Merge tag 'sci.1.81.1_api.38.0.0' into refactor-history-2-dev5

Migrate parameter file switches to the host land models namelists

This includes merge commits for both NGEET#1344 and NGEET#1300

Author: samsrabin

biogeochem/EDCanopyStructureMod.F90

@@ -27,7 +27,6 @@ module EDCanopyStructureMod
   use FatesCohortMod,         only : fates_cohort_type
   use EDParamsMod            , only : nclmax
   use EDParamsMod            , only : nlevleaf
-  use EDParamsMod           , only : radiation_model
   use EDtypesMod            , only : AREA
   use EDLoggingMortalityMod , only : UpdateHarvestC
   use FatesGlobals          , only : endrun => fates_endrun
@@ -1314,10 +1313,11 @@ subroutine canopy_summarization( nsites, sites, bc_in )
     ! ---------------------------------------------------------------------------------
 
     use FatesInterfaceTypesMod    , only : hlm_use_cohort_age_tracking
+    use FatesInterfaceTypesMod    , only : hlm_radiation_model
     use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
     use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
-    use EDtypesMod           , only : area
-    use FatesConstantsMod    , only : itrue
+    use EDtypesMod                , only : area
+    use FatesConstantsMod         , only : itrue
 
     ! !ARGUMENTS
     integer                 , intent(in)            :: nsites
@@ -1451,7 +1451,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )
 
        call leaf_area_profile(sites(s))
 
-       if(radiation_model.eq.twostr_solver) then
+       if(hlm_radiation_model.eq.twostr_solver) then
           call FatesConstructRadElements(sites(s),bc_in(s)%fcansno_pa,bc_in(s)%coszen_pa)
        end if
 
@@ -2266,6 +2266,13 @@ subroutine UpdateCohortLAI(currentCohort, canopy_layer_tlai, total_canopy_area)
 
    ! Number of actual vegetation layers in this cohort's crown
    currentCohort%nv =  count((currentCohort%treelai+currentCohort%treesai) .gt. dlower_vai(:)) + 1
+
+   if( currentCohort%nv .ne. minloc(dlower_vai, DIM=1, MASK=(dlower_vai>(currentCohort%treelai+currentCohort%treesai))) ) then
+      write(fates_log(),*) 'We use two methods of finding maximum leaf layers, and they are not equivalent'
+      write(fates_log(),*) 'count method:',currentCohort%nv
+      write(fates_log(),*) 'minloc method:',minloc(dlower_vai, DIM=1, MASK=(dlower_vai>(currentCohort%treelai+currentCohort%treesai)))
+      call endrun(msg=errMsg(sourcefile, __LINE__))
+   end if
 
   end subroutine UpdateCohortLAI
 

biogeochem/EDMortalityFunctionsMod.F90

@@ -12,7 +12,6 @@ module EDMortalityFunctionsMod
    use FatesCohortMod        , only : fates_cohort_type
    use EDTypesMod            , only : ed_site_type
    use EDParamsMod,            only : maxpft
-   use EDParamsMod           , only : mort_cstarvation_model
    use FatesConstantsMod     , only : itrue,ifalse
    use FatesConstantsMod     , only : cstarvation_model_lin
    use FatesConstantsMod     , only : cstarvation_model_exp
@@ -68,6 +67,7 @@ subroutine mortality_rates( cohort_in,bc_in, btran_ft, mean_temp,             &
     use FatesConstantsMod,      only : fates_check_param_set
     use DamageMainMod,          only : GetDamageMortality
     use EDParamsmod,            only : soil_tfrz_thresh
+    use FatesInterfaceTypesMod, only : hlm_mort_cstarvation_model
 
     type (fates_cohort_type), intent(in) :: cohort_in 
     type (bc_in_type), intent(in) :: bc_in
@@ -204,7 +204,7 @@ subroutine mortality_rates( cohort_in,bc_in, btran_ft, mean_temp,             &
           call storage_fraction_of_target(target_leaf_c, store_c, frac)
 
