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Add mortality and productivity aboveground carbon fluxes as history variables #926

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merged 9 commits into from
Feb 2, 2023
Merged

Add mortality and productivity aboveground carbon fluxes as history variables #926

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0bef167
Add two new history variables - aboveground woody mortality and
Oct 15, 2022
f8910dc
[ Shorten history names - too many characters was causing an error ]
JessicaNeedham Oct 18, 2022
f972400
[ Tidy up names, add leaves ]
JessicaNeedham Oct 21, 2022
8a07cbd
[ Add termination mortality to total carbon flux mortality ]
JessicaNeedham Oct 21, 2022
4010842
[ Tidy up spacing ]
JessicaNeedham Oct 21, 2022
9f228fd
[ Remove repro_m that wasn't needed ]
JessicaNeedham Oct 21, 2022
891bbf8
Merge branch 'master' into JessicaNeedham-IO-bagw-vars
Nov 3, 2022
47c539a
remove extra closing paranthesis in associate statement
glemieux Jan 31, 2023
6422668
add missing line continuation in restart
glemieux Feb 1, 2023
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6 changes: 6 additions & 0 deletions biogeochem/EDCohortDynamicsMod.F90
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Expand Up @@ -873,6 +873,12 @@ subroutine terminate_cohort(currentSite, currentPatch, currentCohort, bc_in)
currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
end if

currentSite%term_abg_flux(currentCohort%size_class, currentCohort%pft) = &
currentSite%term_abg_flux(currentCohort%size_class, currentCohort%pft) + &
currentCohort%n * ( (struct_c+sapw_c+store_c) * prt_params%allom_agb_frac(currentCohort%pft) + &
leaf_c )


! put the litter from the terminated cohorts
! straight into the fragmenting pools

Expand Down
16 changes: 16 additions & 0 deletions biogeochem/EDPatchDynamicsMod.F90
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Expand Up @@ -725,6 +725,14 @@ subroutine spawn_patches( currentSite, bc_in)
(nc%n * ED_val_understorey_death / hlm_freq_day ) * &
total_c * g_per_kg * days_per_sec * years_per_day * ha_per_m2

currentSite%imort_abg_flux(currentCohort%size_class, currentCohort%pft) = &
currentSite%imort_abg_flux(currentCohort%size_class, currentCohort%pft) + &
(nc%n * ED_val_understorey_death / hlm_freq_day ) * &
( (sapw_c + struct_c + store_c) * prt_params%allom_agb_frac(currentCohort%pft) + &
leaf_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...
Expand Down Expand Up @@ -815,6 +823,14 @@ subroutine spawn_patches( currentSite, bc_in)
total_c * g_per_kg * days_per_sec * ha_per_m2
end if

currentSite%fmort_abg_flux(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_abg_flux(currentCohort%size_class, currentCohort%pft) + &
(nc%n * currentCohort%fire_mort) * &
( (sapw_c + struct_c + store_c) * prt_params%allom_agb_frac(currentCohort%pft) + &
leaf_c ) * &
g_per_kg * days_per_sec * ha_per_m2


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
Expand Down
8 changes: 8 additions & 0 deletions main/EDInitMod.F90
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Expand Up @@ -162,6 +162,10 @@ subroutine init_site_vars( site_in, bc_in, bc_out )
allocate(site_in%fmort_carbonflux_canopy(1:numpft))
allocate(site_in%fmort_carbonflux_ustory(1:numpft))

allocate(site_in%term_abg_flux(1:nlevsclass,1:numpft))
allocate(site_in%imort_abg_flux(1:nlevsclass,1:numpft))
allocate(site_in%fmort_abg_flux(1:nlevsclass,1:numpft))

site_in%nlevsoil = bc_in%nlevsoil
allocate(site_in%rootfrac_scr(site_in%nlevsoil))
allocate(site_in%zi_soil(0:site_in%nlevsoil))
Expand Down Expand Up @@ -277,6 +281,10 @@ subroutine zero_site( site_in )
site_in%fmort_carbonflux_ustory(:) = 0._r8
site_in%fmort_rate_cambial(:,:) = 0._r8
site_in%fmort_rate_crown(:,:) = 0._r8
site_in%term_abg_flux(:,:) = 0._r8
site_in%imort_abg_flux(:,:) = 0._r8
site_in%fmort_abg_flux(:,:) = 0._r8


