2/gC]
     leafcn        => pftcon%leafcn                                    , & ! leaf C:N (gC/gN)        
+    jmaxb0        => pftcon%jmaxb0                                    , & ! Baseline proportion of nitrogen allocated for electron transport (J)
     jmaxb1        => pftcon%jmaxb1                                    , & ! Coefficient determining the response of electron transport rate to light availability (-)
+    wc2wjb0       => pftcon%wc2wjb0                                   , & ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
     forc_pbot10   => atm2lnd_inst%forc_pbot240_downscaled_patch       , & ! Input:  [real(r8) (:)   ] 10 day mean atmospheric pressure(Pa)  
     CO2_p240      => atm2lnd_inst%forc_pco2_240_patch                 , & ! Input:  [real(r8) (:)   ] 10-day mean CO2 partial pressure (Pa)
     O2_p240       => atm2lnd_inst%forc_po2_240_patch                  , & ! Input:  [real(r8) (:)   ] 10-day mean O2 partial pressure (Pa)    
@@ -383,7 +379,7 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
                          PNcbold   = 0.0_r8                                     
                          call NitrogenAllocation(FNCa,forc_pbot10(p), relh10, CO2a10, O2a10, PARi10, PARimx10, rb10v, hourpd, &
                               tair10, tleafd10, tleafn10, &
-                              jmaxb1(ft), PNlcold, PNetold, PNrespold, PNcbold, dayl_factor(p), &
+                              jmaxb0(ft), jmaxb1(ft), wc2wjb0(ft), PNlcold, PNetold, PNrespold, PNcbold, dayl_factor(p), &
                               o3coefjmax(p), PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
                          vcmx25_opt= PNcbopt * FNCa * Fc25
                          jmx25_opt= PNetopt * FNCa * Fj25
@@ -769,7 +765,7 @@ end subroutine Clear24_Climate_LUNA
 !************************************************************************************************************************************************
 !Use the LUNA model to calculate the Nitrogen partioning 
 subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PARimx10,rb10, hourpd, tair10, tleafd10, tleafn10, &
-     jmaxb1, PNlcold, PNetold, PNrespold, PNcbold, dayl_factor,o3coefjmax, &
+     jmaxb0, jmaxb1, wc2wjb0, PNlcold, PNetold, PNrespold, PNcbold, dayl_factor,o3coefjmax, &
      PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
   implicit none
   real(r8), intent (in) :: FNCa                       !Area based functional nitrogen content (g N/m2 leaf)
@@ -784,7 +780,9 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
   real(r8), intent (in) :: tair10                     !10-day running mean of the 2m temperature (oC)
   real(r8), intent (in) :: tleafd10                   !10-day running mean of daytime leaf temperature (oC) 
   real(r8), intent (in) :: tleafn10                   !10-day running mean of nighttime leaf temperature (oC) 
+  real(r8), intent (in) :: jmaxb0                     !Baseline proportion of nitrogen allocated for electron transport (J)
   real(r8), intent (in) :: jmaxb1                     !coefficient determining the response of electron transport rate to light availability (unitless) 
+  real(r8), intent (in) :: wc2wjb0                    !The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
   real(r8), intent (in) :: PNlcold                    !old value of the proportion of nitrogen allocated to light capture (unitless)
   real(r8), intent (in) :: PNetold                    !old value of the proportion of nitrogen allocated to electron transport (unitless)
   real(r8), intent (in) :: PNrespold                  !old value of the proportion of nitrogen allocated to respiration (unitless)
@@ -886,7 +884,7 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
      call Nitrogen_investments (KcKjFlag,FNCa, Nlc, forc_pbot10, relh10, CO2a10,O2a10, PARi10c, PARimx10c,rb10, hourpd, tair10, &
           tleafd10c,tleafn10c, &
           Kj2Kc, JmaxCoef, Fc,Fj, NUEc, NUEj, NUEcref, NUEjref, NUEr, o3coefjmax, & 
-          Kc, Kj, ci, &
+          jmaxb0, wc2wjb0, Kc, Kj, ci, &
           Vcmax, Jmax,JmeanL,JmaxL, Net, Ncb, Nresp, PSN, RESP)
 
      Npsntarget = Nlc + Ncb + Net                                                         !target nitrogen allocated to photosynthesis, which may be lower or higher than Npsn_avail
@@ -901,7 +899,7 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
         call Nitrogen_investments (KcKjFlag,FNCa, Nlc2, forc_pbot10, relh10, CO2a10,O2a10, PARi10c, PARimx10c,rb10, hourpd, &
              tair10, tleafd10c,tleafn10c, &
              Kj2Kc, JmaxCoef, Fc,Fj, NUEc, NUEj, NUEcref, NUEjref,NUEr, o3coefjmax, &
-             Kc, Kj, ci, &
+             jmaxb0, wc2wjb0, Kc, Kj, ci, &
              Vcmax, Jmax,JmeanL,JmaxL, Net2, Ncb2, Nresp2, PSN2, RESP2)
 
         Npsntarget2 = Nlc2 + Ncb2 + Net2
@@ -930,7 +928,7 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
         call Nitrogen_investments (KcKjFlag,FNCa, Nlc1,forc_pbot10, relh10, CO2a10,O2a10, PARi10c, PARimx10c,rb10, hourpd, &
              tair10, tleafd10c,tleafn10c, &
              Kj2Kc, JmaxCoef, Fc,Fj, NUEc, NUEj, NUEcref, NUEjref,NUEr, o3coefjmax, &
-             Kc, Kj, ci,&
+             jmaxb0, wc2wjb0, Kc, Kj, ci,&
              Vcmax, Jmax,JmeanL,JmaxL, Net1, Ncb1, Nresp1, PSN1, RESP1)
         Npsntarget1 = Nlc1 + Ncb1 + Net1
         Carboncost1 = (Npsntarget - Npsntarget1) * NMCp25 * Cv * (RespTBernacchi(tleafd10c) * hourpd + &
@@ -961,7 +959,7 @@ end subroutine NitrogenAllocation
 subroutine Nitrogen_investments (KcKjFlag, FNCa, Nlc, forc_pbot10, relh10, &
      CO2a10, O2a10, PARi10, PARimx10, rb10, hourpd, tair10, tleafd10, tleafn10, &
      Kj2Kc, JmaxCoef, Fc, Fj, NUEc, NUEj, NUEcref, NUEjref, NUEr, o3coefjmax, &
-     Kc,  Kj, ci, Vcmax, Jmax, JmeanL, JmaxL, Net, Ncb, Nresp, PSN, RESP)
+     jmaxb0, wc2wjb0, Kc,  Kj, ci, Vcmax, Jmax, JmeanL, JmaxL, Net, Ncb, Nresp, PSN, RESP)
   implicit none
   integer,  intent (in) :: KcKjFlag                   !flag to indicate whether to update the Kc and Kj using the photosynthesis subroutine; 0--Kc and Kj need to be calculated; 1--Kc and Kj is prescribed.
   real(r8), intent (in) :: FNCa                       !Area based functional nitrogen content (g N/m2 leaf)
@@ -987,6 +985,8 @@ subroutine Nitrogen_investments (KcKjFlag, FNCa, Nlc, forc_pbot10, relh10, &
   real(r8), intent (in) :: NUEjref                    !nitrogen use efficiency for electron transport under reference climates
   real(r8), intent (in) :: NUEr                       !nitrogen use efficiency for respiration
   real(r8), intent (in) :: o3coefjmax                 !ozone coef jmax 
+  real(r8), intent (in) :: jmaxb0                     !Baseline proportion of nitrogen allocated for electron transport (J)
+  real(r8), intent (in) :: wc2wjb0                    !The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
 
   real(r8), intent (inout) :: Kc                      !conversion factors from Vc,max to Wc 
   real(r8), intent (inout) :: Kj                      !conversion factor from electron transport rate to Wj 
@@ -1016,7 +1016,7 @@ subroutine Nitrogen_investments (KcKjFlag, FNCa, Nlc, forc_pbot10, relh10, &
   
   theta = 0.292_r8 / (1.0_r8 + 0.076_r8 / (Nlc * Cb))
   ELTRNabsorb = theta * PARi10
-  Jmaxb0act = params_inst%jmaxb0 * FNCa * Fj
+  Jmaxb0act = jmaxb0 * FNCa * Fj
 
   ! Default value of o3coefjmax is 1 -->
   ! o3coefjmax is only different from 1 if ozone_inst%stress_method == 'stress_falk'
@@ -1026,7 +1026,7 @@ subroutine Nitrogen_investments (KcKjFlag, FNCa, Nlc, forc_pbot10, relh10, &
 
   JmaxL = theta * PARimx10 / (sqrt(1.0_r8 + (theta * PARimx10 / Jmax)**2.0_r8))        
   NUEchg = (NUEc / NUEcref) * (NUEjref / NUEj)
-  Wc2Wj = params_inst%wc2wjb0 * (NUEchg**0.5_r8)
+  Wc2Wj = wc2wjb0 * (NUEchg**0.5_r8)
   Vcmax = Wc2Wj * JmaxL * Kj2Kc
   JmeanL = theta * PARi10 / (sqrt(1.0_r8 + (ELTRNabsorb / Jmax)**2.0_r8))
   if(KcKjFlag.eq.0)then      !update the Kc,Kj, anc ci information
diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90
index 4f8a7f16fc..0bb9ef23da 100644
--- a/src/main/pftconMod.F90
+++ b/src/main/pftconMod.F90
@@ -164,7 +164,10 @@ module pftconMod
      real(r8), allocatable :: wood_density  (:)   ! wood density (kg/m3)
      real(r8), allocatable :: crit_onset_gdd_sf(:)! scale factor for crit_onset_gdd
      real(r8), allocatable :: ndays_on(:)         ! number of days to complete leaf onset
+     real(r8), allocatable :: jmaxb0(:)           ! Baseline proportion of nitrogen allocated for electron transport (J)
      real(r8), allocatable :: jmaxb1(:)           ! Coefficient determining the response of electron transport rate to light availability
+     real(r8), allocatable :: wc2wjb0(:)          ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
+     real(r8), allocatable :: r_mort(:)           ! Mortality rate (1/year)
 
      !  crop
 
@@ -507,7 +510,10 @@ subroutine InitAllocate (this)
     allocate( this%wood_density  (0:mxpft) )
     allocate( this%crit_onset_gdd_sf (0:mxpft) )
     allocate( this%ndays_on      (0:mxpft) )
+    allocate( this%jmaxb0        (0:mxpft) )
     allocate( this%jmaxb1        (0:mxpft) )
+    allocate( this%wc2wjb0       (0:mxpft) )
+    allocate( this%r_mort        (0:mxpft) )
  
   end subroutine InitAllocate
 
@@ -1019,9 +1025,18 @@ subroutine InitRead(this)
     call ncd_io('medlynintercept', this%medlynintercept, 'read', ncid, readvar=readv)  
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
+    call ncd_io('jmaxb0', this%jmaxb0, 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
     call ncd_io('jmaxb1', this%jmaxb1, 'read', ncid, readvar=readv)
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
+    call ncd_io('wc2wjb0', this%wc2wjb0, 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
+    call ncd_io('r_mort', this%r_mort, 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
     call ncd_io('mxmat', this%mxmat, 'read', ncid, readvar=readv)  
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
@@ -1601,7 +1616,10 @@ subroutine Clean(this)
     deallocate( this%taper)
     deallocate( this%crit_onset_gdd_sf)
     deallocate( this%ndays_on)
+    deallocate( this%jmaxb0)
     deallocate( this%jmaxb1)
+    deallocate( this%wc2wjb0)
+    deallocate( this%r_mort)
   end subroutine Clean
 
 end module pftconMod

From b7121a6704265cd58fe1af493cf6b668d29aabe9 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Tue, 22 Oct 2024 10:46:46 -0600
Subject: [PATCH 1209/1248] ncd_io not needed after all

---
 src/biogeophys/LunaMod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biogeophys/LunaMod.F90 b/src/biogeophys/LunaMod.F90
index 04bcf8256e..366fa68f4b 100644
--- a/src/biogeophys/LunaMod.F90
+++ b/src/biogeophys/LunaMod.F90
@@ -92,7 +92,7 @@ module LunaMod
   subroutine readParams( ncid )
     !
     ! !USES:
-    use ncdio_pio, only: file_desc_t,ncd_io
+    use ncdio_pio, only: file_desc_t
     use paramUtilMod, only: readNcdioScalar
     !
     ! !ARGUMENTS:

From 3f4936c91a8ca79c3fce486b34c6bbcdf074210b Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Tue, 22 Oct 2024 10:52:34 -0600
Subject: [PATCH 1210/1248] Other variables not needed after all

---
 src/biogeophys/LunaMod.F90 | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/biogeophys/LunaMod.F90 b/src/biogeophys/LunaMod.F90
index 366fa68f4b..21e05dc0c6 100644
--- a/src/biogeophys/LunaMod.F90
+++ b/src/biogeophys/LunaMod.F90
@@ -12,7 +12,7 @@ module LunaMod
   use clm_varcon            , only : rgas, tfrz,spval
   use abortutils            , only : endrun
   use clm_varctl            , only : iulog
-  use clm_varpar            , only : nlevcan, mxpft
+  use clm_varpar            , only : nlevcan
   use decompMod             , only : bounds_type, subgrid_level_patch
   use pftconMod             , only : pftcon
   use FrictionvelocityMod   , only : frictionvel_type 
@@ -101,10 +101,6 @@ subroutine readParams( ncid )
     !
     ! !LOCAL VARIABLES:
     character(len=*), parameter :: subname = 'readParams_Luna'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: temp1d(0:mxpft) ! temporary to read in parameter
-    character(len=100) :: tString ! temp. var for reading
     !--------------------------------------------------------------------
 
     ! CO2 compensation point at 25°C at present day O2 levels
@@ -170,7 +166,7 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
   
     ! !USES:
     use clm_time_manager      , only : get_step_size_real
-    use clm_varpar            , only : nlevsoi, mxpft
+    use clm_varpar            , only : nlevsoi
     use perf_mod              , only : t_startf, t_stopf
     use clm_varctl            , only : use_cn
     use quadraticMod          , only : quadratic

From bc3d51892d4e701cd8b5a57f8010c30dc6de7d49 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Tue, 22 Oct 2024 11:04:17 -0600
Subject: [PATCH 1211/1248] Consistent naming of units

---
 src/biogeophys/LunaMod.F90          | 2 +-
 src/biogeophys/SnowHydrologyMod.F90 | 2 +-
 src/main/pftconMod.F90              | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/biogeophys/LunaMod.F90 b/src/biogeophys/LunaMod.F90
index 21e05dc0c6..0727e84e7a 100644
--- a/src/biogeophys/LunaMod.F90
+++ b/src/biogeophys/LunaMod.F90
@@ -777,7 +777,7 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
   real(r8), intent (in) :: tleafd10                   !10-day running mean of daytime leaf temperature (oC) 
   real(r8), intent (in) :: tleafn10                   !10-day running mean of nighttime leaf temperature (oC) 
   real(r8), intent (in) :: jmaxb0                     !Baseline proportion of nitrogen allocated for electron transport (J)
-  real(r8), intent (in) :: jmaxb1                     !coefficient determining the response of electron transport rate to light availability (unitless) 
+  real(r8), intent (in) :: jmaxb1                     !coefficient determining the response of electron transport rate to light availability (-) 
   real(r8), intent (in) :: wc2wjb0                    !The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
   real(r8), intent (in) :: PNlcold                    !old value of the proportion of nitrogen allocated to light capture (unitless)
   real(r8), intent (in) :: PNetold                    !old value of the proportion of nitrogen allocated to electron transport (unitless)
diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90
index 57e9088ece..578769d9ea 100644
--- a/src/biogeophys/SnowHydrologyMod.F90
+++ b/src/biogeophys/SnowHydrologyMod.F90
@@ -87,7 +87,7 @@ module SnowHydrologyMod
       real(r8) :: scvng_fct_mlt_dst4    ! scavenging factor for dust species 4 inclusion in meltwater  [frc]
       real(r8) :: ceta                  ! Overburden compaction constant (kg/m3)
       real(r8) :: snw_rds_min  ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns]
-      real(r8) :: upplim_destruct_metamorph ! Upper limit on destructive metamorphism compaction
+      real(r8) :: upplim_destruct_metamorph ! Upper limit on destructive metamorphism compaction (kg/m3)
   end type params_type
   type(params_type), private ::  params_inst
 
diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90
index 0bb9ef23da..965b21ec70 100644
--- a/src/main/pftconMod.F90
+++ b/src/main/pftconMod.F90
@@ -165,7 +165,7 @@ module pftconMod
      real(r8), allocatable :: crit_onset_gdd_sf(:)! scale factor for crit_onset_gdd
      real(r8), allocatable :: ndays_on(:)         ! number of days to complete leaf onset
      real(r8), allocatable :: jmaxb0(:)           ! Baseline proportion of nitrogen allocated for electron transport (J)
-     real(r8), allocatable :: jmaxb1(:)           ! Coefficient determining the response of electron transport rate to light availability
+     real(r8), allocatable :: jmaxb1(:)           ! Coefficient determining the response of electron transport rate to light availability (-)
      real(r8), allocatable :: wc2wjb0(:)          ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
      real(r8), allocatable :: r_mort(:)           ! Mortality rate (1/year)
 

From e5100a4d5949a0676103dc99d393478fc6aaf258 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Wed, 23 Oct 2024 08:33:36 -0600
Subject: [PATCH 1212/1248] New versions of specialized parameter files

---
 cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm  | 2 +-
 .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
index 3462b802c7..5aa0b903d0 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
@@ -1,2 +1,2 @@
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240814.nc'
+paramfile = '/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm51_ciso_cwd_hr_params.c241017.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
index d51360c82b..c41856fb01 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240822.nc'
+paramfile = '/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm60_params_cn30.c241017.nc'

From 28d552efb06a8bb345458e4fcbfbc73692a3fb8d Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Thu, 24 Oct 2024 09:41:35 -0600
Subject: [PATCH 1213/1248] Reinstate
 SMS_Lm1.f10_f10_mg37.I1850Clm60Bgc.derecho_intel.clm-clm60_monthly_matrixcn_soilCN30

---
 cime_config/testdefs/testlist_clm.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 490748c7e7..b178570add 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -863,6 +863,15 @@
       <option name="comment"  >Run matrix solution fast spinup for restart beyond a year (to trigger next year logic) turning off extra options to make faster (so without crop or isotopes). This test would've caught a previous bug.</option>
     </options>
   </test>
+  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/clm60_monthly_matrixcn_soilCN30">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:20:00</option>
+      <option name="comment"  >Smoke test of soil CN-matrix on with soil CN ratio set to 30</option>
+    </options>
+  </test>
   <test name="ERS_D" grid="f19_g17" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

From bfed0e0f4b55ff6f3191d52bd91ff2a7f1a702e8 Mon Sep 17 00:00:00 2001
From: seleneonowe <106543520+seleneonowe@users.noreply.github.com>
Date: Sat, 26 Oct 2024 15:30:12 +0100
Subject: [PATCH 1214/1248] Fix numbering error in CLM50_Tech_Note_Fluxes.rst

A link that should be to an equation for leaf boundary layer resistance was instead pointing to one for canopy air temperature.
---
 doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst
index c759d11f92..05b35d8b34 100644
--- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst
+++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst
@@ -1213,7 +1213,7 @@ The numerical solution for vegetation temperature and the fluxes of momentum, se
 
 #. Magnitude of the wind velocity incident on the leaves :math:`U_{av}` (:eq:`5.117` )
 
-#. Leaf boundary layer resistance :math:`r_{b}` (:eq:`5.136` )
+#. Leaf boundary layer resistance :math:`r_{b}` (:eq:`5.122` )
 
 #. Aerodynamic resistances :math:`r_{ah} ^{{'} }` and :math:`r_{aw} ^{{'} }`(:eq:`5.116` )
 

From 157107632490551b79bc5542db5d3d3e47b5a94b Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Sat, 26 Oct 2024 09:01:55 -0600
Subject: [PATCH 1215/1248] Move read of jmaxb0,jmaxb1,wc2wjb0 from pftcon to
 LunaMod and r_mort to CNGapMortality

---
 src/biogeochem/CNGapMortalityMod.F90 | 38 +++++++++++++++++--
 src/biogeophys/LunaMod.F90           | 56 ++++++++++++++++++++++++----
 src/main/pftconMod.F90               | 24 ------------
 3 files changed, 84 insertions(+), 34 deletions(-)

diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90
index 70709bce8b..73ff0bc911 100644
--- a/src/biogeochem/CNGapMortalityMod.F90
+++ b/src/biogeochem/CNGapMortalityMod.F90
@@ -9,9 +9,11 @@ module CNGapMortalityMod
   !
   ! !USES:
   use shr_kind_mod                   , only : r8 => shr_kind_r8
+  use shr_infnan_mod                 , only : nan => shr_infnan_nan, assignment(=)
   use decompMod                      , only : bounds_type
   use abortutils                     , only : endrun
   use shr_log_mod                    , only : errMsg => shr_log_errMsg
+  use clm_varpar                     , only : mxpft
   use pftconMod                      , only : pftcon
   use CNDVType                       , only : dgvs_type
   use CNVegCarbonStateType           , only : cnveg_carbonstate_type, spinup_factor_deadwood
@@ -35,6 +37,9 @@ module CNGapMortalityMod
 
   type, private :: params_type
      real(r8):: k_mort ! coeff. of growth efficiency in mortality equation
+     real(r8), allocatable :: r_mort(:)  ! Mortality rate (1/year)
+  contains
+     procedure, private :: allocParams    ! Allocate the parameters
   end type params_type
   !
   type(params_type), private :: params_inst
@@ -48,6 +53,24 @@ module CNGapMortalityMod
 
 contains
 
+  !-----------------------------------------------------------------------
+  subroutine allocParams ( this )
+    !
+    implicit none
+
+    ! !ARGUMENTS:
+    class(params_type) :: this
+    !
+    ! !LOCAL VARIABLES:
+    character(len=32)  :: subname = 'allocParams'
+    !-----------------------------------------------------------------------
+
+    ! allocate parameters
+
+    allocate( this%r_mort    (0:mxpft) )          ; this%r_mort(:)   = nan
+
+  end subroutine allocParams
+
   !-----------------------------------------------------------------------
   subroutine readParams ( ncid )
     !
@@ -66,6 +89,7 @@ subroutine readParams ( ncid )
     character(len=100) :: errCode = '-Error reading in parameters file:'
     logical            :: readv ! has variable been read in or not
     real(r8)           :: tempr ! temporary to read in constant
+    real(r8)           :: temp1d(0:mxpft) ! temporary to read in parameter
     character(len=100) :: tString ! temp. var for reading
     !-----------------------------------------------------------------------
 
