Merge pull request #514 from rgknox/consolidated-pft-file

consolidation of parameter files

Author: rgknox

main/EDMainMod.F90

@@ -40,7 +40,6 @@ module EDMainMod
   use EDtypesMod               , only : ed_site_type
   use EDtypesMod               , only : ed_patch_type
   use EDtypesMod               , only : ed_cohort_type
-  use EDTypesMod               , only : do_ed_phenology
   use EDTypesMod               , only : AREA
   use FatesConstantsMod        , only : itrue,ifalse
   use FatesConstantsMod        , only : primaryforest, secondaryforest
@@ -135,11 +134,15 @@ subroutine ed_ecosystem_dynamics(currentSite, bc_in)
 
 
     call ed_total_balance_check(currentSite, 0)
-    
-    if (do_ed_phenology) then
+
+    ! We do not allow phenology while in ST3 mode either, it is hypothetically
+    ! possible to allow this, but we have not plugged in the litter fluxes
+    ! of flushing or turning over leaves for non-dynamics runs
+    if (hlm_use_ed_st3.eq.ifalse) then
        call phenology(currentSite, bc_in )
     end if
 
+
     if (hlm_use_ed_st3.eq.ifalse) then   ! Bypass if ST3
        call fire_model(currentSite, bc_in) 
 
@@ -346,7 +349,6 @@ subroutine ed_integrate_state_variables(currentSite, bc_in )
 
           currentSite%flux_in = currentSite%flux_in + currentCohort%npp_acc * currentCohort%n
 
-
           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, &
@@ -356,7 +358,8 @@ subroutine ed_integrate_state_variables(currentSite, bc_in )
                currentPatch%canopy_layer_tlai, currentCohort%treelai,currentCohort%vcmax25top,6 )
 
 
-          ! Conducte Maintenance Turnover (parteh)
+          ! Conduct Maintenance Turnover (parteh)
+
           call currentCohort%prt%CheckMassConservation(ft,3)
           call PRTMaintTurnover(currentCohort%prt,ft,currentSite%is_drought)
           call currentCohort%prt%CheckMassConservation(ft,4)

main/EDTypesMod.F90

@@ -80,18 +80,6 @@ module EDTypesMod
                                         ! its leaves and should not be trying to allocate
                                         ! towards any growth.
 
-  ! Switches that turn on/off ED dynamics process (names are self explanatory)
-  ! IMPORTANT NOTE!!! THESE SWITCHES ARE EXPERIMENTAL.  
-  ! THEY SHOULD CORRECTLY TURN OFF OR ON THE PROCESS, BUT.. THERE ARE VARIOUS 
-  ! ASPECTS REGARDING DIAGNOSING RATES AND HOW THEY ARE REPORTED WHEN THESE 
-  ! PROCESSES ARE OFF THAT NEED TO BE DISCUSSED AND CONSIDERED.
-  ! TO-DO: THESE SHOULD BE PARAMETERS IN THE FILE OR NAMELIST - ADDING THESE
-  ! WAS OUTSIDE THE SCOPE OF THE VERY LARGE CHANGESET WHERE THESE WERE FIRST
-  ! INTRODUCED (RGK 03-2017)
-
-  logical, parameter :: do_ed_phenology   = .true.
-
-
   ! Flag to turn on/off salinity effects on the effective "btran"
   ! btran stress function.
 

main/FatesHistoryInterfaceMod.F90

@@ -1887,51 +1887,50 @@ subroutine update_history_dyn(this,nc,nsites,sites)
                     hio_npp_stor_si_scpf(io_si,scpf) = hio_npp_stor_si_scpf(io_si,scpf) + &
                                                        store_c_net_alloc*n_perm2
 
