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Multiple updates to drought deciduous phenology #801

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Multiple updates to drought deciduous phenology #801

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229b5dc
Added LAI by size class and PFT to the list of output variables.
mpaiao Aug 13, 2021
d44620c
A few bug fixes and updates in carbon allocation (see issue #784).
mpaiao Oct 30, 2021
9ee0831
First set of changes in the drought deciduous phenology to improve it…
mpaiao Oct 30, 2021
3ebf2b9
Merge branch 'master' into carbon-alloc
mpaiao Oct 30, 2021
1df54a4
Merge branch 'master' into drgt-decid
mpaiao Oct 30, 2021
cf6b05b
Updated reproduction, the routine had not been updated with the new d…
mpaiao Nov 1, 2021
aabf4fe
Merge branch 'drgt-decid' of https://github.com/mpaiao/fates into drg…
mpaiao Nov 1, 2021
4eba25f
Added option (hlm_parteh_mode = 0) to use the simpler carbon allocati…
mpaiao Nov 3, 2021
45f5584
Merge branch 'carbon-alloc' into drgt-decid
mpaiao Nov 3, 2021
40bb0cc
Merge branch 'carbon-alloc' of https://github.com/mpaiao/fates into c…
mpaiao Nov 3, 2021
089bf23
Resolved conflict that I had forgotten to resolve.
mpaiao Nov 3, 2021
befe169
Merge branch 'carbon-alloc' into drgt-decid
mpaiao Nov 3, 2021
944455a
Fixed ctrl-c ctrl-v mistake when resolving conflicts (sigh).
mpaiao Nov 3, 2021
b98a3db
Merge branch 'carbon-alloc' into drgt-decid
mpaiao Nov 3, 2021
0ad213d
Deleted if statement that was replaced with select case (sigh again).
mpaiao Nov 3, 2021
ff3fa95
Merge branch 'carbon-alloc' into drgt-decid
mpaiao Nov 3, 2021
d653c83
Fixing another typo in PRTParamsFATESMod.F90 (forgot to replace end i…
mpaiao Nov 3, 2021
9e0896f
Merge branch 'carbon-alloc' into drgt-decid
mpaiao Nov 3, 2021
80377eb
Revised soil water stress tracking for drought deciduous.
mpaiao Nov 11, 2021
f3643aa
Added option for semi-drought deciduous, similar to the ED2 drought d…
mpaiao Feb 15, 2022
a97fb77
Merge branch 'mainline' into drgt-decid
mpaiao Apr 1, 2022
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84 changes: 66 additions & 18 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@ module EDCohortDynamicsMod
use FatesAllometryMod , only : tree_lai, tree_sai
use FatesAllometryMod , only : set_root_fraction
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_csimpler_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : prt_vartypes
use PRTGenericMod, only : all_carbon_elements
Expand All @@ -85,14 +86,21 @@ module EDCohortDynamicsMod
use PRTGenericMod, only : SetState

use PRTAllometricCarbonMod, only : callom_prt_vartypes
use PRTAllometricCarbonMod, only : csimpler_allom_prt_vartypes
use PRTAllometricCarbonMod, only : ac_bc_inout_id_netdc
use PRTAllometricCarbonMod, only : ac_bc_in_id_pft
use PRTAllometricCarbonMod, only : ac_bc_in_id_ctrim
use PRTAllometricCarbonMod, only : ac_bc_inout_id_dbh
use PRTAllometricCarbonMod, only : ac_bc_in_id_lstat
use PRTAllometricCarbonMod, only : ac_bc_in_id_efleaf
use PRTAllometricCarbonMod, only : ac_bc_in_id_effnrt
use PRTAllometricCarbonMod, only : ac_bc_in_id_efstem
use PRTAllometricCNPMod, only : cnp_allom_prt_vartypes
use PRTAllometricCNPMod, only : acnp_bc_in_id_pft, acnp_bc_in_id_ctrim
use PRTAllometricCNPMod, only : acnp_bc_in_id_lstat, acnp_bc_inout_id_dbh
use PRTAllometricCNPMod, only : acnp_bc_in_id_efleaf
use PRTAllometricCNPMod, only : acnp_bc_in_id_effnrt
use PRTAllometricCNPMod, only : acnp_bc_in_id_efstem
use PRTAllometricCNPMod, only : acnp_bc_inout_id_rmaint_def, acnp_bc_in_id_netdc
use PRTAllometricCNPMod, only : acnp_bc_in_id_netdnh4, acnp_bc_in_id_netdno3, acnp_bc_in_id_netdp
use PRTAllometricCNPMod, only : acnp_bc_out_id_cefflux, acnp_bc_out_id_nefflux
Expand Down Expand Up @@ -147,8 +155,9 @@ module EDCohortDynamicsMod


