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Carbon starvation termination mortality reporting #1142

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merged 17 commits into from
Jan 30, 2024
Merged

Carbon starvation termination mortality reporting #1142

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5d0dddc
adding C-starvation termination mortality to carbon starvation diagno…
ckoven Oct 17, 2023
91bf5b4
Merge remote-tracking branch 'ckoven/cstarv_term_reporting' into jkow…
Nov 22, 2023
ad307d2
debug
Nov 22, 2023
019fa58
added comments
Nov 22, 2023
e5f6160
debug
Nov 22, 2023
ae8f117
bug fix
Dec 18, 2023
85e7c18
corrected comments
Dec 21, 2023
052d52c
fixed error in variable declaration, added c-starve related terminati…
Dec 21, 2023
d9113d1
bug fix
Dec 21, 2023
d9edfc5
bug fix; added error check for termination_type
Dec 21, 2023
f479db4
bug fix
Dec 21, 2023
d514afb
Merge tag 'sci.1.70.0_api.32.0.0' into jkowalcz-ckoven-cstarv_term_re…
glemieux Jan 4, 2024
27691d2
Merge tag 'sci.1.71.0_api.33.0.0' into jkowalcz-ckoven-cstarv_term_re…
glemieux Jan 18, 2024
a470a43
shorten history variable name
Jan 19, 2024
4d052e7
clean up loops to avoid duplication
Jan 19, 2024
d3e850e
update long name for termination mortality history variables
Jan 19, 2024
b01c842
update comments
Jan 19, 2024
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3 changes: 2 additions & 1 deletion biogeochem/EDCanopyStructureMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ module EDCanopyStructureMod
use PRTGenericMod, only : struct_organ
use PRTGenericMod, only : SetState
use PRTGenericMod, only : carbon12_element
use FatesConstantsMod, only : i_term_mort_type_canlev

! CIME Globals
use shr_log_mod , only : errMsg => shr_log_errMsg
Expand Down Expand Up @@ -736,7 +737,7 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr,bc_in)
if(currentCohort%canopy_layer>nclmax )then
! put the litter from the terminated cohorts
! straight into the fragmenting pools
call terminate_cohort(currentSite,currentPatch,currentCohort,bc_in)
call terminate_cohort(currentSite,currentPatch,currentCohort,bc_in,i_term_mort_type_canlev)
deallocate(currentCohort, stat=istat, errmsg=smsg)
if (istat/=0) then
write(fates_log(),*) 'dealloc012: fail on deallocate(currentCohort):'//trim(smsg)
Expand Down
36 changes: 27 additions & 9 deletions biogeochem/EDCohortDynamicsMod.F90
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Expand Up @@ -120,6 +120,10 @@ Module EDCohortDynamicsMod
use PRTAllometricCNPMod, only : acnp_bc_out_id_pefflux, acnp_bc_out_id_limiter
use PRTAllometricCNPMod, only : acnp_bc_in_id_cdamage
use DamageMainMod, only : undamaged_class
use FatesConstantsMod, only : n_term_mort_types
use FatesConstantsMod, only : i_term_mort_type_cstarv
use FatesConstantsMod, only : i_term_mort_type_canlev
use FatesConstantsMod, only : i_term_mort_type_numdens

use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
use shr_log_mod, only : errMsg => shr_log_errMsg
Expand Down Expand Up @@ -382,12 +386,14 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
integer :: terminate ! do we terminate (itrue) or not (ifalse)
integer :: istat ! return status code
character(len=255) :: smsg
integer :: termination_type
!----------------------------------------------------------------------

currentCohort => currentPatch%shortest
do while (associated(currentCohort))

