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EDPatchDynamicsMod.F90
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module EDPatchDynamicsMod
! ============================================================================
! Controls formation, creation, fusing and termination of patch level processes.
! ============================================================================
use FatesGlobals , only : fates_log
use FatesGlobals , only : FatesWarn,N2S,A2S
use FatesInterfaceTypesMod , only : hlm_freq_day
use EDPftvarcon , only : EDPftvarcon_inst
use EDPftvarcon , only : GetDecompyFrac
use PRTParametersMod , only : prt_params
use EDCohortDynamicsMod , only : fuse_cohorts, sort_cohorts, insert_cohort
use EDCohortDynamicsMod , only : DeallocateCohort
use EDTypesMod , only : area_site => area
use ChecksBalancesMod , only : PatchMassStock
use FatesLitterMod , only : ncwd
use FatesLitterMod , only : ndcmpy
use FatesLitterMod , only : litter_type
use EDTypesMod , only : homogenize_seed_pfts
use EDTypesMod , only : n_dbh_bins, area, patchfusion_dbhbin_loweredges
use EDtypesMod , only : force_patchfuse_min_biomass
use EDTypesMod , only : ed_site_type, ed_patch_type, ed_cohort_type
use EDTypesMod , only : site_massbal_type
use EDTypesMod , only : site_fluxdiags_type
use EDTypesMod , only : min_patch_area
use EDTypesMod , only : min_patch_area_forced
use EDTypesMod , only : nclmax
use EDTypesMod , only : maxpft
use EDTypesMod , only : dtype_ifall
use EDTypesMod , only : dtype_ilog
use EDTypesMod , only : dtype_ifire
use EDTypesMod , only : ican_upper
use PRTGenericMod , only : num_elements
use PRTGenericMod , only : element_list
use EDTypesMod , only : lg_sf
use EDTypesMod , only : dl_sf
use EDTypesMod , only : dump_patch
use EDTypesMod , only : N_DIST_TYPES
use EDTypesMod , only : AREA_INV
use FatesConstantsMod , only : rsnbl_math_prec
use FatesConstantsMod , only : fates_tiny
use FatesInterfaceTypesMod , only : hlm_use_planthydro
use FatesInterfaceTypesMod , only : hlm_numSWb
use FatesInterfaceTypesMod , only : bc_in_type
use FatesInterfaceTypesMod , only : hlm_days_per_year
use FatesInterfaceTypesMod , only : numpft
use FatesInterfaceTypesMod , only : hlm_stepsize
use FatesInterfaceTypesMod , only : hlm_use_sp
use FatesInterfaceTypesMod , only : hlm_use_nocomp
use FatesInterfaceTypesMod , only : hlm_use_fixed_biogeog
use FatesGlobals , only : endrun => fates_endrun
use FatesConstantsMod , only : r8 => fates_r8
use FatesConstantsMod , only : itrue, ifalse
use FatesConstantsMod , only : t_water_freeze_k_1atm
use FatesPlantHydraulicsMod, only : InitHydrCohort
use FatesPlantHydraulicsMod, only : AccumulateMortalityWaterStorage
use FatesPlantHydraulicsMod, only : DeallocateHydrCohort
use EDLoggingMortalityMod, only : logging_litter_fluxes
use EDLoggingMortalityMod, only : logging_time
use EDLoggingMortalityMod, only : get_harvest_rate_area
use EDParamsMod , only : fates_mortality_disturbance_fraction
use FatesAllometryMod , only : carea_allom
use FatesAllometryMod , only : set_root_fraction
use FatesConstantsMod , only : g_per_kg
use FatesConstantsMod , only : ha_per_m2
use FatesConstantsMod , only : days_per_sec
use FatesConstantsMod , only : years_per_day
use FatesConstantsMod , only : nearzero
use FatesConstantsMod , only : primaryforest, secondaryforest
use FatesConstantsMod , only : n_anthro_disturbance_categories
use FatesConstantsMod , only : fates_unset_r8
use FatesConstantsMod , only : fates_unset_int
use EDCohortDynamicsMod , only : InitPRTObject
use EDCohortDynamicsMod , only : InitPRTBoundaryConditions
use ChecksBalancesMod, only : SiteMassStock
use PRTGenericMod, only : all_carbon_elements
use PRTGenericMod, only : carbon12_element
use PRTGenericMod, only : leaf_organ
use PRTGenericMod, only : fnrt_organ
use PRTGenericMod, only : sapw_organ
use PRTGenericMod, only : store_organ
use PRTGenericMod, only : repro_organ
use PRTGenericMod, only : struct_organ
use PRTLossFluxesMod, only : PRTBurnLosses
use FatesInterfaceTypesMod, only : hlm_parteh_mode
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use SFParamsMod, only : SF_VAL_CWD_FRAC
use EDParamsMod, only : logging_event_code
use EDParamsMod, only : logging_export_frac
use EDParamsMod, only : maxpatch_primary
use EDParamsMod, only : maxpatch_secondary
use EDParamsMod, only : maxpatch_total
use FatesRunningMeanMod, only : ema_24hr, fixed_24hr, ema_lpa
! CIME globals
use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
use shr_log_mod , only : errMsg => shr_log_errMsg
!