subroutine create_cohort(currentSite, patchptr, pft, nn, hite, coage, dbh, &
prt, laimemory, sapwmemory, structmemory, &
status, recruitstatus,ctrim, carea, clayer, spread, bc_in)
prt, leafmemory, fnrtmemory, sapwmemory, structmemory, &
elongf_leaf, elongf_fnrt, elongf_stem, status, &
recruitstatus, ctrim, carea, clayer, spread, bc_in)
!
! !DESCRIPTION:
! create new cohort
Expand All @@ -171,17 +180,25 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, coage, dbh, &
integer, intent(in) :: clayer ! canopy status of cohort
! (1 = canopy, 2 = understorey, etc.)
integer, intent(in) :: status ! growth status of plant
! (2 = leaves on , 1 = leaves off)
! (1 = abscissing, 2 = flushing)
integer, intent(in) :: recruitstatus ! recruit status of plant
! (1 = recruitment , 0 = other)
real(r8), intent(in) :: nn ! number of individuals in cohort
! per 'area' (10000m2 default)
real(r8), intent(in) :: hite ! height: meters
real(r8), intent(in) :: coage ! cohort age in years
real(r8), intent(in) :: dbh ! dbh: cm
real(r8), intent(in) :: elongf_leaf ! leaf elongation factor (fraction)
real(r8), intent(in) :: elongf_fnrt ! fine-root "elongation factor" (fraction)
real(r8), intent(in) :: elongf_stem ! stem "elongation factor" (fraction)
! For all elongation factors:
! 0 means fully abscissed
! 1 means fully flushed
class(prt_vartypes),target :: prt ! The allocated PARTEH
! object
real(r8), intent(in) :: laimemory ! target leaf biomass- set from
real(r8), intent(in) :: leafmemory ! target leaf biomass- set from
! previous year: kGC per indiv
real(r8), intent(in) :: fnrtmemory ! target fine root biomass- set from
! previous year: kGC per indiv
real(r8), intent(in) :: sapwmemory ! target sapwood biomass- set from
! previous year: kGC per indiv
Expand Down Expand Up @@ -230,14 +247,18 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, coage, dbh, &

new_cohort%pft = pft
new_cohort%status_coh = status
new_cohort%efleaf_coh = elongf_leaf
new_cohort%effnrt_coh = elongf_fnrt
new_cohort%efstem_coh = elongf_stem
new_cohort%n = nn
new_cohort%hite = hite
new_cohort%dbh = dbh
new_cohort%coage = coage
new_cohort%canopy_trim = ctrim
new_cohort%canopy_layer = clayer
new_cohort%canopy_layer_yesterday = real(clayer, r8)
new_cohort%laimemory = laimemory
new_cohort%leafmemory = leafmemory
new_cohort%fnrtmemory = fnrtmemory
new_cohort%sapwmemory = sapwmemory
new_cohort%structmemory = structmemory

Expand Down Expand Up @@ -400,7 +421,7 @@ subroutine InitPRTBoundaryConditions(new_cohort)


select case(hlm_parteh_mode)
case (prt_carbon_allom_hyp)
case (prt_csimpler_allom_hyp,prt_carbon_allom_hyp)

! Register boundary conditions for the Carbon Only Allometric Hypothesis

Expand All @@ -409,12 +430,18 @@ subroutine InitPRTBoundaryConditions(new_cohort)
call new_cohort%prt%RegisterBCIn(ac_bc_in_id_pft,bc_ival = new_cohort%pft)
call new_cohort%prt%RegisterBCIn(ac_bc_in_id_ctrim,bc_rval = new_cohort%canopy_trim)
call new_cohort%prt%RegisterBCIn(ac_bc_in_id_lstat,bc_ival = new_cohort%status_coh)
call new_cohort%prt%RegisterBCIn(ac_bc_in_id_efleaf,bc_rval = new_cohort%efleaf_coh)
call new_cohort%prt%RegisterBCIn(ac_bc_in_id_effnrt,bc_rval = new_cohort%effnrt_coh)
call new_cohort%prt%RegisterBCIn(ac_bc_in_id_efstem,bc_rval = new_cohort%efstem_coh)

