Merge pull request #1300 from glemieux/parameter-switch-migration

Migrate parameter file switches that are moving to HLM namelist

biogeochem/EDCanopyStructureMod.F90

@@ -27,7 +27,6 @@ module EDCanopyStructureMod
   use FatesCohortMod,         only : fates_cohort_type
   use EDParamsMod            , only : nclmax
   use EDParamsMod            , only : nlevleaf
-  use EDParamsMod           , only : radiation_model
   use EDtypesMod            , only : AREA
   use EDLoggingMortalityMod , only : UpdateHarvestC
   use FatesGlobals          , only : endrun => fates_endrun
@@ -1314,10 +1313,11 @@ subroutine canopy_summarization( nsites, sites, bc_in )
     ! ---------------------------------------------------------------------------------
 
     use FatesInterfaceTypesMod    , only : hlm_use_cohort_age_tracking
+    use FatesInterfaceTypesMod    , only : hlm_radiation_model
     use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
     use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
-    use EDtypesMod           , only : area
-    use FatesConstantsMod    , only : itrue
+    use EDtypesMod                , only : area
+    use FatesConstantsMod         , only : itrue
 
     ! !ARGUMENTS
     integer                 , intent(in)            :: nsites
@@ -1451,7 +1451,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )
 
        call leaf_area_profile(sites(s))
 
-       if(radiation_model.eq.twostr_solver) then
+       if(hlm_radiation_model.eq.twostr_solver) then
           call FatesConstructRadElements(sites(s),bc_in(s)%fcansno_pa,bc_in(s)%coszen_pa)
        end if
 

biogeochem/EDMortalityFunctionsMod.F90

@@ -12,7 +12,6 @@ module EDMortalityFunctionsMod
    use FatesCohortMod        , only : fates_cohort_type
    use EDTypesMod            , only : ed_site_type
    use EDParamsMod,            only : maxpft
-   use EDParamsMod           , only : mort_cstarvation_model
    use FatesConstantsMod     , only : itrue,ifalse
    use FatesConstantsMod     , only : cstarvation_model_lin
    use FatesConstantsMod     , only : cstarvation_model_exp
@@ -68,6 +67,7 @@ subroutine mortality_rates( cohort_in,bc_in, btran_ft, mean_temp,             &
     use FatesConstantsMod,      only : fates_check_param_set
     use DamageMainMod,          only : GetDamageMortality
     use EDParamsmod,            only : soil_tfrz_thresh
+    use FatesInterfaceTypesMod, only : hlm_mort_cstarvation_model
 
     type (fates_cohort_type), intent(in) :: cohort_in 
     type (bc_in_type), intent(in) :: bc_in
@@ -204,7 +204,7 @@ subroutine mortality_rates( cohort_in,bc_in, btran_ft, mean_temp,             &
           call storage_fraction_of_target(target_leaf_c, store_c, frac)
 
           ! Select the carbon starvation mortality model (linear or exponential)s.
-          select case (mort_cstarvation_model)
+          select case (hlm_mort_cstarvation_model)
           case (cstarvation_model_lin)
              ! Linear model. Carbon starvation mortality will be zero when fraction of
              ! storage is greater than or equal to mort_upthresh_cstarvation, and will
@@ -223,7 +223,7 @@ subroutine mortality_rates( cohort_in,bc_in, btran_ft, mean_temp,             &
 
           case default
               write(fates_log(),*) &
-                 'Invalid carbon starvation model (',mort_cstarvation_model,').'
+                 'Invalid carbon starvation model (',hlm_mort_cstarvation_model,').'
               call endrun(msg=errMsg(sourcefile, __LINE__))
           end select
 

biogeochem/EDPatchDynamicsMod.F90

@@ -30,7 +30,7 @@ module EDPatchDynamicsMod
   use EDTypesMod           , only : elem_diag_type
   use EDTypesMod           , only : min_patch_area
   use EDTypesMod           , only : min_patch_area_forced
-  use EDParamsMod          , only : regeneration_model
+  use FatesInterfaceTypesMod, only : hlm_regeneration_model
   use FatesInterfaceTypesMod, only : numpft
   use FatesConstantsMod     , only : dtype_ifall
   use FatesConstantsMod     , only : dtype_ilog
@@ -682,7 +682,7 @@ subroutine spawn_patches( currentSite, bc_in)
 
                    call newPatch%Create(age, site_areadis, i_landusechange_receiverpatchlabel, i_nocomp_pft, &
                                          num_swb, numpft, currentSite%nlevsoil, hlm_current_tod,              &
-                                         regeneration_model)
+                                         hlm_regeneration_model)
 
