Merge pull request #1114 from rgknox/hetresp_restart_v2

fixes required for FATES-E3SM soil coupling restarts
NGEET · Nov 6, 2023 · 1874511 · 1874511
2 parents 1d18bb6 + c925928
commit 1874511
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Showing 7 changed files with 39 additions and 26 deletions.
diff --git a/biogeochem/FatesCohortMod.F90 b/biogeochem/FatesCohortMod.F90
@@ -476,13 +476,18 @@ subroutine ZeroValues(this)
       this%size_class_lasttimestep = 0
       this%gpp_tstep               = 0._r8
       this%gpp_acc                 = 0._r8
-      this%gpp_acc_hold            = 0._r8
       this%npp_tstep               = 0._r8
       this%npp_acc                 = 0._r8
-      this%npp_acc_hold            = 0._r8
       this%resp_tstep              = 0._r8
       this%resp_acc                = 0._r8
-      this%resp_acc_hold           = 0._r8
+
+      ! do not zero these, they are not built
+      ! so more appropriate to leave unzerod
+      ! to prevent uninitialized use
+      ! this%gpp_acc_hold            = nan
+      ! this%npp_acc_hold            = nan
+      ! this%resp_acc_hold           = nan
+
       this%c13disc_clm             = 0._r8
       this%c13disc_acc             = 0._r8
 

diff --git a/biogeophys/EDAccumulateFluxesMod.F90 b/biogeophys/EDAccumulateFluxesMod.F90
@@ -63,7 +63,11 @@ subroutine AccumulateFluxes_ED(nsites, sites, bc_in, bc_out, dt_time)
     do s = 1, nsites
 
        ifp = 0
-
+
+       ! Note: Do not attempt to accumulate or log any
+       ! heterotrophic respiration fluxes from the HLM here
+       ! It is likely this has not been calculated yet (ELM/CLM)
+
        cpatch => sites(s)%oldest_patch
        do while (associated(cpatch))                 
           if(cpatch%nocomp_pft_label.ne.nocomp_bareground)then

diff --git a/main/EDInitMod.F90 b/main/EDInitMod.F90
@@ -309,7 +309,6 @@ subroutine zero_site( site_in )
     site_in%imort_abg_flux(:,:) = 0._r8
     site_in%fmort_abg_flux(:,:) = 0._r8
 
-
     ! fusoin-induced growth flux of individuals
     site_in%growthflux_fusion(:,:) = 0._r8
 

diff --git a/main/EDTypesMod.F90 b/main/EDTypesMod.F90
@@ -256,6 +256,7 @@ module EDTypesMod
      ! Total area of patches in each age bin [m2]
      real(r8), allocatable :: area_by_age(:)
 
+
      ! Nutrient relevant 
      real(r8), allocatable :: rec_l2fr(:,:) ! A running mean of the l2fr's for the newly
                                             ! recruited, pft x canopy_layer

diff --git a/main/FatesHistoryInterfaceMod.F90 b/main/FatesHistoryInterfaceMod.F90
@@ -3047,20 +3047,6 @@ subroutine update_history_dyn(this,nc,nsites,sites,bc_in)
                   ccohort%c_area * AREA_INV
             end if
 
-            ! update pft-resolved NPP and GPP fluxes
-            hio_gpp_si_pft(io_si, ft) = hio_gpp_si_pft(io_si, ft) + &
-               ccohort%gpp_acc_hold * n_perm2 / days_per_year / sec_per_day
-
-            hio_npp_si_pft(io_si, ft) = hio_npp_si_pft(io_si, ft) + &
-               ccohort%npp_acc_hold * n_perm2 / days_per_year / sec_per_day
-
-            if ( cpatch%anthro_disturbance_label .eq. secondaryforest ) then
-               hio_gpp_sec_si_pft(io_si, ft) = hio_gpp_sec_si_pft(io_si, ft) + &
-                  ccohort%gpp_acc_hold * n_perm2 / days_per_year / sec_per_day
-               hio_npp_sec_si_pft(io_si, ft) = hio_npp_sec_si_pft(io_si, ft) + &
-                  ccohort%npp_acc_hold * n_perm2 / days_per_year / sec_per_day
-            end if
-
             ! Site by Size-Class x PFT (SCPF)
             ! ------------------------------------------------------------------------
 
@@ -3070,6 +3056,20 @@ subroutine update_history_dyn(this,nc,nsites,sites,bc_in)
             ! have any meaning, otherwise they are just inialization values
             notnew: if( .not.(ccohort%isnew) ) then
 
