Merge pull request #523 from huangmy/SF_fuels_refactor

Sf fuels refactor + bole harvest litter logic fix/export frac
NGEET · May 23, 2019 · f1d4bc5 · f1d4bc5
2 parents d2f0907 + 2299587
commit f1d4bc5
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Showing 8 changed files with 235 additions and 176 deletions.
diff --git a/biogeochem/EDLoggingMortalityMod.F90 b/biogeochem/EDLoggingMortalityMod.F90
@@ -59,6 +59,9 @@ module EDLoggingMortalityMod
 
    character(len=*), parameter, private :: sourcefile = &
          __FILE__
+
+
+   real(r8), public, parameter :: logging_export_frac = 0.8_r8
 
    public :: LoggingMortality_frac
    public :: logging_litter_fluxes
@@ -170,6 +173,8 @@ subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
       real(r8), parameter   :: adjustment = 1.0 ! adjustment for mortality rates
 
       if (logging_time) then 
+
+
          if(EDPftvarcon_inst%woody(pft_i) == 1)then ! only set logging rates for trees
 
             ! Pass logging rates to cohort level 
@@ -192,8 +197,14 @@ subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
 
             ! Collateral damage to smaller plants below the canopy layer
             ! will be applied via "understory_death" via the disturbance algorithm
+            ! Important: Degredation rates really only have an impact when
+            ! applied to the canopy layer. So we don't add to degredation
+            ! for collateral damage, even understory collateral damage.
+
             if (canopy_layer .eq. 1) then
                lmort_collateral = logging_collateral_frac * adjustment
+            else
+               lmort_collateral = 0._r8
             endif
 
          else
@@ -202,6 +213,7 @@ subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
             lmort_infra      = 0.0_r8
             l_degrad         = 0.0_r8
          end if
+
       else 
          lmort_direct    = 0.0_r8
          lmort_collateral = 0.0_r8
@@ -309,10 +321,19 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
                   (currentCohort%lmort_collateral + currentCohort%lmort_infra)
 
          else
+
+            ! This routine is only called during disturbance.  The litter
+            ! fluxes from non-disturbance generating mortality are 
+            ! handled in EDPhysiology.  Disturbance generating mortality
+            ! are those cohorts in the top canopy layer, or those
+            ! plants that were impacted. Thus, no direct dead can occur
+            ! here, and indirect are impacts.
+
             if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
                direct_dead   = 0.0_r8
-               indirect_dead = logging_coll_under_frac * currentCohort%n * &
-                     (patch_site_areadis/currentPatch%area)  !kgC/site/day
+               indirect_dead = logging_coll_under_frac * &
+                    (1._r8-currentPatch%fract_ldist_not_harvested) * currentCohort%n * &
+                    (patch_site_areadis/currentPatch%area)   !kgC/site/day
             else
                ! If the cohort of interest is grass, it will not experience
                ! any mortality associated with the logging disturbance

diff --git a/biogeochem/EDMortalityFunctionsMod.F90 b/biogeochem/EDMortalityFunctionsMod.F90
@@ -200,15 +200,18 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
                                currentCohort%lmort_infra,                        &
                                currentCohort%l_degrad)
 
+
+
+
     if (currentCohort%canopy_layer > 1)then 
-
        ! Include understory logging mortality rates not associated with disturbance
        dndt_logging = (currentCohort%lmort_direct     + &
                        currentCohort%lmort_collateral + &
                        currentCohort%lmort_infra)/hlm_freq_day
-
        currentCohort%dndt = -1.0_r8 * (cmort+hmort+bmort+frmort+dndt_logging) * currentCohort%n
     else
+       ! Mortality from logging in the canopy is ONLY disturbance generating, don't
+       ! update number densities via non-disturbance inducing death
        currentCohort%dndt = -(1.0_r8 - fates_mortality_disturbance_fraction) &
             * (cmort+hmort+bmort+frmort) * currentCohort%n
     endif

diff --git a/biogeochem/EDPatchDynamicsMod.F90 b/biogeochem/EDPatchDynamicsMod.F90
@@ -20,6 +20,7 @@ module EDPatchDynamicsMod
   use EDTypesMod           , only : dtype_ilog
   use EDTypesMod           , only : dtype_ifire
   use EDTypesMod           , only : ican_upper
+  use EDTypesMod           , only : lg_sf
   use FatesInterfaceMod    , only : hlm_use_planthydro
   use FatesInterfaceMod    , only : hlm_numSWb
   use FatesInterfaceMod    , only : bc_in_type
@@ -151,7 +152,7 @@ subroutine disturbance_rates( site_in, bc_in)
           call LoggingMortality_frac(currentCohort%pft, currentCohort%dbh, currentCohort%canopy_layer, &
                 lmort_direct,lmort_collateral,lmort_infra,l_degrad )
 