@@ -73,6 +97,13 @@ subroutine readParams ( ncid )
     call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
     if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
     params_inst%k_mort=tempr   
+
+    call params_inst%allocParams()
+
+    tString='r_mort'
+    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
+    params_inst%r_mort=temp1d
     
   end subroutine readParams
 
@@ -134,7 +165,6 @@ subroutine CNGapMortality (bounds, num_soilp, filter_soilp, &
          
          leafcn                   => pftcon%leafcn               , & ! Input:  [real(r8) (:)]  leaf C:N (gC/gN)                        
          livewdcn                 => pftcon%livewdcn             , & ! Input:  [real(r8) (:)]  live wood (phloem and ray parenchyma) C:N (gC/gN) 
-         r_mort                   => pftcon%r_mort               , & ! Input:  [real(r8) (:)]  Mortality rate (1/year)
          laisun                   => canopystate_inst%laisun_patch  , & ! Input:  [real(r8) (:)   ]  sunlit projected leaf area index      
          laisha                   => canopystate_inst%laisha_patch  , & ! Input:  [real(r8) (:)   ]  shaded projected leaf area index   
          nind                     => dgvs_inst%nind_patch                           , & ! Output:[real(r8)(:)] number of individuals (#/m2) added by F. Li and S. Levis
@@ -209,12 +239,14 @@ subroutine CNGapMortality (bounds, num_soilp, filter_soilp, &
                am = min(1._r8, am + heatstress(p))
             else ! lpj didn't set this for grasses; cn does
                ! set the mortality rate based on annual rate
-               am = r_mort(ivt(p))
+               am = params_inst%r_mort(ivt(p))
             end if
 
+         else
+            am = params_inst%r_mort(ivt(p)) 
          end if
 
-         m  = r_mort(ivt(p))/(get_average_days_per_year() * secspday)
+         m  = am/(get_average_days_per_year() * secspday)
 
          !------------------------------------------------------
          ! patch-level gap mortality carbon fluxes
diff --git a/src/biogeophys/LunaMod.F90 b/src/biogeophys/LunaMod.F90
index 0727e84e7a..5641846309 100644
--- a/src/biogeophys/LunaMod.F90
+++ b/src/biogeophys/LunaMod.F90
@@ -9,10 +9,11 @@ module LunaMod
   ! !USES:
   use shr_kind_mod          , only : r8  => shr_kind_r8
   use shr_log_mod           , only : errMsg  => shr_log_errMsg
+  use shr_infnan_mod        , only : nan => shr_infnan_nan, assignment(=)
   use clm_varcon            , only : rgas, tfrz,spval
   use abortutils            , only : endrun
   use clm_varctl            , only : iulog
-  use clm_varpar            , only : nlevcan
+  use clm_varpar            , only : nlevcan, mxpft
   use decompMod             , only : bounds_type, subgrid_level_patch
   use pftconMod             , only : pftcon
   use FrictionvelocityMod   , only : frictionvel_type 
@@ -49,6 +50,11 @@ module LunaMod
       real(r8) :: enzyme_turnover_daily ! The daily turnover rate for photosynthetic enzyme at 25oC in view of ~7 days of half-life time for Rubisco (Suzuki et al. 2001) (unitless)
       real(r8) :: relhExp       ! Specifies the impact of relative humidity on electron transport rate (unitless)
       real(r8) :: minrelh       ! Minimum relative humidity for nitrogen optimization (fraction)
+      real(r8), allocatable :: jmaxb0(:)  ! Baseline proportion of nitrogen allocated for electron transport (J)
+      real(r8), allocatable :: jmaxb1(:)  ! Coefficient determining the response of electron transport rate to light availability (-)
+      real(r8), allocatable :: wc2wjb0(:) ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
+  contains    
+      procedure, private :: allocParams    ! Allocate the parameters
   end type params_type
   type(params_type), private ::  params_inst
 
@@ -88,11 +94,31 @@ module LunaMod
   
   contains
 
+  !-----------------------------------------------------------------------
+  subroutine allocParams ( this )
+    !
+    implicit none
+
+    ! !ARGUMENTS:
+    class(params_type) :: this
+    !
+    ! !LOCAL VARIABLES:
+    character(len=32)  :: subname = 'allocParams'
+    !-----------------------------------------------------------------------
+
+    ! allocate parameters
+
+    allocate( this%jmaxb0    (0:mxpft) )          ; this%jmaxb0(:)   = nan
+    allocate( this%jmaxb1    (0:mxpft) )          ; this%jmaxb1(:)   = nan
+    allocate( this%wc2wjb0   (0:mxpft) )          ; this%wc2wjb0(:)  = nan
+
+  end subroutine allocParams
+
 !----------------------------------------------------------------------------
   subroutine readParams( ncid )
     !
     ! !USES:
-    use ncdio_pio, only: file_desc_t
+    use ncdio_pio, only: file_desc_t,ncd_io
     use paramUtilMod, only: readNcdioScalar
     !
     ! !ARGUMENTS:
@@ -101,6 +127,10 @@ subroutine readParams( ncid )
     !
     ! !LOCAL VARIABLES:
     character(len=*), parameter :: subname = 'readParams_Luna'
+    character(len=100) :: errCode = '-Error reading in parameters file:'
+    logical            :: readv ! has variable been read in or not
+    real(r8)           :: temp1d(0:mxpft) ! temporary to read in parameter
+    character(len=100) :: tString ! temp. var for reading
     !--------------------------------------------------------------------
 
     ! CO2 compensation point at 25°C at present day O2 levels
@@ -121,6 +151,21 @@ subroutine readParams( ncid )
     ! Minimum relative humidity for nitrogen optimization (fraction)
     call readNcdioScalar(ncid, 'minrelh', subname, params_inst%minrelh)
 
+    call params_inst%allocParams()
+
+    tString = "jmaxb0"
+    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
+    params_inst%jmaxb0=temp1d
+    tString = "jmaxb1"
+    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
+    params_inst%jmaxb1=temp1d
+    tString = "wc2wjb0"
+    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
+    params_inst%wc2wjb0=temp1d
+
    end subroutine readParams
 
   !-----------------------------------------------------------------------
@@ -247,9 +292,6 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
     c3psn         => pftcon%c3psn                                     , & ! photosynthetic pathway: 0.  =  c4, 1.  =  c3
     slatop        => pftcon%slatop                                    , & ! specific leaf area at top of canopy, projected area basis [m^2/gC]
     leafcn        => pftcon%leafcn                                    , & ! leaf C:N (gC/gN)        
-    jmaxb0        => pftcon%jmaxb0                                    , & ! Baseline proportion of nitrogen allocated for electron transport (J)
-    jmaxb1        => pftcon%jmaxb1                                    , & ! Coefficient determining the response of electron transport rate to light availability (-)
-    wc2wjb0       => pftcon%wc2wjb0                                   , & ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
     forc_pbot10   => atm2lnd_inst%forc_pbot240_downscaled_patch       , & ! Input:  [real(r8) (:)   ] 10 day mean atmospheric pressure(Pa)  
     CO2_p240      => atm2lnd_inst%forc_pco2_240_patch                 , & ! Input:  [real(r8) (:)   ] 10-day mean CO2 partial pressure (Pa)
     O2_p240       => atm2lnd_inst%forc_po2_240_patch                  , & ! Input:  [real(r8) (:)   ] 10-day mean O2 partial pressure (Pa)    
@@ -375,7 +417,8 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
                          PNcbold   = 0.0_r8                                     
                          call NitrogenAllocation(FNCa,forc_pbot10(p), relh10, CO2a10, O2a10, PARi10, PARimx10, rb10v, hourpd, &
                               tair10, tleafd10, tleafn10, &
-                              jmaxb0(ft), jmaxb1(ft), wc2wjb0(ft), PNlcold, PNetold, PNrespold, PNcbold, dayl_factor(p), &
+                              params_inst%jmaxb0(ft), params_inst%jmaxb1(ft), params_inst%wc2wjb0(ft), PNlcold, PNetold, &
+                              PNrespold, PNcbold, dayl_factor(p), &
                               o3coefjmax(p), PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
                          vcmx25_opt= PNcbopt * FNCa * Fc25
                          jmx25_opt= PNetopt * FNCa * Fj25
@@ -1362,7 +1405,6 @@ subroutine  Quadratic(a,b,c,r1,r2)
   end if
         
 end subroutine Quadratic
-	
 
 end module LunaMod
 
diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90
index 965b21ec70..b987879c03 100644
--- a/src/main/pftconMod.F90
+++ b/src/main/pftconMod.F90
@@ -164,10 +164,6 @@ module pftconMod
      real(r8), allocatable :: wood_density  (:)   ! wood density (kg/m3)
      real(r8), allocatable :: crit_onset_gdd_sf(:)! scale factor for crit_onset_gdd
      real(r8), allocatable :: ndays_on(:)         ! number of days to complete leaf onset
-     real(r8), allocatable :: jmaxb0(:)           ! Baseline proportion of nitrogen allocated for electron transport (J)
-     real(r8), allocatable :: jmaxb1(:)           ! Coefficient determining the response of electron transport rate to light availability (-)
-     real(r8), allocatable :: wc2wjb0(:)          ! The baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj) (-)
-     real(r8), allocatable :: r_mort(:)           ! Mortality rate (1/year)
 
      !  crop
 
@@ -510,10 +506,6 @@ subroutine InitAllocate (this)
     allocate( this%wood_density  (0:mxpft) )
     allocate( this%crit_onset_gdd_sf (0:mxpft) )
     allocate( this%ndays_on      (0:mxpft) )
-    allocate( this%jmaxb0        (0:mxpft) )
-    allocate( this%jmaxb1        (0:mxpft) )
-    allocate( this%wc2wjb0       (0:mxpft) )
-    allocate( this%r_mort        (0:mxpft) )
  
   end subroutine InitAllocate
 
@@ -1025,18 +1017,6 @@ subroutine InitRead(this)
     call ncd_io('medlynintercept', this%medlynintercept, 'read', ncid, readvar=readv)  
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
-    call ncd_io('jmaxb0', this%jmaxb0, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('jmaxb1', this%jmaxb1, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('wc2wjb0', this%wc2wjb0, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('r_mort', this%r_mort, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
     call ncd_io('mxmat', this%mxmat, 'read', ncid, readvar=readv)  
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
@@ -1616,10 +1596,6 @@ subroutine Clean(this)
     deallocate( this%taper)
     deallocate( this%crit_onset_gdd_sf)
     deallocate( this%ndays_on)
-    deallocate( this%jmaxb0)
-    deallocate( this%jmaxb1)
-    deallocate( this%wc2wjb0)
-    deallocate( this%r_mort)
   end subroutine Clean
 
 end module pftconMod

From 0fd1a04d9a59c8e92d516cb0bbb992cba602589e Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Sun, 27 Oct 2024 14:15:24 -0600
Subject: [PATCH 1216/1248] Final paths for parameter files

---
 bld/namelist_files/namelist_defaults_ctsm.xml             | 8 ++++----
 .../testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm    | 2 +-
 .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm       | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index c93c4f5696..54d3afd5c1 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -544,10 +544,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm60_params.c241017.nc</paramfile>
-<paramfile phys="clm5_1" >/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm51_params.c241017.nc</paramfile>
-<paramfile phys="clm5_0" >/glade/campaign/cgd/tss/people/oleson/modify_param/clm50_params.c241017.nc</paramfile>
-<paramfile phys="clm4_5" >/glade/campaign/cgd/tss/people/oleson/modify_param/clm45_params.c241017.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241017.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c241017.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241017.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241017.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
index 5aa0b903d0..edeb0fce21 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
@@ -1,2 +1,2 @@
-paramfile = '/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm51_ciso_cwd_hr_params.c241017.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c241017.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
index c41856fb01..b1d856797d 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '/glade/campaign/cgd/tss/people/oleson/modify_param/ctsm60_params_cn30.c241017.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c241017.nc'

From ebf5f26df700f378522b020b4b3bf31ea008eb78 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Tue, 29 Oct 2024 10:49:17 -0700
Subject: [PATCH 1217/1248] exclude fates element error from ST3 testdefs

This addresses #2580
---
 cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm
index eca76c4b9c..860656e8d8 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm
@@ -1 +1,2 @@
 use_fates_ed_st3= .true.
+hist_fexcl1 = 'FATES_ERROR_EL'

From 127fa7b37376499e97852bd906c7cfe580cf09cf Mon Sep 17 00:00:00 2001
From: adrifoster <adrifost@ucar.edu>
Date: Tue, 29 Oct 2024 15:19:15 -0600
Subject: [PATCH 1218/1248] update nfsc name

---
 src/fates                           |  2 +-
 src/main/histFileMod.F90            | 10 +++++-----
 src/utils/clmfates_interfaceMod.F90 |  6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/fates b/src/fates
index 825579d0b4..b4367834ab 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit 825579d0b406fe99344591b5ed8356e5c7aeebec
+Subproject commit b4367834abf505eb4e5f53af9bc7e4b83af4685c
diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
index 69dcbe3b8e..4d1f514cb0 100644
--- a/src/main/histFileMod.F90
+++ b/src/main/histFileMod.F90
@@ -28,7 +28,7 @@ module histFileMod
   use FatesInterfaceTypesMod , only : nlevheight
   use FatesInterfaceTypesMod , only : nlevdamage
   use FatesConstantsMod      , only : n_landuse_cats
-  use FatesFuelClassesMod    , only : nfsc
+  use FatesFuelClassesMod    , only : num_fuel_classes
   use FatesLitterMod         , only : ncwd
   use PRTGenericMod          , only : num_elements_fates  => num_elements
   use FatesInterfaceTypesMod , only : numpft_fates => numpft
@@ -2504,7 +2504,7 @@ subroutine htape_create (t, histrest)
        call ncd_defdim(lnfid, 'fates_levpft', numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levage', nlevage, dimid)
        call ncd_defdim(lnfid, 'fates_levheight', nlevheight, dimid)
-       call ncd_defdim(lnfid, 'fates_levfuel', nfsc, dimid)
+       call ncd_defdim(lnfid, 'fates_levfuel', num_fuel_classes, dimid)
        call ncd_defdim(lnfid, 'fates_levcwdsc', ncwd, dimid)
        call ncd_defdim(lnfid, 'fates_levscpf', nlevsclass*numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levcapf', nlevcoage*numpft_fates, dimid)
@@ -2519,7 +2519,7 @@ subroutine htape_create (t, histrest)
        call ncd_defdim(lnfid, 'fates_levelpft', num_elements_fates * numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levelcwd', num_elements_fates * ncwd, dimid)
        call ncd_defdim(lnfid, 'fates_levelage', num_elements_fates * nlevage, dimid)
-       call ncd_defdim(lnfid, 'fates_levagefuel', nlevage * nfsc, dimid)
+       call ncd_defdim(lnfid, 'fates_levagefuel', nlevage * num_fuel_classes, dimid)
        call ncd_defdim(lnfid, 'fates_levclscpf', nclmax*nlevsclass*numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levlanduse', n_landuse_cats, dimid)
        call ncd_defdim(lnfid, 'fates_levlulu', n_landuse_cats * n_landuse_cats, dimid)
@@ -5595,7 +5595,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
     case ('fates_levheight')
        num2d = nlevheight
     case ('fates_levfuel')
-       num2d = nfsc
+       num2d = num_fuel_classes
     case ('fates_levcwdsc')
        num2d = ncwd
     case ('fates_levscpf')
@@ -5635,7 +5635,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
     case ('fates_levelage')
        num2d = num_elements_fates*nlevage
     case ('fates_levagefuel')
-       num2d = nlevage*nfsc
+       num2d = nlevage*num_fuel_classes
     case('fates_levclscpf')
        num2d = nclmax * nclmax * numpft_fates
     case ('fates_levlanduse')
diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
index 10fabeed23..269189d1b7 100644
--- a/src/utils/clmfates_interfaceMod.F90
+++ b/src/utils/clmfates_interfaceMod.F90
@@ -3622,7 +3622,7 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates)
    use FatesInterfaceTypesMod, only : nlevsclass, nlevage, nlevcoage
    use FatesInterfaceTypesMod, only : nlevheight
    use FatesInterfaceTypesMod, only : nlevdamage
-   use FatesFuelClassesMod,    only : nfsc
+   use FatesFuelClassesMod,    only : num_fuel_classes
    use FatesLitterMod,         only : ncwd
    use EDParamsMod,            only : nlevleaf, nclmax
    use FatesInterfaceTypesMod, only : numpft_fates => numpft
@@ -3674,7 +3674,7 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates)
    fates%sizeagepft_class_end   = nlevsclass * nlevage * numpft_fates
 
    fates%fuel_begin = 1
-   fates%fuel_end = nfsc
+   fates%fuel_end = num_fuel_classes
 
    fates%cwdsc_begin = 1
    fates%cwdsc_end = ncwd
@@ -3701,7 +3701,7 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates)
    fates%elage_end   = num_elements * nlevage
 
    fates%agefuel_begin = 1
-   fates%agefuel_end   = nlevage * nfsc
+   fates%agefuel_end   = nlevage * num_fuel_classes
 
    fates%cdpf_begin = 1
    fates%cdpf_end = nlevdamage * numpft_fates * nlevsclass

From 152f5d6d814272bd1aee2a76e0069093999de6ef Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 29 Oct 2024 18:29:17 -0600
Subject: [PATCH 1219/1248] Remove/replace refs to DATM_C*_YR_* variables

---
 ...tmospheric-forcing-to-spinup-the-model.rst |  4 +--
 .../customizing-the-clm-configuration.rst     | 34 ++++++-------------
 src/main/clm_varctl.F90                       |  2 +-
 tools/contrib/run_clm_historical              | 12 +++----
 tools/contrib/run_clmtowers                   | 14 ++++----
 5 files changed, 27 insertions(+), 39 deletions(-)

diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
index 769755937d..a81465c699 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
@@ -10,7 +10,7 @@ Because it takes so long to spinup the CN model (as we just saw previously), if
 
 In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on Cheyenne. There are several simulations that have high frequency data for which we can do this. You can also do this on a machine other than Cheyenne, but would need to download the data from the Earth System Grid and change the datapath similar to Example :numref:`eg-sim-data-from-prev-sim`.
 
-Example: Simulation with MOAR Data on cheyenne
+Example: Simulation with MOAR Data on derecho
 -------------------------------------------------------------
 ::
 
@@ -21,7 +21,7 @@ Example: Simulation with MOAR Data on cheyenne
    > ./xmlchange DATM_CPL_CASE=b40.1850.track1.1deg.006a
    # The following sets the align year and years to run over for atm forcing
    #  (you could also use an editor)
-   > ./xmlchange DATM_CPL_YR_ALIGN=1,DATM_CPL_YR_START=960,DATM_CPL_YR_END=1030
+   > ./xmlchange DATM_YR_ALIGN=1,DATM_YR_START=960,DATM_YR_END=1030
    > ./case.setup
    # Now build and run as normal
    > ./case.build
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index 7cd8ce9c9c..11e996ae5d 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -510,13 +510,10 @@ For running "I" cases there are several other noteworthy configuration items tha
    CCSM_BGC
    DATM_MODE
    DATM_PRESAERO
-   DATM_CLMNCEP_YR_ALIGN
-   DATM_CLMNCEP_YR_START
-   DATM_CLMNCEP_YR_END
+   DATM_YR_ALIGN
+   DATM_YR_START
+   DATM_YR_END
    DATM_CPL_CASE
-   DATM_CPL_YR_ALIGN
-   DATM_CPL_YR_START
-   DATM_CPL_YR_END
 
 ``CCSM_CO2_PPMV``
    Sets the mixing ratio of CO2 in parts per million by volume for ALL CESM components to use. Note that most compsets already set this value to something reasonable. Also note that some compsets may tell the atmosphere model to override this value with either historic or ramped values. If the ``CCSM_BGC`` variable is set to something other than "none" the atmosphere model will determine CO2, and CLM will listen and use what the atmosphere sends it. On the CLM side the namelist item ``co2_type`` tells CLM to use the value sent from the atmosphere rather than a value set on it's own namelist.
@@ -569,36 +566,27 @@ For running "I" cases there are several other noteworthy configuration items tha
 
   ``pt1_pt1`` = read in single-point or regional datasets
 
-DATM_CLMNCEP_YR_START
-  ``DATM_CLMNCEP_YR_START`` sets the beginning year to cycle the atmospheric data over for ``CLM_QIAN`` or ``CLMCRUNCEP`` modes.
+DATM_YR_START
+  ``DATM_YR_START`` sets the beginning year to cycle the atmospheric data over for ``CLM_QIAN`` or ``CLMCRUNCEP`` or ``CPLHISTForcing`` modes.
 
-DATM_CLMNCEP_YR_END
-  ``DATM_CLMNCEP_YR_END`` sets the ending year to cycle the atmospheric data over for ``CLM_QIAN`` or ``CLMCRUNCEP`` modes.
+DATM_YR_END
+  ``DATM_YR_END`` sets the ending year to cycle the atmospheric data over for ``CLM_QIAN`` or ``CLMCRUNCEP`` or ``CPLHISTForcing`` modes.
 
-DATM_CLMNCEP_YR_ALIGN
-  ``DATM_CLMNCEP_YR_START`` and ``DATM_CLMNCEP_YR_END`` determine the range of years to cycle the atmospheric data over, and ``DATM_CLMNCEP_YR_ALIGN`` determines which year in that range of years the simulation will start with.
+DATM_YR_ALIGN
+  ``DATM_YR_START`` and ``DATM_YR_END`` determine the range of years to cycle the atmospheric data over, and ``DATM_YR_ALIGN`` determines which year in that range of years the simulation will start with.
 
 DATM_CPL_CASE
   ``DATM_CPL_CASE`` sets the casename to use for the ``CPLHISTForcing`` mode.
 
-DATM_CPL_YR_START
-  ``DATM_CPL_YR_START`` sets the beginning year to cycle the atmospheric data over for the ``CPLHISTForcing`` mode.
-
-DATM_CPL_YR_END
-  ``DATM_CPL_YR_END`` sets the ending year to cycle the atmospheric data over for the ``CPLHISTForcing`` mode.
-
-DATM_CPL_YR_ALIGN
-  ``DATM_CPL_YR_START`` and ``DATM_CPL_YR_END`` determine the range of years to cycle the atmospheric data over, and ``DATM_CPL_YR_ALIGN`` determines which year in that range of years the simulation will start with.
-
 -----------------------------
 Downloading DATM Forcing Data
 -----------------------------
 
 In Chapter One of the `CESM User's Guide <link-to-CESM-UG>`_ there is a section on "Downloading input data". The normal process of setting up cases will use the "scripts/ccsm_utils/Tools/check_input_data" script to retrieve data from the CESM subversion inputdata repository. This is true for the standard `CLM_QIAN` forcing as well.
 
-The `CLMCRUNCEP` data is uploaded into the subversion inputdata repository as well -- but as it is 1.1 Terabytes of data downloading it is problematic (*IT WILL TAKE SEVERAL DAYS TO DOWNLOAD THE ENTIRE DATASET USING SUBVERSION*). Because of its size you may also need to download it onto a separate disk space. We have done that on cheyenne for example where it resides in ``$ENV{CESMROOT}/lmwg`` while the rest of the input data resides in ``$ENV{CESMDATAROOT}/inputdata``. The data is also already available on: janus, franklin, and hopper. If you download the data, we recommend that you break your download into several chunks, by setting up a case and setting the year range for ``DATM_CPL_YR_START`` and ``DATM_CPL_YR_END`` in say 20 year sections over 1901 to 2010, and then use ``check_input_data`` to export the data.
+The `CLMCRUNCEP` data is uploaded into the subversion inputdata repository as well -- but as it is 1.1 Terabytes of data downloading it is problematic (*IT WILL TAKE SEVERAL DAYS TO DOWNLOAD THE ENTIRE DATASET USING SUBVERSION*). Because of its size you may also need to download it onto a separate disk space. We have done that on derecho for example where it resides in ``$ENV{CESMROOT}/lmwg`` while the rest of the input data resides in ``$ENV{CESMDATAROOT}/inputdata``. The data is also already available on: janus, franklin, and hopper. If you download the data, we recommend that you break your download into several chunks, by setting up a case and setting the year range for ``DATM_YR_START`` and ``DATM_YR_END`` in say 20 year sections over 1901 to 2010, and then use ``check_input_data`` to export the data.
 
