Merge pull request #610 from olyson/hrv_xsmrpool_to_atm

Add option to dribble XSMRPOOL at crop harvest to atmosphere over a half year
ESCOMP · Jan 15, 2019 · 02f0af2 · 02f0af2
2 parents aea3cfa + 1989e97
commit 02f0af2
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diff --git a/Externals.cfg b/Externals.cfg
@@ -30,7 +30,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime_cesm2_1_rel_05
+tag = cime_cesm2_1_rel_06
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -1705,6 +1705,10 @@ sub process_namelist_inline_logic {
   ################################################
   setup_logic_century_soilbgcdecompcascade($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
 
+  #############################
+  # namelist group: cngeneral #
+  #############################
+  setup_logic_cngeneral($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   ####################################
   # namelist group: cnvegcarbonstate #
   ####################################
@@ -3502,29 +3506,33 @@ sub setup_logic_lai_streams {
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
   if ( $physv->as_long() >= $physv->as_long("clm4_5") ) {
-    if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl_flags->{'use_lai_streams'}) ) {
+
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
+
+    if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams'))  ) {
       $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true.");
     }
     if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
 
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
-                  'hgrid'=>$nl_flags->{'res'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lai',
-                  'sim_year'=>$nl_flags->{'sim_year'},
-                  'sim_year_range'=>$nl_flags->{'sim_year_range'});
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lai',
-                  'sim_year'=>$nl_flags->{'sim_year'},
-                  'sim_year_range'=>$nl_flags->{'sim_year_range'});
-      # Set align year, if first and last years are different
-      if ( $nl->get_value('stream_year_first_lai') !=
-           $nl->get_value('stream_year_last_lai') ) {
-           add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-                       'model_year_align_lai', 'sim_year'=>$nl_flags->{'sim_year'},
-                       'sim_year_range'=>$nl_flags->{'sim_year_range'});
+      if ( &value_is_true($nl->get_value('use_lai_streams')) ) {
+         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
+                     'hgrid'=>$nl_flags->{'res'} );
+         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lai',
+                     'sim_year'=>$nl_flags->{'sim_year'},
+                     'sim_year_range'=>$nl_flags->{'sim_year_range'});
+         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lai',
+                     'sim_year'=>$nl_flags->{'sim_year'},
+                     'sim_year_range'=>$nl_flags->{'sim_year_range'});
+         # Set align year, if first and last years are different
+         if ( $nl->get_value('stream_year_first_lai') !=
+              $nl->get_value('stream_year_last_lai') ) {
+              add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+                          'model_year_align_lai', 'sim_year'=>$nl_flags->{'sim_year'},
+                          'sim_year_range'=>$nl_flags->{'sim_year_range'});
+         }
+         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lai',
+                     'hgrid'=>"360x720cru" );
       }
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lai',
-                  'hgrid'=>"360x720cru" );
     } else {
       # If bgc is CN/CNDV then make sure none of the LAI settings are set
       if ( defined($nl->get_value('stream_year_first_lai')) ||
@@ -3598,6 +3606,32 @@ sub setup_logic_cnvegcarbonstate {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_cngeneral {
+  # Must be set after setup_logic_co2_type
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  if ( $physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true($nl->get_value('use_cn')) ) {
+    if ( &value_is_true($nl->get_value('use_crop')) ) {
+       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dribble_crophrv_xsmrpool_2atm', 
+                   'co2_type' => remove_leading_and_trailing_quotes($nl->get_value('co2_type')), 
+                   'use_crop' => $nl->get_value('use_crop')  );
+    } else {
+      if ( defined($nl->get_value('dribble_crophrv_xsmrpool_2atm')) ) {
+        $log->fatal_error("When CROP is NOT on dribble_crophrv_xsmrpool_2atm can NOT be set\n" );
+      }
+    }
+  } else {
+    if ( defined($nl->get_value('reseed_dead_plants')) ||
+         defined($nl->get_value('dribble_crophrv_xsmrpool_2atm'))   ) {
+             $log->fatal_error("When CN is not on none of the following can be set: ,\n" .
+                  "dribble_crophrv_xsmrpool_2atm nor reseed_dead_plantsr\n" .
+                  "(eg. don't use these options with SP mode).");
+    }
+  }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_rooting_profile {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;

diff --git a/bld/namelist_files/namelist_defaults_clm4_5.xml b/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -447,6 +447,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_hydrstress phys="clm4_5"                 >.false.</use_hydrstress>
 <use_hydrstress phys="clm5_0" use_fates=".true." >.false.</use_hydrstress>
 <use_hydrstress phys="clm5_0" use_fates=".false.">.true.</use_hydrstress>
+
+<!-- General CN options -->
+<dribble_crophrv_xsmrpool_2atm co2_type="prognostic" use_crop=".true.">.true.</dribble_crophrv_xsmrpool_2atm>
+<dribble_crophrv_xsmrpool_2atm                       use_crop=".true.">.false.</dribble_crophrv_xsmrpool_2atm>
+
 <!--
 