                    ! Initialize the litter pools to zero, these
                    ! pools will be populated by looping over the existing patches
@@ -1371,7 +1371,7 @@ subroutine spawn_patches( currentSite, bc_in)
 
                 call buffer_patch%Create(0._r8, 0._r8, i_land_use_label, 0, &
                      num_swb, numpft, currentSite%nlevsoil, hlm_current_tod,              &
-                     regeneration_model)
+                     hlm_regeneration_model)
 
                 ! Initialize the litter pools to zero
                 do el=1,num_elements
@@ -1559,7 +1559,7 @@ subroutine spawn_patches( currentSite, bc_in)
                    if ( .not. buffer_patch_in_linked_list) then
                       if (buffer_patch%area .lt. rsnbl_math_prec) then
                          ! here we need to deallocate the buffer patch so that we don't get a memory leak.
-                         call buffer_patch%FreeMemory(regeneration_model, numpft)
+                         call buffer_patch%FreeMemory(hlm_regeneration_model, numpft)
                          deallocate(buffer_patch, stat=istat, errmsg=smsg)
                          if (istat/=0) then
                             write(fates_log(),*) 'dealloc: fail on deallocate(dp):'//trim(smsg)
@@ -1576,7 +1576,7 @@ subroutine spawn_patches( currentSite, bc_in)
                    end if
                 else
                    ! buffer patch was never even used. deallocate.
-                   call buffer_patch%FreeMemory(regeneration_model, numpft)
+                   call buffer_patch%FreeMemory(hlm_regeneration_model, numpft)
                    deallocate(buffer_patch, stat=istat, errmsg=smsg)
                    if (istat/=0) then
                       write(fates_log(),*) 'dealloc: fail on deallocate(dp):'//trim(smsg)
@@ -1664,7 +1664,7 @@ subroutine split_patch(currentSite, currentPatch, new_patch, fraction_to_keep, a
     call new_patch%Create(0._r8, temp_area, &
          currentPatch%land_use_label, currentPatch%nocomp_pft_label, &
          num_swb, numpft, currentSite%nlevsoil, hlm_current_tod, &
-         regeneration_model)
+         hlm_regeneration_model)
 
     ! Initialize the litter pools to zero, these
     ! pools will be populated shortly
@@ -3188,7 +3188,7 @@ subroutine fuse_2_patches(csite, dp, rp)
     call rp%tveg24%FuseRMean(dp%tveg24,rp%area*inv_sum_area)
     call rp%tveg_lpa%FuseRMean(dp%tveg_lpa,rp%area*inv_sum_area)
 
-    if ( regeneration_model == TRS_regeneration ) then
+    if ( hlm_regeneration_model == TRS_regeneration ) then
        call rp%seedling_layer_par24%FuseRMean(dp%seedling_layer_par24,rp%area*inv_sum_area)
        call rp%sdlng_mort_par%FuseRMean(dp%sdlng_mort_par,rp%area*inv_sum_area)
        call rp%sdlng2sap_par%FuseRMean(dp%sdlng2sap_par,rp%area*inv_sum_area)
@@ -3259,7 +3259,7 @@ subroutine fuse_2_patches(csite, dp, rp)
     end if
 
     ! We have no need for the dp pointer anymore, we have passed on it's legacy
-    call dp%FreeMemory(regeneration_model, numpft)
+    call dp%FreeMemory(hlm_regeneration_model, numpft)
     deallocate(dp, stat=istat, errmsg=smsg)
     if (istat/=0) then
        write(fates_log(),*) 'dealloc006: fail on deallocate(dp):'//trim(smsg)
@@ -3810,7 +3810,7 @@ subroutine CopyPatchMeansTimers(dp, rp)
     call rp%tveg_lpa%CopyFromDonor(dp%tveg_lpa)
     call rp%tveg_longterm%CopyFromDonor(dp%tveg_longterm)
 
