Merge pull request #3627 from ekluzek/carbon_isotopes_in_streams

Carbon isotopes in streams

Author: ekluzek

bld/CLMBuildNamelist.pm

@@ -3746,6 +3746,8 @@ 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 +3767,7 @@ 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 +3787,8 @@ 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 +3797,7 @@ 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 +3829,8 @@ 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 +3840,23 @@ 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 +3866,30 @@ 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'});
+  }
 }
 
 #-------------------------------------------------------------------------------
@@ -5937,6 +5986,27 @@ 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.

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -149,6 +149,58 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <atm_c14_filename use_c14=".true." use_c14_bombspike =".true." ssp_rcp="SSP5-3.4" >lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP534os_3x1_global_1850-2100_yearly_c181209.nc</atm_c14_filename>
 <atm_c14_filename use_c14=".true." use_c14_bombspike =".true." ssp_rcp="SSP5-8.5" >lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP5B_3x1_global_1850-2100_yearly_c181209.nc</atm_c14_filename>
 
+<!-- Settings for Carbon Isotope streams -->
+<stream_fldfilename_atm_c14 use_c14=".true." use_c14_bombspike =".true." ssp_rcp="hist" >lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C14_CMIP7_360x720_1700-2023_yearly_v3.0_c251117.nc</stream_fldfilename_atm_c14>
+<stream_meshfile_atm_c14    use_c14=".true." use_c14_bombspike =".true." >share/meshes/360x720_120830_ESMFmesh_c20210507.nc</stream_meshfile_atm_c14>
+
+<!-- The following are only set if both use_c14 and use_c14_bombspike are TRUE -->
+<stream_year_first_atm_c14 sim_year="2018" sim_year_range="constant">2018</stream_year_first_atm_c14>
+<stream_year_last_atm_c14  sim_year="2018" sim_year_range="constant">2018</stream_year_last_atm_c14>
+
+<stream_year_first_atm_c14 sim_year="2010" sim_year_range="constant">2010</stream_year_first_atm_c14>
+<stream_year_last_atm_c14  sim_year="2010" sim_year_range="constant">2010</stream_year_last_atm_c14>
+
+<stream_year_first_atm_c14 sim_year="2000" sim_year_range="constant">2000</stream_year_first_atm_c14>
+<stream_year_last_atm_c14  sim_year="2000" sim_year_range="constant">2000</stream_year_last_atm_c14>
+
+<stream_year_first_atm_c14 sim_year="1979" sim_year_range="constant">1850</stream_year_first_atm_c14>
+<stream_year_last_atm_c14  sim_year="1979" sim_year_range="constant">1850</stream_year_last_atm_c14>
+
+<stream_year_first_atm_c14 sim_year="1850" sim_year_range="constant">1850</stream_year_first_atm_c14>
+<stream_year_last_atm_c14  sim_year="1850" sim_year_range="constant">1850</stream_year_last_atm_c14>
+
+<stream_year_first_atm_c14 sim_year="PtVg" sim_year_range="constant">1700</stream_year_first_atm_c14>
+<stream_year_last_atm_c14  sim_year="PtVg" sim_year_range="constant">1700</stream_year_last_atm_c14>
+
+<stream_year_first_atm_c14 sim_year_range="1850-2000" >1700</stream_year_first_atm_c14>
+<stream_year_last_atm_c14  sim_year_range="1850-2000" >2023</stream_year_last_atm_c14>
+<stream_model_year_align_atm_c14  sim_year_range="1850-2000" >1700</stream_model_year_align_atm_c14>
+
+<stream_fldfilename_atm_c13 use_c13=".true." use_c13_timeseries=".true." ssp_rcp="hist" >lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C13_CMIP7_global_1700-2023_yearly_v3.0_c251013.nc</stream_fldfilename_atm_c13>
+
+<!-- The following are only set if both use_c13 and use_c13_bonbspike are TRUE -->
+<stream_year_first_atm_c13 sim_year="2018" sim_year_range="constant" >2018</stream_year_first_atm_c13>
+<stream_year_last_atm_c13  sim_year="2018" sim_year_range="constant" >2018</stream_year_last_atm_c13>
+
+<stream_year_first_atm_c13 sim_year="2010" sim_year_range="constant" >2010</stream_year_first_atm_c13>
+<stream_year_last_atm_c13  sim_year="2010" sim_year_range="constant" >2010</stream_year_last_atm_c13>
+
+<stream_year_first_atm_c13 sim_year="2000" sim_year_range="constant" >2000</stream_year_first_atm_c13>
+<stream_year_last_atm_c13  sim_year="2000" sim_year_range="constant" >2000</stream_year_last_atm_c13>
+
+<stream_year_first_atm_c13 sim_year="1979" sim_year_range="constant" >1850</stream_year_first_atm_c13>
+<stream_year_last_atm_c13  sim_year="1979" sim_year_range="constant" >1850</stream_year_last_atm_c13>
+
+<stream_year_first_atm_c13 sim_year="1850" sim_year_range="constant" >1850</stream_year_first_atm_c13>
+<stream_year_last_atm_c13  sim_year="1850" sim_year_range="constant" >1850</stream_year_last_atm_c13>
+
+<stream_year_first_atm_c13 sim_year="PtVg" sim_year_range="constant" >1700</stream_year_first_atm_c13>
+<stream_year_last_atm_c13  sim_year="PtVg" sim_year_range="constant" >1700</stream_year_last_atm_c13>
+
+<stream_year_first_atm_c13 sim_year_range="1850-2000" >1700</stream_year_first_atm_c13>
+<stream_year_last_atm_c13  sim_year_range="1850-2000" >2023</stream_year_last_atm_c13>
+<stream_model_year_align_atm_c13  sim_year_range="1850-2000" >1700</stream_model_year_align_atm_c13>
+
 <!-- Irrigation default (Note, the use-cases also set this) -->
 <irrigate                                                             >.false.</irrigate>
 <irrigate               use_cndv=".false."  sim_year_range="1850-2100">.true.</irrigate>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -1818,19 +1818,37 @@ First year to loop over for atmospheric C14 isotope delta data
 
