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Size- and age- dependent mortality #599

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merged 31 commits into from
Mar 26, 2020
Merged

Size- and age- dependent mortality #599

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7223c9b
Squashed commit of the following:
Jan 9, 2020
18bcd44
[ Fix bug in parameter file - cohort age classes must be defined ]
Jan 9, 2020
7b34903
[ Update FatesPFTindexSwapper to be compatible with python 3]
Jan 9, 2020
cfb431c
[ Change the logic for how the size and age mortality functions are
Jan 9, 2020
17a60ef
[Fix bug in FatesHistoryInterfaceMod ]
Jan 10, 2020
0789867
[Fix the small simple things like indentations and forgotten _r8s ]
Jan 17, 2020
d8e7935
[Change the switch for age dependent mortality ]
Jan 20, 2020
7a5bebe
[Update param file with metadata and add checks on param values ]
JessicaNeedham Jan 20, 2020
9e5ab32
[ Fix bug in flags for mortality params ]
Jan 21, 2020
b01c136
[In EDCohortDynamicsMod increase maxCohortsPerPatch to 300 if cohort
JessicaNeedham Jan 21, 2020
e45153c
[ More detailed flags for mortality parameter checks in
JessicaNeedham Jan 21, 2020
fb52c50
[ Change the cap on mortality ]
Jan 22, 2020
ab6fc20
[ Remove cap on mortality ]
Jan 23, 2020
dd28a9b
[Change check on initialised params to use the check_initialized
Jan 30, 2020
63c2958
[ Fix some minor bugs/make changes suggested by Rosie Fisher ]
JessicaNeedham Mar 11, 2020
774b105
[ Cohort age units to years ]
JessicaNeedham Mar 11, 2020
c83725a
[ Bug fix - .eqv. to .TRUE. for cohort_age_tracking check ]
JessicaNeedham Mar 11, 2020
aef198f
[Remove the cohort age tracking parameter and make
JessicaNeedham Mar 12, 2020
9345e67
[Fix bug with hlm_use_cohort_age_tracking flag ]
JessicaNeedham Mar 12, 2020
50f6efe
Merge remote-tracking branch 'ngeet_repo/master'
Mar 14, 2020
cbc4c17
Merge branch 'master' into JessicaNeedham-IO-sizeagemortality
Mar 14, 2020
54e8dfb
[Add one additional test to ensure age-dependent
JessicaNeedham Mar 17, 2020
fc733f9
[ Fix bug in error message for cohort age tracking flag ]
JessicaNeedham Mar 18, 2020
eed4545
[ifalse to 0 in a test of hlm_use_cohort_age_flag ]
Mar 18, 2020
22eb568
[ Update parameter file]
JessicaNeedham Mar 19, 2020
337ec13
[ Remove checks on cohort age bin edges ]
JessicaNeedham Mar 20, 2020
dd4d196
Merge branch 'master' into JessicaNeedham-IO-sizeagemortality-merged
rgknox Mar 24, 2020
f4afdf2
Fixed order of operations on mortality condition for age mortality, c…
rgknox Mar 24, 2020
cec41c7
Merge pull request #1 from rgknox/JessicaNeedham-IO-sizeagemortality-…
JessicaNeedham Mar 24, 2020
ee90e0f
[ Fix bug in mortality change in number density - logging
JessicaNeedham Mar 24, 2020
10809b9
[Change maxCohortsPerPatch back to 100]
JessicaNeedham Mar 26, 2020
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18 changes: 14 additions & 4 deletions biogeochem/EDCanopyStructureMod.F90
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Expand Up @@ -29,7 +29,8 @@ module EDCanopyStructureMod
use FatesInterfaceMod , only : numpft
use FatesPlantHydraulicsMod, only : UpdateH2OVeg,InitHydrCohort, RecruitWaterStorage
use EDTypesMod , only : maxCohortsPerPatch

use EDParamsMod , only : cohort_age_tracking

use PRTGenericMod, only : leaf_organ
use PRTGenericMod, only : all_carbon_elements
use PRTGenericMod, only : leaf_organ
Expand Down Expand Up @@ -1258,9 +1259,12 @@ subroutine canopy_summarization( nsites, sites, bc_in )
use FatesInterfaceMod , only : bc_in_type
use EDPatchDynamicsMod , only : set_patchno
use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
use EDtypesMod , only : area
use EDPftvarcon , only : EDPftvarcon_inst

use EDParamsMod , only : cohort_age_tracking
use FatesConstantsMod , only : itrue

