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Small updates to output variables, addition of FATES_FRACTION variable #854

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merged 10 commits into from
Jul 15, 2022
Merged

Small updates to output variables, addition of FATES_FRACTION variable #854

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a2eaf30
typo fix and remove 'event'
Jan 13, 2022
1c33686
update UNDERSTORY to USTORY
Feb 15, 2022
6a5d0c6
added FATES_FRACTION variable to keep track of what gridcell fraction…
ckoven Feb 15, 2022
d08dd7e
Merge branch 'fates_area_var' into history_interface_ilamb
Feb 15, 2022
dd380e5
update history variables
Mar 8, 2022
a318cfa
Merge branch 'master' into history_interface_ilamb
Apr 12, 2022
6ef2c84
Merge branch 'master' into history_interface_ilamb
glemieux May 31, 2022
8078b3a
adjusting check to avoid segfault if flush_to_zero is not present
glemieux Jun 1, 2022
e88d0fb
Merge tag 'sci.1.58.0_api.24.0.0' into history_interface_ilamb
glemieux Jul 6, 2022
9d9c192
zero cohort water balance error during cohort creation
glemieux Jul 8, 2022
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3 changes: 3 additions & 0 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -332,6 +332,9 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, coage, dbh, &
! This allocates array spaces
call InitHydrCohort(currentSite,new_cohort)

! zero out the water balance error
new_cohort%co_hydr%errh2o = 0._r8

! This calculates node heights
call UpdatePlantHydrNodes(new_cohort,new_cohort%pft, &
new_cohort%hite,currentSite%si_hydr)
Expand Down
53 changes: 37 additions & 16 deletions main/FatesHistoryInterfaceMod.F90
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Expand Up @@ -193,6 +193,8 @@ module FatesHistoryInterfaceMod
integer :: ih_area_plant_si
integer :: ih_area_trees_si

integer :: ih_fates_fraction_si

integer :: ih_cwd_elcwd

integer :: ih_litter_in_si ! carbon only
Expand Down Expand Up @@ -1504,7 +1506,7 @@ end subroutine flush_hvars
! =====================================================================================

subroutine set_history_var(this, vname, units, long, use_default, avgflag, vtype, &
hlms, upfreq, ivar, initialize, index)
hlms, upfreq, ivar, initialize, index, flush_to_zero)

use FatesUtilsMod, only : check_hlm_list
use FatesInterfaceTypesMod, only : hlm_name
Expand All @@ -1528,6 +1530,7 @@ subroutine set_history_var(this, vname, units, long, use_default, avgflag, vtype
! explict name (for fast reference during update)
! A zero is passed back when the variable is
! not used
logical, intent(in), optional :: flush_to_zero

! locals
integer :: ub1, lb1, ub2, lb2 ! Bounds for allocating the var
Expand All @@ -1539,8 +1542,15 @@ subroutine set_history_var(this, vname, units, long, use_default, avgflag, vtype
! Flushing to the ignore val coerces all FATES diagnostics to be
! relevant only on FATES sites. This way we do not average zero's
! at locations not on FATES columns
! We make one exception to this rule, for the fates_fraction variable. That way
! we can always know what fraction of the gridcell FATES is occupying.

flushval = hlm_hio_ignore_val
if (present(flush_to_zero)) then
if (flush_to_zero) then
flushval = 0.0_r8
endif
endif

write_var = check_hlm_list(trim(hlms), trim(hlm_name))
if( write_var ) then
Expand Down Expand Up @@ -1796,6 +1806,7 @@ subroutine update_history_dyn(this,nc,nsites,sites)
hio_trimming_si => this%hvars(ih_trimming_si)%r81d, &
hio_area_plant_si => this%hvars(ih_area_plant_si)%r81d, &
hio_area_trees_si => this%hvars(ih_area_trees_si)%r81d, &
hio_fates_fraction_si => this%hvars(ih_fates_fraction_si)%r81d, &
hio_canopy_spread_si => this%hvars(ih_canopy_spread_si)%r81d, &
hio_biomass_si_pft => this%hvars(ih_biomass_si_pft)%r82d, &
hio_leafbiomass_si_pft => this%hvars(ih_leafbiomass_si_pft)%r82d, &
Expand Down Expand Up @@ -2049,6 +2060,10 @@ subroutine update_history_dyn(this,nc,nsites,sites)

io_si = sites(s)%h_gid

! set the fates fraction to one, since it is zero on non-fates columns, &
! the average is the total gridcell fates fraction
hio_fates_fraction_si(io_si) = 1._r8

