MIMICS into vertically resolved CTSM

bld/CLMBuildNamelist.pm

@@ -90,7 +90,7 @@ OPTIONS
                                 sp    = Satellite Phenology (SP)
                                     This toggles off the namelist variable: use_cn
                                 bgc   = Carbon Nitrogen with methane, nitrification, vertical soil C,
-                                        CENTURY decomposition
+                                        CENTURY or MIMICS decomposition
                                     This toggles on the namelist variables:
                                           use_cn, use_lch4, use_nitrif_denitrif
                                 fates = FATES/Ecosystem Demography with below ground BGC
@@ -852,7 +852,6 @@ sub setup_cmdl_bgc {
      $log->fatal_error("The namelist variable use_fates is inconsistent with the -bgc option");
   }
 
-
   # Now set use_cn and use_fates
   foreach $var ( "use_cn", "use_fates" ) {
      $val = $nl_flags->{$var};
@@ -876,7 +875,7 @@ sub setup_cmdl_bgc {
         $log->fatal_error("$var must NOT be None if use_cn or use_fates are on");
      }
   } elsif ( $soil_decomp_method ne "None" ) {
-     $log->fatal_error("$var must be None if use_cn or use_fates are not");
+     $log->fatal_error("$var must be None if use_cn and use_fates are off");
   }
   #
   # Soil decomposition control variables, methane and Nitrification-Denitrification
@@ -2760,7 +2759,6 @@ sub setup_logic_bgc_shared {
   if ( $nl_flags->{'bgc_mode'} ne "sp" ) {
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'constrain_stress_deciduous_onset', 'phys'=>$physv->as_string() );
   }
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'decomp_depth_efolding', 'phys'=>$physv->as_string() );
 }
 
 #-------------------------------------------------------------------------------

bld/listDefaultNamelist.pl

@@ -270,11 +270,17 @@ sub GetListofNeededFiles {
 
            my @bgcsettings   = $definition->get_valid_values( "bgc_mode", 'noquotes'=>1 );
            print "bgc=@bgcsettings\n" if $printing;
+           print "decomp=@decompsettings\n" if $printing;
            #
            # Loop over all possible BGC settings
            #
            foreach my $bgc ( @bgcsettings ) {
               $settings{'bgc'} = $bgc;
+              if ( $bgc eq "bgc" || $bgc eq "fates" ) {
+                foreach my $decomp ( @decompsettings ) {
+                  $settings{'decomp'} = $decomp;
+                }
+              }
               my @crop_vals;
               if ( $bgc =~ /^cn/ ) {
                  @crop_vals = ( "on", "off" );

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -481,9 +481,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210923.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210803.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210803.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c211106.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c211106.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c211106.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -566,11 +566,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <onset_thresh_depends_on_veg                                    >.false.</onset_thresh_depends_on_veg>
 <min_critical_dayl_method                                       >Constant</min_critical_dayl_method>
 
-<!-- turnover time modifications    -->
-<decomp_depth_efolding phys="clm4_5" >0.5</decomp_depth_efolding>
-<decomp_depth_efolding phys="clm5_0" >10.0</decomp_depth_efolding>
-<decomp_depth_efolding phys="clm5_1" >10.0</decomp_depth_efolding>
-
 <!-- use additional stress deciduous onset trigger    -->
 <constrain_stress_deciduous_onset phys="clm4_5" >.false.</constrain_stress_deciduous_onset>
 <constrain_stress_deciduous_onset phys="clm5_0" >.true.</constrain_stress_deciduous_onset>
@@ -2534,7 +2529,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 >lnd/clm2/paramdata/finundated_inversiondata_0.9x1_ESMFmesh_cdf5_130621.nc</stream_meshfile_ch4finundated>
 
 <!-- =========================================  -->
-<!-- Defaults for different BGC modes           -->
+<!-- Defaults for different BGC/decomp modes    -->
 <!-- =========================================  -->
 
 <soil_decomp_method use_cn=".true."    >CENTURYKoven2013</soil_decomp_method>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -2118,12 +2118,6 @@ Base advective flux (downwards) for SOM.
 Maximum depth to mix soils to by croturbation, in permafrost soils.
 </entry>
 
-<!-- turnover time modifications    -->
-<entry id="decomp_depth_efolding" type="real" category="clm_vertcn"
-       group="bgc_shared" valid_values="" >
-E-folding depth over which decomposition is slowed with depth in all soils.
-</entry>
-
 <entry id="anoxia" type="logical" category="clm_vertcn"
        group="clm_inparm" valid_values="" >
 If TRUE, reduce heterotrophic respiration according to available oxygen predicted by CH4 submodel.
@@ -2160,10 +2154,11 @@ Number of days over which to use exponential relaxation of NPP in N fixation cal
 
 <!-- Soil decomposition options  -->
 <entry id="soil_decomp_method" type="char*20" category="clm_physics"
-       group="soilbgc_decomp" valid_values="None,CENTURYKoven2013" >
+       group="soilbgc_decomp" valid_values="None,CENTURYKoven2013,MIMICSWieder2015" >
 Soil decomposition method
   None --  No soil decomposition is done
   CENTURYKoven2013 -- CENTURY model in CTSM from Koven et. al. 2013
+  MIMICSWieder2015 -- MIMICS model in CTSM from Wieder et. al. 2015
 