implicit none
private
!
public :: create_patch
public :: spawn_patches
public :: zero_patch
public :: fuse_patches
public :: terminate_patches
public :: patch_pft_size_profile
public :: disturbance_rates
public :: check_patch_area
public :: set_patchno
private:: fuse_2_patches
public :: get_frac_site_primary
character(len=*), parameter, private :: sourcefile = &
__FILE__
logical, parameter :: debug = .false.
! When creating new patches from other patches, we need to send some of the
! litter from the old patch to the new patch. Likewise, when plants die
! from the disturbance, we need to send some amount from the old patch to
! the new patch. If the plant matter falls straight down, then that
! would make a case for all of the litter going to the new patch.
! This would be localization=1
! But if we think some of the plant matter drifts, or a tall tree lands
! outside of its gap, or are afraid of newly formed patches having
! too much burnable material, then we drop the localization from 1 down
! a notch.
! Note that in all cases, a localization of 0, suggests that litter
! is dispensed randomly in space among the area of the new and old
! patch combined. A localization of 1 suggests that
! all litter is sent to the new patch.
real(r8), parameter :: existing_litt_localization = 1.0_r8
real(r8), parameter :: treefall_localization = 0.0_r8
real(r8), parameter :: burn_localization = 0.0_r8
character(len=512) :: msg ! Message string for warnings and logging
! 10/30/09: Created by Rosie Fisher
! ============================================================================
contains
! ============================================================================
subroutine disturbance_rates( site_in, bc_in)
!
! !DESCRIPTION:
! Calculates the fire and mortality related disturbance rates for each patch,
! and then determines which is the larger at the patch scale (for now, there an only
! be one disturbance type for each timestep.
! all disturbance rates here are per daily timestep.
! 2016-2017
! Modify to add logging disturbance
! !USES:
use EDMortalityFunctionsMod , only : mortality_rates
use EDMortalityFunctionsMod , only : ExemptTreefallDist
! loging flux
use EDLoggingMortalityMod , only : LoggingMortality_frac
! !ARGUMENTS:
type(ed_site_type) , intent(inout), target :: site_in
type(bc_in_type) , intent(in) :: bc_in
!
! !LOCAL VARIABLES:
type (ed_patch_type) , pointer :: currentPatch
type (ed_cohort_type), pointer :: currentCohort
real(r8) :: cmort
real(r8) :: bmort
real(r8) :: hmort
real(r8) :: frmort
real(r8) :: smort
real(r8) :: asmort
real(r8) :: lmort_direct
real(r8) :: lmort_collateral
real(r8) :: lmort_infra
real(r8) :: 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)
real(r8) :: dist_rate_ldist_notharvested
integer :: threshold_sizeclass
integer :: i_dist
real(r8) :: frac_site_primary
real(r8) :: harvest_rate
real(r8) :: tempsum
!----------------------------------------------------------------------------------------------
! Calculate Mortality Rates (these were previously calculated during growth derivatives)
! And the same rates in understory plants have already been applied to %dndt
!----------------------------------------------------------------------------------------------
! first calculate the fractino of the site that is primary land
call get_frac_site_primary(site_in, frac_site_primary)
currentPatch => site_in%oldest_patch
do while (associated(currentPatch))
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
! Mortality for trees in the understorey.