 <entry id="stream_year_last_atm_c14" type="integer" category="datasets"
        group="carbon_isotope_streams" valid_values="" >
-Last year to loop over for data atmospheric C14 isotope delta data
+Last year to loop over for atmospheric C14 isotope delta data
 </entry>
 
 <entry id="stream_model_year_align_atm_c14" type="integer" category="datasets"
        group="carbon_isotope_streams" valid_values="" >
 Simulation year that aligns with stream_year_first_atm_c14 value
 </entry>
 
+<entry id="stream_tintalgo_atm_c14" type="char*256" category="datasets"
+       group="carbon_isotope_streams" valid_values="linear,nearest,lower,upper" >
+Time interpolation method to use for atmospheric C14 delta data
+</entry>
+
+<entry id="stream_taxmode_atm_c14" type="char*80" category="datasets"
+       group="carbon_isotope_streams" valid_values="cycle,extend,limit" >
+Time interpolation mode for atmospheric C14 delta data to determine how to handle data before and after the times in the file
+    cycle   = Always cycle over the data
+    extend  = Use the first time before the available data, and use the last time after the available data
+    limit   = Only use the data within the times available -- abort if the model tries to go outside it
+</entry>
+
 <entry id="stream_fldfilename_atm_c14" type="char*512" category="datasets"
        input_pathname="abs" group="carbon_isotope_streams" valid_values="" >
 Filename of input stream data for atmospheric C14 isotope delta data
 </entry>
 
+<entry id="stream_meshfile_atm_c14" type="char*512" category="datasets"
+       input_pathname="abs" group="carbon_isotope_streams" valid_values="" >
+Filename of input stream mesh for atmospheric C14 isotope delta data
+</entry>
+
 <entry id="stream_year_first_atm_c13" type="integer" category="datasets"
        group="carbon_isotope_streams" valid_values="" >
 First year to loop over for atmospheric C13 isotope delta data
@@ -1846,6 +1864,19 @@ Last year to loop over for data atmospheric C13 isotope delta data
 Simulation year that aligns with stream_year_first_atm_c13 value
 </entry>
 
+<entry id="stream_tintalgo_atm_c13" type="char*256" category="datasets"
+       group="carbon_isotope_streams" valid_values="linear,nearest,lower,upper" >
+Time interpolation method to use for atmospheric C13 delta data
+</entry>
+
+<entry id="stream_taxmode_atm_c13" type="char*80" category="datasets"
+       group="carbon_isotope_streams" valid_values="cycle,extend,limit" >
+Time interpolation mode for atmospheric C13 delta data to determine how to handle data before and after the times in the file
+    cycle   = Always cycle over the data
+    extend  = Use the first time before the available data, and use the last time after the available data
+    limit   = Only use the data within the times available -- abort if the model tries to go outside it
+</entry>
+
 <entry id="stream_fldfilename_atm_c13" type="char*512" category="datasets"
        input_pathname="abs" group="carbon_isotope_streams" valid_values="" >
 Filename of input stream data for atmospheric C13 isotope delta data