case (prt_cnp_flex_allom_hyp)

call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_pft,bc_ival = new_cohort%pft)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_ctrim,bc_rval = new_cohort%canopy_trim)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_lstat,bc_ival = new_cohort%status_coh)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_efleaf,bc_rval = new_cohort%efleaf_coh)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_effnrt,bc_rval = new_cohort%effnrt_coh)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_efstem,bc_rval = new_cohort%efstem_coh)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdc, bc_rval = new_cohort%npp_acc)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdnh4, bc_rval = new_cohort%daily_nh4_uptake)
call new_cohort%prt%RegisterBCIn(acnp_bc_in_id_netdno3, bc_rval = new_cohort%daily_no3_uptake)
Expand Down Expand Up @@ -463,10 +490,16 @@ subroutine InitPRTObject(prt)

! Potential Extended types
class(callom_prt_vartypes), pointer :: c_allom_prt
class(csimpler_allom_prt_vartypes), pointer :: csimpler_allom_prt
class(cnp_allom_prt_vartypes), pointer :: cnp_allom_prt


select case(hlm_parteh_mode)
case (prt_csimpler_allom_hyp)

allocate(csimpler_allom_prt)
prt => csimpler_allom_prt

case (prt_carbon_allom_hyp)

allocate(c_allom_prt)
Expand Down Expand Up @@ -530,7 +563,10 @@ subroutine nan_cohort(cc_p)
currentCohort%canopy_layer = fates_unset_int ! canopy status of cohort (1 = canopy, 2 = understorey, etc.)
currentCohort%canopy_layer_yesterday = nan ! recent canopy status of cohort (1 = canopy, 2 = understorey, etc.)
currentCohort%NV = fates_unset_int ! Number of leaf layers: -
currentCohort%status_coh = fates_unset_int ! growth status of plant (2 = leaves on , 1 = leaves off)
currentCohort%status_coh = fates_unset_int ! growth status of plant (2 = flushing , 1 = fully abscissed, 3 = abscissing)
currentCohort%efleaf_coh = nan ! leaf elongation factor (fraction from 0 (fully abscissed) to 1 (fully flushed)
currentCohort%effnrt_coh = nan ! fine-root "elongation factor" (fraction from 0 (fully abscissed) to 1 (fully flushed)
currentCohort%efstem_coh = nan ! stem "elongation factor" (fraction from 0 (fully abscissed) to 1 (fully flushed)
currentCohort%size_class = fates_unset_int ! size class index
currentCohort%size_class_lasttimestep = fates_unset_int ! size class index
currentCohort%size_by_pft_class = fates_unset_int ! size by pft classification index
Expand All @@ -540,8 +576,9 @@ subroutine nan_cohort(cc_p)
currentCohort%n = nan ! number of individuals in cohort per 'area' (10000m2 default)
currentCohort%dbh = nan ! 'diameter at breast height' in cm
currentCohort%coage = nan ! age of the cohort in years
currentCohort%hite = nan ! height: meters
currentCohort%laimemory = nan ! target leaf biomass- set from previous year: kGC per indiv
currentCohort%hite = nan ! height: meters
currentCohort%leafmemory = nan ! target leaf biomass- set from previous year: kGC per indiv
currentCohort%fnrtmemory = nan ! target fine-root biomass- set from previous year: kGC per indiv
currentCohort%sapwmemory = nan ! target sapwood biomass- set from previous year: kGC per indiv
currentCohort%structmemory = nan ! target structural biomass- set from previous year: kGC per indiv
currentCohort%lai = nan ! leaf area index of cohort m2/m2
Expand Down Expand Up @@ -647,6 +684,9 @@ subroutine zero_cohort(cc_p)

currentCohort%NV = 0
currentCohort%status_coh = 0
currentCohort%efleaf_coh = 0._r8
currentCohort%effnrt_coh = 0._r8
currentCohort%efstem_coh = 0._r8
currentCohort%rdark = 0._r8
currentCohort%resp_m = 0._r8
currentCohort%resp_m_def = 0._r8
Expand Down Expand Up @@ -765,7 +805,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
if (currentcohort%n < min_n_safemath .and. level == 1) then
terminate = itrue
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 0',currentCohort%n/currentPatch%area,currentCohort%dbh,call_index
write(fates_log(),*) 'terminating cohorts 0',currentCohort%n/currentPatch%area,currentCohort%dbh,currentCohort%pft,call_index
endif
endif

