ESCOMP · ekluzek · May 4, 2022 · Feb 9, 2022 · Feb 14, 2022 · Feb 14, 2022
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -901,6 +901,12 @@ sub setup_cmdl_bgc {
            $log->warning("$var normally use_nitrif_denitrif should only be FALSE if FATES is on, it has NOT been validated for being off for BGC mode" );
         }
      }
+     # if MIMICS is on and use_fates = .true. then use_lch4 must = .true.
+     if ( (! &value_is_true($nl_flags->{'use_lch4'})) && &value_is_true($nl_flags->{'use_fates'}) ) {
+        if ( $soil_decomp_method eq "MIMICSWieder2015" ) {
+           $log->warning("If MIMICS is on and use_fates = .true. then use_lch4 must be .true. and currently it's not" );
+        }
+     }
   }
   #
   # Set FUN for BGC

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -1961,6 +1961,16 @@
       <option name="comment">30 day exact restart test activating FATES size and age mortality mode on an f45 grid.</option>
     </options>
   </test>
+  <test name="ERP_P144x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/mimicsFatesColdDef">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="cheyenne" compiler="intel" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment">30 day exact restart test with threading, running FATES-MIMICS on an f45 grid.</option>
+    </options>
+  </test>
   <test name="SMS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50BgcCrop" testmods="clm/irrig_alternate">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm">

diff --git a/cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/include_user_mods
@@ -0,0 +1,2 @@
+../Fates
+../mimics
diff --git a/cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/shell_commands b/cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/shell_commands
@@ -0,0 +1 @@
+./xmlchange CLM_FORCE_COLDSTART="on"
diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,72 @@
 ===============================================================
+Tag name: ctsm5.1.dev093
+Originator(s): slevis (Samuel Levis)
+Date: Tue May  3 21:50:20 MDT 2022
+One-line Summary: Modifications for FATES-MIMICS to work
+
+Purpose and description of changes
+----------------------------------
+
+ 1) For FATES-MIMICS cases, use ligninNratioAvg calculated by FATES.
+ 2) For FATES-MIMICS cases, use annsum_npp_col calculated by FATES.
+ 3) Small modification to allow carbon-only to work with MIMICS.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(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_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+Issues fixed (include CTSM Issue #): 
+   Fixes #1636 -- FATES tests fail with MIMICS active
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+ MIMICS-FATES now do work together, but only as long as use_lch4 = .true.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ To confirm that MIMICS-FATES works, I added the testmod mimicsFatesColdDef.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- PASS
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+ ...but made history variable CWDC_HR active.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/1643
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev092
 Originator(s): sacks (Bill Sacks)
 Date: Fri Apr 29 18:31:48 MDT 2022

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev093   slevis 05/03/2022 Modifications for FATES-MIMICS to work
     ctsm5.1.dev092    sacks 04/29/2022 Refactor NutrientCompetition / CNAllocation to provide hooks for AgSys
     ctsm5.1.dev091   rgknox 04/22/2022 clm decomp method is now passed to fates to enabled mimics coupling
     ctsm5.1.dev090 samrabin 03/31/2022 Fix misleading name of "gddplant"

diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90
@@ -42,6 +42,8 @@ module CNDriverMod
   use SaturatedExcessRunoffMod        , only : saturated_excess_runoff_type
   use ActiveLayerMod                  , only : active_layer_type
   use SoilWaterRetentionCurveMod      , only : soil_water_retention_curve_type
+  use CLMFatesInterfaceMod            , only : hlm_fates_interface_type
+  use CropReprPoolsMod                    , only : nrepr
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -96,7 +98,7 @@ subroutine CNDriverNoLeaching(bounds,
        c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst,            &
        soilbiogeochem_state_inst,                                                          &
        soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst,                &
-       active_layer_inst,                                                                  &
+       active_layer_inst, clm_fates,                                                       &
        atm2lnd_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, waterfluxbulk_inst,    &
        wateratm2lndbulk_inst, canopystate_inst, soilstate_inst, temperature_inst,          &
        soil_water_retention_curve, crop_inst, ch4_inst,            &
@@ -200,6 +202,7 @@ subroutine CNDriverNoLeaching(bounds,
     class(nutrient_competition_method_type) , intent(inout) :: nutrient_competition_method
     class(fire_method_type)                 , intent(inout) :: cnfire_method
     logical                                 , intent(in)    :: dribble_crophrv_xsmrpool_2atm
+    type(hlm_fates_interface_type)          , intent(inout) :: clm_fates
     !
     ! !LOCAL VARIABLES:
     real(r8):: cn_decomp_pools(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_pools)
@@ -322,6 +325,7 @@ subroutine CNDriverNoLeaching(bounds,
             soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst)
     else if (decomp_method == mimics_decomp) then
        call decomp_rates_mimics(bounds, num_soilc, filter_soilc, &
+            num_soilp, filter_soilp, clm_fates, &
             soilstate_inst, temperature_inst, cnveg_carbonflux_inst, ch4_inst, &
             soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst)
     end if
@@ -1056,12 +1060,14 @@ subroutine CNDriverSummarizeFluxes(bounds, &
     type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst
     !
     ! !LOCAL VARIABLES:
+    integer :: begp,endp
     integer :: begc,endc
     integer :: begg,endg
 
