Nutrient Enabled Aquisition (parteh pt 3)

biogeochem/EDCanopyStructureMod.F90

@@ -12,6 +12,7 @@ module EDCanopyStructureMod
   use FatesConstantsMod     , only : rsnbl_math_prec
   use FatesGlobals          , only : fates_log
   use EDPftvarcon           , only : EDPftvarcon_inst
+  use PRTParametersMod      , only : prt_params
   use FatesAllometryMod     , only : carea_allom
   use EDCohortDynamicsMod   , only : copy_cohort, terminate_cohorts, fuse_cohorts
   use EDCohortDynamicsMod   , only : InitPRTObject
@@ -280,12 +281,12 @@ subroutine canopy_structure( currentSite , bc_in )
                   write(fates_log(),*) 'coh n:',currentCohort%n
                   write(fates_log(),*) 'coh carea:',currentCohort%c_area
 		  ipft=currentCohort%pft
-		  write(fates_log(),*) 'maxh:',EDPftvarcon_inst%allom_dbh_maxheight(ipft)
-                  write(fates_log(),*) 'lmode: ',EDPftvarcon_inst%allom_lmode(ipft)
-		  write(fates_log(),*) 'd2bl2: ',EDPftvarcon_inst%allom_d2bl2(ipft)
-		  write(fates_log(),*) 'd2bl_ediff: ',EDPftvarcon_inst%allom_blca_expnt_diff(ipft)
-		  write(fates_log(),*) 'd2ca_min: ',EDPftvarcon_inst%allom_d2ca_coefficient_min(ipft)
-		  write(fates_log(),*) 'd2ca_max: ',EDPftvarcon_inst%allom_d2ca_coefficient_max(ipft)
+		  write(fates_log(),*) 'maxh:',prt_params%allom_dbh_maxheight(ipft)
+                  write(fates_log(),*) 'lmode: ',prt_params%allom_lmode(ipft)
+		  write(fates_log(),*) 'd2bl2: ',prt_params%allom_d2bl2(ipft)
+		  write(fates_log(),*) 'd2bl_ediff: ',prt_params%allom_blca_expnt_diff(ipft)
+		  write(fates_log(),*) 'd2ca_min: ',prt_params%allom_d2ca_coefficient_min(ipft)
+		  write(fates_log(),*) 'd2ca_max: ',prt_params%allom_d2ca_coefficient_max(ipft)
                   currentCohort => currentCohort%shorter
                enddo
                call endrun(msg=errMsg(sourcefile, __LINE__))
@@ -1223,7 +1224,7 @@ subroutine canopy_spread( currentSite )
        do while (associated(currentCohort))
           call carea_allom(currentCohort%dbh,currentCohort%n, &
                 currentSite%spread,currentCohort%pft,currentCohort%c_area)
-          if( (EDPftvarcon_inst%woody(currentCohort%pft) .eq. 1 ) .and. &
+          if( ( int(prt_params%woody(currentCohort%pft)) .eq. itrue ) .and. &
               (currentCohort%canopy_layer .eq. 1 ) ) then
              sitelevel_canopyarea = sitelevel_canopyarea + currentCohort%c_area
           endif
@@ -1262,9 +1263,8 @@ subroutine canopy_summarization( nsites, sites, bc_in )
     use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
     use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
     use EDtypesMod           , only : area
-    use EDPftvarcon          , only : EDPftvarcon_inst
     use FatesConstantsMod    , only : itrue
-    
+
     ! !ARGUMENTS    
     integer                 , intent(in)            :: nsites
     type(ed_site_type)      , intent(inout), target :: sites(nsites)
@@ -1342,7 +1342,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )
 
              if(currentCohort%canopy_layer==1)then
                 currentPatch%total_canopy_area = currentPatch%total_canopy_area + currentCohort%c_area
-                if(EDPftvarcon_inst%woody(ft)==1)then
+                if( int(prt_params%woody(ft))==itrue)then
                    currentPatch%total_tree_area = currentPatch%total_tree_area + currentCohort%c_area
                 endif
              endif
@@ -1875,8 +1875,6 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
      use EDTypesMod        , only : ed_patch_type, ed_cohort_type, &
                                     ed_site_type, AREA
      use FatesInterfaceTypesMod , only : bc_out_type
-     use EDPftvarcon       , only : EDPftvarcon_inst
-
 
      !
      ! !ARGUMENTS    

biogeochem/EDLoggingMortalityMod.F90

@@ -28,8 +28,9 @@ module EDLoggingMortalityMod
    use EDTypesMod        , only : dtype_ifire
    use EDPftvarcon       , only : EDPftvarcon_inst
    use EDPftvarcon       , only : GetDecompyFrac
-   use EDTypesMod        , only : num_elements
-   use EDTypesMod        , only : element_list
+   use PRTParametersMod  , only : prt_params
+   use PRTGenericMod     , only : num_elements
+   use PRTGenericMod     , only : element_list
    use EDParamsMod       , only : logging_export_frac
    use EDParamsMod       , only : logging_event_code
    use EDParamsMod       , only : logging_dbhmin
@@ -220,6 +221,7 @@ subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
       ! todo: implement harvested carbon inputs
 
       if (logging_time) then 
+
          ! Pass logging rates to cohort level 
 
          if (hlm_use_lu_harvest == ifalse) then
@@ -255,7 +257,7 @@ subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
 