           ! Select the carbon starvation mortality model (linear or exponential)s.
-          select case (mort_cstarvation_model)
+          select case (hlm_mort_cstarvation_model)
           case (cstarvation_model_lin)
              ! Linear model. Carbon starvation mortality will be zero when fraction of
              ! storage is greater than or equal to mort_upthresh_cstarvation, and will
@@ -223,7 +223,7 @@ subroutine mortality_rates( cohort_in,bc_in, btran_ft, mean_temp,             &
 
           case default
               write(fates_log(),*) &
-                 'Invalid carbon starvation model (',mort_cstarvation_model,').'
+                 'Invalid carbon starvation model (',hlm_mort_cstarvation_model,').'
               call endrun(msg=errMsg(sourcefile, __LINE__))
           end select
 

biogeochem/EDPatchDynamicsMod.F90

@@ -30,7 +30,7 @@ module EDPatchDynamicsMod
   use EDTypesMod           , only : elem_diag_type
   use EDTypesMod           , only : min_patch_area
   use EDTypesMod           , only : min_patch_area_forced
-  use EDParamsMod          , only : regeneration_model
+  use FatesInterfaceTypesMod, only : hlm_regeneration_model
   use FatesInterfaceTypesMod, only : numpft
   use FatesConstantsMod     , only : dtype_ifall
   use FatesConstantsMod     , only : dtype_ilog
@@ -682,7 +682,7 @@ subroutine spawn_patches( currentSite, bc_in)
 
                    call newPatch%Create(age, site_areadis, i_landusechange_receiverpatchlabel, i_nocomp_pft, &
                                          num_swb, numpft, currentSite%nlevsoil, hlm_current_tod,              &
-                                         regeneration_model)
+                                         hlm_regeneration_model)
 
                    ! Initialize the litter pools to zero, these
                    ! pools will be populated by looping over the existing patches
@@ -1371,7 +1371,7 @@ subroutine spawn_patches( currentSite, bc_in)
 
                 call buffer_patch%Create(0._r8, 0._r8, i_land_use_label, 0, &
                      num_swb, numpft, currentSite%nlevsoil, hlm_current_tod,              &
-                     regeneration_model)
+                     hlm_regeneration_model)
 
                 ! Initialize the litter pools to zero
                 do el=1,num_elements
@@ -1559,7 +1559,7 @@ subroutine spawn_patches( currentSite, bc_in)
                    if ( .not. buffer_patch_in_linked_list) then
                       if (buffer_patch%area .lt. rsnbl_math_prec) then
                          ! here we need to deallocate the buffer patch so that we don't get a memory leak.
-                         call buffer_patch%FreeMemory(regeneration_model, numpft)
+                         call buffer_patch%FreeMemory(hlm_regeneration_model, numpft)
                          deallocate(buffer_patch, stat=istat, errmsg=smsg)
                          if (istat/=0) then
                             write(fates_log(),*) 'dealloc: fail on deallocate(dp):'//trim(smsg)
@@ -1576,7 +1576,7 @@ subroutine spawn_patches( currentSite, bc_in)
                    end if
                 else
                    ! buffer patch was never even used. deallocate.
-                   call buffer_patch%FreeMemory(regeneration_model, numpft)
+                   call buffer_patch%FreeMemory(hlm_regeneration_model, numpft)
                    deallocate(buffer_patch, stat=istat, errmsg=smsg)
                    if (istat/=0) then
                       write(fates_log(),*) 'dealloc: fail on deallocate(dp):'//trim(smsg)
@@ -1664,7 +1664,7 @@ subroutine split_patch(currentSite, currentPatch, new_patch, fraction_to_keep, a
     call new_patch%Create(0._r8, temp_area, &
          currentPatch%land_use_label, currentPatch%nocomp_pft_label, &
          num_swb, numpft, currentSite%nlevsoil, hlm_current_tod, &
-         regeneration_model)
+         hlm_regeneration_model)
 