-                    ! Woody State Variables (basal area and number density and mortality)
+                    ! Woody State Variables (basal area growth increment)
                     if (EDPftvarcon_inst%woody(ft) == 1) then
-                       
-                       hio_m1_si_scpf(io_si,scpf) = hio_m1_si_scpf(io_si,scpf) + ccohort%bmort*ccohort%n
-                       hio_m2_si_scpf(io_si,scpf) = hio_m2_si_scpf(io_si,scpf) + ccohort%hmort*ccohort%n
-                       hio_m3_si_scpf(io_si,scpf) = hio_m3_si_scpf(io_si,scpf) + ccohort%cmort*ccohort%n
-                       hio_m7_si_scpf(io_si,scpf) = hio_m7_si_scpf(io_si,scpf) + &
-                            (ccohort%lmort_direct+ccohort%lmort_collateral+ccohort%lmort_infra) * ccohort%n
-                       hio_m8_si_scpf(io_si,scpf) = hio_m8_si_scpf(io_si,scpf) + ccohort%frmort*ccohort%n
-
-                       hio_m1_si_scls(io_si,scls) = hio_m1_si_scls(io_si,scls) + ccohort%bmort*ccohort%n
-                       hio_m2_si_scls(io_si,scls) = hio_m2_si_scls(io_si,scls) + ccohort%hmort*ccohort%n
-                       hio_m3_si_scls(io_si,scls) = hio_m3_si_scls(io_si,scls) + ccohort%cmort*ccohort%n
-		       hio_m7_si_scls(io_si,scls) = hio_m7_si_scls(io_si,scls) + &
-                             (ccohort%lmort_direct+ccohort%lmort_collateral+ccohort%lmort_infra) * ccohort%n
-                       hio_m8_si_scls(io_si,scls) = hio_m8_si_scls(io_si,scls) + &
-                             ccohort%frmort*ccohort%n
-			     
-		       !C13 discrimination
-                       if(gpp_cached + ccohort%gpp_acc_hold > 0.0_r8)then
-
-                           hio_c13disc_si_scpf(io_si,scpf) = ((hio_c13disc_si_scpf(io_si,scpf) * gpp_cached) + &
-			     (ccohort%c13disc_acc * ccohort%gpp_acc_hold)) / (gpp_cached + ccohort%gpp_acc_hold)
-		       else
-		           hio_c13disc_si_scpf(io_si,scpf) = 0.0_r8
-                       endif
-			
-			     
 
                        ! basal area  [m2/ha]
                        hio_ba_si_scpf(io_si,scpf) = hio_ba_si_scpf(io_si,scpf) + &
                             0.25_r8*3.14159_r8*((dbh/100.0_r8)**2.0_r8)*ccohort%n
+
                        ! also by size class only
                        hio_ba_si_scls(io_si,scls) = hio_ba_si_scls(io_si,scls) + &
                             0.25_r8*3.14159_r8*((dbh/100.0_r8)**2.0_r8)*ccohort%n
-                       
-                       ! number density [/ha]
-                       hio_nplant_si_scpf(io_si,scpf) = hio_nplant_si_scpf(io_si,scpf) + ccohort%n
-                       
+
                        ! growth increment
                        hio_ddbh_si_scpf(io_si,scpf) = hio_ddbh_si_scpf(io_si,scpf) + &
                             ccohort%ddbhdt*ccohort%n
 
                     end if
 
+                    hio_m1_si_scpf(io_si,scpf) = hio_m1_si_scpf(io_si,scpf) + ccohort%bmort*ccohort%n
+                    hio_m2_si_scpf(io_si,scpf) = hio_m2_si_scpf(io_si,scpf) + ccohort%hmort*ccohort%n
+                    hio_m3_si_scpf(io_si,scpf) = hio_m3_si_scpf(io_si,scpf) + ccohort%cmort*ccohort%n
+                    hio_m7_si_scpf(io_si,scpf) = hio_m7_si_scpf(io_si,scpf) + &
+                         (ccohort%lmort_direct+ccohort%lmort_collateral+ccohort%lmort_infra) * ccohort%n
+                    hio_m8_si_scpf(io_si,scpf) = hio_m8_si_scpf(io_si,scpf) + ccohort%frmort*ccohort%n
+
+                    hio_m1_si_scls(io_si,scls) = hio_m1_si_scls(io_si,scls) + ccohort%bmort*ccohort%n
+                    hio_m2_si_scls(io_si,scls) = hio_m2_si_scls(io_si,scls) + ccohort%hmort*ccohort%n
+                    hio_m3_si_scls(io_si,scls) = hio_m3_si_scls(io_si,scls) + ccohort%cmort*ccohort%n
+                    hio_m7_si_scls(io_si,scls) = hio_m7_si_scls(io_si,scls) + &
+                         (ccohort%lmort_direct+ccohort%lmort_collateral+ccohort%lmort_infra) * ccohort%n
+                    hio_m8_si_scls(io_si,scls) = hio_m8_si_scls(io_si,scls) + &
+                         ccohort%frmort*ccohort%n
+
+                    !C13 discrimination
+                    if(gpp_cached + ccohort%gpp_acc_hold > 0.0_r8)then
+                       hio_c13disc_si_scpf(io_si,scpf) = ((hio_c13disc_si_scpf(io_si,scpf) * gpp_cached) + &
+                            (ccohort%c13disc_acc * ccohort%gpp_acc_hold)) / (gpp_cached + ccohort%gpp_acc_hold)
+                    else
+                       hio_c13disc_si_scpf(io_si,scpf) = 0.0_r8
+                    endif
+
+                    ! number density [/ha]
+                    hio_nplant_si_scpf(io_si,scpf) = hio_nplant_si_scpf(io_si,scpf) + ccohort%n
+
+
                     hio_agb_si_scls(io_si,scls) = hio_agb_si_scls(io_si,scls) + &
                           total_c * ccohort%n * EDPftvarcon_inst%allom_agb_frac(ccohort%pft) * AREA_INV
 