      Initial condition files to use and or interpolate from

diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -1788,7 +1788,7 @@ Representative concentration pathway for future scenarios [radiative forcing at
 -999.9 means do NOT use a future scenario, just use historical data.
 </entry> 
 
-<entry id="ssp-rcp" type="character*8" category="default_settings"
+<entry id="ssp_rcp" type="character*8" category="default_settings"
        group="default_settings"  
        valid_values="hist,SSP1-2.6,SSP3-7.0,SSP5-3.4,SSP2-4.5,SSP1-1.9,SSP4-3.4,SSP4-6.0,SSP5-8.5">
 Shared Socioeconomic Pathway (SSP) and Representative Concentration Pathway (RCP) combination for future scenarios 
@@ -1970,6 +1970,11 @@ Number of days over which to use exponential relaxation of NPP in N fixation cal
 Flag to reseed any dead plants on startup from reading the initial conditions file
 </entry>
 
+<entry id="dribble_crophrv_xsmrpool_2atm" type="logical" category="clm_physics"
+       group="cn_general" valid_values="" >
+Harvest the XSMR pool at crop harvest time to the atmosphere slowly at an exponential rate
+</entry>
+
 <!-- C isotope flags    -->
 <entry id="use_c13" type="logical" category="clm_isotope"
        group="clm_inparm" valid_values="" >

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -123,7 +123,7 @@ sub make_env_run {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 947;
+my $ntests = 950;
 if ( defined($opts{'compare'}) ) {
    $ntests += 600;
 }
@@ -387,6 +387,21 @@ sub make_env_run {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      conopts=>"-phys clm4_5",
                                    },
+     "reseed without CN"         =>{ options=>" -envxml_dir . -bgc sp",
+                                     namelst=>"reseed_dead_plants=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     conopts=>"-phys clm5_0",
+                                   },
+     "dribble_crphrv w/o CN"     =>{ options=>" -envxml_dir . -bgc sp",
+                                     namelst=>"dribble_crophrv_xsmrpool_2atm=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     conopts=>"-phys clm5_0",
+                                   },
+     "dribble_crphrv w/o crop"   =>{ options=>" -envxml_dir . -bgc cn -no-crop",
+                                     namelst=>"dribble_crophrv_xsmrpool_2atm=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     conopts=>"-phys clm5_0",
+                                   },
      "CNDV with flanduse_timeseries"         =>{ options=>" -envxml_dir .",
                                      namelst=>"flanduse_timeseries='my_flanduse_timeseries_file.nc'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

diff --git a/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0001 b/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0001
@@ -10,4 +10,4 @@
  hist_type1d_pertape = ' ',' ',' '
 
  use_init_interp = .true.
- finidat = '/glade/p_old/image/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0001.r.2001-01-01-00000.nc'
+ finidat = '/glade/p/cisl/dares/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0001.r.2001-01-01-00000.nc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0002 b/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0002
@@ -10,4 +10,4 @@
  hist_type1d_pertape = ' ',' ',' '
 
  use_init_interp = .true.
- finidat = '/glade/p_old/image/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0002.r.2001-01-01-00000.nc'
+ finidat = '/glade/p/cisl/dares/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0002.r.2001-01-01-00000.nc'
diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+release-clm5.0.16     erik 01/15/2019 PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere
 release-clm5.0.15    sacks 12/06/2018 Option for rain-to-snow to immediately run off in some regions
 release-clm5.0.14     erik 11/29/2018 Update cime and fix surface dataset for f05 1850 non-crop case
 release-clm5.0.13     erik 11/14/2018 Update externals with new CO2/presearo/rtm/mosart, add science_support, change testing

