ctsm5.2.0 -- ctsm5.2.mksurfdata

.git-blame-ignore-revs

@@ -30,3 +30,11 @@ d866510188d26d51bcd6d37239283db690af7e82
 8a168bb0895f4f2421608dd2589398e13a6663e6
 183fc26a6691bbdf87f515dc47924a64be3ced9b
 6fccf682eaf718615407d9bacdd3903b8786a03d
+a0d014fae9550dd9ffbc934abd29ef16176f8208
+c7b7ca1d94ac19abb9ecea9fb5b712ddbdd6645d
+b565b55ce7a9f8d812a573d716a5fd3d78cfea81
+fdf72cd011e2ba318987a1e100efc5a1847c9d04
+de9a30bfbbec36f9dcacc4380005ab596da47af4
+cda0cf1412212e6f4363e6e8eb39f74c944b454d
+aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
+6c6f57e948bfa31e60b383536cc21663fedb8b70

.gitignore

@@ -79,25 +79,32 @@ test_driver_*.sh
 
 # mksurfdata output
 surfdata_*.log
-surfdata_*.namelist
-landuse.timeseries_*.namelist
+*.namelist
+mksurfdata.o*
 landuse.timeseries_*.log
 landuse_timeseries_*.txt
 ctsm.input_data_list
 ctsm.input_data_list.previous
 *.stdout.txt.o*
+/tools/mksurfdata_esmf/PET*
+/tools/mksurfdata_esmf/job_name.o*
+/tools/mksurfdata_esmf/mksurfdata_in
+/tools/mksurfdata_esmf/surfdata_*.nc
+/tools/mksurfdata_esmf/landuse.timeseries_*.nc
+/tools/mksurfdata_esmf/mksurfdata_jobscript_multi
+/tools/mksurfdata_esmf/mksurfdata_jobscript_single
+/tools/mksurfdata_esmf/pio_iotype.txt
+/tools/mksurfdata_esmf/*.sh
+/tools/mksurfdata_esmf/mksrf_*.o*
+/tools/mksurfdata_esmf/tool_bld
+/tools/mksurfdata_esmf/pio_iotype.txt
 
 # mksurfdata unit tests
 unit_test_build
 
 # Tools executables
-/tools/mksurfdata_map/mksurfdata_map
 /tools/mkprocdata_map/mkprocdata_map
 
-# mksurfdata output files
-/tools/mksurfdata_map/surfdata_*.nc
-/tools/mksurfdata_map/landuse.timeseries_*.nc
-
 # mkmapdata output files
 /tools/mkmapdata/PET*.RegridWeightGen.Log
 /tools/mkmapdata/regrid.*.out

README

@@ -53,6 +53,7 @@ Directory structure only for a CTSM checkout:
 components -------- Other active sub-components needed for CTSM to run (river routing and land-ice models)
 libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO
 share ------------- CESM shared code
+ccs_config -------- CIME configure files (for grids, compsets, and machines) for CESM
 
 cime/scripts --------------- cesm/cime driver scripts
 
@@ -133,13 +134,12 @@ cime_config/usermods_dirs -------- Directories of sets of user-modification subd
 test/tools/test_driver.sh -- Script for general software testing of 
                              CTSM's offline tools.
 
-tools/mksurfdata_map ---------- Directory to build program to create surface dataset 
+tools/mksurfdata_esmf --------- Directory to build program to create surface dataset 
                                 at any resolution.
-tools/mkdatadomain ------------ Directory to build program to create datm7 or docn7 
-                                domain files from clm files.
 tools/mkprocdata_map ---------- Process history data from unstructed grids to a gridded 
                                 format.
 tools/mkmapgrids -------------- NCL script to create a SCRIP grid file for a regular lat/lon grid
+tools/modify_fsurdat ---------- Script to modify existing surface datasets in standard ways
 tools/ncl_scripts  ------------ Directory of NCL and perl scripts to do various
                                 tasks. Most notably to plot perturbation error growth
                                 testing and to extract regional information from

