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Fire mortality diagnostics update #431

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merged 21 commits into from
Jan 12, 2019
Merged

Fire mortality diagnostics update #431

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44544db
Merge remote-tracking branch 'ngeet_repo/master'
jkshuman Sep 25, 2018
3c8e46e
changed diagnostic calculation of fmort to correct for changing N. a…
ckoven Aug 20, 2018
7ec0472
stratified site-level fire mort by canopy, incldued carbon flux term,…
ckoven Aug 20, 2018
eff4c3f
Typo update in support of fire mortality diagnostics
jkshuman Oct 3, 2018
040a2c4
Correct typo for diffuse surface albedo
jkshuman Oct 3, 2018
8577d46
Conflict Resolutions with PARTEH
rgknox Oct 24, 2018
6f0efd1
Merge pull request #1 from rgknox/fire_mortality
jkshuman Oct 25, 2018
2b5330b
Conflict resolutions, and fixing some diagnostics that sum over nclmax
rgknox Jan 7, 2019
1828428
Minor fixes related to new fire mortality diagnostics
rgknox Jan 8, 2019
898ac97
Merge pull request #2 from rgknox/fire_mortality
jkshuman Jan 8, 2019
90b603e
Remove SF_alpha_FMC, add SF_drying_ratio
Jan 8, 2019
b47e931
Remove extra space
Jan 8, 2019
0641a3e
Fix typo
Jan 8, 2019
f686da8
Updated termination diagnostic arrays to fill over canopy layer
rgknox Jan 8, 2019
b349a79
Merge pull request #3 from rgknox/fire_mortality
jkshuman Jan 8, 2019
5f7a452
Correct dimensions for drying_ratio
Jan 9, 2019
5c77081
Add missing comma to SFParamsMod
Jan 9, 2019
c079597
Half-way through adding new restarts for site level diagnostics
rgknox Jan 10, 2019
82be6b0
First pass through adding site diagnostics fmort/nindivs etc, to rest…
rgknox Jan 11, 2019
3df34c2
Fixed various problems with first implementation of site level diagno…
rgknox Jan 11, 2019
be04146
Merge pull request #4 from rgknox/fire_mortality
jkshuman Jan 11, 2019
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29 changes: 16 additions & 13 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ module EDCohortDynamicsMod
use EDTypesMod , only : min_npm2, min_nppatch
use EDTypesMod , only : min_n_safemath
use EDTypesMod , only : nlevleaf
use EDTypesMod , only : ican_upper
use FatesInterfaceMod , only : hlm_use_planthydro
use FatesInterfaceMod , only : hlm_parteh_mode
use FatesPlantHydraulicsMod, only : FuseCohortHydraulics
Expand Down Expand Up @@ -602,19 +603,23 @@ subroutine terminate_cohorts( currentSite, currentPatch, level )
endif ! if (.not.currentCohort%isnew .and. level == 2) then

if (terminate == 1) then

! preserve a record of the to-be-terminated cohort for mortality accounting
if (currentCohort%canopy_layer .eq. 1) then
levcan = 1
else
levcan = 2
endif
levcan = currentCohort%canopy_layer

currentSite%terminated_nindivs(currentCohort%size_class,currentCohort%pft,levcan) = &
currentSite%terminated_nindivs(currentCohort%size_class,currentCohort%pft,levcan) + currentCohort%n
!
currentSite%termination_carbonflux(levcan) = currentSite%termination_carbonflux(levcan) + &
currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)

if(levcan==ican_upper) then
currentSite%term_nindivs_canopy(currentCohort%size_class,currentCohort%pft) = &
currentSite%term_nindivs_canopy(currentCohort%size_class,currentCohort%pft) + currentCohort%n

currentSite%term_carbonflux_canopy = currentSite%term_carbonflux_canopy + &
currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
else
currentSite%term_nindivs_ustory(currentCohort%size_class,currentCohort%pft) = &
currentSite%term_nindivs_ustory(currentCohort%size_class,currentCohort%pft) + currentCohort%n

currentSite%term_carbonflux_ustory = currentSite%term_carbonflux_ustory + &
currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
end if

