Merge pull request #552 from ekluzek/transcrop2rel

Move fix for transient non-crop to release-clm5.0 branch

CTSMMasterChecklist

@@ -0,0 +1,71 @@
+Checklist of steps to do to make a CTSM Trunk Tag        Oct/1st/2018
+
+CTSM Software Management team.
+
+See the wiki page for this on:
+
+https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow
+
+(1) Update your branch to latest version of ESCOMP/ctsm master branch (git fetch followed
+    by git merge)
+
+(2) Make sure you have the latest version of code in your testing sandbox
+
+   2a -- run 'git pull' to pull in the latest version from GitHub
+   2b -- run 'git status' and/or 'git diff' to make sure you don't have any uncommitted
+         local changes
+   2c -- run './manage_externals/checkout_externals -S' to make sure all externals are
+         updated and don't have any uncommitted changes. (If any are marked with 's' in
+         the first column, run ./manage_externals/checkout_externals to update them.)
+
+(3) Do all testing on your fork/feature-branch
+
+   3a -- make sure any new failing tests are either fixed or approved as a new expected
+         fail
+   3b -- update the ExpectedFails list if expected fails changes in 1a
+        $EDITOR cime_config/testdefs/ExpectedTestFails.xml
+   3c -- make sure you understand any changes to the baselines -- to document in ChangeLog
+
+(4) Use diff and status to make sure any new files are in the repo and only the correct
+    changes are on the branch
+
+   4a -- 'git status' to check that you've added any new files and haven't
+         added any non source files that aren't needed in the repository
+   4b -- 'git diff' to check that your changes are correct and you didn't accidentally
+         add something unintentionally
+
+(5) Update ChangeLog
+
+   5a -- From the 'doc' directory, run './UpdateChangelog.pl TAGNAME "one-line summary"'.
+         This will open an editor with the ChangeLog. You can edit it now (step 4b) or
+         exit your editor and then reopen it manually.
+   5b -- Fill in the ChangeLog entry
+   5c -- Update date stamp on ChangeLog
+        ./UpDateChangeLog.pl -update
+   5d -- Commit new change files
+
+(6) Submit a pull request (PR) for the changes
+    Have someone review it if you are able. At minimum review it youself. The PR mechanism
+    on git is an excellent way to code review code for both yourself and others. Also make
+    sure all your changes are correct, changes that shouldn't have gone in don't, and all new
+    files are added in.
+
+---- THE FOLLOWING CAN ONLY BE DONE BY INTEGRATORS ----
+
+(7) Merge the PR to master when review is approved
+
+(8) Compare master to branch show that they are identical
+
+git diff master remote/feature-branch
+
+This should show no diffs
+
+(9) Make an annotated tag on master
+
+(10) Push master and tag to ESCOMP/ctsm
+
+---- NOTES ----
+
+(3) -- Always test on your fork with a feature-branch so that we can change tag order if needed. Put 
+baselines in the next tag name, as we can easily change afterwards if needed.
+

bld/CLMBuildNamelist.pm

@@ -1880,7 +1880,11 @@ sub setup_logic_irrigate {
   if ( $physv->as_long() >= $physv->as_long("clm4_5") ) {
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'irrigate',
                 'use_crop'=>$nl_flags->{'use_crop'}, 'use_cndv'=>$nl_flags->{'use_cndv'} );
-    $nl_flags->{'irrigate'} = lc($nl->get_value('irrigate'));
+    if ( &value_is_true($nl->get_value('irrigate') ) ) {
+       $nl_flags->{'irrigate'} = ".true."
+    } else {
+       $nl_flags->{'irrigate'} = ".false."
+    }
   }
 }
 
@@ -2074,6 +2078,9 @@ sub setup_logic_create_crop_landunit {
     if ( &value_is_true($nl_flags->{'use_fates'}) && &value_is_true($nl->get_value($var)) ) {
          $log->fatal_error( "$var is true and yet use_fates is being set, which contradicts that (use_fates requires $var to be .false." );
     }
+    if ( (! &value_is_true($nl_flags->{'use_fates'})) && (! &value_is_true($nl->get_value($var))) ) {
+         $log->fatal_error( "$var is false which is ONLY allowed when FATES is being used" );
+    }
   }
 }
 