currentCohort%patchptr => currentPatch
call mortality_rates(currentCohort,bc_in,cmort,hmort,bmort,frmort,smort,asmort)
currentCohort%dmort = cmort+hmort+bmort+frmort+smort+asmort
call carea_allom(currentCohort%dbh,currentCohort%n,site_in%spread,currentCohort%pft, &
currentCohort%c_area)
! Initialize diagnostic mortality rates
currentCohort%cmort = cmort
currentCohort%bmort = bmort
currentCohort%hmort = hmort
currentCohort%frmort = frmort
currentCohort%smort = smort
currentCohort%asmort = asmort
call LoggingMortality_frac(currentCohort%pft, currentCohort%dbh, currentCohort%canopy_layer, &
lmort_direct,lmort_collateral,lmort_infra,l_degrad,&
bc_in%hlm_harvest_rates, &
bc_in%hlm_harvest_catnames, &
bc_in%hlm_harvest_units, &
currentPatch%anthro_disturbance_label, &
currentPatch%age_since_anthro_disturbance, &
frac_site_primary)
currentCohort%lmort_direct = lmort_direct
currentCohort%lmort_collateral = lmort_collateral
currentCohort%lmort_infra = lmort_infra
currentCohort%l_degrad = l_degrad
currentCohort => currentCohort%taller
end do
currentPatch => currentPatch%younger
end do
! ---------------------------------------------------------------------------------------------
! Calculate Disturbance Rates based on the mortality rates just calculated
! ---------------------------------------------------------------------------------------------
! zero the diagnostic disturbance rate fields
site_in%potential_disturbance_rates(1:N_DIST_TYPES) = 0._r8
! Recalculate total canopy area prior to resolving the disturbance
currentPatch => site_in%oldest_patch
do while (associated(currentPatch))
currentPatch%total_canopy_area = 0._r8
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
if(currentCohort%canopy_layer==1)then
currentPatch%total_canopy_area = currentPatch%total_canopy_area + currentCohort%c_area
end if
currentCohort => currentCohort%taller
end do
currentPatch => currentPatch%younger
end do
currentPatch => site_in%oldest_patch
do while (associated(currentPatch))
currentPatch%disturbance_rates(dtype_ifall) = 0.0_r8
currentPatch%disturbance_rates(dtype_ilog) = 0.0_r8
currentPatch%disturbance_rates(dtype_ifire) = 0.0_r8
dist_rate_ldist_notharvested = 0.0_r8
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
if(currentCohort%canopy_layer == 1)then
! Treefall Disturbance Rate. Only count this for trees, not grasses
if ( .not. ExemptTreefallDist(currentCohort) ) then
currentPatch%disturbance_rates(dtype_ifall) = currentPatch%disturbance_rates(dtype_ifall) + &
fates_mortality_disturbance_fraction * &
min(1.0_r8,currentCohort%dmort)*hlm_freq_day*currentCohort%c_area/currentPatch%area
end if
! Logging Disturbance Rate
currentPatch%disturbance_rates(dtype_ilog) = currentPatch%disturbance_rates(dtype_ilog) + &
min(1.0_r8, currentCohort%lmort_direct + &
currentCohort%lmort_collateral + &
currentCohort%lmort_infra + &
currentCohort%l_degrad ) * &
currentCohort%c_area/currentPatch%area
! Non-harvested part of the logging disturbance rate
dist_rate_ldist_notharvested = dist_rate_ldist_notharvested + currentCohort%l_degrad * &
currentCohort%c_area/currentPatch%area
endif
currentCohort => currentCohort%taller
enddo !currentCohort
! for non-closed-canopy areas subject to logging, add an additional increment of area disturbed
! equivalent to the fradction logged to account for transfer of interstitial ground area to new secondary lands
if ( logging_time .and. &
(currentPatch%area - currentPatch%total_canopy_area) .gt. fates_tiny ) then
! The canopy is NOT closed.
call get_harvest_rate_area (currentPatch%anthro_disturbance_label, bc_in%hlm_harvest_catnames, &
bc_in%hlm_harvest_rates, frac_site_primary, currentPatch%age_since_anthro_disturbance, harvest_rate)
currentPatch%disturbance_rates(dtype_ilog) = currentPatch%disturbance_rates(dtype_ilog) + &
(currentPatch%area - currentPatch%total_canopy_area) * harvest_rate / currentPatch%area
! Non-harvested part of the logging disturbance rate
dist_rate_ldist_notharvested = dist_rate_ldist_notharvested + &
(currentPatch%area - currentPatch%total_canopy_area) * harvest_rate / currentPatch%area
endif
! fraction of the logging disturbance rate that is non-harvested
if (currentPatch%disturbance_rates(dtype_ilog) .gt. nearzero) then
currentPatch%fract_ldist_not_harvested = dist_rate_ldist_notharvested / &
currentPatch%disturbance_rates(dtype_ilog)
endif
! Fire Disturbance Rate
currentPatch%disturbance_rates(dtype_ifire) = currentPatch%frac_burnt
! calculate a disgnostic sum of disturbance rates for different classes of disturbance across all patches in this site.
do i_dist = 1,N_DIST_TYPES
site_in%potential_disturbance_rates(i_dist) = site_in%potential_disturbance_rates(i_dist) + &
currentPatch%disturbance_rates(i_dist) * currentPatch%area * AREA_INV
end do
! Fires can't burn the whole patch, as this causes /0 errors.
if (currentPatch%disturbance_rates(dtype_ifire) > 0.98_r8)then
msg = 'very high fire areas'//trim(A2S(currentPatch%disturbance_rates(:)))//trim(N2S(currentPatch%frac_burnt))
call FatesWarn(msg,index=2)
endif
! if the sum of all disturbance rates is such that they will exceed total patch area on this day, then reduce them all proportionally.
if ( sum(currentPatch%disturbance_rates(:)) .gt. 1.0_r8 ) then
tempsum = sum(currentPatch%disturbance_rates(:))
do i_dist = 1,N_DIST_TYPES
currentPatch%disturbance_rates(i_dist) = currentPatch%disturbance_rates(i_dist) / tempsum
end do
endif
currentPatch => currentPatch%younger
enddo !patch loop
end subroutine disturbance_rates
! ============================================================================
subroutine spawn_patches( currentSite, bc_in)
!
