Merge remote-tracking branch 'glemieux/fates-spmode-filterfix'

This PR includes a number of minor fixes and updates associated with FATES.
A duplicate filter for all soils that was introduced during the the initial
implementation of FATES-SP mode is removed.  A small set of FATES history
variable names have been updated necessitating an update to the testmod
user namelists.  The ccs_config and cime externals have been updated to
include the FATES development workstation, lobata.  The cime tag update
is necessary to include a fix enabling support for module initilization
on certain linux distributions (ESMCI/cime#4260).
Finally, a minor fix was included to the initialization of the fates_levcdam
dimension that was introduced with the last fates api update.

Fixes #1794

Fixes #1488

Externals.cfg

@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.36
+tag = ccs_config_cesm0.0.38
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,7 +44,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.27
+tag = cime6.0.40
 required = True
 
 [cmeps]

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.57.4_api.24.0.0
+tag = sci.1.58.1_api.24.1.0
 required = True
 
 [externals_description]

cime_config/testdefs/ExpectedTestFails.xml

@@ -39,20 +39,6 @@
 
   <!-- fates test suite failures -->
 
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdDefHydro">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>NGEET/fates#795</issue>
-    </phase>
-  </test>
-
-  <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdDefHydro">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#1525</issue>
-    </phase>
-  </test>
-
   <test name="ERS_D_Lm12.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesFireLightningPopDens">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>

cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm

@@ -23,9 +23,9 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX',
 'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP',
 'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY',
-'FATES_AUTORESP_CANOPY', 'FATES_GPP_UNDERSTORY', 'FATES_AUTORESP_UNDERSTORY',
+'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY',
 'FATES_DEMOTION_CARBONFLUX', 'FATES_PROMOTION_CARBONFLUX',
-'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_UNDERSTORY',
+'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY',
 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
 'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',

cime_config/usermods_dirs/fates_sp/user_nl_clm

@@ -23,8 +23,8 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FA
               'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S', 'FATES_DISTURBANCE_RATE_S2S',
               'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
               'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY',
-              'FATES_GPP_UNDERSTORY', 'FATES_AUTORESP_UNDERSTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX',
-              'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_UNDERSTORY', 
+              'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX',
+              'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY', 
               'FATES_DDBH_CANOPY_SZ', 'FATES_DDBH_USTORY_SZ', 'FATES_BASALAREA_SZ',
               'FATES_VEGC_ABOVEGROUND_SZ', 'FATES_LAI_CANOPY_SZ', 'FATES_MORTALITY_CANOPY_SZ', 'FATES_NPLANT_USTORY_SZ',
               'FATES_LAI_USTORY_SZ', 'FATES_NPLANT_SZ', 'FATES_NPLANT_AC', 'FATES_MORTALITY_BACKGROUND_SZ',

doc/ChangeLog

@@ -1,4 +1,100 @@
 ===============================================================
+Tag name: ctsm5.1.dev104
+Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049)
+Date: Mon Jul 18 15:45:00 MDT 2022
+One-line Summary: Update to fates history names and machine configuration
+
+Purpose and description of changes
+----------------------------------
+
+This PR includes a number of minor fixes and updates associated with FATES.
+A duplicate filter for all soils that was introduced during the the initial
+implementation of FATES-SP mode is removed.  A small set of FATES history
+variable names have been updated necessitating an update to the testmod
+user namelists.  The ccs_config and cime externals have been updated to
+include the FATES development workstation, lobata.  The cime tag update
+is necessary to include a fix enabling support for module initilization
+on certain linux distributions (https://github.com/ESMCI/cime/issues/4260).
+Finally, a minor fix was included to the initialization of the fates_levcdam
+dimension that was introduced with the last fates api update.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+CTSM issues fixed (include CTSM Issue #):
+    Fixes #1794 -- Get lobata in ccs_config and working with NUOPC
+    Fixes #1488 -- Remove all_soil_patches filter and use and filter_inactive_and_active(nc)%soilp in it's place
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  tools-tests (test/tools) (if tools have been changed):
+
+    cheyenne - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    cheyenne - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    cheyenne ---- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+  FATES tests run against fates-sci.1.58.0_api.24.0.0-ctsm5.1.dev103 baseline
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+    Changes answers due to a correction only for a subset of fates testmods for the fates_levcdam dimension.
+    NLCOMP and FIELDLIST differences only due to expected ccs_config and fates updates.
+
+Other details
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+
+- CIME: cime6.0.27 -> cime6.0.40
+- ccs_config: ccs_config_cesm0.0.36 -> ccs_config_cesm0.0.38
+- FATES: sci.1.58.0_api.24.0.0 -> sci.1.58.1_api.24.1.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+https://github.com/ESCOMP/CTSM/pull/1515
+https://github.com/NGEET/fates/pull/854
+
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev103
 Originator(s): sacks (Bill Sacks)
 Date: Tue Jul 12 22:27:30 MDT 2022