@@ -2566,9 +2573,6 @@ sub setup_logic_do_transient_crops {
       if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
          $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
       }
-      elsif (!&value_is_true($nl->get_value('use_crop'))) {
-         $cannot_be_true = "$var can only be set to true when running with use_crop = true";
-      }
       elsif (&value_is_true($nl->get_value('use_fates'))) {
          # In principle, use_fates should be compatible with
          # do_transient_crops. However, this hasn't been tested, so to be safe,
@@ -2594,6 +2598,13 @@ sub setup_logic_do_transient_crops {
          $log->fatal_error($cannot_be_true);
       }
 
+      my $dopft = "do_transient_pfts";
+      # Make sure the value agrees with the do_transient_pft flag
+      if ( (  &value_is_true($nl->get_value($var))) && (! &value_is_true($nl->get_value($dopft))) ||
+           (! &value_is_true($nl->get_value($var))) && (  &value_is_true($nl->get_value($dopft))) ) {
+         $log->fatal_error("$var and $dopft do NOT agree and need to");
+      }
+
    }
 }
 
@@ -3047,9 +3058,12 @@ sub setup_logic_fertilizer {
    my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
    if ( $physv->as_long() >= $physv->as_long("clm4_5") ) {
-     $nl_flags->{'use_crop'} = $nl->get_value('use_crop');
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fertilizer',
      'use_crop'=>$nl_flags->{'use_crop'} );
+     my $use_fert = $nl->get_value('use_fertilizer');
+     if ( (! &value_is_true($nl_flags->{'use_crop'})) && &value_is_true($use_fert) ) {
+       $log->fatal_error("use_ferilizer can NOT be on without prognostic crop\n" );
+     }
   }
 }
 
@@ -3062,9 +3076,11 @@ sub setup_logic_grainproduct {
    my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
    if ( $physv->as_long() >= $physv->as_long("clm4_5") ) {
-     $nl_flags->{'use_crop'} = $nl->get_value('use_crop');
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_grainproduct',
      'use_crop'=>$nl_flags->{'use_crop'}, 'phys'=>$physv->as_string() );
+     if ( (! &value_is_true($nl_flags->{'use_crop'})) && &value_is_true($nl->get_value('use_grainproduct') ) ) {
+       $log->fatal_error("use_grainproduct can NOT be on without prognostic crop\n" );
+     }
   }
 }
 

bld/namelist_files/createMkSrfEntry.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+import os, sys
+
+class mksrfDataEntry_prog:
+
+   # Class data
+   year_start = 2016
+   year_end   = 2100
+   ssp_rcp    = "SSP5-8.5"
+   subdir     = "pftcftdynharv.0.25x0.25.SSP5-8.5.simyr2016-2100.c171005"
+   cdate      = 171005
+   desc       = "SSP5RCP85_clm5"
+
+   def parse_cmdline_args( self ):
+      "Parse the command line arguments for create data entry list"
+      from optparse import OptionParser, OptionGroup
+
+      parser   = OptionParser( usage="%prog [options]" )
+      options = OptionGroup( parser, "Options" )
+      options.add_option( "-s", "--year_start", dest="year_start", default=self.year_start, \
+                        help="Start year" )
+      options.add_option( "-f", "--year_end", dest="year_end", default=self.year_end, \
+                        help="End year" )
+      options.add_option( "-d", "--subdir", dest="subdir", default=self.subdir, \
+                        help="Subdirectory" )
+      options.add_option( "--cdate", dest="cdate", default=self.cdate, \
+                        help="Creation date" )
+      options.add_option( "--desc", dest="desc", default=self.desc, \
+                        help="Description string" )
+      parser.add_option_group(options)
+      (options, args) = parser.parse_args()
+      if len(args) != 0:
+          parser.error("incorrect number of arguments")
+
+      self.year_start = options.year_start
+      self.year_end   = options.year_end
+      self.subdir     = options.subdir
+      self.cdate      = options.cdate
+      self.desc       = options.desc
+
+   def printentry( self, year ):
+      "Print a single entry"
+      print '<mksrf_fvegtyp hgrid="0.25x0.25" ssp_rcp="%s" sim_year="%d" crop="on"' % (self.ssp_rcp, year)
+      print '>lnd/clm2/rawdata/%s/mksrf_landuse_%s_%s.c%s.nc' % (self.subdir, self.desc, year, self.cdate)
+      print '</mksrf_fvegtyp>\n'
+
+entry = mksrfDataEntry_prog()
+entry.parse_cmdline_args()
+
+for year in range(entry.year_start, entry.year_end+1):
+   entry.printentry( year )
+
+
+
+