Merge pull request #343 from xuchongang/bchristo-planthydro-longlived

Bchristo planthydro longlived

Author: rgknox

biogeochem/EDCanopyStructureMod.F90

@@ -6,6 +6,7 @@ module EDCanopyStructureMod
   ! =====================================================================================
 
   use FatesConstantsMod     , only : r8 => fates_r8
+  use FatesConstantsMod     , only : itrue, ifalse
   use FatesGlobals          , only : fates_log
   use EDPftvarcon           , only : EDPftvarcon_inst
   use FatesAllometryMod     , only : carea_allom
@@ -18,8 +19,9 @@ module EDCanopyStructureMod
   use EDtypesMod            , only : AREA
   use FatesGlobals          , only : endrun => fates_endrun
   use FatesInterfaceMod     , only : hlm_days_per_year
+  use FatesInterfaceMod     , only : hlm_use_planthydro
   use FatesInterfaceMod     , only : numpft
-
+  use FatesPlantHydraulicsMod, only : UpdateH2OVeg,InitHydrCohort
 
   ! CIME Globals
   use shr_log_mod           , only : errMsg => shr_log_errMsg
@@ -172,7 +174,7 @@ subroutine canopy_structure( currentSite , bc_in )
             ! Remove cohorts that are incredibly sparse
             call terminate_cohorts(currentSite, currentPatch, 1)
 
-            call fuse_cohorts(currentPatch, bc_in)
+            call fuse_cohorts(currentSite, currentPatch, bc_in)
 
             ! Remove cohorts for various other reasons
             call terminate_cohorts(currentSite, currentPatch, 2)
@@ -196,7 +198,7 @@ subroutine canopy_structure( currentSite , bc_in )
                ! Remove cohorts that are incredibly sparse
                call terminate_cohorts(currentSite, currentPatch, 1)
 
-               call fuse_cohorts(currentPatch, bc_in)
+               call fuse_cohorts(currentSite, currentPatch, bc_in)
 
                ! Remove cohorts for various other reasons
                call terminate_cohorts(currentSite, currentPatch, 2)
@@ -390,6 +392,9 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
                      ! otherwise currentPatch%spread(i_lyr+1) will be higher and the area will change...!!! 
 
                      allocate(copyc)
+		     if( hlm_use_planthydro.eq.itrue ) then
+                         call InitHydrCohort(copyc)
+                     endif
                      call copy_cohort(currentCohort, copyc) !
 
                      newarea = currentCohort%c_area - cc_loss
@@ -715,6 +720,9 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
                   !-----------Split and copy boundary cohort-----------------!
                   if(cc_gain < currentCohort%c_area)then
                      allocate(copyc)
+		     if( hlm_use_planthydro.eq.itrue ) then
+                         call InitHydrCohort(copyc)
+                     endif
 
                      call copy_cohort(currentCohort, copyc) !makes an identical copy...
                      ! n.b this needs to happen BEFORE the cohort goes into the new layer, otherwise currentPatch
@@ -1588,10 +1596,14 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
         if(abs(total_patch_area-1.0_r8)>1e-9)then
            write(fates_log(),*) 'total area is wrong in update_hlm_dynamics',total_patch_area
         endif
-        
 
      end do
 
+     ! If hydraulics is turned on, update the amount of water bound in vegetation
+     if (hlm_use_planthydro.eq.itrue) then
+        call UpdateH2OVeg(nsites,sites,bc_out)
+     end if
+
 
   end subroutine update_hlm_dynamics
 

biogeochem/EDCohortDynamicsMod.F90

@@ -29,6 +29,7 @@ module EDCohortDynamicsMod
   use FatesPlantHydraulicsMod, only : initTreeHydStates
   use FatesPlantHydraulicsMod, only : InitHydrCohort
   use FatesPlantHydraulicsMod, only : DeallocateHydrCohort
+  use FatesPlantHydraulicsMod, only : AccumulateMortalityWaterStorage
   use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
   use FatesAllometryMod  , only : bsap_allom
   use FatesAllometryMod  , only : bleaf
@@ -64,19 +65,23 @@ module EDCohortDynamicsMod
 contains
 