-The ``CPLHISTForcing`` DATM forcing data is unique -- because it is large compared to the rest of the input data, and we only have a disk copy on cheyenne. The DATM assumes the path for the previous NCAR machine cheyenne of ``/glade/p/cesm/shared_outputdata/cases/ccsm4/$DATM_CPLHIST_CASE`` for the data. So you will need to change this path in order to run on any other machine. You can download the data itself from NCAR HPSS from ``/CCSM/csm/$DATM_CPLHIST_CASE``.
+The ``CPLHISTForcing`` DATM forcing data is unique -- because it is large compared to the rest of the input data, and we only have a disk copy on derecho. The DATM assumes the path for derecho of ``/glade/p/cesm/shared_outputdata/cases/ccsm4/$DATM_CPLHIST_CASE`` for the data. So you will need to change this path in order to run on any other machine. You can download the data itself from NCAR HPSS from ``/CCSM/csm/$DATM_CPLHIST_CASE``.
 
 --------------------------------------
 Customizing via the build script files
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index 5fa2602e5a..9539060200 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -289,7 +289,7 @@ module clm_varctl
   logical, public :: spinup_matrixcn = .false.  !.false.              ! true => use acc spinup
   logical, public :: hist_wrt_matrixcn_diag = .false.!.false.              ! true => use acc spinup
   ! SASU 
-  integer, public :: nyr_forcing  = 10   ! length of forcing years for the spin up. eg. if DATM_CLMNCEP_YR_START=1901;DATM_CLMNCEP_YR_END=1920, then nyr_forcing = 20
+  integer, public :: nyr_forcing  = 10   ! length of forcing years for the spin up. eg. if DATM_YR_START=1901;DATM_YR_END=1920, then nyr_forcing = 20
   integer, public :: nyr_SASU     = 1    ! length of each semi-analytic solution. eg. nyr_SASU=5, analytic solutions will be calculated every five years.
                                          ! nyr_SASU=1: the fastest SASU, but inaccurate; nyr_SASU=nyr_forcing(eg. 20): the lowest SASU but accurate
   integer, public :: iloop_avg    = -999 ! The restart file will be based on the average of all analytic solutions within the iloop_avg^th loop. 
diff --git a/tools/contrib/run_clm_historical b/tools/contrib/run_clm_historical
index cd293d5867..8dc9269d3b 100755
--- a/tools/contrib/run_clm_historical
+++ b/tools/contrib/run_clm_historical
@@ -76,9 +76,9 @@ cp original_user_nl_clm user_nl_clm
 ./xmlchange STOP_N=21
 ./xmlchange CONTINUE_RUN=FALSE
 ./xmlchange RESUBMIT=0
-./xmlchange DATM_CLMNCEP_YR_ALIGN=1901
-./xmlchange DATM_CLMNCEP_YR_START=1901
-./xmlchange DATM_CLMNCEP_YR_END=1920
+./xmlchange DATM_YR_ALIGN=1901
+./xmlchange DATM_YR_START=1901
+./xmlchange DATM_YR_END=1920
 
 # need to use user_nl_datm files to get years right
 cp user_nl_datm1901-1920 user_nl_datm
@@ -203,9 +203,9 @@ gzip $DDIR$CASENAME*.bin
 # we have to resubmit the job 3 times.
 ./xmlchange STOP_OPTION=nyears
 ./xmlchange STOP_N=22
-./xmlchange DATM_CLMNCEP_YR_ALIGN=1901
-./xmlchange DATM_CLMNCEP_YR_START=1901
-./xmlchange DATM_CLMNCEP_YR_END=2014
+./xmlchange DATM_YR_ALIGN=1901
+./xmlchange DATM_YR_START=1901
+./xmlchange DATM_YR_END=2014
 ./xmlchange CONTINUE_RUN=TRUE
 ./xmlchange RESUBMIT=3
 
diff --git a/tools/contrib/run_clmtowers b/tools/contrib/run_clmtowers
index e4dd2519ff..7e9dbbc426 100755
--- a/tools/contrib/run_clmtowers
+++ b/tools/contrib/run_clmtowers
@@ -211,9 +211,9 @@ foreach mysite ( $sites )
     ./xmlchange --id STOP_OPTION --val nyears
     ./xmlchange --id STOP_N --val $numyears
     ./xmlchange --id RUN_STARTDATE --val $startyear[$cnt]-01-01
-    ./xmlchange --id DATM_CLMNCEP_YR_ALIGN --val $startyear[$cnt]
-    ./xmlchange --id DATM_CLMNCEP_YR_START --val $startyear[$cnt]
-    ./xmlchange --id DATM_CLMNCEP_YR_END --val $endyear[$cnt]
+    ./xmlchange --id DATM_YR_ALIGN --val $startyear[$cnt]
+    ./xmlchange --id DATM_YR_START --val $startyear[$cnt]
+    ./xmlchange --id DATM_YR_END --val $endyear[$cnt]
     ./xmlchange --id CALENDAR --val GREGORIAN
     if ($BGC == ON) then
       ./xmlchange --id CLM_BLDNML_OPTS --val "-mask navy -bgc bgc -crop"
@@ -240,9 +240,9 @@ foreach mysite ( $sites )
       else
         ./xmlchange --id RUN_STARTDATE --val $startyear[$cnt]-01-01
       endif
-      ./xmlchange --id DATM_CLMNCEP_YR_ALIGN --val $alignyear
-      ./xmlchange --id DATM_CLMNCEP_YR_START --val $startyears
-      ./xmlchange --id DATM_CLMNCEP_YR_END --val $endyears
+      ./xmlchange --id DATM_YR_ALIGN --val $alignyear
+      ./xmlchange --id DATM_YR_START --val $startyears
+      ./xmlchange --id DATM_YR_END --val $endyears
       if ($alignyear == 1) then
         ./xmlchange --id CALENDAR --val NO_LEAP
       endif
@@ -263,7 +263,7 @@ foreach mysite ( $sites )
   ./preview_namelists
   # Have to force this for some reason
   if ($SPINUP_P1 == FALSE) then
-    ./xmlchange --id DATM_CLMNCEP_YR_END --val $endyear[$cnt]
+    ./xmlchange --id DATM_YR_END --val $endyear[$cnt]
     ./preview_namelists
   endif
   if ( $status != 0 )then

From f2a8ce051099244efd3cbd38279865ea04f1d61f Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 29 Oct 2024 18:46:45 -0600
Subject: [PATCH 1220/1248] Remove some more DATM_C..._YR_...

---
 cime_config/buildnml | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/cime_config/buildnml b/cime_config/buildnml
index e9b7a610cd..e06b9388c7 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -52,16 +52,8 @@ def buildnml(case, caseroot, compname):
     clm_accelerated_spinup = case.get_value("CLM_ACCELERATED_SPINUP")
     comp_interface = case.get_value("COMP_INTERFACE")
     lilac_mode = case.get_value("LILAC_MODE")
-    if comp_interface == "nuopc":
-        yr_start = case.get_value("DATM_YR_START")
-        yr_end = case.get_value("DATM_YR_END")
-    else:
-        yr_start = case.get_value("DATM_CLMNCEP_YR_START")
-        yr_end = case.get_value("DATM_CLMNCEP_YR_END")
-
-    if yr_start != None and yr_start < 0:
-        yr_start = case.get_value("DATM_CPLHIST_YR_START")
-        yr_end = case.get_value("DATM_CPLHIST_YR_END")
+    yr_start = case.get_value("DATM_YR_START")
+    yr_end = case.get_value("DATM_YR_END")
 
     # For LILAC
     if yr_start == None or lilac_mode == "on":

From c697c76a5bec4837075f82eacef45ef36b7eeab0 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Tue, 29 Oct 2024 18:51:47 -0600
Subject: [PATCH 1221/1248] Remove additional DATM_C..._YR_...

---
 .../running-special-cases/Running-with-anomaly-forcing.rst      | 2 +-
 ...us-simulation-as-atmospheric-forcing-to-spinup-the-model.rst | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst b/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst
index 0c6009f3fe..2efa65893d 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst
@@ -42,4 +42,4 @@ For single point simulations, the global anomaly forcing files can be used, but
 
     mapalgo = 'nn','nn','nn','nn','nn','nn','nn','nn','nn','nn','nn','nn','nn' (the number of 'nn' values will depend on the number of original streams plus the number of anomaly forcing streams)
 
-The cycling of the present-day (base) climate is controlled through the DATM\_CLMNCEP\_YR\_START and DATM_CLMNCEP\_YR\_END variables in env\_run.xml.
+The cycling of the present-day (base) climate is controlled through the DATM\_YR\_START and DATM\_YR\_END variables in env\_run.xml.
diff --git a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst
index 2a55cbed1e..88d209c0d1 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst
@@ -51,7 +51,7 @@ Example: Simulation Forced with Data from the Previous Simulation
    > ./xmlchange DATM_CPLHIST_CASE="myB1850"
    # The following sets the align year and years to run over for atm forcing
    #  (you could also use an editor)
-   > ./xmlchange DATM_CPLHIST_YR_ALIGN="1",DATM_CPLHIST_YR_START=1,DATM_CPLHIST_YR_END=20
+   > ./xmlchange DATM_YR_ALIGN="1",DATM_YR_START=1,DATM_YR_END=20
    # Set the strm_datdir in the namelist_defaults_datm.xml
    # file to the archival path of the case above in the form of: /glade/home/achive/$USER/$DATM_CPLHIST_CASE/cpl/hist
    # NOTE: THIS WILL CHANGE THE PATH FOR ALL I1850Clm50BgcSpinup COMPSET CASES MADE AFTER THIS!

From 862739bcbd044133e12afb9a60c0562d67bece44 Mon Sep 17 00:00:00 2001
From: Samuel Levis <slevis@ucar.edu>
Date: Wed, 30 Oct 2024 10:47:32 -0600
Subject: [PATCH 1222/1248] Replace outdated DATM_CPL_CASE with
 DATM_CPLHIST_CASE

---
 ...AR-data-as-atmospheric-forcing-to-spinup-the-model.rst | 2 +-
 .../customizing-the-clm-configuration.rst                 | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
index a81465c699..cf9fbc773c 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
@@ -18,7 +18,7 @@ Example: Simulation with MOAR Data on derecho
    > ./create_newcase -case MOARforce1850 -res f19_g17_gl4 -compset I1850Clm50BgcSpinup
    > cd MOARforce1850
    # The following sets the casename to point to for atm forcing (you could also use an editor)
-   > ./xmlchange DATM_CPL_CASE=b40.1850.track1.1deg.006a
+   > ./xmlchange DATM_CPLHIST_CASE=b40.1850.track1.1deg.006a
    # The following sets the align year and years to run over for atm forcing
    #  (you could also use an editor)
    > ./xmlchange DATM_YR_ALIGN=1,DATM_YR_START=960,DATM_YR_END=1030
diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
index 11e996ae5d..ec28a0d624 100644
--- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
+++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst
@@ -513,7 +513,7 @@ For running "I" cases there are several other noteworthy configuration items tha
    DATM_YR_ALIGN
    DATM_YR_START
    DATM_YR_END
-   DATM_CPL_CASE
+   DATM_CPLHIST_CASE
 
 ``CCSM_CO2_PPMV``
    Sets the mixing ratio of CO2 in parts per million by volume for ALL CESM components to use. Note that most compsets already set this value to something reasonable. Also note that some compsets may tell the atmosphere model to override this value with either historic or ramped values. If the ``CCSM_BGC`` variable is set to something other than "none" the atmosphere model will determine CO2, and CLM will listen and use what the atmosphere sends it. On the CLM side the namelist item ``co2_type`` tells CLM to use the value sent from the atmosphere rather than a value set on it's own namelist.
@@ -575,8 +575,8 @@ DATM_YR_END
 DATM_YR_ALIGN
   ``DATM_YR_START`` and ``DATM_YR_END`` determine the range of years to cycle the atmospheric data over, and ``DATM_YR_ALIGN`` determines which year in that range of years the simulation will start with.
 
-DATM_CPL_CASE
-  ``DATM_CPL_CASE`` sets the casename to use for the ``CPLHISTForcing`` mode.
+DATM_CPLHIST_CASE
+  ``DATM_CPLHIST_CASE`` sets the casename to use for the ``CPLHISTForcing`` mode.
 
 -----------------------------
 Downloading DATM Forcing Data
@@ -586,7 +586,7 @@ In Chapter One of the `CESM User's Guide <link-to-CESM-UG>`_ there is a section
 
 The `CLMCRUNCEP` data is uploaded into the subversion inputdata repository as well -- but as it is 1.1 Terabytes of data downloading it is problematic (*IT WILL TAKE SEVERAL DAYS TO DOWNLOAD THE ENTIRE DATASET USING SUBVERSION*). Because of its size you may also need to download it onto a separate disk space. We have done that on derecho for example where it resides in ``$ENV{CESMROOT}/lmwg`` while the rest of the input data resides in ``$ENV{CESMDATAROOT}/inputdata``. The data is also already available on: janus, franklin, and hopper. If you download the data, we recommend that you break your download into several chunks, by setting up a case and setting the year range for ``DATM_YR_START`` and ``DATM_YR_END`` in say 20 year sections over 1901 to 2010, and then use ``check_input_data`` to export the data.
 
-The ``CPLHISTForcing`` DATM forcing data is unique -- because it is large compared to the rest of the input data, and we only have a disk copy on derecho. The DATM assumes the path for derecho of ``/glade/p/cesm/shared_outputdata/cases/ccsm4/$DATM_CPLHIST_CASE`` for the data. So you will need to change this path in order to run on any other machine. You can download the data itself from NCAR HPSS from ``/CCSM/csm/$DATM_CPLHIST_CASE``.
+The ``CPLHISTForcing`` DATM forcing data is unique -- because it is large compared to the rest of the input data, and we only have a disk copy on derecho. The DATM assumes the path for derecho of ``/glade/p/cesm/shared_outputdata/cases/ccsm4/$DATM_CPLHIST_CASE`` for the data. So you will need to change this path in order to run on any other machine.
 
 --------------------------------------
 Customizing via the build script files

From c6157d500078ffe06ac4a1bdeb3b67cce07c6905 Mon Sep 17 00:00:00 2001
From: adrifoster <adrifost@ucar.edu>
Date: Thu, 31 Oct 2024 10:15:53 -0600
Subject: [PATCH 1223/1248] updates

---
 src/fates | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fates b/src/fates
index b4367834ab..de61028847 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit b4367834abf505eb4e5f53af9bc7e4b83af4685c
+Subproject commit de6102884790bb60681b11d20151fb462c1a70b5

From 5ba87240eac03a0b5d26973fb7c5f4cef8fe06cb Mon Sep 17 00:00:00 2001
From: adrifoster <adrifost@ucar.edu>
Date: Thu, 31 Oct 2024 10:16:13 -0600
Subject: [PATCH 1224/1248] updates

---
 components/cdeps | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/cdeps b/components/cdeps
index 7b0b3a8272..7476950699 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit 7b0b3a827241c53d296ec877cb1f59966bf5e5bf
+Subproject commit 7476950699909813d1938a34bd8d71bf5bfbf1e9

From 32fc16737e7b0b4b9f35b4f74d92e66dacbded24 Mon Sep 17 00:00:00 2001
From: Gregory Lemieux <glemieux@users.noreply.github.com>
Date: Thu, 31 Oct 2024 13:08:32 -0700
Subject: [PATCH 1225/1248] Revert "temporarily convert fates seed dispersal
 test to use f10"

This reverts commit e9fb075891f90f97159071d03b376ed44c451bfc.
---
 cime_config/testdefs/testlist_clm.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 4654f53c45..0077221573 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -2670,7 +2670,7 @@
       <option name="comment"  >5x5_amazon grid with FATES and latest CLM</option>
     </options>
   </test>
-  <test name="ERS_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="ERS_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
@@ -2679,7 +2679,7 @@
       <option name="comment"  >This test should be converted to an ERP test once the PEM version of this test is passing COMPARE_base_modpes. Also change to 5x5_amazon once ccs_config updated to allow it</option>
     </options>
   </test>
-  <test name="PEM_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="PEM_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>

From 16d83c15cce709955a44ca75115e718e84bc6a7f Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Fri, 1 Nov 2024 12:42:17 -0600
Subject: [PATCH 1226/1248] Add warning box to MOAR User's Guide page.

---
 ...th-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
index cf9fbc773c..7c18cee009 100644
--- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
+++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst
@@ -6,6 +6,9 @@
  Running with MOAR data
 ========================
 
+.. warning::
+    These instructions are outdated and will not work. This page will be either updated or removed as part of the CTSM6/CLM3 release.
+
 Because it takes so long to spinup the CN model (as we just saw previously), if you are doing fully coupled simulations with active atmosphere and ocean, you will want to do the spinup portion of this "offline". So instead of doing expensive fully coupled simulations for the spinup duration, you run CLM in a very cheap "I" compset using atmospheric forcing from a shorter fully coupled simulation (or a simulation run previously by someone else).
 
 In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on Cheyenne. There are several simulations that have high frequency data for which we can do this. You can also do this on a machine other than Cheyenne, but would need to download the data from the Earth System Grid and change the datapath similar to Example :numref:`eg-sim-data-from-prev-sim`.

From a4d23b512a9173af78cd00d182bbcedd332f7f38 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Mon, 4 Nov 2024 13:29:54 -0700
Subject: [PATCH 1227/1248] Make ALBGRD and ALBGRI active by default

---
 src/biogeophys/SurfaceAlbedoType.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90
index e90caeecbb..10819a47b6 100644
--- a/src/biogeophys/SurfaceAlbedoType.F90
+++ b/src/biogeophys/SurfaceAlbedoType.F90
@@ -242,12 +242,12 @@ subroutine InitHistory(this, bounds)
     this%albgrd_col(begc:endc,:) = spval
     call hist_addfld2d (fname='ALBGRD', units='proportion', type2d='numrad', &
          avgflag='A', long_name='ground albedo (direct)', &
-         ptr_col=this%albgrd_col, default='inactive')
+         ptr_col=this%albgrd_col, default='active')
 
     this%albgri_col(begc:endc,:) = spval
     call hist_addfld2d (fname='ALBGRI', units='proportion', type2d='numrad', &
          avgflag='A', long_name='ground albedo (indirect)', &
-         ptr_col=this%albgri_col, default='inactive')
+         ptr_col=this%albgri_col, default='active')
 
     if (use_SSRE) then
        this%albdSF_patch(begp:endp,:) = spval

From e72e947773ce7ca6035c7ba37fc58072c080ae17 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Wed, 6 Nov 2024 12:37:51 -0700
Subject: [PATCH 1228/1248] Implement urbanl and urbanc coszen filters

---
 src/biogeophys/UrbanAlbedoMod.F90 | 219 +++++++++++++++++-------------
 1 file changed, 122 insertions(+), 97 deletions(-)

diff --git a/src/biogeophys/UrbanAlbedoMod.F90 b/src/biogeophys/UrbanAlbedoMod.F90
index 2e854a0497..25555b2da8 100644
--- a/src/biogeophys/UrbanAlbedoMod.F90
+++ b/src/biogeophys/UrbanAlbedoMod.F90
@@ -78,9 +78,14 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
     type(surfalb_type)     , intent(inout) :: surfalb_inst
     !
     ! !LOCAL VARIABLES:
-    integer  :: fl,fp,fc,g,l,p,c,ib                                  ! indices
+    integer  :: fl,fp,fc,g,l,p,c,ib,f,fn                             ! indices and counters
     integer  :: ic                                                   ! 0=unit incoming direct; 1=unit incoming diffuse
-    integer  :: num_solar                                            ! counter
+    integer, allocatable :: filter_urbanl_coszen_gt0(:)              ! filter for urban landunits with coszen > 0
+    integer  :: num_urbanl_coszen_gt0                                ! number of urban landunits with coszen > 0
+    integer, allocatable :: filter_nourbanl_coszen_gt0(:)            ! filter for urban landunits with coszen <= 0
+    integer  :: num_nourbanl_coszen_gt0                              ! number of urban landunits with coszen <= 0
+    integer, allocatable :: filter_urbanc_coszen_gt0(:)              ! filter for urban columns with coszen > 0
+    integer  :: num_urbanc_coszen_gt0                                ! number of urban columns with coszen > 0
     real(r8) :: coszen             (bounds%begl:bounds%endl)         ! cosine solar zenith angle for next time step (landunit)
     real(r8) :: zen                (bounds%begl:bounds%endl)         ! solar zenith angle (radians)
     real(r8) :: sdir               (bounds%begl:bounds%endl, numrad) ! direct beam solar radiation on horizontal surface
@@ -165,9 +170,19 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
          begl               => bounds%begl                          , &
          vf_sr              => urbanparams_inst%vf_sr               , & ! Input:  [real(r8) (:) ]  view factor of sky for road
          vf_sw              => urbanparams_inst%vf_sw               , & ! Input:  [real(r8) (:) ]  view factor of sky for one wall
-         endl               => bounds%endl                            &
+         endl               => bounds%endl                          , &
+         begc               => bounds%begc                          , &
+         endc               => bounds%endc                            &
          )
 
+      !TODO KO - Indentation needs to be done properly throughout this module.  Will do later
+      ! to make the changes easier to review now.
+
+      ! Allocate urbanl and urbanc coszen filters
+      allocate(filter_urbanl_coszen_gt0(bounds%endl-bounds%begl+1))
+      allocate(filter_nourbanl_coszen_gt0(bounds%endl-bounds%begl+1))
+      allocate(filter_urbanc_coszen_gt0(bounds%endc-bounds%begc+1))
+
       ! ----------------------------------------------------------------------------
       ! Solar declination and cosine solar zenith angle and zenith angle for 
       ! next time step
@@ -228,15 +243,36 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
          end do
       end do
 
-      ! ----------------------------------------------------------------------------
-      ! Urban Code
-      ! ----------------------------------------------------------------------------
-
-      num_solar = 0
+      ! Populate urbanl and urbanc coszen filters
+      f = 0
+      fn = 0
       do fl = 1,num_urbanl
          l = filter_urbanl(fl)
-         if (coszen(l) > 0._r8) num_solar = num_solar + 1
+         if (coszen(l) > 0._r8) then
+            f = f + 1
+            filter_urbanl_coszen_gt0(f) = l
+         else
+            fn = fn + 1
+            filter_nourbanl_coszen_gt0(fn) = l
+         end if
       end do
+      num_urbanl_coszen_gt0 = f
+      num_nourbanl_coszen_gt0 = fn
+
+      f = 0
+      do fc = 1,num_urbanc
+         c = filter_urbanc(fc)
+         l = col%landunit(c)
+         if (coszen(l) > 0._r8) then
+            f = f + 1
+            filter_urbanc_coszen_gt0(f) = c
+         end if
+      end do
+      num_urbanc_coszen_gt0 = f
+
+      ! ----------------------------------------------------------------------------
+      ! Urban Code
+      ! ----------------------------------------------------------------------------
 
       do ib = 1,numrad
          do fl = 1,num_urbanl
@@ -267,16 +303,15 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
       end do
 
       ! ----------------------------------------------------------------------------
-      ! Only do the rest if all coszen are positive 
+      ! Use the urban coszen filters to only calculate quantities when coszen > 0
       ! ----------------------------------------------------------------------------
 
-      if (num_solar > 0)then
 
          ! Set constants - solar fluxes are per unit incoming flux
 
          do ib = 1,numrad
-            do fl = 1,num_urbanl
-               l = filter_urbanl(fl)
+            do fl = 1,num_urbanl_coszen_gt0
+               l = filter_urbanl_coszen_gt0(fl)
                sdir(l,ib) = 1._r8
                sdif(l,ib) = 1._r8
             end do
@@ -287,9 +322,11 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
 
          if (num_urbanl > 0) then
             call incident_direct (bounds, &
-                 num_urbanl, filter_urbanl, &
+                 num_urbanl_coszen_gt0, &
+                 filter_urbanl_coszen_gt0, &
+                 num_nourbanl_coszen_gt0, &
+                 filter_nourbanl_coszen_gt0, &
                  canyon_hwr(begl:endl), &
-                 coszen(begl:endl), &
                  zen(begl:endl), &
                  sdir(begl:endl, :), &
                  sdir_road(begl:endl, :), &
@@ -300,9 +337,10 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
          ! Incident diffuse radiation for 
          ! (a) roof and (b) road and both walls in urban canyon.
 
