Merge pull request ESCOMP#7 from rgknox/yi-logging-v4

Yi logging v4
NordicESMhub · Sep 22, 2017 · 13178d7 · 13178d7
2 parents e1fe601 + 6d210ea
commit 13178d7
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Showing 2 changed files with 17 additions and 10 deletions.
diff --git a/biogeochem/EDLoggingMortalityMod.F90 b/biogeochem/EDLoggingMortalityMod.F90
@@ -147,9 +147,9 @@ subroutine LoggingMortality_frac( pft_i, dbh, lmort_logging,lmort_collateral,lmo
       ! Arguments
       integer,  intent(in)  :: pft_i            ! pft index 
       real(r8), intent(in)  :: dbh              ! diameter at breast height (cm)
-      real(r8), intent(out) :: lmort_logging    ! logging mortality_rates, share same size class
-      real(r8), intent(out) :: lmort_collateral ! logging impact mortality_rates, share same size class
-      real(r8), intent(out) :: lmort_infra      ! infrastructure mortality_rates, share same size class
+      real(r8), intent(out) :: lmort_logging    ! direct (harvestable) mortality fraction
+      real(r8), intent(out) :: lmort_collateral ! collateral damage mortality fraction
+      real(r8), intent(out) :: lmort_infra      ! infrastructure mortality fraction
 
       ! Parameters
       real(r8), parameter   :: adjustment = 1.0 ! adjustment for mortality rates
@@ -161,12 +161,18 @@ subroutine LoggingMortality_frac( pft_i, dbh, lmort_logging,lmort_collateral,lmo
 
             if (dbh >= logging_dbhmin ) then
                lmort_logging = logging_direct_frac * adjustment
+               lmort_collateral = logging_collateral_frac * adjustment
             else
-               lmort_logging = 0.0_r8
+               lmort_logging = 0.0_r8 
+               lmort_collateral = 0.0_r8
             end if
-            lmort_collateral = logging_collateral_frac * adjustment
+
             lmort_infra      = logging_mechanical_frac * adjustment
             !damage rates for size class < & > threshold_size need to be specified seperately
+
+            ! Collateral damage to smaller plants below the direct logging size threshold
+            ! will be applied via "understory_death" via the disturbance algorithm
+
          else
             lmort_logging    = 0.0_r8
             lmort_collateral = 0.0_r8

diff --git a/biogeochem/EDPatchDynamicsMod.F90 b/biogeochem/EDPatchDynamicsMod.F90
@@ -178,8 +178,8 @@ subroutine disturbance_rates( site_in)
 
 
        ! ------------------------------------------------------------------------------------------
-       ! Determine which disturbance is dominant, and force mortality in the upper canopy to be
-       ! zero for the non-dominant mode.  Note: upper-canopy tree-fall mortality is 
+       ! Determine which disturbance is dominant, and force mortality diagnostics in the upper 
+       ! canopy to be zero for the non-dominant mode.  Note: upper-canopy tree-fall mortality is 
        ! not always disturbance generating, so when tree-fall mort is non-dominant, make sure
        ! to still diagnose and track the non-disturbance rate
        ! ------------------------------------------------------------------------------------------
@@ -190,6 +190,7 @@ subroutine disturbance_rates( site_in)
 
           currentPatch%disturbance_rate = currentPatch%disturbance_rates(dtype_ilog)
 
+          ! Update diagnostics
           currentCohort => currentPatch%shortest
           do while(associated(currentCohort))
              if(currentCohort%canopy_layer == 1)then
@@ -209,7 +210,7 @@ subroutine disturbance_rates( site_in)
 
           currentPatch%disturbance_rate = currentPatch%disturbance_rates(dtype_ifire)
 
-          ! Zero non-fire mortality rates
+          ! Update diagnostics, zero non-fire mortality rates
           currentCohort => currentPatch%shortest
           do while(associated(currentCohort))
              if(currentCohort%canopy_layer == 1)then
@@ -236,7 +237,7 @@ subroutine disturbance_rates( site_in)
 
           currentPatch%disturbance_rate = currentPatch%disturbance_rates(dtype_ifall)
 
-          ! Zero non-treefall mortality rates
+          ! Update diagnostics, zero non-treefall mortality rates
           currentCohort => currentPatch%shortest
           do while(associated(currentCohort))
              if(currentCohort%canopy_layer == 1)then
@@ -345,7 +346,7 @@ 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
 
-          call average_patch_properties(currentPatch, new_patch, patch_site_areadis)  ! MAY BE REDUNDANT CALL
+          call average_patch_properties(currentPatch, new_patch, patch_site_areadis)
 
           if (currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) .and. &
                 currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifire) ) then