-          currentCohort%lmort_direct    = lmort_direct
+          currentCohort%lmort_direct     = lmort_direct
           currentCohort%lmort_collateral = lmort_collateral
           currentCohort%lmort_infra      = lmort_infra
           currentCohort%l_degrad         = l_degrad
@@ -186,7 +187,7 @@ subroutine disturbance_rates( site_in, bc_in)
 
              ! Logging Disturbance Rate
              currentPatch%disturbance_rates(dtype_ilog) = currentPatch%disturbance_rates(dtype_ilog) + &
-                   min(1.0_r8, currentCohort%lmort_direct +                         & 
+                   min(1.0_r8, currentCohort%lmort_direct +                          & 
                                currentCohort%lmort_collateral +                      &
                                currentCohort%lmort_infra +                           &
                                currentCohort%l_degrad ) *                            &
@@ -226,7 +227,7 @@ subroutine disturbance_rates( site_in, bc_in)
        ! to still diagnose and track the non-disturbance rate
        ! ------------------------------------------------------------------------------------------
 
-
+       ! DISTURBANCE IS LOGGING
        if (currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) .and. &
              currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifire) ) then 
 
@@ -245,7 +246,7 @@ subroutine disturbance_rates( site_in, bc_in)
              currentCohort => currentCohort%taller
           enddo !currentCohort
 
-          ! DISTURBANCE IS FIRE
+       ! DISTURBANCE IS FIRE
        elseif (currentPatch%disturbance_rates(dtype_ifire) > currentPatch%disturbance_rates(dtype_ifall) .and. &
              currentPatch%disturbance_rates(dtype_ifire) > currentPatch%disturbance_rates(dtype_ilog) ) then  
 
@@ -275,7 +276,7 @@ subroutine disturbance_rates( site_in, bc_in)
              currentCohort => currentCohort%taller
           enddo !currentCohort
 
-       else  ! If fire and loggin are not greater than treefall, just set disturbance rate to tree-fall
+       else  ! If fire and logging are not greater than treefall, just set disturbance rate to tree-fall
              ! which is most likely a 0.0
 
           currentPatch%disturbance_rate = currentPatch%disturbance_rates(dtype_ifall)
@@ -477,6 +478,8 @@ subroutine spawn_patches( currentSite, bc_in)
 
                 call logging_litter_fluxes(currentSite, currentPatch, new_patch, patch_site_areadis)
 
+                if(debug) write(fates_log(),*) "Logging disturbance generated:",patch_site_areadis
+
              elseif ((currentPatch%disturbance_rates(dtype_ifire) > &
                       currentPatch%disturbance_rates(dtype_ifall)) .and. &
                      (currentPatch%disturbance_rates(dtype_ifire) > &
@@ -681,7 +684,7 @@ subroutine spawn_patches( currentSite, bc_in)
                    nc%lmort_infra      = currentCohort%lmort_infra
 
 
-                   ! Logging is the dominant disturbance  
+                ! Logging is the dominant disturbance  
                 elseif ((currentPatch%disturbance_rates(dtype_ilog) > &
                          currentPatch%disturbance_rates(dtype_ifall)) .and. &
                         (currentPatch%disturbance_rates(dtype_ilog) > &
@@ -756,7 +759,7 @@ subroutine spawn_patches( currentSite, bc_in)
                          ! LOGGING SURVIVORSHIP OF UNDERSTORY PLANTS IS SET AS A NEW PARAMETER 
                          ! in the fatesparameter files 
                          nc%n = nc%n * (1.0_r8 - &
-                               currentPatch%fract_ldist_not_harvested * logging_coll_under_frac)
+                              (1.0_r8-currentPatch%fract_ldist_not_harvested) * logging_coll_under_frac)
 
                          ! Step 3: Reduce the number count of cohorts in the 
                          !         original/donor/non-disturbed patch to reflect the area change
@@ -1085,7 +1088,7 @@ subroutine fire_litter_fluxes(currentSite, cp_target, new_patch_target, patch_si
        !************************************/ 
        do c = 1,ncwd
           burned_litter = new_patch%cwd_ag(c) * patch_site_areadis/new_patch%area * &
-                currentPatch%burnt_frac_litter(c+1) !kG/m2/day
+                currentPatch%burnt_frac_litter(c) !kG/m2/day
           new_patch%cwd_ag(c) = new_patch%cwd_ag(c) - burned_litter
           currentSite%flux_out = currentSite%flux_out + burned_litter * new_patch%area !kG/site/day
           currentSite%total_burn_flux_to_atm = currentSite%total_burn_flux_to_atm + &
@@ -1240,7 +1243,7 @@ subroutine fire_litter_fluxes(currentSite, cp_target, new_patch_target, patch_si
           if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
              burned_leaves = leaf_c * currentCohort%fraction_crown_burned
           else
-             burned_leaves = leaf_c * currentPatch%burnt_frac_litter(6)
+             burned_leaves = leaf_c * currentPatch%burnt_frac_litter(lg_sf)
           endif
 
           if (burned_leaves > 0.0_r8) then