Merge pull request #454 from ckoven/secondary_forest

Track secondary forest area to keep primary and secondary patches distinct

Author: rgknox

biogeochem/EDCohortDynamicsMod.F90

@@ -515,9 +515,12 @@ subroutine nan_cohort(cc_p)
 
     ! ALLOCATION
     currentCohort%dmort              = nan ! proportional mortality rate. (year-1)
+
+    ! logging
     currentCohort%lmort_direct       = nan
     currentCohort%lmort_infra        = nan
     currentCohort%lmort_collateral   = nan
+    currentCohort%l_degrad           = nan
 
 
     currentCohort%seed_prod          = nan ! reproduction seed and clonal: KgC/indiv/year
@@ -589,6 +592,7 @@ subroutine zero_cohort(cc_p)
     currentCohort%lmort_direct       = 0._r8
     currentCohort%lmort_infra        = 0._r8
     currentCohort%lmort_collateral   = 0._r8
+    currentCohort%l_degrad           = 0._r8    
     currentCohort%leaf_cost          = 0._r8
     currentcohort%excl_weight        = 0._r8
     currentcohort%prom_weight        = 0._r8
@@ -1152,12 +1156,6 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
 
                                    currentCohort%dmort          = (currentCohort%n*currentCohort%dmort       + &
                                          nextc%n*nextc%dmort)/newn
-                                   currentCohort%lmort_direct     = (currentCohort%n*currentCohort%lmort_direct     + &
-                                         nextc%n*nextc%lmort_direct)/newn
-                                   currentCohort%lmort_infra      = (currentCohort%n*currentCohort%lmort_infra      + &
-                                         nextc%n*nextc%lmort_infra)/newn
-                                   currentCohort%lmort_collateral = (currentCohort%n*currentCohort%lmort_collateral + &
-                                         nextc%n*nextc%lmort_collateral)/newn
 
                                    currentCohort%fire_mort      = (currentCohort%n*currentCohort%fire_mort   + &
                                          nextc%n*nextc%fire_mort)/newn
@@ -1175,7 +1173,9 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
                                          nextc%n*nextc%lmort_collateral)/newn
                                    currentCohort%lmort_infra = (currentCohort%n*currentCohort%lmort_infra + &
                                          nextc%n*nextc%lmort_infra)/newn
-
+                                   currentCohort%l_degrad = (currentCohort%n*currentCohort%l_degrad + &
+                                         nextc%n*nextc%l_degrad)/newn
+                                   
                                    ! biomass and dbh tendencies
                                    currentCohort%ddbhdt     = (currentCohort%n*currentCohort%ddbhdt  + &
                                          nextc%n*nextc%ddbhdt)/newn
@@ -1550,9 +1550,6 @@ subroutine copy_cohort( currentCohort,copyc )
 
     ! ALLOCATION
     n%dmort           = o%dmort
-    n%lmort_direct    = o%lmort_direct
-    n%lmort_infra     = o%lmort_infra
-    n%lmort_collateral= o%lmort_collateral
     n%seed_prod       = o%seed_prod
     n%treelai         = o%treelai
     n%treesai         = o%treesai
@@ -1565,9 +1562,10 @@ subroutine copy_cohort( currentCohort,copyc )
     n%frmort = o%frmort
 
     ! logging mortalities, Yi Xu
-    n%lmort_direct=o%lmort_direct
+    n%lmort_direct     =o%lmort_direct
     n%lmort_collateral =o%lmort_collateral
-    n%lmort_infra =o%lmort_infra
+    n%lmort_infra      =o%lmort_infra
+    n%l_degrad         =o%l_degrad    
 
     ! Flags
     n%isnew = o%isnew

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
 
@@ -151,14 +151,20 @@ end subroutine IsItLoggingTime
 
    ! ======================================================================================
 
-   subroutine LoggingMortality_frac( pft_i, dbh, lmort_direct,lmort_collateral,lmort_infra )
+   subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
+        lmort_collateral, lmort_infra, l_degrad )
 
       ! Arguments
       integer,  intent(in)  :: pft_i            ! pft index 
       real(r8), intent(in)  :: dbh              ! diameter at breast height (cm)
+      integer,  intent(in)  :: canopy_layer     ! canopy layer of this cohort
       real(r8), intent(out) :: lmort_direct     ! direct (harvestable) mortality fraction
       real(r8), intent(out) :: lmort_collateral ! collateral damage mortality fraction
       real(r8), intent(out) :: lmort_infra      ! infrastructure mortality fraction
+      real(r8), intent(out) :: l_degrad         ! fraction of trees that are not killed
+                                                ! but suffer from forest degradation (i.e. they
+                                                ! are moved to newly-anthro-disturbed secondary
+                                                ! forest patch)
 
       ! Parameters
       real(r8), parameter   :: adjustment = 1.0 ! adjustment for mortality rates
@@ -170,31 +176,37 @@ subroutine LoggingMortality_frac( pft_i, dbh, lmort_direct,lmort_collateral,lmor
 
             if (dbh >= logging_dbhmin ) then
                lmort_direct = logging_direct_frac * adjustment
-               lmort_collateral = logging_collateral_frac * adjustment
+               l_degrad = 0._r8
             else
                lmort_direct = 0.0_r8 
-               lmort_collateral = 0.0_r8
+               l_degrad = logging_direct_frac * adjustment
             end if
 
             if (dbh >= logging_dbhmax_infra) then
                lmort_infra      = 0.0_r8
+               l_degrad         = l_degrad + logging_mechanical_frac * adjustment
             else
                lmort_infra      = logging_mechanical_frac * adjustment
             end if
             !damage rates for size class < & > threshold_size need to be specified seperately
 
-            ! Collateral damage to smaller plants below the direct logging size threshold
+            ! Collateral damage to smaller plants below the canopy layer
             ! will be applied via "understory_death" via the disturbance algorithm
+            if (canopy_layer .eq. 1) then
+               lmort_collateral = logging_collateral_frac * adjustment
+            endif
 
          else
             lmort_direct    = 0.0_r8
             lmort_collateral = 0.0_r8
             lmort_infra      = 0.0_r8
+            l_degrad         = 0.0_r8
          end if
       else 
          lmort_direct    = 0.0_r8
          lmort_collateral = 0.0_r8
          lmort_infra      = 0.0_r8
+         l_degrad         = 0.0_r8
       end if
 
    end subroutine LoggingMortality_frac

biogeochem/EDMortalityFunctionsMod.F90

@@ -194,10 +194,11 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
     ! Mortality for trees in the understorey. 
     !if trees are in the canopy, then their death is 'disturbance'. This probably needs a different terminology
     call mortality_rates(currentCohort,bc_in,cmort,hmort,bmort,frmort)
-    call LoggingMortality_frac(ipft, currentCohort%dbh, &
+    call LoggingMortality_frac(ipft, currentCohort%dbh, currentCohort%canopy_layer, &
                                currentCohort%lmort_direct,                       &
                                currentCohort%lmort_collateral,                    &
-                               currentCohort%lmort_infra )
+                               currentCohort%lmort_infra,                        &
+                               currentCohort%l_degrad)
 
     if (currentCohort%canopy_layer > 1)then