resolved trivial merge conflict

Author: ckoven

biogeochem/EDCanopyStructureMod.F90

@@ -25,7 +25,7 @@ module EDCanopyStructureMod
   use FatesInterfaceMod     , only : hlm_days_per_year
   use FatesInterfaceMod     , only : hlm_use_planthydro
   use FatesInterfaceMod     , only : numpft
-  use FatesPlantHydraulicsMod, only : UpdateH2OVeg,InitHydrCohort
+  use FatesPlantHydraulicsMod, only : UpdateH2OVeg,InitHydrCohort, RecruitWaterStorage
   use EDTypesMod            , only : maxCohortsPerPatch
 
   use PRTGenericMod,          only : leaf_organ
@@ -587,6 +587,7 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
                   ! demoted to the understory
 
                   allocate(copyc)
+
                   call InitPRTCohort(copyc)
                   if( hlm_use_planthydro.eq.itrue ) then
                      call InitHydrCohort(currentSite,copyc)
@@ -1011,6 +1012,7 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
                   elseif ( cc_gain > nearzero .and. cc_gain < currentCohort%c_area) then
 
                      allocate(copyc)
+
                      call InitPRTCohort(copyc)
                      if( hlm_use_planthydro.eq.itrue ) then
                         call InitHydrCohort(CurrentSite,copyc)
@@ -1920,6 +1922,7 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
 
      ! If hydraulics is turned on, update the amount of water bound in vegetation
      if (hlm_use_planthydro.eq.itrue) then
+        call RecruitWaterStorage(nsites,sites,bc_out)
         call UpdateH2OVeg(nsites,sites,bc_out)
      end if
 

biogeochem/EDCohortDynamicsMod.F90

@@ -8,6 +8,7 @@ module EDCohortDynamicsMod
   use FatesGlobals          , only : fates_log
   use FatesInterfaceMod     , only : hlm_freq_day
   use FatesInterfaceMod     , only : bc_in_type
+  use FatesInterfaceMod     , only : hlm_use_planthydro
   use FatesConstantsMod     , only : r8 => fates_r8
   use FatesConstantsMod     , only : fates_unset_int
   use FatesConstantsMod     , only : itrue,ifalse
@@ -21,6 +22,7 @@ module EDCohortDynamicsMod
   use EDTypesMod            , only : min_npm2, min_nppatch
   use EDTypesMod            , only : min_n_safemath
   use EDTypesMod            , only : nlevleaf
+  use EDTypesMod            , only : ican_upper
   use FatesInterfaceMod      , only : hlm_use_planthydro
   use FatesInterfaceMod      , only : hlm_parteh_mode
   use FatesPlantHydraulicsMod, only : FuseCohortHydraulics
@@ -30,6 +32,9 @@ module EDCohortDynamicsMod
   use FatesPlantHydraulicsMod, only : InitHydrCohort
   use FatesPlantHydraulicsMod, only : DeallocateHydrCohort
   use FatesPlantHydraulicsMod, only : AccumulateMortalityWaterStorage
+  use FatesPlantHydraulicsMod, only : UpdateTreeHydrNodes
+  use FatesPlantHydraulicsMod, only : UpdateTreeHydrLenVolCond
+  use FatesPlantHydraulicsMod, only : SavePreviousCompartmentVolumes
   use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
   use FatesAllometryMod  , only : bleaf
   use FatesAllometryMod  , only : bfineroot
@@ -97,6 +102,13 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, dbh, bleaf, bfine
     !
     ! !DESCRIPTION:
     ! create new cohort
+    ! There are 4 places this is called
+    ! 1) Initializing new cohorts at the beginning of a cold-start simulation
+    ! 2) Initializing new recruits during dynamics
+    ! 3) Initializing new cohorts at the beginning of a inventory read
+    ! 4) Initializing new cohorts during restart
+    !
+    ! It is assumed that in the first 3, this is called with a reasonable amount of starter information.
     !
     ! !USES:
     !
@@ -124,7 +136,8 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, dbh, bleaf, bfine
     ! !LOCAL VARIABLES:
     type(ed_cohort_type), pointer :: new_cohort         ! Pointer to New Cohort structure.
     type(ed_cohort_type), pointer :: storesmallcohort 
-    type(ed_cohort_type), pointer :: storebigcohort   
+    type(ed_cohort_type), pointer :: storebigcohort  
+    integer :: nlevsoi_hyd                      ! number of hydraulically active soil layers 
     integer :: tnull,snull                      ! are the tallest and shortest cohorts allocate
     !----------------------------------------------------------------------
 
@@ -241,12 +254,31 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, dbh, bleaf, bfine
     new_cohort%isnew = .true.
 
