Merge branch 'cropresidues3' into tillage-and-residues3

bld/CLMBuildNamelist.pm

@@ -2182,8 +2182,13 @@ sub setup_logic_crop_inparm {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting",
                  'use_crop'=>$nl->get_value('use_crop') );
+
+     my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac');
+     if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) {
+        $log->fatal_error("crop_residue_removal_frac must be in range [0, 1]");
+     }
   } else {
-     error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept" );
+     error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept", "crop_residue_removal_frac" );
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_fsat_equals_zero' );
   }
 }

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -544,6 +544,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_grainproduct use_crop=".true." phys="clm5_0" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
 <use_grainproduct use_crop=".true." phys="clm5_1" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
 
+<crop_residue_removal_frac>0.d+0</crop_residue_removal_frac>
+
 <!-- Crop model options -->
 <baset_mapping           use_crop=".true." phys="clm4_5" >constant</baset_mapping>
 <baset_mapping           use_crop=".true." phys="clm5_0" >varytropicsbylat</baset_mapping>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -1089,6 +1089,13 @@ Toggle to turn on the prognostic fertilizer for crop model
 Toggle to turn on the 1-year grain product pool in the crop model 
 </entry>
 
+<entry id="crop_residue_removal_frac" type="real" category="physics"
+       group="clm_inparm" valid_values="" value="0.0d00">
+Fraction of post-harvest crop residues (leaf and stem) to move to 
+1-year product pool instead of letting them fall as litter.
+<default>Default: 0.0</default>
+</entry>
+
 <entry id="baset_mapping" type="char*20" category="physics"
        group="crop_inparm" valid_values="constant,varytropicsbylat" value="constant">
 Type of mapping to use for base temperature for prognostic crop model

src/biogeochem/CNCIsoFluxMod.F90

@@ -428,6 +428,16 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp,         &
               iso_cnveg_cs%livestemc_patch                  , cnveg_cs%livestemc_patch, &
               num_soilp                                     , filter_soilp, 1._r8, 0, isotope)
 
+         call CIsoFluxCalc(&
+              iso_cnveg_cf%leafc_to_removedresiduec_patch   , cnveg_cf%leafc_to_removedresiduec_patch, &
+              iso_cnveg_cs%leafc_patch                      , cnveg_cs%leafc_patch, &
+              num_soilp                                     , filter_soilp, 1._r8, 0, isotope)
+
+         call CIsoFluxCalc(&
+              iso_cnveg_cf%livestemc_to_removedresiduec_patch, cnveg_cf%livestemc_to_removedresiduec_patch, &
+              iso_cnveg_cs%livestemc_patch                  , cnveg_cs%livestemc_patch, &
+              num_soilp                                     , filter_soilp, 1._r8, 0, isotope)
+
          call CIsoFluxCalc(&
               iso_cnveg_cf%repr_grainc_to_seed_patch        , cnveg_cf%repr_grainc_to_seed_patch, &
               iso_cnveg_cs%reproductivec_patch              , cnveg_cs%reproductivec_patch, &
@@ -497,7 +507,9 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp,         &
             p = filter_soilp(fp)
             iso_cnveg_cf%crop_harvestc_to_cropprodc_patch(p) = &
                  iso_cnveg_cf%leafc_to_biofuelc_patch(p) + &
-                 iso_cnveg_cf%livestemc_to_biofuelc_patch(p)
+                 iso_cnveg_cf%livestemc_to_biofuelc_patch(p) + &
+                 iso_cnveg_cf%leafc_to_removedresiduec_patch(p) + &
+                 iso_cnveg_cf%livestemc_to_removedresiduec_patch(p)
          end do
 
          if (use_grainproduct) then

src/biogeochem/CNCStateUpdate1Mod.F90

@@ -320,8 +320,10 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
            end if
            if (ivt(p) >= npcropmin) then ! skip 2 generic crops
               cs_veg%livestemc_patch(p)  = cs_veg%livestemc_patch(p)  - cf_veg%livestemc_to_litter_patch(p)*dt
-              cs_veg%livestemc_patch(p)  = cs_veg%livestemc_patch(p)  - cf_veg%livestemc_to_biofuelc_patch(p)*dt
-              cs_veg%leafc_patch(p)      = cs_veg%leafc_patch(p)      - cf_veg%leafc_to_biofuelc_patch(p)*dt
+              cs_veg%livestemc_patch(p)  = cs_veg%livestemc_patch(p)  - &
+                   (cf_veg%livestemc_to_biofuelc_patch(p) + cf_veg%livestemc_to_removedresiduec_patch(p))*dt
+              cs_veg%leafc_patch(p)      = cs_veg%leafc_patch(p)      - &
+                   (cf_veg%leafc_to_biofuelc_patch(p) + cf_veg%leafc_to_removedresiduec_patch(p))*dt
               cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) &
                    - cf_veg%crop_seedc_to_leaf_patch(p) * dt
               do k = repr_grain_min, repr_grain_max

