clm4_5_14_r215

Use new rawdatasets from Peter Lawrence that have crop landunit changing in size as well as specific crop and natural vegetation types. Modify mksurfdata_map to use new fields for fertilizer for each crop type. Add in harvest fields to both surface dataset as well as landuse.timeseries dataset. Also add in two new fields: UNREPRESENTED_PFT_LULCC, UNREPRESENTED_CFT_LULCC for the impact of landuse changes for natural and crop vegetation types. Currently these two fields are zeroed out. But, they will be added in with a new update to the datasets. Implement crop fertilizer for each crop type into CLM. The fertilizer is also moved from one crop type to another by the mapping system between the different crop types (to handle unrepresented crop types by mapping them to one that is represented). The new datasets also have harvest fields in units by mass rather than area. This requires new surface and landuse.timeseries datasets. We have hand-edited versions from Peter Lawrence for f09 and f19. The older datasets for other resolutions still work, but they don't have the new fertilizer field so anthropogenic fertilizer is zeroed out. NOTE: Capability to create rcp scenarios for landuse.timeseries was removed from mksurfdata_map.
slevis-lmwg · Dec 19, 2017 · 0123b55 · 0123b55
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diff --git a/SVN_EXTERNAL_DIRECTORIES.standalone b/SVN_EXTERNAL_DIRECTORIES.standalone
@@ -1,5 +1,5 @@
 cime                                    https://github.com/CESM-Development/cime/tags/cime5.2.0-alpha.9
-components/clm/tools/shared/gen_domain  https://github.com/CESM-Development/cime/tags/cime5.2.0-alpha.9/tools/mapping/gen_domain_files
+components/clm/tools/gen_domain         https://github.com/CESM-Development/cime/tags/cime5.2.0-alpha.9/tools/mapping/gen_domain_files
 components/cism                         https://svn-ccsm-models.cgd.ucar.edu/glc/trunk_tags/cism2_1_24
 components/rtm                          https://svn-ccsm-models.cgd.ucar.edu/rivrtm/trunk_tags/rtm1_0_59
 components/mosart                       https://svn-ccsm-models.cgd.ucar.edu/mosart/trunk_tags/mosart1_0_19
diff --git a/bld/README b/bld/README
@@ -44,7 +44,6 @@ unit_testers --- Directory of scripts to test scipts in this directory
 
 ---------- XML Files describing namelists in namelist_files
 namelist_files/namelist_defaults_clm4_0.xml ------- List of default values for the clm4_0 namelist
-namelist_files/namelist_defaults_clm4_0_tools.xml - List of default values for the clm4_0 tools.
 namelist_files/namelist_defaults_clm4_5.xml ------- List of default values for the clm4_5 namelist
 namelist_files/namelist_defaults_clm4_5_tools.xml - List of default values for the clm4_5 tools.
 namelist_files/namelist_defaults_overall.xml ------ List of default values for overall settings

diff --git a/bld/listDefaultNamelist.pl b/bld/listDefaultNamelist.pl
@@ -69,7 +69,6 @@ sub usage {
 OPTIONS
      -help  [or -h]                       Display this help.
      -csmdata [or -d]                     Path to CSMDATA.
-     -phys "name"                         Model physics (either clm4_0 or clm4_5) (default clm4_0)
      -res  "resolution1,resolution2,..."  List of resolution to use for files.
                                           (At least one resolution is required)
                                           (If res is "all" will run over all resolutions)
@@ -157,7 +156,7 @@ sub GetListofNeededFiles {
                list       => $list,
                usrdat     => undef,
                help       => undef,
-               phys       => "clm4_0",
+               phys       => "clm4_5",
              );
 
   my $cmdline = "@ARGV";
@@ -167,7 +166,6 @@ sub GetListofNeededFiles {
         "s|silent"     => \$opts{'silent'},
         "u|usrdat=s"   => \$opts{'usrdat'},
         "h|elp"        => \$opts{'help'},
-        "phys=s"       => \$opts{'phys'},
   ) or usage();
 
   # Check for unparsed arguments
@@ -290,11 +288,7 @@ sub GetListofNeededFiles {
                  foreach my $crop ( @crop_vals ) {
                    $settings{'crop'} = $crop;
                    if ( $crop eq "on" ) {
-                     if ($phys eq "clm4_0") { 
-                       $settings{'maxpft'} = 21;
-                     } else {
-                       $settings{'maxpft'} = 25;
-                     }
+                     $settings{'maxpft'} = 78;
                    } else {
                      $settings{'maxpft'} = 17;
                    }

diff --git a/bld/namelist_files/namelist_defaults_clm4_0_tools.xml b/bld/namelist_files/namelist_defaults_clm4_0_tools.xml
diff --git a/bld/namelist_files/namelist_defaults_clm4_5.xml b/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -540,9 +540,9 @@ lnd/clm2/surfdata_map/surfdata_ne30np4_16pfts_simyr1850_c160127.nc</fsurdat>
 