-         if (num_urbanl > 0) then
+         if (num_urbanl_coszen_gt0 > 0) then
             call incident_diffuse (bounds, &
-                 num_urbanl, filter_urbanl, &
+                 num_urbanl_coszen_gt0, &
+                 filter_urbanl_coszen_gt0, &
                  canyon_hwr(begl:endl), &
                  sdif(begl:endl, :), &
                  sdif_road(begl:endl, :), &
@@ -316,7 +354,8 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
             ic = 0
             call SnowAlbedo(bounds, &
                  num_urbanc, filter_urbanc, &
-                 coszen(begl:endl), &
+                 num_urbanc_coszen_gt0, &
+                 filter_urbanc_coszen_gt0, &
                  ic, &
                  albsnd_roof(begl:endl, :), &
                  albsnd_improad(begl:endl, :), &
@@ -326,7 +365,8 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
             ic = 1
             call SnowAlbedo(bounds, &
                  num_urbanc, filter_urbanc, &
-                 coszen(begl:endl), &
+                 num_urbanc_coszen_gt0, &
+                 filter_urbanc_coszen_gt0, &
                  ic, &
                  albsni_roof(begl:endl, :), &
                  albsni_improad(begl:endl, :), &
@@ -336,8 +376,8 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
 
          ! Combine snow-free and snow albedos
          do ib = 1,numrad
-            do fc = 1,num_urbanc
-               c = filter_urbanc(fc)
+            do fc = 1,num_urbanc_coszen_gt0
+               c = filter_urbanc_coszen_gt0(fc)
                l = col%landunit(c)
                if (ctype(c) == icol_roof) then    
                   alb_roof_dir_s(l,ib) = alb_roof_dir(l,ib)*(1._r8-frac_sno(c))  &
@@ -362,10 +402,10 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
          ! for road and both walls in urban canyon allowing for multiple reflection
          ! Reflected and absorbed solar radiation per unit incident radiation for roof
 
-         if (num_urbanl > 0) then
+         if (num_urbanl_coszen_gt0 > 0) then
             call net_solar (bounds, &
-                 num_urbanl, filter_urbanl, &
-                 coszen             (begl:endl), &
+                 num_urbanl_coszen_gt0, &
+                 filter_urbanl_coszen_gt0, &
                  canyon_hwr         (begl:endl), &
                  wtroad_perv        (begl:endl), &
                  sdir               (begl:endl, :), &
@@ -423,6 +463,7 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
                   albgrd(c,ib) = sref_improad_dir(l,ib)
                   albgri(c,ib) = sref_improad_dif(l,ib)
                endif
+               !TODO KO - Clean up these SNICAR comments (not needed?)
 ! add new snicar albedo variables for history fields
                if (coszen(l) > 0._r8) then
                   albgrd_hst(c,ib) = albgrd(c,ib)
@@ -444,7 +485,6 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
 ! end add new snicar
             end do
          end do
-      end if
 
     end associate
 
@@ -452,7 +492,7 @@ end subroutine UrbanAlbedo
 
   !-----------------------------------------------------------------------
   subroutine SnowAlbedo (bounds          , &
-       num_urbanc, filter_urbanc, coszen, ind , &
+       num_urbanc, filter_urbanc, num_urbanc_coszen_gt0, filter_urbanc_coszen_gt0, ind , &
        albsn_roof, albsn_improad, albsn_perroad, &
        waterstatebulk_inst)
     !
@@ -466,8 +506,9 @@ subroutine SnowAlbedo (bounds          , &
     type(bounds_type), intent(in) :: bounds                     
     integer , intent(in) :: num_urbanc                          ! number of urban columns in clump
     integer , intent(in) :: filter_urbanc(:)                    ! urban column filter
+    integer , intent(in) :: num_urbanc_coszen_gt0               ! number of urban columns with coszen > 0
+    integer , intent(in) :: filter_urbanc_coszen_gt0(:)         ! filter for urban columns with coszen > 0
     integer , intent(in) :: ind                                 ! 0=direct beam, 1=diffuse radiation
-    real(r8), intent(in) :: coszen        ( bounds%begl: )      ! cosine solar zenith angle [landunit]
     real(r8), intent(out):: albsn_roof    ( bounds%begl: , 1: ) ! roof snow albedo by waveband [landunit, numrad]
     real(r8), intent(out):: albsn_improad ( bounds%begl: , 1: ) ! impervious road snow albedo by waveband [landunit, numrad]
     real(r8), intent(out):: albsn_perroad ( bounds%begl: , 1: ) ! pervious road snow albedo by waveband [landunit, numrad]
@@ -488,7 +529,6 @@ subroutine SnowAlbedo (bounds          , &
     SHR_ASSERT_ALL_FL(numrad == 2, sourcefile, __LINE__)
 
     ! Enforce expected array sizes
-    SHR_ASSERT_ALL_FL((ubound(coszen)        == (/bounds%endl/)),         sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(albsn_roof)    == (/bounds%endl, numrad/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(albsn_improad) == (/bounds%endl, numrad/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(albsn_perroad) == (/bounds%endl, numrad/)), sourcefile, __LINE__)
@@ -497,10 +537,10 @@ subroutine SnowAlbedo (bounds          , &
          caller = 'UrbanAlbedoMod:SnowAlbedo', &
          h2osno_total = h2osno_total(bounds%begc:bounds%endc))
 
-    do fc = 1,num_urbanc
-       c = filter_urbanc(fc)
+    do fc = 1,num_urbanc_coszen_gt0
+       c = filter_urbanc_coszen_gt0(fc)
        l = col%landunit(c)
-       if (coszen(l) > 0._r8 .and. h2osno_total(c) > 0._r8) then
+       if (h2osno_total(c) > 0._r8) then
           if (col%itype(c) == icol_roof) then
              albsn_roof(l,1) = snal0
              albsn_roof(l,2) = snal1
@@ -528,8 +568,9 @@ subroutine SnowAlbedo (bounds          , &
   end subroutine SnowAlbedo
 
   !-----------------------------------------------------------------------
-  subroutine incident_direct (bounds                      ,                    &
-       num_urbanl, filter_urbanl, canyon_hwr, coszen, zen ,                    &
+  subroutine incident_direct (bounds,                                        &
+       num_urbanl_coszen_gt0, filter_urbanl_coszen_gt0,                      &
+       num_nourbanl_coszen_gt0, filter_nourbanl_coszen_gt0, canyon_hwr, zen, &
        sdir, sdir_road, sdir_sunwall, sdir_shadewall)
     !
     ! !DESCRIPTION: 
@@ -567,10 +608,11 @@ subroutine incident_direct (bounds                      ,                    &
     !
     ! !ARGUMENTS:
     type(bounds_type), intent(in) :: bounds                      
-    integer , intent(in)  :: num_urbanl                          ! number of urban landunits
-    integer , intent(in)  :: filter_urbanl(:)                    ! urban landunit filter
+    integer , intent(in)  :: num_urbanl_coszen_gt0               ! number of urban landunits with coszen > 0
+    integer , intent(in)  :: filter_urbanl_coszen_gt0(:)         ! filter for urban landunits with coszen > 0
+    integer , intent(in)  :: num_nourbanl_coszen_gt0             ! number of urban landunits with coszen <= 0
+    integer , intent(in)  :: filter_nourbanl_coszen_gt0(:)       ! filter for urban landunits with coszen <= 0
     real(r8), intent(in)  :: canyon_hwr( bounds%begl: )          ! ratio of building height to street width [landunit]
-    real(r8), intent(in)  :: coszen( bounds%begl: )              ! cosine solar zenith angle [landunit]
     real(r8), intent(in)  :: zen( bounds%begl: )                 ! solar zenith angle (radians) [landunit]
     real(r8), intent(in)  :: sdir( bounds%begl: , 1: )           ! direct beam solar radiation incident on horizontal surface [landunit, numrad]
     real(r8), intent(out) :: sdir_road( bounds%begl: , 1: )      ! direct beam solar radiation incident on road per unit incident flux [landunit, numrad]
@@ -595,26 +637,22 @@ subroutine incident_direct (bounds                      ,                    &
 
     ! Enforce expected array sizes
     SHR_ASSERT_ALL_FL((ubound(canyon_hwr)     == (/bounds%endl/)),         sourcefile, __LINE__)
-    SHR_ASSERT_ALL_FL((ubound(coszen)         == (/bounds%endl/)),         sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(zen)            == (/bounds%endl/)),         sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(sdir)           == (/bounds%endl, numrad/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(sdir_road)      == (/bounds%endl, numrad/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(sdir_sunwall)   == (/bounds%endl, numrad/)), sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(sdir_shadewall) == (/bounds%endl, numrad/)), sourcefile, __LINE__)
 
-    do fl = 1,num_urbanl
-       l = filter_urbanl(fl)
-       if (coszen(l) > 0._r8) then
-          theta0(l) = asin(min( (1._r8/(canyon_hwr(l)*tan(max(zen(l),0.000001_r8)))), 1._r8 ))
-          tanzen(l) = tan(zen(l))
-       end if
+    do fl = 1,num_urbanl_coszen_gt0
+       l = filter_urbanl_coszen_gt0(fl)
+       theta0(l) = asin(min( (1._r8/(canyon_hwr(l)*tan(max(zen(l),0.000001_r8)))), 1._r8 ))
+       tanzen(l) = tan(zen(l))
     end do
 
     do ib = 1,numrad
 
-       do fl = 1,num_urbanl
-          l = filter_urbanl(fl)
-          if (coszen(l) > 0._r8) then
+       do fl = 1,num_urbanl_coszen_gt0
+          l = filter_urbanl_coszen_gt0(fl)
              sdir_shadewall(l,ib) = 0._r8
 
              ! incident solar radiation on wall and road integrated over all canyon orientations (0 <= theta <= pi/2)
@@ -628,21 +666,20 @@ subroutine incident_direct (bounds                      ,                    &
 
              swall_projected = (sdir_shadewall(l,ib) + sdir_sunwall(l,ib)) * canyon_hwr(l)
              err1(l) = sdir(l,ib) - (sdir_road(l,ib) + swall_projected)
-          else
-             sdir_road(l,ib) = 0._r8
-             sdir_sunwall(l,ib) = 0._r8
-             sdir_shadewall(l,ib) = 0._r8
-          endif
+       end do
+       do fl = 1,num_nourbanl_coszen_gt0
+          l = filter_nourbanl_coszen_gt0(fl)
+          sdir_road(l,ib) = 0._r8
+          sdir_sunwall(l,ib) = 0._r8
+          sdir_shadewall(l,ib) = 0._r8
        end do
 
-       do fl = 1,num_urbanl
-          l = filter_urbanl(fl)
-          if (coszen(l) > 0._r8) then
-             if (abs(err1(l)) > 0.001_r8) then
-                write (iulog,*) 'urban direct beam solar radiation balance error',err1(l)
-                write (iulog,*) 'clm model is stopping'
-                call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
-             endif
+       do fl = 1,num_urbanl_coszen_gt0
+          l = filter_urbanl_coszen_gt0(fl)
+          if (abs(err1(l)) > 0.001_r8) then
+             write (iulog,*) 'urban direct beam solar radiation balance error',err1(l)
+             write (iulog,*) 'clm model is stopping'
+             call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
           endif
        end do
 
@@ -650,9 +687,8 @@ subroutine incident_direct (bounds                      ,                    &
        ! sum sroad and swall over all canyon orientations (0 <= theta <= pi/2)
 
        if (numchk) then
-          do fl = 1,num_urbanl
-             l = filter_urbanl(fl)
-             if (coszen(l) > 0._r8) then
+          do fl = 1,num_urbanl_coszen_gt0
+             l = filter_urbanl_coszen_gt0(fl)
                 sumr = 0._r8
                 sumw = 0._r8
                 num  = 0._r8
@@ -670,11 +706,9 @@ subroutine incident_direct (bounds                      ,                    &
                 end do
                 err2(l) = sumr/num - sdir_road(l,ib)
                 err3(l) = sumw/num - sdir_sunwall(l,ib)
-             endif
           end do
-          do fl = 1,num_urbanl
-             l = filter_urbanl(fl)
-             if (coszen(l) > 0._r8) then
+          do fl = 1,num_urbanl_coszen_gt0
+             l = filter_urbanl_coszen_gt0(fl)
                 if (abs(err2(l)) > 0.0006_r8 ) then
                    write (iulog,*) 'urban road incident direct beam solar radiation error',err2(l)
                    write (iulog,*) 'clm model is stopping'
@@ -685,7 +719,6 @@ subroutine incident_direct (bounds                      ,                    &
                    write (iulog,*) 'clm model is stopping'
                    call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
                 end if
-             end if
           end do
        end if
 
@@ -695,7 +728,7 @@ end subroutine incident_direct
 
   !-----------------------------------------------------------------------
   subroutine incident_diffuse (bounds, &
-       num_urbanl, filter_urbanl, canyon_hwr, &
+       num_urbanl_coszen_gt0, filter_urbanl_coszen_gt0, canyon_hwr, &
        sdif, sdif_road, sdif_sunwall, sdif_shadewall, &
        urbanparams_inst)
     !
@@ -707,8 +740,8 @@ subroutine incident_diffuse (bounds, &
     !
     ! !ARGUMENTS:
     type(bounds_type)     , intent(in)  :: bounds                      
-    integer               , intent(in)  :: num_urbanl                           ! number of urban landunits
-    integer               , intent(in)  :: filter_urbanl(:)                     ! urban landunit filter
+    integer               , intent(in)  :: num_urbanl_coszen_gt0                ! number of urban landunits with coszen > 0
+    integer               , intent(in)  :: filter_urbanl_coszen_gt0(:)          ! filter for urban landunits with coszen > 0
     real(r8)              , intent(in)  :: canyon_hwr     ( bounds%begl: )      ! ratio of building height to street width [landunit]
     real(r8)              , intent(in)  :: sdif           ( bounds%begl: , 1: ) ! diffuse solar radiation incident on horizontal surface [landunit, numrad]
     real(r8)              , intent(out) :: sdif_road      ( bounds%begl: , 1: ) ! diffuse solar radiation incident on road [landunit, numrad]
@@ -738,8 +771,8 @@ subroutine incident_diffuse (bounds, &
          
          ! diffuse solar and conservation check. need to convert wall fluxes to ground area
          
-         do fl = 1,num_urbanl
-            l = filter_urbanl(fl)
+         do fl = 1,num_urbanl_coszen_gt0
+            l = filter_urbanl_coszen_gt0(fl)
             sdif_road(l,ib)      = sdif(l,ib) * vf_sr(l)
             sdif_sunwall(l,ib)   = sdif(l,ib) * vf_sw(l) 
             sdif_shadewall(l,ib) = sdif(l,ib) * vf_sw(l) 
@@ -750,8 +783,8 @@ subroutine incident_diffuse (bounds, &
 
          ! error check
 
-         do fl = 1, num_urbanl
-            l = filter_urbanl(fl)
+         do fl = 1, num_urbanl_coszen_gt0
+            l = filter_urbanl_coszen_gt0(fl)
             if (abs(err(l)) > 0.001_r8) then
                write (iulog,*) 'urban diffuse solar radiation balance error',err(l) 
                write (iulog,*) 'clm model is stopping'
@@ -767,7 +800,7 @@ end subroutine incident_diffuse
 
   !-----------------------------------------------------------------------
   subroutine net_solar (bounds                                                                 , &
-       num_urbanl, filter_urbanl, coszen, canyon_hwr, wtroad_perv, sdir, sdif                  , &
+       num_urbanl_coszen_gt0, filter_urbanl_coszen_gt0, canyon_hwr, wtroad_perv, sdir, sdif    , &
        alb_improad_dir, alb_perroad_dir, alb_wall_dir, alb_roof_dir                            , &
        alb_improad_dif, alb_perroad_dif, alb_wall_dif, alb_roof_dif                            , &
        sdir_road, sdir_sunwall, sdir_shadewall,                                                  &
@@ -782,9 +815,8 @@ subroutine net_solar (bounds
     !
     ! !ARGUMENTS:
     type (bounds_type), intent(in) :: bounds                            
-    integer , intent(in)    :: num_urbanl                               ! number of urban landunits
-    integer , intent(in)    :: filter_urbanl(:)                         ! urban landunit filter
-    real(r8), intent(in)    :: coszen             ( bounds%begl: )      ! cosine solar zenith angle [landunit]
+    integer,  intent(in)    :: num_urbanl_coszen_gt0                    ! number of urban landunits with coszen > 0
+    integer,  intent(in)    :: filter_urbanl_coszen_gt0(:)              ! filter for urban landunits with coszen > 0
     real(r8), intent(in)    :: canyon_hwr         ( bounds%begl: )      ! ratio of building height to street width [landunit]
     real(r8), intent(in)    :: wtroad_perv        ( bounds%begl: )      ! weight of pervious road wrt total road [landunit]
     real(r8), intent(in)    :: sdir               ( bounds%begl: , 1: ) ! direct beam solar radiation incident on horizontal surface [landunit, numrad]
@@ -897,7 +929,6 @@ subroutine net_solar (bounds
     !-----------------------------------------------------------------------
 
     ! Enforce expected array sizes
-    SHR_ASSERT_ALL_FL((ubound(coszen)             == (/bounds%endl/)),         sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(canyon_hwr)         == (/bounds%endl/)),         sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(wtroad_perv)        == (/bounds%endl/)),         sourcefile, __LINE__)
     SHR_ASSERT_ALL_FL((ubound(sdir)               == (/bounds%endl, numrad/)), sourcefile, __LINE__)
@@ -948,15 +979,14 @@ subroutine net_solar (bounds
 
       ! Calculate impervious road
       
-      do fl = 1,num_urbanl 
-         l = filter_urbanl(fl)
+      do fl = 1,num_urbanl_coszen_gt0
+         l = filter_urbanl_coszen_gt0(fl)
          wtroad_imperv(l) = 1._r8 - wtroad_perv(l)
       end do
 
       do ib = 1,numrad
-         do fl = 1,num_urbanl
-            l = filter_urbanl(fl)
-            if (coszen(l) > 0._r8) then
+         do fl = 1,num_urbanl_coszen_gt0
+            l = filter_urbanl_coszen_gt0(fl)
 
                ! initial absorption and reflection for road and both walls. 
                ! distribute reflected radiation to sky, road, and walls 
@@ -1057,7 +1087,6 @@ subroutine net_solar (bounds
                sref_perroad_dif(l,ib)   = perroad_r_sky_dif(l)
                sref_sunwall_dif(l,ib)   = sunwall_r_sky_dif(l)
                sref_shadewall_dif(l,ib) = shadewall_r_sky_dif(l)
-            endif
 
          end do
 
@@ -1080,9 +1109,8 @@ subroutine net_solar (bounds
          !
          ! do separately for direct beam and diffuse
 
-         do fl = 1,num_urbanl
-            l = filter_urbanl(fl)
-            if (coszen(l) > 0._r8) then
+         do fl = 1,num_urbanl_coszen_gt0
+            l = filter_urbanl_coszen_gt0(fl)
 
                ! reflected direct beam
 
@@ -1279,20 +1307,17 @@ subroutine net_solar (bounds
 
                canyon_alb_dif(l) = sref_canyon_dif(l) / max(stot_dif(l), 1.e-06_r8)
                canyon_alb_dir(l) = sref_canyon_dir(l) / max(stot_dir(l), 1.e-06_r8)
-            end if
 
          end do   ! end of landunit loop
 
          ! Refected and absorbed solar radiation per unit incident radiation for roof
 
-         do fl = 1,num_urbanl
-            l = filter_urbanl(fl)
-            if (coszen(l) > 0._r8) then
-               sref_roof_dir(l,ib) = alb_roof_dir(l,ib) * sdir(l,ib)
-               sref_roof_dif(l,ib) = alb_roof_dif(l,ib) * sdif(l,ib)
-               sabs_roof_dir(l,ib) = sdir(l,ib) - sref_roof_dir(l,ib)
-               sabs_roof_dif(l,ib) = sdif(l,ib) - sref_roof_dif(l,ib)
-            end if
+         do fl = 1,num_urbanl_coszen_gt0
+            l = filter_urbanl_coszen_gt0(fl)
+            sref_roof_dir(l,ib) = alb_roof_dir(l,ib) * sdir(l,ib)
+            sref_roof_dif(l,ib) = alb_roof_dif(l,ib) * sdif(l,ib)
+            sabs_roof_dir(l,ib) = sdir(l,ib) - sref_roof_dir(l,ib)
+            sabs_roof_dif(l,ib) = sdif(l,ib) - sref_roof_dif(l,ib)
          end do
 
       end do   ! end of radiation band loop

From 956d41d7bfeb94d6d15a4999a614ba16a621d2b2 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Thu, 7 Nov 2024 13:28:38 -0700
Subject: [PATCH 1229/1248] adding expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 7049e9672b..ba7b945767 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -188,6 +188,13 @@
       <issue>#2454</issue>
     </phase>
   </test>
+  
+  <test name="ERS_Ld60.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdST3">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2867</issue>
+    </phase>
+  </test>
 
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">

From 58ae949b74d82f52d1c2e93ef211b669ae870f80 Mon Sep 17 00:00:00 2001
From: Keith Oleson <oleson@ucar.edu>
Date: Thu, 7 Nov 2024 17:52:24 -0700
Subject: [PATCH 1230/1248] Fix indentation