! !ARGUMENTS
integer , intent(in) :: nsites
type(ed_site_type) , intent(inout), target :: sites(nsites)
Expand All @@ -1279,8 +1283,9 @@ subroutine canopy_summarization( nsites, sites, bc_in )
real(r8) :: sapw_c ! sapwood carbon [kg]
real(r8) :: store_c ! storage carbon [kg]
real(r8) :: struct_c ! structure carbon [kg]
!----------------------------------------------------------------------

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

if ( debug ) then
write(fates_log(),*) 'in canopy_summarization'
endif
Expand Down Expand Up @@ -1319,8 +1324,13 @@ subroutine canopy_summarization( nsites, sites, bc_in )
! Update the cohort's index within the size bin classes
! Update the cohort's index within the SCPF classification system
call sizetype_class_index(currentCohort%dbh,currentCohort%pft, &
currentCohort%size_class,currentCohort%size_by_pft_class)
currentCohort%size_class,currentCohort%size_by_pft_class)

if (cohort_age_tracking) then
call coagetype_class_index(currentCohort%coage,currentCohort%pft, &
currentCohort%coage_class,currentCohort%coage_by_pft_class)
end if

call carea_allom(currentCohort%dbh,currentCohort%n,sites(s)%spread,&
currentCohort%pft,currentCohort%c_area)

Expand Down
108 changes: 87 additions & 21 deletions biogeochem/EDCohortDynamicsMod.F90
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89 changes: 76 additions & 13 deletions biogeochem/EDMortalityFunctionsMod.F90
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Expand Up @@ -42,28 +42,34 @@ module EDMortalityFunctionsMod



subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )
subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmort )

! ============================================================================
! Calculate mortality rates from carbon storage, hydraulic cavitation,
! background and freezing
! background and freezing and size dependent senescence
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and size and age dependent senescence maybe?

Also, is it me, or is 'senescence' really, really, hard to spell?

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Added 'age' in there. And yes! It is a terrible word to have to type repeatedly.

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Ha ha. Glad it isn't just my brain senescing, or whatever.

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

use FatesConstantsMod, only : tfrz => t_water_freeze_k_1atm

use FatesInterfaceMod , only : hlm_hio_ignore_val

type (ed_cohort_type), intent(in) :: cohort_in
type (bc_in_type), intent(in) :: bc_in
real(r8),intent(out) :: bmort ! background mortality : Fraction per year
real(r8),intent(out) :: cmort ! carbon starvation mortality
real(r8),intent(out) :: hmort ! hydraulic failure mortality
real(r8),intent(out) :: frmort ! freezing stress mortality
real(r8),intent(out) :: smort ! size dependent senescence term
real(r8),intent(out) :: asmort ! age dependent senescence term

real(r8) :: frac ! relativised stored carbohydrate
real(r8) :: leaf_c_target ! target leaf biomass kgC
real(r8) :: store_c
real(r8) :: hf_sm_threshold ! hydraulic failure soil moisture threshold
real(r8) :: hf_flc_threshold ! hydraulic failure fractional loss of conductivity threshold
real(r8) :: mort_ip_size_senescence ! inflection point for increase in mortality with dbh
real(r8) :: mort_r_size_senescence ! rate of mortality increase with dbh in senesence term
real(r8) :: mort_ip_age_senescence ! inflection point for increase in mortality with age
real(r8) :: mort_r_age_senescence ! rate of mortality increase with age in senescence term
real(r8) :: temp_dep_fraction ! Temp. function (freezing mortality)
real(r8) :: temp_in_C ! Daily averaged temperature in Celcius
real(r8) :: min_fmc_ag ! minimum fraction of maximum conductivity for aboveground
Expand All @@ -75,12 +81,41 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )
logical, parameter :: test_zero_mortality = .false. ! Developer test which
! may help to debug carbon imbalances
! and the like

! Size Dependent Senescence
! rate (r) and inflection point (ip) define the increase in mortality rate with dbh
mort_r_size_senescence = EDPftvarcon_inst%mort_r_size_senescence(cohort_in%pft)
mort_ip_size_senescence = EDPftvarcon_inst%mort_ip_size_senescence(cohort_in%pft)

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I'm worried that a user will set mort_r_size_senescence to 0 and think that will turn off size dependent senescence. I think that value generates an smort of 0.5. Will check how this is read in.