terminate = ifalse
termination_type = 0
tallerCohort => currentCohort%taller

leaf_c = currentCohort%prt%GetState(leaf_organ, carbon12_element)
Expand All @@ -400,6 +406,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
! Check if number density is so low is breaks math (level 1)
if (currentcohort%n < min_n_safemath .and. level == 1) then
terminate = itrue
termination_type = i_term_mort_type_numdens
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 0',currentCohort%n/currentPatch%area,currentCohort%dbh,currentCohort%pft,call_index
endif
Expand All @@ -413,6 +420,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
currentCohort%n <= min_nppatch .or. &
(currentCohort%dbh < 0.00001_r8 .and. store_c < 0._r8) ) then
terminate = itrue
termination_type = i_term_mort_type_numdens
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 1',currentCohort%n/currentPatch%area,currentCohort%dbh,currentCohort%pft,call_index
endif
Expand All @@ -421,6 +429,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
! Outside the maximum canopy layer
if (currentCohort%canopy_layer > nclmax ) then
terminate = itrue
termination_type = i_term_mort_type_canlev
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 2', currentCohort%canopy_layer,currentCohort%pft,call_index
endif
Expand All @@ -430,6 +439,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
if ( ( sapw_c+leaf_c+fnrt_c ) < 1e-10_r8 .or. &
store_c < 1e-10_r8) then
terminate = itrue
termination_type = i_term_mort_type_cstarv
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 3', &
sapw_c,leaf_c,fnrt_c,store_c,currentCohort%pft,call_index
Expand All @@ -439,6 +449,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
! Total cohort biomass is negative
if ( ( struct_c+sapw_c+leaf_c+fnrt_c+store_c ) < 0._r8) then
terminate = itrue
termination_type = i_term_mort_type_cstarv
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 4', &
struct_c,sapw_c,leaf_c,fnrt_c,store_c,currentCohort%pft,call_index
Expand All @@ -448,7 +459,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
endif ! if (.not.currentCohort%isnew .and. level == 2) then

if (terminate == itrue) then
call terminate_cohort(currentSite, currentPatch, currentCohort, bc_in)
call terminate_cohort(currentSite, currentPatch, currentCohort, bc_in, termination_type)
deallocate(currentCohort, stat=istat, errmsg=smsg)
if (istat/=0) then
write(fates_log(),*) 'dealloc001: fail on terminate_cohorts:deallocate(currentCohort):'//trim(smsg)
Expand All @@ -461,7 +472,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
end subroutine terminate_cohorts

!-------------------------------------------------------------------------------------!
subroutine terminate_cohort(currentSite, currentPatch, currentCohort, bc_in)
subroutine terminate_cohort(currentSite, currentPatch, currentCohort, bc_in, termination_type)
!
! !DESCRIPTION:
! Terminates an individual cohort and updates the site-level
Expand All @@ -474,6 +485,7 @@ subroutine terminate_cohort(currentSite, currentPatch, currentCohort, bc_in)
type (fates_patch_type) , intent(inout), target :: currentPatch
type (fates_cohort_type), intent(inout), target :: currentCohort
type(bc_in_type), intent(in) :: bc_in
integer, intent(in) :: termination_type

! !LOCAL VARIABLES:
type (fates_cohort_type) , pointer :: shorterCohort
Expand All @@ -491,6 +503,12 @@ subroutine terminate_cohort(currentSite, currentPatch, currentCohort, bc_in)

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

! check termination_type; it should not be 0
if (termination_type == 0) then
write(fates_log(),*) 'termination_type=0'
call endrun(msg=errMsg(sourcefile, __LINE__))
endif

leaf_c = currentCohort%prt%GetState(leaf_organ, carbon12_element)
store_c = currentCohort%prt%GetState(store_organ, carbon12_element)
sapw_c = currentCohort%prt%GetState(sapw_organ, carbon12_element)
Expand All @@ -506,16 +524,16 @@ subroutine terminate_cohort(currentSite, currentPatch, currentCohort, bc_in)

! Update the site-level carbon flux and individuals count for the appropriate canopy layer
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_nindivs_canopy(termination_type,currentCohort%size_class,currentCohort%pft) = &
currentSite%term_nindivs_canopy(termination_type,currentCohort%size_class,currentCohort%pft) + currentCohort%n

currentSite%term_carbonflux_canopy(currentCohort%pft) = currentSite%term_carbonflux_canopy(currentCohort%pft) + &
currentSite%term_carbonflux_canopy(termination_type,currentCohort%pft) = currentSite%term_carbonflux_canopy(termination_type,currentCohort%pft) + &
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_nindivs_ustory(termination_type,currentCohort%size_class,currentCohort%pft) = &
currentSite%term_nindivs_ustory(termination_type,currentCohort%size_class,currentCohort%pft) + currentCohort%n

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

Expand Down Expand Up @@ -553,7 +571,7 @@ subroutine terminate_cohort(currentSite, currentPatch, currentCohort, bc_in)

call currentCohort%FreeMemory()

end subroutine terminate_cohort
end subroutine terminate_cohort

! =====================================================================================

Expand Down
17 changes: 9 additions & 8 deletions main/EDInitMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,7 @@ module EDInitMod
use PRTGenericMod, only : SetState
use FatesSizeAgeTypeIndicesMod,only : get_age_class_index
use DamageMainMod, only : undamaged_class
use FatesConstantsMod, only : n_term_mort_types
use FatesInterfaceTypesMod , only : hlm_num_luh2_transitions

