Merge tag 'ctsm5.1.dev048' into neon_modify_dev

I used existing infrastructure to add descriptive strings to certain history fields that I had labeled by number in ESCOMP#1340. While doing this, I applied the change to a bunch of other history fields that needed it. Some variable names for pools was also changed to use terms consistent with the new names as well.
negin513 · Jul 23, 2021 · 81288cc · 81288cc
2 parents e503179 + 05c1eae
commit 81288cc
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diff --git a/Externals.cfg b/Externals.cfg
@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cism2_1_78
+tag = cismwrap_2_1_83
 externals = Externals_CISM.cfg
 required = True
 
@@ -37,21 +37,22 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = branch_tags/cime5.8.42_a01
+tag = branch_tags/cime5.8.47_a01
 required = True
 
 [cmeps]
 local_path = cime/src/drivers/nuopc/
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
-tag = v0.9.0
+tag = cmeps0.13.2
 required = True
 
 [cdeps]
 local_path = components/cdeps
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
-tag = v0.6.0
+tag = cdeps0.12.11
+externals = Externals_CDEPS.cfg
 required = True
 
 [doc-builder]

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.1.45.0_api.15.0.0
+tag = sci.1.46.2_api.16.1.0
 required = True
 
 [PTCLM]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -83,6 +83,7 @@ REQUIRED OPTIONS
                               (default 2000)
      -structure "structure"   The overall structure being used [ standard | fast ]
 OPTIONS
+     -driver "value"          mct or nuopc
      -bgc "value"             Build CLM with BGC package [ sp | cn | bgc | fates ]
                               (default is sp).
                                 CLM Biogeochemistry mode
@@ -242,7 +243,7 @@ sub process_commandline {
   # Save the command line arguments to the script. NOTE: this must be
   # before GetOptions() is called because items are removed from from
   # the array!
-  $nl_flags->{'cmdline'} = "@ARGV";
+  $nl_flags->{'cmdline'} = "@ARGV\n";
 
   my %opts = ( cimeroot              => undef,
                config                => "config_cache.xml",
@@ -252,6 +253,7 @@ sub process_commandline {
                co2_type              => undef,
                co2_ppmv              => undef,
                clm_demand            => "null",
+               driver                => "mct",
                help                  => 0,
                glc_nec               => "default",
                glc_use_antarctica    => 0,
@@ -284,6 +286,7 @@ sub process_commandline {
 
   GetOptions(
              "cimeroot=s"                => \$opts{'cimeroot'},
+             "driver=s"                  => \$opts{'driver'},
              "clm_demand=s"              => \$opts{'clm_demand'},
              "co2_ppmv=f"                => \$opts{'co2_ppmv'},
              "co2_type=s"                => \$opts{'co2_type'},
@@ -1645,11 +1648,6 @@ sub process_namelist_inline_logic {
   #############################################
   setup_logic_friction_vel($opts,  $nl_flags, $definition, $defaults, $nl);
 
