Merge tag 'ctsm5.1.dev142' into tillage

b4b changes to Python scripts, history lists, tech note, and clm_time_manager. * Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081) * Rework master_list* files etc. (ESCOMP#2087) * Fixes to methane Tech Note (ESCOMP#2091) * Add is_doy_in_interval() function (ESCOMP#2158) * Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125) Closes issues: * Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079) * Rework master_list_(no)?fates.rst? (ESCOMP#2083) * conda run -n can fail if a conda environment is already active (ESCOMP#2109) * conda fails to load for SystemTests (ESCOMP#2111)
samsrabin · Oct 2, 2023 · d43c617 · d43c617
2 parents 3c24b25 + 2e2434d
commit d43c617
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,4 +1,5 @@
 # Ran python directory through black python formatter
+d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 4cd83cb3ee6d85eb909403487abf5eeaf4d98911
 0aa2957c1f8603c63fa30b11295c06cfddff44a5
 2cdb380febb274478e84cd90945aee93f29fa2e6
@@ -10,5 +11,11 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 b771971e3299c4fa56534b93421f7a2b9c7282fd
 9de88bb57ea9855da408cbec1dc8acb9079eda47
 8bc4688e52ea23ef688e283698f70a44388373eb
+0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
+810cb346f05ac1aabfff931ab1a2b7b584add241
+5933b0018f8e29413e30dda9b906370d147bad45
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
+8056ae649c1b37f5e10aaaac79005d6e3a8b2380
+540b256d1f3382f4619d7b0877c32d54ce5c40b6
+8a168bb0895f4f2421608dd2589398e13a6663e6
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -16,6 +16,22 @@ jobs:
              # Use options and version identical to the conda environment
              # Using pyproject.toml makes sure this testing is consistent with our python directory testing
              options: "--check --config python/pyproject.toml"
-             src:     "./python"
+             src: "./python"
              # Version should be coordinated with the ctsm_pylib conda environment under the python directory
              version: "22.3.0"
+          # Actions identical to above for each directory and source file we need to check (arrays aren't allowed for src: field)
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/SystemTests"
+             version: "22.3.0"
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/buildlib"
+             version: "22.3.0"
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/buildnml"
+             version: "22.3.0"
diff --git a/Externals.cfg b/Externals.cfg
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.64
+tag = ccs_config_cesm0.0.65
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config

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.1.66.1_api.25.5.0
+tag = sci.1.67.2_api.27.0.0
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -91,11 +91,13 @@ OPTIONS
                                     This toggles off the namelist variable: use_cn
                                 bgc   = Carbon Nitrogen with methane, nitrification, vertical soil C,
                                         CENTURY or MIMICS decomposition
-                                    This toggles on the namelist variables:
+				        This toggles on the namelist variables:
                                           use_cn, use_lch4, use_nitrif_denitrif
-                                fates = FATES/Ecosystem Demography with below ground BGC
-                                    This toggles on the namelist variables:
-                                          use_fates
+				fates = FATES/Ecosystem Demography with below ground BGC
+				        CENTURY or MIMICS decomposition
+                                        This toggles on the namelist variables:
+				        use_fates. use_lch4 and use_nitrif_denitrif are optional
+				 
                               (Only for CLM4.5/CLM5.0)
      -[no-]chk_res            Also check [do NOT check] to make sure the resolution and
                               land-mask is valid.
@@ -763,26 +765,12 @@ sub setup_cmdl_fates_mode {
           }
        }
 
-      # The following variables may be set by the user and are compatible with use_fates
-      # no need to set defaults, covered in a different routine
-      my @list  = (  "use_lch4" );
-      foreach my $var ( @list ) {
-	  if ( defined($nl->get_value($var))  ) {
-	      $nl_flags->{$var} = $nl->get_value($var);
-	      $val = $nl_flags->{$var};
-	      my $group = $definition->get_group_name($var);
-	      $nl->set_variable_value($group, $var, $val);
-	      if (  ! $definition->is_valid_value( $var, $val ) ) {
-		  my @valid_values   = $definition->get_valid_values( $var );
-		  $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
-	      }
-	  }
-      }
     } else {
        # dis-allow fates specific namelist items with non-fates runs
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
-                      "use_fates_cohort_age_tracking",
-                      "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode","use_fates_tree_damage" );
+                      "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
+		      "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
+		      "fates_parteh_mode","use_fates_tree_damage" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -1592,6 +1580,7 @@ sub process_namelist_inline_logic {
   setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_fates($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_z0param($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl);
 
   #########################################
@@ -3009,24 +2998,30 @@ sub setup_logic_supplemental_nitrogen {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" && &value_is_true($nl_flags->{'use_crop'}) ) {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-                'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});
-  }
+      # If this is non-fates, non-sp and crop is active
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+		  'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});
 