bld/CLMBuildNamelist.pm

@@ -1961,9 +1961,12 @@ sub setup_logic_irrigate {
                 'use_crop'=>$nl_flags->{'use_crop'}, 'use_cndv'=>$nl_flags->{'use_cndv'},
                 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, );
   if ( &value_is_true($nl->get_value('irrigate') ) ) {
-     $nl_flags->{'irrigate'} = ".true."
+     $nl_flags->{'irrigate'} = ".true.";
+     if ( $nl_flags->{'sim_year'} eq "PtVg" ) {
+        $log->fatal_error("irrigate=TRUE does NOT make sense with the Potential Vegetation dataset, leave irrigate=FALSE");
+     }
   } else {
-     $nl_flags->{'irrigate'} = ".false."
+     $nl_flags->{'irrigate'} = ".false.";
   }
 }
 
@@ -2161,6 +2164,7 @@ sub setup_logic_subgrid {
 
    my $var = 'run_zero_weight_urban';
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
+   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'convert_ocean_to_land');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'collapse_urban',
                'structure'=>$nl_flags->{'structure'});
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'n_dom_landunits',
@@ -2383,17 +2387,15 @@ sub setup_logic_demand {
     if ( $item eq "finidat" ) {
         $log->fatal_error( "Do NOT put findat in the clm_demand list, set the clm_start_type=startup so initial conditions are required");
     }
-    # For landuse.timeseries try with crop and irrigate on first, if found use it, otherwise try with exact settings
+    # 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{'irrigate'} = ".true.";
        $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{'nofail'}   = 0;
-       $settings{'irrigate'} = $nl_flags->{'irrigate'};
        $settings{'use_crop'} = $nl_flags->{'use_crop'};
        if ( ! defined($nl->get_value( $item )) ) {
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $item, %settings );
@@ -2436,8 +2438,8 @@ sub setup_logic_surface_dataset {
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
                  'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'},
                  'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
-                 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.", 'use_vichydro'=>$nl_flags->{'use_vichydro'},
-                 'use_crop'=>".true.", 'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'}, 'nofail'=>1);
+                 'sim_year'=>$nl_flags->{'sim_year'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'},
+                 'use_crop'=>".true.", 'use_fates'=>$nl_flags->{'use_fates'}, 'nofail'=>1);
   }
   # If didn't find the crop version check for the exact match
   my $fsurdat = $nl->get_value($var);
@@ -2447,17 +2449,9 @@ sub setup_logic_surface_dataset {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
                  'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'},
-                 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'}, 'use_fates'=>$nl_flags->{'use_fates'},
-                 'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
-                 'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'}, 'nofail'=>1 );
-     if ( ! defined($fsurdat) ) {
-        $log->verbose_message( "Exact match of $var NOT found, searching for version with irrigate true" );
-     }
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                 'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'},
-                 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.", 'use_fates'=>$nl_flags->{'use_fates'}, 
+                 'sim_year'=>$nl_flags->{'sim_year'}, 'use_fates'=>$nl_flags->{'use_fates'},
                  'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
-                 'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'} );
+                 'use_crop'=>$nl_flags->{'use_crop'} );
   }
   #
   # Expand the XML variables for NEON cases so that NEONSITE will be used
@@ -2507,11 +2501,17 @@ sub setup_logic_initial_conditions {
   }
   my $useinitvar = "use_init_interp";
 