     ! Initialize the litter pools to zero, these
     ! pools will be populated shortly
@@ -3188,7 +3188,7 @@ subroutine fuse_2_patches(csite, dp, rp)
     call rp%tveg24%FuseRMean(dp%tveg24,rp%area*inv_sum_area)
     call rp%tveg_lpa%FuseRMean(dp%tveg_lpa,rp%area*inv_sum_area)
 
-    if ( regeneration_model == TRS_regeneration ) then
+    if ( hlm_regeneration_model == TRS_regeneration ) then
        call rp%seedling_layer_par24%FuseRMean(dp%seedling_layer_par24,rp%area*inv_sum_area)
        call rp%sdlng_mort_par%FuseRMean(dp%sdlng_mort_par,rp%area*inv_sum_area)
        call rp%sdlng2sap_par%FuseRMean(dp%sdlng2sap_par,rp%area*inv_sum_area)
@@ -3259,7 +3259,7 @@ subroutine fuse_2_patches(csite, dp, rp)
     end if
 
     ! We have no need for the dp pointer anymore, we have passed on it's legacy
-    call dp%FreeMemory(regeneration_model, numpft)
+    call dp%FreeMemory(hlm_regeneration_model, numpft)
     deallocate(dp, stat=istat, errmsg=smsg)
     if (istat/=0) then
        write(fates_log(),*) 'dealloc006: fail on deallocate(dp):'//trim(smsg)
@@ -3810,7 +3810,7 @@ subroutine CopyPatchMeansTimers(dp, rp)
     call rp%tveg_lpa%CopyFromDonor(dp%tveg_lpa)
     call rp%tveg_longterm%CopyFromDonor(dp%tveg_longterm)
 
-    if ( regeneration_model == TRS_regeneration ) then
+    if ( hlm_regeneration_model == TRS_regeneration ) then
        call rp%seedling_layer_par24%CopyFromDonor(dp%seedling_layer_par24)
        call rp%sdlng_mort_par%CopyFromDonor(dp%sdlng_mort_par)
        call rp%sdlng2sap_par%CopyFromDonor(dp%sdlng2sap_par)

biogeochem/EDPhysiologyMod.F90

@@ -98,7 +98,6 @@ module EDPhysiologyMod
   use EDParamsMod           , only : q10_mr
   use EDParamsMod           , only : q10_froz
   use EDParamsMod           , only : logging_export_frac
-  use EDParamsMod           , only : regeneration_model
   use EDParamsMod           , only : sdlng_mort_par_timescale
   use FatesPlantHydraulicsMod  , only : AccumulateMortalityWaterStorage
   use FatesConstantsMod     , only : itrue,ifalse
@@ -143,7 +142,8 @@ module EDPhysiologyMod
   use FatesParameterDerivedMod, only : param_derived
   use FatesPlantHydraulicsMod, only : InitHydrCohort
   use PRTInitParamsFatesMod, only : NewRecruitTotalStoichiometry
-  use FatesInterfaceTypesMod    , only : hlm_use_luh
+  use FatesInterfaceTypesMod, only : hlm_use_luh
+  use FatesInterfaceTypesMod, only : hlm_regeneration_model
 
   implicit none
   private
@@ -2157,7 +2157,7 @@ subroutine SeedUpdate( currentSite )
                 litt%seed_in_local(pft) = litt%seed_in_local(pft) + site_seed_rain(pft)*(1.0_r8-site_disp_frac(pft))/area ![kg/m2/day]
 
                 ! If we are using the Tree Recruitment Scheme (TRS) with or w/o seedling dynamics
-                if ( any(regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
+                if ( any(hlm_regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
                      prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees) then
 
                    ! Send a fraction of reproductive carbon to litter to account for 
@@ -2215,7 +2215,7 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
     !
     ! !DESCRIPTION:
     ! 1. Flux from seed pool into leaf litter pool
-    ! 2. If the TRS with seedling dynamics is on (regeneration_model = 3)
+    ! 2. If the TRS with seedling dynamics is on (hlm_regeneration_model = 3)
     !    then we calculate seedling mortality here (i.e. flux from seedling pool
     !    (into leaf litter pool)   
     !
@@ -2249,7 +2249,7 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
 