          ! transfer of area to secondary land is based on overall area affected, not just logged crown area
          ! l_degrad accounts for the affected area between logged crowns
-         if(EDPftvarcon_inst%woody(pft_i) == 1)then ! only set logging rates for trees
+         if(int(prt_params%woody(pft_i)) == 1)then ! only set logging rates for trees
 
             ! direct logging rates, based on dbh min and max criteria
             if (dbh >= logging_dbhmin .and. .not. &
@@ -534,7 +536,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
                ! plants that were impacted. Thus, no direct dead can occur
                ! here, and indirect are impacts.
 
-               if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
+               if(int(prt_params%woody(pft)) == itrue) then
                   direct_dead   = 0.0_r8
                   indirect_dead = logging_coll_under_frac * &
                        (1._r8-currentPatch%fract_ldist_not_harvested) * currentCohort%n * &
@@ -565,9 +567,9 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
             call set_root_fraction(currentSite%rootfrac_scr, pft, currentSite%zi_soil)
 
             ag_wood = (direct_dead+indirect_dead) * (struct_m + sapw_m ) * &
-                  EDPftvarcon_inst%allom_agb_frac(currentCohort%pft)
+                  prt_params%allom_agb_frac(currentCohort%pft)
             bg_wood = (direct_dead+indirect_dead) * (struct_m + sapw_m ) * &
-                  (1._r8 - EDPftvarcon_inst%allom_agb_frac(currentCohort%pft))
+                  (1._r8 - prt_params%allom_agb_frac(currentCohort%pft))
 
             do c = 1,ncwd-1
 
@@ -608,9 +610,9 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
             ! ----------------------------------------------------------------------------------------
 
             ag_wood = indirect_dead * (struct_m + sapw_m ) * &
-                  EDPftvarcon_inst%allom_agb_frac(currentCohort%pft)
+                  prt_params%allom_agb_frac(currentCohort%pft)
             bg_wood = indirect_dead * (struct_m + sapw_m ) * &
-                  (1._r8 - EDPftvarcon_inst%allom_agb_frac(currentCohort%pft))
+                  (1._r8 - prt_params%allom_agb_frac(currentCohort%pft))
 
             new_litt%ag_cwd(ncwd) = new_litt%ag_cwd(ncwd) + ag_wood * &
                   SF_val_CWD_frac(ncwd) * donate_frac/newPatch%area
@@ -646,7 +648,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
             ! ----------------------------------------------------------------------------------------
 
             bg_wood = direct_dead * (struct_m + sapw_m ) * SF_val_CWD_frac(ncwd) * &
-                  (1._r8 - EDPftvarcon_inst%allom_agb_frac(currentCohort%pft))
+                  (1._r8 - prt_params%allom_agb_frac(currentCohort%pft))
 
             do ilyr = 1,nlevsoil
                 new_litt%bg_cwd(ncwd,ilyr) = new_litt%bg_cwd(ncwd,ilyr) + &
@@ -671,7 +673,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
             ! ----------------------------------------------------------------------------------------
 
             ag_wood = direct_dead * (struct_m + sapw_m ) * &
-                  EDPftvarcon_inst%allom_agb_frac(currentCohort%pft) * &
+                  prt_params%allom_agb_frac(currentCohort%pft) * &
                   SF_val_CWD_frac(ncwd)
 
             trunk_product_site = trunk_product_site + &

biogeochem/EDPatchDynamicsMod.F90

@@ -7,6 +7,7 @@ module EDPatchDynamicsMod
   use FatesInterfaceTypesMod    , only : hlm_freq_day
   use EDPftvarcon          , only : EDPftvarcon_inst
   use EDPftvarcon          , only : GetDecompyFrac
+  use PRTParametersMod      , only : prt_params
   use EDCohortDynamicsMod  , only : fuse_cohorts, sort_cohorts, insert_cohort
   use EDCohortDynamicsMod  , only : DeallocateCohort
   use EDTypesMod           , only : area_site => area
@@ -30,9 +31,8 @@ module EDPatchDynamicsMod
   use EDTypesMod           , only : dtype_ilog
   use EDTypesMod           , only : dtype_ifire
   use EDTypesMod           , only : ican_upper
-  use EDTypesMod           , only : num_elements
-  use EDTypesMod           , only : element_list
-  use EDTypesMod           , only : element_pos
+  use PRTGenericMod        , only : num_elements
+  use PRTGenericMod        , only : element_list
   use EDTypesMod           , only : lg_sf
   use EDTypesMod           , only : dl_sf
   use EDTypesMod           , only : dump_patch
@@ -231,7 +231,7 @@ subroutine disturbance_rates( site_in, bc_in)
                   currentCohort%lmort_direct * currentCohort%n * &
                   ( currentCohort%prt%GetState(sapw_organ, all_carbon_elements) + &
                   currentCohort%prt%GetState(struct_organ, all_carbon_elements)) * &
-                  EDPftvarcon_inst%allom_agb_frac(currentCohort%pft) * &
+                  prt_params%allom_agb_frac(currentCohort%pft) * &
                   SF_val_CWD_frac(ncwd) * logging_export_frac
           endif
 
