ESCOMP · ekluzek · Aug 6, 2020 · May 20, 2020 · May 20, 2020 · May 20, 2020
diff --git a/Externals.cfg b/Externals.cfg
@@ -16,14 +16,14 @@ required = True
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_71
+tag = rtm1_0_72
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_36
+tag = mosart1_0_37
 required = True
 
 [cime]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -1817,7 +1817,8 @@ sub setup_logic_co2_type {
       my $group = $definition->get_group_name($var);
       $nl->set_variable_value($group, $var, $opts->{$var});
     } else {
-      add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'sim_year'=>$nl_flags->{'sim_year'} );
+      add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'sim_year'=>$nl_flags->{'sim_year'},
+                  'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
     }
   }
 }
@@ -2187,7 +2188,7 @@ sub setup_logic_surface_dataset {
      $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with ecosystem dynamics (use_fates=.true)." );
   }
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsurdat',
-              'hgrid'=>$nl_flags->{'res'},
+              'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'},
               'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'},
               'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'});
 }
@@ -2244,11 +2245,11 @@ sub setup_logic_initial_conditions {
        $settings{'sim_year'}     = $nl_flags->{'sim_year'};
        $opts->{'ignore_ic_year'} = 1; 
     } else {
-       delete( $settings{'sim_year'} );
+       $settings{'sim_year'}     = $st_year;
     }
     foreach my $item ( "mask", "maxpft", "irrigate", "glc_nec", "use_crop", "use_cn", "use_cndv", 
                        "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp", "use_fates",
-                       "lnd_tuning_mode"
+                       "lnd_tuning_mode", 
                      ) {
        $settings{$item}    = $nl_flags->{$item};
     }
@@ -2296,10 +2297,8 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
              my $how_close = undef;
              if ( $nl_flags->{'sim_year'} eq "PtVg" ) {
                 $how_close = abs(1850 - $sim_yr);
-             # EBK 07/20/2020 -- This makes sure the sim_year matched is based on the sim-year
-             #                   rather than  the start year.
-             #} elsif ( $nl_flags->{'flanduse_timeseries'} eq "null" ) {
-             #   $how_close = abs($nl_flags->{'sim_year'} - $sim_yr);
+             } elsif ( $nl_flags->{'flanduse_timeseries'} eq "null" ) {
+                $how_close = abs($nl_flags->{'sim_year'} - $sim_yr);
              } else {
                 $how_close = abs($st_year - $sim_yr);
              }
@@ -2321,7 +2320,7 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
           }    # SIMYR:
           $settings{'sim_year'} = $closest_sim_year;
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $useinitvar,
-                      'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(),
+                      'use_cndv'=>$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);
@@ -3127,9 +3126,17 @@ sub setup_logic_nitrogen_deposition {
                 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
                 'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 );
     if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) {
+       # Also check at f19 resolution
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'},
                    'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
-                   'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+                   'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 );
+       # If not found report an error
+       if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) {
+          $log->warning("Did NOT find the Nitrogen-deposition forcing file (stream_fldfilename_ndep) for this ssp_rcp\n" .
+                        "One way to get around this is to point to a file for another existing ssp_rcp in your user_nl_clm file.\n" .
+                        "If you are running with CAM and WACCM chemistry Nitrogen deposition will come through the coupler.\n" .
+                        "This file won't be used, so it doesn't matter what it points to -- but it's required to point to something.\n" )
+       }
     }
   } else {
     # If bgc is NOT CN/CNDV then make sure none of the ndep settings are set!

diff --git a/bld/namelist_files/namelist_defaults_ctsm_tools.xml b/bld/namelist_files/namelist_defaults_ctsm_tools.xml
@@ -271,6 +271,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <mksrf_furban   hgrid="3x3min"   lmask="LandScan2004"
 >lnd/clm2/rawdata/mksrf_urban_0.05x0.05_simyr2000.c120621.nc</mksrf_furban>
 
+<mksrf_furban   hgrid="3x3min"   lmask="LandScan2004" sim_year="PtVg"
+>lnd/clm2/rawdata/mksrf_urban_0.05x0.05_zerourbanpct.c181014.nc</mksrf_furban>
+
 <!-- mksrf_fglacier % glacier land-unit -->
 <!-- WJS (9-26-12): 
      There are two versions of this dataset: the "standard" version uses
@@ -300,6 +303,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- fire-related datasets -->
 <mksrf_fgdp hgrid="0.5x0.5" lmask="AVHRR"
 >lnd/clm2/rawdata/mksrf_gdp_0.5x0.5_AVHRR_simyr2000.c130228.nc</mksrf_fgdp>
+<mksrf_fgdp hgrid="0.5x0.5" lmask="AVHRR" sim_year="PtVg"
+>lnd/clm2/rawdata/mksrf_gdp_0.5x0_zerogdp.c200413.nc</mksrf_fgdp>
 