   !-------------------------------------------------------------------------------------!
-  subroutine create_cohort(patchptr, pft, nn, hite, dbh, bleaf, bfineroot, bsap, &
-                           bdead, bstore, laimemory, status, ctrim, clayer, spread, bc_in)
+
+  subroutine create_cohort(currentSite, patchptr, pft, nn, hite, dbh, bleaf, bfineroot, bsap, &
+                           bdead, bstore, laimemory, status, recruitstatus,ctrim, clayer, spread, bc_in)
+
     !
     ! !DESCRIPTION:
     ! create new cohort
     !
     ! !USES:
     !
     ! !ARGUMENTS    
+    type(ed_site_type), intent(inout),   target :: currentSite
     type(ed_patch_type), intent(inout), pointer :: patchptr
     integer,  intent(in)   :: pft       ! Cohort Plant Functional Type
     integer,  intent(in)   :: clayer    ! canopy status of cohort (1 = canopy, 2 = understorey, etc.)
     integer,  intent(in)   :: status    ! growth status of plant  (2 = leaves on , 1 = leaves off)
+    integer,  intent(in)   :: recruitstatus    ! recruit status of plant  (1 = recruitment , 0 = other)
     real(r8), intent(in)   :: nn        ! number of individuals in cohort per 'area' (10000m2 default)
     real(r8), intent(in)   :: hite      ! height: meters
     real(r8), intent(in)   :: dbh       ! dbh: cm
@@ -89,6 +94,7 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, bleaf, bfineroot, bsap, &
     real(r8), intent(in)   :: ctrim     ! What is the fraction of the maximum leaf biomass that we are targeting? :-
     real(r8), intent(in)   :: spread    ! The community assembly effects how spread crowns are in horizontal space
     type(bc_in_type), intent(in) :: bc_in ! External boundary conditions
+     
     !
     ! !LOCAL VARIABLES:
     type(ed_cohort_type), pointer :: new_cohort         ! Pointer to New Cohort structure.
@@ -180,7 +186,10 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, bleaf, bfineroot, bsap, &
     if( hlm_use_planthydro.eq.itrue ) then
        call InitHydrCohort(new_cohort)
        call updateSizeDepTreeHydProps(new_cohort, bc_in) 
-       call initTreeHydStates(new_cohort, bc_in) 
+       call initTreeHydStates(currentSite,new_cohort, bc_in)
+       if(recruitstatus==1)then
+          new_cohort%co_hydr%is_newly_recuited = .true.
+       endif
     endif
 
     call insert_cohort(new_cohort, patchptr%tallest, patchptr%shortest, tnull, snull, &
@@ -535,6 +544,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level )
              if(associated(shorterCohort)) shorterCohort%taller => null()
           else 
              tallerCohort%shorter => shorterCohort
+
           endif
 
           if (.not. associated(shorterCohort)) then
@@ -557,7 +567,7 @@ end subroutine terminate_cohorts
 
   !-------------------------------------------------------------------------------------!
 
-  subroutine fuse_cohorts(currentPatch, bc_in)  
+  subroutine fuse_cohorts(currentSite, currentPatch, bc_in)  
 
      !
      ! !DESCRIPTION:
@@ -567,7 +577,8 @@ subroutine fuse_cohorts(currentPatch, bc_in)
      use EDParamsMod , only :  ED_val_cohort_fusion_tol
      use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
      !
-     ! !ARGUMENTS    
+     ! !ARGUMENTS   
+     type (ed_site_type), intent(inout),  target :: currentSite 
      type (ed_patch_type), intent(inout), target :: currentPatch
      type (bc_in_type), intent(in)               :: bc_in
      !
@@ -711,7 +722,7 @@ subroutine fuse_cohorts(currentPatch, bc_in)
                                 call sizetype_class_index(currentCohort%dbh,currentCohort%pft, &
                                       currentCohort%size_class,currentCohort%size_by_pft_class)
 
-                                if(hlm_use_planthydro.eq.itrue) call FuseCohortHydraulics(currentCohort,nextc,bc_in,newn)
+                                if(hlm_use_planthydro.eq.itrue) call FuseCohortHydraulics(currentSite,currentCohort,nextc,bc_in,newn)
 
                                 ! recent canopy history
                                 currentCohort%canopy_layer_yesterday  = (currentCohort%n*currentCohort%canopy_layer_yesterday  + &
@@ -1209,7 +1220,9 @@ subroutine copy_cohort( currentCohort,copyc )
 
     ! Plant Hydraulics
 
-    if( hlm_use_planthydro.eq.itrue ) call CopyCohortHydraulics(n,o)
+    if( hlm_use_planthydro.eq.itrue ) then
+      call CopyCohortHydraulics(n,o)
+    endif
 