        ! If the TRS is switched off or the pft can't get big enough to be considered a tree 
        ! then use FATES default regeneration.
-       if ( regeneration_model == default_regeneration .or. &
+       if ( hlm_regeneration_model == default_regeneration .or. &
             prt_params%allom_dbh_maxheight(pft) < min_max_dbh_for_trees ) then
 
           ! Default seed decay (TRS is off)
@@ -2261,7 +2261,7 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
        ! If the TRS is switched on and the pft is a tree then add non-seed reproductive biomass
        ! to the seed decay flux. This was added to litt%seed_decay in the previously called SeedIn 
        ! subroutine
-       if ( any(regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
+       if ( any(hlm_regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
             prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees ) then
 
           litt%seed_decay(pft) = litt%seed_decay(pft) + &! From non-seed reproductive biomass (added in
@@ -2271,9 +2271,9 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
        end if 
 
 
-       ! If the TRS is switched on with seedling dynamics (regeneration_model = 2) 
+       ! If the TRS is switched on with seedling dynamics (hlm_regeneration_model = 2)
        ! then calculate seedling mortality.
-       if_trs_germ_decay: if ( regeneration_model == TRS_regeneration .and. &
+       if_trs_germ_decay: if ( hlm_regeneration_model == TRS_regeneration .and. &
             prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees ) then
 
           !----------------------------------------------------------------------
@@ -2379,16 +2379,16 @@ subroutine SeedGermination( litt, cold_stat, drought_stat, bc_in, currentPatch )
 
        ! If the TRS's seedling dynamics is switched off, then we use FATES's default approach
        ! to germination 
-       if_tfs_or_def: if ( regeneration_model == default_regeneration .or. &
-            regeneration_model == TRS_no_seedling_dyn .or. & 
+       if_tfs_or_def: if ( hlm_regeneration_model == default_regeneration .or. &
+            hlm_regeneration_model == TRS_no_seedling_dyn .or. &
             prt_params%allom_dbh_maxheight(pft) < min_max_dbh_for_trees ) then
 
           litt%seed_germ_in(pft) =  min(litt%seed(pft) * EDPftvarcon_inst%germination_rate(pft), &  
                max_germination)*years_per_day
 
           ! If TRS seedling dynamics is switched on we calculate seedling emergence (i.e. germination)
           ! as a pft-specific function of understory light and soil moisture.
-       else if ( regeneration_model == TRS_regeneration .and. &
+       else if ( hlm_regeneration_model == TRS_regeneration .and. &
             prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees ) then	    
 
           ! Step 1. Calculate how germination rate is modified by understory light
@@ -2634,15 +2634,15 @@ subroutine recruitment(currentSite, currentPatch, bc_in)
 
                   ! If TRS seedling dynamics is switched off then the available mass to make new recruits
                   ! is everything in the seed_germ pool.
-                  if (regeneration_model == default_regeneration .or.          &
-                     regeneration_model == TRS_no_seedling_dyn .or.            & 
+                  if (hlm_regeneration_model == default_regeneration .or.          &
+                     hlm_regeneration_model == TRS_no_seedling_dyn .or.            &
                      prt_params%allom_dbh_maxheight(ft) < min_max_dbh_for_trees) then
 
                      mass_avail = currentPatch%area * currentPatch%litter(el)%seed_germ(ft)
 