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev104 glemieux 07/15/2022 Update to FATES history names and machine configuration
     ctsm5.1.dev103    sacks 07/12/2022 Fix accumulation variables when changing model time step
     ctsm5.1.dev102    sacks 07/11/2022 Fix LILAC interface to PIO
     ctsm5.1.dev101 samrabin 07/11/2022 Fix winter wheat sowing window bugs

src/biogeochem/SatellitePhenologyMod.F90

@@ -105,8 +105,8 @@ subroutine SatellitePhenology(bounds, num_filter, filter, &
     !
     ! !ARGUMENTS:
     type(bounds_type)              , intent(in)    :: bounds
-    integer                        , intent(in)    :: num_filter                        ! number of column non-lake points in patch filter
-    integer                        , intent(in)    :: filter(bounds%endp-bounds%begp+1) ! patch filter for non-lake points
+    integer                        , intent(in)    :: num_filter                        ! number of column points in patch filter
+    integer                        , intent(in)    :: filter(bounds%endp-bounds%begp+1) ! patch filter points
     type(waterdiagnosticbulk_type) , intent(in)    :: waterdiagnosticbulk_inst
     type(canopystate_type)         , intent(inout) :: canopystate_inst
     !

src/main/clm_driver.F90

@@ -1036,9 +1036,17 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
 
        if (use_fates_sp.and.doalb) then
           call t_startf('SatellitePhenology')
-          call SatellitePhenology(bounds_clump, filter(nc)%num_all_soil_patches, filter(nc)%all_soil_patches, &
+
+          ! FATES satellite phenology mode needs to include all active and inactive patch-level soil
+          ! filters due to the translation between the hlm pfts and the fates pfts.
+          ! E.g. in FATES, an active PFT vector of 1, 0, 0, 0, 1, 0, 1, 0 would be mapped into
+          ! the host land model as 1, 1, 1, 0, 0, 0, 0.  As such, the 'active' filter would only
+          ! use the first three points, which would incorrectly represent the interpolated values.
+          call SatellitePhenology(bounds_clump, &
+               filter_inactive_and_active(nc)%num_soilp, filter_inactive_and_active(nc)%soilp, &
                water_inst%waterdiagnosticbulk_inst, canopystate_inst)
           call t_stopf('SatellitePhenology')
+
        end if
 
        ! Dry Deposition of chemical tracers (Wesely (1998) parameterizaion)

src/main/clm_initializeMod.F90

@@ -209,7 +209,7 @@ subroutine initialize2(ni,nj)
     ! Get processor bounds for gridcells
     call get_proc_bounds(bounds_proc)
     begg = bounds_proc%begg; endg = bounds_proc%endg
-    
+
     ! Initialize glc behavior
     call glc_behavior%Init(begg, endg, NLFilename)
 
