post5.4: Carbon isotope b4b changes to ctsm5.4

.gitmodules

@@ -68,7 +68,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.61
+fxtag = ccs_config_cesm1.0.61_add_domain_ne3np4.pg2_1
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git

bld/CLMBuildNamelist.pm

@@ -735,6 +735,14 @@ sub setup_cmdl_resolution {
     $log->verbose_message( "This is NOT a NEON site" );
   }
 
+  #
+  # To determine CMIP era
+  # TODO slevis: Ideally this line would occupy a new subroutine, e.g.
+  #              subr. process_envxml_flags that would get called from
+  #              process_namelist_user_input. This would allow other such
+  #              XML variables to be set in the same place in the future (issue #3547).
+  $nl_flags->{'cmip_era'} = $envxml_ref->{'CLM_CMIP_ERA'};
+
 }
 
 #-------------------------------------------------------------------------------
@@ -2367,6 +2375,7 @@ sub setup_logic_urban {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'init_interp_fill_missing_urban_with_HD');
 }
 
 #-------------------------------------------------------------------------------
@@ -2513,11 +2522,13 @@ sub setup_logic_demand {
     # For landuse.timeseries try with crop on first eise try with exact settings
     # Logic for this is identical for fsurdat
     if ( $item eq "flanduse_timeseries" ) {
+       $settings{'cmip_era'} = $nl_flags->{'cmip_era'};
        $settings{'use_crop'} = ".true.";
        $settings{'nofail'}   = 1;
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $item, %settings );
     if ( $item eq "flanduse_timeseries" ) {
+       $settings{'cmip_era'} = $nl_flags->{'cmip_era'};
        $settings{'nofail'}   = 0;
        $settings{'use_crop'} = $nl_flags->{'use_crop'};
        if ( ! defined($nl->get_value( $item )) ) {
@@ -2567,6 +2578,7 @@ sub setup_logic_surface_dataset {
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
                  'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'},
                  'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
+                 'cmip_era'=>$nl_flags->{'cmip_era'},
                  'sim_year'=>$nl_flags->{'sim_year'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'},
                  'use_crop'=>".true.", 'use_fates'=>$nl_flags->{'use_fates'}, 'nofail'=>1);
   }
@@ -2580,6 +2592,7 @@ sub setup_logic_surface_dataset {
                  'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'},
                  'sim_year'=>$nl_flags->{'sim_year'}, 'use_fates'=>$nl_flags->{'use_fates'},
                  'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
+                 'cmip_era'=>$nl_flags->{'cmip_era'},
                  'use_crop'=>$nl_flags->{'use_crop'} );
   }
   #
@@ -3746,6 +3759,8 @@ sub setup_logic_c_isotope {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14', 
               'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'},
               'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, ssp_rcp=>$nl_flags->{'ssp_rcp'} );
+  &add_logical_to_nl_flags( $nl_flags, $nl, "use_c13" );
+  &add_logical_to_nl_flags( $nl_flags, $nl, "use_c14" );
   my $use_c13 = $nl->get_value('use_c13');
   my $use_c14 = $nl->get_value('use_c14');
   if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" ) {
@@ -3765,6 +3780,7 @@ sub setup_logic_c_isotope {
       $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
       if ( &value_is_true($use_c14_bombspike) ) {
          if ( defined($stream_fldfilename_atm_c14) ) {
+            &add_logical_to_nl_flags( $nl_flags, $nl, "use_c14_bombspike" );
             setup_logic_c14_streams($opts, $nl_flags, $definition, $defaults, $nl);
          } else {
             add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
@@ -3784,6 +3800,8 @@ sub setup_logic_c_isotope {
         $log->fatal_error("use_c14 is FALSE and use_c14_bombspike, stream_fldfilename_atm_c14 or atm_c14_filename set");
       }
     }
+    &add_logical_to_nl_flags( $nl_flags, $nl, "use_c14_bombspike" );
+
     my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
     my $stream_fldfilename_atm_c13 = $nl->get_value('stream_fldfilename_atm_c13');
     my $atm_c13_filename = $nl->get_value('atm_c13_filename');
@@ -3792,6 +3810,7 @@ sub setup_logic_c_isotope {
       $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
       if ( &value_is_true($use_c13_timeseries) ) {
          if ( defined($stream_fldfilename_atm_c13) ) {
+            &add_logical_to_nl_flags( $nl_flags, $nl, "use_c13_timeseries" );
             setup_logic_c13_streams($opts, $nl_flags, $definition, $defaults, $nl);
          } else {
             add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
@@ -3823,6 +3842,8 @@ sub setup_logic_c_isotope {
            $log->fatal_error("bgc=sp and C isotope  namelist variables were set, both can't be used at the same time");
     }
   }
+  &add_logical_to_nl_flags( $nl_flags, $nl, "use_c13_timeseries" );
+  &add_logical_to_nl_flags( $nl_flags, $nl, "use_c13_bombspike" );
 }
 
