some more bugfixes and diagnostics on secondary forest tracking

biogeochem/EDLoggingMortalityMod.F90

@@ -112,7 +112,7 @@ subroutine IsItLoggingTime(is_master,currentSite)
 
       else if(icode < 0 .and. icode > -366) then
          ! Logging event every year on specific day of year
-         if(hlm_day_of_year .eq. icode  ) then
+         if(hlm_day_of_year .eq. abs(icode)  ) then
             logging_time = .true.
          end if
 

biogeochem/EDPatchDynamicsMod.F90

@@ -358,9 +358,11 @@ subroutine spawn_patches( currentSite, bc_in)
           call endrun(msg=errMsg(sourcefile, __LINE__))          
        end if
 
+       ! figure out whether the receiver patch for disturbance from this patch will be primary or secondary land
+       ! receiver patch is primary forest only if both the donor patch is primary forest and the dominant disturbance type is not logging
        if (currentPatch%anthro_disturbance_label .eq. primaryforest .and. &
-            currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifall) .and. &
-            currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifire) ) then
+            (currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifall) .or. &
+            currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifire)) ) then
 
           site_areadis_primary = site_areadis_primary + currentPatch%area * currentPatch%disturbance_rate
        else
@@ -379,6 +381,7 @@ subroutine spawn_patches( currentSite, bc_in)
        age = 0.0_r8
 
        ! create two empty patches, to absorb newly disturbed primary and secondary forest area
+       ! first create patch to receive primary forest area
        if ( site_areadis_primary .gt. 0.0_r8) then
           allocate(new_patch_primary)
           call create_patch(currentSite, new_patch_primary, age, site_areadis_primary, &
@@ -388,6 +391,7 @@ subroutine spawn_patches( currentSite, bc_in)
           new_patch_primary%shortest => null()
        endif
 
+       ! next create patch to receive secondary forest area
        if ( site_areadis_secondary .gt. 0.0_r8) then
           allocate(new_patch_secondary)
           call create_patch(currentSite, new_patch_secondary, age, site_areadis_secondary, &
@@ -402,9 +406,10 @@ subroutine spawn_patches( currentSite, bc_in)
        do while(associated(currentPatch))   
 
           ! figure out whether the receiver patch for disturbance from this patch will be primary or secondary land
+          ! receiver patch is primary forest only if both the donor patch is primary forest and the dominant disturbance type is not logging
           if (currentPatch%anthro_disturbance_label .eq. primaryforest .and. &
-               currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifall) .and. &
-               currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifire) ) then
+               (currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifall) .or. &
+               currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifire) ) ) then
              new_patch => new_patch_primary
           else
              new_patch => new_patch_secondary
@@ -413,11 +418,11 @@ subroutine spawn_patches( currentSite, bc_in)
           ! This is the amount of patch area that is disturbed, and donated by the donor
           patch_site_areadis = currentPatch%area * currentPatch%disturbance_rate
 
-          ! for the secondary forest case, if the dominant disturbance from this patch is non-anthropogenic,
+          ! for the case where the donating patch is secondary forest, if the dominant disturbance from this patch is non-anthropogenic,
           ! we need to average in the time-since-anthropogenic-disturbance from the donor patch into that of the receiver patch
           if ( currentPatch%anthro_disturbance_label .eq. secondaryforest .and. &
-               currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifall) .and. &
-               currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifire) ) then
+               (currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifall) .or. &
+               currentPatch%disturbance_rates(dtype_ilog) .lt. currentPatch%disturbance_rates(dtype_ifire) ) ) then
 
              new_patch%age_since_anthro_disturbance = new_patch%age_since_anthro_disturbance + &
                   currentPatch%age_since_anthro_disturbance * (patch_site_areadis / site_areadis_secondary)

main/FatesHistoryInterfaceMod.F90

@@ -153,6 +153,8 @@ module FatesHistoryInterfaceMod
   integer, private :: ih_livestem_mr_si
   integer, private :: ih_livecroot_mr_si
   integer, private :: ih_fraction_secondary_forest_si
+  integer, private :: ih_biomass_secondary_forest_si
+  integer, private :: ih_woodproduct_si
 