! CIME GLOBALS
Expand Down Expand Up @@ -133,8 +134,8 @@ subroutine init_site_vars( site_in, bc_in, bc_out )
integer :: el

!
allocate(site_in%term_nindivs_canopy(1:nlevsclass,1:numpft))
allocate(site_in%term_nindivs_ustory(1:nlevsclass,1:numpft))
allocate(site_in%term_nindivs_canopy(1:n_term_mort_types,1:nlevsclass,1:numpft))
allocate(site_in%term_nindivs_ustory(1:n_term_mort_types,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))
Expand Down Expand Up @@ -170,8 +171,8 @@ subroutine init_site_vars( site_in, bc_in, bc_out )
allocate(site_in%fmort_cflux_ustory_damage(1,1))
end if

allocate(site_in%term_carbonflux_canopy(1:numpft))
allocate(site_in%term_carbonflux_ustory(1:numpft))
allocate(site_in%term_carbonflux_canopy(1:n_term_mort_types,1:numpft))
allocate(site_in%term_carbonflux_ustory(1:n_term_mort_types,1:numpft))
allocate(site_in%imort_carbonflux(1:numpft))
allocate(site_in%fmort_carbonflux_canopy(1:numpft))
allocate(site_in%fmort_carbonflux_ustory(1:numpft))
Expand Down Expand Up @@ -288,15 +289,15 @@ subroutine zero_site( site_in )
site_in%ema_npp = -9999.9_r8

! termination and recruitment info
site_in%term_nindivs_canopy(:,:) = 0._r8
site_in%term_nindivs_ustory(:,:) = 0._r8
site_in%term_nindivs_canopy(:,:,:) = 0._r8
site_in%term_nindivs_ustory(:,:,:) = 0._r8
site_in%term_crownarea_canopy = 0._r8
site_in%term_crownarea_ustory = 0._r8
site_in%imort_crownarea = 0._r8
site_in%fmort_crownarea_canopy = 0._r8
site_in%fmort_crownarea_ustory = 0._r8
site_in%term_carbonflux_canopy(:) = 0._r8
site_in%term_carbonflux_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
Expand Down
18 changes: 9 additions & 9 deletions main/EDTypesMod.F90
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Expand Up @@ -363,15 +363,15 @@ module EDTypesMod
real(r8) :: fmort_crownarea_canopy ! crownarea of canopy indivs killed due to fire per year. [m2/sec]
real(r8) :: fmort_crownarea_ustory ! crownarea of understory indivs killed due to fire per year [m2/sec]

real(r8), allocatable :: term_nindivs_canopy(:,:) ! number of canopy individuals that were in cohorts which
! were terminated this timestep, on size x pft
real(r8), allocatable :: term_nindivs_ustory(:,:) ! number of understory individuals that were in cohorts which
! were terminated this timestep, on size x pft

real(r8), allocatable :: term_carbonflux_canopy(:) ! carbon flux from live to dead pools associated
! with termination mortality, per canopy level. [kgC/ha/day]
real(r8), allocatable :: term_carbonflux_ustory(:) ! carbon flux from live to dead pools associated
! with termination mortality, per canopy level. [kgC/ha/day]
real(r8), allocatable :: term_nindivs_canopy(:,:,:) ! number of canopy individuals that were in cohorts which
! were terminated this timestep, by termination type, size x pft
real(r8), allocatable :: term_nindivs_ustory(:,:,:) ! number of understory individuals that were in cohorts which
! were terminated this timestep, by termination type, size x pft

real(r8), allocatable :: term_carbonflux_canopy(:,:) ! carbon flux from live to dead pools associated
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! with termination mortality, by termination type and per canopy level. [kgC/ha/day]
real(r8), allocatable :: term_carbonflux_ustory(:,:) ! carbon flux from live to dead pools associated
! with termination mortality, by termination type and per canopy level. [kgC/ha/day]
real(r8), allocatable :: imort_carbonflux(:) ! biomass of individuals killed due to impact mortality per year. [kgC/m2/sec]
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]
Expand Down
7 changes: 6 additions & 1 deletion main/FatesConstantsMod.F90
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Expand Up @@ -338,5 +338,10 @@ module FatesConstantsMod

real(fates_r8), parameter, public :: lmr_r_2 = -0.0402_fates_r8 ! (umol CO2/m**2/s/degree C)


! some integers related to termination mortality
integer, parameter, public :: n_term_mort_types = 3
integer, parameter, public :: i_term_mort_type_cstarv = 1
integer, parameter, public :: i_term_mort_type_canlev = 2
integer, parameter, public :: i_term_mort_type_numdens = 3

end module FatesConstantsMod
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