     if( hlm_use_planthydro.eq.itrue ) then
-       call InitHydrCohort(CurrentSite,new_cohort)
-       call updateSizeDepTreeHydProps(CurrentSite,new_cohort, bc_in) 
-       call initTreeHydStates(CurrentSite,new_cohort, bc_in)
+
+       nlevsoi_hyd = currentSite%si_hydr%nlevsoi_hyd
+
+       ! This allocates array spaces
+       call InitHydrCohort(currentSite,new_cohort)
+
+       ! This calculates node heights
+       call UpdateTreeHydrNodes(new_cohort%co_hydr,new_cohort%pft, &
+                                new_cohort%hite,nlevsoi_hyd,bc_in)
+
+       ! This calculates volumes, lengths and max conductances
+       call UpdateTreeHydrLenVolCond(new_cohort,nlevsoi_hyd,bc_in)
+       
+       ! Since this is a newly initialized plant, we set the previous compartment-size
+       ! equal to the ones we just calculated.
+       call SavePreviousCompartmentVolumes(new_cohort%co_hydr)
+       
+       ! This comes up with starter suctions and then water contents
+       ! based on the soil values
+       call initTreeHydStates(currentSite,new_cohort, bc_in)
+
        if(recruitstatus==1)then
-          new_cohort%co_hydr%is_newly_recuited = .true.
+          new_cohort%co_hydr%is_newly_recruited = .true.
        endif
+
     endif
 
     call insert_cohort(new_cohort, patchptr%tallest, patchptr%shortest, tnull, snull, &
@@ -602,19 +634,26 @@ subroutine terminate_cohorts( currentSite, currentPatch, level )
       endif    !  if (.not.currentCohort%isnew .and. level == 2) then
 
       if (terminate == 1) then 
+         
           ! preserve a record of the to-be-terminated cohort for mortality accounting
-          if (currentCohort%canopy_layer .eq. 1) then
-             levcan = 1
-          else
-             levcan = 2
-          endif
+          levcan = currentCohort%canopy_layer
 
-          currentSite%terminated_nindivs(currentCohort%size_class,currentCohort%pft,levcan) = &
-               currentSite%terminated_nindivs(currentCohort%size_class,currentCohort%pft,levcan) + currentCohort%n
-          !
-          currentSite%termination_carbonflux(levcan) = currentSite%termination_carbonflux(levcan) + &
-                currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
-          
+          if( hlm_use_planthydro == itrue ) &
+             call AccumulateMortalityWaterStorage(currentSite,currentCohort,currentCohort%n)
+
+          if(levcan==ican_upper) then
+             currentSite%term_nindivs_canopy(currentCohort%size_class,currentCohort%pft) = &
+                   currentSite%term_nindivs_canopy(currentCohort%size_class,currentCohort%pft) + currentCohort%n
+ 
+             currentSite%term_carbonflux_canopy = currentSite%term_carbonflux_canopy + &
+                   currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
+          else
+             currentSite%term_nindivs_ustory(currentCohort%size_class,currentCohort%pft) = &
+                   currentSite%term_nindivs_ustory(currentCohort%size_class,currentCohort%pft) + currentCohort%n
+ 
+             currentSite%term_carbonflux_ustory = currentSite%term_carbonflux_ustory + &
+                   currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
+          end if
 
           !put the litter from the terminated cohorts straight into the fragmenting pools
           if (currentCohort%n.gt.0.0_r8) then
@@ -729,6 +768,7 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
      real(r8) :: newn
      real(r8) :: diff
      real(r8) :: dynamic_fusion_tolerance
+     real(r8) :: leaf_c             ! leaf carbon [kg]
 
      integer  :: largersc, smallersc, sc_i        ! indices for tracking the growth flux caused by fusion
      real(r8) :: larger_n, smaller_n
@@ -845,8 +885,11 @@ subroutine fuse_cohorts(currentSite, 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(currentSite,currentCohort,nextc,bc_in,newn)
+                                if(hlm_use_planthydro.eq.itrue) then			  					  				  
+				    call FuseCohortHydraulics(currentSite,currentCohort,nextc,bc_in,newn)				    
+				 endif
 
                                 ! recent canopy history
                                 currentCohort%canopy_layer_yesterday  = (currentCohort%n*currentCohort%canopy_layer_yesterday  + &
@@ -927,7 +970,6 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
                                    currentCohort%cmort = (currentCohort%n*currentCohort%cmort + nextc%n*nextc%cmort)/newn
                                    currentCohort%hmort = (currentCohort%n*currentCohort%hmort + nextc%n*nextc%hmort)/newn
                                    currentCohort%bmort = (currentCohort%n*currentCohort%bmort + nextc%n*nextc%bmort)/newn
-                                   currentCohort%fmort = (currentCohort%n*currentCohort%fmort + nextc%n*nextc%fmort)/newn
                                    currentCohort%frmort = (currentCohort%n*currentCohort%frmort + nextc%n*nextc%frmort)/newn
 
                                    ! logging mortality, Yi Xu
@@ -976,7 +1018,18 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
                                 endif
 