-  ################################################
-  # namelist group: century_soilbgcdecompcascade #
-  ################################################
-  setup_logic_century_soilbgcdecompcascade($opts,  $nl_flags, $definition, $defaults, $nl);
-
   #############################
   # namelist group: cngeneral #
   #############################
@@ -2925,15 +2923,13 @@ sub setup_logic_methane {
   if ( &value_is_true($nl_flags->{'use_lch4'}) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'finundation_method',
                 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} );
-    #
-    # Get resolution to read streams file for
-    #
     my $finundation_method = remove_leading_and_trailing_quotes($nl->get_value('finundation_method' ));
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'finundation_res', 
-             'finundation_method'=>$finundation_method );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ch4finundated', 
-             'finundation_method'=>$finundation_method,
-             'finundation_res'=>$nl->get_value('finundation_res') );
+             'finundation_method'=>$finundation_method);
+    if ($opts->{'driver'} eq "nuopc" ) {
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ch4finundated', 
+                    'finundation_method'=>$finundation_method);
+    }
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_aereoxid_prog',
                 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} );
     #
@@ -3216,7 +3212,6 @@ sub setup_logic_nitrogen_deposition {
   #
   # Nitrogen deposition for bgc=CN
   #
-
   if ( $nl_flags->{'bgc_mode'} =~/cn|bgc/ ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'},
                 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'},
@@ -3242,17 +3237,32 @@ sub setup_logic_nitrogen_deposition {
                 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
                 'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 );
     if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) {
-       # Also check at f19 resolution
-       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'},
-                   'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
-                   'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 );
-       # If not found report an error
-       if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) {
-          $log->warning("Did NOT find the Nitrogen-deposition forcing file (stream_fldfilename_ndep) for this ssp_rcp\n" .
-                        "One way to get around this is to point to a file for another existing ssp_rcp in your user_nl_clm file.\n" .
-                        "If you are running with CAM and WACCM chemistry Nitrogen deposition will come through the coupler.\n" .
-                        "This file won't be used, so it doesn't matter what it points to -- but it's required to point to something.\n" )
-       }
+        # Also check at f19 resolution
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'},
+                    'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
+                    'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 );
+        # If not found report an error
+        if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) {
+            $log->warning("Did NOT find the Nitrogen-deposition forcing file (stream_fldfilename_ndep) for this ssp_rcp\n" .
+                          "One way to get around this is to point to a file for another existing ssp_rcp in your user_nl_clm file.\n" .
+                          "If you are running with CAM and WACCM chemistry Nitrogen deposition will come through the coupler.\n" .
+                          "This file won't be used, so it doesn't matter what it points to -- but it's required to point to something.\n" )
+        }
+    }
+    if ($opts->{'driver'} eq "nuopc" ) {
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ndep', 'phys'=>$nl_flags->{'phys'},
+                    'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
+                    'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 );
+        if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) {
+            # Also check at f19 resolution
+            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ndep', 'phys'=>$nl_flags->{'phys'},
+                        'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
+                        'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 );
+            # If not found report an error
+            if ( ! defined($nl->get_value('stream_meshfile_ndep') ) ) {
+                $log->warning("Did NOT find the Nitrogen-deposition meshfile file (stream_meshfilee_ndep) for this ssp_rcp. \n")
+            }
+        }
     }
   } else {
     # If bgc is NOT CN/CNDV then make sure none of the ndep settings are set!
@@ -3363,6 +3373,29 @@ sub setup_logic_popd_streams {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'},
                  'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+     # 
+     # TODO (mvertens, 2021-06-22) the following is needed for MCT since a use case enforces this  - so for now stream_meshfile_popdens will be added to the mct 
+     # stream namelist but simply not used
+    if ($opts->{'driver'} eq "nuopc" ) {
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_popdens', 'hgrid'=>"0.5x0.5");  
+        my $inputdata_rootdir = $nl_flags->{'inputdata_rootdir'};
+        my $default_value = $nl->get_value('stream_meshfile_popdens');
+        my $none_filename = $inputdata_rootdir . '/none';
+        my $none_filename = &quote_string($none_filename);
+        if ($default_value eq $none_filename) {
+            my $var = 'stream_meshfile_popdens'; 
+            my $group = $definition->get_group_name($var);
+            my $val = "none";
+            $val = &quote_string( $val );
+            $nl->set_variable_value($group, $var, $val);
+        }
+    } else {
+        my $var = 'stream_meshfile_popdens'; 
+        my $group = $definition->get_group_name($var);
+        my $val = "none";
+        $val = &quote_string( $val );
+        $nl->set_variable_value($group, $var, $val);
+    }
   } else {
      # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set
      if ( defined($nl->get_value('stream_year_first_popdens')) ||
@@ -3399,6 +3432,10 @@ sub setup_logic_urbantv_streams {
   }
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_urbantv', 'phys'=>$nl_flags->{'phys'},
               'hgrid'=>"0.9x1.25" );
+  if ($opts->{'driver'} eq "nuopc" ) {
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_urbantv', 'phys'=>$nl_flags->{'phys'},
+                  'hgrid'=>"0.9x1.25" );
+  }
 }
 
 #-------------------------------------------------------------------------------
@@ -3425,6 +3462,10 @@ sub setup_logic_lightning_streams {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng', 
                  'hgrid'=>$nl_flags->{'light_res'} );
+      if ($opts->{'driver'} eq "nuopc" ) {
+          add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_lightng', 
+                      'hgrid'=>$nl_flags->{'light_res'} );
+      }
   } else {
      # If bgc is NOT CN/CNDV then make sure none of the Lightng settings are set
      if ( defined($nl->get_value('stream_year_first_lightng')) ||
@@ -3582,6 +3623,10 @@ sub setup_logic_lai_streams {
        }
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lai',
                    'hgrid'=>"360x720cru" );
+       if ($opts->{'driver'} eq "nuopc" ) {
+           add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_lai',
+                       'hgrid'=>"360x720cru" );
+       }
      }
   } else {
      # If bgc is CN/CNDV then make sure none of the LAI settings are set
@@ -3621,23 +3666,6 @@ sub setup_logic_soilwater_movement {
 }
 #-------------------------------------------------------------------------------
 