   ! Indices to (site x scpf) variables
   integer, private :: ih_nplant_si_scpf
@@ -1499,9 +1501,11 @@ subroutine update_history_dyn(this,nc,nsites,sites)
                hio_npatches_si_age     => this%hvars(ih_npatches_si_age)%r82d, &
                hio_zstar_si_age        => this%hvars(ih_zstar_si_age)%r82d, &
                hio_biomass_si_age        => this%hvars(ih_biomass_si_age)%r82d, &
-               hio_fraction_secondary_forest_si  => this%hvars(ih_fraction_secondary_forest_si)%r81d, &
-               hio_agesince_anthrodist_si_age    => this%hvars(ih_agesince_anthrodist_si_age)%r82d, &
-               hio_secondaryforest_area_si_age  => this%hvars(ih_secondaryforest_area_si_age)%r82d, &
+               hio_fraction_secondary_forest_si   => this%hvars(ih_fraction_secondary_forest_si)%r81d, &
+               hio_biomass_secondary_forest_si    => this%hvars(ih_biomass_secondary_forest_si)%r81d, &
+               hio_woodproduct_si                 => this%hvars(ih_woodproduct_si)%r81d, &
+               hio_agesince_anthrodist_si_age     => this%hvars(ih_agesince_anthrodist_si_age)%r82d, &
+               hio_secondaryforest_area_si_age    => this%hvars(ih_secondaryforest_area_si_age)%r82d, &
                hio_canopy_height_dist_si_height   => this%hvars(ih_canopy_height_dist_si_height)%r82d, &
                hio_leaf_height_dist_si_height     => this%hvars(ih_leaf_height_dist_si_height)%r82d, &
                hio_litter_moisture_si_fuel        => this%hvars(ih_litter_moisture_si_fuel)%r82d, &
@@ -1549,6 +1553,9 @@ subroutine update_history_dyn(this,nc,nsites,sites)
          hio_seed_bank_si(io_si) = sum(sites(s)%seed_bank) * g_per_kg
 
          hio_canopy_spread_si(io_si)        = sites(s)%spread
+
+         ! track total wood product accumulation at the site level
+         hio_woodproduct_si(io_si)          = sites(s)%resources_management%trunk_product_site * AREA_INV
 
          ipa = 0
          cpatch => sites(s)%oldest_patch
@@ -1714,6 +1721,12 @@ subroutine update_history_dyn(this,nc,nsites,sites)
                hio_biomass_si_age(io_si,cpatch%age_class) = hio_biomass_si_age(io_si,cpatch%age_class) &
                     + total_c * ccohort%n * AREA_INV
 
+               ! track the total biomass on all secondary lands
+               if ( cpatch%anthro_disturbance_label .eq. secondaryforest ) then
+                  hio_biomass_secondary_forest_si(io_si) = hio_biomass_secondary_forest_si(io_si) + &
+                       total_c * ccohort%n * AREA_INV
+               endif
+
                ! Site by Size-Class x PFT (SCPF) 
                ! ------------------------------------------------------------------------
 
@@ -3236,7 +3249,18 @@ subroutine define_history_vars(this, initialize_variables)
          avgflag='A', vtype=site_r8, hlms='CLM:ALM', flushval=0.0_r8, upfreq=1, &
          ivar=ivar, initialize=initialize_variables, index = ih_fraction_secondary_forest_si )
 
-    call this%set_history_var(vname='SECONDARY_AREA_BY_AGE_SINCE_ANTHRO_DIST', units='m2/m2', &
+    call this%set_history_var(vname='WOOD_PRODUCT', units='kgC/m2', &
+         long='Total wood product from logging', use_default='inactive', &
+         avgflag='A', vtype=site_r8, hlms='CLM:ALM', flushval=0.0_r8, upfreq=1, &
+         ivar=ivar, initialize=initialize_variables, index = ih_woodproduct_si )
+
+    call this%set_history_var(vname='SECONDARY_FOREST_BIOMASS', units='kgC/m2', &
+         long='Biomass on secondary lands (per total site area, mult by SECONDARY_FOREST_FRACTION to get per secondary forest area)',&
+         use_default='inactive', &
+         avgflag='A', vtype=site_r8, hlms='CLM:ALM', flushval=0.0_r8, upfreq=1, &
+         ivar=ivar, initialize=initialize_variables, index = ih_biomass_secondary_forest_si )
+
+    call this%set_history_var(vname='SECONDARY_AREA_AGE_ANTHRO_DIST', units='m2/m2', &
          long='Secondary forest patch area age distribution since anthropgenic disturbance', use_default='inactive', &
          avgflag='A', vtype=site_age_r8, hlms='CLM:ALM', flushval=0.0_r8, upfreq=1, &
          ivar=ivar, initialize=initialize_variables, index = ih_agesince_anthrodist_si_age )