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Sf fuels refactor + bole harvest litter logic fix/export frac #523

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merged 15 commits into from
May 23, 2019
Merged

Sf fuels refactor + bole harvest litter logic fix/export frac #523

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c653988
SF fuels refactor
Mar 5, 2019
f241751
Update index for CWD flux to decomposing litter pool
Mar 6, 2019
f95b448
Correct parameter values for fate_max_decomp
Mar 6, 2019
2990d2d
commit changes from Jackies Shuman's SPITFIRE fuel refactoring
Apr 22, 2019
c1c2afa
Deleted all FATES parameter files other than the default one
Apr 22, 2019
113aaf6
Commit parameter ordering changes for SPITFIRE fuel refactoring
Apr 22, 2019
7e6d3dd
fix the bole harvest litter logic
Apr 23, 2019
ac4d646
Removed non-disturbance CWD flux from canopy layer logging, which sho…
rgknox Apr 26, 2019
1015c4b
Continued: Removed non-disturbance CWD flux from canopy layer logging…
rgknox Apr 26, 2019
12a6c7e
Merge pull request #3 from rgknox/SF_fuels_refactor
Apr 29, 2019
476ffbc
Some syntax improvements, but mostly a fix for understory impact from…
rgknox May 4, 2019
2c046e4
Removed degredation rate on impact mortality calculations.
rgknox May 4, 2019
9e13025
Merge pull request #4 from rgknox/SF_fuels_refactor_degfixes
May 6, 2019
69d6277
Fixed indexing on the maximum decomposition rate
rgknox May 22, 2019
2299587
Merge pull request #5 from rgknox/SF_fuels_refactor
May 22, 2019
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25 changes: 23 additions & 2 deletions biogeochem/EDLoggingMortalityMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down
7 changes: 5 additions & 2 deletions biogeochem/EDMortalityFunctionsMod.F90
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Expand Up @@ -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
Expand Down
21 changes: 12 additions & 9 deletions biogeochem/EDPatchDynamicsMod.F90
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 ) * &
Expand Down Expand Up @@ -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

Expand All @@ -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

Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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) > &
Expand Down Expand Up @@ -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) > &
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 + &
Expand Down Expand Up @@ -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
Expand Down
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