src/biogeochem/CNNStateUpdate1Mod.F90

@@ -257,8 +257,10 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
                ns_veg%frootn_patch(p)       = ns_veg%frootn_patch(p)     - nf_veg%frootn_to_retransn_patch(p)*dt
                ns_veg%retransn_patch(p)     = ns_veg%retransn_patch(p)   + nf_veg%frootn_to_retransn_patch(p)*dt
                ns_veg%livestemn_patch(p)    = ns_veg%livestemn_patch(p)  - nf_veg%livestemn_to_litter_patch(p)*dt
-               ns_veg%livestemn_patch(p)    = ns_veg%livestemn_patch(p)  - nf_veg%livestemn_to_biofueln_patch(p)*dt
-               ns_veg%leafn_patch(p)        = ns_veg%leafn_patch(p)      - nf_veg%leafn_to_biofueln_patch(p)*dt
+               ns_veg%livestemn_patch(p)    = ns_veg%livestemn_patch(p)  - &
+                  (nf_veg%livestemn_to_biofueln_patch(p) + nf_veg%livestemn_to_removedresiduen_patch(p))*dt
+               ns_veg%leafn_patch(p)        = ns_veg%leafn_patch(p)      - &
+                  (nf_veg%leafn_to_biofueln_patch(p) + nf_veg%leafn_to_removedresiduen_patch(p))*dt
                ns_veg%livestemn_patch(p)    = ns_veg%livestemn_patch(p)  - nf_veg%livestemn_to_retransn_patch(p)*dt
                ns_veg%retransn_patch(p)     = ns_veg%retransn_patch(p)   + nf_veg%livestemn_to_retransn_patch(p)*dt
             !

src/biogeochem/CNPhenologyMod.F90

@@ -2983,7 +2983,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
     use pftconMod        , only : nmiscanthus, nirrig_miscanthus, nswitchgrass, nirrig_switchgrass
 
     use CNSharedParamsMod, only : use_fun
-    use clm_varctl       , only : CNratio_floating    
+    use clm_varctl       , only : CNratio_floating, crop_residue_removal_frac
     !
     ! !ARGUMENTS:
     integer                       , intent(in)    :: num_soilp       ! number of soil patches in filter
@@ -3008,6 +3008,9 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
     real(r8) :: cropseedc_deficit_to_restore ! amount of crop seed C deficit that will be restored from this grain pool (gC/m2)
     real(r8) :: cropseedn_deficit_to_restore ! amount of crop seed N deficit that will be restored from this grain pool (gN/m2)
     real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s)
+    real(r8) :: leafc_remaining, livestemc_remaining
+    real(r8) :: leafn_remaining, livestemn_remaining
+    real(r8) :: removedresidue_fraction
     !-----------------------------------------------------------------------
 
     associate(                                                                           & 
@@ -3052,6 +3055,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
          repr_structurec_to_litter   => cnveg_carbonflux_inst%repr_structurec_to_litter_patch,   & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s)
          leafc_to_biofuelc     =>    cnveg_carbonflux_inst%leafc_to_biofuelc_patch     , & ! Output: [real(r8) (:) ]  leaf C to biofuel C (gC/m2/s)
          livestemc_to_biofuelc =>    cnveg_carbonflux_inst%livestemc_to_biofuelc_patch , & ! Output: [real(r8) (:) ]  livestem C to biofuel C (gC/m2/s)
+         leafc_to_removedresiduec     => cnveg_carbonflux_inst%leafc_to_removedresiduec_patch     , & ! Output: [real(r8) (:) ]  leaf C to removed residue C (gC/m2/s)
+         livestemc_to_removedresiduec => cnveg_carbonflux_inst%livestemc_to_removedresiduec_patch , & ! Output: [real(r8) (:) ]  livestem C to removed residue C (gC/m2/s)
          leafn                 =>    cnveg_nitrogenstate_inst%leafn_patch              , & ! Input:  [real(r8) (:) ]  (gN/m2) leaf N      
          frootn                =>    cnveg_nitrogenstate_inst%frootn_patch             , & ! Input:  [real(r8) (:) ]  (gN/m2) fine root N                        
 