 #-------------------------------------------------------------------------------
@@ -3832,6 +3853,23 @@ sub setup_logic_c13_streams {
   #
   # C13 stream file settings
   #
+  # Just return if use_c13 and use_c13_timeseries aren't both TRUE
+  if ( ! &value_is_true($nl_flags->{'use_c13'}) ) { return; }
+  if ( ! &value_is_true($nl_flags->{'use_c13_timeseries'}) ) { return; }
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_atm_c13',
+              'use_c13'=>$nl_flags->{'use_c13'}, 'use_c13_timeseries'=>$nl_flags->{'use_c13_timeseries'},
+              'ssp_rcp'=>$nl_flags->{'ssp_rcp'});
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_atm_c13',
+              'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_atm_c13',
+              'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  # Set align year, if first and last years are different
+  if ( $nl->get_value('stream_year_first_atm_c13') != $nl->get_value('stream_year_last_atm_c13') ) {
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_model_year_align_atm_c13',
+                'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  }
 }
 
 #-------------------------------------------------------------------------------
@@ -3841,6 +3879,30 @@ sub setup_logic_c14_streams {
   #
   # C14 stream file settings
   #
+  # Just return if use_c14 and use_c14_bombspike aren't both TRUE
+  if ( ! &value_is_true($nl_flags->{'use_c14'}) ) { return; }
+  if ( ! &value_is_true($nl_flags->{'use_c14_bombspike'}) ) { return; }
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_atm_c14',
+              'use_c14'=>$nl_flags->{'use_c14'}, 'use_c14_bombspike'=>$nl_flags->{'use_c14_bombspike'},
+              'ssp_rcp'=>$nl_flags->{'ssp_rcp'});
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_atm_c14',
+              'use_c14'=>$nl_flags->{'use_c14'}, 'use_c14_bombspike'=>$nl_flags->{'use_c14_bombspike'});
+   if ( &remove_leading_and_trailing_quotes( $nl->get_value( "stream_meshfile_atm_c14") ) eq "none" ) {
+      # TODP: Change this to a fatal when we start using this
+      $log->warning( "stream_meshfile_atm_c14 is set to 'none' which will only copy the first latitude to the globe")
+   }
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_atm_c14',
+              'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_atm_c14',
+              'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  # Set align year, if first and last years are different
+  if ( $nl->get_value('stream_year_first_atm_c14') != $nl->get_value('stream_year_last_atm_c14') ) {
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_model_year_align_atm_c14',
+                'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  }
 }
 
 #-------------------------------------------------------------------------------
@@ -4430,7 +4492,9 @@ sub setup_logic_cropcal_streams {
   if ( &value_is_true($cropcals_rx) or &value_is_true($cropcals_rx_adapt) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_start');
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_swindow_end');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds');
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds',
+       'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}
+       );
     if ( &value_is_true($cropcals_rx_adapt) ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline', 'stream_gdd20_seasons'=>$stream_gdd20_seasons);
     }
@@ -5495,7 +5559,7 @@ sub add_default {
                   "            Are defaults provided for this resolution and land mask?" );
         } else {
           $log->fatal_error("No default value found for $var.\n" .
-                      "            Are defaults provided for this resolution and land mask?");
+                      "      Are defaults provided in namelist_defaults for this resolution, land mask, and CLM_CMIP_ERA (set in env_run.xml)?");
         }
       }
       else {
@@ -5937,6 +6001,27 @@ sub logical_to_fortran {
 
 #-------------------------------------------------------------------------------
 
+sub add_logical_to_nl_flags {
+   # Add a logical setting to the $nl_flsgs hash, so can be used in attribute checking
+   # This is important to do to make sure that the attribute is matched exactly as
+   # either: .true. or .false.
+   # Also sets nl_flags to .false. when the namelist variable is NOT set
+   my ($nl_flags, $nl, $var) = @_;
+
+   my $val = $nl->get_value($var);
+   if ( defined($val) ) {
+      if ( &value_is_true($val)) {
+         $nl_flags->{$var} = ".true.";
+      } else {
+         $nl_flags->{$var} = ".false.";
+      }
+   } else {
+      $nl_flags->{$var} = ".false.";
+   }
+}
+
+#-------------------------------------------------------------------------------
+
 sub string_is_undef_or_empty {
    # Return true if the given string is undefined or only spaces, false otherwise.
    # A quoted empty string (' ' or " ") is treated as being empty.