!put the litter from the terminated cohorts straight into the fragmenting pools
if (currentCohort%n.gt.0.0_r8) then
Expand Down Expand Up @@ -927,7 +932,6 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
currentCohort%cmort = (currentCohort%n*currentCohort%cmort + nextc%n*nextc%cmort)/newn
currentCohort%hmort = (currentCohort%n*currentCohort%hmort + nextc%n*nextc%hmort)/newn
currentCohort%bmort = (currentCohort%n*currentCohort%bmort + nextc%n*nextc%bmort)/newn
currentCohort%fmort = (currentCohort%n*currentCohort%fmort + nextc%n*nextc%fmort)/newn
currentCohort%frmort = (currentCohort%n*currentCohort%frmort + nextc%n*nextc%frmort)/newn

! logging mortality, Yi Xu
Expand Down Expand Up @@ -1303,7 +1307,6 @@ subroutine copy_cohort( currentCohort,copyc )
! Mortality diagnostics
n%cmort = o%cmort
n%bmort = o%bmort
n%fmort = o%fmort
n%hmort = o%hmort
n%frmort = o%frmort

Expand Down
58 changes: 41 additions & 17 deletions biogeochem/EDPatchDynamicsMod.F90
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Expand Up @@ -17,6 +17,7 @@ module EDPatchDynamicsMod
use EDTypesMod , only : dtype_ifall
use EDTypesMod , only : dtype_ilog
use EDTypesMod , only : dtype_ifire
use EDTypesMod , only : ican_upper
use FatesInterfaceMod , only : hlm_use_planthydro
use FatesInterfaceMod , only : hlm_numSWb
use FatesInterfaceMod , only : bc_in_type
Expand Down Expand Up @@ -139,7 +140,6 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort%bmort = bmort
currentCohort%hmort = hmort
currentCohort%frmort = frmort
currentCohort%fmort = 0.0_r8 ! Fire mortality is initialized as zero, but may be changed

call LoggingMortality_frac(currentCohort%pft, currentCohort%dbh, &
lmort_direct,lmort_collateral,lmort_infra )
Expand Down Expand Up @@ -216,7 +216,6 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
if(currentCohort%canopy_layer == 1)then
currentCohort%fmort = 0.0_r8
currentCohort%cmort = currentCohort%cmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%hmort = currentCohort%hmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%bmort = currentCohort%bmort*(1.0_r8 - fates_mortality_disturbance_fraction)
Expand Down Expand Up @@ -267,7 +266,6 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort%lmort_direct = 0.0_r8
currentCohort%lmort_collateral = 0.0_r8
currentCohort%lmort_infra = 0.0_r8
currentCohort%fmort = 0.0_r8
end if
currentCohort => currentCohort%taller
enddo !currentCohort
Expand Down Expand Up @@ -323,13 +321,15 @@ subroutine spawn_patches( currentSite, bc_in)
real(r8) :: leaf_litter_local(maxpft) ! initial value of leaf litter. KgC/m2
real(r8) :: cwd_ag_local(ncwd) ! initial value of above ground coarse woody debris. KgC/m2
real(r8) :: cwd_bg_local(ncwd) ! initial value of below ground coarse woody debris. KgC/m2
integer :: levcan ! canopy level
real(r8) :: leaf_c ! leaf carbon [kg]
real(r8) :: fnrt_c ! fineroot carbon [kg]
real(r8) :: sapw_c ! sapwood carbon [kg]
real(r8) :: store_c ! storage carbon [kg]
real(r8) :: struct_c ! structure carbon [kg]
real(r8) :: total_c ! total carbon of plant [kg]
real(r8) :: fnrt_c ! fineroot carbon [kg]
real(r8) :: sapw_c ! sapwood carbon [kg]
real(r8) :: store_c ! storage carbon [kg]
real(r8) :: struct_c ! structure carbon [kg]
real(r8) :: total_c ! total carbon of plant [kg]

