Merge pull request #3 from rgknox/rgknox-cxu-dynamic-hydro-restart-me…

…rged

restarts

biogeochem/EDCohortDynamicsMod.F90

@@ -31,6 +31,9 @@ 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
@@ -98,6 +101,13 @@ 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:
     !
@@ -125,7 +135,8 @@ 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
     !----------------------------------------------------------------------
 
@@ -242,12 +253,31 @@ 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_recruited = .true.
        endif
+
     endif
 
     call insert_cohort(new_cohort, patchptr%tallest, patchptr%shortest, tnull, snull, &

biogeochem/EDPhysiologyMod.F90

@@ -1002,13 +1002,12 @@ subroutine recruitment( currentSite, currentPatch, bc_in )
        endif
 
        if (temp_cohort%n > 0.0_r8 )then
-          if ( debug ) write(fates_log(),*) 'EDPhysiologyMod.F90 call create_cohort '
+
           call create_cohort(currentSite,currentPatch, temp_cohort%pft, temp_cohort%n, temp_cohort%hite, temp_cohort%dbh, &
                 b_leaf, b_fineroot, b_sapwood, b_dead, b_store, &  
                 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
 

biogeochem/FatesAllometryMod.F90

@@ -117,6 +117,7 @@ module FatesAllometryMod
   public :: decay_coeff_kn
   public :: StructureResetOfDH ! Method to set DBH to sync with structure biomass
   public :: CheckIntegratedAllometries
+  public :: CrownDepth
   public :: set_root_fraction  ! Generic wrapper to calculate normalized
                                ! root profiles
 
@@ -1843,6 +1844,33 @@ subroutine h2d_martcano(h,p1,p2,p3,d,dddh)
     return
   end subroutine h2d_martcano
 
+  ! =====================================================================================
+
+
+  subroutine CrownDepth(height,crown_depth)
+
+    ! -----------------------------------------------------------------------------------
+    ! This routine returns the depth of a plant's crown.  Which is the length
+    ! from the bottom of the crown to the top in the vertical dimension.
+    ! 
+    ! This code may be used as a wrapper if different hypotheses are wished to be
+    ! optioned.
+    ! -----------------------------------------------------------------------------------
+
+    real(r8),intent(in)  :: height   ! The height of the plant   [m]
+    real(r8),intent(out) :: crown_depth ! The depth of the crown [m]
+
+    ! Alternative Hypothesis:
+    ! crown depth from Poorter, Bongers & Bongers
+    ! crown_depth = exp(-1.169_r8)*cCohort%hite**1.098_r8   
+
+    crown_depth               = min(height,0.1_r8)
+
+    return
+ end subroutine CrownDepth
+
+
+
   ! =============================================================================
   ! Specific diameter to crown area allometries
   ! =============================================================================