@@ -3062,6 +3067,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
          repr_structuren_to_litter   => cnveg_nitrogenflux_inst%repr_structuren_to_litter_patch,   & ! Output: [real(r8) (:,:) ] reproductive structure N to litter (gN/m2/s)
          leafn_to_biofueln     =>    cnveg_nitrogenflux_inst%leafn_to_biofueln_patch   , & ! Output: [real(r8) (:) ]  leaf N to biofuel N (gN/m2/s)
          livestemn_to_biofueln =>    cnveg_nitrogenflux_inst%livestemn_to_biofueln_patch, & ! Output: [real(r8) (:) ]  livestem N to biofuel N (gN/m2/s)     
+         leafn_to_removedresiduen     => cnveg_nitrogenflux_inst%leafn_to_removedresiduen_patch    , & ! Output: [real(r8) (:) ]  leaf N to removed residue N (gN/m2/s)
+         livestemn_to_removedresiduen => cnveg_nitrogenflux_inst%livestemn_to_removedresiduen_patch, & ! Output: [real(r8) (:) ]  livestem N to removed residue N (gN/m2/s)     
          leafn_to_litter       =>    cnveg_nitrogenflux_inst%leafn_to_litter_patch     , & ! Output: [real(r8) (:) ]  leaf N litterfall (gN/m2/s)                       
          leafn_to_retransn     =>    cnveg_nitrogenflux_inst%leafn_to_retransn_patch   , & ! Input: [real(r8) (:) ]  leaf N to retranslocated N pool (gN/m2/s)         
          free_retransn_to_npool=>    cnveg_nitrogenflux_inst%free_retransn_to_npool_patch  , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s)          
@@ -3074,7 +3081,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
 
       ! The litterfall transfer rate starts at 0.0 and increases linearly
       ! over time, with displayed growth going to 0.0 on the last day of litterfall
-      
+
       do fp = 1,num_soilp
          p = filter_soilp(fp)
 
@@ -3085,9 +3092,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                t1 = 1.0_r8 / dt
                frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p)
 
-               ! biofuel_harvfrac is only non-zero for prognostic crops.
-               leafc_to_litter(p)  = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p)))  + cpool_to_leafc(p)
-
                ! leafc_litter and frootc_to_litter for matrix
                if (use_matrixcn) then
                else
@@ -3152,13 +3156,34 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                   ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of leaf C
                   ! and move this fration of leaf C to biofuel C, rather than move it to litter
                   leafc_to_biofuelc(p) = t1 * leafc(p) * biofuel_harvfrac(ivt(p))
+                  leafc_remaining = leafc(p)*(1._r8-biofuel_harvfrac(ivt(p)))
                   leafn_to_biofueln(p) = t1 * leafn(p) * biofuel_harvfrac(ivt(p))
+                  leafn_remaining = leafn(p)*(1._r8-biofuel_harvfrac(ivt(p)))
 
                   ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of livestem C
                   ! and move this fration of leaf C to biofuel C, rather than move it to litter
-                  livestemc_to_litter(p)   = t1 * livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p)))  + cpool_to_livestemc(p)
                   livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p))
                   livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p))
+                  livestemc_remaining = livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p)))
+                  livestemn_remaining = livestemn(p)*(1._r8-biofuel_harvfrac(ivt(p)))
+
+                  ! Remove residues
+                  leafc_to_removedresiduec(p) = t1 * leafc_remaining * crop_residue_removal_frac
+                  leafn_to_removedresiduen(p) = t1 * leafn_remaining * crop_residue_removal_frac
+                  livestemc_to_removedresiduec(p) = t1 * livestemc_remaining * crop_residue_removal_frac
+                  livestemn_to_removedresiduen(p) = t1 * livestemn_remaining * crop_residue_removal_frac
+                  leafc_remaining     = leafc_remaining     * (1._r8 - crop_residue_removal_frac)
+                  leafn_remaining     = leafn_remaining     * (1._r8 - crop_residue_removal_frac)
+                  livestemc_remaining = livestemc_remaining * (1._r8 - crop_residue_removal_frac)
+                  livestemn_remaining = livestemn_remaining * (1._r8 - crop_residue_removal_frac)
+
+                  leafc_to_litter(p)  = t1 * leafc_remaining  + cpool_to_leafc(p)
+                  livestemc_to_litter(p)   = t1 * livestemc_remaining  + cpool_to_livestemc(p)
+                  livestemn_to_litter(p)   = t1 * livestemn_remaining
+                  ! Sam Rabin 2023-09-11:
+                  ! leafn_to_litter is calculated below based on leafc_to_litter (updated above)
+                  ! as well as leaf C:N ratio (unaffected by biofuel harvest). It thus does not
+                  ! need to be updated here.
 