diff --git a/doc/release-clm5.0.ChangeLog b/doc/release-clm5.0.ChangeLog
@@ -1,4 +1,103 @@
 ===============================================================
+Tag name:  release-clm5.0.16
+Originator(s):  erik (Erik Kluzek)
+Date: Tue Jan 15 15:13:43 MST 2019
+One-line Summary: PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere
+
+Purpose of this version:
+------------------------
+
+no-anthro changes on release branch. Update of mksurfdata for Antarctic. Also start adding in newly created SSP-RCP datasets that are easy to add in.
+Also add in new option for dribble_crophrv_xsmrpool_2atm.
+
+CTSM Master Tag This Corresponds To: N/A
+
+Summary of changes:
+-------------------
+
+Issues fixed (include CTSM Issue #): #553 #533 #589 #547 #545
+  #553 -- More robust mksurfdata_map logic for determining where to put wetlands
+  #533 -- Add -no-anthro option to mksurfdata_map
+  #589 -- Existence of content in the lai_streams namelist makes it confusing to users
+  #547 -- Add conus_30_x8 grid as valid option for CTSM and mksurfdata_map
+  #545 -- Antarctica ice shelves are being treated as wetlands rather than glaciers
+
+Science changes since: release-clm5.0.15
+  mksurfdata now properly makes Antarctica teated as glacier rather than wetland
+  Add in option to create all of the SSP-RCP future scenarios in mksurfdata_map
+  Add dribble_crophrv_xsmrpool_2atm, to do slow release of crop harvested XSMRPOOL to atmosphere
+    (only active by default when co2_type="prognostic")
+
+Software changes since: release-clm5.0.15
+  Add no-anthro option for mksurfdata_map
+
+Changes to User Interface since: release-clm5.0.15
+  New namelist option: dribble_crophrv_xsmrpool_2atm
+  Add SSP-RCP future scenarios can be done in mksurfdata_map
+
+Testing:
+--------
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - PASS
+
+  unit-tests (components/clm/src):
+
+    cheyenne - PASS
+    hobart --- PASS
+
+  tools-tests (components/clm/test/tools):
+
+    cheyenne - PASS
+    hobart ---
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     cheyenne - PASS
+
+  regular tests (aux_clm):
+
+    cheyenne_intel ---- OK
+    cheyenne_gnu ------ OK
+    hobart_nag -------- OK
+    hobart_pgi -------- OK
+    hobart_intel ------ OK
+
+Summary of Answer changes:
+-------------------------
+
+Baseline version for comparison: release-clm5.0.15
+
+Changes answers relative to baseline: No bit-for-bit
+
+Detailed list of changes:
+------------------------
+
+Externals being used:
+
+   cism:   release-cesm2.0.04
+   rtm:    release-cesm2.0.02
+   mosart: release-cesm2.0.03
+   cime:   cime_cesm2_1_rel_06
+   FATES:  fates_s1.8.1_a3.0.0
+   PTCLM:  PTCLM2_180611
+
+CTSM Tag versions pulled over from master development branch: N/A
+
+Pull Requests that document the changes (include PR ids):  #567 #561 #564 #616 #610
+(https://github.com/ESCOMP/ctsm/pull)
+
+   #616 -- No anthro options to tools, and all future scenarios in place, plus a few small issue fixes
+   #610 -- Add option to dribble XSMRPOOL at crop harvest to atmosphere over a half year
+   #567 -- ignore patterns for vim
+   #564 -- Update mksurfdata_map to include glaciers outside of pft landmask
+   #561 -- Add list of checks for new surface datasets
+
+===============================================================
+===============================================================
 Tag name:  release-clm5.0.15
 Originator(s):  sacks (Bill Sacks)
 Date: Thu Dec  6 10:14:30 MST 2018

diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90
@@ -146,7 +146,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
          er                      =>    cnveg_carbonflux_inst%er_col                     , & ! Input:  [real(r8) (:) ]  (gC/m2/s) total ecosystem respiration, autotrophic + heterotrophic
          col_fire_closs          =>    cnveg_carbonflux_inst%fire_closs_col             , & ! Input:  [real(r8) (:) ]  (gC/m2/s) total column-level fire C loss
          col_hrv_xsmrpool_to_atm =>    cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_col    , & ! Input:  [real(r8) (:) ]  (gC/m2/s) excess MR pool harvest mortality 
-
+         col_xsmrpool_to_atm     =>   cnveg_carbonflux_inst%xsmrpool_to_atm_col         , & ! Input:  [real(r8) (:) ]  (gC/m2/s) excess MR pool crop harvest loss to atm
          som_c_leached           =>    soilbiogeochem_carbonflux_inst%som_c_leached_col , & ! Input:  [real(r8) (:) ]  (gC/m2/s) total SOM C loss from vertical transport 
 
          totcolc                 =>    cnveg_carbonstate_inst%totc_col                    & ! Input:  [real(r8) (:) ]  (gC/m2) total column carbon, incl veg and cpool
@@ -167,7 +167,8 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
 
          ! calculate total column-level outputs
          ! er = ar + hr, col_fire_closs includes patch-level fire losses
-         col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c)
+         col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + &
+              col_xsmrpool_to_atm(c)
 
          ! Fluxes to product pools are included in column-level outputs: the product
          ! pools are not included in totcolc, so are outside the system with respect to
@@ -211,6 +212,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
          write(iulog,*)'er                       = ',er(c)*dt
          write(iulog,*)'col_fire_closs           = ',col_fire_closs(c)*dt
          write(iulog,*)'col_hrv_xsmrpool_to_atm  = ',col_hrv_xsmrpool_to_atm(c)*dt
+         write(iulog,*)'col_xsmrpool_to_atm      = ',col_xsmrpool_to_atm(c)*dt
          write(iulog,*)'wood_harvestc            = ',wood_harvestc(c)*dt
          write(iulog,*)'grainc_to_cropprodc      = ',grainc_to_cropprodc(c)*dt
          write(iulog,*)'-1*som_c_leached         = ',som_c_leached(c)*dt