! Total carbon model error [kgC/day -> kgC/s]
hio_cbal_err_fates_si(io_si) = &
sites(s)%mass_balance(element_pos(carbon12_element))%err_fates / sec_per_day
Expand Down Expand Up @@ -2165,7 +2180,7 @@ subroutine update_history_dyn(this,nc,nsites,sites)
! 24hr veg temperature
hio_tveg24(io_si) = hio_tveg24(io_si) + &
(cpatch%tveg24%GetMean()- t_water_freeze_k_1atm)*cpatch%area*AREA_INV

! Increment some patch-age-resolved diagnostics

hio_lai_si_age(io_si,cpatch%age_class) = hio_lai_si_age(io_si,cpatch%age_class) &
Expand Down Expand Up @@ -3606,7 +3621,7 @@ subroutine update_history_hifrq(this,nc,nsites,sites,bc_in,dt_tstep)
hio_parsun_top_si_can => this%hvars(ih_parsun_top_si_can)%r82d, &
hio_parsha_top_si_can => this%hvars(ih_parsha_top_si_can)%r82d, &
hio_tveg => this%hvars(ih_tveg_si)%r81d)

! Flush the relevant history variables
call this%flush_hvars(nc,upfreq_in=2)

Expand Down Expand Up @@ -4436,6 +4451,12 @@ subroutine define_history_vars(this, initialize_variables)
upfreq=1, ivar=ivar, initialize=initialize_variables, &
index=ih_area_trees_si)

call this%set_history_var(vname='FATES_FRACTION', units='m2 m-2', &
long='total gridcell fraction which FATES is running over', use_default='active', &
avgflag='A', vtype=site_r8, hlms='CLM:ALM', &
upfreq=1, ivar=ivar, initialize=initialize_variables, &
index=ih_fates_fraction_si, flush_to_zero=.true.)

call this%set_history_var(vname='FATES_COLD_STATUS', units='', &
long='site-level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not too cold', &
use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM', &
Expand Down Expand Up @@ -4755,7 +4776,7 @@ subroutine define_history_vars(this, initialize_variables)
avgflag='A', vtype=site_r8, hlms='CLM:ALM', upfreq=1, ivar=ivar, &
initialize=initialize_variables, index = ih_fire_fuel_eff_moist_si)

call this%set_history_var(vname='FATES_FUEL_SAV', units='per m', &
call this%set_history_var(vname='FATES_FUEL_SAV', units='m-1', &
long='spitfire fuel surface area to volume ratio', &
use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM', &
upfreq=1, ivar=ivar, initialize=initialize_variables, &
Expand Down Expand Up @@ -5162,19 +5183,19 @@ subroutine define_history_vars(this, initialize_variables)
ivar=ivar, initialize=initialize_variables, index = ih_c_lblayer_si)

! Temperature

call this%set_history_var(vname='FATES_TVEG24', units='degree_Celsius', &
long='fates 24-hr running mean vegetation temperature by site', &
use_default='active', &
avgflag='A', vtype=site_r8, hlms='CLM:ALM', upfreq=1, &
ivar=ivar, initialize=initialize_variables, index = ih_tveg24_si )

call this%set_history_var(vname='FATES_TVEG', units='degree_Celsius', &
long='fates instantaneous mean vegetation temperature by site', &
use_default='active', &
avgflag='A', vtype=site_r8, hlms='CLM:ALM', upfreq=2, &
ivar=ivar, initialize=initialize_variables, index = ih_tveg_si )