! fusoin-induced growth flux of individuals
site_in%growthflux_fusion(:,:) = 0._r8
Expand Down
5 changes: 5 additions & 0 deletions main/EDTypesMod.F90
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Expand Up @@ -808,6 +808,11 @@ module EDTypesMod
real(r8), allocatable :: fmort_carbonflux_canopy(:) ! biomass of canopy indivs killed due to fire per year. [gC/m2/sec]
real(r8), allocatable :: fmort_carbonflux_ustory(:) ! biomass of understory indivs killed due to fire per year [gC/m2/sec]

real(r8), allocatable :: term_abg_flux(:,:) ! aboveground biomass lost due to termination mortality x size x pft
real(r8), allocatable :: imort_abg_flux(:,:) ! aboveground biomass lost due to impact mortality x size x pft
real(r8), allocatable :: fmort_abg_flux(:,:) ! aboveground biomass lost due to fire mortality x size x pft


real(r8) :: demotion_carbonflux ! biomass of demoted individuals from canopy to understory [kgC/ha/day]
real(r8) :: promotion_carbonflux ! biomass of promoted individuals from understory to canopy [kgC/ha/day]
real(r8) :: recruitment_rate(1:maxpft) ! number of individuals that were recruited into new cohorts
Expand Down
60 changes: 58 additions & 2 deletions main/FatesHistoryInterfaceMod.F90
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Expand Up @@ -426,6 +426,9 @@ module FatesHistoryInterfaceMod
integer :: ih_crownfiremort_si_scpf
integer :: ih_cambialfiremort_si_scpf

integer :: ih_abg_mortality_cflux_si_scpf
integer :: ih_abg_productivity_cflux_si_scpf

integer :: ih_m10_si_capf
integer :: ih_nplant_si_capf

Expand Down Expand Up @@ -2068,6 +2071,9 @@ subroutine update_history_dyn(this,nc,nsites,sites)
hio_crownfiremort_si_scpf => this%hvars(ih_crownfiremort_si_scpf)%r82d, &
hio_cambialfiremort_si_scpf => this%hvars(ih_cambialfiremort_si_scpf)%r82d, &

hio_abg_mortality_cflux_si_scpf => this%hvars(ih_abg_mortality_cflux_si_scpf)%r82d, &
hio_abg_productivity_cflux_si_scpf => this%hvars(ih_abg_productivity_cflux_si_scpf)%r82d, &

hio_fire_c_to_atm_si => this%hvars(ih_fire_c_to_atm_si)%r81d, &
hio_burn_flux_elem => this%hvars(ih_burn_flux_elem)%r82d, &

Expand Down Expand Up @@ -2694,6 +2700,7 @@ subroutine update_history_dyn(this,nc,nsites,sites)
hio_npp_stor_si_scpf(io_si,scpf) = hio_npp_stor_si_scpf(io_si,scpf) + &
store_m_net_alloc*n_perm2 / days_per_year / sec_per_day


! Woody State Variables (basal area growth increment)
if ( prt_params%woody(ft) == itrue) then

Expand Down Expand Up @@ -2744,6 +2751,9 @@ subroutine update_history_dyn(this,nc,nsites,sites)
ccohort%asmort*ccohort%n / m2_per_ha
end if




hio_m1_si_scls(io_si,scls) = hio_m1_si_scls(io_si,scls) + ccohort%bmort*ccohort%n / m2_per_ha
hio_m2_si_scls(io_si,scls) = hio_m2_si_scls(io_si,scls) + ccohort%hmort*ccohort%n / m2_per_ha
hio_m3_si_scls(io_si,scls) = hio_m3_si_scls(io_si,scls) + ccohort%cmort*ccohort%n / m2_per_ha
Expand Down Expand Up @@ -2821,12 +2831,30 @@ subroutine update_history_dyn(this,nc,nsites,sites)
(ccohort%lmort_direct + ccohort%lmort_collateral + ccohort%lmort_infra) * total_m * &
ccohort%n * ha_per_m2