! !DESCRIPTION:
! In this subroutine, the following happens
! 1) the total area disturbed is calculated
! 2) a new patch is created
! 3) properties are averaged
! 4) litter fluxes from fire and mortality are added
! 5) For mortality, plants in existing patch canopy are killed.
! 6) For mortality, Plants in new and existing understorey are killed
! 7) For fire, burned plants are killed, and unburned plants are added to new patch.
! 8) New cohorts are added to new patch and sorted.
! 9) New patch is added into linked list
! 10) Area checked, and patchno recalculated.
!
! !USES:
use EDParamsMod , only : ED_val_understorey_death, logging_coll_under_frac
use EDCohortDynamicsMod , only : zero_cohort, copy_cohort, terminate_cohorts
use FatesConstantsMod , only : rsnbl_math_prec
!
! !ARGUMENTS:
type (ed_site_type), intent(inout), target :: currentSite
type (bc_in_type), intent(in) :: bc_in
!
! !LOCAL VARIABLES:
type (ed_patch_type) , pointer :: new_patch
type (ed_patch_type) , pointer :: new_patch_primary
type (ed_patch_type) , pointer :: new_patch_secondary
type (ed_patch_type) , pointer :: currentPatch
type (ed_cohort_type), pointer :: currentCohort
type (ed_cohort_type), pointer :: nc
type (ed_cohort_type), pointer :: storesmallcohort
type (ed_cohort_type), pointer :: storebigcohort
real(r8) :: site_areadis_primary ! total area disturbed (to primary forest) in m2 per site per day
real(r8) :: site_areadis_secondary ! total area disturbed (to secondary forest) in m2 per site per day
real(r8) :: patch_site_areadis ! total area disturbed in m2 per patch per day
real(r8) :: age ! notional age of this patch in years
integer :: el ! element loop index
integer :: tnull ! is there a tallest cohort?
integer :: snull ! is there a shortest cohort?
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) :: leaf_burn_frac ! fraction of leaves burned in fire
! for both woody and grass species
real(r8) :: leaf_m ! leaf mass during partial burn calculations
logical :: found_youngest_primary ! logical for finding the first primary forest patch
integer :: min_nocomp_pft, max_nocomp_pft, i_nocomp_pft
integer :: i_disturbance_type, i_dist2 ! iterators for looping over disturbance types
real(r8) :: disturbance_rate ! rate of disturbance being resolved [fraction of patch area / day]
real(r8) :: oldarea ! old patch area prior to disturbance
!---------------------------------------------------------------------
storesmallcohort => null() ! storage of the smallest cohort for insertion routine
storebigcohort => null() ! storage of the largest cohort for insertion routine
if (hlm_use_nocomp .eq. itrue) then
min_nocomp_pft = 0
max_nocomp_pft = numpft
else
min_nocomp_pft = fates_unset_int
max_nocomp_pft = fates_unset_int
endif
! zero the diagnostic disturbance rate fields
currentSite%disturbance_rates_primary_to_primary(1:N_DIST_TYPES) = 0._r8
currentSite%disturbance_rates_primary_to_secondary(1:N_DIST_TYPES) = 0._r8
currentSite%disturbance_rates_secondary_to_secondary(1:N_DIST_TYPES) = 0._r8
! in the nocomp cases, since every patch has a PFT identity, it can only receive patch area from patches
! that have the same identity. In order to allow this, we have this very high level loop over nocomp PFTs
! and only do the disturbance for any patches that have that nocomp PFT identity.