 <!-- pre-industrial with crop -->
 <fsurdat hgrid="0.9x1.25"  sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_simyr1850_c160127.nc</fsurdat>
+lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_simyr1850_c161128.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"   sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/surfdata_1.9x2.5_78pfts_simyr1850_c160127.nc</fsurdat>
+lnd/clm2/surfdata_map/surfdata_1.9x2.5_78pfts_simyr1850_c161128.nc</fsurdat>
 <fsurdat hgrid="10x15"     sim_year="1850" use_crop=".true." >
 lnd/clm2/surfdata_map/surfdata_10x15_78pfts_simyr1850_c160127.nc</fsurdat>
 <fsurdat hgrid="4x5"       sim_year="1850" use_crop=".true." >
@@ -584,6 +584,10 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_simyr1850_c160216.nc</fsurdat>
 
 <!-- Dynamic PFT surface datasets for crop -->
 
+<flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000"
+ use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_simyr1850-2015_c161128.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000"
+ use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_simyr1850-2015_c161216.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000"
  use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_simyr1850-2005_c160127.nc</flanduse_timeseries>
 

diff --git a/bld/namelist_files/namelist_defaults_clm4_5_tools.xml b/bld/namelist_files/namelist_defaults_clm4_5_tools.xml
diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -961,7 +961,7 @@ in its attributes. (Only used if scripgriddata_src_type = UGRID.)
 <!--                                                   -->
 <entry id="mksrf_filename" type="char*256" category="mksurfdata"
        group="default_settings" 
-       valid_values="mksrf_fsoitex,mksrf_forganic,mksrf_flakwat,mksrf_fwetlnd,mksrf_fmax,mksrf_fmax,mksrf_fglacier,mksrf_fglacierregion,mksrf_fvocef,mksrf_furbtopo,firrig,mksrf_furban,mksrf_fvegtyp,mksrf_fsoicol,mksrf_flai,mksrf_fgdp,mksrf_fpeat,mksrf_fsoildepth,mksrf_fabm,mksrf_ftopostats,mksrf_fvic,mksrf_fch4" >
+       valid_values="mksrf_fsoitex,mksrf_forganic,mksrf_flakwat,mksrf_fwetlnd,mksrf_fmax,mksrf_fmax,mksrf_fglacier,mksrf_fglacierregion,mksrf_fvocef,mksrf_furbtopo,firrig,mksrf_furban,mksrf_fvegtyp,mksrf_fhrvtyp,mksrf_fsoicol,mksrf_flai,mksrf_fgdp,mksrf_fpeat,mksrf_fsoildepth,mksrf_fabm,mksrf_ftopostats,mksrf_fvic,mksrf_fch4" >
 Filename for mksurfdata_map to remap raw data into the output surface dataset
 </entry>
 
@@ -970,6 +970,11 @@ Filename for mksurfdata_map to remap raw data into the output surface dataset
 Plant Function Type dataset for mksurfdata
 </entry>
 
+<entry id="mksrf_fhrvtyp" type="char*256" category="mksurfdata"
+       input_pathname="abs" group="clmexp" valid_values="" >
+Harvest dataset for mksurfdata
+</entry>
+
 <entry id="mksrf_fglacier" type="char*256" category="mksurfdata"
        input_pathname="abs" group="clmexp" valid_values="" >
 Dataset for percent glacier land-unit for mksurfdata

diff --git a/bld/unit_testers/NMLTest/CompFiles.pm b/bld/unit_testers/NMLTest/CompFiles.pm
@@ -76,8 +76,8 @@ sub comparefiles {
    my $compdir   = shift;
    my $nm = ref($self)."\:\:comparefiles";
 
-   $type      =~ s#[ '&/]#+#g;
-   $comp_mode =~ s#[ '&/]#+#g;
+   $type      =~ s#[ '"&/]#+#g;
+   $comp_mode =~ s#[ '"&/]#+#g;
    my $confdir  = $self->{'dir'};
    my $diffref   = $self->{'diffref'};
    if ( ! defined($type)    ) {
@@ -126,8 +126,8 @@ sub copyfiles {
    my $mode    = shift;
    my $nm = ref($self)."\:\:copyfiles";
 
