Merge branch 'b4b-dev' into fix-generate_gdd20_baseline

Author: samsrabin

.gitmodules

@@ -28,15 +28,15 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.88.0_api.42.0.0
+fxtag = sci.1.89.0_api.43.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates
 
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_010
+fxtag = cismwrap_2_2_011
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
@@ -68,15 +68,15 @@ 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_add_domain_ne3np4.pg2_1
+fxtag = ccs_config_cesm1.0.66
 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
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.144
+fxtag = cime6.1.145
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime

WhatsNewInCTSM5.4.md

@@ -1,4 +1,4 @@
-# What's new in CTSM 5.4 (tag `ctsm5.4.0xx`)
+# What's new in CTSM 5.4 (tag `ctsm5.4.002`)
 
 # Purpose and description of changes since CTSM 5.3 (tag `ctsm5.3.021`)
 
@@ -37,21 +37,23 @@ Changes to defaults for \`clm6\` physics:
 * See “Changes to FATES and the FATES parameter file” below.  
 * Namelist defaults change so that  
   * use\_c13/use\_c14 are on only for HistClm60Bgc compsets with CRUJRA2024 or CAM7 forcing; examples of when use\_c13/use\_c14 are now off include SSP and single-point compsets, as well as cases using older forcings, such as CAM6, GSWP3v1, Qian, and CRUv7  
-  * when use\_c13 or use\_c14 is on, turn on the corresponding time series file  
+  * when use\_c13 or use\_c14 is on, turn on the corresponding time series file  (responding to the CLM_CMIP_ERA flag)
+  * C13/C14 CMIP7 data is done using streams with new namelist variables (stream_*_atm_c13, stream_*_atm_c14)
   * irrigation is on for transient cases (1850-2000, 1850-2100, but not for clm4\_5).
 
 Changes for all physics versions:
 
 * Parameters updated: Added MIMICS parameter \`mimics\_fi\` (fraction of litter inputs that bypass litter pools, directly contributing to SOM) and updated other MIMICS parameters (https://github.com/ESCOMP/CTSM/pull/2365) to remove NPP control on turnover, fix density dependent control on turnover, add litterfall fluxes that bypass litter pools and contribute directly to soil organic matter.  
 * FATES parameter file updated: ([PR \#2965](https://github.com/ESCOMP/CTSM/pull/2965), [PR \#2904](https://github.com/ESCOMP/CTSM/pull/2904), [PR \#1344](https://github.com/NGEET/fates/pull/1344), [PR \#3087](https://github.com/ESCOMP/CTSM/pull/3087)). See “FATES parameter file” section below for details.  
 * New surface datasets and landuse timeseries files (see “surface datasets” section below).
+* CMIP7 C13/C14 atmospheric timeseries data
 
 ## Heads up
 
 * History tapes now split into two files from hX to hXi and hXa, where X is the tape number (e.g. h0i/h0a) and where "i" stands for history file containing instantaneous fields, while "a" stands for history file containing non-instantaneous fields. Details in the “history files” section below and in the PRs https://github.com/ESCOMP/ctsm/pull/2445 https://github.com/ESCOMP/MOSART/pull/117 https://github.com/ESCOMP/RTM/pull/61 and the corresponding issues.  
 * Adding time to 1d weighting fields in transient simulations PR https://github.com/ESCOMP/CTSM/pull/3328  
 * Regarding CMIP7 vs. CMIP6 inputs:  
-  * We supply only CMIP7 C13/C14 isotope datasets, so these get used regardless of CLM\_CMIP\_ERA setting.  
+  * C13/C14 isotope datasets are the new CMIP7 datasets using streams, while when CLM_CMIP_ERA==cmip6, the older cmip6 files are used
   * We supply only CMIP7 population density with clm6 physics in non-SSP cases, because the fire model is calibrated to that; conversely, we supply only CMIP6 population density for pre-clm6 physics and for SSP cases.  
   * We supply only CESM2 nitrogen deposition (ndep), so this gets used regardless of CLM\_CMIP\_ERA setting.  
   * For DATM we supply only CMIP6 aerosols.  
@@ -147,4 +149,3 @@ The former is calculated as a function of the latter and can be time-evolving de
 * ne30 with \`Clm60BgcCropCruJra\`: https://github.com/NCAR/LMWG_dev/issues/123 (123\_HIST\_popDens)  
 * ne30 SP https://github.com/NCAR/LMWG_dev/issues/126  
 * f09 SP https://github.com/NCAR/LMWG_dev/issues/127
-

bld/CLMBuildNamelist.pm

@@ -60,6 +60,7 @@ SYNOPSIS
      Create the namelist for CLM
 REQUIRED OPTIONS
      -cimeroot "directory"    Path to cime directory
+     -landroot "directory"    Path to the land models parent directory, ie <>/ctsm
      -config "filepath"       Read the given CLM configuration cache file.
                               Default: "config_cache.xml".
      -configuration "cfg"     The overall configuration being used [ clm | nwp ]
@@ -259,6 +260,7 @@ sub process_commandline {
   $nl_flags->{'cmdline'} = "@ARGV\n";
 
   my %opts = ( cimeroot              => undef,
+	       landroot              => undef,
                config                => "config_cache.xml",
                configuration         => undef,
                csmdata               => undef,
@@ -300,6 +302,7 @@ sub process_commandline {
 