! If nocomp is not enabled, then this is not much of a loop, it only passes through once.
nocomp_pft_loop: do i_nocomp_pft = min_nocomp_pft,max_nocomp_pft
disturbance_type_loop: do i_disturbance_type = 1,N_DIST_TYPES
! calculate area of disturbed land, in this timestep, by summing contributions from each existing patch.
currentPatch => currentSite%youngest_patch
site_areadis_primary = 0.0_r8
site_areadis_secondary = 0.0_r8
do while(associated(currentPatch))
cp_nocomp_matches_1_if: if ( hlm_use_nocomp .eq. ifalse .or. &
currentPatch%nocomp_pft_label .eq. i_nocomp_pft ) then
disturbance_rate = currentPatch%disturbance_rates(i_disturbance_type)
if(disturbance_rate > (1.0_r8 + rsnbl_math_prec)) then
write(fates_log(),*) 'patch disturbance rate > 1 ?',disturbance_rate
call dump_patch(currentPatch)
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
! Only create new patches that have non-negligible amount of land
if((currentPatch%area*disturbance_rate) > nearzero ) then
! figure out whether the receiver patch for disturbance from this patch will be
! primary or secondary land receiver patch is primary forest only if both the
! donor patch is primary forest and the current disturbance type is not logging
if ( currentPatch%anthro_disturbance_label .eq. primaryforest .and. &
(i_disturbance_type .ne. dtype_ilog) ) then
site_areadis_primary = site_areadis_primary + currentPatch%area * disturbance_rate
! track disturbance rates to output to history
currentSite%disturbance_rates_primary_to_primary(i_disturbance_type) = &
currentSite%disturbance_rates_primary_to_primary(i_disturbance_type) + &
currentPatch%area * disturbance_rate * AREA_INV
else
site_areadis_secondary = site_areadis_secondary + currentPatch%area * disturbance_rate
! track disturbance rates to output to history
if (currentPatch%anthro_disturbance_label .eq. secondaryforest) then
currentSite%disturbance_rates_secondary_to_secondary(i_disturbance_type) = &
currentSite%disturbance_rates_secondary_to_secondary(i_disturbance_type) + &
currentPatch%area * disturbance_rate * AREA_INV
else
currentSite%disturbance_rates_primary_to_secondary(i_disturbance_type) = &
currentSite%disturbance_rates_primary_to_secondary(i_disturbance_type) + &
currentPatch%area * disturbance_rate * AREA_INV
endif
endif
end if
end if cp_nocomp_matches_1_if
currentPatch => currentPatch%older
enddo ! end loop over patches. sum area disturbed for all patches.
! It is possible that no disturbance area was generated
if ( (site_areadis_primary + site_areadis_secondary) > nearzero) then
age = 0.0_r8
! create two empty patches, to absorb newly disturbed primary and secondary forest area
! first create patch to receive primary forest area
if ( site_areadis_primary .gt. nearzero ) then
allocate(new_patch_primary)
call create_patch(currentSite, new_patch_primary, age, &
site_areadis_primary, primaryforest, i_nocomp_pft)
! Initialize the litter pools to zero, these
! pools will be populated by looping over the existing patches
! and transfering in mass
do el=1,num_elements
call new_patch_primary%litter(el)%InitConditions(init_leaf_fines=0._r8, &
init_root_fines=0._r8, &
init_ag_cwd=0._r8, &
init_bg_cwd=0._r8, &
init_seed=0._r8, &
init_seed_germ=0._r8)
end do
new_patch_primary%tallest => null()
new_patch_primary%shortest => null()
endif
! next create patch to receive secondary forest area
if ( site_areadis_secondary .gt. nearzero) then
allocate(new_patch_secondary)
call create_patch(currentSite, new_patch_secondary, age, &
site_areadis_secondary, secondaryforest,i_nocomp_pft)
! Initialize the litter pools to zero, these
! pools will be populated by looping over the existing patches
! and transfering in mass
do el=1,num_elements
call new_patch_secondary%litter(el)%InitConditions(init_leaf_fines=0._r8, &
init_root_fines=0._r8, &
init_ag_cwd=0._r8, &
init_bg_cwd=0._r8, &
init_seed=0._r8, &
init_seed_germ=0._r8)
end do
new_patch_secondary%tallest => null()
new_patch_secondary%shortest => null()
endif
! loop round all the patches that contribute surviving indivduals and litter
! pools to the new patch. We only loop the pre-existing patches, so
! quit the loop if the current patch is either null, or matches the
! two new pointers.