---
 src/biogeophys/UrbanAlbedoMod.F90 | 960 +++++++++++++++---------------
 1 file changed, 476 insertions(+), 484 deletions(-)

diff --git a/src/biogeophys/UrbanAlbedoMod.F90 b/src/biogeophys/UrbanAlbedoMod.F90
index 25555b2da8..3e84f73176 100644
--- a/src/biogeophys/UrbanAlbedoMod.F90
+++ b/src/biogeophys/UrbanAlbedoMod.F90
@@ -175,9 +175,6 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
          endc               => bounds%endc                            &
          )
 
-      !TODO KO - Indentation needs to be done properly throughout this module.  Will do later
-      ! to make the changes easier to review now.
-
       ! Allocate urbanl and urbanc coszen filters
       allocate(filter_urbanl_coszen_gt0(bounds%endl-bounds%begl+1))
       allocate(filter_nourbanl_coszen_gt0(bounds%endl-bounds%begl+1))
@@ -307,184 +304,179 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, &
       ! ----------------------------------------------------------------------------
 
 
-         ! Set constants - solar fluxes are per unit incoming flux
+      ! Set constants - solar fluxes are per unit incoming flux
 
-         do ib = 1,numrad
-            do fl = 1,num_urbanl_coszen_gt0
-               l = filter_urbanl_coszen_gt0(fl)
-               sdir(l,ib) = 1._r8
-               sdif(l,ib) = 1._r8
-            end do
+      do ib = 1,numrad
+         do fl = 1,num_urbanl_coszen_gt0
+            l = filter_urbanl_coszen_gt0(fl)
+            sdir(l,ib) = 1._r8
+            sdif(l,ib) = 1._r8
          end do
+      end do
 
-         ! Incident direct beam radiation for 
-         ! (a) roof and (b) road and both walls in urban canyon
-
-         if (num_urbanl > 0) then
-            call incident_direct (bounds, &
-                 num_urbanl_coszen_gt0, &
-                 filter_urbanl_coszen_gt0, &
-                 num_nourbanl_coszen_gt0, &
-                 filter_nourbanl_coszen_gt0, &
-                 canyon_hwr(begl:endl), &
-                 zen(begl:endl), &
-                 sdir(begl:endl, :), &
-                 sdir_road(begl:endl, :), &
-                 sdir_sunwall(begl:endl, :), &
-                 sdir_shadewall(begl:endl, :))
-         end if
-
-         ! Incident diffuse radiation for 
-         ! (a) roof and (b) road and both walls in urban canyon.
-
-         if (num_urbanl_coszen_gt0 > 0) then
-            call incident_diffuse (bounds, &
-                 num_urbanl_coszen_gt0, &
-                 filter_urbanl_coszen_gt0, &
-                 canyon_hwr(begl:endl), &
-                 sdif(begl:endl, :), &
-                 sdif_road(begl:endl, :), &
-                 sdif_sunwall(begl:endl, :), &
-                 sdif_shadewall(begl:endl, :), &
-                 urbanparams_inst)
-         end if
-
-         ! Get snow albedos for roof and impervious and pervious road
-         if (num_urbanl > 0) then
-            ic = 0
-            call SnowAlbedo(bounds, &
-                 num_urbanc, filter_urbanc, &
-                 num_urbanc_coszen_gt0, &
-                 filter_urbanc_coszen_gt0, &
-                 ic, &
-                 albsnd_roof(begl:endl, :), &
-                 albsnd_improad(begl:endl, :), &
-                 albsnd_perroad(begl:endl, :), &
-                 waterstatebulk_inst)
-
-            ic = 1
-            call SnowAlbedo(bounds, &
-                 num_urbanc, filter_urbanc, &
-                 num_urbanc_coszen_gt0, &
-                 filter_urbanc_coszen_gt0, &
-                 ic, &
-                 albsni_roof(begl:endl, :), &
-                 albsni_improad(begl:endl, :), &
-                 albsni_perroad(begl:endl, :), &
-                 waterstatebulk_inst)
-         end if
-
-         ! Combine snow-free and snow albedos
-         do ib = 1,numrad
-            do fc = 1,num_urbanc_coszen_gt0
-               c = filter_urbanc_coszen_gt0(fc)
-               l = col%landunit(c)
-               if (ctype(c) == icol_roof) then    
-                  alb_roof_dir_s(l,ib) = alb_roof_dir(l,ib)*(1._r8-frac_sno(c))  &
-                       + albsnd_roof(l,ib)*frac_sno(c)
-                  alb_roof_dif_s(l,ib) = alb_roof_dif(l,ib)*(1._r8-frac_sno(c))  &
-                       + albsni_roof(l,ib)*frac_sno(c)
-               else if (ctype(c) == icol_road_imperv) then    
-                  alb_improad_dir_s(l,ib) = alb_improad_dir(l,ib)*(1._r8-frac_sno(c))  &
-                       + albsnd_improad(l,ib)*frac_sno(c)
-                  alb_improad_dif_s(l,ib) = alb_improad_dif(l,ib)*(1._r8-frac_sno(c))  &
-                       + albsni_improad(l,ib)*frac_sno(c)
-               else if (ctype(c) == icol_road_perv) then    
-                  alb_perroad_dir_s(l,ib) = alb_perroad_dir(l,ib)*(1._r8-frac_sno(c))  &
-                       + albsnd_perroad(l,ib)*frac_sno(c)
-                  alb_perroad_dif_s(l,ib) = alb_perroad_dif(l,ib)*(1._r8-frac_sno(c))  &
-                       + albsni_perroad(l,ib)*frac_sno(c)
-               end if
-            end do
+      ! Incident direct beam radiation for 
+      ! (a) roof and (b) road and both walls in urban canyon
+
+      if (num_urbanl > 0) then
+         call incident_direct (bounds, &
+              num_urbanl_coszen_gt0, &
+              filter_urbanl_coszen_gt0, &
+              num_nourbanl_coszen_gt0, &
+              filter_nourbanl_coszen_gt0, &
+              canyon_hwr(begl:endl), &
+              zen(begl:endl), &
+              sdir(begl:endl, :), &
+              sdir_road(begl:endl, :), &
+              sdir_sunwall(begl:endl, :), &
+              sdir_shadewall(begl:endl, :))
+      end if
+
+      ! Incident diffuse radiation for 
+      ! (a) roof and (b) road and both walls in urban canyon.
+
+      if (num_urbanl_coszen_gt0 > 0) then
+         call incident_diffuse (bounds, &
+              num_urbanl_coszen_gt0, &
+              filter_urbanl_coszen_gt0, &
+              canyon_hwr(begl:endl), &
+              sdif(begl:endl, :), &
+              sdif_road(begl:endl, :), &
+              sdif_sunwall(begl:endl, :), &
+              sdif_shadewall(begl:endl, :), &
+              urbanparams_inst)
+      end if
+
+      ! Get snow albedos for roof and impervious and pervious road
+      if (num_urbanl > 0) then
+         ic = 0
+         call SnowAlbedo(bounds, &
+              num_urbanc, filter_urbanc, &
+              num_urbanc_coszen_gt0, &
+              filter_urbanc_coszen_gt0, &
+              ic, &
+              albsnd_roof(begl:endl, :), &
+              albsnd_improad(begl:endl, :), &
+              albsnd_perroad(begl:endl, :), &
+              waterstatebulk_inst)
+
+         ic = 1
+         call SnowAlbedo(bounds, &
+              num_urbanc, filter_urbanc, &
+              num_urbanc_coszen_gt0, &
+              filter_urbanc_coszen_gt0, &
+              ic, &
+              albsni_roof(begl:endl, :), &
+              albsni_improad(begl:endl, :), &
+              albsni_perroad(begl:endl, :), &
+              waterstatebulk_inst)
+      end if
+
+      ! Combine snow-free and snow albedos
+      do ib = 1,numrad
+         do fc = 1,num_urbanc_coszen_gt0
+            c = filter_urbanc_coszen_gt0(fc)
+            l = col%landunit(c)
+            if (ctype(c) == icol_roof) then    
+               alb_roof_dir_s(l,ib) = alb_roof_dir(l,ib)*(1._r8-frac_sno(c))  &
+                    + albsnd_roof(l,ib)*frac_sno(c)
+               alb_roof_dif_s(l,ib) = alb_roof_dif(l,ib)*(1._r8-frac_sno(c))  &
+                    + albsni_roof(l,ib)*frac_sno(c)
+            else if (ctype(c) == icol_road_imperv) then    
+               alb_improad_dir_s(l,ib) = alb_improad_dir(l,ib)*(1._r8-frac_sno(c))  &
+                    + albsnd_improad(l,ib)*frac_sno(c)
+               alb_improad_dif_s(l,ib) = alb_improad_dif(l,ib)*(1._r8-frac_sno(c))  &
+                    + albsni_improad(l,ib)*frac_sno(c)
+            else if (ctype(c) == icol_road_perv) then    
+               alb_perroad_dir_s(l,ib) = alb_perroad_dir(l,ib)*(1._r8-frac_sno(c))  &
+                    + albsnd_perroad(l,ib)*frac_sno(c)
+               alb_perroad_dif_s(l,ib) = alb_perroad_dif(l,ib)*(1._r8-frac_sno(c))  &
+                    + albsni_perroad(l,ib)*frac_sno(c)
+            end if
          end do
+      end do
 
-         ! Reflected and absorbed solar radiation per unit incident radiation 
-         ! for road and both walls in urban canyon allowing for multiple reflection
-         ! Reflected and absorbed solar radiation per unit incident radiation for roof
+      ! Reflected and absorbed solar radiation per unit incident radiation 
+      ! for road and both walls in urban canyon allowing for multiple reflection
+      ! Reflected and absorbed solar radiation per unit incident radiation for roof
+
+      if (num_urbanl_coszen_gt0 > 0) then
+         call net_solar (bounds, &
+              num_urbanl_coszen_gt0, &
+              filter_urbanl_coszen_gt0, &
+              canyon_hwr         (begl:endl), &
+              wtroad_perv        (begl:endl), &
+              sdir               (begl:endl, :), &
+              sdif               (begl:endl, :), &
+              alb_improad_dir_s  (begl:endl, :), &
+              alb_perroad_dir_s  (begl:endl, :), &
+              alb_wall_dir       (begl:endl, :), &
+              alb_roof_dir_s     (begl:endl, :), &
+              alb_improad_dif_s  (begl:endl, :), &
+              alb_perroad_dif_s  (begl:endl, :), &
+              alb_wall_dif       (begl:endl, :), &
+              alb_roof_dif_s     (begl:endl, :), &
+              sdir_road          (begl:endl, :), &
+              sdir_sunwall       (begl:endl, :), &
+              sdir_shadewall     (begl:endl, :),  &
+              sdif_road          (begl:endl, :), &
+              sdif_sunwall       (begl:endl, :), &
+              sdif_shadewall     (begl:endl, :),  &
+              sref_improad_dir   (begl:endl, :), &
+              sref_perroad_dir   (begl:endl, :), &
+              sref_sunwall_dir   (begl:endl, :), &
+              sref_shadewall_dir (begl:endl, :), &
+              sref_roof_dir      (begl:endl, :), &
+              sref_improad_dif   (begl:endl, :), &
+              sref_perroad_dif   (begl:endl, :), &
+              sref_sunwall_dif   (begl:endl, :), &
+              sref_shadewall_dif (begl:endl, :), &
+              sref_roof_dif      (begl:endl, :), &
+              urbanparams_inst, solarabs_inst)
+      end if
 
-         if (num_urbanl_coszen_gt0 > 0) then
-            call net_solar (bounds, &
-                 num_urbanl_coszen_gt0, &
-                 filter_urbanl_coszen_gt0, &
-                 canyon_hwr         (begl:endl), &
-                 wtroad_perv        (begl:endl), &
-                 sdir               (begl:endl, :), &
-                 sdif               (begl:endl, :), &
-                 alb_improad_dir_s  (begl:endl, :), &
-                 alb_perroad_dir_s  (begl:endl, :), &
-                 alb_wall_dir       (begl:endl, :), &
-                 alb_roof_dir_s     (begl:endl, :), &
-                 alb_improad_dif_s  (begl:endl, :), &
-                 alb_perroad_dif_s  (begl:endl, :), &
-                 alb_wall_dif       (begl:endl, :), &
-                 alb_roof_dif_s     (begl:endl, :), &
-                 sdir_road          (begl:endl, :), &
-                 sdir_sunwall       (begl:endl, :), &
-                 sdir_shadewall     (begl:endl, :),  &
-                 sdif_road          (begl:endl, :), &
-                 sdif_sunwall       (begl:endl, :), &
-                 sdif_shadewall     (begl:endl, :),  &
-                 sref_improad_dir   (begl:endl, :), &
-                 sref_perroad_dir   (begl:endl, :), &
-                 sref_sunwall_dir   (begl:endl, :), &
-                 sref_shadewall_dir (begl:endl, :), &
-                 sref_roof_dir      (begl:endl, :), &
-                 sref_improad_dif   (begl:endl, :), &
-                 sref_perroad_dif   (begl:endl, :), &
-                 sref_sunwall_dif   (begl:endl, :), &
-                 sref_shadewall_dif (begl:endl, :), &
-                 sref_roof_dif      (begl:endl, :), &
-                 urbanparams_inst, solarabs_inst)
-         end if
+      ! ----------------------------------------------------------------------------
+      ! Map urban output to surfalb_inst components 
+      ! ----------------------------------------------------------------------------
 
-         ! ----------------------------------------------------------------------------
-         ! Map urban output to surfalb_inst components 
-         ! ----------------------------------------------------------------------------
-
-         !  Set albgrd and albgri (ground albedos) and albd and albi (surface albedos)
-
-         do ib = 1,numrad
-            do fc = 1,num_urbanc
-               c = filter_urbanc(fc)
-               l = col%landunit(c)
-               if (ctype(c) == icol_roof) then    
-                  albgrd(c,ib) = sref_roof_dir(l,ib) 
-                  albgri(c,ib) = sref_roof_dif(l,ib) 
-               else if (ctype(c) == icol_sunwall) then   
-                  albgrd(c,ib) = sref_sunwall_dir(l,ib)
-                  albgri(c,ib) = sref_sunwall_dif(l,ib)
-               else if (ctype(c) == icol_shadewall) then 
-                  albgrd(c,ib) = sref_shadewall_dir(l,ib)
-                  albgri(c,ib) = sref_shadewall_dif(l,ib)
-               else if (ctype(c) == icol_road_perv) then
-                  albgrd(c,ib) = sref_perroad_dir(l,ib)
-                  albgri(c,ib) = sref_perroad_dif(l,ib)
-               else if (ctype(c) == icol_road_imperv) then
-                  albgrd(c,ib) = sref_improad_dir(l,ib)
-                  albgri(c,ib) = sref_improad_dif(l,ib)
-               endif
-               !TODO KO - Clean up these SNICAR comments (not needed?)
-! add new snicar albedo variables for history fields
-               if (coszen(l) > 0._r8) then
-                  albgrd_hst(c,ib) = albgrd(c,ib)
-                  albgri_hst(c,ib) = albgri(c,ib)
-               end if
-! end add new snicar
-            end do
-            do fp = 1,num_urbanp
-               p = filter_urbanp(fp)
-               c = patch%column(p)
-               l = patch%landunit(p)
-               albd(p,ib) = albgrd(c,ib)
-               albi(p,ib) = albgri(c,ib)
-! add new snicar albedo variables for history fields
-               if (coszen(l) > 0._r8) then
-                  albd_hst(p,ib) = albd(p,ib)
-                  albi_hst(p,ib) = albi(p,ib)
-               end if
-! end add new snicar
-            end do
+      !  Set albgrd and albgri (ground albedos) and albd and albi (surface albedos)
+
+      do ib = 1,numrad
+         do fc = 1,num_urbanc
+            c = filter_urbanc(fc)
+            l = col%landunit(c)
+            if (ctype(c) == icol_roof) then    
+               albgrd(c,ib) = sref_roof_dir(l,ib) 
+               albgri(c,ib) = sref_roof_dif(l,ib) 
+            else if (ctype(c) == icol_sunwall) then   
+               albgrd(c,ib) = sref_sunwall_dir(l,ib)
+               albgri(c,ib) = sref_sunwall_dif(l,ib)
+            else if (ctype(c) == icol_shadewall) then 
+               albgrd(c,ib) = sref_shadewall_dir(l,ib)
+               albgri(c,ib) = sref_shadewall_dif(l,ib)
+            else if (ctype(c) == icol_road_perv) then
+               albgrd(c,ib) = sref_perroad_dir(l,ib)
+               albgri(c,ib) = sref_perroad_dif(l,ib)
+            else if (ctype(c) == icol_road_imperv) then
+               albgrd(c,ib) = sref_improad_dir(l,ib)
+               albgri(c,ib) = sref_improad_dif(l,ib)
+            endif
+            if (coszen(l) > 0._r8) then
+               albgrd_hst(c,ib) = albgrd(c,ib)
+               albgri_hst(c,ib) = albgri(c,ib)
+            end if
+         end do
+         do fp = 1,num_urbanp
+            p = filter_urbanp(fp)
+            c = patch%column(p)
+            l = patch%landunit(p)
+            albd(p,ib) = albgrd(c,ib)
+            albi(p,ib) = albgri(c,ib)
+            if (coszen(l) > 0._r8) then
+               albd_hst(p,ib) = albd(p,ib)
+               albi_hst(p,ib) = albi(p,ib)
+            end if
          end do
+      end do
 
     end associate
 
@@ -653,19 +645,19 @@ subroutine incident_direct (bounds,                                        &
 
        do fl = 1,num_urbanl_coszen_gt0
           l = filter_urbanl_coszen_gt0(fl)
-             sdir_shadewall(l,ib) = 0._r8
+          sdir_shadewall(l,ib) = 0._r8
 
-             ! incident solar radiation on wall and road integrated over all canyon orientations (0 <= theta <= pi/2)
+          ! incident solar radiation on wall and road integrated over all canyon orientations (0 <= theta <= pi/2)
 
-             sdir_road(l,ib) = sdir(l,ib) *                                    &
-                  (2._r8*theta0(l)/rpi - 2./rpi*canyon_hwr(l)*tanzen(l)*(1._r8-cos(theta0(l))))
-             sdir_sunwall(l,ib) = 2._r8 * sdir(l,ib) * ((1._r8/canyon_hwr(l))* &
-                  (0.5_r8-theta0(l)/rpi) + (1._r8/rpi)*tanzen(l)*(1._r8-cos(theta0(l))))
+          sdir_road(l,ib) = sdir(l,ib) *                                    &
+               (2._r8*theta0(l)/rpi - 2./rpi*canyon_hwr(l)*tanzen(l)*(1._r8-cos(theta0(l))))
+          sdir_sunwall(l,ib) = 2._r8 * sdir(l,ib) * ((1._r8/canyon_hwr(l))* &
+               (0.5_r8-theta0(l)/rpi) + (1._r8/rpi)*tanzen(l)*(1._r8-cos(theta0(l))))
 
-             ! conservation check for road and wall. need to use wall fluxes converted to ground area
+          ! conservation check for road and wall. need to use wall fluxes converted to ground area
 
-             swall_projected = (sdir_shadewall(l,ib) + sdir_sunwall(l,ib)) * canyon_hwr(l)
-             err1(l) = sdir(l,ib) - (sdir_road(l,ib) + swall_projected)
+          swall_projected = (sdir_shadewall(l,ib) + sdir_sunwall(l,ib)) * canyon_hwr(l)
+          err1(l) = sdir(l,ib) - (sdir_road(l,ib) + swall_projected)
        end do
        do fl = 1,num_nourbanl_coszen_gt0
           l = filter_nourbanl_coszen_gt0(fl)
@@ -689,36 +681,36 @@ subroutine incident_direct (bounds,                                        &
        if (numchk) then
           do fl = 1,num_urbanl_coszen_gt0
              l = filter_urbanl_coszen_gt0(fl)
-                sumr = 0._r8
-                sumw = 0._r8
-                num  = 0._r8
-                do i = 1, 9000
-                   theta = i/100._r8 * rpi/180._r8
-                   zen0 = atan(1._r8/(canyon_hwr(l)*sin(theta)))
-                   if (zen(l) >= zen0) then 
-                      sumr = sumr + 0._r8
-                      sumw = sumw + sdir(l,ib) / canyon_hwr(l)
-                   else
-                      sumr = sumr + sdir(l,ib) * (1._r8-canyon_hwr(l)*sin(theta)*tanzen(l))
-                      sumw = sumw + sdir(l,ib) * sin(theta)*tanzen(l)
-                   end if
-                   num = num + 1._r8
-                end do
-                err2(l) = sumr/num - sdir_road(l,ib)
-                err3(l) = sumw/num - sdir_sunwall(l,ib)
+             sumr = 0._r8
+             sumw = 0._r8
+             num  = 0._r8
+             do i = 1, 9000
+                theta = i/100._r8 * rpi/180._r8
+                zen0 = atan(1._r8/(canyon_hwr(l)*sin(theta)))
+                if (zen(l) >= zen0) then 
+                   sumr = sumr + 0._r8
+                   sumw = sumw + sdir(l,ib) / canyon_hwr(l)
+                else
+                   sumr = sumr + sdir(l,ib) * (1._r8-canyon_hwr(l)*sin(theta)*tanzen(l))
+                   sumw = sumw + sdir(l,ib) * sin(theta)*tanzen(l)
+                end if
+                num = num + 1._r8
+             end do
+             err2(l) = sumr/num - sdir_road(l,ib)
+             err3(l) = sumw/num - sdir_sunwall(l,ib)
           end do
           do fl = 1,num_urbanl_coszen_gt0
              l = filter_urbanl_coszen_gt0(fl)
-                if (abs(err2(l)) > 0.0006_r8 ) then
-                   write (iulog,*) 'urban road incident direct beam solar radiation error',err2(l)
-                   write (iulog,*) 'clm model is stopping'
-                   call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
-                endif
-                if (abs(err3(l)) > 0.0006_r8 ) then
-                   write (iulog,*) 'urban wall incident direct beam solar radiation error',err3(l)
-                   write (iulog,*) 'clm model is stopping'
-                   call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
-                end if
+             if (abs(err2(l)) > 0.0006_r8 ) then
+                write (iulog,*) 'urban road incident direct beam solar radiation error',err2(l)
+                write (iulog,*) 'clm model is stopping'
+                call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
+             endif
+             if (abs(err3(l)) > 0.0006_r8 ) then
+                write (iulog,*) 'urban wall incident direct beam solar radiation error',err3(l)
+                write (iulog,*) 'clm model is stopping'
+                call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
+             end if
           end do
        end if
 
@@ -803,8 +795,8 @@ subroutine net_solar (bounds
        num_urbanl_coszen_gt0, filter_urbanl_coszen_gt0, canyon_hwr, wtroad_perv, sdir, sdif    , &
        alb_improad_dir, alb_perroad_dir, alb_wall_dir, alb_roof_dir                            , &
        alb_improad_dif, alb_perroad_dif, alb_wall_dif, alb_roof_dif                            , &
-       sdir_road, sdir_sunwall, sdir_shadewall,                                                  &
-       sdif_road, sdif_sunwall, sdif_shadewall,                                                  &
+       sdir_road, sdir_sunwall, sdir_shadewall                                                 , &
+       sdif_road, sdif_sunwall, sdif_shadewall                                                 , &
        sref_improad_dir, sref_perroad_dir, sref_sunwall_dir, sref_shadewall_dir, sref_roof_dir , &
        sref_improad_dif, sref_perroad_dif, sref_sunwall_dif, sref_shadewall_dif, sref_roof_dif , &
        urbanparams_inst, solarabs_inst)
@@ -988,329 +980,329 @@ subroutine net_solar (bounds
          do fl = 1,num_urbanl_coszen_gt0
             l = filter_urbanl_coszen_gt0(fl)
 