 <mksrf_fpeat hgrid="0.5x0.5" lmask="AVHRR"
 >lnd/clm2/rawdata/mksrf_peatf_0.5x0.5_AVHRR_simyr2000.c130228.nc</mksrf_fpeat>
@@ -309,6 +314,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <mksrf_fabm hgrid="0.5x0.5" lmask="AVHRR"
 >lnd/clm2/rawdata/mksrf_abm_0.5x0.5_AVHRR_simyr2000.c130201.nc</mksrf_fabm>
+<mksrf_fabm hgrid="0.5x0.5" lmask="AVHRR" sim_year="PtVg"
+>lnd/clm2/rawdata/mksrf_abm_0.5x0.5_missingabm.c200413.nc</mksrf_fabm>
+
 
 <mksrf_ftopostats hgrid="1km-merge-10min" lmask="HYDRO1K-merge-nomask"
 >lnd/clm2/rawdata/mksrf_topostats_1km-merge-10min_HYDRO1K-merge-nomask_simyr2000.c130402.nc</mksrf_ftopostats>
@@ -4672,7 +4680,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </mksrf_fvegtyp>
 
 <!-- 
-      Future scenarios 
+      Future scenarios  (up to 2100)
 -->
 
 <!-- SSP1-RCP 2.6 -->

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -2024,7 +2024,7 @@ How close in years to use when looking for an initial condition file (finidat) i
 </entry>
 
 <entry id="init_interp_sim_years" type="integer(6)"  category="default_settings"
-       group="default_settings" valid_values="1850,1979,1982,2000,2010,2013" >
+       group="default_settings" valid_values="1850,1979,2000,2010,2013" >
 Simulation years you can look for in initial condition files (finidat) if interpolation is turned on (use_init_interp is .true.)
 </entry>
 

diff --git a/bld/namelist_files/use_cases/2010_control.xml b/bld/namelist_files/use_cases/2010_control.xml
@@ -12,6 +12,11 @@
 <irrigate use_crop=".true." phys="clm5_0" use_cndv=".true." >.false.</irrigate>
 <irrigate use_crop=".true." phys="clm4_5"                   >.false.</irrigate>
 
+<finidat use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0" phys="clm5_0"
+>lnd/clm2/initdata_map/clmi.BHIST.2010-01-01.0.9x1.25_gx1v7_simyr2010_c181015.nc
+</finidat>
+<use_init_interp use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0" phys="clm5_0">.true.</use_init_interp>
+
 <stream_year_first_ndep phys="clm4_0" bgc="cn"   >2010</stream_year_first_ndep>
 <stream_year_last_ndep  phys="clm4_0" bgc="cn"   >2010</stream_year_last_ndep>
 

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -138,9 +138,9 @@ sub make_config_cache {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 890;
+my $ntests = 889;
 if ( defined($opts{'compare'}) ) {
-   $ntests += 549;
+   $ntests += 546;
 }
 plan( tests=>$ntests );
 
@@ -1043,6 +1043,11 @@ sub make_config_cache {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "missing_ndep_file"         =>{ options=>"-envxml_dir . -bgc bgc -ssp_rcp SSP5-3.4",
+                                     namelst=>"",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
      "bad_megan_spec"            =>{ options=>"-envxml_dir . -bgc bgc -megan",
                                      namelst=>"megan_specifier='ZZTOP=zztop'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1244,7 +1249,7 @@ sub make_config_cache {
 $phys = "clm4_5";
 $mode = "-phys $phys";
 &make_config_cache($phys);
-my @glc_res = ( "48x96", "0.9x1.25", "1.9x2.5" );
+my @glc_res = ( "0.9x1.25", "1.9x2.5" );
 my @use_cases = ( "1850-2100_SSP1-2.6_transient",
                   "1850-2100_SSP2-4.5_transient",
                   "1850-2100_SSP3-7.0_transient",
@@ -1286,7 +1291,7 @@ sub make_config_cache {
 $phys = "clm5_0";
 $mode = "-phys $phys";
 &make_config_cache($phys);
-my @tran_res = ( "48x96", "0.9x1.25", "1.9x2.5", "ne30np4", "10x15" );
+my @tran_res = ( "0.9x1.25", "1.9x2.5", "ne30np4", "10x15" );
 my $usecase  = "20thC_transient";
 my $GLC_NEC         = 10;
 foreach my $res ( @tran_res ) {

