Merge remote-tracking branch 'escomp/master' into new_params_file

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.68.2_api.30.0.0
+tag = sci.1.68.2_api.31.0.0
 required = True
 
 [externals_description]

cime_config/testdefs/ExpectedTestFails.xml

@@ -59,26 +59,6 @@
 
   <!-- fates test suite failures -->
 
-  <test name="ERS_Lm12.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesFireLightningPopDens">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>#667</issue>
-    </phase>
-  </test>
-
-    <test name="ERS_Lm13.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-FatesColdNoComp">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>FATES#897</issue>
-    </phase>
-  </test>
-
-  <test name="ERS_Lm13.f10_f10_mg37.I2000Clm50Fates.cheyenne_gnu.clm-FatesCold">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>FATES#897</issue>
-    </phase>
-  </test>
 
     <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
     <phase name="COMPARE_base_rest">
@@ -103,7 +83,7 @@
 
   <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdPRT2">
     <phase name="RUN">
-      <status>FAIL</status>
+      <status>PEND</status>
       <issue>FATES#983</issue>
       <comment>This job should time out on izumi, seems to be hanging on history output.</comment>
     </phase>

cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands

@@ -39,3 +39,5 @@ fi
 
 # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way)
 ./xmlchange PIO_TYPENAME=netcdf
+
+./xmlchange NEONVERSION="v2"

cime_config/usermods_dirs/NEON/defaults/shell_commands

@@ -43,3 +43,5 @@ fi
 
 # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way)
 ./xmlchange PIO_TYPENAME=netcdf
+
+./xmlchange NEONVERSION="v2"

doc/ChangeLog

@@ -1,4 +1,69 @@
 ===============================================================
+Tag name: ctsm5.1.dev153
+Originator(s): afoster (Adrianna Foster) and johnpaulalex (John Paul Alex)
+Date: Fri Nov 17 11:53:14 MST 2023
+One-line Summary: Call new FATES-side FatesReadParameters
+
+Purpose and description of changes
+----------------------------------
+
+Have CTSM use the new code path in FATES that allows passing in a `fates_param_reader_type`, which does the actual work reading the parameter files, in lieu of calling CTSM methods.
+
+Also updated NEON usermods to use version 2 data by default, rather than latest.
+
+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.)
+
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Bugs fixed or introduced
+------------------------
+
+Some progress towards CTSM#2006 and FATES#1076
+
+Testing summary:
+----------------
+
+  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
+
+    fates baseline: `fates-sci.1.68.2_api.31.0.0-ctsm5.1.dev153`
+
+
+Answer changes
+--------------
+
+None
+
+
+Other details
+--------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates
+
+Pull Requests that document the changes (include PR ids): 
+https://github.com/NGEET/fates/pull/1096
+https://github.com/ESCOMP/CTSM/pull/2198
+
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev152
 Originator(s): multiple (tking (Teagan King); slevis (Sam Levis); AdrienDams (Adrien Damseaux); afoster (Adrianna Foster); samrabin (Sam Rabin); ekluzek (Erik Kluzek); wwieder (Will Wieder); sacks (Bill Sacks); a few others listed below)
 Date: Tue Nov 14 17:09:43 MST 2023

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev153  afoster 11/17/2023 Call new FATES-side FatesReadParameters
     ctsm5.1.dev152 multiple 11/14/2023 Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors
     ctsm5.1.dev151   rgknox 11/11/2023 Fixes to FATES long run restarts
     ctsm5.1.dev150   rgknox 11/06/2023 FATES API fix to support future fates npp-fixation coupling, and urgent coupling fixes with E3SM.

src/utils/clmfates_interfaceMod.F90

@@ -7,11 +7,9 @@ module CLMFatesInterfaceMod
    !
    ! This is also the only location where CLM code is allowed to see FATES memory
    ! structures.
-   ! The routines here, that call FATES library routines, will not pass any types defined
-   ! by the driving land model (HLM).
-   !
-   ! either native type arrays (int,real,log, etc) or packed into fates boundary condition
-   ! structures.
+   ! The routines here, that call FATES library routines, cannot pass most types defined
+   ! by the driving land model (HLM), only native type arrays (int,real,log, etc), implementations
+   ! of fates abstract classes, and references into fates boundary condition structures.
    !
    ! Note that CLM/ALM does use Shared Memory Parallelism (SMP), where processes such as
    ! the update of state variables are forked.  However, IO is not assumed to be
@@ -112,6 +110,7 @@ module CLMFatesInterfaceMod
    use shr_log_mod       , only : errMsg => shr_log_errMsg
    use clm_varcon        , only : dzsoi_decomp
    use FuncPedotransferMod, only: get_ipedof
+   use CLMFatesParamInterfaceMod, only: fates_param_reader_ctsm_impl
 !   use SoilWaterPlantSinkMod, only : Compute_EffecRootFrac_And_VertTranSink_Default
 
    ! Used FATES Modules
@@ -128,6 +127,10 @@ module CLMFatesInterfaceMod
    use FatesInterfaceMod     , only : set_fates_ctrlparms
    use FatesInterfaceMod     , only : UpdateFatesRMeansTStep
    use FatesInterfaceMod     , only : InitTimeAveragingGlobals
+
+   use FatesParametersInterface, only : fates_param_reader_type
+   use FatesParametersInterface, only : fates_parameters_type
+
    use FatesInterfaceMod     , only : DetermineGridCellNeighbors
 
    use FatesHistoryInterfaceMod, only : fates_hist
@@ -283,6 +286,7 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches)
      integer                                        :: pass_sp
      integer                                        :: pass_masterproc
      logical                                        :: verbose_output
+     type(fates_param_reader_ctsm_impl)             :: var_reader
 
      call t_startf('fates_globals1')
 