hio_hydraulicmortality_carbonflux_si_pft(io_si,ccohort%pft) = hio_hydraulicmortality_carbonflux_si_pft(io_si,ccohort%pft) + &
ccohort%hmort * total_m * ccohort%n * days_per_sec * years_per_day * ha_per_m2

hio_cstarvmortality_carbonflux_si_pft(io_si,ccohort%pft) = hio_cstarvmortality_carbonflux_si_pft(io_si,ccohort%pft) + &
ccohort%cmort * total_m * ccohort%n * days_per_sec * years_per_day * ha_per_m2

! Aboveground mortality
hio_abg_mortality_cflux_si_scpf(io_si,scpf) = hio_abg_mortality_cflux_si_scpf(io_si,scpf) + &
(ccohort%bmort + ccohort%hmort + ccohort%cmort + &
ccohort%frmort + ccohort%smort + ccohort%asmort) * &
( (sapw_m + struct_m + store_m ) * prt_params%allom_agb_frac(ccohort%pft) + &
leaf_m ) * ccohort%n * days_per_sec * years_per_day * ha_per_m2 + &
(ccohort%lmort_direct + ccohort%lmort_collateral + ccohort%lmort_infra) * &
( (sapw_m + struct_m + store_m ) * prt_params%allom_agb_frac(ccohort%pft) + &
leaf_m ) * ccohort%n * ha_per_m2

! Aboveground woody productivity
hio_abg_productivity_cflux_si_scpf(io_si,scpf) = hio_abg_productivity_cflux_si_scpf(io_si,scpf) + &
( (sapw_m_net_alloc + struct_m_net_alloc + store_m_net_alloc) * prt_params%allom_agb_frac(ccohort%pft) + &
leaf_m_net_alloc ) * n_perm2 / &
days_per_year / sec_per_day


! number density by size and biomass
hio_agb_si_scls(io_si,scls) = hio_agb_si_scls(io_si,scls) + &
total_m * ccohort%n * prt_params%allom_agb_frac(ccohort%pft) * AREA_INV
Expand Down Expand Up @@ -3239,6 +3267,7 @@ subroutine update_history_dyn(this,nc,nsites,sites)
cpatch => cpatch%younger
end do patchloop !patch loop


! divide basal-area-weighted height by basal area to get mean
if ( sum(hio_ba_si_scpf(io_si,:)) .gt. nearzero ) then
hio_ba_weighted_height_si(io_si) = hio_ba_weighted_height_si(io_si) / sum(hio_ba_si_scpf(io_si,:))
Expand Down Expand Up @@ -3363,11 +3392,23 @@ subroutine update_history_dyn(this,nc,nsites,sites)
hio_mortality_carbonflux_si_pft(io_si,i_pft) = hio_mortality_carbonflux_si_pft(io_si,i_pft) + &
(sites(s)%fmort_carbonflux_canopy(i_pft) + &
sites(s)%fmort_carbonflux_ustory(i_pft) + &
sites(s)%imort_carbonflux(i_pft) ) / g_per_kg !cdk

sites(s)%imort_carbonflux(i_pft) ) / g_per_kg ! cdk
hio_firemortality_carbonflux_si_pft(io_si,i_pft) = sites(s)%fmort_carbonflux_canopy(i_pft) / g_per_kg
end do

