Merge remote-tracking branch 'escomp/master' into ctsm5.2_to_5.1.dev166

ekluzek · Feb 2, 2024 · e4b769f · e4b769f
2 parents 1e0bca4 + e611238
commit e4b769f
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -21,6 +21,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630
 025d5e7c2e80263717fb029101d65cbbf261c3c4
 a9d96219902cf609636886c7073a84407f450d9a
 d866510188d26d51bcd6d37239283db690af7e82
+0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml
@@ -0,0 +1,23 @@
+name: Auto Assign to Project(s)
+
+on:
+  issues:
+    types: [opened, labeled]
+  pull_request:
+    types: [opened, labeled]
+  issue_comment:
+    types: [created]
+
+jobs:
+  assign_high_priority:
+    runs-on: ubuntu-latest
+    name: Assign to High Priority project
+    steps:
+    - name: Assign issues and pull requests with priority-high label to project 25
+      uses: srggrs/[email protected]
+      if: |
+        contains(github.event.issue.labels.*.name, 'priority: high') ||
+        contains(github.event.pull_request.labels.*.name, 'priority: high')
+      with:
+        project: 'https://github.com/ESCOMP/CTSM/projects/25'
+        column_name: 'Needs triage'
diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.70.0_api.32.0.0
+tag = sci.1.71.0_api.33.0.0
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -1571,6 +1571,7 @@ sub process_namelist_inline_logic {
   setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_start_type($opts, $nl_flags, $nl);
   setup_logic_decomp_performance($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_roughness_methods($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_snicar_methods($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl,  $envxml_ref);
@@ -1636,7 +1637,7 @@ sub process_namelist_inline_logic {
   ###############################
   # namelist group: tillage     #
   ###############################
-  setup_logic_tillage($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_tillage($opts, $nl_flags, $definition, $defaults, $nl, $physv);
 
   ###############################
   # namelist group: ch4par_in   #
@@ -2005,6 +2006,25 @@ sub setup_logic_decomp_performance {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_roughness_methods {
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method',
+              'phys'=>$nl_flags->{'phys'} );
+
+  my $var = remove_leading_and_trailing_quotes( $nl->get_value("z0param_method") );
+  if ( $var ne "Meier2022" && $var ne "ZengWang2007" ) {
+    $log->fatal_error("$var is incorrect entry for the namelist variable z0param_method; expected Meier2022 or ZengWang2007");
+  }
+  my $phys = $physv->as_string();
+  if ( $phys eq "clm4_5" || $phys eq "clm5_0" ) {
+    if ( $var eq "Meier2022" ) {
+      $log->fatal_error("z0param_method = $var and phys = $phys, but this method has been tested only with clm5_1 and later versions; to use with earlier versions, disable this error, and add Meier2022 parameters to the corresponding params file");
+    }
+  }
+}
+#-------------------------------------------------------------------------------
+
 sub setup_logic_snicar_methods {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -2246,6 +2266,7 @@ sub setup_logic_crop_inparm {
                  'use_crop'=>$nl->get_value('use_crop') );
 
      my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac');
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_residue_removal_frac' );
      if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) {
         $log->fatal_error("crop_residue_removal_frac must be in range [0, 1]");
      }
@@ -2258,10 +2279,13 @@ sub setup_logic_crop_inparm {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_tillage {
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'tillage_mode',
+              'use_crop'=>$nl_flags->{'use_crop'}, 'phys'=>$physv->as_string() );
 
   my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) );
-  if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) {
+  if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl_flags->{'use_crop'}) ) {
       $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." );
   }
 }

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -503,6 +503,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- ================================================================== -->
 
 <z0param_method>ZengWang2007</z0param_method>
+<z0param_method phys="clm5_1">Meier2022</z0param_method>
 
 <use_z0m_snowmelt z0param_method="Meier2022" >.true.</use_z0m_snowmelt>
 <use_z0m_snowmelt >.false.</use_z0m_snowmelt>
@@ -558,6 +559,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_grainproduct use_crop=".true." phys="clm5_1" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
 
 <crop_residue_removal_frac>0.d+0</crop_residue_removal_frac>
+<crop_residue_removal_frac phys="clm5_1">0.5d00</crop_residue_removal_frac>
 
 <!-- Crop model options -->
 <baset_mapping           use_crop=".true." phys="clm4_5" >constant</baset_mapping>
@@ -2037,6 +2039,8 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- =========================================  -->
 
 <tillage_mode>off</tillage_mode>
+<tillage_mode use_crop=".true." phys="clm5_1">low</tillage_mode>
+
 <use_original_tillage_phases>.false.</use_original_tillage_phases>
 <max_tillage_depth>0.26d00</max_tillage_depth>
 

diff --git a/cime_config/buildlib b/cime_config/buildlib
@@ -140,6 +140,7 @@ def _main_func():
                 os.path.join(lnd_root, "src", "fates", "biogeochem"),
                 os.path.join(lnd_root, "src", "fates", "fire"),
                 os.path.join(lnd_root, "src", "fates", "parteh"),
+                os.path.join(lnd_root, "src", "fates", "radiation"),
                 os.path.join(lnd_root, "src", "utils"),
                 os.path.join(lnd_root, "src", "cpl"),
                 os.path.join(lnd_root, "src", "cpl", "utils"),

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -150,6 +150,13 @@
 
   <!-- fates test suite failures -->
 
+  <test name="SMS_D_Ld3.f09_g17.I2000Clm51FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen_prescribed">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2321</issue>
+    </phase>
+  </test>
+
   <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
@@ -221,4 +228,25 @@
     </phase>
   </test>
 
