Merge pull request ESCOMP#2009 from glemieux/fates-drdt-decid-updates

FATES parameter file and test definition updates

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.65.3_api.25.4.0
+tag = sci.1.66.1_api.25.5.0
 required = True
 
 [externals_description]

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->

cime_config/testdefs/testlist_clm.xml

@@ -1569,7 +1569,7 @@
       <option name="comment">Want to keep a little single-point testing on cheyenne</option>
     </options>
   </test>
-  <test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/default--clm/NEON/NIWO">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/default--clm/NEON/NIWO">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
     </machines>
@@ -1579,7 +1579,7 @@
       <option name="comment"  >Add at least one test of a NEON site</option>
     </options>
   </test>
-  <test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51SpRs" testmods="clm/default--clm/NEON/TOOL">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51SpRs" testmods="clm/default--clm/NEON/TOOL">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
     </machines>
@@ -1589,7 +1589,7 @@
       <option name="comment"  >Add at least one test of a NEON site with SP</option>
     </options>
   </test>
-  <test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/NEON/MOAB--clm/PRISM">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/NEON/MOAB--clm/PRISM">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
     </machines>
@@ -1599,7 +1599,7 @@
       <option name="comment"  >Add at least one test of a NEON site with PRISM precipitation</option>
     </options>
   </test>
-  <test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesFireLightningPopDens--clm/NEON/FATES/NIWO">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesFireLightningPopDens--clm/NEON/FATES/NIWO">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
       <machine name="izumi"    compiler="nag"   category="fates"/>
@@ -1610,7 +1610,7 @@
       <option name="comment"  >Add at least one test of a FATES NEON site that needs lightning data</option>
     </options>
   </test>
-  <test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesPRISM--clm/NEON/FATES/YELL">
+  <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesPRISM--clm/NEON/FATES/YELL">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
       <machine name="izumi"    compiler="nag"   category="fates"/>

cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm

@@ -5,10 +5,8 @@ hist_empty_htapes = .true.
 hist_ndens = 1
 fates_spitfire_mode = 1
 hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
-'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD',
-'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF',
-'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF',
-'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN',
+'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD',
+'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON',
 'FATES_CANOPY_SPREAD', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI',
 'FATES_ROS','FATES_EFFECT_WSPEED', 'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY',
 'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF',

cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm

@@ -71,4 +71,7 @@ hist_fincl1       = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF',
 'FATES_CROOTMAINTAR_USTORY_SZ', 'FATES_FROOTMAINTAR_USTORY_SZ',
 'FATES_GROWAR_USTORY_SZ', 'FATES_MAINTAR_USTORY_SZ', 'FATES_VEGC_SZPF',
 'FATES_LEAFC_SZPF', 'FATES_FROOTC_SZPF', 'FATES_SAPWOODC_SZPF',
-'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF'
+'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF', 'FATES_DROUGHT_STATUS_PF',
+'FATES_DAYSINCE_DROUGHTLEAFOFF_PF', 'FATES_DAYSINCE_DROUGHTLEAFON_PF',
+'FATES_MEANLIQVOL_DROUGHTPHEN_PF', 'FATES_MEANSMP_DROUGHTPHEN_PF',
+'FATES_ELONG_FACTOR_PF'

cime_config/usermods_dirs/fates_sp/user_nl_clm

@@ -8,9 +8,9 @@ use_fates_fixed_biogeog = .true.
 use_fates_nocomp = .true.
 hist_ndens = 1
 ! Turn off a list of fields that are not needed for FATES-SP mode
-hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS',
-              'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF',
-              'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN', 'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF',
+hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS',
+              'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON',
+              'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF',
               'FATES_STOREC_PF', 'FATES_RECRUITMENT_PF', 'FATES_MORTALITY_PF', 'FATES_PATCHAREA_AP', 'FATES_LAI_AP',
               'FATES_CANOPYAREA_AP', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI', 'FATES_ROS', 'FATES_EFFECT_WSPEED',
               'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY', 'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF',

doc/ChangeLog

@@ -1,4 +1,97 @@
 ===============================================================
+Tag name: ctsm5.1.dev130
+Originator(s): glemieux (Greg Lemieux,LBL/NGEET,510-486-5049)
+Date: Sun Jul  9 23:24:29 MDT 2023
+One-line Summary: FATES parameter file and test definition update
+
+Purpose and description of changes
+----------------------------------
+
+This tag incorporates updates to the FATES parameter file and test
+definitions to be consistent with updates to the drought deciduous
+phenology model in FATES.  This also updates the external FATES
+pointer to the tag associated with the drought deciduous phenology
+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
+------------------------
+
+CTSM issues fixed (include CTSM Issue #):
+   Fixes #2043 -- Five izumi NEON tests fail (for me) because the testnames include L10d instead of Ld10
+
+Known bugs found since the previous tag (include issue #):
+   #2049 -- Use of 0.01_r8 as a magic number
+   #2042 -- Issue running SystemTests due to "conda activate" error
+   #2039 -- Conditional for NEON usermods is too broad
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+
+   FATES parameter file default updated to fates_params_api.25.5.0_12pft_c230628.nc
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  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
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES for FATES tests only
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: FATES
+    - what platforms/compilers: ALL
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+
+      See FATES #958 for discussion.  The update increased the dimensions of
+      some FATES history output from site-level to pft-level.  As such, these
+      have been removed from some test cases to keep the test light weight and
+      added to the AllVars test to maintain coverage.
+
+      Note that this FATES update also incorporates a number of additional science updates
+      since the previous tag.
+
+Other details
+-------------
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates
+  fates: sci.1.65.3_api.25.4.0 -> fates-sci.1.66.0_api.25.5.0
+
+Pull Requests that document the changes (include PR ids):
+  https://github.com/ESCOMP/ctsm/pull/2009
+  https://github.com/NGEET/fates/pull/958
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev129
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Thu Jun 22 01:21:56 MDT 2023
@@ -329,7 +422,7 @@ https://github.com/ESCOMP/CTSM/pull/2005
 ===============================================================
 Tag name: ctsm5.1.dev125
 Originator(s): jpalex (John Alex)
-Date: Wed May 17 08:56:41 MDT 2023
+Date: Sun Jul  9 21:04:13 MDT 2023
 One-line Summary: Added cache for clock step_size in clm_time_manager.F90
 