-    if ( regeneration_model == TRS_regeneration ) then
+    if ( hlm_regeneration_model == TRS_regeneration ) then
        call rp%seedling_layer_par24%CopyFromDonor(dp%seedling_layer_par24)
        call rp%sdlng_mort_par%CopyFromDonor(dp%sdlng_mort_par)
        call rp%sdlng2sap_par%CopyFromDonor(dp%sdlng2sap_par)

biogeochem/EDPhysiologyMod.F90

@@ -98,7 +98,6 @@ module EDPhysiologyMod
   use EDParamsMod           , only : q10_mr
   use EDParamsMod           , only : q10_froz
   use EDParamsMod           , only : logging_export_frac
-  use EDParamsMod           , only : regeneration_model
   use EDParamsMod           , only : sdlng_mort_par_timescale
   use FatesPlantHydraulicsMod  , only : AccumulateMortalityWaterStorage
   use FatesConstantsMod     , only : itrue,ifalse
@@ -143,7 +142,8 @@ module EDPhysiologyMod
   use FatesParameterDerivedMod, only : param_derived
   use FatesPlantHydraulicsMod, only : InitHydrCohort
   use PRTInitParamsFatesMod, only : NewRecruitTotalStoichiometry
-  use FatesInterfaceTypesMod    , only : hlm_use_luh
+  use FatesInterfaceTypesMod, only : hlm_use_luh
+  use FatesInterfaceTypesMod, only : hlm_regeneration_model
 
   implicit none
   private
@@ -2157,7 +2157,7 @@ subroutine SeedUpdate( currentSite )
                 litt%seed_in_local(pft) = litt%seed_in_local(pft) + site_seed_rain(pft)*(1.0_r8-site_disp_frac(pft))/area ![kg/m2/day]
 
                 ! If we are using the Tree Recruitment Scheme (TRS) with or w/o seedling dynamics
-                if ( any(regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
+                if ( any(hlm_regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
                      prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees) then
 
                    ! Send a fraction of reproductive carbon to litter to account for 
@@ -2215,7 +2215,7 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
     !
     ! !DESCRIPTION:
     ! 1. Flux from seed pool into leaf litter pool
-    ! 2. If the TRS with seedling dynamics is on (regeneration_model = 3)
+    ! 2. If the TRS with seedling dynamics is on (hlm_regeneration_model = 3)
     !    then we calculate seedling mortality here (i.e. flux from seedling pool
     !    (into leaf litter pool)   
     !
@@ -2249,7 +2249,7 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
 
        ! If the TRS is switched off or the pft can't get big enough to be considered a tree 
        ! then use FATES default regeneration.
-       if ( regeneration_model == default_regeneration .or. &
+       if ( hlm_regeneration_model == default_regeneration .or. &
             prt_params%allom_dbh_maxheight(pft) < min_max_dbh_for_trees ) then
 
           ! Default seed decay (TRS is off)
@@ -2261,7 +2261,7 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
        ! If the TRS is switched on and the pft is a tree then add non-seed reproductive biomass
        ! to the seed decay flux. This was added to litt%seed_decay in the previously called SeedIn 
        ! subroutine
-       if ( any(regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
+       if ( any(hlm_regeneration_model == [TRS_regeneration, TRS_no_seedling_dyn]) .and. &
             prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees ) then
 
           litt%seed_decay(pft) = litt%seed_decay(pft) + &! From non-seed reproductive biomass (added in
@@ -2271,9 +2271,9 @@ subroutine SeedDecay( litt , currentPatch, bc_in )
        end if 
 