                   ! Matrix for grain, livestem to litter and biofuel
                   if(use_matrixcn)then
@@ -3296,18 +3321,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                endif    
             end if
 
-            if (ivt(p) >= npcropmin) then
-               ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn
-               !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p))
-               ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead
-               livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p)))
-
-               ! Matrix update for livestemn to litter
-               if(use_matrixcn)then
-               else
-               end if
-            end if
-
             ! save the current litterfall fluxes
             prev_leafc_to_litter(p)  = leafc_to_litter(p)
             prev_frootc_to_litter(p) = frootc_to_litter(p)
@@ -3650,10 +3663,14 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil
           p = filter_soilp(fp)
           cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) = &
                cnveg_carbonflux_inst%leafc_to_biofuelc_patch(p) + &
-               cnveg_carbonflux_inst%livestemc_to_biofuelc_patch(p)
+               cnveg_carbonflux_inst%livestemc_to_biofuelc_patch(p) + &
+               cnveg_carbonflux_inst%leafc_to_removedresiduec_patch(p) + &
+               cnveg_carbonflux_inst%livestemc_to_removedresiduec_patch(p)
           cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) = &
                cnveg_nitrogenflux_inst%leafn_to_biofueln_patch(p) + &
-               cnveg_nitrogenflux_inst%livestemn_to_biofueln_patch(p)
+               cnveg_nitrogenflux_inst%livestemn_to_biofueln_patch(p) + &
+               cnveg_nitrogenflux_inst%leafn_to_removedresiduen_patch(p) + &
+               cnveg_nitrogenflux_inst%livestemn_to_removedresiduen_patch(p)
        end do
 
        if (use_grainproduct) then

src/biogeochem/CNVegCarbonFluxType.F90

@@ -147,6 +147,8 @@ module CNVegCarbonFluxType
 
      real(r8), pointer :: leafc_to_biofuelc_patch                   (:)     ! leaf C to biofuel C (gC/m2/s)
      real(r8), pointer :: livestemc_to_biofuelc_patch               (:)     ! livestem C to biofuel C (gC/m2/s)
+     real(r8), pointer :: leafc_to_removedresiduec_patch            (:)     ! leaf C to removed residues C (gC/m2/s)
+     real(r8), pointer :: livestemc_to_removedresiduec_patch        (:)     ! livestem C to removed residues C (gC/m2/s)
      real(r8), pointer :: repr_grainc_to_seed_patch               (:,:)     ! grain C to seed for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max]
 
      ! maintenance respiration fluxes     
@@ -662,6 +664,8 @@ subroutine InitAllocate(this, bounds, carbon_type)
     this%repr_structurec_to_litter_patch(:,:) = nan
     allocate(this%leafc_to_biofuelc_patch                   (begp:endp)) ; this%leafc_to_biofuelc_patch                   (:) = nan
     allocate(this%livestemc_to_biofuelc_patch               (begp:endp)) ; this%livestemc_to_biofuelc_patch               (:) = nan
+    allocate(this%leafc_to_removedresiduec_patch            (begp:endp)) ; this%leafc_to_removedresiduec_patch            (:) = nan
+    allocate(this%livestemc_to_removedresiduec_patch        (begp:endp)) ; this%livestemc_to_removedresiduec_patch        (:) = nan
     allocate(this%repr_grainc_to_seed_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_seed_patch (:,:) = nan
     allocate(this%reproductivec_xfer_to_reproductivec_patch(begp:endp, nrepr))
     this%reproductivec_xfer_to_reproductivec_patch(:,:) = nan
@@ -967,6 +971,16 @@ subroutine InitHistory(this, bounds, carbon_type)
                avgflag='A', long_name='livestem C to biofuel C', &
                ptr_patch=this%livestemc_to_biofuelc_patch)
 
+          this%leafc_to_removedresiduec_patch(begp:endp) = spval
+          call hist_addfld1d (fname='LEAFC_TO_REMOVEDRESIDUEC', units='gC/m^2/s', &
+               avgflag='A', long_name='leaf C to removed residue C', &
+               ptr_patch=this%leafc_to_removedresiduec_patch)
+
+          this%livestemc_to_removedresiduec_patch(begp:endp) = spval
+          call hist_addfld1d (fname='LIVESTEMC_TO_REMOVEDRESIDUEC', units='gC/m^2/s', &
+               avgflag='A', long_name='livestem C to removed residue C', &
+               ptr_patch=this%livestemc_to_removedresiduec_patch)
+
           this%repr_grainc_to_seed_patch(begp:endp,:) = spval
           do k = repr_grain_min, repr_grain_max
              data1dptr => this%repr_grainc_to_seed_patch(:,k)
@@ -4143,6 +4157,8 @@ subroutine SetValues ( this, nvegcpool, &
           this%livestemc_to_litter_patch(i)     = value_patch
           this%leafc_to_biofuelc_patch(i)       = value_patch
           this%livestemc_to_biofuelc_patch(i)   = value_patch
+          this%leafc_to_removedresiduec_patch(i)     = value_patch
+          this%livestemc_to_removedresiduec_patch(i) = value_patch
        end do
 
        do k = 1, nrepr