! radiation error

call this%set_history_var(vname='FATES_RAD_ERROR', units='W m-2 ', &
Expand Down Expand Up @@ -5254,14 +5275,14 @@ subroutine define_history_vars(this, initialize_variables)
upfreq=2, ivar=ivar, initialize=initialize_variables, &
index = ih_ar_canopy_si)

call this%set_history_var(vname='FATES_GPP_UNDERSTORY', &
call this%set_history_var(vname='FATES_GPP_USTORY', &
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units='kg m-2 s-1', &
long='gross primary production of understory plants in kg carbon per m2 per second', &
use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM', &
upfreq=2, ivar=ivar, initialize=initialize_variables, &
index = ih_gpp_understory_si)

call this%set_history_var(vname='FATES_AUTORESP_UNDERSTORY', &
call this%set_history_var(vname='FATES_AUTORESP_USTORY', &
units='kg m-2 s-1', &
long='autotrophic respiration of understory plants in kg carbon per m2 per second', &
use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM', &
Expand Down Expand Up @@ -5481,7 +5502,7 @@ subroutine define_history_vars(this, initialize_variables)
upfreq=1, ivar=ivar, initialize=initialize_variables, &
index = ih_canopy_mortality_carbonflux_si)

call this%set_history_var(vname='FATES_MORTALITY_CFLUX_UNDERSTORY', &
call this%set_history_var(vname='FATES_MORTALITY_CFLUX_USTORY', &
units = 'kg m-2 s-1', &
long='flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbon per m2 per second', &
use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM', &
Expand Down Expand Up @@ -5802,7 +5823,7 @@ subroutine define_history_vars(this, initialize_variables)

call this%set_history_var(vname='FATES_MORTALITY_LOGGING_SZPF', &
units = 'm-2 yr-1', &
long='logging mortality by pft/size in number of plants per m2 per ', &
long='logging mortality by pft/size in number of plants per m2 per year', &
use_default='inactive', &
avgflag='A', vtype=site_size_pft_r8, hlms='CLM:ALM', upfreq=1, &
ivar=ivar, initialize=initialize_variables, index = ih_m7_si_scpf)
Expand Down Expand Up @@ -6167,21 +6188,21 @@ subroutine define_history_vars(this, initialize_variables)

call this%set_history_var(vname='FATES_MORTALITY_LOGGING_SZ', &
units = 'm-2 yr-1', &
long='logging mortality by size in number of plants per m2 per event', &
long='logging mortality by size in number of plants per m2 per year', &
use_default='active', avgflag='A', vtype=site_size_r8, &
hlms='CLM:ALM', upfreq=1, ivar=ivar, &
initialize=initialize_variables, index = ih_m7_si_scls)

call this%set_history_var(vname='FATES_MORTALITY_FREEZING_SZ', &
units = 'm-2 event-1', &
long='freezing mortality by size in number of plants per m2 per event', &
units = 'm-2 yr-1', &
long='freezing mortality by size in number of plants per m2 per year', &
use_default='active', avgflag='A', vtype=site_size_r8, &
hlms='CLM:ALM', upfreq=1, ivar=ivar, &
initialize=initialize_variables, index = ih_m8_si_scls)

call this%set_history_var(vname='FATES_MORTALITY_SENESCENCE_SZ', &
units = 'm-2 yr-1', &
long='senescence mortality by size in number of plants per m2 per event', &
long='senescence mortality by size in number of plants per m2 per year', &
use_default='active', avgflag='A', vtype=site_size_r8, &
hlms='CLM:ALM', upfreq=1, ivar=ivar, &
initialize=initialize_variables, index = ih_m9_si_scls)
Expand Down Expand Up @@ -6775,7 +6796,7 @@ subroutine define_history_vars(this, initialize_variables)
hlms='CLM:ALM', upfreq=1, ivar=ivar, &
initialize=initialize_variables, index = ih_storeptfrac_canopy_scpf)

call this%set_history_var(vname='FATES_STOREP_TF_USTORY_SZPF', &
call this%set_history_var(vname='FATES_STOREP_TF_USTORY_SZPF', &
units='1', &
long='storage phosphorus fraction (0-1) of target, in understory, by size-class x pft', &
use_default='inactive', avgflag='A', vtype=site_size_pft_r8, &
Expand Down