     character(len=*), parameter :: subname = 'CNDriverSummarizeFluxes'
     !-----------------------------------------------------------------------
 
+    begp = bounds%begp; endp= bounds%endp
     begc = bounds%begc; endc= bounds%endc
     begg = bounds%begg; endg = bounds%endg
 
@@ -1071,12 +1077,30 @@ subroutine CNDriverSummarizeFluxes(bounds, &
     ! soilbiogeochem carbon/nitrogen flux summary
     ! ----------------------------------------------
 
-    call soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc)
+    call soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, &
+         num_soilp, filter_soilp, &
+         soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), &
+         soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), &
+         soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), &
+         leafc_to_litter_patch=cnveg_carbonflux_inst%leafc_to_litter_patch(begp:endp), &
+         frootc_to_litter_patch=cnveg_carbonflux_inst%frootc_to_litter_patch(begp:endp))
     if ( use_c13 ) then
-       call c13_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc)
+       call c13_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, &
+         num_soilp, filter_soilp, &
+         c13_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), &
+         c13_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), &
+         soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), &
+         leafc_to_litter_patch=c13_cnveg_carbonflux_inst%leafc_to_litter_patch(begp:endp), &
+         frootc_to_litter_patch=c13_cnveg_carbonflux_inst%frootc_to_litter_patch(begp:endp))
     end if
     if ( use_c14 ) then
-       call c14_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc)
+       call c14_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, &
+         num_soilp, filter_soilp, &
+         c14_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), &
+         c14_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), &
+         soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), &
+         leafc_to_litter_patch=c14_cnveg_carbonflux_inst%leafc_to_litter_patch(begp:endp), &
+         frootc_to_litter_patch=c14_cnveg_carbonflux_inst%frootc_to_litter_patch(begp:endp))
     end if
     call soilbiogeochem_nitrogenflux_inst%Summary(bounds, num_soilc, filter_soilc)
 
@@ -1092,8 +1116,6 @@ subroutine CNDriverSummarizeFluxes(bounds, &
          soilbiogeochem_lithr_col=soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), &  
          soilbiogeochem_decomp_cascade_ctransfer_col=&
          soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), &
-         soilbiogeochem_cwdc_col=soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), &
-         soilbiogeochem_cwdn_col=soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), &
          product_closs_grc=c_products_inst%product_loss_grc(begg:endg))
 
     if ( use_c13 ) then
@@ -1104,8 +1126,6 @@ subroutine CNDriverSummarizeFluxes(bounds, &
             soilbiogeochem_lithr_col=c13_soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), &  
             soilbiogeochem_decomp_cascade_ctransfer_col=&
             c13_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), &
-            soilbiogeochem_cwdc_col=c13_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), &
-            soilbiogeochem_cwdn_col=soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), &
             product_closs_grc=c13_products_inst%product_loss_grc(begg:endg))
     end if
 
@@ -1117,8 +1137,6 @@ subroutine CNDriverSummarizeFluxes(bounds, &
             soilbiogeochem_lithr_col=c14_soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), &  
             soilbiogeochem_decomp_cascade_ctransfer_col=&
             c14_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), &
-            soilbiogeochem_cwdc_col=c14_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), &
-            soilbiogeochem_cwdn_col=soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), &
             product_closs_grc=c14_products_inst%product_loss_grc(begg:endg))
     end if
     call t_stopf('CNvegCflux_summary')

diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90
@@ -11,7 +11,7 @@ module CNVegCarbonFluxType
   use decompMod                          , only : bounds_type
   use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
   use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools
-  use clm_varpar                         , only : nlevdecomp_full, nlevdecomp, i_litr_min, i_litr_max, i_cwdl2
+  use clm_varpar                         , only : nlevdecomp_full, nlevdecomp, i_litr_min, i_litr_max
   use clm_varcon                         , only : spval, dzsoi_decomp
   use clm_varctl                         , only : use_cndv, use_c13, use_nitrif_denitrif, use_crop
   use clm_varctl                         , only : use_grainproduct
@@ -338,9 +338,6 @@ module CNVegCarbonFluxType
      real(r8), pointer :: nbp_grc        (:) ! (gC/m2/s) net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux, positive for sink (same as net carbon exchange between land and atmosphere)
      real(r8), pointer :: nee_grc        (:) ! (gC/m2/s) net ecosystem exchange of carbon, includes fire and hrv_xsmrpool, excludes landuse and harvest flux, positive for source 
 