!---------------------------------------------------------------------

storesmallcohort => null() ! storage of the smallest cohort for insertion routine
storebigcohort => null() ! storage of the largest cohort for insertion routine
Expand Down Expand Up @@ -449,7 +449,6 @@ subroutine spawn_patches( currentSite, bc_in)
nc%cmort = nan ! The mortality diagnostics are set to nan because the cohort should dissappear
nc%hmort = nan
nc%bmort = nan
nc%fmort = nan
nc%frmort = nan
nc%lmort_direct = nan
nc%lmort_collateral = nan
Expand Down Expand Up @@ -492,7 +491,6 @@ subroutine spawn_patches( currentSite, bc_in)
! number density in EDCLMLink, and the number density of this new patch is donated
! so with the number density must come the effective mortality rates.

nc%fmort = 0.0_r8 ! Should had also been zero in the donor
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -517,7 +515,6 @@ subroutine spawn_patches( currentSite, bc_in)
! Those remaining in the existing
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)

nc%fmort = 0.0_r8
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -540,11 +537,40 @@ subroutine spawn_patches( currentSite, bc_in)
! loss of individuals from source patch due to area shrinking
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)

levcan = currentCohort%canopy_layer

if(levcan==ican_upper) then

! before changing number densities, track total rate of trees that died
! due to fire, as well as from each fire mortality term
currentSite%fmort_rate_canopy(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_canopy(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%fire_mort / hlm_freq_day

currentSite%fmort_carbonflux_canopy = currentSite%fmort_carbonflux_canopy + &
(nc%n * currentCohort%fire_mort) * &
total_c * g_per_kg * days_per_sec * ha_per_m2

else
currentSite%fmort_rate_ustory(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_ustory(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%fire_mort / hlm_freq_day

currentSite%fmort_carbonflux_ustory = currentSite%fmort_carbonflux_ustory + &
(nc%n * currentCohort%fire_mort) * &
total_c * g_per_kg * days_per_sec * ha_per_m2
end if

currentSite%fmort_rate_cambial(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_cambial(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%cambial_mort / hlm_freq_day
currentSite%fmort_rate_crown(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_crown(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%crownfire_mort / hlm_freq_day

! loss of individual from fire in new patch.
nc%n = nc%n * (1.0_r8 - currentCohort%fire_mort)

nc%fmort = currentCohort%fire_mort/hlm_freq_day

nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -553,7 +579,8 @@ subroutine spawn_patches( currentSite, bc_in)
nc%lmort_direct = currentCohort%lmort_direct
nc%lmort_collateral = currentCohort%lmort_collateral
nc%lmort_infra = currentCohort%lmort_infra



! Logging is the dominant disturbance
elseif (currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) .and. &
currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifire)) then ! Logging
Expand All @@ -574,7 +601,6 @@ subroutine spawn_patches( currentSite, bc_in)
nc%hmort = nan
nc%bmort = nan
nc%frmort = nan
nc%fmort = nan
nc%lmort_direct = nan
nc%lmort_collateral = nan
nc%lmort_infra = nan
Expand Down Expand Up @@ -616,7 +642,6 @@ subroutine spawn_patches( currentSite, bc_in)
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)


nc%fmort = 0.0_r8
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -636,7 +661,6 @@ subroutine spawn_patches( currentSite, bc_in)
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)

! No grass impact mortality imposed on the newly created patch
nc%fmort = 0.0_r8
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand Down
11 changes: 7 additions & 4 deletions fire/SFMainMod.F90
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Expand Up @@ -158,14 +158,15 @@ end subroutine fire_danger_index
subroutine charecteristics_of_fuel ( currentSite )
!*****************************************************************

use SFParamsMod, only : SF_val_alpha_FMC, SF_val_SAV, SF_val_FBD
use SFParamsMod, only : SF_val_drying_ratio, SF_val_SAV, SF_val_FBD

type(ed_site_type), intent(in), target :: currentSite

type(ed_patch_type), pointer :: currentPatch
type(ed_cohort_type), pointer :: currentCohort

real(r8) timeav_swc
real(r8) timeav_swc
real(r8) alpha_FMC(nfsc) ! Relative fuel moisture adjusted per drying ratio
real(r8) fuel_moisture(nfsc) ! Scaled moisture content of small litter fuels.
real(r8) MEF(nfsc) ! Moisture extinction factor of fuels integer n