currentPatch => currentSite%oldest_patch
do while(associated(currentPatch))
cp_nocomp_matches_2_if: if ( hlm_use_nocomp .eq. ifalse .or. &
currentPatch%nocomp_pft_label .eq. i_nocomp_pft ) then
! This is the amount of patch area that is disturbed, and donated by the donor
disturbance_rate = currentPatch%disturbance_rates(i_disturbance_type)
patch_site_areadis = currentPatch%area * disturbance_rate
if ( patch_site_areadis > nearzero ) then
! figure out whether the receiver patch for disturbance from this patch
! will be primary or secondary land receiver patch is primary forest
! only if both the donor patch is primary forest and the current
! disturbance type is not logging
if (currentPatch%anthro_disturbance_label .eq. primaryforest .and. &
(i_disturbance_type .ne. dtype_ilog)) then
new_patch => new_patch_primary
else
new_patch => new_patch_secondary
endif
if(.not.associated(new_patch))then
write(fates_log(),*) 'Patch spawning has attempted to point to'
write(fates_log(),*) 'an un-allocated patch'
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
! for the case where the donating patch is secondary forest, if
! the current disturbance from this patch is non-anthropogenic,
! we need to average in the time-since-anthropogenic-disturbance
! from the donor patch into that of the receiver patch
if ( currentPatch%anthro_disturbance_label .eq. secondaryforest .and. &
(i_disturbance_type .ne. dtype_ilog) ) then
new_patch%age_since_anthro_disturbance = new_patch%age_since_anthro_disturbance + &
currentPatch%age_since_anthro_disturbance * (patch_site_areadis / site_areadis_secondary)
endif
! Transfer the litter existing already in the donor patch to the new patch
! This call will only transfer non-burned litter to new patch
! and burned litter to atmosphere. Thus it is important to zero burnt_frac_litter when
! fire is not the current disturbance regime.
if(i_disturbance_type .ne. dtype_ifire) then
currentPatch%burnt_frac_litter(:) = 0._r8
end if
call TransLitterNewPatch( currentSite, currentPatch, new_patch, patch_site_areadis)
! Transfer in litter fluxes from plants in various contexts of death and destruction
if(i_disturbance_type .eq. dtype_ilog) then
call logging_litter_fluxes(currentSite, currentPatch, &
new_patch, patch_site_areadis,bc_in)
elseif(i_disturbance_type .eq. dtype_ifire) then
call fire_litter_fluxes(currentSite, currentPatch, &
new_patch, patch_site_areadis,bc_in)
else
call mortality_litter_fluxes(currentSite, currentPatch, &
new_patch, patch_site_areadis,bc_in)
endif
! Copy any means or timers from the original patch to the new patch
! These values will inherit all info from the original patch
! --------------------------------------------------------------------------
call new_patch%tveg24%CopyFromDonor(currentPatch%tveg24)
call new_patch%tveg_lpa%CopyFromDonor(currentPatch%tveg_lpa)
! --------------------------------------------------------------------------
! The newly formed patch from disturbance (new_patch), has now been given
! some litter from dead plants and pre-existing litter from the donor patches.
!
! Next, we loop through the cohorts in the donor patch, copy them with
! area modified number density into the new-patch, and apply survivorship.
! -------------------------------------------------------------------------
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
allocate(nc)
if(hlm_use_planthydro.eq.itrue) call InitHydrCohort(CurrentSite,nc)
! Initialize the PARTEH object and point to the
! correct boundary condition fields
nc%prt => null()
call InitPRTObject(nc%prt)
call InitPRTBoundaryConditions(nc)
! (Keeping as an example)
! Allocate running mean functions
!allocate(nc%tveg_lpa)
!call nc%tveg_lpa%InitRMean(ema_lpa,init_value=new_patch%tveg_lpa%GetMean())
call zero_cohort(nc)
! nc is the new cohort that goes in the disturbed patch (new_patch)... currentCohort
! is the curent cohort that stays in the donor patch (currentPatch)
call copy_cohort(currentCohort, nc)
!this is the case as the new patch probably doesn't have a closed canopy, and
! even if it does, that will be sorted out in canopy_structure.
nc%canopy_layer = 1
nc%canopy_layer_yesterday = 1._r8
sapw_c = currentCohort%prt%GetState(sapw_organ, all_carbon_elements)
struct_c = currentCohort%prt%GetState(struct_organ, all_carbon_elements)
leaf_c = currentCohort%prt%GetState(leaf_organ, all_carbon_elements)
fnrt_c = currentCohort%prt%GetState(fnrt_organ, all_carbon_elements)
store_c = currentCohort%prt%GetState(store_organ, all_carbon_elements)
total_c = sapw_c + struct_c + leaf_c + fnrt_c + store_c
! treefall mortality is the current disturbance
if(i_disturbance_type .eq. dtype_ifall) then
if(currentCohort%canopy_layer == 1)then
! In the donor patch we are left with fewer trees because the area has decreased
! the plant density for large trees does not actually decrease in the donor patch
! because this is the part of the original patch where no trees have actually fallen
! The diagnostic cmort,bmort,hmort, and frmort rates have already been saved
currentCohort%n = currentCohort%n * (1.0_r8 - fates_mortality_disturbance_fraction * &
min(1.0_r8,currentCohort%dmort * hlm_freq_day))
nc%n = 0.0_r8 ! kill all of the trees who caused the disturbance.
nc%cmort = nan ! The mortality diagnostics are set to nan
! because the cohort should dissappear
nc%hmort = nan
nc%bmort = nan
nc%frmort = nan
nc%smort = nan
nc%asmort = nan
nc%lmort_direct = nan
nc%lmort_collateral = nan
nc%lmort_infra = nan
nc%l_degrad = nan
else
! small trees
if( prt_params%woody(currentCohort%pft) == itrue)then
! Survivorship of undestory woody plants. Two step process.