-     ! Plant C to N ratios
-     real(r8), pointer :: ligninNratioAvg_col(:)  ! Average of leaf, fine root, and CWD lignin to N ratio
-
      ! Dynamic landcover fluxnes
      real(r8), pointer :: landuseflux_grc(:) ! (gC/m2/s) dwt_conv_cflux+product_closs
      real(r8), pointer :: npp_Nactive_patch                         (:)     ! C used by mycorrhizal uptake    (gC/m2/s)
@@ -709,8 +706,6 @@ subroutine InitAllocate(this, bounds, carbon_type)
     allocate(this%annsum_npp_col          (begc:endc)) ; this%annsum_npp_col          (:) = nan
     allocate(this%lag_npp_col             (begc:endc)) ; this%lag_npp_col             (:) = spval
 
-    allocate(this%ligninNratioAvg_col     (begc:endc)) ; this%ligninNratioAvg_col     (:) = nan
-
     allocate(this%nep_col                 (begc:endc)) ; this%nep_col                 (:) = nan
     allocate(this%nbp_grc                 (begg:endg)) ; this%nbp_grc                 (:) = nan
     allocate(this%nee_grc                 (begg:endg)) ; this%nee_grc                 (:) = nan
@@ -3439,12 +3434,10 @@ subroutine InitCold(this, bounds)
 
        if (lun%ifspecial(l)) then
           this%annsum_npp_col(c) = spval
-          this%ligninNratioAvg_col(c) = spval
        end if
 
        if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
           this%annsum_npp_col(c) = 0._r8   
-          this%ligninNratioAvg_col(c) = 0._r8
        end if
     end do
 
@@ -3670,11 +3663,6 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag )
          long_name='', units='', &
          interpinic_flag='interp', readvar=readvar, data=this%annsum_npp_col) 
 
-    call restartvar(ncid=ncid, flag=flag, varname='ligninNratioAvg', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%ligninNratioAvg_col)
-
     call restartvar(ncid=ncid, flag=flag, varname='tempsum_litfall', xtype=ncd_double,  &
          dim1name='pft', &
          long_name='', units='', &
@@ -4108,7 +4096,6 @@ subroutine Summary_carbonflux(this, &
        bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, isotope, &
        soilbiogeochem_hr_col, soilbiogeochem_cwdhr_col, soilbiogeochem_lithr_col, &
        soilbiogeochem_decomp_cascade_ctransfer_col, &
-       soilbiogeochem_cwdc_col, soilbiogeochem_cwdn_col, &
        product_closs_grc)
     !
     ! !DESCRIPTION:
@@ -4119,8 +4106,8 @@ subroutine Summary_carbonflux(this, &
     use clm_varcon                         , only: secspday
     use clm_varctl                         , only: nfix_timeconst, carbon_resp_opt
     use subgridAveMod                      , only: p2c, c2g
-    use SoilBiogeochemDecompCascadeConType , only: decomp_cascade_con, mimics_decomp, decomp_method
-    use CNSharedParamsMod                  , only: use_fun, CNParamsShareInst
+    use SoilBiogeochemDecompCascadeConType , only: decomp_cascade_con
+    use CNSharedParamsMod                  , only: use_fun
     !
     ! !ARGUMENTS:
     class(cnveg_carbonflux_type)   :: this
@@ -4134,22 +4121,13 @@ subroutine Summary_carbonflux(this, &
     real(r8)          , intent(in) :: soilbiogeochem_cwdhr_col(bounds%begc:)
     real(r8)          , intent(in) :: soilbiogeochem_lithr_col(bounds%begc:)
     real(r8)          , intent(in) :: soilbiogeochem_decomp_cascade_ctransfer_col(bounds%begc:,1:)
-    real(r8)          , intent(in) :: soilbiogeochem_cwdc_col(bounds%begc:)
-    real(r8)          , intent(in) :: soilbiogeochem_cwdn_col(bounds%begc:)
     real(r8)          , intent(in) :: product_closs_grc(bounds%begg:)
     !
     ! !LOCAL VARIABLES:
     integer  :: c,p,j,k,l,g     ! indices
     integer  :: fp,fc           ! lake filter indices
     real(r8) :: nfixlags, dtime ! temp variables for making lagged npp
     real(r8) :: maxdepth        ! depth to integrate soil variables
-    real(r8) :: ligninNratio_cwd  ! lignin to N ratio of CWD
-    real(r8) :: ligninNratio_leaf_patch(bounds%begp:bounds%endp)  ! lignin to N ratio of leaves, patch level
-    real(r8) :: ligninNratio_froot_patch(bounds%begp:bounds%endp)  ! lignin to N ratio of fine roots, patch level
-    real(r8) :: ligninNratio_leaf_col(bounds%begc:bounds%endc)  ! lignin to N ratio of leaves, column level
-    real(r8) :: ligninNratio_froot_col(bounds%begc:bounds%endc)  ! lignin to N ratio of fine roots, column level
-    real(r8) :: leafc_to_litter_col(bounds%begc:bounds%endc)  ! leaf C to litter C, column level
-    real(r8) :: frootc_to_litter_col(bounds%begc:bounds%endc)  ! fine root C to litter C, column level
     real(r8) :: nep_grc(bounds%begg:bounds%endg)        ! nep_col averaged to gridcell
     real(r8) :: fire_closs_grc(bounds%begg:bounds%endg) ! fire_closs_col averaged to gridcell
     real(r8) :: hrv_xsmrpool_to_atm_grc(bounds%begg:bounds%endg) ! hrv_xsmrpool_to_atm_col averaged to gridcell (gC/m2/s)
@@ -4539,17 +4517,6 @@ subroutine Summary_carbonflux(this, &
             this%hrv_gresp_storage_to_litter_patch(p)      + &
             this%hrv_gresp_xfer_to_litter_patch(p)
 