 
-       ! If the TRS is switched on with seedling dynamics (regeneration_model = 2) 
+       ! If the TRS is switched on with seedling dynamics (hlm_regeneration_model = 2)
        ! then calculate seedling mortality.
-       if_trs_germ_decay: if ( regeneration_model == TRS_regeneration .and. &
+       if_trs_germ_decay: if ( hlm_regeneration_model == TRS_regeneration .and. &
             prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees ) then
 
           !----------------------------------------------------------------------
@@ -2379,16 +2379,16 @@ subroutine SeedGermination( litt, cold_stat, drought_stat, bc_in, currentPatch )
 
        ! If the TRS's seedling dynamics is switched off, then we use FATES's default approach
        ! to germination 
-       if_tfs_or_def: if ( regeneration_model == default_regeneration .or. &
-            regeneration_model == TRS_no_seedling_dyn .or. & 
+       if_tfs_or_def: if ( hlm_regeneration_model == default_regeneration .or. &
+            hlm_regeneration_model == TRS_no_seedling_dyn .or. &
             prt_params%allom_dbh_maxheight(pft) < min_max_dbh_for_trees ) then
 
           litt%seed_germ_in(pft) =  min(litt%seed(pft) * EDPftvarcon_inst%germination_rate(pft), &  
                max_germination)*years_per_day
 
           ! If TRS seedling dynamics is switched on we calculate seedling emergence (i.e. germination)
           ! as a pft-specific function of understory light and soil moisture.
-       else if ( regeneration_model == TRS_regeneration .and. &
+       else if ( hlm_regeneration_model == TRS_regeneration .and. &
             prt_params%allom_dbh_maxheight(pft) > min_max_dbh_for_trees ) then	    
 
           ! Step 1. Calculate how germination rate is modified by understory light
@@ -2634,15 +2634,15 @@ subroutine recruitment(currentSite, currentPatch, bc_in)
 
                   ! If TRS seedling dynamics is switched off then the available mass to make new recruits
                   ! is everything in the seed_germ pool.
-                  if (regeneration_model == default_regeneration .or.          &
-                     regeneration_model == TRS_no_seedling_dyn .or.            & 
+                  if (hlm_regeneration_model == default_regeneration .or.          &
+                     hlm_regeneration_model == TRS_no_seedling_dyn .or.            &
                      prt_params%allom_dbh_maxheight(ft) < min_max_dbh_for_trees) then
 
                      mass_avail = currentPatch%area * currentPatch%litter(el)%seed_germ(ft)
 
                      ! If TRS seedling dynamics is on then calculate the available mass to make new recruits
                      ! as a pft-specific function of light and soil moisture in the seedling layer.
-                  else if (regeneration_model == TRS_regeneration .and.        &
+                  else if (hlm_regeneration_model == TRS_regeneration .and.        &
                      prt_params%allom_dbh_maxheight(ft) > min_max_dbh_for_trees) then
 
                      sdlng2sap_par = currentPatch%sdlng2sap_par%GetMean()*     &

biogeophys/FatesPlantHydraulicsMod.F90

@@ -49,7 +49,6 @@ module FatesPlantHydraulicsMod
   use EDParamsMod       , only : hydr_psi0
   use EDParamsMod       , only : hydr_psicap
   use EDParamsMod       , only : hydr_htftype_node
-  use EDParamsMod       , only : hydr_solver
 
   use EDTypesMod        , only : ed_site_type
   use FatesPatchMod     , only : fates_patch_type
@@ -64,6 +63,7 @@ module FatesPlantHydraulicsMod
   use FatesInterfaceTypesMod  , only : hlm_ipedof
   use FatesInterfaceTypesMod  , only : numpft
   use FatesInterfaceTypesMod  , only : nlevsclass
+  use FatesInterfaceTypesMod  , only : hlm_hydr_solver
 
   use FatesAllometryMod, only    : bleaf
   use FatesAllometryMod, only    : bsap_allom
@@ -1419,7 +1419,7 @@ subroutine InitHydrSites(sites,bc_in)
      case(rhizlayer_aggmeth_none)
 