     ! indices for binning
     n%size_class      = o%size_class

biogeochem/EDLoggingMortalityMod.F90

@@ -38,12 +38,14 @@ module EDLoggingMortalityMod
    use FatesInterfaceMod , only : hlm_model_day
    use FatesInterfaceMod , only : hlm_day_of_year 
    use FatesInterfaceMod , only : hlm_days_per_year
-   use FatesInterfaceMod , only : hlm_use_logging
+   use FatesInterfaceMod , only : hlm_use_logging 
+   use FatesInterfaceMod , only : hlm_use_planthydro
    use FatesConstantsMod , only : itrue,ifalse
    use FatesGlobals      , only : endrun => fates_endrun 
    use FatesGlobals      , only : fates_log
    use shr_log_mod       , only : errMsg => shr_log_errMsg
-
+   use FatesPlantHydraulicsMod, only : AccumulateMortalityWaterStorage
+   
    implicit none
    private
 
@@ -296,6 +298,12 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
          litter_area = currentPatch%area 
          np_mult     = patch_site_areadis/newPatch%area
 
+         
+         if( hlm_use_planthydro == itrue ) then
+            call AccumulateMortalityWaterStorage(currentSite,currentCohort,(direct_dead+indirect_dead))
+         end if
+         
+
          ! ----------------------------------------------------------------------------------------
          ! Handle woody litter flux for non-bole components of biomass
          ! This litter is distributed between the current and new patches, &

biogeochem/EDPatchDynamicsMod.F90

@@ -28,6 +28,7 @@ module EDPatchDynamicsMod
   use FatesConstantsMod    , only : r8 => fates_r8
   use FatesConstantsMod    , only : itrue
   use FatesPlantHydraulicsMod, only : InitHydrCohort
+  use FatesPlantHydraulicsMod, only : AccumulateMortalityWaterStorage
   use FatesPlantHydraulicsMod, only : DeallocateHydrCohort
   use EDLoggingMortalityMod, only : logging_litter_fluxes 
   use EDLoggingMortalityMod, only : logging_time
@@ -655,7 +656,7 @@ subroutine spawn_patches( currentSite, bc_in)
           ! the second call removes for all other reasons (sparse culling must happen
           ! before fusion)
           call terminate_cohorts(currentSite, currentPatch, 1)
-          call fuse_cohorts(currentPatch, bc_in)
+          call fuse_cohorts(currentSite,currentPatch, bc_in)
           call terminate_cohorts(currentSite, currentPatch, 2)
           call sort_cohorts(currentPatch)
 
@@ -678,7 +679,7 @@ subroutine spawn_patches( currentSite, bc_in)
        ! the second call removes for all other reasons (sparse culling must happen
        ! before fusion)
        call terminate_cohorts(currentSite, new_patch, 1)
-       call fuse_cohorts(new_patch, bc_in)
+       call fuse_cohorts(currentSite,new_patch, bc_in)
        call terminate_cohorts(currentSite, new_patch, 2)
        call sort_cohorts(new_patch)
 
@@ -866,6 +867,10 @@ subroutine fire_litter_fluxes(currentSite, cp_target, new_patch_target, patch_si
              bcroot = (currentCohort%bsw + currentCohort%bdead) * (1.0_r8 - EDPftvarcon_inst%allom_agb_frac(p) )
              ! density of dead trees per m2. 
              dead_tree_density  = (currentCohort%fire_mort * currentCohort%n*patch_site_areadis/currentPatch%area) / AREA  
+             
+             if( hlm_use_planthydro == itrue ) then
+                call AccumulateMortalityWaterStorage(currentSite,currentCohort,dead_tree_density*AREA)
+             end if
 
              ! Unburned parts of dead tree pool. 
              ! Unburned leaves and roots    
@@ -1041,6 +1046,10 @@ subroutine mortality_litter_fluxes(currentSite, cp_target, new_patch_target, pat
              canopy_mortality_root_litter(p) = canopy_mortality_root_litter(p) + &
                   canopy_dead*(currentCohort%br+currentCohort%bstore)
 
+             if( hlm_use_planthydro == itrue ) then
+                call AccumulateMortalityWaterStorage(currentSite,currentCohort, canopy_dead)
+             end if
+
          else 
              if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
 
@@ -1051,6 +1060,10 @@ subroutine mortality_litter_fluxes(currentSite, cp_target, new_patch_target, pat
                      understorey_dead* currentCohort%bl 
                 canopy_mortality_root_litter(p)= canopy_mortality_root_litter(p)+ &
                       understorey_dead*(currentCohort%br+currentCohort%bstore)
+                
+                if( hlm_use_planthydro == itrue ) then
+                   call AccumulateMortalityWaterStorage(currentSite,currentCohort, understorey_dead)
+                end if
 