+               ! update pft-resolved NPP and GPP fluxes
+               hio_gpp_si_pft(io_si, ft) = hio_gpp_si_pft(io_si, ft) + &
+                    ccohort%gpp_acc_hold * n_perm2 / days_per_year / sec_per_day
+
+               hio_npp_si_pft(io_si, ft) = hio_npp_si_pft(io_si, ft) + &
+                    ccohort%npp_acc_hold * n_perm2 / days_per_year / sec_per_day
+
+               if ( cpatch%anthro_disturbance_label .eq. secondaryforest ) then
+                  hio_gpp_sec_si_pft(io_si, ft) = hio_gpp_sec_si_pft(io_si, ft) + &
+                       ccohort%gpp_acc_hold * n_perm2 / days_per_year / sec_per_day
+                  hio_npp_sec_si_pft(io_si, ft) = hio_npp_sec_si_pft(io_si, ft) + &
+                       ccohort%npp_acc_hold * n_perm2 / days_per_year / sec_per_day
+               end if
+
                ! Turnover pools [kgC/day] * [day/yr] = [kgC/yr]
                sapw_m_turnover   = ccohort%prt%GetTurnover(sapw_organ, carbon12_element) * days_per_year
                store_m_turnover  = ccohort%prt%GetTurnover(store_organ, carbon12_element) * days_per_year
@@ -4509,7 +4509,7 @@ subroutine update_history_hifrq(this,nc,nsites,sites,bc_in,dt_tstep)
 
       do s = 1,nsites
 
-        call this%zero_site_hvars(sites(s), upfreq_in=2)
+         call this%zero_site_hvars(sites(s), upfreq_in=2)
 
          io_si  = sites(s)%h_gid
 

diff --git a/main/FatesInterfaceMod.F90 b/main/FatesInterfaceMod.F90
@@ -1976,14 +1976,15 @@ end subroutine FatesReportParameters
 
    ! =====================================================================================
 
-   subroutine UpdateFatesRMeansTStep(sites,bc_in)
+   subroutine UpdateFatesRMeansTStep(sites,bc_in, bc_out)
 
      ! In this routine, we update any FATES buffers where
      ! we calculate running means. It is assumed that this buffer is updated
      ! on the model time-step.
 
      type(ed_site_type), intent(inout) :: sites(:)
      type(bc_in_type), intent(in)      :: bc_in(:)
+     type(bc_out_type), intent(inout)  :: bc_out(:)
 
      type(fates_patch_type),  pointer :: cpatch
      type(fates_cohort_type), pointer :: ccohort
@@ -2060,11 +2061,11 @@ subroutine UpdateFatesRMeansTStep(sites,bc_in)
            ccohort => cpatch%tallest
            do while (associated(ccohort))
               !   call ccohort%tveg_lpa%UpdateRMean(bc_in(s)%t_veg_pa(ifp))
-
-              ! [kgC/plant/yr] -> [gC/m2/s]
-              site_npp = site_npp + ccohort%npp_acc_hold * ccohort%n*area_inv * &
-                   g_per_kg * hlm_days_per_year / sec_per_day
-
+              if(.not.ccohort%isnew)then
+                 ! [kgC/plant/yr] -> [gC/m2/s]
+                 site_npp = site_npp + ccohort%npp_acc_hold * ccohort%n*area_inv * &
+                      g_per_kg * hlm_days_per_year / sec_per_day
+              end if
               ccohort => ccohort%shorter
            end do
 
@@ -2080,6 +2081,8 @@ subroutine UpdateFatesRMeansTStep(sites,bc_in)
         sites(s)%ema_npp = (1._r8-1._r8/ema_npp_tscale)*sites(s)%ema_npp + (1._r8/ema_npp_tscale)*site_npp
      end if
 
+     bc_out(s)%ema_npp = sites(s)%ema_npp
+
   end do
 
   return

diff --git a/main/FatesRestartInterfaceMod.F90 b/main/FatesRestartInterfaceMod.F90
@@ -97,6 +97,7 @@ module FatesRestartInterfaceMod
   integer :: ir_gdd_si
   integer :: ir_snow_depth_si
   integer :: ir_trunk_product_si
+
   integer :: ir_ncohort_pa
   integer :: ir_canopy_layer_co
   integer :: ir_canopy_layer_yesterday_co