+  } elsif ( $nl_flags->{'bgc_mode'} eq "fates" && not &value_is_true( $nl_flags->{'use_fates_sp'})  ) {
+      # Or... if its fates but not fates-sp
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+		  'suplnitro', 'use_fates'=>$nl_flags->{'use_fates'});
+  }
+
   #
   # Error checking for suplnitro
   #
   my $suplnitro = $nl->get_value('suplnitro');
   if ( defined($suplnitro) ) {
     if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
-      $log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV is active!");
+      $log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV nor FATES is active!");
     }
     if ( ! &value_is_true($nl_flags->{'use_crop'}) && $suplnitro =~ /PROG_CROP_ONLY/i ) {
       $log->fatal_error("supplemental Nitrogen is set to run over prognostic crops, but prognostic crop is NOT active!");
     }
 
     if ( $suplnitro =~ /ALL/i ) {
-      if ( $nl_flags->{'bgc_spinup'} eq "on" ) {
+      if ( $nl_flags->{'bgc_spinup'} eq "on" && $nl_flags->{'bgc_mode'} ne "fates" ) {
         $log->warning("There is no need to use a bgc_spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen" );
       }
     }
@@ -3343,6 +3338,12 @@ sub setup_logic_luna {
                  'use_cn'=>$nl_flags->{'use_cn'} );
   }
   $nl_flags->{'use_luna'} = $nl->get_value('use_luna');
+
+  # LUNA can NOT be on with FATES
+  if ( &value_is_true( $nl_flags->{'use_luna'} ) && &value_is_true( $nl_flags->{'use_fates'} )) {
+     $log->fatal_error("Cannot turn use_luna to true when bgc=fates" );
+  }
+
   my $vcmax_opt= $nl->get_value('vcmax_opt');
   # lnc_opt only applies if luna is on or for vcmax_opt=3/4
   if ( &value_is_true( $nl_flags->{'use_luna'} ) || $vcmax_opt == 3 || $vcmax_opt == 4 ) {
@@ -3509,18 +3510,18 @@ sub setup_logic_nitrogen_deposition {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   #
-  # Nitrogen deposition for bgc=CN
+  # Nitrogen deposition for bgc=CN or fates
   #
-  if ( $nl_flags->{'bgc_mode'} =~/bgc/ ) {
+  if ( ($nl_flags->{'bgc_mode'} =~/bgc/) ) {   # or  ($nl_flags->{'bgc_mode'} =~/fates/) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'},
                 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'},
                 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'},
-                'use_cn'=>$nl_flags->{'use_cn'},
-                'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
+		'use_cn'=>$nl_flags->{'use_cn'}, 
+		'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'},
-                'use_cn'=>$nl_flags->{'use_cn'},
-                'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
+		'use_cn'=>$nl_flags->{'use_cn'}, 
+		'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'},
                 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
@@ -3908,8 +3909,7 @@ sub setup_logic_lai_streams {
   if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams'))  ) {
     $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true.");
   }
-  if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
-
+  if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) {
      if ( &value_is_true($nl->get_value('use_lai_streams')) ) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
@@ -3935,15 +3935,20 @@ sub setup_logic_lai_streams {
        }
      }
   } else {
-     # If bgc is CN/CNDV then make sure none of the LAI settings are set
-     if ( defined($nl->get_value('stream_year_first_lai')) ||
-          defined($nl->get_value('stream_year_last_lai'))  ||
-          defined($nl->get_value('model_year_align_lai'))  ||
-          defined($nl->get_value('lai_tintalgo'        ))  ||
+     # If bgc is BGC/BGCDV then make sure none of the LAI settings are set
+     if ( &value_is_true($nl->get_value('use_lai_streams'))) {
+        $log->fatal_error("When not in SP mode use_lai_streams cannot be .true.\n" .
+                          "(eg. don't use this option with BGC or non-SP FATES), \n" .
+                          "Update compset to use SP)");
+     }
+     if ( defined($nl->get_value('stream_year_first_lai'))  ||
+          defined($nl->get_value('stream_year_last_lai'))   ||
+          defined($nl->get_value('model_year_align_lai'))   ||
+          defined($nl->get_value('lai_tintalgo'        ))   ||
           defined($nl->get_value('stream_fldfilename_lai'))   ) {
-        $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" .
+        $log->fatal_error("When not in SP mode none of the following can be set: stream_year_first_lai,\n" .
                           "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" .
-                          "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV).");
+                          "stream_fldfilename_lai (eg. don't use this option with BGC or FATES-SP).");
      }
   }
 }
@@ -4297,6 +4302,13 @@ sub setup_logic_fates {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
         }
+        my $suplnitro = $nl->get_value('suplnitro');
+        my $parteh_mode = $nl->get_value('fates_parteh_mode');
+        if ( ($parteh_mode == 1) &&  ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+          $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " . 
+                            "but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" . 
+                            "Change suplnitro back to ALL");
+        }
         #
         # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
         # And also check for other settings that can't be trigged on as well
@@ -4381,6 +4393,28 @@ sub setup_logic_exice {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_z0param {
+   #
+   # Set default z0 paramterization
+   #
+   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method');
+
+   my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' ));
+   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0m_snowmelt',
+           'z0param_method'=>$z0param_method );
+
+   my $use_z0m_snowmelt = $nl->get_value( 'use_z0m_snowmelt' );
+
+   if ( $z0param_method eq "ZengWang2007" && defined($use_z0m_snowmelt) && value_is_true($use_z0m_snowmelt)) {
+      $log->fatal_error("use_z0m_snowmelt must be .false. when z0param_method = $z0param_method.\n $@");
+   }
+
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_misc {
    #
    # Set some misc options
@@ -4398,7 +4432,7 @@ sub setup_logic_misc {
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_use_second_grain_pool');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_use_repr_structure_pool');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_no_crop_seed_replenishment');
-   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_master_list_file');
+   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_fields_list_file');
 }
 