! Step 1: Reduce current number of plants to reflect the
! change in area.
! The number density per square are doesn't change,
! but since the patch is smaller and cohort counts
! are absolute, reduce this number.
nc%n = currentCohort%n * patch_site_areadis/currentPatch%area
! because the mortality rate due to impact for the cohorts which
! had been in the understory and are now in the newly-
! disturbed patch is very high, passing the imort directly to history
! results in large numerical errors, on account of the sharply
! reduced number densities. so instead pass this info via a
! site-level diagnostic variable before reducing the number density.
currentSite%imort_rate(currentCohort%size_class, currentCohort%pft) = &
currentSite%imort_rate(currentCohort%size_class, currentCohort%pft) + &
nc%n * ED_val_understorey_death / hlm_freq_day
currentSite%imort_carbonflux(currentCohort%pft) = &
currentSite%imort_carbonflux(currentCohort%pft) + &
(nc%n * ED_val_understorey_death / hlm_freq_day ) * &
total_c * g_per_kg * days_per_sec * years_per_day * ha_per_m2
! Step 2: Apply survivor ship function based on the understory death fraction
! remaining of understory plants of those that are knocked over
! by the overstorey trees dying...
nc%n = nc%n * (1.0_r8 - ED_val_understorey_death)
! since the donor patch split and sent a fraction of its members
! to the new patch and a fraction to be preserved in itself,
! when reporting diagnostic rates, we must carry over the mortality rates from
! the donor that were applied before the patch split. Remember this is only
! for diagnostics. But think of it this way, the rates are weighted by
! 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%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
nc%frmort = currentCohort%frmort
nc%smort = currentCohort%smort
nc%asmort = currentCohort%asmort
nc%dmort = currentCohort%dmort
nc%lmort_direct = currentCohort%lmort_direct
nc%lmort_collateral = currentCohort%lmort_collateral
nc%lmort_infra = currentCohort%lmort_infra
! understory trees that might potentially be knocked over in the disturbance.
! The existing (donor) patch should not have any impact mortality, it should
! only lose cohorts due to the decrease in area. This is not mortality.
! Besides, the current and newly created patch sum to unity
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)
else
! grass is not killed by mortality disturbance events. Just move it into the new patch area.
! Just split the grass into the existing and new patch structures
nc%n = currentCohort%n * patch_site_areadis/currentPatch%area
! Those remaining in the existing
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
nc%frmort = currentCohort%frmort
nc%smort = currentCohort%smort
nc%asmort = currentCohort%asmort
nc%dmort = currentCohort%dmort
nc%lmort_direct = currentCohort%lmort_direct
nc%lmort_collateral = currentCohort%lmort_collateral
nc%lmort_infra = currentCohort%lmort_infra
endif
endif
! Fire is the current disturbance
elseif (i_disturbance_type .eq. dtype_ifire ) then
! Number of members in the new patch, before we impose fire survivorship
nc%n = currentCohort%n * patch_site_areadis/currentPatch%area
! 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(currentCohort%pft) = &
currentSite%fmort_carbonflux_canopy(currentCohort%pft) + &
(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(currentCohort%pft) = &
currentSite%fmort_carbonflux_ustory(currentCohort%pft) + &
(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%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
nc%frmort = currentCohort%frmort
nc%smort = currentCohort%smort
nc%asmort = currentCohort%asmort
nc%dmort = currentCohort%dmort
nc%lmort_direct = currentCohort%lmort_direct
nc%lmort_collateral = currentCohort%lmort_collateral
nc%lmort_infra = currentCohort%lmort_infra
! Some of of the leaf mass from living plants has been
! burned off. Here, we remove that mass, and
! tally it in the flux we sent to the atmosphere
if(prt_params%woody(currentCohort%pft) == itrue)then
leaf_burn_frac = currentCohort%fraction_crown_burned
else
! Grasses determine their fraction of leaves burned here
leaf_burn_frac = currentPatch%burnt_frac_litter(lg_sf)
endif
! Perform a check to make sure that spitfire gave
! us reasonable mortality and burn fraction rates
if( (leaf_burn_frac < 0._r8) .or. &
(leaf_burn_frac > 1._r8) .or. &
(currentCohort%fire_mort < 0._r8) .or. &
(currentCohort%fire_mort > 1._r8)) then
write(fates_log(),*) 'unexpected fire fractions'
write(fates_log(),*) prt_params%woody(currentCohort%pft)