-   $type =~ s#[ '&/]#+#g;
-   $mode =~ s#[ '&/]#+#g;
+   $type =~ s#[ '"&/]#+#g;
+   $mode =~ s#[ '"&/]#+#g;
    my $diffref   = $self->{'diffref'};
    my $filesref = $self->{'files'};
    my $confdir  = $self->{'dir'};
@@ -151,8 +151,8 @@ sub shownmldiff {
    my $comp_mode = shift;
    my $nm = ref($self)."\:\:shownmldiff";
 
-   $type      =~ s#[ '&/]#+#g;
-   $comp_mode =~ s#[ '&/]#+#g;
+   $type      =~ s#[ '"&/]#+#g;
+   $comp_mode =~ s#[ '"&/]#+#g;
    my $filesref = $self->{'files'};
    my $confdir  = $self->{'dir'};
    foreach my $file ( @$filesref ) {
@@ -184,8 +184,8 @@ sub dodiffonfile {
   my $mode    = shift;
   my $nm = ref($self)."\:\:dodiffonfile";
 
-  $type =~ s#[ '&/]#+#g;
-  $mode =~ s#[ '&/]#+#g;
+  $type =~ s#[ '"&/]#+#g;
+  $mode =~ s#[ '"&/]#+#g;
   my $diffref   = $self->{'diffref'};
   if ( ! defined($type) ) {
      $type = "default";
@@ -204,8 +204,8 @@ sub doNOTdodiffonfile {
   my $mode    = shift;
   my $nm = ref($self)."\:\:doNOTdodiffonfile";
 
-  $type =~ s#[ '&/]#+#g;
-  $mode =~ s#[ '&/]#+#g;
+  $type =~ s#[ '"&/]#+#g;
+  $mode =~ s#[ '"&/]#+#g;
   my $diffref   = $self->{'diffref'};
   if ( ! defined($type) ) {
      $type = "default";

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -233,7 +233,7 @@ sub make_env_run {
    # Compare to baseline
    if ( defined($opts{'compare'}) ) {
       $cfiles->dodiffonfile(      "lnd_in",    "most_options", $mode );
-      $cfiles->doNOTdodiffonfile( "$real_par_file", "most_options", $mode );
+      $cfiles->dodiffonfile( "$real_par_file", "most_options", $mode );
       $cfiles->doNOTdodiffonfile( "$tempfile", "most_options", $mode );
       $cfiles->comparefiles( "most_options", $mode, $opts{'compare'} );
    }
@@ -295,7 +295,7 @@ sub make_env_run {
    }
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->doNOTdodiffonfile( "$real_par_file", "$options", $mode );
+      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -324,6 +324,8 @@ sub make_env_run {
    $cfiles->shownmldiff( "default", $mode );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+      $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
+      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -909,7 +911,7 @@ sub make_env_run {
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->doNOTdodiffonfile( "$real_par_file", "$options", $mode );
+      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
 
@@ -996,7 +998,7 @@ sub make_env_run {
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$res", $mode );
-      $cfiles->doNOTdodiffonfile( "$real_par_file", "$res", $mode );
+      $cfiles->dodiffonfile( "$real_par_file", "$res", $mode );
       $cfiles->comparefiles( "$res", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -1022,7 +1024,7 @@ sub make_env_run {
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->doNOTdodiffonfile( "$real_par_file", "$options", $mode );
+      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -1080,7 +1082,7 @@ sub make_env_run {
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->doNOTdodiffonfile( "$real_par_file", "$options", $mode );
+      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -1102,7 +1104,7 @@ sub make_env_run {
       $cfiles->shownmldiff( "default", "standard" );
       if ( defined($opts{'compare'}) ) {
          $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-         $cfiles->doNOTdodiffonfile( "$real_par_file", "$options", $mode );
+         $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
          $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
       }
       if ( defined($opts{'generate'}) ) {

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
@@ -385,6 +385,11 @@
     <lname>1850_DATM%CRU_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2_SWAV</lname>
   </compset>
 
+  <compset grid="g%gland">
+    <alias>IGMHISTCRUCLM50BGCCROP</alias>
+    <lname>HIST_DATM%CRU_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2_SWAV</lname>
+  </compset>
+
   <compset grid="g%gland">
     <alias>IGM1850CRUCLM50BGC</alias>
     <lname>1850_DATM%CRU_CLM50%BGC_SICE_SOCN_MOSART_CISM2_SWAV</lname>