-               ! initial absorption and reflection for road and both walls. 
-               ! distribute reflected radiation to sky, road, and walls 
-               ! according to appropriate view factor. radiation reflected to 
-               ! road and walls will undergo multiple reflections within the canyon. 
-               ! do separately for direct beam and diffuse radiation.
+            ! initial absorption and reflection for road and both walls. 
+            ! distribute reflected radiation to sky, road, and walls 
+            ! according to appropriate view factor. radiation reflected to 
+            ! road and walls will undergo multiple reflections within the canyon. 
+            ! do separately for direct beam and diffuse radiation.
+
+            ! direct beam
+
+            road_a_dir(l)              = 0.0_r8
+            road_r_dir(l)              = 0.0_r8
+            improad_a_dir(l)           = (1._r8-alb_improad_dir(l,ib)) * sdir_road(l,ib) 
+            improad_r_dir(l)           =     alb_improad_dir(l,ib)  * sdir_road(l,ib) 
+            improad_r_sky_dir(l)       = improad_r_dir(l) * vf_sr(l)
+            improad_r_sunwall_dir(l)   = improad_r_dir(l) * vf_wr(l)
+            improad_r_shadewall_dir(l) = improad_r_dir(l) * vf_wr(l)
+            road_a_dir(l)              = road_a_dir(l) + improad_a_dir(l)*wtroad_imperv(l)
+            road_r_dir(l)              = road_r_dir(l) + improad_r_dir(l)*wtroad_imperv(l)
+
+            perroad_a_dir(l)           = (1._r8-alb_perroad_dir(l,ib)) * sdir_road(l,ib) 
+            perroad_r_dir(l)           =     alb_perroad_dir(l,ib)  * sdir_road(l,ib) 
+            perroad_r_sky_dir(l)       = perroad_r_dir(l) * vf_sr(l)
+            perroad_r_sunwall_dir(l)   = perroad_r_dir(l) * vf_wr(l)
+            perroad_r_shadewall_dir(l) = perroad_r_dir(l) * vf_wr(l)
+            road_a_dir(l)              = road_a_dir(l) + perroad_a_dir(l)*wtroad_perv(l)
+            road_r_dir(l)              = road_r_dir(l) + perroad_r_dir(l)*wtroad_perv(l)
+
+            road_r_sky_dir(l)          = road_r_dir(l) * vf_sr(l)
+            road_r_sunwall_dir(l)      = road_r_dir(l) * vf_wr(l)
+            road_r_shadewall_dir(l)    = road_r_dir(l) * vf_wr(l)
+
+            sunwall_a_dir(l)           = (1._r8-alb_wall_dir(l,ib)) * sdir_sunwall(l,ib)
+            sunwall_r_dir(l)           =     alb_wall_dir(l,ib)  * sdir_sunwall(l,ib)
+            sunwall_r_sky_dir(l)       = sunwall_r_dir(l) * vf_sw(l)
+            sunwall_r_road_dir(l)      = sunwall_r_dir(l) * vf_rw(l)
+            sunwall_r_shadewall_dir(l) = sunwall_r_dir(l) * vf_ww(l)
+
+            shadewall_a_dir(l)         = (1._r8-alb_wall_dir(l,ib)) * sdir_shadewall(l,ib)
+            shadewall_r_dir(l)         =     alb_wall_dir(l,ib)  * sdir_shadewall(l,ib)
+            shadewall_r_sky_dir(l)     = shadewall_r_dir(l) * vf_sw(l)
+            shadewall_r_road_dir(l)    = shadewall_r_dir(l) * vf_rw(l)
+            shadewall_r_sunwall_dir(l) = shadewall_r_dir(l) * vf_ww(l)
+
+            ! diffuse
+
+            road_a_dif(l)              = 0.0_r8
+            road_r_dif(l)              = 0.0_r8
+            improad_a_dif(l)           = (1._r8-alb_improad_dif(l,ib)) * sdif_road(l,ib) 
+            improad_r_dif(l)           =     alb_improad_dif(l,ib)  * sdif_road(l,ib) 
+            improad_r_sky_dif(l)       = improad_r_dif(l) * vf_sr(l)
+            improad_r_sunwall_dif(l)   = improad_r_dif(l) * vf_wr(l)
+            improad_r_shadewall_dif(l) = improad_r_dif(l) * vf_wr(l)
+            road_a_dif(l)              = road_a_dif(l) + improad_a_dif(l)*wtroad_imperv(l)
+            road_r_dif(l)              = road_r_dif(l) + improad_r_dif(l)*wtroad_imperv(l)
+
+            perroad_a_dif(l)           = (1._r8-alb_perroad_dif(l,ib)) * sdif_road(l,ib) 
+            perroad_r_dif(l)           =     alb_perroad_dif(l,ib)  * sdif_road(l,ib) 
+            perroad_r_sky_dif(l)       = perroad_r_dif(l) * vf_sr(l)
+            perroad_r_sunwall_dif(l)   = perroad_r_dif(l) * vf_wr(l)
+            perroad_r_shadewall_dif(l) = perroad_r_dif(l) * vf_wr(l)
+            road_a_dif(l)              = road_a_dif(l) + perroad_a_dif(l)*wtroad_perv(l)
+            road_r_dif(l)              = road_r_dif(l) + perroad_r_dif(l)*wtroad_perv(l)
+
+            road_r_sky_dif(l)          = road_r_dif(l) * vf_sr(l)
+            road_r_sunwall_dif(l)      = road_r_dif(l) * vf_wr(l)
+            road_r_shadewall_dif(l)    = road_r_dif(l) * vf_wr(l)
+
+            sunwall_a_dif(l)           = (1._r8-alb_wall_dif(l,ib)) * sdif_sunwall(l,ib)
+            sunwall_r_dif(l)           =     alb_wall_dif(l,ib)  * sdif_sunwall(l,ib)
+            sunwall_r_sky_dif(l)       = sunwall_r_dif(l) * vf_sw(l)
+            sunwall_r_road_dif(l)      = sunwall_r_dif(l) * vf_rw(l)
+            sunwall_r_shadewall_dif(l) = sunwall_r_dif(l) * vf_ww(l)
+
+            shadewall_a_dif(l)         = (1._r8-alb_wall_dif(l,ib)) * sdif_shadewall(l,ib)
+            shadewall_r_dif(l)         =     alb_wall_dif(l,ib)  * sdif_shadewall(l,ib)
+            shadewall_r_sky_dif(l)     = shadewall_r_dif(l) * vf_sw(l)
+            shadewall_r_road_dif(l)    = shadewall_r_dif(l) * vf_rw(l) 
+            shadewall_r_sunwall_dif(l) = shadewall_r_dif(l) * vf_ww(l) 
+
+            ! initialize sum of direct and diffuse solar absorption and reflection for road and both walls
+
+            sabs_improad_dir(l,ib)   = improad_a_dir(l)
+            sabs_perroad_dir(l,ib)   = perroad_a_dir(l)
+            sabs_sunwall_dir(l,ib)   = sunwall_a_dir(l)
+            sabs_shadewall_dir(l,ib) = shadewall_a_dir(l)
+
+            sabs_improad_dif(l,ib)   = improad_a_dif(l)
+            sabs_perroad_dif(l,ib)   = perroad_a_dif(l)
+            sabs_sunwall_dif(l,ib)   = sunwall_a_dif(l)
+            sabs_shadewall_dif(l,ib) = shadewall_a_dif(l)
+
+            sref_improad_dir(l,ib)   = improad_r_sky_dir(l) 
+            sref_perroad_dir(l,ib)   = perroad_r_sky_dir(l) 
+            sref_sunwall_dir(l,ib)   = sunwall_r_sky_dir(l) 
+            sref_shadewall_dir(l,ib) = shadewall_r_sky_dir(l) 
+
+            sref_improad_dif(l,ib)   = improad_r_sky_dif(l)
+            sref_perroad_dif(l,ib)   = perroad_r_sky_dif(l)
+            sref_sunwall_dif(l,ib)   = sunwall_r_sky_dif(l)
+            sref_shadewall_dif(l,ib) = shadewall_r_sky_dif(l)
+
+         end do
+
+         ! absorption and reflection for walls and road with multiple reflections
+         ! (i.e., absorb and reflect initial reflection in canyon and allow for 
+         ! subsequent scattering)
+         !
+         ! (1) absorption and reflection of scattered solar radiation
+         !     road: reflected fluxes from walls need to be projected to ground area
+         !     wall: reflected flux from road needs to be projected to wall area
+         !
+         ! (2) add absorbed radiation for ith reflection to total absorbed
+         !
+         ! (3) distribute reflected radiation to sky, road, and walls according to view factors
+         !
+         ! (4) add solar reflection to sky for ith reflection to total reflection
+         !
+         ! (5) stop iteration when absorption for ith reflection is less than some nominal amount. 
+         !     small convergence criteria is required to ensure solar radiation is conserved
+         !
+         ! do separately for direct beam and diffuse
+
+         do fl = 1,num_urbanl_coszen_gt0
+            l = filter_urbanl_coszen_gt0(fl)
+
+            ! reflected direct beam
+
+            do iter_dir = 1, n
+               ! step (1)
+
+               stot(l) = (sunwall_r_road_dir(l) + shadewall_r_road_dir(l))*canyon_hwr(l)
+
+               road_a_dir(l) = 0.0_r8
+               road_r_dir(l) = 0.0_r8
+               improad_a_dir(l) = (1._r8-alb_improad_dir(l,ib)) * stot(l) 
+               improad_r_dir(l) =     alb_improad_dir(l,ib)  * stot(l) 
+               road_a_dir(l)    = road_a_dir(l) + improad_a_dir(l)*wtroad_imperv(l)
+               road_r_dir(l)    = road_r_dir(l) + improad_r_dir(l)*wtroad_imperv(l)
+               perroad_a_dir(l) = (1._r8-alb_perroad_dir(l,ib)) * stot(l) 
+               perroad_r_dir(l) =     alb_perroad_dir(l,ib)  * stot(l) 
+               road_a_dir(l)    = road_a_dir(l) + perroad_a_dir(l)*wtroad_perv(l)
+               road_r_dir(l)    = road_r_dir(l) + perroad_r_dir(l)*wtroad_perv(l)
+
+               stot(l) = road_r_sunwall_dir(l)/canyon_hwr(l) + shadewall_r_sunwall_dir(l)
+               sunwall_a_dir(l) = (1._r8-alb_wall_dir(l,ib)) * stot(l)
+               sunwall_r_dir(l) =     alb_wall_dir(l,ib)  * stot(l)
+
+               stot(l) = road_r_shadewall_dir(l)/canyon_hwr(l) + sunwall_r_shadewall_dir(l)
+               shadewall_a_dir(l) = (1._r8-alb_wall_dir(l,ib)) * stot(l)
+               shadewall_r_dir(l) =     alb_wall_dir(l,ib)  * stot(l)
+
+               ! step (2)
 
-               ! direct beam
+               sabs_improad_dir(l,ib)   = sabs_improad_dir(l,ib)   + improad_a_dir(l)
+               sabs_perroad_dir(l,ib)   = sabs_perroad_dir(l,ib)   + perroad_a_dir(l)
+               sabs_sunwall_dir(l,ib)   = sabs_sunwall_dir(l,ib)   + sunwall_a_dir(l)
+               sabs_shadewall_dir(l,ib) = sabs_shadewall_dir(l,ib) + shadewall_a_dir(l)
+
+               ! step (3)
 
-               road_a_dir(l)              = 0.0_r8
-               road_r_dir(l)              = 0.0_r8
-               improad_a_dir(l)           = (1._r8-alb_improad_dir(l,ib)) * sdir_road(l,ib) 
-               improad_r_dir(l)           =     alb_improad_dir(l,ib)  * sdir_road(l,ib) 
                improad_r_sky_dir(l)       = improad_r_dir(l) * vf_sr(l)
                improad_r_sunwall_dir(l)   = improad_r_dir(l) * vf_wr(l)
                improad_r_shadewall_dir(l) = improad_r_dir(l) * vf_wr(l)
-               road_a_dir(l)              = road_a_dir(l) + improad_a_dir(l)*wtroad_imperv(l)
-               road_r_dir(l)              = road_r_dir(l) + improad_r_dir(l)*wtroad_imperv(l)
 
-               perroad_a_dir(l)           = (1._r8-alb_perroad_dir(l,ib)) * sdir_road(l,ib) 
-               perroad_r_dir(l)           =     alb_perroad_dir(l,ib)  * sdir_road(l,ib) 
                perroad_r_sky_dir(l)       = perroad_r_dir(l) * vf_sr(l)
                perroad_r_sunwall_dir(l)   = perroad_r_dir(l) * vf_wr(l)
                perroad_r_shadewall_dir(l) = perroad_r_dir(l) * vf_wr(l)
-               road_a_dir(l)              = road_a_dir(l) + perroad_a_dir(l)*wtroad_perv(l)
-               road_r_dir(l)              = road_r_dir(l) + perroad_r_dir(l)*wtroad_perv(l)
 
                road_r_sky_dir(l)          = road_r_dir(l) * vf_sr(l)
                road_r_sunwall_dir(l)      = road_r_dir(l) * vf_wr(l)
                road_r_shadewall_dir(l)    = road_r_dir(l) * vf_wr(l)
 
-               sunwall_a_dir(l)           = (1._r8-alb_wall_dir(l,ib)) * sdir_sunwall(l,ib)
-               sunwall_r_dir(l)           =     alb_wall_dir(l,ib)  * sdir_sunwall(l,ib)
                sunwall_r_sky_dir(l)       = sunwall_r_dir(l) * vf_sw(l)
                sunwall_r_road_dir(l)      = sunwall_r_dir(l) * vf_rw(l)
                sunwall_r_shadewall_dir(l) = sunwall_r_dir(l) * vf_ww(l)
 
-               shadewall_a_dir(l)         = (1._r8-alb_wall_dir(l,ib)) * sdir_shadewall(l,ib)
-               shadewall_r_dir(l)         =     alb_wall_dir(l,ib)  * sdir_shadewall(l,ib)
                shadewall_r_sky_dir(l)     = shadewall_r_dir(l) * vf_sw(l)
                shadewall_r_road_dir(l)    = shadewall_r_dir(l) * vf_rw(l)
                shadewall_r_sunwall_dir(l) = shadewall_r_dir(l) * vf_ww(l)
 
-               ! diffuse
+               ! step (4)
+
+               sref_improad_dir(l,ib)   = sref_improad_dir(l,ib) + improad_r_sky_dir(l)
+               sref_perroad_dir(l,ib)   = sref_perroad_dir(l,ib) + perroad_r_sky_dir(l)
+               sref_sunwall_dir(l,ib)   = sref_sunwall_dir(l,ib) + sunwall_r_sky_dir(l)
+               sref_shadewall_dir(l,ib) = sref_shadewall_dir(l,ib) + shadewall_r_sky_dir(l)
+
+               ! step (5)
+
+               crit = max(road_a_dir(l), sunwall_a_dir(l), shadewall_a_dir(l))
+               if (crit < errcrit) exit
+            end do
+            if (iter_dir >= n) then
+               write (iulog,*) 'urban net solar radiation error: no convergence, direct beam'
+               write (iulog,*) 'clm model is stopping'
+               call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
+            endif
+
+            ! reflected diffuse
+
+            do iter_dif = 1, n
+               ! step (1)
+
+               stot(l) = (sunwall_r_road_dif(l) + shadewall_r_road_dif(l))*canyon_hwr(l)
+               road_a_dif(l)    = 0.0_r8
+               road_r_dif(l)    = 0.0_r8
+               improad_a_dif(l) = (1._r8-alb_improad_dif(l,ib)) * stot(l) 
+               improad_r_dif(l) =     alb_improad_dif(l,ib)  * stot(l) 
+               road_a_dif(l)    = road_a_dif(l) + improad_a_dif(l)*wtroad_imperv(l)
+               road_r_dif(l)    = road_r_dif(l) + improad_r_dif(l)*wtroad_imperv(l)
+               perroad_a_dif(l) = (1._r8-alb_perroad_dif(l,ib)) * stot(l) 
+               perroad_r_dif(l) =     alb_perroad_dif(l,ib)  * stot(l) 
+               road_a_dif(l)    = road_a_dif(l) + perroad_a_dif(l)*wtroad_perv(l)
+               road_r_dif(l)    = road_r_dif(l) + perroad_r_dif(l)*wtroad_perv(l)
+
+               stot(l) = road_r_sunwall_dif(l)/canyon_hwr(l) + shadewall_r_sunwall_dif(l)
+               sunwall_a_dif(l) = (1._r8-alb_wall_dif(l,ib)) * stot(l)
+               sunwall_r_dif(l) =     alb_wall_dif(l,ib)  * stot(l)
+
+               stot(l) = road_r_shadewall_dif(l)/canyon_hwr(l) + sunwall_r_shadewall_dif(l)
+               shadewall_a_dif(l) = (1._r8-alb_wall_dif(l,ib)) * stot(l)
+               shadewall_r_dif(l) =     alb_wall_dif(l,ib)  * stot(l)
+
+               ! step (2)
+
+               sabs_improad_dif(l,ib)   = sabs_improad_dif(l,ib)   + improad_a_dif(l)
+               sabs_perroad_dif(l,ib)   = sabs_perroad_dif(l,ib)   + perroad_a_dif(l)
+               sabs_sunwall_dif(l,ib)   = sabs_sunwall_dif(l,ib)   + sunwall_a_dif(l)
+               sabs_shadewall_dif(l,ib) = sabs_shadewall_dif(l,ib) + shadewall_a_dif(l)
+
+               ! step (3)
 
-               road_a_dif(l)              = 0.0_r8
-               road_r_dif(l)              = 0.0_r8
-               improad_a_dif(l)           = (1._r8-alb_improad_dif(l,ib)) * sdif_road(l,ib) 
-               improad_r_dif(l)           =     alb_improad_dif(l,ib)  * sdif_road(l,ib) 
                improad_r_sky_dif(l)       = improad_r_dif(l) * vf_sr(l)
                improad_r_sunwall_dif(l)   = improad_r_dif(l) * vf_wr(l)
                improad_r_shadewall_dif(l) = improad_r_dif(l) * vf_wr(l)
-               road_a_dif(l)              = road_a_dif(l) + improad_a_dif(l)*wtroad_imperv(l)
-               road_r_dif(l)              = road_r_dif(l) + improad_r_dif(l)*wtroad_imperv(l)
 
-               perroad_a_dif(l)           = (1._r8-alb_perroad_dif(l,ib)) * sdif_road(l,ib) 
-               perroad_r_dif(l)           =     alb_perroad_dif(l,ib)  * sdif_road(l,ib) 
                perroad_r_sky_dif(l)       = perroad_r_dif(l) * vf_sr(l)
                perroad_r_sunwall_dif(l)   = perroad_r_dif(l) * vf_wr(l)
                perroad_r_shadewall_dif(l) = perroad_r_dif(l) * vf_wr(l)
-               road_a_dif(l)              = road_a_dif(l) + perroad_a_dif(l)*wtroad_perv(l)
-               road_r_dif(l)              = road_r_dif(l) + perroad_r_dif(l)*wtroad_perv(l)
 
                road_r_sky_dif(l)          = road_r_dif(l) * vf_sr(l)
                road_r_sunwall_dif(l)      = road_r_dif(l) * vf_wr(l)
                road_r_shadewall_dif(l)    = road_r_dif(l) * vf_wr(l)
 
-               sunwall_a_dif(l)           = (1._r8-alb_wall_dif(l,ib)) * sdif_sunwall(l,ib)
-               sunwall_r_dif(l)           =     alb_wall_dif(l,ib)  * sdif_sunwall(l,ib)
                sunwall_r_sky_dif(l)       = sunwall_r_dif(l) * vf_sw(l)
                sunwall_r_road_dif(l)      = sunwall_r_dif(l) * vf_rw(l)
                sunwall_r_shadewall_dif(l) = sunwall_r_dif(l) * vf_ww(l)
 
-               shadewall_a_dif(l)         = (1._r8-alb_wall_dif(l,ib)) * sdif_shadewall(l,ib)
-               shadewall_r_dif(l)         =     alb_wall_dif(l,ib)  * sdif_shadewall(l,ib)
                shadewall_r_sky_dif(l)     = shadewall_r_dif(l) * vf_sw(l)
-               shadewall_r_road_dif(l)    = shadewall_r_dif(l) * vf_rw(l) 
-               shadewall_r_sunwall_dif(l) = shadewall_r_dif(l) * vf_ww(l) 
-
-               ! initialize sum of direct and diffuse solar absorption and reflection for road and both walls
-
-               sabs_improad_dir(l,ib)   = improad_a_dir(l)
-               sabs_perroad_dir(l,ib)   = perroad_a_dir(l)
-               sabs_sunwall_dir(l,ib)   = sunwall_a_dir(l)
-               sabs_shadewall_dir(l,ib) = shadewall_a_dir(l)
-
-               sabs_improad_dif(l,ib)   = improad_a_dif(l)
-               sabs_perroad_dif(l,ib)   = perroad_a_dif(l)
-               sabs_sunwall_dif(l,ib)   = sunwall_a_dif(l)
-               sabs_shadewall_dif(l,ib) = shadewall_a_dif(l)
-
-               sref_improad_dir(l,ib)   = improad_r_sky_dir(l) 
-               sref_perroad_dir(l,ib)   = perroad_r_sky_dir(l) 
-               sref_sunwall_dir(l,ib)   = sunwall_r_sky_dir(l) 
-               sref_shadewall_dir(l,ib) = shadewall_r_sky_dir(l) 
-
-               sref_improad_dif(l,ib)   = improad_r_sky_dif(l)
-               sref_perroad_dif(l,ib)   = perroad_r_sky_dif(l)
-               sref_sunwall_dif(l,ib)   = sunwall_r_sky_dif(l)
-               sref_shadewall_dif(l,ib) = shadewall_r_sky_dif(l)
-
-         end do
-
-         ! absorption and reflection for walls and road with multiple reflections
-         ! (i.e., absorb and reflect initial reflection in canyon and allow for 
-         ! subsequent scattering)
-         !
-         ! (1) absorption and reflection of scattered solar radiation
-         !     road: reflected fluxes from walls need to be projected to ground area
-         !     wall: reflected flux from road needs to be projected to wall area
-         !
-         ! (2) add absorbed radiation for ith reflection to total absorbed
-         !
-         ! (3) distribute reflected radiation to sky, road, and walls according to view factors
-         !
-         ! (4) add solar reflection to sky for ith reflection to total reflection
-         !
-         ! (5) stop iteration when absorption for ith reflection is less than some nominal amount. 
-         !     small convergence criteria is required to ensure solar radiation is conserved
-         !
-         ! do separately for direct beam and diffuse
-
-         do fl = 1,num_urbanl_coszen_gt0
-            l = filter_urbanl_coszen_gt0(fl)
-
-               ! reflected direct beam
-
-               do iter_dir = 1, n
-                  ! step (1)
-
-                  stot(l) = (sunwall_r_road_dir(l) + shadewall_r_road_dir(l))*canyon_hwr(l)
+               shadewall_r_road_dif(l)    = shadewall_r_dif(l) * vf_rw(l)
+               shadewall_r_sunwall_dif(l) = shadewall_r_dif(l) * vf_ww(l)
 