 An active soil decomposition method requires the BGC or FATES model to work 
 And both BGC and FATES models require an active soil decomposition model

cime_config/testdefs/testlist_clm.xml

@@ -538,6 +538,24 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/mimics">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
+    </options>
+  </test>
+  <test name="SMS_Ld5_Mmpi-serial" grid="1x1_brazil" compset="IHistClm50BgcQianRs" testmods="clm/mimics">
+    <machines>
+      <machine name="izumi" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
+    </options>
+  </test>
   <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>

cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/README

@@ -1,5 +1,5 @@
 This points to an alternate params file with
-rf_cwdl2_bgc = 0.5
+rf_cwdl2     = 0.5
 rf_cwdl3_bgc = 0.5
 while by default these parameters equal zero.
 

cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm

@@ -1,2 +1,2 @@
-paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_params.c210827.nc'
+paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c211106.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'

cime_config/testdefs/testmods_dirs/clm/mimics/README

@@ -0,0 +1,2 @@
+This test mod turns on the MIMICS instead of the CENTURY below-ground
+biogeochemistry.

cime_config/testdefs/testmods_dirs/clm/mimics/include_user_mods

@@ -0,0 +1 @@
+../coldStart

cime_config/testdefs/testmods_dirs/clm/mimics/user_nl_clm

@@ -0,0 +1 @@
+soil_decomp_method = 'MIMICSWieder2015'

cime_config/usermods_dirs/newton_krylov_spinup/shell_commands

@@ -0,0 +1,3 @@
+#!/bin/bash
+./xmlchange CLM_FORCE_COLDSTART="on"
+

cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm

@@ -0,0 +1,15 @@
+hist_dov2xy = .true.,.false.
+hist_nhtfrq = 0,-175200
+hist_mfilt = 1,1
+hist_fincl2 = 'FPI_vr', 'K_PAS_SOM', 'K_SLO_SOM', 'K_ACT_SOM',
+              'K_CWD', 'K_CEL_LIT', 'K_LIG_LIT', 'K_MET_LIT',
+              'CWD_PATHFRAC_L2_vr', 'CWD_RESP_FRAC_L2_vr',
+              'CWD_PATHFRAC_L3_vr', 'CWD_RESP_FRAC_L3_vr',
+              'L1_PATHFRAC_S1_vr', 'L1_RESP_FRAC_S1_vr',
+              'L2_PATHFRAC_S1_vr', 'L2_RESP_FRAC_S1_vr',
+              'L3_PATHFRAC_S2_vr', 'L3_RESP_FRAC_S2_vr',
+              'S1_PATHFRAC_S2_vr', 'S1_RESP_FRAC_S2_vr'
+              'S1_PATHFRAC_S3_vr', 'S1_RESP_FRAC_S3_vr'
+              'S2_PATHFRAC_S1_vr', 'S2_RESP_FRAC_S1_vr'
+              'S2_PATHFRAC_S3_vr', 'S2_RESP_FRAC_S3_vr'
+              'S3_PATHFRAC_S1_vr', 'S3_RESP_FRAC_S1_vr'

src/biogeochem/CNBalanceCheckMod.F90

@@ -325,7 +325,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
       do g = bounds%begg, bounds%endg
          ! calculate gridcell-level carbon storage for mass conservation check
          ! Notes:
-         ! totgrcc = totcolc = totc_p2c_col(c) + soilbiogeochem_cwdc_col(c) + soilbiogeochem_totlitc_col(c) + soilbiogeochem_totsomc_col(c) + soilbiogeochem_ctrunc_col(c)
+         ! totgrcc = totcolc = totc_p2c_col(c) + soilbiogeochem_cwdc_col(c) + soilbiogeochem_totlitc_col(c) + soilbiogeochem_totmicc_col(c) + soilbiogeochem_totsomc_col(c) + soilbiogeochem_ctrunc_col(c)
          ! totc_p2c_col = totc_patch = totvegc_patch(p) + xsmrpool_patch(p) + ctrunc_patch(p) + cropseedc_deficit_patch(p)
          ! Not including seedc_grc in grc_begcb and grc_endcb because
          ! seedc_grc forms out of thin air, for now, and equals
@@ -540,7 +540,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, &
          write(iulog,*)'output mass              = ',col_noutputs(c)*dt
          write(iulog,*)'net flux                 = ',(col_ninputs(c)-col_noutputs(c))*dt
          write(iulog,*)'inputs,ffix,nfix,ndep    = ',ffix_to_sminn(c)*dt,nfix_to_sminn(c)*dt,ndep_to_sminn(c)*dt
-         write(iulog,*)'outputs,ffix,nfix,ndep   = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt
+         write(iulog,*)'outputs,lch,roff,dnit    = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt
          call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, msg=errMsg(sourcefile, __LINE__))
       end if