bld/unit_testers/build-namelist_test.pl

@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3400;
+my $ntests = 3403;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2061;
@@ -1421,6 +1421,11 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"use_soil_moisture_streams=T,soilm_tintalgo='linear'",
                                      phys=>"clm5_0",
                                    },
+     "c14_meshfile_none"         =>{ options=>"-envxml_dir . -bgc bgc",
+                                     namelst=>"stream_fldfilename_atm_c14='/dev/null', " .
+                                              "stream_meshfile_atm_c14='none'",
+                                     phys=>"clm6_0",
+                                   },
      "missing_ndep_file"         =>{ options=>"-envxml_dir . -bgc bgc -ssp_rcp SSP5-3.4",
                                      namelst=>"",
                                      phys=>"clm5_0",
@@ -1611,9 +1616,9 @@ sub cat_and_create_namelistinfile {
    &cleanup(); print "\n";
 }
 
-print "\n==================================================\n";
-print " Test all use-cases over all physics options\n";
-print "==================================================\n";
+print "\n=============================================================\n";
+print   " Test all use-cases over all physics options for f09 and SP \n";
+print   "=============================================================\n";
 
 # Run over all use-cases for f09 and all physics...
 my $list = `$bldnml -use_case list 2>&1 | grep "use case"`;
@@ -1634,7 +1639,8 @@ sub cat_and_create_namelistinfile {
    &make_config_cache($phys);
    foreach my $usecase ( @usecases ) {
       print "usecase = $usecase\n";
-      $options = "-res 0.9x1.25 -use_case $usecase  -envxml_dir .";
+      # Just do SP here as some use-cases can't do crop (nonanthro), and some not BGC (stdurbpt)
+      $options = "-res 0.9x1.25 -use_case $usecase --bgc bgc -envxml_dir .";
       &make_env_run();
       my $expect_fail = undef;
       foreach my $failusecase ( @expect_fails ) {
@@ -1940,6 +1946,12 @@ sub cat_and_create_namelistinfile {
      my @clmres = ( "10x15", "4x5", "360x720cru", "0.9x1.25", "1.9x2.5", "ne3np4", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
      foreach my $res ( @clmres ) {
         $options = "-res $res -envxml_dir . ";
+        # For clm6_0 and BGC use Carbon isotope streams
+        if ( ($phys eq "clm6_0") && ($clmopts =~ /bgc bgc/) ) {
+           $options = "$options --namelist \"&a stream_fldfilename_atm_c14 = '/dev/null'," .
+                      "stream_meshfile_atm_c14 = '/dev/null', " .
+                      "stream_fldfilename_atm_c13 = '/dev/null' /\"";
+        }
         &make_env_run( );
         eval{ system( "$bldnml $options $clmopts > $tempfile 2>&1 " ); };
         is( $@, '', "$options $clmopts" );

cime_config/testdefs/testmods_dirs/clm/ciso_cmip7_monthly_2013Start/README

@@ -0,0 +1,6 @@
+This tests with the new CMIP7 Carbon isotope datasets as streams.
+
+However, this uses the initial version of C14 and hence C14 is constant with the value
+over the southern pole latitude band. When we can change answers the ignore-warning should
+be removed and the CMIP7 defaults setup to use the streams rather than default to the
+CMIP6 version.

cime_config/testdefs/testmods_dirs/clm/ciso_cmip7_monthly_2013Start/shell_commands

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append
+

cime_config/testdefs/testmods_dirs/clm/ciso_cmip7_monthly_2013Start/user_nl_clm

@@ -1,6 +1,9 @@
  stream_fldfilename_atm_c13 = '$DIN_LOC_ROOT/lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C13_CMIP7_global_1700-2023_yearly_v3.0_c251013.nc'
+ ! NOTE: This file is the one with only 4 latitude bands, and can't be used by streams for regridding
+ ! The one copied to a half degree grid can be used to regrid the bands properly
  stream_fldfilename_atm_c14 = '$DIN_LOC_ROOT/lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C14_CMIP7_4x1_global_1700-2023_yearly_v3.0_c251013.nc'
  stream_year_first_atm_c14 = 2013
+ stream_meshfile_atm_c14 = 'none' ! NOTE: By NOT using a mesh file this means the first value will be copied to the whole grid rather than regridded
  stream_model_year_align_atm_c14 = 2013
  stream_year_first_atm_c13 = 2013
  stream_model_year_align_atm_c13 = 2013