@@ -661,8 +661,16 @@ subroutine initialize2(ni,nj)
           !$OMP PARALLEL DO PRIVATE (nc, bounds_clump)
           do nc = 1,nclumps
              call get_clump_bounds(nc, bounds_clump)
-             call SatellitePhenology(bounds_clump, filter(nc)%num_nolakep, filter(nc)%nolakep, &
+
+             ! FATES satellite phenology mode needs to include all active and inactive patch-level soil
+             ! filters due to the translation between the hlm pfts and the fates pfts.
+             ! E.g. in FATES, an active PFT vector of 1, 0, 0, 0, 1, 0, 1, 0 would be mapped into
+             ! the host land model as 1, 1, 1, 0, 0, 0, 0.  As such, the 'active' filter would only
+             ! use the first three points, which would incorrectly represent the interpolated values.
+             call SatellitePhenology(bounds_clump, &
+                  filter_inactive_and_active(nc)%num_soilp, filter_inactive_and_active(nc)%soilp, &
                   water_inst%waterdiagnosticbulk_inst, canopystate_inst)
+
           end do
           !$OMP END PARALLEL DO
        end if

src/main/filterMod.F90

@@ -204,7 +204,6 @@ subroutine allocFiltersOneGroup(this_filter)
        allocate(this_filter(nc)%lakep(bounds%endp-bounds%begp+1))
        allocate(this_filter(nc)%nolakep(bounds%endp-bounds%begp+1))
        allocate(this_filter(nc)%nolakeurbanp(bounds%endp-bounds%begp+1))
-       allocate(this_filter(nc)%all_soil_patches(bounds%endp-bounds%begp+1))
 
        allocate(this_filter(nc)%lakec(bounds%endc-bounds%begc+1))
        allocate(this_filter(nc)%nolakec(bounds%endc-bounds%begc+1))
@@ -320,7 +319,6 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio
     integer :: fnl,fnlu    ! non-lake filter index
     integer :: fs          ! soil filter index
     integer :: f, fn       ! general indices
-    integer :: f_asp       ! all soil patches index
     integer :: g           !gridcell index
     !------------------------------------------------------------------------
 
@@ -441,25 +439,6 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio
           end if
        end if
     end do
-
-    ! thise filter will include all soil P's irrespective of whether or not they are active.
-    ! its purpose is to allow the TLAI, TSAI and HTOP drivers to be interpolated when in
-    ! FATES-SP mode.
-    ! e.g. in FATES, an active PFT vector of 1, 0, 0, 0, 1, 0, 1, 0
-    ! would be mapped inot the host land model as
-    ! 1, 1, 1, 0, 0, 0, 0
-    ! thus the 'active' filter will only use the first three points.
-    ! this filter will stay on for all the
-    f_asp = 0
-    do p = bounds%begp,bounds%endp
-       l =patch%landunit(p)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          f_asp = f_asp +1
-          this_filter(nc)%all_soil_patches(f_asp) = p
-       end if
-    enddo
-    this_filter(nc)%num_all_soil_patches = f_asp
-
     this_filter(nc)%num_pcropp   = fl
     this_filter(nc)%num_soilnopcropp = fnl   ! This wasn't being set before...
 

src/main/histFileMod.F90

@@ -2997,6 +2997,7 @@ subroutine htape_timeconst(t, mode)
     use FatesInterfaceTypesMod, only : fates_hdim_agmap_levagepft
     use FatesInterfaceTypesMod, only : fates_hdim_pftmap_levagepft
     use FatesInterfaceTypesMod, only : fates_hdim_levfuel
+    use FatesInterfaceTypesMod, only : fates_hdim_levdamage
     use FatesInterfaceTypesMod, only : fates_hdim_levcwdsc
     use FatesInterfaceTypesMod, only : fates_hdim_levcan
     use FatesInterfaceTypesMod, only : fates_hdim_levleaf
@@ -3175,6 +3176,7 @@ subroutine htape_timeconst(t, mode)
              call ncd_io(varname='fates_levheight',data=fates_hdim_levheight, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levpft',data=fates_hdim_levpft, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levfuel',data=fates_hdim_levfuel, ncid=nfid(t), flag='write')
+             call ncd_io(varname='fates_levcdam',data=fates_hdim_levdamage, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levcwdsc',data=fates_hdim_levcwdsc, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levcan',data=fates_hdim_levcan, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levleaf',data=fates_hdim_levleaf, ncid=nfid(t), flag='write')