 Purpose and description of changes

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update
     ctsm5.1.dev129     erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml
     ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision
     ctsm5.1.dev127    sacks 05/19/2023 Fix nuopc cplhist test

src/main/clm_driver.F90

@@ -1151,7 +1151,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
                   atm2lnd_inst, soilstate_inst, temperature_inst, active_layer_inst, &
                   water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, &
                   water_inst%wateratm2lndbulk_inst, canopystate_inst, soilbiogeochem_carbonflux_inst, &
-                  frictionvel_inst)
+                  frictionvel_inst, soil_water_retention_curve)
 
              ! TODO(wjs, 2016-04-01) I think this setFilters call should be replaced by a
              ! call to reweight_wrapup, if it's needed at all.

src/utils/clmfates_interfaceMod.F90

@@ -97,6 +97,7 @@ module CLMFatesInterfaceMod
                                   get_clump_bounds
    use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, decomp_method
    use SoilBiogeochemDecompCascadeConType , only : no_soil_decomp, century_decomp
+   use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type
    use GridCellType      , only : grc
    use ColumnType        , only : col
    use LandunitType      , only : lun
@@ -808,7 +809,8 @@ end subroutine check_hlm_active
    subroutine dynamics_driv(this, nc, bounds_clump,      &
          atm2lnd_inst, soilstate_inst, temperature_inst, active_layer_inst, &
          waterstatebulk_inst, waterdiagnosticbulk_inst, wateratm2lndbulk_inst, &
-         canopystate_inst, soilbiogeochem_carbonflux_inst, frictionvel_inst)
+         canopystate_inst, soilbiogeochem_carbonflux_inst, frictionvel_inst, &
+         soil_water_retention_curve)
 
       ! This wrapper is called daily from clm_driver
       ! This wrapper calls ed_driver, which is the daily dynamics component of FATES
@@ -834,11 +836,13 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
       type(canopystate_type)  , intent(inout)        :: canopystate_inst
       type(soilbiogeochem_carbonflux_type), intent(inout) :: soilbiogeochem_carbonflux_inst
       type(frictionvel_type)  , intent(inout)        :: frictionvel_inst
+      class(soil_water_retention_curve_type), intent(in) :: soil_water_retention_curve
 
       ! !LOCAL VARIABLES:
       integer  :: s                        ! site index
       integer  :: g                        ! grid-cell index (HLM)
       integer  :: c                        ! column index (HLM)
+      integer  :: j                        ! Soil layer index
       integer  :: ifp                      ! patch index ft
       integer  :: p                        ! HLM patch index
       integer  :: nlevsoil                 ! number of soil layers at the site
@@ -849,6 +853,7 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
       integer  :: ier
       integer  :: begg,endg
       real(r8) :: harvest_rates(bounds_clump%begg:bounds_clump%endg,num_harvest_inst)
+      real(r8) :: s_node, smp_node         ! local for relative water content and potential
       logical  :: after_start_of_harvest_ts
       integer  :: iharv
       !-----------------------------------------------------------------------
@@ -933,6 +938,24 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
          this%fates(nc)%bc_in(s)%max_rooting_depth_index_col = &
               min(nlevsoil, active_layer_inst%altmax_lastyear_indx_col(c))
 
+         nlevsoil = this%fates(nc)%bc_in(s)%nlevsoil
+         do j = 1,nlevsoil
+            this%fates(nc)%bc_in(s)%tempk_sl(j) = temperature_inst%t_soisno_col(c,j)
+         end do
+
+         call get_active_suction_layers(this%fates(nc)%nsites, &
+             this%fates(nc)%sites,  &
+             this%fates(nc)%bc_in,  &
+             this%fates(nc)%bc_out)
+
+         do j = 1,nlevsoil
+            if(this%fates(nc)%bc_out(s)%active_suction_sl(j)) then
+               s_node = max(waterstatebulk_inst%h2osoi_vol_col(c,j)/soilstate_inst%eff_porosity_col(c,j) ,0.01_r8)
+               call soil_water_retention_curve%soil_suction(c,j,s_node, soilstate_inst, smp_node)
+               this%fates(nc)%bc_in(s)%smp_sl(j)           = smp_node
+            end if
+         end do
+
 
          do ifp = 1, this%fates(nc)%sites(s)%youngest_patch%patchno !for vegetated patches
             ! Mapping between  IFP space (1,2,3) and HLM P space (looping by IFP)
@@ -1998,8 +2021,6 @@ subroutine wrap_btran(this,nc,fn,filterc,soilstate_inst, &
       !
       ! ---------------------------------------------------------------------------------
 
-      use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type
-
       implicit none
 
       ! Arguments