         csite_hydr%nlevrhiz = bc_in(s)%nlevsoil
-        call sites(s)%si_hydr%InitHydrSite(numpft,nlevsclass,hydr_solver,bc_in(s)%nlevsoil)
+        call sites(s)%si_hydr%InitHydrSite(numpft,nlevsclass,hlm_hydr_solver,bc_in(s)%nlevsoil)
 
         do j=1,csite_hydr%nlevrhiz
            csite_hydr%map_r2s(j,1) = j
@@ -1431,7 +1431,7 @@ subroutine InitHydrSites(sites,bc_in)
      case(rhizlayer_aggmeth_combine12)
 
         csite_hydr%nlevrhiz     = max(1,bc_in(s)%nlevsoil-1)
-        call sites(s)%si_hydr%InitHydrSite(numpft,nlevsclass,hydr_solver,bc_in(s)%nlevsoil)
+        call sites(s)%si_hydr%InitHydrSite(numpft,nlevsclass,hlm_hydr_solver,bc_in(s)%nlevsoil)
 
         csite_hydr%map_r2s(1,1) = 1
         j_bc                 = min(2,bc_in(s)%nlevsoil) ! this protects 1 soil layer
@@ -1449,7 +1449,7 @@ subroutine InitHydrSites(sites,bc_in)
      case(rhizlayer_aggmeth_balN)
 
         csite_hydr%nlevrhiz = min(aggN,bc_in(s)%nlevsoil)
-        call sites(s)%si_hydr%InitHydrSite(numpft,nlevsclass,hydr_solver,bc_in(s)%nlevsoil)
+        call sites(s)%si_hydr%InitHydrSite(numpft,nlevsclass,hlm_hydr_solver,bc_in(s)%nlevsoil)
 
         ntoagg = int(ceiling(real(bc_in(s)%nlevsoil)/real(csite_hydr%nlevrhiz)-nearzero))
 
@@ -2583,21 +2583,21 @@ subroutine hydraulics_bc ( nsites, sites, bc_in, bc_out, dtime)
               ! from leaf to the current soil layer.  This does NOT
               ! update cohort%th_*
 
-              if(hydr_solver == hydr_solver_2DNewton) then
+              if(hlm_hydr_solver == hydr_solver_2DNewton) then
 
                  call MatSolve2D(csite_hydr,ccohort,ccohort_hydr, &
                       dtime,qflx_tran_veg_indiv, &
                       sapflow,rootuptake(1:nlevrhiz),wb_err_plant,dwat_plant, &
                       dth_layershell_col)
 
-              elseif(hydr_solver == hydr_solver_2DPicard) then
+              elseif(hlm_hydr_solver == hydr_solver_2DPicard) then
 
                  call PicardSolve2D(csite_hydr,ccohort,ccohort_hydr, &
                       dtime,qflx_tran_veg_indiv, &
                       sapflow,rootuptake(1:nlevrhiz),wb_err_plant,dwat_plant, &
                       dth_layershell_col,csite_hydr%num_nodes)
 
-              elseif(hydr_solver == hydr_solver_1DTaylor ) then
+              elseif(hlm_hydr_solver == hydr_solver_1DTaylor ) then
 
                  ! ---------------------------------------------------------------------------------
                  ! Approach: do nlevsoi_hyd sequential solutions to Richards' equation,
@@ -4938,7 +4938,7 @@ subroutine MatSolve2D(csite_hydr,cohort,cohort_hydr, &
 
 
    ! This NaN's the scratch arrays
-   call csite_hydr%FlushSiteScratch(hydr_solver)
+   call csite_hydr%FlushSiteScratch(hlm_hydr_solver)
 
    ! This is the maximum number of iterations needed for this cohort
    ! (each soil layer has a different number, this saves the max)
@@ -5714,7 +5714,7 @@ subroutine PicardSolve2D(csite_hydr,cohort,cohort_hydr, &
        ft           => cohort%pft)
 
     ! This NaN's the scratch arrays
-    call csite_hydr%FlushSiteScratch(hydr_solver)
+    call csite_hydr%FlushSiteScratch(hlm_hydr_solver)
 
     ! This is the maximum number of iterations needed for this cohort
     ! (each soil layer has a different number, this saves the max)