Merge pull request #751 from rgknox/fix-decay-restarts

Fix decay restarts

biogeochem/EDPatchDynamicsMod.F90

@@ -1396,7 +1396,6 @@ subroutine TransLitterNewPatch(currentSite,        &
                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

biogeochem/FatesSoilBGCFluxMod.F90

@@ -997,9 +997,9 @@ 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(:)
@@ -1022,13 +1022,12 @@ subroutine FluxIntoLitterPools(csite, bc_in, bc_out)
 
        end select
 
-
        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
@@ -1039,7 +1038,7 @@ subroutine FluxIntoLitterPools(csite, bc_in, bc_out)
                 elseif(element_list(el).eq.phosphorus_element) then
                    efflux_ptr => currentCohort%daily_p_efflux
                 end if
-
+                
                 ! Unit conversion
                 ! kg/plant/day * plant/ha * ha/m2 -> kg/m2/day
 
@@ -1050,7 +1049,8 @@ subroutine FluxIntoLitterPools(csite, bc_in, bc_out)
              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

@@ -151,6 +151,8 @@ 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
@@ -944,6 +946,17 @@ 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_frag', vtype=cohort_r8, &
+            long_name_base='seed bank fragmentation flux (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_frag', vtype=cohort_r8, &
+           long_name_base='seed bank fragmentation flux (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, &
@@ -1940,6 +1953,8 @@ 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
 
@@ -2705,6 +2720,8 @@ 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