Merge pull request #5 from rgknox/yi-logging-v3

removed unused patch logging variables, initialized site logging variables

biogeochem/EDPatchDynamicsMod.F90

@@ -9,7 +9,7 @@ module EDPatchDynamicsMod
   use EDCohortDynamicsMod  , only : fuse_cohorts, sort_cohorts, insert_cohort
   use EDtypesMod           , only : ncwd, n_dbh_bins, ntol, area, dbhmax
   use EDTypesMod           , only : maxPatchesPerSite
-  use EDTypesMod           , only : ed_site_type, ed_patch_type, ed_cohort_type, ed_resources_management_type
+  use EDTypesMod           , only : ed_site_type, ed_patch_type, ed_cohort_type
   use EDTypesMod           , only : min_patch_area
   use EDTypesMod           , only : nclmax
   use EDTypesMod           , only : maxpft
@@ -86,8 +86,6 @@ subroutine disturbance_rates( site_in)
     type (ed_patch_type) , pointer :: currentPatch
     type (ed_cohort_type), pointer :: currentCohort
 
-    type (ed_resources_management_type) :: resources_management
-
     real(r8) :: cmort
     real(r8) :: bmort
     real(r8) :: hmort
@@ -142,7 +140,7 @@ subroutine disturbance_rates( site_in)
           !  Yi Xu  2017
           ! ---------------------------------------------------------------
 
-          if (currentPatch%logging==1 .and. logging_time) then 
+          if (logging_time) then 
 
              ! always call this function if turn on logging at the beginning 
              call LoggingMortality_rates(site_in, currentCohort%pft, currentCohort%dbh, &
@@ -630,11 +628,6 @@ subroutine spawn_patches( currentSite, bc_in)
           call terminate_cohorts(currentSite, currentPatch, 2)
           call sort_cohorts(currentPatch)
 
-           if (currentPatch%logging==1 .and. logging_time) then            
-                 currentPatch%after_spawn_patch= 1
-          else
-                 currentPatch%after_spawn_patch= 0
-          endif
           currentPatch => currentPatch%younger
 
        enddo ! currentPatch patch loop. 
@@ -1294,13 +1287,6 @@ subroutine zero_patch(cp_p)
     currentPatch%sabs_dif(:)                = 0.0_r8
     currentPatch%zstar                      = 0.0_r8
 
-    !LOGGING 
-    !kGC/m2
-    currentPatch%trunk_product              = 0.0_r8
-    currentPatch%logging	            = 1        ! Currently, assume all patch=1, need to change in future
-    currentPatch%after_spawn_patch	    = 0
-
-
   end subroutine zero_patch
 
   ! ============================================================================

main/EDInitMod.F90

@@ -107,6 +107,9 @@ subroutine zero_site( site_in )
     site_in%CWD_BG_diagnostic_input_carbonflux(:) = 0._r8
     site_in%leaf_litter_diagnostic_input_carbonflux(:) = 0._r8
     site_in%root_litter_diagnostic_input_carbonflux(:) = 0._r8
+
+    ! Resources management (logging/harvesting, etc)
+    site_in%resources_management%trunk_product_site  = 0.0_r8
 
   end subroutine zero_site
 

main/EDMainMod.F90

@@ -88,7 +88,7 @@ subroutine ed_ecosystem_dynamics(currentSite, bc_in)
 
     ! Call a routine that simply identifies if logging should occur
     ! This is limited to a global event until more structured event handling is enabled
-    call IsItLoggingTime(hlm_masterproc)
+    call IsItLoggingTime(hlm_masterproc,currentSite)
 
     !**************************************************************************
     ! Fire, growth, biogeochemistry. 
@@ -500,19 +500,6 @@ subroutine ed_total_balance_check (currentSite, call_index )
 
        enddo !end cohort loop 
 
-       ! Modify biomass for logging
-       ! Yi Xu
-       ! 03/2017
-
-	if (currentPatch%logging==1 .and. currentPatch%after_spawn_patch==1) then  
-
-	   ! turn off this flag after spawn patch , since flux_in and flux_out are cleaned in every balance check 
-	   currentPatch%after_spawn_patch = 0
-
-	end if 
-
-
-
        currentPatch => currentPatch%younger
 
     enddo !end patch loop

main/EDTypesMod.F90

@@ -443,12 +443,6 @@ module EDTypesMod
      ! PLANT HYDRAULICS     
      type(ed_patch_hydr_type) , pointer :: pa_hydr                 ! All patch hydraulics data, see FatesHydraulicsMemMod.F90
 