@@ -3206,6 +3205,12 @@ subroutine update_history_hydraulics(this,nc,nsites,sites,dt_tstep)
          if(hlm_use_ed_st3.eq.ifalse) then
             do scpf=1,nlevsclass*numpft
                if( abs(hio_nplant_si_scpf(io_si, scpf)-ncohort_scpf(scpf)) > 1.0E-8_r8 ) then
+                  write(fates_log(),*) 'numpft:',numpft
+                  write(fates_log(),*) 'nlevsclass:',nlevsclass
+                  write(fates_log(),*) 'scpf:',scpf
+                  write(fates_log(),*) 'io_si:',io_si
+                  write(fates_log(),*) 'hio_nplant_si_scpf:',hio_nplant_si_scpf(io_si, scpf)
+                  write(fates_log(),*) 'ncohort_scpf:',ncohort_scpf(scpf)
                   write(fates_log(),*) 'nplant check on hio_nplant_si_scpf fails during hydraulics history updates'
                   call endrun(msg=errMsg(sourcefile, __LINE__))
                end if

main/FatesRestartInterfaceMod.F90

@@ -96,6 +96,7 @@ module FatesRestartInterfaceMod
   integer, private :: ir_canopy_trim_co
   integer, private :: ir_size_class_lasttimestep_co
   integer, private :: ir_dbh_co
+  integer, private :: ir_g_sb_laweight_co
   integer, private :: ir_height_co
   integer, private :: ir_laimemory_co
   integer, private :: ir_nplant_co
@@ -804,6 +805,10 @@ subroutine define_restart_vars(this, initialize_variables)
          units='0/1', flushval = flushone, &
          hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_isnew_co )
 
+    call this%set_restart_var(vname='fates_gsblaweight',vtype=cohort_r8, &
+         long_name='ed cohort - leaf-area weighted total stomatal+blayer conductance', &
+         units='[m/s]*[m2]', flushval = flushzero, &
+         hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_g_sb_laweight_co)
 
     ! Mixed dimension variables using the cohort vector
     ! -----------------------------------------------------------------------------------
@@ -1468,6 +1473,7 @@ subroutine set_restart_vectors(this,nc,nsites,sites)
            rio_canopy_trim_co          => this%rvars(ir_canopy_trim_co)%r81d, &
            rio_size_class_lasttimestep => this%rvars(ir_size_class_lasttimestep_co)%int1d, &
            rio_dbh_co                  => this%rvars(ir_dbh_co)%r81d, &
+           rio_g_sb_laweight_co        => this%rvars(ir_g_sb_laweight_co)%r81d, &
            rio_height_co               => this%rvars(ir_height_co)%r81d, &
            rio_laimemory_co            => this%rvars(ir_laimemory_co)%r81d, &
            rio_nplant_co               => this%rvars(ir_nplant_co)%r81d, &
@@ -1654,6 +1660,7 @@ subroutine set_restart_vectors(this,nc,nsites,sites)
                 rio_dbh_co(io_idx_co)          = ccohort%dbh
                 rio_height_co(io_idx_co)       = ccohort%hite
                 rio_laimemory_co(io_idx_co)    = ccohort%laimemory
+                rio_g_sb_laweight_co(io_idx_co)= ccohort%g_sb_laweight
 
                 rio_nplant_co(io_idx_co)       = ccohort%n
                 rio_gpp_acc_co(io_idx_co)      = ccohort%gpp_acc
@@ -2179,6 +2186,7 @@ subroutine get_restart_vectors(this, nc, nsites, sites)
           rio_canopy_trim_co          => this%rvars(ir_canopy_trim_co)%r81d, &
           rio_size_class_lasttimestep => this%rvars(ir_size_class_lasttimestep_co)%int1d, &
           rio_dbh_co                  => this%rvars(ir_dbh_co)%r81d, &
+          rio_g_sb_laweight_co        => this%rvars(ir_g_sb_laweight_co)%r81d, &
           rio_height_co               => this%rvars(ir_height_co)%r81d, &
           rio_laimemory_co            => this%rvars(ir_laimemory_co)%r81d, &
           rio_nplant_co               => this%rvars(ir_nplant_co)%r81d, &
@@ -2326,6 +2334,7 @@ subroutine get_restart_vectors(this, nc, nsites, sites)
                 ccohort%canopy_trim  = rio_canopy_trim_co(io_idx_co)
                 ccohort%size_class_lasttimestep = rio_size_class_lasttimestep(io_idx_co)
                 ccohort%dbh          = rio_dbh_co(io_idx_co)
+                ccohort%g_sb_laweight= rio_g_sb_laweight_co(io_idx_co)
                 ccohort%hite         = rio_height_co(io_idx_co)
                 ccohort%laimemory    = rio_laimemory_co(io_idx_co)
                 ccohort%n            = rio_nplant_co(io_idx_co)