                                 ! At this point, nothing should be pointing to current Cohort
-                                if (hlm_use_planthydro.eq.itrue) call DeallocateHydrCohort(nextc)
+				! update hydraulics quantities that are functions of hite & biomasses
+				! deallocate the hydro structure of nextc
+                                if (hlm_use_planthydro.eq.itrue) then				    
+				    call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread, &
+				          currentCohort%pft,currentCohort%c_area)
+                                    leaf_c   = currentCohort%prt%GetState(leaf_organ, all_carbon_elements)
+                                    currentCohort%treelai = tree_lai(leaf_c,             &
+                                       currentCohort%pft, currentCohort%c_area, currentCohort%n, &
+                                       currentCohort%canopy_layer, currentPatch%canopy_layer_tlai )			    
+				   call updateSizeDepTreeHydProps(currentSite,currentCohort, bc_in)  				   
+				   call DeallocateHydrCohort(nextc)
+				endif
 
                                 ! Deallocate the cohort's PRT structure
                                 call nextc%prt%DeallocatePRTVartypes()
@@ -1303,7 +1356,6 @@ subroutine copy_cohort( currentCohort,copyc )
     ! Mortality diagnostics
     n%cmort = o%cmort
     n%bmort = o%bmort
-    n%fmort = o%fmort
     n%hmort = o%hmort
     n%frmort = o%frmort
 

biogeochem/EDMortalityFunctionsMod.F90

@@ -16,6 +16,7 @@ module EDMortalityFunctionsMod
    use FatesInterfaceMod     , only : bc_in_type
    use FatesInterfaceMod     , only : hlm_use_ed_prescribed_phys
    use FatesInterfaceMod     , only : hlm_freq_day
+   use FatesInterfaceMod     , only : hlm_use_planthydro
    use EDLoggingMortalityMod , only : LoggingMortality_frac
    use EDParamsMod           , only : fates_mortality_disturbance_fraction
    use FatesInterfaceMod     , only : bc_in_type
@@ -62,8 +63,14 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )
     real(r8) :: leaf_c_target      ! target leaf biomass kgC
     real(r8) :: store_c
     real(r8) :: hf_sm_threshold    ! hydraulic failure soil moisture threshold 
+    real(r8) :: hf_flc_threshold   ! hydraulic failure fractional loss of conductivity threshold
     real(r8) :: temp_dep_fraction  ! Temp. function (freezing mortality)
     real(r8) :: temp_in_C          ! Daily averaged temperature in Celcius
+    real(r8) :: min_fmc_ag         ! minimum fraction of maximum conductivity for aboveground
+    real(r8) :: min_fmc_tr         ! minimum fraction of maximum conductivity for transporting root
+    real(r8) :: min_fmc_ar         ! minimum fraction of maximum conductivity for absorbing root
+    real(r8) :: min_fmc            ! minimum fraction of maximum conductivity for whole plant
+    real(r8) :: flc                ! fractional loss of conductivity 
     real(r8), parameter :: frost_mort_buffer = 5.0_r8  ! 5deg buffer for freezing mortality
     logical, parameter :: test_zero_mortality = .false. ! Developer test which
                                                         ! may help to debug carbon imbalances
@@ -77,12 +84,28 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )
 
     ! Proxy for hydraulic failure induced mortality. 
     hf_sm_threshold = EDPftvarcon_inst%hf_sm_threshold(cohort_in%pft)
-
-    if(cohort_in%patchptr%btran_ft(cohort_in%pft) <= hf_sm_threshold)then 
+    hf_flc_threshold = EDPftvarcon_inst%hf_flc_threshold(cohort_in%pft)
+    if(hlm_use_planthydro.eq.itrue)then
+     !note the flc is set as the fraction of max conductivity in hydro
+     min_fmc_ag = minval(cohort_in%co_hydr%flc_ag(:))
+     min_fmc_tr = minval(cohort_in%co_hydr%flc_troot(:))
+     min_fmc_ar = minval(cohort_in%co_hydr%flc_aroot(:))
+     min_fmc = min(min_fmc_ag, min_fmc_tr)
+     min_fmc = min(min_fmc, min_fmc_ar)
+     flc = 1.0_r8-min_fmc
+     if(flc >= hf_flc_threshold .and. hf_flc_threshold < 1.0_r8 )then 
+       hmort = (flc-hf_flc_threshold)/(1.0_r8-hf_flc_threshold) * &
+           EDPftvarcon_inst%mort_scalar_hydrfailure(cohort_in%pft)
+     else
+       hmort = 0.0_r8
+     endif      
+    else
+     if(cohort_in%patchptr%btran_ft(cohort_in%pft) <= hf_sm_threshold)then 
        hmort = EDPftvarcon_inst%mort_scalar_hydrfailure(cohort_in%pft)
      else
        hmort = 0.0_r8
-     endif 
+     endif
+    endif 
 
     ! Carbon Starvation induced mortality.
     if ( cohort_in%dbh  >  0._r8 ) then