Expand Down Expand Up @@ -235,13 +236,15 @@ subroutine charecteristics_of_fuel ( currentSite )
! Equation 6 in Thonicke et al. 2010. across leaves,twig, small branch, and large branch
! dead leaves and twigs included in 1hr pool per Thonicke (2010)
! Calculate fuel moisture for trunks to hold value for fuel consumption
fuel_moisture(dl_sf:tr_sf) = exp(-1.0_r8 * SF_val_alpha_FMC(dl_sf:tr_sf) * currentSite%acc_NI)
alpha_FMC(dl_sf:tr_sf) = SF_val_SAV(dl_sf:tr_sf)/SF_val_drying_ratio

fuel_moisture(dl_sf:tr_sf) = exp(-1.0_r8 * alpha_FMC(dl_sf:tr_sf) * currentSite%acc_NI)

if(write_SF == itrue)then
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'ff3 ',currentPatch%fuel_frac
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'fm ',fuel_moisture
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'csa ',currentSite%acc_NI
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'sfv ',SF_val_alpha_FMC
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'sfv ',alpha_FMC
endif
! FIX(RF,032414): needs refactoring.
! average water content !is this the correct metric?
Expand Down
18 changes: 9 additions & 9 deletions fire/SFParamsMod.F90
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Expand Up @@ -23,7 +23,7 @@ module SFParamsMod
real(r8),protected :: SF_val_miner_damp
real(r8),protected :: SF_val_max_durat
real(r8),protected :: SF_val_durat_slope
real(r8),protected :: SF_val_alpha_FMC(NFSC)
real(r8),protected :: SF_val_drying_ratio
real(r8),protected :: SF_val_CWD_frac(NCWD)
real(r8),protected :: SF_val_max_decomp(NFSC)
real(r8),protected :: SF_val_SAV(NFSC)
Expand All @@ -44,7 +44,7 @@ module SFParamsMod
character(len=param_string_length),parameter :: SF_name_miner_damp = "fates_miner_damp"
character(len=param_string_length),parameter :: SF_name_max_durat = "fates_max_durat"
character(len=param_string_length),parameter :: SF_name_durat_slope = "fates_durat_slope"
character(len=param_string_length),parameter :: SF_name_alpha_FMC = "fates_alpha_FMC"
character(len=param_string_length),parameter :: SF_name_drying_ratio = "fates_drying_ratio"
character(len=param_string_length),parameter :: SF_name_CWD_frac = "fates_CWD_frac"
character(len=param_string_length),parameter :: SF_name_max_decomp = "fates_max_decomp"
character(len=param_string_length),parameter :: SF_name_SAV = "fates_SAV"
Expand Down Expand Up @@ -88,10 +88,10 @@ subroutine SpitFireParamsInit()
SF_val_miner_damp = nan
SF_val_max_durat = nan
SF_val_durat_slope = nan
SF_val_drying_ratio = nan

SF_val_CWD_frac(:) = nan

SF_val_alpha_FMC(:) = nan
SF_val_max_decomp(:) = nan

SF_val_SAV(:) = nan
Expand Down Expand Up @@ -174,6 +174,9 @@ subroutine SpitFireRegisterScalars(fates_params)
call fates_params%RegisterParameter(name=SF_name_durat_slope, dimension_shape=dimension_shape_scalar, &
dimension_names=dim_names_scalar)

call fates_params%RegisterParameter(name=SF_name_drying_ratio, dimension_shape=dimension_shape_scalar, &
dimension_names=dim_names_scalar)

end subroutine SpitFireRegisterScalars

!-----------------------------------------------------------------------
Expand Down Expand Up @@ -212,6 +215,9 @@ subroutine SpitFireReceiveScalars(fates_params)
call fates_params%RetreiveParameter(name=SF_name_durat_slope, &
data=SF_val_durat_slope)