              ! FIX(SPM,040114) - clarify this comment
              ! grass is not killed by canopy mortality disturbance events.
@@ -1059,6 +1072,9 @@ subroutine mortality_litter_fluxes(currentSite, cp_target, new_patch_target, pat
                 ! no-op
              endif
           endif
+
+          
+
 
 
        currentCohort => currentCohort%taller      
@@ -1462,7 +1478,7 @@ subroutine fuse_patches( csite, bc_in )
                    if(fuse_flag  ==  1)then 
                       tmpptr => currentPatch%older       
                       call fuse_2_patches(csite, currentPatch, tpp)
-                      call fuse_cohorts(tpp, bc_in)
+                      call fuse_cohorts(csite,tpp, bc_in)
                       call sort_cohorts(tpp)
                       currentPatch => tmpptr
                    else

biogeochem/EDPhysiologyMod.F90

@@ -12,6 +12,7 @@ module EDPhysiologyMod
   use FatesInterfaceMod, only    : hlm_freq_day
   use FatesInterfaceMod, only    : hlm_day_of_year
   use FatesInterfaceMod, only    : numpft
+  use FatesInterfaceMod, only    : hlm_use_planthydro
   use FatesConstantsMod, only    : r8 => fates_r8
   use EDPftvarcon      , only    : EDPftvarcon_inst
   use FatesInterfaceMod, only    : bc_in_type
@@ -34,6 +35,8 @@ module EDPhysiologyMod
   use FatesGlobals          , only : fates_log
   use FatesGlobals          , only : endrun => fates_endrun
   use EDParamsMod           , only : fates_mortality_disturbance_fraction
+
+  use FatesPlantHydraulicsMod  , only : AccumulateMortalityWaterStorage
   use FatesConstantsMod     , only : itrue,ifalse
   use FatesConstantsMod     , only : calloc_abs_error
 
@@ -1586,14 +1589,15 @@ subroutine recruitment( currentSite, currentPatch, bc_in )
     use FatesInterfaceMod, only : hlm_use_ed_prescribed_phys
     !
     ! !ARGUMENTS    
-    type(ed_site_type), intent(inout), target  :: currentSite
+    type(ed_site_type), intent(inout), target   :: currentSite
     type(ed_patch_type), intent(inout), pointer :: currentPatch
     type(bc_in_type), intent(in)                :: bc_in
     !
     ! !LOCAL VARIABLES:
     integer :: ft
     type (ed_cohort_type) , pointer :: temp_cohort
     integer :: cohortstatus
+    integer,parameter :: recruitstatus = 1 !weather it the new created cohorts is recruited or initialized
     real(r8) :: b_leaf
     real(r8) :: b_fineroot    ! fine root biomass [kgC]
     real(r8) :: b_sapwood     ! sapwood biomass [kgC]
@@ -1655,14 +1659,14 @@ subroutine recruitment( currentSite, currentPatch, bc_in )
           currentSite%flux_out = currentSite%flux_out + currentPatch%area * currentPatch%seed_germination(ft)*hlm_freq_day
        endif
 
-
        if (temp_cohort%n > 0.0_r8 )then
           if ( DEBUG ) write(fates_log(),*) 'EDPhysiologyMod.F90 call create_cohort '
-          call create_cohort(currentPatch, temp_cohort%pft, temp_cohort%n, temp_cohort%hite, temp_cohort%dbh, &
+          call create_cohort(currentSite,currentPatch, temp_cohort%pft, temp_cohort%n, temp_cohort%hite, temp_cohort%dbh, &
                 b_leaf, b_fineroot, b_sapwood, temp_cohort%bdead, temp_cohort%bstore,  &
-                temp_cohort%laimemory, cohortstatus, temp_cohort%canopy_trim, currentPatch%NCL_p, &
+                temp_cohort%laimemory, cohortstatus,recruitstatus, temp_cohort%canopy_trim, currentPatch%NCL_p, &
                 currentSite%spread, bc_in)
 
+
           ! keep track of how many individuals were recruited for passing to history
           currentSite%recruitment_rate(ft) = currentSite%recruitment_rate(ft) + temp_cohort%n
 
@@ -1779,6 +1783,11 @@ subroutine CWD_Input( currentSite, currentPatch)
                 (dead_n_ilogging+dead_n_dlogging) * & 
                 hlm_freq_day * currentPatch%area
 
+          if( hlm_use_planthydro == itrue ) then
+             call AccumulateMortalityWaterStorage(currentSite,currentCohort,dead_n)
+          end if
+          
+
           do c = 1,ncwd
 
              currentPatch%cwd_BG_in(c) = currentPatch%cwd_BG_in(c) + (currentCohort%bdead+currentCohort%bsw) * &