@@ -733,7 +733,7 @@ subroutine spawn_patches( currentSite, bc_in)
 
                    else
                       ! small trees 
-                      if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
+                      if( int(prt_params%woody(currentCohort%pft)) == itrue)then
 
 
                          ! Survivorship of undestory woody plants.  Two step process.
@@ -873,7 +873,7 @@ subroutine spawn_patches( currentSite, bc_in)
                    ! burned off.  Here, we remove that mass, and
                    ! tally it in the flux we sent to the atmosphere
 
-                   if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
+                   if(int(prt_params%woody(currentCohort%pft)) == itrue)then
                        leaf_burn_frac = currentCohort%fraction_crown_burned
                    else
 
@@ -890,7 +890,7 @@ subroutine spawn_patches( currentSite, bc_in)
                        (currentCohort%fire_mort < 0._r8) .or. &
                        (currentCohort%fire_mort > 1._r8)) then
                        write(fates_log(),*) 'unexpected fire fractions'
-                       write(fates_log(),*) EDPftvarcon_inst%woody(currentCohort%pft)
+                       write(fates_log(),*) prt_params%woody(currentCohort%pft)
                        write(fates_log(),*) leaf_burn_frac
                        write(fates_log(),*) currentCohort%fire_mort
                        call endrun(msg=errMsg(sourcefile, __LINE__))
@@ -951,7 +951,7 @@ subroutine spawn_patches( currentSite, bc_in)
                       ! WHat to do with cohorts in the understory of a logging generated
                       ! disturbance patch?
 
-                      if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
+                      if(int(prt_params%woody(currentCohort%pft)) == itrue)then
 
 
                          ! Survivorship of undestory woody plants.  Two step process.
@@ -1682,7 +1682,7 @@ subroutine fire_litter_fluxes(currentSite, currentPatch, newPatch, patch_site_ar
                   (fnrt_m + store_m) * num_dead_trees
 
              ! coarse root biomass per tree
-             bcroot = (sapw_m + struct_m) * (1.0_r8 - EDPftvarcon_inst%allom_agb_frac(pft) )
+             bcroot = (sapw_m + struct_m) * (1.0_r8 - prt_params%allom_agb_frac(pft) )
 
              ! below ground coarse woody debris from burned trees
              do c = 1,ncwd
@@ -1703,7 +1703,7 @@ subroutine fire_litter_fluxes(currentSite, currentPatch, newPatch, patch_site_ar
              end do
 
              ! stem biomass per tree
-             bstem  = (sapw_m + struct_m) * EDPftvarcon_inst%allom_agb_frac(pft)
+             bstem  = (sapw_m + struct_m) * prt_params%allom_agb_frac(pft)
 
              ! Above ground coarse woody debris from twigs and small branches
              ! a portion of this pool may burn
@@ -1829,7 +1829,7 @@ subroutine mortality_litter_fluxes(currentSite, currentPatch, newPatch, patch_si
              num_dead = currentCohort%n * min(1.0_r8,currentCohort%dmort * &
                    hlm_freq_day * fates_mortality_disturbance_fraction)
 
-          elseif(EDPftvarcon_inst%woody(pft) == itrue) then
+          elseif(int(prt_params%woody(pft)) == itrue) then
 
              ! Understorey trees. The total dead is based on their survivorship
              ! function, and the total area of disturbance.
@@ -1864,8 +1864,8 @@ subroutine mortality_litter_fluxes(currentSite, currentPatch, newPatch, patch_si
           end do
 
           ! Pre-calculate Structural and sapwood, below and above ground, total mass [kg]
-          ag_wood = num_dead * (struct_m + sapw_m) * EDPftvarcon_inst%allom_agb_frac(pft)
-          bg_wood = num_dead * (struct_m + sapw_m) * (1.0_r8-EDPftvarcon_inst%allom_agb_frac(pft))
+          ag_wood = num_dead * (struct_m + sapw_m) * prt_params%allom_agb_frac(pft)
+          bg_wood = num_dead * (struct_m + sapw_m) * (1.0_r8-prt_params%allom_agb_frac(pft))
 
           call set_root_fraction(currentSite%rootfrac_scr, pft, currentSite%zi_soil)