! add imort and fmort to aboveground woody mortality
do i_pft = 1, numpft
do i_scls = 1,nlevsclass
i_scpf = (i_pft-1)*nlevsclass + i_scls
hio_abg_mortality_cflux_si_scpf(io_si,i_scpf) = hio_abg_mortality_cflux_si_scpf(io_si,i_scpf) + &
(sites(s)%fmort_abg_flux(i_scls,i_pft) / g_per_kg ) + &
(sites(s)%imort_abg_flux(i_scls,i_pft) / g_per_kg) + &
(sites(s)%term_abg_flux(i_scls,i_pft) * days_per_sec * ha_per_m2 ) ! jfn
end do
end do


if(hlm_use_tree_damage .eq. itrue) then

do i_pft = 1, numpft
Expand Down Expand Up @@ -3413,6 +3454,9 @@ subroutine update_history_dyn(this,nc,nsites,sites)
sites(s)%fmort_rate_cambial(:,:) = 0._r8
sites(s)%fmort_rate_crown(:,:) = 0._r8
sites(s)%growthflux_fusion(:,:) = 0._r8
sites(s)%fmort_abg_flux(:,:) = 0._r8
sites(s)%imort_abg_flux(:,:) = 0._r8
sites(s)%term_abg_flux(:,:) = 0._r8

sites(s)%imort_rate_damage(:,:,:) = 0.0_r8
sites(s)%term_nindivs_canopy_damage(:,:,:) = 0.0_r8
Expand Down Expand Up @@ -5902,6 +5946,18 @@ subroutine define_history_vars(this, initialize_variables)
upfreq=1, ivar=ivar, initialize=initialize_variables, &
index=ih_cstarvmortality_carbonflux_si_pft)

call this%set_history_var(vname='FATES_ABOVEGROUND_MORT_SZPF', units='kg m-2 s-1', &
long='Aboveground flux of carbon from AGB to necromass due to mortality', &
use_default='inactive', avgflag='A', vtype=site_size_pft_r8, hlms='CLM:ALM', &
upfreq=1, ivar=ivar, initialize=initialize_variables, &
index=ih_abg_mortality_cflux_si_scpf)

call this%set_history_var(vname='FATES_ABOVEGROUND_PROD_SZPF', units='kg m-2 s-1', &
long='Aboveground carbon productivity', &
use_default='inactive', avgflag='A', vtype=site_size_pft_r8, hlms='CLM:ALM', &
upfreq=1, ivar=ivar, initialize=initialize_variables, &
index=ih_abg_productivity_cflux_si_scpf)

call this%set_history_var(vname='MORTALITY_CROWNAREA_CANOPY', &
units = 'm2/ha/year', &
long='Crown area of canopy trees that died', &
Expand Down
38 changes: 36 additions & 2 deletions main/FatesRestartInterfaceMod.F90
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Expand Up @@ -221,6 +221,9 @@ module FatesRestartInterfaceMod
integer :: ir_imortcflux_sipft
integer :: ir_fmortcflux_cano_sipft
integer :: ir_fmortcflux_usto_sipft
integer :: ir_abg_term_flux_siscpf
integer :: ir_abg_imort_flux_siscpf
integer :: ir_abg_fmort_flux_siscpf

integer :: ir_cwdagin_flxdg
integer :: ir_cwdbgin_flxdg
Expand Down Expand Up @@ -1284,7 +1287,22 @@ subroutine define_restart_vars(this, initialize_variables)
call this%set_restart_var(vname='fates_termcflux_ustory', vtype=cohort_r8, &
long_name='fates diagnostic term carbon flux understory', &
units='', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_termcflux_usto_sipft )
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_termcflux_usto_sipft )

call this%set_restart_var(vname='fates_abg_term_flux', vtype=cohort_r8, &
long_name='fates aboveground biomass loss from termination mortality', &
units='', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_abg_term_flux_siscpf )

call this%set_restart_var(vname='fates_abg_imort_flux', vtype=cohort_r8, &
long_name='fates aboveground biomass loss from impact mortality', &
units='', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_abg_imort_flux_siscpf )

call this%set_restart_var(vname='fates_abg_fmort_flux', vtype=cohort_r8, &
long_name='fates aboveground biomass loss from fire mortality', &
units='', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_abg_fmort_flux_siscpf )