call fates_params%RetreiveParameter(name=SF_name_drying_ratio, &
data=SF_val_drying_ratio)

end subroutine SpitFireReceiveScalars

!-----------------------------------------------------------------------
Expand Down Expand Up @@ -279,9 +285,6 @@ subroutine SpitFireRegisterNFSC(fates_params)
call fates_params%RegisterParameter(name=SF_name_mid_moisture_Slope, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names)

call fates_params%RegisterParameter(name=SF_name_alpha_FMC, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names)

call fates_params%RegisterParameter(name=SF_name_max_decomp, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names)

Expand Down Expand Up @@ -321,9 +324,6 @@ subroutine SpitFireReceiveNFSC(fates_params)
call fates_params%RetreiveParameter(name=SF_name_mid_moisture_Slope, &
data=SF_val_mid_moisture_Slope)

call fates_params%RetreiveParameter(name=SF_name_alpha_FMC, &
data=SF_val_alpha_FMC)

call fates_params%RetreiveParameter(name=SF_name_max_decomp, &
data=SF_val_max_decomp)

Expand Down
20 changes: 17 additions & 3 deletions main/EDInitMod.F90
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Expand Up @@ -70,11 +70,17 @@ subroutine init_site_vars( site_in )
! !LOCAL VARIABLES:
!----------------------------------------------------------------------
!
allocate(site_in%terminated_nindivs(1:nlevsclass,1:numpft,2))
allocate(site_in%term_nindivs_canopy(1:nlevsclass,1:numpft))
allocate(site_in%term_nindivs_ustory(1:nlevsclass,1:numpft))
allocate(site_in%demotion_rate(1:nlevsclass))
allocate(site_in%promotion_rate(1:nlevsclass))
allocate(site_in%imort_rate(1:nlevsclass,1:numpft))
allocate(site_in%fmort_rate_canopy(1:nlevsclass,1:numpft))
allocate(site_in%fmort_rate_ustory(1:nlevsclass,1:numpft))
allocate(site_in%fmort_rate_cambial(1:nlevsclass,1:numpft))
allocate(site_in%fmort_rate_crown(1:nlevsclass,1:numpft))
allocate(site_in%growthflux_fusion(1:nlevsclass,1:numpft))

!
end subroutine init_site_vars

Expand Down Expand Up @@ -123,11 +129,19 @@ subroutine zero_site( site_in )
site_in%fates_to_bgc_last_ts = 0.0_r8

! termination and recruitment info
site_in%terminated_nindivs(:,:,:) = 0._r8
site_in%termination_carbonflux(:) = 0._r8
site_in%term_nindivs_canopy(:,:) = 0._r8
site_in%term_nindivs_ustory(:,:) = 0._r8
site_in%term_carbonflux_canopy = 0._r8
site_in%term_carbonflux_ustory = 0._r8
site_in%recruitment_rate(:) = 0._r8
site_in%imort_rate(:,:) = 0._r8
site_in%imort_carbonflux = 0._r8
site_in%fmort_rate_canopy(:,:) = 0._r8
site_in%fmort_rate_ustory(:,:) = 0._r8
site_in%fmort_carbonflux_canopy = 0._r8
site_in%fmort_carbonflux_ustory = 0._r8
site_in%fmort_rate_cambial(:,:) = 0._r8
site_in%fmort_rate_crown(:,:) = 0._r8

! fusoin-induced growth flux of individuals
site_in%growthflux_fusion(:,:) = 0._r8
Expand Down
1 change: 0 additions & 1 deletion main/EDMainMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -686,7 +686,6 @@ subroutine bypass_dynamics(currentSite)
currentCohort%bmort = 0.0_r8
currentCohort%hmort = 0.0_r8
currentCohort%cmort = 0.0_r8
currentCohort%fmort = 0.0_r8
currentCohort%frmort = 0.0_r8

currentCohort%dndt = 0.0_r8
Expand Down
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