                      ! If TRS seedling dynamics is on then calculate the available mass to make new recruits
                      ! as a pft-specific function of light and soil moisture in the seedling layer.
-                  else if (regeneration_model == TRS_regeneration .and.        &
+                  else if (hlm_regeneration_model == TRS_regeneration .and.        &
                      prt_params%allom_dbh_maxheight(ft) > min_max_dbh_for_trees) then
 
                      sdlng2sap_par = currentPatch%sdlng2sap_par%GetMean()*     &
@@ -2799,7 +2799,9 @@ subroutine CWDInput( currentSite, currentPatch, litt, bc_in)
     ! and turnover in dying trees.
     !
     ! !USES:
-
+    use EDParamsMod           , only : landuse_grazing_carbon_use_eff
+    use EDParamsMod           , only : landuse_grazing_nitrogen_use_eff
+    use EDParamsMod           , only : landuse_grazing_phosphorus_use_eff
     !
     ! !ARGUMENTS
     type(ed_site_type), intent(inout), target :: currentSite
@@ -2846,6 +2848,8 @@ subroutine CWDInput( currentSite, currentPatch, litt, bc_in)
     integer  :: numlevsoil        ! Actual number of soil layers
 
     real(r8) :: SF_val_CWD_frac_adj(4) !SF_val_CWD_frac adjusted based on cohort dbh
+    real(r8) :: leaf_herbivory  ! leaf that is eaten by grazers [kg]
+    real(r8) :: herbivory_element_use_efficiency   ! fraction of grazed biomass that is returned to litter pool versus atmosphere
     !----------------------------------------------------------------------
 
     ! -----------------------------------------------------------------------------------
@@ -2856,6 +2860,15 @@ subroutine CWDInput( currentSite, currentPatch, litt, bc_in)
 
     element_id = litt%element_id
 
+    select case(element_id)
+       case (carbon12_element)
+          herbivory_element_use_efficiency = landuse_grazing_carbon_use_eff
+       case (nitrogen_element)
+          herbivory_element_use_efficiency = landuse_grazing_nitrogen_use_eff
+       case (phosphorus_element)
+          herbivory_element_use_efficiency = landuse_grazing_phosphorus_use_eff
+    end select
+
     ! Object tracking flux diagnostics for each element
     elflux_diags => currentSite%flux_diags%elem(element_pos(element_id))
 
@@ -2881,6 +2894,8 @@ subroutine CWDInput( currentSite, currentPatch, litt, bc_in)
        fnrt_m          = currentCohort%prt%GetState(fnrt_organ,element_id)
        repro_m         = currentCohort%prt%GetState(repro_organ,element_id)
 
+       leaf_herbivory  = currentCohort%prt%GetHerbivory(leaf_organ, element_id)
+
        if (prt_params%woody(currentCohort%pft) == itrue) then
           ! Assumption: for woody plants fluxes from deadwood and sapwood go together in CWD pool
           leaf_m_turnover   = currentCohort%prt%GetTurnover(leaf_organ,element_id)
@@ -2925,7 +2940,9 @@ subroutine CWDInput( currentSite, currentPatch, litt, bc_in)
        do dcmpy=1,ndcmpy
           dcmpy_frac = GetDecompyFrac(pft,leaf_organ,dcmpy)
           litt%leaf_fines_in(dcmpy) = litt%leaf_fines_in(dcmpy) + &
-               (leaf_m_turnover+repro_m_turnover) * plant_dens * dcmpy_frac
+               (leaf_m_turnover+repro_m_turnover + &
+               leaf_herbivory * herbivory_element_use_efficiency) * &
+               plant_dens * dcmpy_frac
 
           dcmpy_frac = GetDecompyFrac(pft,fnrt_organ,dcmpy)
           do ilyr = 1, numlevsoil
@@ -2938,6 +2955,11 @@ subroutine CWDInput( currentSite, currentPatch, litt, bc_in)
             elflux_diags%root_litter_input(pft) +  &
             (fnrt_m_turnover + store_m_turnover ) * currentCohort%n
 
+       ! send the part of the herbivory flux that doesn't go to litter to the atmosphere
+
+       site_mass%herbivory_flux_out = &
+            site_mass%herbivory_flux_out + &
+            leaf_herbivory * (1._r8 - herbivory_element_use_efficiency) * currentCohort%n
 
        ! Assumption: turnover from deadwood and sapwood are lumped together in CWD pool