+  my %settings;
+  my $use_init_interp_default = $nl->get_value($useinitvar);
+  $settings{$useinitvar} = $use_init_interp_default;
+  if ( string_is_undef_or_empty( $use_init_interp_default ) ) {
+    $use_init_interp_default = $defaults->get_value($useinitvar, \%settings);
+    $settings{$useinitvar} = ".false.";
+  }
   if (not defined $finidat ) {
     my $ic_date = $nl->get_value('start_ymd');
     my $st_year = $nl_flags->{'st_year'};
     my $nofail = 1;
-    my %settings;
     $settings{'hgrid'}   = $nl_flags->{'res'};
     $settings{'phys'}    = $physv->as_string();
     $settings{'nofail'}  = $nofail;
@@ -2548,12 +2548,6 @@ sub setup_logic_initial_conditions {
     }
     my $try = 0;
     my $done = 2;
-    my $use_init_interp_default = $nl->get_value($useinitvar);
-    $settings{$useinitvar} = $use_init_interp_default;
-    if ( string_is_undef_or_empty( $use_init_interp_default ) ) {
-      $use_init_interp_default = $defaults->get_value($useinitvar, \%settings);
-      $settings{$useinitvar} = ".false.";
-    }
     do {
        $try++;
        add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, %settings );
@@ -2600,14 +2594,24 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
              }
           }    # SIMYR:
           $settings{'sim_year'} = $closest_sim_year;
+          # Add options set here to the "$set" variable below...
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $useinitvar,
                       'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(), 'hgrid'=>$nl_flags->{'res'},
                       'sim_year'=>$settings{'sim_year'}, 'nofail'=>1, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
                       'use_fates'=>$nl_flags->{'use_fates'} );
           $settings{$useinitvar} = $nl->get_value($useinitvar);
           if ( ! &value_is_true($nl->get_value($useinitvar) ) ) {
-             if ( $nl_flags->{'clm_start_type'} =~ /startup/  ) {
-                $log->fatal_error("clm_start_type is startup so an initial conditions ($var) file is required, but can't find one without $useinitvar being set to true");
+             if ( $nl_flags->{'clm_start_type'} =~ /startup/ ) {
+                my $err_msg = "clm_start_type is startup so an initial conditions ($var) file is required,";
+                if ( defined($use_init_interp_default) ) {
+                   $log->fatal_error($err_msg." but can't find one without $useinitvar being set to true, change it to true in your user_nl_clm file in your case");
+                } else {
+                   my $set = "Relevent settings: use_cndv = ". $nl_flags->{'use_cndv'} . " phys = " . 
+                              $physv->as_string() . " hgrid = " . $nl_flags->{'res'} . " sim_year = " . 
+                              $settings{'sim_year'} . " lnd_tuning_mode = " . $nl_flags->{'lnd_tuning_mode'} .
+                              "use_fates = " . $nl_flags->{'use_fates'};
+                   $log->fatal_error($err_msg." but the default setting of $useinitvar is false, so set both $var to a startup file and $useinitvar==TRUE, or developers should modify the namelist_defaults file".$set);
+                }
              }
           } else {
              my $stat = add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_attributes",
@@ -2616,15 +2620,15 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
                                  'hgrid'=>$nl_flags->{'res'},
                                  'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'nofail'=>1 );
              if ( $stat ) {
-                $log->fatal_error("$useinitvar is NOT synchronized with init_interp_attributes");
+                $log->fatal_error("$useinitvar is NOT synchronized with init_interp_attributes in the namelist_defaults file, this should be corrected there");
              }
              my $attributes = $nl->get_value("init_interp_attributes");
              my $attributes_string = remove_leading_and_trailing_quotes($attributes);
              foreach my $pair ( split( /\s/, $attributes_string) ) {
                 if ( $pair =~ /^([a-z_]+)=([a-zA-Z._0-9]+)$/ ) {
                    $settings{$1} = $2;
                 } else {
-                   $log->fatal_error("Problem interpreting init_interp_attributes: $pair");
+                   $log->fatal_error("Problem interpreting init_interp_attributes from the namelist_defaults file: $pair");
                 }
              }
           }
@@ -2639,7 +2643,11 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
   }
   $finidat = $nl->get_value($var);
   if ( &value_is_true($nl->get_value($useinitvar) ) && string_is_undef_or_empty($finidat) ) {
-     $log->fatal_error("$useinitvar is set BUT $var is NOT, need to set both" );
+     if ( ! defined($use_init_interp_default) ) {
+        $log->fatal_error("You set $useinitvar but a $var file could not be found for this case, try setting $var explicitly, and/or removing the setting for $useinitvar" );
+     } else {
+        $log->fatal_error("$useinitvar is being set for you but a $var was not found, so $useinitvar, init_interp_attributes, and finidat must not be set correctly for this configuration in the namelist_default file" );
+     }
   }
 } # end initial conditions
 