-                  road_a_dir(l) = 0.0_r8
-                  road_r_dir(l) = 0.0_r8
-                  improad_a_dir(l) = (1._r8-alb_improad_dir(l,ib)) * stot(l) 
-                  improad_r_dir(l) =     alb_improad_dir(l,ib)  * stot(l) 
-                  road_a_dir(l)    = road_a_dir(l) + improad_a_dir(l)*wtroad_imperv(l)
-                  road_r_dir(l)    = road_r_dir(l) + improad_r_dir(l)*wtroad_imperv(l)
-                  perroad_a_dir(l) = (1._r8-alb_perroad_dir(l,ib)) * stot(l) 
-                  perroad_r_dir(l) =     alb_perroad_dir(l,ib)  * stot(l) 
-                  road_a_dir(l)    = road_a_dir(l) + perroad_a_dir(l)*wtroad_perv(l)
-                  road_r_dir(l)    = road_r_dir(l) + perroad_r_dir(l)*wtroad_perv(l)
+               ! step (4)
 
-                  stot(l) = road_r_sunwall_dir(l)/canyon_hwr(l) + shadewall_r_sunwall_dir(l)
-                  sunwall_a_dir(l) = (1._r8-alb_wall_dir(l,ib)) * stot(l)
-                  sunwall_r_dir(l) =     alb_wall_dir(l,ib)  * stot(l)
+               sref_improad_dif(l,ib)   = sref_improad_dif(l,ib)   + improad_r_sky_dif(l)
+               sref_perroad_dif(l,ib)   = sref_perroad_dif(l,ib)   + perroad_r_sky_dif(l)
+               sref_sunwall_dif(l,ib)   = sref_sunwall_dif(l,ib)   + sunwall_r_sky_dif(l)
+               sref_shadewall_dif(l,ib) = sref_shadewall_dif(l,ib) + shadewall_r_sky_dif(l)
 
-                  stot(l) = road_r_shadewall_dir(l)/canyon_hwr(l) + sunwall_r_shadewall_dir(l)
-                  shadewall_a_dir(l) = (1._r8-alb_wall_dir(l,ib)) * stot(l)
-                  shadewall_r_dir(l) =     alb_wall_dir(l,ib)  * stot(l)
+               ! step (5)
 
-                  ! step (2)
-
-                  sabs_improad_dir(l,ib)   = sabs_improad_dir(l,ib)   + improad_a_dir(l)
-                  sabs_perroad_dir(l,ib)   = sabs_perroad_dir(l,ib)   + perroad_a_dir(l)
-                  sabs_sunwall_dir(l,ib)   = sabs_sunwall_dir(l,ib)   + sunwall_a_dir(l)
-                  sabs_shadewall_dir(l,ib) = sabs_shadewall_dir(l,ib) + shadewall_a_dir(l)
+               crit = max(road_a_dif(l), sunwall_a_dif(l), shadewall_a_dif(l))
+               if (crit < errcrit) exit
+            end do
+            if (iter_dif >= n) then
+               write (iulog,*) 'urban net solar radiation error: no convergence, diffuse'
+               write (iulog,*) 'clm model is stopping'
+               call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
+            endif
 
-                  ! step (3)
+            ! total reflected by canyon - sum of solar reflection to sky from canyon.
+            ! project wall fluxes to horizontal surface
+
+            sref_canyon_dir(l) = 0.0_r8
+            sref_canyon_dif(l) = 0.0_r8
+            sref_canyon_dir(l) = sref_canyon_dir(l) + sref_improad_dir(l,ib)*wtroad_imperv(l)
+            sref_canyon_dif(l) = sref_canyon_dif(l) + sref_improad_dif(l,ib)*wtroad_imperv(l)
+            sref_canyon_dir(l) = sref_canyon_dir(l) + sref_perroad_dir(l,ib)*wtroad_perv(l)
+            sref_canyon_dif(l) = sref_canyon_dif(l) + sref_perroad_dif(l,ib)*wtroad_perv(l)
+            sref_canyon_dir(l) = sref_canyon_dir(l) + (sref_sunwall_dir(l,ib) + sref_shadewall_dir(l,ib))*canyon_hwr(l)
+            sref_canyon_dif(l) = sref_canyon_dif(l) + (sref_sunwall_dif(l,ib) + sref_shadewall_dif(l,ib))*canyon_hwr(l)
+
+            ! total absorbed by canyon. project wall fluxes to horizontal surface
+
+            sabs_canyon_dir(l) = 0.0_r8
+            sabs_canyon_dif(l) = 0.0_r8
+            sabs_canyon_dir(l) = sabs_canyon_dir(l) + sabs_improad_dir(l,ib)*wtroad_imperv(l)
+            sabs_canyon_dif(l) = sabs_canyon_dif(l) + sabs_improad_dif(l,ib)*wtroad_imperv(l)
+            sabs_canyon_dir(l) = sabs_canyon_dir(l) + sabs_perroad_dir(l,ib)*wtroad_perv(l)
+            sabs_canyon_dif(l) = sabs_canyon_dif(l) + sabs_perroad_dif(l,ib)*wtroad_perv(l)
+            sabs_canyon_dir(l) = sabs_canyon_dir(l) + (sabs_sunwall_dir(l,ib) + sabs_shadewall_dir(l,ib))*canyon_hwr(l)
+            sabs_canyon_dif(l) = sabs_canyon_dif(l) + (sabs_sunwall_dif(l,ib) + sabs_shadewall_dif(l,ib))*canyon_hwr(l)
+
+            ! conservation check. note: previous conservation checks confirm partioning of total direct
+            ! beam and diffuse radiation from atmosphere to road and walls is conserved as
+            !    sdir (from atmosphere) = sdir_road + (sdir_sunwall + sdir_shadewall)*canyon_hwr
+            !    sdif (from atmosphere) = sdif_road + (sdif_sunwall + sdif_shadewall)*canyon_hwr
+
+            stot_dir(l) = sdir_road(l,ib) + (sdir_sunwall(l,ib) + sdir_shadewall(l,ib))*canyon_hwr(l)
+            stot_dif(l) = sdif_road(l,ib) + (sdif_sunwall(l,ib) + sdif_shadewall(l,ib))*canyon_hwr(l)
+
+            err = stot_dir(l) + stot_dif(l) &
+                 - (sabs_canyon_dir(l) + sabs_canyon_dif(l) + sref_canyon_dir(l) + sref_canyon_dif(l))
+            if (abs(err) > 0.001_r8 ) then
+               write(iulog,*)'urban net solar radiation balance error for ib=',ib,' err= ',err
+               write(iulog,*)' l= ',l,' ib= ',ib 
+               write(iulog,*)' stot_dir        = ',stot_dir(l)
+               write(iulog,*)' stot_dif        = ',stot_dif(l)
+               write(iulog,*)' sabs_canyon_dir = ',sabs_canyon_dir(l)
+               write(iulog,*)' sabs_canyon_dif = ',sabs_canyon_dif(l)
+               write(iulog,*)' sref_canyon_dir = ',sref_canyon_dir(l)
+               write(iulog,*)' sref_canyon_dif = ',sref_canyon_dir(l)
+               write(iulog,*) 'clm model is stopping'
+               call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
+            endif
 
-                  improad_r_sky_dir(l)       = improad_r_dir(l) * vf_sr(l)
-                  improad_r_sunwall_dir(l)   = improad_r_dir(l) * vf_wr(l)
-                  improad_r_shadewall_dir(l) = improad_r_dir(l) * vf_wr(l)
+            ! canyon albedo
 
-                  perroad_r_sky_dir(l)       = perroad_r_dir(l) * vf_sr(l)
-                  perroad_r_sunwall_dir(l)   = perroad_r_dir(l) * vf_wr(l)
-                  perroad_r_shadewall_dir(l) = perroad_r_dir(l) * vf_wr(l)
-
-                  road_r_sky_dir(l)          = road_r_dir(l) * vf_sr(l)
-                  road_r_sunwall_dir(l)      = road_r_dir(l) * vf_wr(l)
-                  road_r_shadewall_dir(l)    = road_r_dir(l) * vf_wr(l)
-
-                  sunwall_r_sky_dir(l)       = sunwall_r_dir(l) * vf_sw(l)
-                  sunwall_r_road_dir(l)      = sunwall_r_dir(l) * vf_rw(l)
-                  sunwall_r_shadewall_dir(l) = sunwall_r_dir(l) * vf_ww(l)
-
-                  shadewall_r_sky_dir(l)     = shadewall_r_dir(l) * vf_sw(l)
-                  shadewall_r_road_dir(l)    = shadewall_r_dir(l) * vf_rw(l)
-                  shadewall_r_sunwall_dir(l) = shadewall_r_dir(l) * vf_ww(l)
-
-                  ! step (4)
-
-                  sref_improad_dir(l,ib)   = sref_improad_dir(l,ib) + improad_r_sky_dir(l)
-                  sref_perroad_dir(l,ib)   = sref_perroad_dir(l,ib) + perroad_r_sky_dir(l)
-                  sref_sunwall_dir(l,ib)   = sref_sunwall_dir(l,ib) + sunwall_r_sky_dir(l)
-                  sref_shadewall_dir(l,ib) = sref_shadewall_dir(l,ib) + shadewall_r_sky_dir(l)
-
-                  ! step (5)
-
-                  crit = max(road_a_dir(l), sunwall_a_dir(l), shadewall_a_dir(l))
-                  if (crit < errcrit) exit
-               end do
-               if (iter_dir >= n) then
-                  write (iulog,*) 'urban net solar radiation error: no convergence, direct beam'
-                  write (iulog,*) 'clm model is stopping'
-                  call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
-               endif
-
-               ! reflected diffuse
-
-               do iter_dif = 1, n
-                  ! step (1)
-
-                  stot(l) = (sunwall_r_road_dif(l) + shadewall_r_road_dif(l))*canyon_hwr(l)
-                  road_a_dif(l)    = 0.0_r8
-                  road_r_dif(l)    = 0.0_r8
-                  improad_a_dif(l) = (1._r8-alb_improad_dif(l,ib)) * stot(l) 
-                  improad_r_dif(l) =     alb_improad_dif(l,ib)  * stot(l) 
-                  road_a_dif(l)    = road_a_dif(l) + improad_a_dif(l)*wtroad_imperv(l)
-                  road_r_dif(l)    = road_r_dif(l) + improad_r_dif(l)*wtroad_imperv(l)
-                  perroad_a_dif(l) = (1._r8-alb_perroad_dif(l,ib)) * stot(l) 
-                  perroad_r_dif(l) =     alb_perroad_dif(l,ib)  * stot(l) 
-                  road_a_dif(l)    = road_a_dif(l) + perroad_a_dif(l)*wtroad_perv(l)
-                  road_r_dif(l)    = road_r_dif(l) + perroad_r_dif(l)*wtroad_perv(l)
-
-                  stot(l) = road_r_sunwall_dif(l)/canyon_hwr(l) + shadewall_r_sunwall_dif(l)
-                  sunwall_a_dif(l) = (1._r8-alb_wall_dif(l,ib)) * stot(l)
-                  sunwall_r_dif(l) =     alb_wall_dif(l,ib)  * stot(l)
-
-                  stot(l) = road_r_shadewall_dif(l)/canyon_hwr(l) + sunwall_r_shadewall_dif(l)
-                  shadewall_a_dif(l) = (1._r8-alb_wall_dif(l,ib)) * stot(l)
-                  shadewall_r_dif(l) =     alb_wall_dif(l,ib)  * stot(l)
-
-                  ! step (2)
-
-                  sabs_improad_dif(l,ib)   = sabs_improad_dif(l,ib)   + improad_a_dif(l)
-                  sabs_perroad_dif(l,ib)   = sabs_perroad_dif(l,ib)   + perroad_a_dif(l)
-                  sabs_sunwall_dif(l,ib)   = sabs_sunwall_dif(l,ib)   + sunwall_a_dif(l)
-                  sabs_shadewall_dif(l,ib) = sabs_shadewall_dif(l,ib) + shadewall_a_dif(l)
-
-                  ! step (3)
-
-                  improad_r_sky_dif(l)       = improad_r_dif(l) * vf_sr(l)
-                  improad_r_sunwall_dif(l)   = improad_r_dif(l) * vf_wr(l)
-                  improad_r_shadewall_dif(l) = improad_r_dif(l) * vf_wr(l)
-
-                  perroad_r_sky_dif(l)       = perroad_r_dif(l) * vf_sr(l)
-                  perroad_r_sunwall_dif(l)   = perroad_r_dif(l) * vf_wr(l)
-                  perroad_r_shadewall_dif(l) = perroad_r_dif(l) * vf_wr(l)
-
-                  road_r_sky_dif(l)          = road_r_dif(l) * vf_sr(l)
-                  road_r_sunwall_dif(l)      = road_r_dif(l) * vf_wr(l)
-                  road_r_shadewall_dif(l)    = road_r_dif(l) * vf_wr(l)
-
-                  sunwall_r_sky_dif(l)       = sunwall_r_dif(l) * vf_sw(l)
-                  sunwall_r_road_dif(l)      = sunwall_r_dif(l) * vf_rw(l)
-                  sunwall_r_shadewall_dif(l) = sunwall_r_dif(l) * vf_ww(l)
-
-                  shadewall_r_sky_dif(l)     = shadewall_r_dif(l) * vf_sw(l)
-                  shadewall_r_road_dif(l)    = shadewall_r_dif(l) * vf_rw(l)
-                  shadewall_r_sunwall_dif(l) = shadewall_r_dif(l) * vf_ww(l)
-
-                  ! step (4)
-
-                  sref_improad_dif(l,ib)   = sref_improad_dif(l,ib)   + improad_r_sky_dif(l)
-                  sref_perroad_dif(l,ib)   = sref_perroad_dif(l,ib)   + perroad_r_sky_dif(l)
-                  sref_sunwall_dif(l,ib)   = sref_sunwall_dif(l,ib)   + sunwall_r_sky_dif(l)
-                  sref_shadewall_dif(l,ib) = sref_shadewall_dif(l,ib) + shadewall_r_sky_dif(l)
-
-                  ! step (5)
-
-                  crit = max(road_a_dif(l), sunwall_a_dif(l), shadewall_a_dif(l))
-                  if (crit < errcrit) exit
-               end do
-               if (iter_dif >= n) then
-                  write (iulog,*) 'urban net solar radiation error: no convergence, diffuse'
-                  write (iulog,*) 'clm model is stopping'
-                  call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
-               endif
-
-               ! total reflected by canyon - sum of solar reflection to sky from canyon.
-               ! project wall fluxes to horizontal surface
-
-               sref_canyon_dir(l) = 0.0_r8
-               sref_canyon_dif(l) = 0.0_r8
-               sref_canyon_dir(l) = sref_canyon_dir(l) + sref_improad_dir(l,ib)*wtroad_imperv(l)
-               sref_canyon_dif(l) = sref_canyon_dif(l) + sref_improad_dif(l,ib)*wtroad_imperv(l)
-               sref_canyon_dir(l) = sref_canyon_dir(l) + sref_perroad_dir(l,ib)*wtroad_perv(l)
-               sref_canyon_dif(l) = sref_canyon_dif(l) + sref_perroad_dif(l,ib)*wtroad_perv(l)
-               sref_canyon_dir(l) = sref_canyon_dir(l) + (sref_sunwall_dir(l,ib) + sref_shadewall_dir(l,ib))*canyon_hwr(l)
-               sref_canyon_dif(l) = sref_canyon_dif(l) + (sref_sunwall_dif(l,ib) + sref_shadewall_dif(l,ib))*canyon_hwr(l)
-
-               ! total absorbed by canyon. project wall fluxes to horizontal surface
-
-               sabs_canyon_dir(l) = 0.0_r8
-               sabs_canyon_dif(l) = 0.0_r8
-               sabs_canyon_dir(l) = sabs_canyon_dir(l) + sabs_improad_dir(l,ib)*wtroad_imperv(l)
-               sabs_canyon_dif(l) = sabs_canyon_dif(l) + sabs_improad_dif(l,ib)*wtroad_imperv(l)
-               sabs_canyon_dir(l) = sabs_canyon_dir(l) + sabs_perroad_dir(l,ib)*wtroad_perv(l)
-               sabs_canyon_dif(l) = sabs_canyon_dif(l) + sabs_perroad_dif(l,ib)*wtroad_perv(l)
-               sabs_canyon_dir(l) = sabs_canyon_dir(l) + (sabs_sunwall_dir(l,ib) + sabs_shadewall_dir(l,ib))*canyon_hwr(l)
-               sabs_canyon_dif(l) = sabs_canyon_dif(l) + (sabs_sunwall_dif(l,ib) + sabs_shadewall_dif(l,ib))*canyon_hwr(l)
-
-               ! conservation check. note: previous conservation checks confirm partioning of total direct
-               ! beam and diffuse radiation from atmosphere to road and walls is conserved as
-               !    sdir (from atmosphere) = sdir_road + (sdir_sunwall + sdir_shadewall)*canyon_hwr
-               !    sdif (from atmosphere) = sdif_road + (sdif_sunwall + sdif_shadewall)*canyon_hwr
-
-               stot_dir(l) = sdir_road(l,ib) + (sdir_sunwall(l,ib) + sdir_shadewall(l,ib))*canyon_hwr(l)
-               stot_dif(l) = sdif_road(l,ib) + (sdif_sunwall(l,ib) + sdif_shadewall(l,ib))*canyon_hwr(l)
-
-               err = stot_dir(l) + stot_dif(l) &
-                    - (sabs_canyon_dir(l) + sabs_canyon_dif(l) + sref_canyon_dir(l) + sref_canyon_dif(l))
-               if (abs(err) > 0.001_r8 ) then
-                  write(iulog,*)'urban net solar radiation balance error for ib=',ib,' err= ',err
-                  write(iulog,*)' l= ',l,' ib= ',ib 
-                  write(iulog,*)' stot_dir        = ',stot_dir(l)
-                  write(iulog,*)' stot_dif        = ',stot_dif(l)
-                  write(iulog,*)' sabs_canyon_dir = ',sabs_canyon_dir(l)
-                  write(iulog,*)' sabs_canyon_dif = ',sabs_canyon_dif(l)
-                  write(iulog,*)' sref_canyon_dir = ',sref_canyon_dir(l)
-                  write(iulog,*)' sref_canyon_dif = ',sref_canyon_dir(l)
-                  write(iulog,*) 'clm model is stopping'
-                  call endrun(subgrid_index=l, subgrid_level=subgrid_level_landunit, msg=errmsg(sourcefile, __LINE__))
-               endif
-
-               ! canyon albedo
-
-               canyon_alb_dif(l) = sref_canyon_dif(l) / max(stot_dif(l), 1.e-06_r8)
-               canyon_alb_dir(l) = sref_canyon_dir(l) / max(stot_dir(l), 1.e-06_r8)
+            canyon_alb_dif(l) = sref_canyon_dif(l) / max(stot_dif(l), 1.e-06_r8)
+            canyon_alb_dir(l) = sref_canyon_dir(l) / max(stot_dir(l), 1.e-06_r8)
 
          end do   ! end of landunit loop
 
-         ! Refected and absorbed solar radiation per unit incident radiation for roof
+         ! Reflected and absorbed solar radiation per unit incident radiation for roof
 
          do fl = 1,num_urbanl_coszen_gt0
             l = filter_urbanl_coszen_gt0(fl)

From 7006d9499920ee0327ab41aa422d41019f64f04a Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Fri, 8 Nov 2024 09:29:53 -0700
Subject: [PATCH 1231/1248] more expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index ba7b945767..dd0068909a 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -304,6 +304,13 @@
       <issue>#2810</issue>
     </phase>
   </test>
+  
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2810</issue>
+    </phase>
+  </test>
 
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 

From 06bcd4aea211554ff847255da02c75acb02bd824 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Fri, 8 Nov 2024 09:32:38 -0700
Subject: [PATCH 1232/1248] expected fails for izumi_nag

---
 cime_config/testdefs/ExpectedTestFails.xml | 32 ++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index dd0068909a..6be21e3e4f 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -311,6 +311,38 @@
       <issue>#2810</issue>
     </phase>
   </test>
+  
+  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+    
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesPRISM--clm-NEON-FATES-YELLO">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+
+
 
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 

From bd8565647f41f0c249ad443295adf23e08b2c7da Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 8 Nov 2024 13:16:00 -0700
Subject: [PATCH 1233/1248] build-namelist_test: Ensure cold starts w/ finidat
 are handled properly.

Currently fails. We want FATES to work and BGC to fail, even when ignoring warnings.
---
 bld/unit_testers/build-namelist_test.pl | 54 +++++++++++++++++++++++--
 1 file changed, 50 insertions(+), 4 deletions(-)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index a1f5e3912f..1bf201d239 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -1318,10 +1318,6 @@ sub cat_and_create_namelistinfile {
 
 my %warntest = (
      # Warnings without the -ignore_warnings option given
-     "coldwfinidat"              =>{ options=>"-envxml_dir . -clm_start_type cold",
-                                     namelst=>"finidat = 'testfile.nc'",
-                                     phys=>"clm5_0",
-                                   },
      "bgcspin_w_suplnitro"       =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup on",
                                      namelst=>"suplnitro='ALL'",
                                      phys=>"clm5_0",
@@ -1402,6 +1398,56 @@ sub cat_and_create_namelistinfile {
    system( "cat $tempfile" );
 }
 
+print "\n===============================================================================\n";
+print "Ensure cold starts with finidat are handled properly \n";
+print "=================================================================================\n";
+
+my %coldwfinidat = (
+     "bgc"   => { options=>"-envxml_dir . -clm_start_type cold",
+                  namelst=>"finidat = 'testfile.nc'",
+                  phys=>"clm5_0",
+                  expected_fail=>1,
+                },
+     "fates" => { options=>"-envxml_dir . -clm_start_type cold -bgc fates -no-megan",
+                  namelst=>"finidat = 'testfile.nc', use_fates = .true.",
+                  phys=>"clm5_0",
+                  expected_fail=>0,
+                },
+);
+my $finidat;
+foreach my $key ( keys(%coldwfinidat) ) {
+   print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "options", "namelst", "expected_fail" ) {
+      if ( not exists $coldwfinidat{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for coldwfinidat $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
+   &make_config_cache($coldwfinidat{$key}{"phys"});
+   my $options  = $coldwfinidat{$key}{"options"};
+   my $namelist = $coldwfinidat{$key}{"namelst"};
+   my $expected_fail = $coldwfinidat{$key}{"expected_fail"};
+   my %settings;
+   &make_env_run( %settings );
+
+   # Should fail if expected to, pass otherwise
+   eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
+   is( $? eq 0, $expected_fail eq 0, "coldwfinidat $key run");
+
+   if ( $expected_fail ) {
+      # Now run with -ignore_warnings and make sure it still doesn't work
+      $options .= " -ignore_warnings";
+      eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
+      isnt( $?, 0, "coldwfinidat $key run -ignore_warnings" );
+   } else {
+      # Check that finidat was correctly set
+      $finidat = `grep finidat lnd_in`;
+      ok ( $finidat =~ "testfile.nc", "coldwfinidat $key finidat? $finidat" );
+   }
+}
+
 #
 # Loop over all physics versions
 #

From f8f3a6f8e01ff356027dd935c70e8bf1efadbc6e Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 8 Nov 2024 13:03:22 -0700
Subject: [PATCH 1234/1248] Ignore finidat for cold-start FATES runs.

