Merge branch 'main' into edge-area-202410

Author: samsrabin

.github/PULL_REQUEST_TEMPLATE.md

@@ -28,6 +28,9 @@ All checklist items must be checked to enable merging this pull request:
 *Integrator*
 - [ ] FATES PASS/FAIL regression tests were run
 - [ ] Evaluation of test results for answer changes was performed and results provided
+- [ ] FATES-CLM6 Code Freeze: satellite phenology regression tests are b4b
+
+*If satellite phenology regressions are **not** b4b, please hold merge and notify the FATES development team.*
 
 ### Documentation
 <!--- If this pull requests warrants an update to the tech doc or user's guide, and said changes have been made paste a link to the documentation pull request below.  -->

biogeochem/EDCanopyStructureMod.F90

@@ -2085,7 +2085,7 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
     ! call during the fast timestep sequence
 
     if (hlm_use_planthydro.eq.itrue) then
-       call RecruitWaterStorage(nsites,sites,bc_out)
+       call RecruitWaterStorage(nsites,sites)
     end if
 
   end subroutine update_hlm_dynamics

biogeochem/EDCohortDynamicsMod.F90

@@ -941,7 +941,7 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
                                         currentCohort%size_class,currentCohort%size_by_pft_class)
 
                                    if(hlm_use_planthydro.eq.itrue) then
-                                      call FuseCohortHydraulics(currentSite,currentCohort,nextc,bc_in,newn)
+                                      call FuseCohortHydraulics(currentSite,currentCohort,nextc,newn)
                                    endif
 
                                    ! recent canopy history
@@ -1118,7 +1118,7 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
                                    ! update hydraulics quantities that are functions of height & biomasses
                                    ! deallocate the hydro structure of nextc
                                    if (hlm_use_planthydro.eq.itrue) then
-                                      call UpdateSizeDepPlantHydProps(currentSite,currentCohort, bc_in)
+                                      call UpdateSizeDepPlantHydProps(currentSite,currentCohort)
                                    endif
 
                                    call nextc%FreeMemory()

biogeochem/EDLoggingMortalityMod.F90

@@ -1145,9 +1145,6 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
          ! This portion is known as "trunk_product_site
 
          if(element_id .eq. carbon12_element) then
-            currentSite%resources_management%trunk_product_site  = &
-                  currentSite%resources_management%trunk_product_site + &
-                  trunk_product_site
 
             currentSite%resources_management%delta_litter_stock  = &
                   currentSite%resources_management%delta_litter_stock + &

biogeochem/EDPatchDynamicsMod.F90

@@ -17,7 +17,6 @@ module EDPatchDynamicsMod
   use FatesLitterMod       , only : litter_type
   use FatesConstantsMod    , only : n_dbh_bins 
   use FatesLitterMod       , only : adjust_SF_CWD_frac
-  use EDTypesMod           , only : homogenize_seed_pfts
   use EDTypesMod           , only : area
   use FatesConstantsMod    , only : patchfusion_dbhbin_loweredges
   use EDtypesMod           , only : force_patchfuse_min_biomass
@@ -482,7 +481,7 @@ end subroutine disturbance_rates
 
     ! ============================================================================
 
-  subroutine spawn_patches( currentSite, bc_in)
+  subroutine spawn_patches( currentSite, bc_in )
     !
     ! !DESCRIPTION:
     ! In this subroutine, the following happens,
@@ -1068,14 +1067,16 @@ subroutine spawn_patches( currentSite, bc_in)
                                           currentSite%mass_balance(el)%burn_flux_to_atm + &
                                           leaf_burn_frac * leaf_m * nc%n
 
-                                     ! This diagnostic only tracks
+                                     ! This term increments the loss flux from surviving trees
                                      currentSite%flux_diags%elem(el)%burned_liveveg = &
                                           currentSite%flux_diags%elem(el)%burned_liveveg + & 
                                           leaf_burn_frac * leaf_m * nc%n * area_inv
 
+                                     
                                   end do
 
-                                  ! Here the mass is removed from the plant
+                                  ! Add burned leaf carbon to the atmospheric carbon flux
+                                  ! for burning.
 
                                   if(int(prt_params%woody(currentCohort%pft)) == itrue)then
                                      call PRTBurnLosses(nc%prt, leaf_organ, leaf_burn_frac)
@@ -1866,7 +1867,6 @@ subroutine TransLitterNewPatch(currentSite,        &
                                                               ! by current patch
     integer,              intent(in)    :: dist_type          ! disturbance type
 
-    
     ! locals
     type(site_massbal_type), pointer :: site_mass
     type(litter_type),pointer :: curr_litt  ! litter object for current patch
@@ -1989,9 +1989,8 @@ subroutine TransLitterNewPatch(currentSite,        &
           curr_litt%ag_cwd(c) = curr_litt%ag_cwd(c) + donatable_mass*retain_m2
 
           site_mass%burn_flux_to_atm = site_mass%burn_flux_to_atm + burned_mass
-             
+
           ! Transfer below ground CWD (none burns)
-          
           do sl = 1,currentSite%nlevsoil
              donatable_mass         = curr_litt%bg_cwd(c,sl) * patch_site_areadis
              new_litt%bg_cwd(c,sl)  = new_litt%bg_cwd(c,sl) + donatable_mass*donate_m2
@@ -2018,7 +2017,7 @@ subroutine TransLitterNewPatch(currentSite,        &
            curr_litt%leaf_fines(dcmpy) = curr_litt%leaf_fines(dcmpy) + donatable_mass*retain_m2
 
            site_mass%burn_flux_to_atm = site_mass%burn_flux_to_atm + burned_mass
-           
+
            ! Transfer root fines (none burns)
            do sl = 1,currentSite%nlevsoil
                donatable_mass = curr_litt%root_fines(dcmpy,sl) * patch_site_areadis             
@@ -2088,7 +2087,7 @@ subroutine fire_litter_fluxes(currentSite, currentPatch, &
     type(fates_patch_type) , intent(inout), target :: newPatch   ! New Patch
     real(r8)            , intent(in)            :: patch_site_areadis ! Area being donated
     type(bc_in_type)    , intent(in)            :: bc_in
-    
+
     !
     ! !LOCAL VARIABLES:
 