write(fates_log(),*) leaf_burn_frac
write(fates_log(),*) currentCohort%fire_mort
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
do el = 1,num_elements
leaf_m = nc%prt%GetState(leaf_organ, element_list(el))
currentSite%mass_balance(el)%burn_flux_to_atm = &
currentSite%mass_balance(el)%burn_flux_to_atm + &
leaf_burn_frac * leaf_m * nc%n
end do
! Here the mass is removed from the plant
call PRTBurnLosses(nc%prt, leaf_organ, leaf_burn_frac)
currentCohort%fraction_crown_burned = 0.0_r8
nc%fraction_crown_burned = 0.0_r8
! Logging is the current disturbance
elseif (i_disturbance_type .eq. dtype_ilog ) then
! If this cohort is in the upper canopy. It generated
if(currentCohort%canopy_layer == 1)then
! calculate the survivorship of disturbed trees because non-harvested
nc%n = currentCohort%n * currentCohort%l_degrad
! nc%n = (currentCohort%l_degrad / (currentCohort%l_degrad + &
! currentCohort%lmort_direct + currentCohort%lmort_collateral +
! currentCohort%lmort_infra) ) * &
! currentCohort%n * patch_site_areadis/currentPatch%area
! Reduce counts in the existing/donor patch according to the logging rate
currentCohort%n = currentCohort%n * &
(1.0_r8 - min(1.0_r8,(currentCohort%lmort_direct + &
currentCohort%lmort_collateral + &
currentCohort%lmort_infra + currentCohort%l_degrad)))
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
nc%frmort = currentCohort%frmort
nc%smort = currentCohort%smort
nc%asmort = currentCohort%asmort
nc%dmort = currentCohort%dmort
! since these are the ones that weren't logged,
! set the logging mortality rates as zero
nc%lmort_direct = 0._r8
nc%lmort_collateral = 0._r8
nc%lmort_infra = 0._r8
else
! What to do with cohorts in the understory of a logging generated
! disturbance patch?
if(prt_params%woody(currentCohort%pft) == itrue)then
! Survivorship of undestory woody plants. Two step process.
! Step 1: Reduce current number of plants to reflect the
! change in area.
! The number density per square are doesn't change,
! but since the patch is smaller
! and cohort counts are absolute, reduce this number.
nc%n = currentCohort%n * patch_site_areadis/currentPatch%area
! because the mortality rate due to impact for the cohorts which had
! been in the understory and are now in the newly-
! disturbed patch is very high, passing the imort directly to
! history results in large numerical errors, on account
! of the sharply reduced number densities. so instead pass this info
! via a site-level diagnostic variable before reducing
! the number density.
currentSite%imort_rate(currentCohort%size_class, currentCohort%pft) = &
currentSite%imort_rate(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentPatch%fract_ldist_not_harvested * &
logging_coll_under_frac / hlm_freq_day
currentSite%imort_carbonflux(currentCohort%pft) = &
currentSite%imort_carbonflux(currentCohort%pft) + &
(nc%n * currentPatch%fract_ldist_not_harvested * &
logging_coll_under_frac/ hlm_freq_day ) * &
total_c * g_per_kg * days_per_sec * years_per_day * ha_per_m2
! Step 2: Apply survivor ship function based on the understory death fraction
! remaining of understory plants of those that are knocked
! over by the overstorey trees dying...
! LOGGING SURVIVORSHIP OF UNDERSTORY PLANTS IS SET AS A NEW PARAMETER
! in the fatesparameter files
nc%n = nc%n * (1.0_r8 - &
(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
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
nc%frmort = currentCohort%frmort
nc%smort = currentCohort%smort
nc%asmort = currentCohort%asmort
nc%dmort = currentCohort%dmort
nc%lmort_direct = currentCohort%lmort_direct
nc%lmort_collateral = currentCohort%lmort_collateral
nc%lmort_infra = currentCohort%lmort_infra
else
! grass is not killed by mortality disturbance events.
! Just move it into the new patch area.
! Just split the grass into the existing and new patch structures
nc%n = currentCohort%n * patch_site_areadis/currentPatch%area
! Those remaining in the existing
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)
! No grass impact mortality imposed on the newly created patch
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
nc%frmort = currentCohort%frmort
nc%smort = currentCohort%smort
nc%asmort = currentCohort%asmort
nc%dmort = currentCohort%dmort
nc%lmort_direct = currentCohort%lmort_direct
nc%lmort_collateral = currentCohort%lmort_collateral
nc%lmort_infra = currentCohort%lmort_infra
endif ! is/is-not woody
endif ! Select canopy layer
else
write(fates_log(),*) 'unknown disturbance mode?'
write(fates_log(),*) 'i_disturbance_type: ',i_disturbance_type
call endrun(msg=errMsg(sourcefile, __LINE__))