-sub setup_logic_century_soilbgcdecompcascade {
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
-
-  if ( (&value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates'))) &&
-       &value_is_true($nl->get_value('use_century_decomp')) ) {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'initial_Cstocks',
-                'use_cn' => $nl->get_value('use_cn'), 'use_fates' => $nl->get_value('use_fates'),
-                'use_century_decomp' => $nl->get_value('use_century_decomp') );
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'initial_Cstocks_depth', 
-                'use_cn' => $nl->get_value('use_cn'), 'use_fates' => $nl->get_value('use_fates'),
-                'use_century_decomp' => $nl->get_value('use_century_decomp') ); 
-  }
-}
-
-#-------------------------------------------------------------------------------
-
 sub setup_logic_cnvegcarbonstate {
   #  MUST be AFTER: setup_logic_dynamic_plant_nitrogen_alloc as depends on mm_nuptake_opt which is set there
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
@@ -4131,7 +4159,7 @@ sub add_default {
       } else {
         if ($is_input_pathname eq 'abs') {
           $val = set_abs_filepath($val, $inputdata_rootdir);
-          if ( $test_files and ($val !~ /null/) and (! -f "$val") ) {
+          if ( $test_files and ($val !~ /null|none/) and (! -f "$val") ) {
             $log->fatal_error("file not found: $var = $val");
           }
         }

diff --git a/bld/namelist_files/checkmapfiles.ncl b/bld/namelist_files/checkmapfiles.ncl
@@ -9,7 +9,7 @@
 ;
 
   print( "Check that datm mapping files are consistent" );
-  resolutions = (/ "128x256", "64x128", "48x96", "32x64", "8x16", "94x192", "0.23x0.31", "0.47x0.63", "0.9x1.25", "1.9x2.5", "2.5x3.33", "4x5", "10x15", "0.125nldas2", "5x5_amazon", "1x1_camdenNJ", "1x1_vancouverCAN", "1x1_mexicocityMEX", "1x1_asphaltjungleNJ", "1x1_brazil", "1x1_urbanc_alpha", "1x1_numaIA", "1x1_smallvilleIA", "ne4np4", "ne16np4", "ne30np4", "ne60np4", "ne120np4", "ne240np4" /);
+  resolutions = (/ "128x256", "64x128", "48x96", "94x192", "0.23x0.31", "0.47x0.63", "0.9x1.25", "1.9x2.5", "2.5x3.33", "4x5", "10x15", "0.125nldas2", "5x5_amazon", "1x1_camdenNJ", "1x1_vancouverCAN", "1x1_mexicocityMEX", "1x1_asphaltjungleNJ", "1x1_brazil", "1x1_urbanc_alpha", "1x1_numaIA", "1x1_smallvilleIA", "ne4np4", "ne16np4", "ne30np4", "ne60np4", "ne120np4", "ne240np4" /);
 
   space  = "      ";
   badres = 0
@@ -82,7 +82,7 @@ begin
   print( "query string="+querynml )
 
 
-  mapgrids = (/"0.5x0.5_MODIS", "0.5x0.5_AVHRR", "0.5x0.5_MODIS", "5x5min_nomask", "5x5min_IGBP-GSDP", "5x5min_ISRIC-WISE", "10x10min_nomask", "3x3min_MODIS", "3x3min_LandScan2004", "3x3min_GLOBE-Gardner", "3x3min_GLOBE-Gardner-mergeGIS", "0.9x1.25_GRDC", "360x720cru_cruncep", "1km-merge-10min_HYDRO1K-merge-nomask"/);
+  mapgrids = (/"0.5x0.5_nomask", "0.25x0.25_nomask", "0.125x0.125_nomask", "3x3min_nomask", "5x5min_nomask", "10x10min_nomask", "0.9x1.25_nomask", "1km-merge-10min_HYDRO1K-merge-nomask"/);
   do i = 0, dimsizes(resolutions)-1
      res = resolutions(i);
      print( "Go through maps for Resolution: "+res );

diff --git a/bld/namelist_files/createMkSrfEntry.py b/bld/namelist_files/createMkSrfEntry.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import os, sys
 
@@ -41,9 +41,9 @@ def parse_cmdline_args( self ):
 
    def printentry( self, year ):
       "Print a single entry"
-      print '<mksrf_fvegtyp hgrid="0.25x0.25" ssp_rcp="%s" sim_year="%d" crop="on"' % (self.ssp_rcp, year)
-      print '>lnd/clm2/rawdata/%s/mksrf_landuse_%s_%s.c%s.nc' % (self.subdir, self.desc, year, self.cdate)
-      print '</mksrf_fvegtyp>\n'
+      print( '<mksrf_fvegtyp hgrid="0.25x0.25" ssp_rcp="%s" sim_year="%d" crop="on"' % (self.ssp_rcp, year) )
+      print( '>lnd/clm2/rawdata/%s/mksrf_landuse_%s_%s.c%s.nc' % (self.subdir, self.desc, year, self.cdate) )
+      print( '</mksrf_fvegtyp>\n' )
 
 entry = mksrfDataEntry_prog()
 entry.parse_cmdline_args()