 #-------------------------------------------------------------------------------

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -67,8 +67,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <for_testing_use_repr_structure_pool>.false.</for_testing_use_repr_structure_pool>
 <for_testing_no_crop_seed_replenishment>.false.</for_testing_no_crop_seed_replenishment>
 
-<!-- Set to .true. in namelist to write hist fields master list file -->
-<hist_master_list_file>.false.</hist_master_list_file>
+<!-- Set to .true. in namelist to write file with all history fields -->
+<hist_fields_list_file>.false.</hist_fields_list_file>
 
 <!-- In accelerated spinup mode reduce the amount of history output -->
 <hist_empty_htapes clm_accelerated_spinup="on">.true.</hist_empty_htapes>
@@ -146,7 +146,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Supplmental Nitrogen mode -->
 <suplnitro use_cn=".true." >NONE</suplnitro>
-<suplnitro use_fates=".true." >NONE</suplnitro>
+<suplnitro use_fates=".true." >ALL</suplnitro>
 
 <!-- Albedo for glaciers -->
 <albice phys="clm5_1" >0.50,0.30</albice>
@@ -213,7 +213,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <zetamaxstable               use_biomass_heat_storage=".true." >2.0d00</zetamaxstable>
 <zetamaxstable phys="clm4_5"                                   >2.0d00</zetamaxstable>
 <zetamaxstable phys="clm5_0"                                   >0.5d00</zetamaxstable>
-<zetamaxstable phys="clm5_1"                                   >0.5d00</zetamaxstable>
+<zetamaxstable phys="clm5_1" z0param_method="ZengWang2007" >0.5d00</zetamaxstable>
+<zetamaxstable phys="clm5_1" z0param_method="Meier2022" >2.0d00</zetamaxstable>
 
 <!-- atm2lnd defaults -->
 <repartition_rain_snow phys="clm5_1" >.true.</repartition_rain_snow>
@@ -324,6 +325,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <itmax_canopy_fluxes structure="standard">40</itmax_canopy_fluxes>
 <itmax_canopy_fluxes structure="fast"    >3</itmax_canopy_fluxes>
 
+
 <!-- Canopy hydrology namelist defaults -->
 <use_clm5_fpi                 phys="clm5_1" >.true.</use_clm5_fpi>
 <interception_fraction        phys="clm5_1" >1.0</interception_fraction>
@@ -495,6 +497,15 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc</fates_paramfile>
 
+<!-- ================================================================== -->
+<!-- Default surface roughness parameterization                         -->
+<!-- ================================================================== -->
+
+<z0param_method>ZengWang2007</z0param_method>
+
+<use_z0m_snowmelt z0param_method="Meier2022" >.true.</use_z0m_snowmelt>
+<use_z0m_snowmelt >.false.</use_z0m_snowmelt>
+
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->
 <!-- ========================================================================================  -->
@@ -510,6 +521,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_luna phys="clm5_0"  >.true.</use_luna>
 <use_luna phys="clm5_0"  use_fates=".true." >.false.</use_luna>
 <use_luna phys="clm4_5"  >.false.</use_luna>
+<use_luna phys="clm4_5"  use_fates=".true." >.false.</use_luna>
 
 <!-- Flexible CN options -->
 <MM_Nuptake_opt             use_flexibleCN=".true." >.true.</MM_Nuptake_opt>
@@ -1128,6 +1140,8 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_C24_hist_78pfts_CMIP6_simyr2000
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"   sim_year="2000" use_crop=".true." use_vichydro=".false.">
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr2000_c190304.nc</fsurdat>
+<fsurdat hgrid="hcru_hcru"   sim_year="2000">
+lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_360x720cru_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
 <fsurdat hgrid="0.125x0.125"  sim_year="2000" use_crop=".true." >
 lnd/clm2/surfdata_map/release-clm5.0.24/surfdata_0.125x0.125_hist_78pfts_CMIP6_simyr2005_c190624.nc</fsurdat>
 <fsurdat hgrid="10x15"     sim_year="2000" use_crop=".true." use_vichydro=".false.">