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Lets add some metadata to the parameter value entry that explains _ turns this off, and what valid ranges are.
https://github.com/NGEET/fates/blob/master/parameter_files/fates_params_default.cdl#L322

There is also this subroutine here, a good place to check if fates parameters are in acceptable ranges (if for instance 0 is an unexpected/invalid, you can have fates gracefully complain and fail):

fates/main/EDPftvarcon.F90

Line 2071 in d8e7935

subroutine FatesCheckParams(is_master, parteh_mode)

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Sounds good. I'll add some metadata to the parameter value entry and some checks in FatesCheckParams.

! if param values have been set then calculate smort
if (mort_ip_size_senescence < 10000.0_r8 ) then
smort = 1.0_r8 / ( 1.0_r8 + exp( -1.0_r8 * mort_r_size_senescence * &
(cohort_in%dbh - mort_ip_size_senescence) ) )
else
smort = 0.0_r8
end if

! if user has set cohort age fusion param to not be _ we calculate age
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What is _ in this sentence? Also why doesn't this use 'cohort_age_tracking'?

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I've changed it to match the comment above for size mortality. The size and age dependent mortality parameters are _ by default in the parameter file. The user has to set them in order to turn on either mortality term. Cohort age tracking is turned on separately with the cohort_age_tracking parameter. This was in case anyone in the future wanted to track cohort age independently of having size or age mortality turned on.

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check_initialized is defined in PRTGenericMod.F90, but that check is designed to work in step with un_initialized. See here:

https://github.com/NGEET/fates/blob/master/parteh/PRTGenericMod.F90#L43

It only works in situations where we are defining uninitialized values with "un_initialized". In this case, the parameter values that have "_" from the file, are not the same as un_initialized.

I remember we thought it was 9.9E36, but there was some confusion if we were importing that value correctly... I had thought that "spval" from CLM/ELM would give us this value.

We have an "ignore" value for history, but that value is not necessarily the "no data" value we get from netcdf: https://github.com/NGEET/fates/blob/master/main/FatesInterfaceMod.F90#L94

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Ah ok, thank you. I misunderstood the un_initialized value. Would it make most sense then for me to define a local arbitrary large number to compare these parameters against, in order to check whether or not they have been set by the user in the parameter file?

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I think the fill values we were printing out when they made there way to FATES were 1E36 right? If so, I think this is is where it is defined...

https://github.com/ESCOMP/CTSM/blob/master/src/main/ncdio_pio.F90.in#L146

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If I print a parameter that is "_" in the parameter file I get 9.9692099...E+036.

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I think it is defined in ./cime/src/externals/pio2/src/flib/pio_types.F90 L234-235

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I've made a new variable called 'fates_check_param_set' defined in FatesConstantsMod to check whether the mortality parameters have been set. This might not be the way to go so happy to change it if there is a better way of doing things. But it seems to be working.

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@rgknox I think the discussion from yesterday is here.

! dependent mortality
if (mort_ip_age_senescence < 10000.0_r8) then
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Is it true that we only want to calculate an aging mortality rate if we are tracking aging and cohort_age_tracking is true? Should we be using that logical here?

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Yes, ageing mortality can only be calculated if cohort age tracking is on. I changed the logic so that cohort age tracking could be on without having ageing mortality. So now the 'cohort_age_tracking' parameter in the param file turns on cohort age tracking. And both size and age dependent mortality get turned on by setting the ip_age/size_senescence parameters. I can put in some flags so that the ip_age_senescence parameter can't be turned on without cohort_age_tracking being on.

! Age Dependent Senescence
! rate and inflection point define the change in mortality with age
mort_r_age_senescence = EDPftvarcon_inst%mort_r_age_senescence(cohort_in%pft)
mort_ip_age_senescence = EDPftvarcon_inst%mort_ip_age_senescence(cohort_in%pft)
asmort = 1.0_r8 / (1.0_r8 + exp(-1.0_r8 * mort_r_age_senescence * &
(cohort_in%coage - mort_ip_age_senescence ) ) )
else
asmort = 0.0_r8
end if

if (hlm_use_ed_prescribed_phys .eq. ifalse) then


if (hlm_use_ed_prescribed_phys .eq. ifalse) then

! 'Background' mortality (can vary as a function of
! density as in ED1.0 and ED2.0, but doesn't here for tractability)
bmort = EDPftvarcon_inst%bmort(cohort_in%pft)

bmort = EDPftvarcon_inst%bmort(cohort_in%pft)