-       if (decomp_method == mimics_decomp) then
-          ! Calculate ligninNratio for leaves and fine roots
-          associate(ivt => patch%itype)  ! Input: [integer (:)] patch plant type
-            ligninNratio_leaf_patch(p) = pftcon%lf_flig(ivt(p)) * &
-                                         pftcon%lflitcn(ivt(p)) * &
-                                         this%leafc_to_litter_patch(p)
-            ligninNratio_froot_patch(p) = pftcon%fr_flig(ivt(p)) * &
-                                          pftcon%frootcn(ivt(p)) * &
-                                          this%frootc_to_litter_patch(p)
-          end associate
-       end if
     end do  ! end of patches loop
 
     !------------------------------------------------
@@ -4594,39 +4561,6 @@ subroutine Summary_carbonflux(this, &
          this%gpp_patch(bounds%begp:bounds%endp), &
          this%gpp_col(bounds%begc:bounds%endc))
 
-    if (decomp_method == mimics_decomp) then
-       call p2c(bounds, num_soilc, filter_soilc, &
-            ligninNratio_leaf_patch(bounds%begp:bounds%endp), &
-            ligninNratio_leaf_col(bounds%begc:bounds%endc))
-       call p2c(bounds, num_soilc, filter_soilc, &
-            ligninNratio_froot_patch(bounds%begp:bounds%endp), &
-            ligninNratio_froot_col(bounds%begc:bounds%endc))
-       call p2c(bounds, num_soilc, filter_soilc, &
-            this%leafc_to_litter_patch(bounds%begp:bounds%endp), &
-            leafc_to_litter_col(bounds%begc:bounds%endc))
-       call p2c(bounds, num_soilc, filter_soilc, &
-            this%frootc_to_litter_patch(bounds%begp:bounds%endp), &
-            frootc_to_litter_col(bounds%begc:bounds%endc))
-
-       ! Calculate ligninNratioAve
-       do fc = 1,num_soilc
-          c = filter_soilc(fc)
-          if (soilbiogeochem_cwdn_col(c) > 0._r8) then
-             ligninNratio_cwd = CNParamsShareInst%cwd_flig * &
-                (soilbiogeochem_cwdc_col(c) / soilbiogeochem_cwdn_col(c)) * &
-                soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2)
-          else
-             ligninNratio_cwd = 0._r8
-          end if
-          this%ligninNratioAvg_col(c) = &
-             (ligninNratio_leaf_col(c) + ligninNratio_froot_col(c) + &
-              ligninNratio_cwd) / &
-              max(1.0e-3_r8, leafc_to_litter_col(c) + &
-                             frootc_to_litter_col(c) + &
-                             soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2))
-       end do
-    end if
-
     ! this code is to calculate an exponentially-relaxed npp value for use in NDynamics code
 
     if ( trim(isotope) == 'bulk') then