Resolves ESCOMP/CTSM#2856, where such runs were getting their finidat overwritten with ' '.
---
 bld/CLMBuildNamelist.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 592699cc2b..f4d60e481b 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2588,7 +2588,7 @@ sub setup_logic_initial_conditions {
   my $finidat = $nl->get_value($var);
   $nl_flags->{'excess_ice_on_finidat'} = "unknown";
   if ( $nl_flags->{'clm_start_type'} =~ /cold/ ) {
-    if (defined $finidat ) {
+    if (defined $finidat && !&value_is_true(($nl->get_value('use_fates')))) {
       $log->warning("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incomptable with using a cold start" .
               " (by setting CLM_FORCE_COLDSTART=on)." );
       $log->warning("Overridding input $var file with one specifying that this is a cold start from arbitrary initial conditions." );

From 33fd95de9ca0e20e30a4e9c5d7eb6caf1c700f6a Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Fri, 8 Nov 2024 13:06:31 -0700
Subject: [PATCH 1235/1248] Don't allow users to supply finidat for cold-start
 non-FATES runs.

Previously, this only produced a warning, which could be overridden.
---
 bld/CLMBuildNamelist.pm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index f4d60e481b..94777d320d 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -2589,11 +2589,8 @@ sub setup_logic_initial_conditions {
   $nl_flags->{'excess_ice_on_finidat'} = "unknown";
   if ( $nl_flags->{'clm_start_type'} =~ /cold/ ) {
     if (defined $finidat && !&value_is_true(($nl->get_value('use_fates')))) {
-      $log->warning("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incomptable with using a cold start" .
+      $log->fatal_error("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incompatible with using a cold start" .
               " (by setting CLM_FORCE_COLDSTART=on)." );
-      $log->warning("Overridding input $var file with one specifying that this is a cold start from arbitrary initial conditions." );
-      my $group = $definition->get_group_name($var);
-      $nl->set_variable_value($group, $var, "' '" );
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
                 $var, 'val'=>"' '", 'no_abspath'=>1);

From 6fbd0cc410fa56643db46f55eee730fe5d9c439d Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Fri, 8 Nov 2024 14:32:59 -0700
Subject: [PATCH 1236/1248] updating expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 7 -------
 components/cdeps                           | 2 +-
 src/fates                                  | 2 +-
 3 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 6be21e3e4f..b53914378f 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -319,13 +319,6 @@
     </phase>
   </test>
   
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-  
     
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesPRISM--clm-NEON-FATES-YELLO">
     <phase name="RUN">
diff --git a/components/cdeps b/components/cdeps
index 7476950699..7b0b3a8272 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit 7476950699909813d1938a34bd8d71bf5bfbf1e9
+Subproject commit 7b0b3a827241c53d296ec877cb1f59966bf5e5bf
diff --git a/src/fates b/src/fates
index de61028847..fb6ab8c2f7 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit de6102884790bb60681b11d20151fb462c1a70b5
+Subproject commit fb6ab8c2f744fdebe42e5ab2881c0c34333180b7

From 000b70d74e627ff457b7353bc88921f3035fdd68 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Sat, 9 Nov 2024 12:42:16 -0700
Subject: [PATCH 1237/1248] adding izumi nag fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 51 ++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 7049e9672b..b403c95b7e 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -283,6 +283,57 @@
       <issue>#2325</issue>
     </phase>
   </test>
+  
+  <!-- izumi nag failures -->
+  <test name="ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+  <test name="SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_nag.clm-ptsRLA">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+  <test name="SMS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm60FatesRs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60SpRs.izumi_nag.clm-default--clm-NEON-TOOL">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
 
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_intel.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">

From bbe061dfa37394d2ffcd541ebd19aaae1dfbef5f Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Sat, 9 Nov 2024 12:54:31 -0700
Subject: [PATCH 1238/1248] changelog

---
 doc/ChangeLog | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 58 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 3620cd8c15..7dcda101aa 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,61 @@
 ===============================================================
+Tag name: ctsm5.3.010
+Originator(s): afoster (Adrianna Foster)
+Date: Sat Nov  9 12:54:18 MST 2024
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+- moves namelist variables to parameter file for PPE and makes some parameter variables pft-dimensioned (resolves ESCOMP/CTSM#2830 and resolves ESCOMP/CTSM#2831)
+- removes/replaces references to DATM_C* _YR_* variables (resolves ESCOMP/CTSM#2743)
+- documents that fincl1 and fexcl1 map to 'h0' history files
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+- ESCOMP/CTSM#2830 (allow LUNA & mortality parameter to vary by PFT; https://github.com/ESCOMP/CTSM/issues/2830)
+- ESCOMP/CTSM#2831 (Move namelist parameters to paramfile; https://github.com/ESCOMP/CTSM/issues/2831)
+- ESCOMP/CTSM#2743 (Docs: Remove refs to DATM_CLMNCEP_YR_* and DATM_CPL_YR_* variables; https://github.com/ESCOMP/CTSM/issues/2743)
+
+
+Testing summary:
+----------------
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2845: PPE parameter work -Addresses issues 2830 and 2831 (https://github.com/ESCOMP/CTSM/pull/2845)
+- ESCOMP/CTSM#2852: Remove/replace refs to DATM_C*_YR_* variables (https://github.com/ESCOMP/CTSM/pull/2852)
+- ESCOMP/CTSM#2866: Document that fincl1 maps to 'h0' history file. And fexcl1 (https://github.com/ESCOMP/CTSM/pull/2866)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.009
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Tue Oct 15 17:35:40 MDT 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index af6e1675b4..46e1176fd3 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.010  afoster 11/09/2024 Merge b4b-dev
        ctsm5.3.009 samrabin 10/15/2024 Reduce outputs from matrixcnOn tests
        ctsm5.3.008   olyson 10/14/2024 PPE change to sa_leaf in CanopyFluxesMod.F90
        ctsm5.3.007   slevis 10/14/2024 Clm60 finidat updates for ne30, f09, f19 grids

From 5ccd3578d5b3ef7d7ba3fd8053a85b08ed113514 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 11 Nov 2024 12:41:09 -0700
Subject: [PATCH 1239/1248] run_sys_tests: Print test list in
 --verbose/--debug.

---
 python/ctsm/run_sys_tests.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py
index 6afc43cd19..3568dcc174 100644
--- a/python/ctsm/run_sys_tests.py
+++ b/python/ctsm/run_sys_tests.py
@@ -8,6 +8,7 @@
 from datetime import datetime
 
 from CIME.test_utils import get_tests_from_xml  # pylint: disable=import-error
+from CIME.test_utils import test_to_string  # pylint: disable=import-error
 from CIME.cs_status_creator import create_cs_status  # pylint: disable=import-error
 
 from ctsm.ctsm_logging import (
@@ -780,6 +781,10 @@ def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests):
         raise RuntimeError(
             "No tests found for suite {} on machine {}".format(suite_name, machine_name)
         )
+    logger.info("Tests:")
+    for test in test_data:
+        test_string = test_to_string(test).split(" ")[1]
+        logger.info("   %s", test_string)
     if not running_ctsm_py_tests:
         _check_py_env([t["testname"] for t in test_data])
         _check_py_env([t["testmods"] for t in test_data if "testmods" in t.keys()])

From e81cbc86951912b0581573ec573155b3140313bb Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 11 Nov 2024 13:03:02 -0700
Subject: [PATCH 1240/1248] Only enter for-loop if verbose+.

---
 python/ctsm/run_sys_tests.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py
index 3568dcc174..7d3ffe8444 100644
--- a/python/ctsm/run_sys_tests.py
+++ b/python/ctsm/run_sys_tests.py
@@ -781,10 +781,11 @@ def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests):
         raise RuntimeError(
             "No tests found for suite {} on machine {}".format(suite_name, machine_name)
         )
-    logger.info("Tests:")
-    for test in test_data:
-        test_string = test_to_string(test).split(" ")[1]
-        logger.info("   %s", test_string)
+    if logger.getEffectiveLevel() <= logging.INFO:
+        logger.info("Tests:")
+        for test in test_data:
+            test_string = test_to_string(test).split(" ")[1]
+            logger.info("   %s", test_string)
     if not running_ctsm_py_tests:
         _check_py_env([t["testname"] for t in test_data])
         _check_py_env([t["testmods"] for t in test_data if "testmods" in t.keys()])

From c60fe19e7d93679a0b3fcaac9d26f1f56e667065 Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Mon, 11 Nov 2024 17:53:58 -0700
Subject: [PATCH 1241/1248] Add some tests to expected fail list.

---
 cime_config/testdefs/ExpectedTestFails.xml | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index b403c95b7e..775ff2c281 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -334,6 +334,19 @@
     </phase>
   </test>
 
+  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
 
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_intel.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">
@@ -349,6 +362,13 @@
     </phase>
   </test>
 
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2810</issue>
+    </phase>
+  </test>
+
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 
   <test name="SMS_Lh3.f10_f10_mg37.I2000Clm51Sp.derecho_intel.mosart-clmAccelSpinupIgnoreWarn">

From ebcd4fb4742c8eb3197a83f19309907b585c28f5 Mon Sep 17 00:00:00 2001
From: Sam Rabin <samrabin@ucar.edu>
Date: Mon, 11 Nov 2024 18:04:18 -0700
Subject: [PATCH 1242/1248] Update ChangeLog and ChangeSum.

---
 doc/ChangeLog | 87 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 88 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 7dcda101aa..c08a55bbd4 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,91 @@
 ===============================================================
+Tag name: ctsm5.3.011
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Mon Nov 11 17:55:57 MST 2024
+One-line Summary: Improve handling of cold-start finidat
+
+Purpose and description of changes
+----------------------------------
+
+This PR changes things so that:
+
+1. Cold-start FATES runs with finidat specified will not require -ignore_warnings, and the supplied finidat will actually be obeyed.
+2. Cold-start non-FATES runs will not be allowed, even with -ignore_warnings.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List of CTSM issues fixed:
+- Resolves ESCOMP/CTSM#2856: FATES will never start from specified finidat (https://github.com/ESCOMP/CTSM/issues/2856)
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Changes to tests or testing:
+Adds three fates suite tests to expected fails:
+- ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold
+- SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro
+- ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests:
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: FATES cold-start runs with finidat
+    - what platforms/compilers: All
+    - nature of change: new climate
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2870: Fix handling of finidat with cold starts (https://github.com/ESCOMP/CTSM/pull/2870)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.010
 Originator(s): afoster (Adrianna Foster)
 Date: Sat Nov  9 12:54:18 MST 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 46e1176fd3..daffdab145 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.011 samrabin 11/11/2024 Improve handling of cold-start finidat
        ctsm5.3.010  afoster 11/09/2024 Merge b4b-dev
        ctsm5.3.009 samrabin 10/15/2024 Reduce outputs from matrixcnOn tests
        ctsm5.3.008   olyson 10/14/2024 PPE change to sa_leaf in CanopyFluxesMod.F90

From bb8a8a035d3c8377a85ab5ff3ad88091350b12aa Mon Sep 17 00:00:00 2001
From: Sam Rabin <sam.rabin@gmail.com>
Date: Tue, 12 Nov 2024 10:13:53 -0700
Subject: [PATCH 1243/1248] Pylint: ignore abstract-class-instantiated in
 cropcal code.

---
 python/ctsm/crop_calendars/cropcal_figs_module.py     | 1 +
 python/ctsm/crop_calendars/generate_gdds_functions.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/python/ctsm/crop_calendars/cropcal_figs_module.py b/python/ctsm/crop_calendars/cropcal_figs_module.py
index d820460175..f26b5975d4 100644
--- a/python/ctsm/crop_calendars/cropcal_figs_module.py
+++ b/python/ctsm/crop_calendars/cropcal_figs_module.py
@@ -1,6 +1,7 @@
 """
 Functions for making crop calendar figures
 """
+# pylint: disable=abstract-class-instantiated
 
 import numpy as np
 
diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index 14bd6b2e40..81c71e2a51 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -1,7 +1,7 @@
 """
 Functions to support generate_gdds.py
 """
-# pylint: disable=too-many-lines,too-many-statements
+# pylint: disable=too-many-lines,too-many-statements,abstract-class-instantiated
 import warnings
 import os
 import glob

From 7d222636cb49ccec8c168ff870caed976205b442 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Wed, 13 Nov 2024 09:09:37 -0700
Subject: [PATCH 1244/1248] remove duplicated expected fails

---
 cime_config/testdefs/ExpectedTestFails.xml | 34 +++-------------------
 src/fates                                  |  2 +-
 2 files changed, 5 insertions(+), 31 deletions(-)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 7631addb80..9cfc3d864b 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -180,6 +180,10 @@
       <status>FAIL</status>
       <issue>#2454</issue>
     </phase>
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
   </test>
 
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
@@ -277,13 +281,6 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>#2325</issue>
-    </phase>
-  </test>
-
   <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
@@ -341,13 +338,6 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
     <phase name="RUN">
       <status>FAIL</status>
@@ -369,13 +359,6 @@
     </phase>
   </test>
   
-  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse">
-    <phase name="SHAREDLIB_BUILD">
-      <status>FAIL</status>
-      <issue>#2810</issue>
-    </phase>
-  </test>
-  
   <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
     <phase name="RUN">
       <status>FAIL</status>
@@ -391,15 +374,6 @@
     </phase>
   </test>
 
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-
-
 
   <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse">
     <phase name="SHAREDLIB_BUILD">
diff --git a/src/fates b/src/fates
index fb6ab8c2f7..bdb253fd92 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit fb6ab8c2f744fdebe42e5ab2881c0c34333180b7
+Subproject commit bdb253fd9262cbb721a3f2ef033e16d73c2cd77e

From 7148a3871682ae24c7f32b36432db8e4264d38f5 Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Wed, 13 Nov 2024 09:14:50 -0700
Subject: [PATCH 1245/1248] another izumi_nag fail

---
 cime_config/testdefs/ExpectedTestFails.xml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index 9cfc3d864b..007468cecc 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -289,6 +289,14 @@
   </test>
   
   <!-- izumi nag failures -->
+
+  <test name="SMS_D.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-ciso_soil_matrixcn_only">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+  
   <test name="ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate">
     <phase name="RUN">
       <status>FAIL</status>

From 836d4701d9acd340558167335c17969bd32df8dc Mon Sep 17 00:00:00 2001
From: Adrianna Foster <afoster@ucar.edu>
Date: Wed, 13 Nov 2024 09:54:08 -0700
Subject: [PATCH 1246/1248] changelog and fates tag

---
 .gitmodules   |  2 +-
 doc/ChangeLog | 58 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 src/fates     |  2 +-
 4 files changed, 61 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 1f6da08484..225f2f75ac 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.3_api.36.1.0
+fxtag = sci.1.79.3_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
diff --git a/doc/ChangeLog b/doc/ChangeLog
index c08a55bbd4..5a2a3c472e 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,62 @@
 ===============================================================
+Tag name: ctsm5.3.012
+Originator(s): afoster (Adrianna Foster,UCAR/TSS,303-497-1728)
+Date: Wed 13 Nov 2024 09:53:51 AM MST
+One-line Summary: update fates tag
+
+Purpose and description of changes
+----------------------------------
+
+Updates FATES tag to latest fates main (sci.1.79.3_api.37.0.0), and updates API to go
+along with latest FATES update to refactor it's fire equations
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+
+
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests:
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+Round-off differences for FATES compsets where fire is active.
+NLCOMP differences for some FATES compsets
+
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2782: Fates fuel refactor (https://github.com/ESCOMP/CTSM/pull/2782)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.011
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Mon Nov 11 17:55:57 MST 2024
diff --git a/doc/ChangeSum b/doc/ChangeSum
index daffdab145..87d5709a68 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.012  afoster 11/13/2024 update fates tag
        ctsm5.3.011 samrabin 11/11/2024 Improve handling of cold-start finidat
        ctsm5.3.010  afoster 11/09/2024 Merge b4b-dev
        ctsm5.3.009 samrabin 10/15/2024 Reduce outputs from matrixcnOn tests
diff --git a/src/fates b/src/fates
index bdb253fd92..e3e7d2cd86 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit bdb253fd9262cbb721a3f2ef033e16d73c2cd77e
+Subproject commit e3e7d2cd86a66f8ca0e8f6dc4a823246a2bdb95b

From 2018fe48dc047d7654fd2e815b1281a30bd7b0a1 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Thu, 21 Nov 2024 12:17:22 -0700
Subject: [PATCH 1247/1248] Squashed '.lib/git-fleximod/' changes from
 02e859950..50bd54c63

50bd54c63 Bump to 0.9.3
1e0c40a46 Merge pull request #66 from ESMCI/poetry_and_test_update
135770709 strip strip
e7f9a261c fix issue 65
b1568e724 update poetry certifi version and update tests failing due to mpi-serial update

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 50bd54c63e38c52e0bfc4a1d6bc6cb0eea6cf645
---
 git_fleximod/cli.py          | 38 ++++++++++++++++++++----------------
 git_fleximod/git_fleximod.py |  2 +-
 git_fleximod/submodule.py    |  2 +-
 poetry.lock                  |  6 +++---
 pyproject.toml               |  2 +-
 tbump.toml                   |  2 +-
 tests/conftest.py            |  4 ++--
 7 files changed, 30 insertions(+), 26 deletions(-)

diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index 208bc04684..ac9493cfc3 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -2,27 +2,31 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.9.2"
+__version__ = "0.9.3"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
     which contains a file called filename """
-    d = Path.cwd()
-    root = Path(d.root)
-    dirlist = []
-    dl = d
-    while dl != root:
-        dirlist.append(dl)
-        dl = dl.parent
-    dirlist.append(root)
-    dirlist.reverse()
-
-    for dl in dirlist:
-        attempt = dl / filename
-        if attempt.is_file():
-            return str(dl)
-    return None
-
+    try:
+        root = utils.execute_subprocess(["git","rev-parse", "--show-toplevel"],
+                                        output_to_caller=True ).rstrip()
+    except:
+        d = Path.cwd()
+        root = Path(d.root)
+        dirlist = []
+        dl = d
+        while dl != root:
+            dirlist.append(dl)
+            dl = dl.parent
+        dirlist.append(root)
+        dirlist.reverse()
+
+        for dl in dirlist:
+            attempt = dl / filename
+            if attempt.is_file():
+                return str(dl)
+        return None
+    return Path(root)
 
 def get_parser():
     description = """
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index 0851e9d095..13f35df959 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -342,7 +342,7 @@ def main():
         excludelist=excludelist,
     )
     if not gitmodules.sections():
-        sys.exit("No submodule components found")
+        sys.exit(f"No submodule components found, root_dir={root_dir}")
     retval = 0
     if action == "update":
         submodules_update(gitmodules, root_dir, fxrequired, force)
diff --git a/git_fleximod/submodule.py b/git_fleximod/submodule.py
index c939d54bc9..75d9dd4eb9 100644
--- a/git_fleximod/submodule.py
+++ b/git_fleximod/submodule.py
@@ -221,7 +221,7 @@ def sparse_checkout(self):
         if superroot:
             gitroot = superroot.strip()
         else:
-            gitroot = self.root_dir.strip()
+            gitroot = self.root_dir
         # Now need to move the .git dir to the submodule location
         rootdotgit = os.path.join(self.root_dir, ".git")
         while os.path.isfile(rootdotgit):
diff --git a/poetry.lock b/poetry.lock
index 3a74effcd1..ac82fb0d97 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -30,13 +30,13 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "certifi"
-version = "2024.6.2"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
-    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
diff --git a/pyproject.toml b/pyproject.toml
index 619cdabe3b..1d0419ad20 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.9.2"
+version = "0.9.3"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/tbump.toml b/tbump.toml
index 920ff0591c..b432206a54 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.9.2"
+current = "0.9.3"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before
diff --git a/tests/conftest.py b/tests/conftest.py
index 81edbe713e..1dd1b86f34 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -32,7 +32,7 @@ def logger():
      "submodule_name": "test_optional",
      "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0 (optional)",
+     "status3" : "test_optional not checked out, out of sync at tag MPIserial_2.5.1, expected tag is MPIserial_2.4.0 (optional)",
      "status4" : "test_optional at tag MPIserial_2.4.0",
      "gitmodules_content": """
      [submodule "test_optional"]
@@ -46,7 +46,7 @@ def logger():
      "submodule_name": "test_alwaysoptional",
      "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
      "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "out of sync at tag None, expected tag is e5cf35c",
+     "status3" : "out of sync at tag MPIserial_2.5.1, expected tag is e5cf35c",
      "status4" : "test_alwaysoptional at hash e5cf35c",
      "gitmodules_content": """
     [submodule "test_alwaysoptional"]

From 4ece589f055a775fa98b346fd07f322be7d0c985 Mon Sep 17 00:00:00 2001
From: Erik Kluzek <erik@ucar.edu>
Date: Tue, 26 Nov 2024 15:22:04 -0700
Subject: [PATCH 1248/1248] Update change files

---
 doc/ChangeLog | 99 +++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/ChangeSum |  1 +
 2 files changed, 100 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 5a2a3c472e..fc4ee9f376 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,103 @@
 ===============================================================
+Tag name: ctsm5.3.013
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Tue 26 Nov 2024 02:59:49 PM MST
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+Bring in latest b4b-dev branch to main CTSM development.
+
+- Update git-fleximod
+- Fix equation number in tech note
+- Implement urbanl and urbanc coszen filters
+- Make ALBGRD and ALBGRI active by default
+- Some adjustments to control pylint for the RXCROPMATURITY python tests
+- Run_sys_tests: Print test list in --verbose/--debug.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes #17 albgrd and albgri history fields depend on decomposition, for urban points
+   Fixes #747 In UrbanAlbedo: Create a filter for coszen>0 and operate over that
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   ALBGRD/ALBGRI are now active by default on the h0 files
+
+Changes to documentation: Fixed equation number
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing:
+    Testlist that will be run is now output when --verbose/--debug is given to run_sys_tests
+
+Testing summary: regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+  #2893 -- Merge b4b-dev
+  #2786 -- git fleximod
+  #2848 -- equation number in tech note
+  #2875 -- run_sys_tests log testlist for --verbose/--debug options
+  #2860 -- Remove num_solar and implement coszen filters in UrbanAlbedoMod.F90
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.012
 Originator(s): afoster (Adrianna Foster,UCAR/TSS,303-497-1728)
 Date: Wed 13 Nov 2024 09:53:51 AM MST
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 87d5709a68..85e347513b 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.013     erik 11/26/2024 Merge b4b-dev
        ctsm5.3.012  afoster 11/13/2024 update fates tag
        ctsm5.3.011 samrabin 11/11/2024 Improve handling of cold-start finidat
        ctsm5.3.010  afoster 11/09/2024 Merge b4b-dev