@@ -2229,8 +2228,6 @@ subroutine fire_litter_fluxes(currentSite, currentPatch, &
 
              site_mass%burn_flux_to_atm = site_mass%burn_flux_to_atm + burned_mass
 
-             
-             
              call set_root_fraction(currentSite%rootfrac_scr, pft, currentSite%zi_soil, &
                   bc_in%max_rooting_depth_index_col)
 
@@ -2301,7 +2298,7 @@ subroutine fire_litter_fluxes(currentSite, currentPatch, &
 
             currentCohort => currentCohort%taller
         enddo
-    end do
+     end do
 
     return
   end subroutine fire_litter_fluxes
@@ -2382,7 +2379,7 @@ subroutine mortality_litter_fluxes(currentSite, currentPatch, &
 
 
     do el = 1,num_elements
-       
+
        element_id = element_list(el)
        site_mass  => currentSite%mass_balance(el)
        elflux_diags => currentSite%flux_diags%elem(el)
@@ -2542,7 +2539,7 @@ end subroutine mortality_litter_fluxes
     ! ============================================================================
 
   subroutine landusechange_litter_fluxes(currentSite, currentPatch, &
-       newPatch, patch_site_areadis, bc_in, &
+       newPatch, patch_site_areadis, bc_in,  &
        clearing_matrix_element)
     !
     ! !DESCRIPTION:
@@ -2596,8 +2593,6 @@ subroutine landusechange_litter_fluxes(currentSite, currentPatch, &
     integer  :: pft                  ! loop index for plant functional types
     integer  :: dcmpy                ! loop index for decomposability pool
     integer  :: element_id           ! parteh compatible global element index
-    real(r8) :: trunk_product_site   ! flux of carbon in trunk products exported off site      [ kgC/site ]
-                                     ! (note we are accumulating over the patch, but scale is site level)
     real(r8) :: woodproduct_mass     ! mass that ends up in wood products [kg]
 
     !---------------------------------------------------------------------
@@ -2640,9 +2635,6 @@ subroutine landusechange_litter_fluxes(currentSite, currentPatch, &
 
        do el = 1,num_elements
 
-          ! Zero some site level accumulator diagnsotics
-          trunk_product_site  = 0.0_r8
-
           element_id = element_list(el)
           site_mass  => currentSite%mass_balance(el)
           elflux_diags => currentSite%flux_diags%elem(el)
@@ -2702,7 +2694,7 @@ subroutine landusechange_litter_fluxes(currentSite, currentPatch, &
              end do
 
              site_mass%burn_flux_to_atm = site_mass%burn_flux_to_atm + burned_mass
-             
+
              call set_root_fraction(currentSite%rootfrac_scr, pft, currentSite%zi_soil, &
                   bc_in%max_rooting_depth_index_col)
 
@@ -2762,6 +2754,7 @@ subroutine landusechange_litter_fluxes(currentSite, currentPatch, &
                         EDPftvarcon_inst%landusechange_frac_burned(pft)
 
                    site_mass%burn_flux_to_atm = site_mass%burn_flux_to_atm + burned_mass
+
                 else ! all other pools can end up as timber products or burn or go to litter
                    donatable_mass = donatable_mass * (1.0_r8-EDPftvarcon_inst%landusechange_frac_exported(pft)) * &
                         (1.0_r8-EDPftvarcon_inst%landusechange_frac_burned(pft))
@@ -2775,9 +2768,6 @@ subroutine landusechange_litter_fluxes(currentSite, currentPatch, &
 
                    site_mass%burn_flux_to_atm = site_mass%burn_flux_to_atm + burned_mass
 
-                   trunk_product_site = trunk_product_site + &
-                        woodproduct_mass
-
                    ! Amount of trunk mass exported off site [kg/m2]
                    elflux_diags%exported_harvest = elflux_diags%exported_harvest + &
                         woodproduct_mass * area_inv
@@ -2794,15 +2784,6 @@ subroutine landusechange_litter_fluxes(currentSite, currentPatch, &
              currentCohort => currentCohort%taller
           enddo
 
-          ! Update the amount of carbon exported from the site through logging.
-
-          if(element_id .eq. carbon12_element) then
-             currentSite%resources_management%trunk_product_site  = &
-                  currentSite%resources_management%trunk_product_site + &
-                  trunk_product_site
-          end if
-
-
        end do
 
     end if clear_veg_if
@@ -3578,12 +3559,8 @@ subroutine DistributeSeeds(currentSite,seed_mass,el,pft)
       do while(associated(currentPatch)) 
           litt => currentPatch%litter(el)
 
-          if(homogenize_seed_pfts) then
-              litt%seed(:) = litt%seed(:) + seed_mass/(area_site*real(numpft,r8))
-          else
-              litt%seed(pft) = litt%seed(pft) + seed_mass/area_site
-          end if
-          
+          litt%seed(pft) = litt%seed(pft) + seed_mass/area_site
+
           currentPatch => currentPatch%younger
       end do