Merge pull request #1 from rgknox/recruiment_into_sizeclasses_v2

conflict resolutions with PARTEH

.gitignore

@@ -0,0 +1,51 @@
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+*.mod
+*.pyc
+*.pdf
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+*.nc
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.out
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Latex/Tex files #
+*.aux
+*.dvi
+*.toc
+
+
+# Old Files
+*~

biogeochem/EDLoggingMortalityMod.F90

@@ -45,7 +45,12 @@ module EDLoggingMortalityMod
    use FatesGlobals      , only : fates_log
    use shr_log_mod       , only : errMsg => shr_log_errMsg
    use FatesPlantHydraulicsMod, only : AccumulateMortalityWaterStorage
-
+
+   use PRTGenericMod     , only : all_carbon_elements
+   use PRTGenericMod     , only : sapw_organ, struct_organ, leaf_organ
+   use PRTGenericMod     , only : fnrt_organ, store_organ, repro_organ
+
+
    implicit none
    private
 
@@ -260,6 +265,11 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
       real(r8) :: leaf_litter         ! Leafy biomass transferred through mortality [kgC/site]
       real(r8) :: root_litter         ! Rooty + storage biomass transferred through mort [kgC/site]
       real(r8) :: agb_frac            ! local copy of the above ground biomass fraction [fraction]
+      real(r8) :: leaf_c              ! leaf carbon [kg]
+      real(r8) :: fnrt_c              ! fineroot carbon [kg]
+      real(r8) :: sapw_c              ! sapwood carbon [kg]
+      real(r8) :: store_c             ! storage carbon [kg]
+      real(r8) :: struct_c            ! structure carbon [kg]
       integer  :: p                   ! pft index
       integer  :: c                   ! cwd index
 
@@ -274,8 +284,13 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
       currentCohort => currentPatch%shortest
       do while(associated(currentCohort))       
          p = currentCohort%pft
+
+         sapw_c   = currentCohort%prt%GetState(sapw_organ, all_carbon_elements)
+         struct_c = currentCohort%prt%GetState(struct_organ, all_carbon_elements)
+         leaf_c   = currentCohort%prt%GetState(leaf_organ, all_carbon_elements)
+         fnrt_c   = currentCohort%prt%GetState(fnrt_organ, all_carbon_elements)
+         store_c  = currentCohort%prt%GetState(store_organ, all_carbon_elements)
 
-
          if(currentCohort%canopy_layer == 1)then         
             direct_dead   = currentCohort%n * currentCohort%lmort_direct
             indirect_dead = currentCohort%n * &
@@ -315,7 +330,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
 
          do c = 1,ncwd-1
             woody_litter = (direct_dead+indirect_dead) * &
-                  (currentCohort%bdead+currentCohort%bsw)
+                  (struct_c + sapw_c ) 
             cwd_litter_density = SF_val_CWD_frac(c) * woody_litter / litter_area
 
             newPatch%cwd_ag(c)     = newPatch%cwd_ag(c)     + agb_frac * cwd_litter_density * np_mult
@@ -344,7 +359,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
          ! collateral damange and infrastructure logging is applied to bole litter
          ! ----------------------------------------------------------------------------------------
 
-         woody_litter =  indirect_dead * (currentCohort%bdead+currentCohort%bsw)
+         woody_litter =  indirect_dead * (struct_c + sapw_c)
 
          cwd_litter_density = SF_val_CWD_frac(ncwd) * woody_litter / litter_area
 
@@ -368,7 +383,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
          ! Handle litter flux for the belowground portion of directly logged boles
          ! ----------------------------------------------------------------------------------------
 
-         woody_litter =  direct_dead * (currentCohort%bdead+currentCohort%bsw)
+         woody_litter =  direct_dead * (struct_c + sapw_c)
          cwd_litter_density = SF_val_CWD_frac(ncwd) * woody_litter / litter_area
 
          newPatch%cwd_bg(ncwd)     = newPatch%cwd_bg(ncwd)     + &
@@ -393,16 +408,16 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
          ! ----------------------------------------------------------------------------------------
 
          trunk_product_site = trunk_product_site + &
-               SF_val_CWD_frac(ncwd) * agb_frac * direct_dead * (currentCohort%bdead+currentCohort%bsw)
+               SF_val_CWD_frac(ncwd) * agb_frac * direct_dead * (struct_c + sapw_c)
 
 
          ! ----------------------------------------------------------------------------------------
          ! Handle fluxes of leaf, root and storage carbon into litter pools. 
          !  (none of these are exported)
          ! ----------------------------------------------------------------------------------------
 
-         leaf_litter = (direct_dead+indirect_dead)*currentCohort%bl
-         root_litter = (direct_dead+indirect_dead)*(currentCohort%br+currentCohort%bstore)
+         leaf_litter = (direct_dead+indirect_dead) * leaf_c
+         root_litter = (direct_dead+indirect_dead) * (fnrt_c + store_c)
 
          newPatch%leaf_litter(p) = newPatch%leaf_litter(p) + leaf_litter / litter_area * np_mult
          newPatch%root_litter(p) = newPatch%root_litter(p) + root_litter / litter_area * np_mult 
@@ -431,7 +446,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
          delta_biomass_stock = delta_biomass_stock + &
                                leaf_litter         + &
                                root_litter         + &
-                               (direct_dead+indirect_dead) * (currentCohort%bdead+currentCohort%bsw)
+                               (direct_dead+indirect_dead) * (struct_c + sapw_c)
 
          delta_individual    = delta_individual    + &
                                direct_dead         + &

biogeochem/EDMortalityFunctionsMod.F90

@@ -20,6 +20,8 @@ module EDMortalityFunctionsMod
    use EDParamsMod           , only : fates_mortality_disturbance_fraction
    use FatesInterfaceMod     , only : bc_in_type
 
+   use PRTGenericMod,          only : all_carbon_elements
+   use PRTGenericMod,          only : store_organ
 
    implicit none
    private
@@ -57,7 +59,8 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )
     real(r8),intent(out) :: frmort ! freezing stress mortality
 
     real(r8) :: frac  ! relativised stored carbohydrate
-    real(r8) :: b_leaf ! target leaf biomass kgC
+    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) :: temp_dep_fraction  ! Temp. function (freezing mortality)
     real(r8) :: temp_in_C          ! Daily averaged temperature in Celcius
@@ -83,8 +86,11 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )
 
     ! Carbon Starvation induced mortality.
     if ( cohort_in%dbh  >  0._r8 ) then
-       call bleaf(cohort_in%dbh,cohort_in%pft,cohort_in%canopy_trim,b_leaf)
-       call storage_fraction_of_target(b_leaf, cohort_in%bstore, frac)
+
+       call bleaf(cohort_in%dbh,cohort_in%pft,cohort_in%canopy_trim,leaf_c_target)
+       store_c = cohort_in%prt%GetState(store_organ,all_carbon_elements)
+
+       call storage_fraction_of_target(leaf_c_target, store_c, frac)
        if( frac .lt. 1._r8) then
           cmort = max(0.0_r8,EDPftvarcon_inst%mort_scalar_cstarvation(cohort_in%pft) * &
                (1.0_r8 - frac))