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -1162,7 +1162,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">01:20:00</option>
       <option name="comment"  >Run ARCTICGRIS for transient case starting in 1979 as for AMIP CAM cases"</option>
     </options>
   </test>
@@ -1171,7 +1171,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:40:00</option>
       <option name="comment"  >Run ARCTICGRIS for future transient case"</option>
     </options>
   </test>
@@ -1189,7 +1189,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:40:00</option>
       <option name="comment"  >Run ne30np4.pg2 to make sure will work for CAM"</option>
     </options>
   </test>
@@ -1198,7 +1198,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:40:00</option>
       <option name="comment"  >Run ne30np4.pg3 to make sure will work for CAM"</option>
     </options>
   </test>

diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/shell_commands
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+./xmlchange LND_TUNING_MODE="clm4_5_cam6.0"
+
diff --git a/cime_config/usermods_dirs/cmip6_waccm_deck/shell_commands b/cime_config/usermods_dirs/cmip6_waccm_deck/shell_commands
@@ -0,0 +1,3 @@
+#!/bin/bash
+# Turn ignore-warnings on, so won't abort on missing ndep file, as WACCM should provide it
+./xmlchange --append CLM_BLDNML_OPTS="--ignore_warnings"
diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,123 @@
 ===============================================================
+Tag name:  ctsm1.0.dev106
+Originator(s):  erik (Erik Kluzek)
+Date: Thu Aug  6 15:35:47 MDT 2020
+One-line Summary: Bit-for-bit updates for the CESM2.2.0 release
+
+Purpose of changes
+------------------
+
+Fix some bit-for-bit things needed for the CESM2.2.0 release
+Bring changes needed from release-clm5.0.31-34 to trunk. ndep change.
+Brings in some changes for PtVg datasets for no-anthro compset.
+Do some refactoring of Fire class so that it makes sense for FATES to use the base class.
+Update RTM and MOSART with NUOPC changes and an update of a NetCDF-4 file to NetCDF-5
+needed for the cesm2.2.0 release.
+
+The 2010 finidat file is now set in the 2010_control use-case rather than relying on the
+finidat dataset matching.
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #): 
+ Fixes #1087 -- wrong finidat file
+ Fixes #1096 -- failing tests
+ Fixes #1036 -- ne30 case fails
+ Fixes #946 --- better error message
+ Fixes #983 --- Fire method renames
+ Fixes #938 --- mscripgrid issue
+
+Known bugs found since the previous tag (include github issue ID): 
+  #1098 -- ARCTICGRIS PE-layout is very slow...
+  #1097 -- xsmrpool_loss should only be written to the restart file if use_crop is true
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations? No
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   if ndep file isn't found die with a warning rather than fatal error.
+   The warning allows you to override with CLM_BLDNML_OPTS="-ignore_warnings"
+
+   finidat file matching will now use the sim_year rather than start-year
+   for a control case (transient cases used the start-year)
+   Add 2010 f09 finidat file for clm5_0_cam6.0
+
+Changes made to namelist defaults (e.g., changed parameter values):
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+
+Substantial timing or memory changes: None
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing: 
+   Add clm45cam6LndTuningMode testmod
+   Some tests needed more wallclock
+
+Code reviewed by: self
+
+
+CTSM testing: regular
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - PASS (one test is different than ctsm1.0.dev105)
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    cheyenne -= PASS
+
+  regular tests (aux_clm):
+
+    cheyenne ---- PASS
+    izumi ------- PASS
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No (bit-for-bit)
+
+Detailed list of changes
+------------------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): rtm, mosart
+  RTM    to rtm1_0_72
+  MOSART to mosart1_0_37
+
+Pull Requests that document the changes (include PR ids): #1079
+(https://github.com/ESCOMP/ctsm/pull)
+  #1079 -- Bit-for-bit updates for the CESM2.2.0 release
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev105
 Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326) / Chris Fischer
 Date: Thu Jul 23 08:59:37 MDT 2020

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,10 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev106     erik 08/06/2020 Bit-for-bit updates for the CESM2.2.0 release
+release-clm5.0.34    erik 04/20/2020 Update doc for release-clm5.0 (SKIPPED), and fix issues with no-anthro surface dataset creation
+release-clm5.0.33    erik 04/07/2020 SKIPPED ON MASTER -- Turn irrigation on for 2300 SSP extensions
+release-clm5.0.32    erik 04/02/2020 SKIPPED ON MASTER -- Extensions to 2300 for SSP5-8.5,SSP5-3.4, and SSP1-2.6
+release-clm5.0.31    erik 03/29/2020 Bring raw 2100-2300 extension (SKIPPED), some other misc. changes
   ctsm1.0.dev105 erik/fis 07/23/2020 Bring in some new SE grids for CAM as well as initial condition files for them
   ctsm1.0.dev104    sacks 07/06/2020 Add LILAC
   ctsm1.0.dev103   slevis 06/29/2020 Gridcell-level error-check for methane (CH4)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,4 @@
		#!/bin/bash

		./xmlchange LND_TUNING_MODE="clm4_5_cam6.0"