! Proxy for hydraulic failure induced mortality.
hf_sm_threshold = EDPftvarcon_inst%hf_sm_threshold(cohort_in%pft)
Expand Down Expand Up @@ -141,9 +176,10 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )

!mortality_rates = bmort + hmort + cmort

else ! i.e. hlm_use_ed_prescribed_phys is true
else ! i.e. hlm_use_ed_prescribed_phys is true

if ( cohort_in%canopy_layer .eq. 1) then
bmort = EDPftvarcon_inst%prescribed_mortality_canopy(cohort_in%pft)
bmort = EDPftvarcon_inst%prescribed_mortality_canopy(cohort_in%pft)
else
bmort = EDPftvarcon_inst%prescribed_mortality_understory(cohort_in%pft)
endif
Expand All @@ -157,6 +193,8 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort )
hmort = 0.0_r8
frmort = 0.0_r8
bmort = 0.0_r8
smort = 0.0_r8
asmort = 0.0_r8
end if

return
Expand All @@ -174,6 +212,7 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
!
! !USES:

use FatesInterfaceMod, only : hlm_freq_day
!
! !ARGUMENTS
type(ed_site_type), intent(inout), target :: currentSite
Expand All @@ -185,6 +224,8 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
real(r8) :: bmort ! background mortality rate (fraction per year)
real(r8) :: hmort ! hydraulic failure mortality rate (fraction per year)
real(r8) :: frmort ! freezing mortality rate (fraction per year)
real(r8) :: smort ! size dependent senescence mortality rate (fraction per year)
real(r8) :: asmort ! age dependent senescence mortality rate (fraction per year)
real(r8) :: dndt_logging ! Mortality rate (per day) associated with the a logging event
integer :: ipft ! local copy of the pft index
!----------------------------------------------------------------------
Expand All @@ -193,7 +234,7 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)

! Mortality for trees in the understorey.
!if trees are in the canopy, then their death is 'disturbance'. This probably needs a different terminology
call mortality_rates(currentCohort,bc_in,cmort,hmort,bmort,frmort)
call mortality_rates(currentCohort,bc_in,cmort,hmort,bmort,frmort,smort, asmort)
call LoggingMortality_frac(ipft, currentCohort%dbh, currentCohort%canopy_layer, &
currentCohort%lmort_direct, &
currentCohort%lmort_collateral, &
Expand All @@ -206,14 +247,36 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
if (currentCohort%canopy_layer > 1)then
! Include understory logging mortality rates not associated with disturbance
dndt_logging = (currentCohort%lmort_direct + &
currentCohort%lmort_collateral + &
currentCohort%lmort_infra)/hlm_freq_day
currentCohort%dndt = -1.0_r8 * (cmort+hmort+bmort+frmort+dndt_logging) * currentCohort%n
currentCohort%lmort_collateral + &
currentCohort%lmort_infra)/hlm_freq_day

! this caps bmort so that daily mortality cannot exceed 0.995
if ((cmort+hmort+bmort+frmort+smort+asmort + dndt_logging)*hlm_freq_day &
> 1.0_r8)then
bmort = (1.0_r8 - ((cmort+hmort+asmort+frmort+smort+dndt_logging)*hlm_freq_day)) &
/hlm_freq_day
endif

currentCohort%dndt = -1.0_r8 * &
(cmort+hmort+bmort+frmort+smort+asmort + dndt_logging) &
* currentCohort%n
else

! cap on bmort for canopy layers - bmort is adjusted so that total mortality
! including disturbance fraction does not exceed 0.995
if(((cmort+hmort+bmort+frmort+smort+asmort)*hlm_freq_day) > &
1.0_r8 - fates_mortality_disturbance_fraction)then
bmort = (1.0_r8 - fates_mortality_disturbance_fraction - &
((cmort+hmort+asmort+frmort+smort)*hlm_freq_day))/hlm_freq_day
endif