@@ -326,6 +330,7 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches)
 
      end if
 
+
      ! The following call reads in the parameter file
      ! and then uses that to determine the number of patches
      ! FATES requires. We pass that to CLM here
@@ -334,7 +339,7 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches)
      ! and allocations on the FATES side, which require
      ! some allocations from CLM (like soil layering)
 
-     call SetFatesGlobalElements1(use_fates,surf_numpft,surf_numcft)
+     call SetFatesGlobalElements1(use_fates,surf_numpft,surf_numcft,var_reader)
 
      maxsoil_patches = fates_maxPatchesPerSite
 
@@ -3590,4 +3595,6 @@ subroutine GetAndSetTime()
 
  end subroutine GetAndSetTime
 
+ !-----------------------------------------------------------------------
+
 end module CLMFatesInterfaceMod

src/utils/clmfates_paraminterfaceMod.F90

@@ -5,17 +5,30 @@ module CLMFatesParamInterfaceMod
   use shr_kind_mod,             only : r8 => shr_kind_r8, SHR_KIND_CL
   use FatesGlobals,             only : fates_log
   use FatesParametersInterface, only : fates_parameters_type
+  use FatesParametersInterface, only : fates_param_reader_type
   use EDParamsMod,              only : FatesRegisterParams, FatesReceiveParams
   use SFParamsMod,              only : SpitFireRegisterParams, SpitFireReceiveParams
   use PRTInitParamsFATESMod,    only : PRTRegisterParams, PRTReceiveParams
   use FatesSynchronizedParamsMod, only : FatesSynchronizedParamsInst
 
   implicit none
+   public :: fates_param_reader_ctsm_impl
+   !
+   type, extends(fates_param_reader_type) :: fates_param_reader_ctsm_impl
+      private
 
-  ! NOTE(bja, 2017-01) these methods can NOT be part of the clmi-fates
-  ! nterface type because they are called before the instance is
+      ! !PRIVATE MEMBER DATA:
+
+    contains
+      ! !PUBLIC MEMBER FUNCTIONS:
+      procedure, public :: Read ! Read params from disk
+
+   end type fates_param_reader_ctsm_impl
+
+
+  ! NOTE(bja, 2017-01) these methods can NOT be part of the clm-fates
+  ! interface type because they are called before the instance is
   ! initialized.
-  public :: FatesReadParameters
   public :: FatesReadPFTs
   private :: ParametersFromNetCDF
   private :: SetParameterDimensions
@@ -28,44 +41,6 @@ module CLMFatesParamInterfaceMod
 
 contains
 
- !-----------------------------------------------------------------------
- subroutine FatesReadParameters()
-  use clm_varctl, only : use_fates, paramfile, fates_paramfile
-  use spmdMod, only : masterproc
-
-   implicit none
-
-   character(len=32)  :: subname = 'FatesReadParameters'
-   class(fates_parameters_type), allocatable :: fates_params
-   logical :: is_host_file
-
-    if (masterproc) then
-      write(fates_log(), *) 'clmfates_interfaceMod.F90::'//trim(subname)//' :: CLM reading ED/FATES '//' parameters '
-    end if
-
-    allocate(fates_params)
-    call fates_params%Init()   ! fates_params class, in FatesParameterInterfaceMod
-    call FatesRegisterParams(fates_params)  !EDParamsMod, only operates on fates_params class
-    call SpitFireRegisterParams(fates_params) !SpitFire Mod, only operates of fates_params class
-    call PRTRegisterParams(fates_params)     ! PRT mod, only operates on fates_params class
-    call FatesSynchronizedParamsInst%RegisterParams(fates_params) !Synchronized params class in Synchronized params mod, only operates on fates_params class
-
-    is_host_file = .false.
-    call ParametersFromNetCDF(fates_paramfile, is_host_file, fates_params)
-
-    is_host_file = .true.
-    call ParametersFromNetCDF(paramfile, is_host_file, fates_params)
-
-    call FatesReceiveParams(fates_params)
-    call SpitFireReceiveParams(fates_params)
-    call PRTReceiveParams(fates_params)
-    call FatesSynchronizedParamsInst%ReceiveParams(fates_params)
-
-    call fates_params%Destroy()
-    deallocate(fates_params)
-
- end subroutine FatesReadParameters
-
  !-----------------------------------------------------------------------
  subroutine FatesReadPFTs()
 
@@ -238,4 +213,23 @@ subroutine ParametersFromNetCDF(filename, is_host_file, fates_params)
  end subroutine ParametersFromNetCDF
  !-----------------------------------------------------------------------
 
+ subroutine Read(this, fates_params )
+    !
+    ! !DESCRIPTION:
+    ! Read 'fates_params' parameters from storage.
+    !
+    ! USES
+    use clm_varctl, only : fname_len, paramfile, fates_paramfile
+    ! !ARGUMENTS:
+    class(fates_param_reader_ctsm_impl) :: this
+    class(fates_parameters_type), intent(inout) :: fates_params
+    !-----------------------------------------------------------------------
+    logical :: is_host_file = .false.
+
+    call ParametersFromNetCDF(fates_paramfile, is_host_file, fates_params)
+
+ end subroutine Read
+
+ !-----------------------------------------------------------------------
+
 end module CLMFatesParamInterfaceMod