   GetOptions(
              "cimeroot=s"                => \$opts{'cimeroot'},
+             "landroot=s"                => \$opts{'landroot'},
              "driver=s"                  => \$opts{'driver'},
              "clm_demand=s"              => \$opts{'clm_demand'},
              "co2_ppmv=f"                => \$opts{'co2_ppmv'},
@@ -3779,15 +3782,14 @@ sub setup_logic_c_isotope {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14_bombspike', 'use_c14'=>$use_c14 );
       $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_logical_to_nl_flags( $nl_flags, $nl, "use_c14_bombspike" );
+         setup_logic_c14_streams($opts, $nl_flags, $definition, $defaults, $nl);
+         $stream_fldfilename_atm_c14 = $nl->get_value('stream_fldfilename_atm_c14');
+         if ( ! defined($stream_fldfilename_atm_c14) ) {
             add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
                     'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
-                    'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+                    'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'cmip_era'=>$nl_flags->{'cmip_era'} );
          }
-         $stream_fldfilename_atm_c14 = $nl->get_value('stream_fldfilename_atm_c14');
          $atm_c14_filename = $nl->get_value('atm_c14_filename');
          if ( defined($stream_fldfilename_atm_c14) && defined($atm_c14_filename) ) {
            $log->fatal_error("Both stream_fldfilename_atm_c14 and atm_c14_filename set, only one should be set");
@@ -3809,15 +3811,14 @@ sub setup_logic_c_isotope {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13_timeseries', 'use_c13'=>$use_c13 );
       $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_logical_to_nl_flags( $nl_flags, $nl, "use_c13_timeseries" );
+         setup_logic_c13_streams($opts, $nl_flags, $definition, $defaults, $nl);
+         $stream_fldfilename_atm_c13 = $nl->get_value('stream_fldfilename_atm_c13');
+         if ( ! defined($nl->get_value('stream_fldfilename_atm_c13')) ) {
             add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
                     'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
                     'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
          }
-         $stream_fldfilename_atm_c13 = $nl->get_value('stream_fldfilename_atm_c13');
          $atm_c13_filename = $nl->get_value('atm_c13_filename');
          if ( defined($stream_fldfilename_atm_c13) && defined($atm_c13_filename) ) {
            $log->fatal_error("Both stream_fldfilename_atm_c13 and atm_c13_filename set, only one should be set");
@@ -3859,7 +3860,11 @@ sub setup_logic_c13_streams {
 
   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'});
+              'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'cmip_era'=>$nl_flags->{'cmip_era'}, 'nofail'=>1);
+  # If stream_fldfilename_atm_c13 is not defined then return and get the cmip6 file format version
+  if ( ! defined( $nl->get_value( "stream_fldfilename_atm_c13") ) ) {
+      return;
+  }
 
   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'});
@@ -3885,13 +3890,16 @@ sub setup_logic_c14_streams {
 
   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'});
+              'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1);
+   # If stream_fldfilename_atm_c14 is not defined then return and get the cmip6 file format version
+   if ( ! defined( $nl->get_value( "stream_fldfilename_atm_c14") ) ) {
+       return;
+   }
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_atm_c14',
+   add_default($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")
+      $log->fatal_error( "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, $nl, 'stream_year_first_atm_c14',
@@ -4493,10 +4501,12 @@ sub setup_logic_cropcal_streams {
     add_default($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, $nl, 'stream_fldfilename_cultivar_gdds',
+       'cropcals_rx'=>$cropcals_rx,
+       'cropcals_rx_adapt'=>$cropcals_rx_adapt,
        'lnd_tuning_mode'=>$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);
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline', 'stream_gdd20_seasons'=>$stream_gdd20_seasons, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'});
     }
   }
 
@@ -5573,17 +5583,22 @@ sub add_default {
     # The default values for input pathnames are relative.  If the namelist
     # variable is defined to be an absolute pathname, then prepend
     # the CESM inputdata root directory.
-    if (not defined $settings{'no_abspath'}) {
-      if (defined $settings{'set_abspath'}) {
-        $val = set_abs_filepath($val, $settings{'set_abspath'});
-      } else {
-        if ($is_input_pathname eq 'abs') {
-          $val = set_abs_filepath($val, $inputdata_rootdir);
-          if ( $test_files and ($val !~ /null|none/) and (! -f "$val") ) {
-            $log->fatal_error("file not found: $var = $val");
-          }
-        }
-      }
+    if ($is_input_pathname eq 'landroot') {
+	#my $landroot = $opts->{'landroot'};
+	$val = set_abs_filepath($val,$opts->{'landroot'});
+    } else {
+	if (not defined $settings{'no_abspath'}) {
+	    if (defined $settings{'set_abspath'}) {
+		$val = set_abs_filepath($val, $settings{'set_abspath'});
+	    } else {
+		if ($is_input_pathname eq 'abs') {
+		    $val = set_abs_filepath($val, $inputdata_rootdir);
+		    if ( $test_files and ($val !~ /null|none/) and (! -f "$val") ) {
+			$log->fatal_error("file not found: $var = $val");
+		    }
+		}
+	    }
+	}
     }
 
     # query the definition to find out if the variable takes a string value.