call this%set_restart_var(vname='fates_democflux', vtype=site_r8, &
long_name='fates diagnostic demotion carbon flux', &
Expand Down Expand Up @@ -1958,6 +1976,10 @@ subroutine set_restart_vectors(this,nc,nsites,sites)
rio_imortcflux_sipft => this%rvars(ir_imortcflux_sipft)%r81d, &
rio_fmortcflux_cano_sipft => this%rvars(ir_fmortcflux_cano_sipft)%r81d, &
rio_fmortcflux_usto_sipft => this%rvars(ir_fmortcflux_usto_sipft)%r81d, &
rio_abg_imort_flux_siscpf => this%rvars(ir_abg_imort_flux_siscpf)%r81d, &
rio_abg_fmort_flux_siscpf => this%rvars(ir_abg_fmort_flux_siscpf)%r81d, &
rio_abg_term_flux_siscpf => this%rvars(ir_abg_term_flux_siscpf)%r81d, &

rio_imortrate_sicdpf => this%rvars(ir_imortrate_sicdpf)%r81d, &
rio_imortcflux_sicdsc => this%rvars(ir_imortcflux_sicdsc)%r81d, &
rio_termcflux_cano_sicdsc => this%rvars(ir_termcflux_cano_sicdsc)%r81d, &
Expand Down Expand Up @@ -2346,6 +2368,10 @@ subroutine set_restart_vectors(this,nc,nsites,sites)
rio_termnindiv_usto_siscpf(io_idx_si_scpf) = sites(s)%term_nindivs_ustory(i_scls,i_pft)
rio_growflx_fusion_siscpf(io_idx_si_scpf) = sites(s)%growthflux_fusion(i_scls, i_pft)

rio_abg_term_flux_siscpf(io_idx_si_scpf) = sites(s)%term_abg_flux(i_scls, i_pft)
rio_abg_imort_flux_siscpf(io_idx_si_scpf) = sites(s)%imort_abg_flux(i_scls, i_pft)
rio_abg_fmort_flux_siscpf(io_idx_si_scpf) = sites(s)%fmort_abg_flux(i_scls, i_pft)

io_idx_si_scpf = io_idx_si_scpf + 1
end do

Expand Down Expand Up @@ -2864,7 +2890,10 @@ subroutine get_restart_vectors(this, nc, nsites, sites)
rio_crownarea_usto_damage_si=> this%rvars(ir_crownarea_usto_si)%r81d, &
rio_imortcflux_sipft => this%rvars(ir_imortcflux_sipft)%r81d, &
rio_fmortcflux_cano_sipft => this%rvars(ir_fmortcflux_cano_sipft)%r81d, &
rio_fmortcflux_usto_sipft => this%rvars(ir_fmortcflux_usto_sipft)%r81d)
rio_fmortcflux_usto_sipft => this%rvars(ir_fmortcflux_usto_sipft)%r81d, &
rio_abg_term_flux_siscpf => this%rvars(ir_abg_term_flux_siscpf)%r81d, &
rio_abg_imort_flux_siscpf => this%rvars(ir_abg_imort_flux_siscpf)%r81d, &
rio_abg_fmort_flux_siscpf => this%rvars(ir_abg_fmort_flux_siscpf)%r81d )


totalcohorts = 0
Expand Down Expand Up @@ -3278,6 +3307,11 @@ subroutine get_restart_vectors(this, nc, nsites, sites)
sites(s)%term_nindivs_canopy(i_scls,i_pft) = rio_termnindiv_cano_siscpf(io_idx_si_scpf)
sites(s)%term_nindivs_ustory(i_scls,i_pft) = rio_termnindiv_usto_siscpf(io_idx_si_scpf)
sites(s)%growthflux_fusion(i_scls, i_pft) = rio_growflx_fusion_siscpf(io_idx_si_scpf)

sites(s)%term_abg_flux(i_scls,i_pft) = rio_abg_term_flux_siscpf(io_idx_si_scpf)
sites(s)%imort_abg_flux(i_scls,i_pft) = rio_abg_imort_flux_siscpf(io_idx_si_scpf)
sites(s)%fmort_abg_flux(i_scls,i_pft) = rio_abg_fmort_flux_siscpf(io_idx_si_scpf)

io_idx_si_scpf = io_idx_si_scpf + 1
end do

Expand Down