! Mortality from logging in the canopy is ONLY disturbance generating, don't
! update number densities via non-disturbance inducing death
currentCohort%dndt = -(1.0_r8 - fates_mortality_disturbance_fraction) &
* (cmort+hmort+bmort+frmort) * currentCohort%n
currentCohort%dndt= -(1.0_r8-fates_mortality_disturbance_fraction) &
* (cmort+hmort+bmort+frmort+smort+asmort+dndt_logging) * &
currentCohort%n

endif

return
Expand Down
28 changes: 25 additions & 3 deletions biogeochem/EDPatchDynamicsMod.F90
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Expand Up @@ -158,6 +158,8 @@ subroutine disturbance_rates( site_in, bc_in)
real(r8) :: bmort
real(r8) :: hmort
real(r8) :: frmort
real(r8) :: smort
real(r8) :: asmort

real(r8) :: lmort_direct
real(r8) :: lmort_collateral
Expand All @@ -181,8 +183,8 @@ subroutine disturbance_rates( site_in, bc_in)
! Mortality for trees in the understorey.
currentCohort%patchptr => currentPatch

call mortality_rates(currentCohort,bc_in,cmort,hmort,bmort,frmort)
currentCohort%dmort = cmort+hmort+bmort+frmort
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)

Expand All @@ -191,6 +193,8 @@ subroutine disturbance_rates( site_in, bc_in)
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 )
Expand Down Expand Up @@ -287,6 +291,8 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort%bmort = currentCohort%bmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%dmort = currentCohort%dmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%frmort = currentCohort%frmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%smort = currentCohort%smort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%asmort = currentCohort%asmort*(1.0_r8 - fates_mortality_disturbance_fraction)
end if
currentCohort => currentCohort%taller
enddo !currentCohort
Expand All @@ -307,6 +313,8 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort%bmort = currentCohort%bmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%dmort = currentCohort%dmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%frmort = currentCohort%frmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%smort = currentCohort%smort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%asmort = currentCohort%asmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%lmort_direct = 0.0_r8
currentCohort%lmort_collateral = 0.0_r8
currentCohort%lmort_infra = 0.0_r8
Expand Down Expand Up @@ -621,6 +629,8 @@ subroutine spawn_patches( currentSite, bc_in)
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
Expand Down Expand Up @@ -673,6 +683,8 @@ subroutine spawn_patches( currentSite, bc_in)
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
Expand All @@ -697,6 +709,8 @@ subroutine spawn_patches( currentSite, bc_in)
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
Expand Down Expand Up @@ -752,6 +766,8 @@ subroutine spawn_patches( currentSite, bc_in)
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
Expand Down Expand Up @@ -825,6 +841,8 @@ subroutine spawn_patches( currentSite, bc_in)
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,
Expand Down Expand Up @@ -884,6 +902,8 @@ subroutine spawn_patches( currentSite, bc_in)
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
Expand All @@ -904,6 +924,8 @@ subroutine spawn_patches( currentSite, bc_in)
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
Expand Down Expand Up @@ -1958,7 +1980,7 @@ subroutine zero_patch(cp_p)


! FIRE
currentPatch%litter_moisture(:) = 0.0_r8 ! litter moisture
currentPatch%litter_moisture(:) = 0.0_r8 ! litter moisture
currentPatch%fuel_eff_moist = 0.0_r8 ! average fuel moisture content of the ground fuel
! (incl. live grasses. omits 1000hr fuels)
currentPatch%livegrass = 0.0_r8 ! total ag grass biomass in patch. 1=c3 grass, 2=c4 grass. gc/m2
Expand Down
4 changes: 2 additions & 2 deletions biogeochem/EDPhysiologyMod.F90
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Expand Up @@ -1361,6 +1361,7 @@ subroutine recruitment( currentSite, currentPatch, bc_in )
temp_cohort%canopy_trim = 0.8_r8 !starting with the canopy not fully expanded
temp_cohort%pft = ft
temp_cohort%hite = EDPftvarcon_inst%hgt_min(ft)
temp_cohort%coage = 0.0_r8
call h2d_allom(temp_cohort%hite,ft,temp_cohort%dbh)

! Initialize live pools
Expand Down Expand Up @@ -1460,7 +1461,6 @@ subroutine recruitment( currentSite, currentPatch, bc_in )
! Initialize the PARTEH object, and determine the initial masses of all
! organs and elements.
! -----------------------------------------------------------------------------

prt => null()
call InitPRTObject(prt)

Expand Down Expand Up @@ -1560,7 +1560,7 @@ subroutine recruitment( currentSite, currentPatch, bc_in )

! This initializes the cohort
call create_cohort(currentSite,currentPatch, temp_cohort%pft, temp_cohort%n, &
temp_cohort%hite, temp_cohort%dbh, prt, &
temp_cohort%hite, temp_cohort%coage, temp_cohort%dbh, prt, &
temp_cohort%laimemory, cohortstatus, recruitstatus, &
temp_cohort%canopy_trim, currentPatch%NCL_p, currentSite%spread, bc_in)

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