Merge branch 'master' into hieight_based_sorting

biogeochem/EDPatchDynamicsMod.F90

@@ -1145,14 +1145,20 @@ subroutine mortality_litter_fluxes(currentSite, cp_target, new_patch_target, pat
              !not right to recalcualte dmort here.
              canopy_dead = currentCohort%n * min(1.0_r8,currentCohort%dmort * hlm_freq_day * fates_mortality_disturbance_fraction)
 
-
-
              canopy_mortality_woody_litter(p)= canopy_mortality_woody_litter(p) + &
                   canopy_dead*(struct_c + sapw_c)
              canopy_mortality_leaf_litter(p) = canopy_mortality_leaf_litter(p) + &
                   canopy_dead*leaf_c
+
+             ! Some plants upon death will transfer storage carbon to seed production
+             ! Storage carbon that is not transferred to seeds goes to root litter flux
+
              canopy_mortality_root_litter(p) = canopy_mortality_root_litter(p) + &
-                  canopy_dead*(fnrt_c + store_c)
+                  canopy_dead*(fnrt_c + store_c*(1.0_r8-EDPftvarcon_inst%allom_frbstor_repro(p)) )
+
+             currentSite%seed_bank(p) = currentSite%seed_bank(p) + &
+                   canopy_dead * store_c * EDPftvarcon_inst%allom_frbstor_repro(p)/AREA
+
 
              if( hlm_use_planthydro == itrue ) then
                 call AccumulateMortalityWaterStorage(currentSite,currentCohort, canopy_dead)
@@ -1316,6 +1322,8 @@ subroutine create_patch(currentSite, new_patch, age, areap,cwd_ag_local,cwd_bg_l
     new_patch%frac_burnt         = 0._r8  
     new_patch%total_tree_area    = 0.0_r8  
     new_patch%NCL_p              = 1
+
+
 
   end subroutine create_patch
 
@@ -1440,6 +1448,12 @@ subroutine zero_patch(cp_p)
     currentPatch%c_stomata                  = 0.0_r8 ! This is calculated immediately before use
     currentPatch%c_lblayer                  = 0.0_r8
 
+    currentPatch%solar_zenith_flag          = .false.
+    currentPatch%solar_zenith_angle         = nan
+
+    currentPatch%gnd_alb_dir(:)             = nan
+    currentPatch%gnd_alb_dif(:)             = nan
+
   end subroutine zero_patch
 
   ! ============================================================================

biogeochem/EDPhysiologyMod.F90

@@ -172,7 +172,7 @@ subroutine non_canopy_derivs( currentSite, currentPatch, bc_in )
     ! update fragmenting pool fluxes
     call cwd_input( currentSite, currentPatch)
     call cwd_out( currentSite, currentPatch, bc_in)
-
+  
     do p = 1,numpft
        currentSite%dseed_dt(p) = currentSite%dseed_dt(p) + &
             (currentPatch%seeds_in(p) - currentPatch%seed_decay(p) - &
@@ -792,6 +792,7 @@ subroutine seeds_in( currentSite, cp_pnt )
     type(ed_cohort_type), pointer :: currentCohort
     integer :: p
     logical :: pft_present(maxpft)
+    real(r8) :: store_c_to_repro   ! carbon sent from storage to reproduction upon death [kg/plant]
     real(r8) :: npfts_present
     !----------------------------------------------------------------------
 
@@ -822,10 +823,18 @@ subroutine seeds_in( currentSite, cp_pnt )
        currentPatch => cp_pnt
        currentCohort => currentPatch%tallest
        do while (associated(currentCohort))
+
+          ! a certain fraction of bstore goes to clonal reproduction when plants die
+          store_c_to_repro = currentCohort%prt%GetState(store_organ,all_carbon_elements) * &
+                EDPftvarcon_inst%allom_frbstor_repro(currentCohort%pft)
+
           do p = 1, numpft
              if (pft_present(p)) then
-                currentPatch%seeds_in(p) = currentPatch%seeds_in(p) +  currentCohort%seed_prod * currentCohort%n / &
-                     (currentPatch%area * npfts_present)
+
+                  currentPatch%seeds_in(p) = currentPatch%seeds_in(p) + &
+                        (currentCohort%seed_prod * currentCohort%n - &
+                        currentCohort%dndt*store_c_to_repro) &
+                        /(currentPatch%area * npfts_present)		  
              endif
           end do
           currentCohort => currentCohort%shorter
@@ -836,8 +845,15 @@ subroutine seeds_in( currentSite, cp_pnt )
     currentCohort => currentPatch%tallest
     do while (associated(currentCohort))
        p = currentCohort%pft
+
+       ! a certain fraction of bstore goes to clonal reproduction when plants die
+       store_c_to_repro = currentCohort%prt%GetState(store_organ,all_carbon_elements) * &
+             EDPftvarcon_inst%allom_frbstor_repro(p)
+
        currentPatch%seeds_in(p) = currentPatch%seeds_in(p) +  &
-             currentCohort%seed_prod * currentCohort%n/currentPatch%area
+           (currentCohort%seed_prod * currentCohort%n - &
+	   currentCohort%dndt*store_c_to_repro)/currentPatch%area
+
        currentCohort => currentCohort%shorter
     enddo !cohort loop
 
@@ -913,13 +929,18 @@ subroutine seed_germination( currentSite, currentPatch )
 
     do p = 1,numpft
        currentPatch%seed_germination(p) =  min(currentSite%seed_bank(p) * &
-             EDPftvarcon_inst%germination_timescale(p),max_germination)
+             EDPftvarcon_inst%germination_timescale(p),max_germination)     
+       !set the germination only under the growing season...c.xu
+       if (EDPftvarcon_inst%season_decid(p) == 1.and.currentSite%status == 1)then 
+             currentPatch%seed_germination(p) = 0.0_r8
+       endif
+       if (EDPftvarcon_inst%stress_decid(p) == 1.and.currentSite%dstatus == 1)then
+             currentPatch%seed_germination(p) = 0.0_r8
+       endif
     enddo
 
   end subroutine seed_germination
 
-  ! ============================================================================
-
   subroutine recruitment( currentSite, currentPatch, bc_in )
     !
     ! !DESCRIPTION:
@@ -1134,9 +1155,8 @@ subroutine CWD_Input( currentSite, currentPatch)
                 ! the litter flux has already been counted since it captured
                 ! the losses of live trees and those flagged for death
 
-
           currentPatch%root_litter_in(pft) = currentPatch%root_litter_in(pft) + &
-               (fnrt_c + store_c ) * dead_n
+               (fnrt_c + store_c*(1._r8-EDPftvarcon_inst%allom_frbstor_repro(pft)) ) * dead_n
 
           ! Update diagnostics that track resource management
           currentSite%resources_management%delta_litter_stock  = &

biogeochem/FatesAllometryMod.F90

@@ -2156,7 +2156,7 @@ subroutine StructureResetOfDH( bdead, ipft, canopy_trim, d, h )
      ! of the diameter increment
      counter = 0
      step_frac = step_frac0
-     do while( (bdead-bt_dead) > calloc_abs_error )
+     do while( (bdead-bt_dead) > calloc_abs_error .and. dbt_dead_dd>0.0_r8)
 
         ! vulnerable to div0
         dd    = step_frac*(bdead-bt_dead)/dbt_dead_dd

biogeophys/EDBtranMod.F90

@@ -25,6 +25,7 @@ module EDBtranMod
 
    public :: btran_ed
    public :: get_active_suction_layers
+   public :: check_layer_water
 
 contains