Add crop residue removal

bld/CLMBuildNamelist.pm

@@ -2235,8 +2235,13 @@ 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

@@ -553,6 +553,8 @@ 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

@@ -1164,6 +1164,13 @@ 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

doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst

@@ -508,45 +508,47 @@ where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the car
 Harvest
 '''''''
 
-Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. Root C and N pools are routed to the litter pools in the same manner as natural vegetation.
+Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`. :eq:`harv_c_to_removed_residue`, :eq:`25.12`, and :eq:`harv_n_to_removed_residue`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation.
+
+In the equations below, subscript :math:`p` refers to either the leaf or live stem biomass pool.
 
 .. math::
    :label: 25.9
 
-     CF_{leaf,biofuel} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf}  \Delta t}} \right.} \Delta t}
+     CF_{p,biofuel} = \left({CS_{p} \mathord{\left/ {\vphantom {CS_{p}  \Delta t}} \right.} \Delta t}
      \right) * biofuel\_harvfrac
 
 .. math::
-   :label: 25.10
+   :label: harv_c_to_removed_residue
 
-     CF_{livestem,biofuel} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf}  \Delta t}} \right.} \Delta t}
-     \right) * biofuel\_harvfrac
+     CF_{p,removed\_residue} = \left({CS_{p} \mathord{\left/ {\vphantom {CS_{p}  \Delta t}} \right.} \Delta t}
+     \right) * (1 - biofuel\_harvfrac) * crop\_residue\_removal\_frac
 
 .. math::
    :label: 25.11
 
-     CF_{livestem,litter} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{livestem}  \Delta t}} \right.} \Delta t}
-     \right) * \left( 1-biofuel\_harvfrac  \right) +CF_{alloc,livestem}
+     CF_{p,litter} = \left({CS_{p} \mathord{\left/ {\vphantom {CS_{p}  \Delta t}} \right.} \Delta t}
+     \right) * \left( 1-biofuel\_harvfrac  \right) * \left( 1-crop\_residue\_removal\_frac  \right) +CF_{p,alloc}
 
 with corresponding nitrogen fluxes:
 
 .. math::
    :label: 25.12
 
-     NF_{leaf,biofuel} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf}  \Delta t}} \right.} \Delta t}
+     NF_{p,biofuel} = \left({NS_{p} \mathord{\left/ {\vphantom {NS_{p}  \Delta t}} \right.} \Delta t}
      \right) * biofuel\_harvfrac
 
 .. math::
-   :label: 25.13
+   :label: harv_n_to_removed_residue
 
-     NF_{livestem,biofuel} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem}  \Delta t}} \right.} \Delta t}
-     \right) *  biofuel\_harvfrac
+     NF_{p,removed\_residue} = \left({NS_{p} \mathord{\left/ {\vphantom {NS_{p}  \Delta t}} \right.} \Delta t}
+     \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac
 
 .. math::
    :label: 25.14
 
-     NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem}  \Delta t}} \right.} \Delta t}
-     \right) *  \left( 1-biofuel\_harvfrac  \right)
+     NF_{p,litter} = \left({NS_{p} \mathord{\left/ {\vphantom {NS_{p}  \Delta t}} \right.} \Delta t}
+     \right) *  \left( 1-biofuel\_harvfrac  \right) *  \left( 1-crop\_residue\_removal\_frac  \right)
 
 where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction of leaf/livestem for biofuel feedstocks.
 
@@ -606,7 +608,7 @@ where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is
  | Switchgrass                      |             0.70           |
  +----------------------------------+----------------------------+
 
-Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, similar in structure to the wood product pools. The biofuel C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year.
+Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, similar in structure to the wood product pools. Biofuel and removed-residue C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year.
 
 Annual food crop yields (g dry matter m\ :sup:`-2`) can be calculated by saving the GRAINC_TO_FOOD_ANN variable once per year, then postprocessing with Equation :eq:`25.15`. This calculation assumes that grain C is 45% of the total dry weight. Additionally, harvest is not typically 100% efficient, so analysis needs to assume that harvest efficiency is less---we use 85%.
 

src/biogeochem/CNCIsoFluxMod.F90

@@ -427,6 +427,16 @@ 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, &
@@ -496,7 +506,9 @@ 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

@@ -280,8 +280,10 @@ 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

@@ -3013,7 +3013,7 @@ 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
@@ -3041,6 +3041,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
     real(r8) :: repr_grainn_to_food_thispool ! amount added to / subtracted from repr_grainn_to_food for the pool in question (gN/m2/s)
     real(r8) :: leafc_remaining, livestemc_remaining
     real(r8) :: leafn_remaining, livestemn_remaining
+    real(r8) :: removedresidue_fraction
     !-----------------------------------------------------------------------
 
     associate(                                                                           & 
@@ -3087,6 +3088,8 @@ 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                        
 
@@ -3101,6 +3104,8 @@ 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)          
@@ -3113,7 +3118,7 @@ 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)
 
@@ -3215,6 +3220,16 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                   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
@@ -3701,10 +3716,14 @@ 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