-     ! LOGGING EFFECTS
-
-     integer  ::  logging                                            ! 1=logging; 0=no logging
-     integer  ::  after_spawn_patch                                  ! 1=after spawn patch; 0=before spawn patch
-     real(r8) ::  trunk_product					     ! kGC/m2
-
    contains
 
   end type ed_patch_type

main/FatesRestartInterfaceMod.F90

@@ -69,6 +69,7 @@ module FatesRestartInterfaceMod
   integer, private :: ir_fates_to_bgc_this_ts_si
   integer, private :: ir_fates_to_bgc_last_ts_si
   integer, private :: ir_seedrainflux_si
+  integer, private :: ir_trunk_product_si
   integer, private :: ir_ncohort_pa
   integer, private :: ir_balive_co
   integer, private :: ir_bdead_co
@@ -591,6 +592,12 @@ subroutine define_restart_vars(this, initialize_variables)
          units='kgC/m2/year', flushval = flushzero, &
          hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_seedrainflux_si )
 
+    call this%set_restart_var(vname='fates_trunk_product_site', vtype=site_r8, &
+         long_name='Accumulate trunk product flux at site', &
+         units='kgC/m2', flushval = flushzero, &
+         hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_trunk_product_si )
+
+
     ! -----------------------------------------------------------------------------------
     ! Variables stored within cohort vectors
     ! Note: Some of these are multi-dimensional variables in the patch/site dimension
@@ -1025,6 +1032,7 @@ subroutine set_restart_vectors(this,nc,nsites,sites)
            rio_fates_to_bgc_this_ts_si => this%rvars(ir_fates_to_bgc_this_ts_si)%r81d, &
            rio_fates_to_bgc_last_ts_si => this%rvars(ir_fates_to_bgc_last_ts_si)%r81d, &
            rio_seedrainflux_si         => this%rvars(ir_seedrainflux_si)%r81d, &
+           rio_trunk_product_si        => this%rvars(ir_trunk_product_si)%r81d, &
            rio_ncohort_pa              => this%rvars(ir_ncohort_pa)%int1d, &
            rio_balive_co               => this%rvars(ir_balive_co)%r81d, &
            rio_bdead_co                => this%rvars(ir_bdead_co)%r81d, &
@@ -1310,8 +1318,11 @@ subroutine set_restart_vectors(this,nc,nsites,sites)
           rio_fates_to_bgc_this_ts_si(io_idx_si) = sites(s)%fates_to_bgc_this_ts
           rio_fates_to_bgc_last_ts_si(io_idx_si) = sites(s)%fates_to_bgc_last_ts
           rio_seedrainflux_si(io_idx_si)         = sites(s)%tot_seed_rain_flux
-
+
+          ! Accumulated trunk product
+          rio_trunk_product_si(io_idx_si) = sites(s)%resources_management%trunk_product_site
           ! set numpatches for this column
+
           rio_npatch_si(io_idx_si)  = patchespersite
 
           do i = 1,numWaterMem ! numWaterMem currently 10
@@ -1611,6 +1622,7 @@ subroutine get_restart_vectors(this, nc, nsites, sites)
           rio_fates_to_bgc_this_ts_si => this%rvars(ir_fates_to_bgc_this_ts_si)%r81d, &
           rio_fates_to_bgc_last_ts_si => this%rvars(ir_fates_to_bgc_last_ts_si)%r81d, &
           rio_seedrainflux_si         => this%rvars(ir_seedrainflux_si)%r81d, &
+          rio_trunk_product_si        => this%rvars(ir_trunk_product_si)%r81d, &
           rio_ncohort_pa              => this%rvars(ir_ncohort_pa)%int1d, &
           rio_balive_co               => this%rvars(ir_balive_co)%r81d, &
           rio_bdead_co                => this%rvars(ir_bdead_co)%r81d, &
@@ -1893,7 +1905,8 @@ subroutine get_restart_vectors(this, nc, nsites, sites)
           sites(s)%fates_to_bgc_this_ts = rio_fates_to_bgc_this_ts_si(io_idx_si)
           sites(s)%fates_to_bgc_last_ts = rio_fates_to_bgc_last_ts_si(io_idx_si)
           sites(s)%tot_seed_rain_flux   = rio_seedrainflux_si(io_idx_si)
-
+          sites(s)%resources_management%trunk_product_site = rio_trunk_product_si(io_idx_si)
+
        end do
 
        if ( DEBUG ) then