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
+  </test>
+
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
+  </test>
+
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
+  </test>
+
 </expectedFails>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -2792,6 +2792,26 @@
       <option name="comment"  >Ensure functionality of the tree damage option in FATES</option>
     </options>
   </test>
+  <test name="ERS_D_Ld15" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdTwoStream">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+      <option name="comment"  >Ensure functionality of two-stream radiation option in FATES</option>
+    </options>
+  </test>
+  <test name="ERS_D_Ld15" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdTwoStreamNoCompFixedBioGeo">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+      <option name="comment"  >Ensure functionality of two-stream radiation option with nocomp-fixedbiogeo in FATES</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -3384,13 +3404,13 @@
     </options>
   </test>
 
-  <test name="SMS_Ld3" grid="f09_g17" compset="I2000Clm51FatesSpCruRsGs" testmods="clm/FatesColdSatPhen_prescribed">
+  <test name="SMS_D_Ld3" grid="f09_g17" compset="I2000Clm51FatesSpCruRsGs" testmods="clm/FatesColdSatPhen_prescribed">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="fates"/>
-      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="cheyenne" compiler="gnu" category="fates"/>
+      <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:30:00</option>
       <option name="comment">Test with prescribed LAI and soil moisture with FatesSP mode</option>
     </options>
   </test>
@@ -3713,6 +3733,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
@@ -17,7 +17,7 @@ hist_fincl1       = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF',
 'FATES_FABI_SUN_CLLLPF', 'FATES_FABI_SHA_CLLLPF', 'FATES_FABD_SUN_CLLL',
 'FATES_FABD_SHA_CLLL', 'FATES_FABI_SUN_CLLL', 'FATES_FABI_SHA_CLLL',
 'FATES_PARPROF_DIR_CLLLPF', 'FATES_PARPROF_DIF_CLLLPF',
-'FATES_PARPROF_DIR_CLLL', 'FATES_PARPROF_DIF_CLLL', 'FATES_FABD_SUN_TOPLF_CL',
+'FATES_FABD_SUN_TOPLF_CL',
 'FATES_FABD_SHA_TOPLF_CL', 'FATES_FABI_SUN_TOPLF_CL', 'FATES_FABI_SHA_TOPLF_CL',
 'FATES_NET_C_UPTAKE_CLLL', 'FATES_CROWNAREA_CLLL', 'FATES_NPLANT_CANOPY_SZAP',
 'FATES_NPLANT_USTORY_SZAP', 'FATES_DDBH_CANOPY_SZAP', 'FATES_DDBH_USTORY_SZAP',

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
@@ -1,11 +1,11 @@
 SRCDIR=`./xmlquery SRCROOT --value`
 CASEDIR=`./xmlquery CASEROOT --value`
-FATESROOT=$SRCDIR/src/fates/
-FATESPARAMFILE=$FATESROOT/parameter_files/fates_params_seeddisp_4x5.nc
+FATESDIR=$SRCDIR/src/fates/
+FATESPARAMFILE=$SRCDIR/fates_params_seeddisp_4x5.nc
 
-ncgen -o $FATESPARAMFILE $FATESROOT/parameter_files/fates_params_default.cdl
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
 
-$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts
-$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts
-$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_scale --val 1e-05 --allpfts
-$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_shape --val 0.1 --allpfts
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_scale --val 1e-05 --allpfts
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_shape --val 0.1 --allpfts
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
@@ -1,3 +1,3 @@
-fates_paramfile = '$SRCROOT/src/fates/parameter_files/fates_params_seeddisp_4x5.nc'
+fates_paramfile = '$SRCROOT/fates_params_seeddisp_4x5.nc'
 fates_seeddisp_cadence = 1
 hist_fincl1       = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/README
@@ -0,0 +1,15 @@
+Testing FATES two-stream radiation scheme is activated by switching the fates_rad_model
+parameter from 1 to 2.  This is all that is needed, both radiation schemes
+1) Norman and 2) two-stream use the same optical parameters.
+
+fates_rad_model
+
+Note that to avoid exceeding the filename string length maximum, the parameter
+file generated on the fly is placed in the $SRCROOT/src/fates/parameter_files
+directory.  This may still run into problems is the $SRCROOT string is too long.
+
+Like the test with seed dispersal activation, the main downside of this method is
+that this file will require a custom update for every fates parameter file API update.
+Addressing CTSM issue #2126 will alleviate
+this issue as it will provide the capability to build the fates parameter file on 
+the fly which with the appropriate values for this test.
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/include_user_mods
@@ -0,0 +1 @@
+../FatesCold
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands
@@ -0,0 +1,8 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates
+FATESPARAMFILE=$CASEDIR/fates_params_twostream.nc
+
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
+
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm
@@ -0,0 +1 @@
+fates_paramfile = '$CASEROOT/fates_params_twostream.nc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/README
@@ -0,0 +1,3 @@
+This tests two-stream radiation crossed with fixed biogeography and nocomp, for
+a description of how two-stream is turned on for tests see
+FatesColdTwoStream/README
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/include_user_mods
@@ -0,0 +1 @@
+../FatesColdNoComp
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands
@@ -0,0 +1,8 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates
+FATESPARAMFILE=$CASEDIR/fates_params_twostream.nc
+
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
+
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm
@@ -0,0 +1,2 @@
+fates_paramfile = '$CASEROOT/fates_params_twostream.nc'
+use_fates_fixed_biogeog=.true.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		fates_paramfile = '$CASEROOT/fates_params_twostream.nc'
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		fates_paramfile = '$CASEROOT/fates_params_twostream.nc'
		use_fates_fixed_biogeog=.true.