Merge tag 'sci.1.44.1_api.14.2.0_patchA' into sci.1.45.2_api.15.0.0_b…

…ranch

Patch tag A. These are fixes that enabled b4b restart cababilities in E3SM. These are applied retroactively to this api which is at present, behind fates master which is api 16 at the time of this log

biogeochem/EDPatchDynamicsMod.F90

@@ -1384,6 +1384,16 @@ subroutine TransLitterNewPatch(currentSite,        &
 
        enddo
 
+       do pft = 1,numpft
+
+          new_litt%seed_decay(pft) = new_litt%seed_decay(pft) + &
+               curr_litt%seed_decay(pft)*patch_site_areadis/newPatch%area
+
+          new_litt%seed_germ_decay(pft) = new_litt%seed_germ_decay(pft) + &
+               curr_litt%seed_germ_decay(pft)*patch_site_areadis/newPatch%area
+
+       end do
+
        ! -----------------------------------------------------------------------------
        ! Distribute the existing litter that was already in place on the donor
        ! patch.  Some of this burns and is sent to the atmosphere, and some goes to the 

biogeochem/FatesSoilBGCFluxMod.F90

@@ -826,9 +826,9 @@ subroutine FluxIntoLitterPools(csite, bc_in, bc_out)
 
        select case (element_list(el))
        case (carbon12_element)
-          bc_out%litt_flux_cel_c_si(:) = 0._r8
-          bc_out%litt_flux_lig_c_si(:) = 0._r8
-          bc_out%litt_flux_lab_c_si(:) = 0._r8
+          bc_out%litt_flux_cel_c_si(:) = 0.0_r8
+          bc_out%litt_flux_lig_c_si(:) = 0.0_r8
+          bc_out%litt_flux_lab_c_si(:) = 0.0_r8
           flux_cel_si => bc_out%litt_flux_cel_c_si(:)
           flux_lab_si => bc_out%litt_flux_lab_c_si(:)
           flux_lig_si => bc_out%litt_flux_lig_c_si(:)
@@ -861,31 +861,16 @@ subroutine FluxIntoLitterPools(csite, bc_in, bc_out)
 
        end select
 
+       ! Add efflux to the litter pool. kg/ha/day -> kg/m2/day                                                                             
+       do id = 1,nlev_eff_decomp
+          flux_lab_si(id) = flux_lab_si(id) + &
+               sum(csite%flux_diags(el)%nutrient_efflux_scpf)*surface_prof(id)*area_inv
+       end do
+
 
        currentPatch => csite%oldest_patch
        do while (associated(currentPatch))
 
-          ! If there is any efflux (from stores overflowing)
-          ! than pass that to the labile litter pool
-
-          currentCohort => currentPatch%tallest
-          do while(associated(currentCohort))
-             if(.not.currentCohort%isnew)then
-                if(element_list(el).eq.carbon12_element) then
-                   efflux_ptr => currentCohort%daily_c_efflux
-                elseif(element_list(el).eq.nitrogen_element) then
-                   efflux_ptr => currentCohort%daily_n_efflux
-                elseif(element_list(el).eq.phosphorus_element) then
-                   efflux_ptr => currentCohort%daily_p_efflux
-                end if
-                do id = 1,nlev_eff_decomp
-                   flux_lab_si(id) = flux_lab_si(id) + &
-                        efflux_ptr*currentCohort%n* AREA_INV * surface_prof(id)
-                end do
-             end if
-             currentCohort => currentCohort%shorter
-          end do
-
           ! Set a pointer to the litter object
           ! for the current element on the current
           ! patch

main/FatesRestartInterfaceMod.F90

@@ -150,6 +150,8 @@ module FatesRestartInterfaceMod
   integer :: ir_fnrt_litt
   integer :: ir_seed_litt
   integer :: ir_seedgerm_litt
+  integer :: ir_seed_decay_litt
+  integer :: ir_seedgerm_decay_litt
   integer :: ir_seed_prod_co
   integer :: ir_livegrass_pa
   integer :: ir_age_pa
@@ -938,6 +940,17 @@ subroutine define_restart_vars(this, initialize_variables)
            units='kg/m2', veclength=num_elements, flushval = flushzero, &
            hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_seedgerm_litt)
 
+
+    call this%RegisterCohortVector(symbol_base='fates_seed_decay', vtype=cohort_r8, &
+            long_name_base='seed bank (non-germinated)',  &
+            units='kg/m2', veclength=num_elements, flushval = flushzero, &
+            hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_seed_decay_litt)
+
+    call this%RegisterCohortVector(symbol_base='fates_seedgerm_decay', vtype=cohort_r8, &
+           long_name_base='seed bank (germinated)',  &
+           units='kg/m2', veclength=num_elements, flushval = flushzero, &
+           hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_seedgerm_decay_litt)
+
     call this%RegisterCohortVector(symbol_base='fates_ag_cwd_frag', vtype=cohort_r8, &
             long_name_base='above ground CWD frag flux',  &
             units='kg/m2/day', veclength=num_elements, flushval = flushzero, &
@@ -1932,6 +1945,8 @@ subroutine set_restart_vectors(this,nc,nsites,sites)
                  do i = 1,numpft
                     this%rvars(ir_seed_litt+el)%r81d(io_idx_pa_pft) = litt%seed(i)
                     this%rvars(ir_seedgerm_litt+el)%r81d(io_idx_pa_pft) = litt%seed_germ(i)
+                    this%rvars(ir_seed_decay_litt+el)%r81d(io_idx_pa_pft) = litt%seed_decay(i)
+                    this%rvars(ir_seedgerm_decay_litt+el)%r81d(io_idx_pa_pft) = litt%seed_germ_decay(i)
                     io_idx_pa_pft = io_idx_pa_pft + 1
                  end do
 
@@ -2694,6 +2709,8 @@ subroutine get_restart_vectors(this, nc, nsites, sites)
                  do i = 1,numpft
                      litt%seed(i)       = this%rvars(ir_seed_litt+el)%r81d(io_idx_pa_pft)
                      litt%seed_germ(i)  = this%rvars(ir_seedgerm_litt+el)%r81d(io_idx_pa_pft)
+                     litt%seed_decay(i)       = this%rvars(ir_seed_decay_litt+el)%r81d(io_idx_pa_pft)
+                     litt%seed_germ_decay(i)  = this%rvars(ir_seedgerm_decay_litt+el)%r81d(io_idx_pa_pft)
                      io_idx_pa_pft      = io_idx_pa_pft + 1
                   end do