Merge pull request ESCOMP#1962 from ckoven/modinitsoilwater

change soil moisture initialization logic for FATES configurations

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.61.0_api.25.0.0
+tag = sci.1.65.3_api.25.4.0
 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.25.0.0_12pft_c221128.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->

cime_config/testdefs/ExpectedTestFails.xml

@@ -51,13 +51,6 @@
     </phase>
   </test>
 
-  <test name="FUNITCTSM_P1x1.f10_f10_mg37.I2000Clm50Sp.cheyenne_intel">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#1972</issue>
-    </phase>
-  </test>
-
   <!-- fates test suite failures -->
 
   <test name="ERS_Lm12.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesFireLightningPopDens">

cime_config/testdefs/testlist_clm.xml

@@ -1876,7 +1876,7 @@
       <machine name="cheyenne" compiler="gnu" category="fates"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:50:00</option>
     </options>
   </test>
   <test name="ERS_Lm13" grid="f45_f45_mg37" compset="I2000Clm50Fates" testmods="clm/FatesColdNoComp">

doc/.ChangeLog_template

@@ -121,15 +121,10 @@ infrastructure should be run when appropriate, as described below.
 
     clm_pymods test suite on cheyenne - 
 
-  regular tests:
-      - aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing
-      - Fortran unit tests on cheyenne (until https://github.com/ESCOMP/CTSM/issues/1972 is resolved): from src, run:
-          ../cime/scripts/fortran_unit_testing/run_tests.py --build-dir `mktemp -d --tmpdir=. unit_tests.XXXXXXXX`
-
-    aux_clm on cheyenne ------------
-    aux_clm on izumi ---------------
-    Fortran unit tests on cheyenne -
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
+    cheyenne ----
+    izumi -------
 
   fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
     cheyenne ----

doc/ChangeLog

@@ -1,4 +1,109 @@
 ===============================================================
+Tag name: ctsm5.1.dev121
+Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049)
+Date: Wed Apr  5 13:34:09 MDT 2023
+One-line Summary: Changes soil moisture initialization logic for FATES
+
+Purpose and description of changes
+----------------------------------
+
+This PR changes the logic for soil moisture initialization to initialize
+with wetter soils (75% of saturated water content, as opposed to 15% of
+absolute water content) for all FATES configurations. The rationale for
+this is that in FATES-nocomp simulations, Jessica Needham was finding very
+high initial mortality rates in some seasonal tropical forest regions which
+she traced it back to the initial soil moisture killing off plants before the
+ecosystem could get established.
+
+This also updates the fates externals pointer to the latest tag which includes
+a number of science updates since the last tag update and updates the the
+default parameter file.
+
+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
+------------------------
+
+Externals issues fixed (include issue #):
+    Partially addresses FATES#994 -- Bare ground establishment problem and increased soil moisture
+
+Known bugs found since the previous tag (include issue #):
+    #1979 -- Need to loosen tolerance on near-zero truncation of h2osoi_ice in UpdateState_TopLayerFluxes
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   fates_paramfile updated to fates_params_api.25.4.0_12pft_c230327.nc
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+    This changes the starting level for a COLD start of soil moisture for ALL FATES cases to a much
+    higher value than for non-FATES. In the long run we'd like to have these the same and/or
+    have the value changable on the namelist.
+
+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
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+  FATES tests run against fates-sci.1.65.3_api.25.4.0-ctsm5.1.dev120 baseline
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+   Changes answers in fates suite for all non-hydro fates tests since the soil
+   moisture initialization matches that of fates hydro now.  Changes answer
+   for all fates testmods in the aux_clm suite as the science tag has iterated
+   forward by 4 minor version updates.  All diffs accounted for with prior fates
+   suite tests.
+
+Other details
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+
+- FATES: sci.1.61.0_api.25.0.0 -> sci.1.65.3_api.25.4.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+  https://github.com/ESCOMP/CTSM/pull/1962 -- Cold start moisture for FATES increased
+  https://github.com/ESCOMP/CTSM/pull/1978 -- revert some commits now that FUNITCTSM works again
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev120
 Originator(s): sacks (Bill Sacks)
 Date: Sat Mar 25 17:49:27 MDT 2023

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev121 glemieux 04/05/2023 Changes soil moisture initialization logic for FATES
     ctsm5.1.dev120    sacks 03/25/2023 Update externals and minor fixes
     ctsm5.1.dev119   slevis 03/16/2023 Allow gross unrepresented land use transition (PR #309)
     ctsm5.1.dev118   slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test

src/biogeophys/WaterStateType.F90

@@ -14,7 +14,7 @@ module WaterStateType
   use decompMod      , only : bounds_type
   use decompMod      , only : subgrid_level_patch, subgrid_level_column, subgrid_level_gridcell
   use clm_varctl     , only : use_bedrock, iulog
-  use clm_varctl     , only : use_fates_planthydro
+  use clm_varctl     , only : use_fates
   use clm_varpar     , only : nlevgrnd, nlevsoi, nlevurb, nlevmaxurbgrnd, nlevsno   
   use clm_varcon     , only : spval
   use LandunitType   , only : lun                
@@ -348,7 +348,7 @@ subroutine InitCold(this, bounds, &
                   if (j > nbedrock) then
                      this%h2osoi_vol_col(c,j) = 0.0_r8
                   else
-                     if(use_fates_planthydro) then
+                     if(use_fates) then
                          this%h2osoi_vol_col(c,j) = 0.75_r8*watsat_col(c,j)*ratio
                      else
                          this%h2osoi_vol_col(c,j) = 0.15_r8*ratio