@@ -2843,6 +2851,13 @@ sub setup_logic_do_transient_lakes {
 
    my $var = 'do_transient_lakes';
 
+   # Start by assuming a default value of '.true.'. Then check a number of
+   # conditions under which do_transient_lakes cannot be true. Under these
+   # conditions: (1) set default value to '.false.'; (2) make sure that the
+   # value is indeed false (e.g., that the user didn't try to set it to true).
+
+   my $default_val = ".true.";
+
    # cannot_be_true will be set to a non-empty string in any case where
    # do_transient_lakes should not be true; if it turns out that
    # do_transient_lakes IS true in any of these cases, a fatal error will be
@@ -2866,7 +2881,7 @@ sub setup_logic_do_transient_lakes {
       # Note that, if the variable cannot be true, we don't call add_default
       # - so that we don't clutter up the namelist with variables that don't
       # matter for this case
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val);
    }
 
    # Make sure the value is false when it needs to be false - i.e., that the
@@ -2908,6 +2923,13 @@ sub setup_logic_do_transient_urban {
 
    my $var = 'do_transient_urban';
 
+   # Start by assuming a default value of '.true.'. Then check a number of
+   # conditions under which do_transient_urban cannot be true. Under these
+   # conditions: (1) set default value to '.false.'; (2) make sure that the
+   # value is indeed false (e.g., that the user didn't try to set it to true).
+
+   my $default_val = ".true.";
+
    # cannot_be_true will be set to a non-empty string in any case where
    # do_transient_urban should not be true; if it turns out that
    # do_transient_urban IS true in any of these cases, a fatal error will be
@@ -2931,7 +2953,7 @@ sub setup_logic_do_transient_urban {
       # Note that, if the variable cannot be true, we don't call add_default
       # - so that we don't clutter up the namelist with variables that don't
       # matter for this case
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val);
    }
 
    # Make sure the value is false when it needs to be false - i.e., that the

bld/README

@@ -19,21 +19,6 @@ build-namelist --- Build the namelists needed
 
 env_run.xml --- Sample case runtime environment variables, so build-namelist can run outside of a case directory.
 
---------- Scripts to query namelist defaults
-listDefaultNamelist.pl -- List the files needed, for a list of resolutions,
-                          to run CLM that are currently NOT on your machine.
-                          This file can then be used by 
-                            cime/CIME/Tools/check_input_data
-                          to retreive them from the inputdata repository.
-                          Setting up cases with create_newcase also does
-                          this -- but only for the exact configuration
-                          given. This tries to get all the files need
-                          for several different resolutions and configurations
-                          at once.
-queryDefaultNamelist.pl - Query default namelist for settings of variables
-queryDefaultXML.pm ------ Subroutines needed by queryDefaultNamelist.pl script
-
-
 --------- Test scripts directory
 unit_testers --- Directory of scripts to test scipts in this directory
                  (most notably build-namelist)
@@ -59,7 +44,5 @@ namelist_files/namelist_definition_drv_flds.xml --- Definition of add driver fie
 
 ---------- XML helper files
 namelist_files/LogMessages.pm  ---- Perl module to handle log output
-namelist_files/checkmapfiles.ncl -- NCL script to check that all of the mapping files are valid
-namelist_files/createMapEntry.pl -- Perl script to create a map entry for the 
 namelist_files/history_fields.xsl - Style sheet for history fields as created by script that lists all of the
                                     history fields from the source files (../src/main/findHistFields.pl)