Expand All @@ -778,15 +818,15 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
(currentCohort%dbh < 0.00001_r8 .and. store_c < 0._r8) ) then
terminate = itrue
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 1',currentCohort%n/currentPatch%area,currentCohort%dbh,call_index
write(fates_log(),*) 'terminating cohorts 1',currentCohort%n/currentPatch%area,currentCohort%dbh,currentCohort%pft,call_index
endif
endif

! Outside the maximum canopy layer
if (currentCohort%canopy_layer > nclmax ) then
terminate = itrue
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 2', currentCohort%canopy_layer,call_index
write(fates_log(),*) 'terminating cohorts 2', currentCohort%canopy_layer,currentCohort%pft,call_index
endif
endif

Expand All @@ -796,7 +836,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
terminate = itrue
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 3', &
sapw_c,leaf_c,fnrt_c,store_c,call_index
sapw_c,leaf_c,fnrt_c,store_c,currentCohort%pft,call_index
endif
endif

Expand All @@ -805,7 +845,7 @@ subroutine terminate_cohorts( currentSite, currentPatch, level , call_index, bc_
terminate = itrue
if ( debug ) then
write(fates_log(),*) 'terminating cohorts 4', &
struct_c,sapw_c,leaf_c,fnrt_c,store_c,call_index
struct_c,sapw_c,leaf_c,fnrt_c,store_c,currentCohort%pft,call_index
endif

endif
Expand Down Expand Up @@ -1196,7 +1236,8 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
write(fates_log(),*) 'Cohort I, Cohort II'
write(fates_log(),*) 'n:',currentCohort%n,nextc%n
write(fates_log(),*) 'isnew:',currentCohort%isnew,nextc%isnew
write(fates_log(),*) 'laimemory:',currentCohort%laimemory,nextc%laimemory
write(fates_log(),*) 'leafmemory:',currentCohort%leafmemory,nextc%leafmemory
write(fates_log(),*) 'fnrtmemory:',currentCohort%fnrtmemory,nextc%fnrtmemory
write(fates_log(),*) 'hite:',currentCohort%hite,nextc%hite
write(fates_log(),*) 'coage:',currentCohort%coage,nextc%coage
write(fates_log(),*) 'dbh:',currentCohort%dbh,nextc%dbh
Expand Down Expand Up @@ -1234,8 +1275,11 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
! -----------------------------------------------------------------
call UpdateCohortBioPhysRates(currentCohort)

currentCohort%laimemory = (currentCohort%n*currentCohort%laimemory &
+ nextc%n*nextc%laimemory)/newn
currentCohort%leafmemory = (currentCohort%n*currentCohort%leafmemory &
+ nextc%n*nextc%leafmemory)/newn

currentCohort%fnrtmemory = (currentCohort%n*currentCohort%fnrtmemory &
+ nextc%n*nextc%fnrtmemory)/newn

currentCohort%sapwmemory = (currentCohort%n*currentCohort%sapwmemory &
+ nextc%n*nextc%sapwmemory)/newn
Expand Down Expand Up @@ -1828,7 +1872,8 @@ subroutine copy_cohort( currentCohort,copyc )
n%dbh = o%dbh
n%coage = o%coage
n%hite = o%hite
n%laimemory = o%laimemory
n%leafmemory = o%leafmemory
n%fnrtmemory = o%fnrtmemory
n%sapwmemory = o%sapwmemory
n%structmemory = o%structmemory
n%lai = o%lai
Expand All @@ -1839,6 +1884,9 @@ subroutine copy_cohort( currentCohort,copyc )
n%canopy_layer_yesterday = o%canopy_layer_yesterday
n%nv = o%nv
n%status_coh = o%status_coh
n%efleaf_coh = o%efleaf_coh
n%effnrt_coh = o%effnrt_coh
n%efstem_coh = o%efstem_coh
n%canopy_trim = o%canopy_trim
n%excl_weight = o%excl_weight
n%prom_weight = o%prom_weight
Expand Down
3 changes: 2 additions & 1 deletion biogeochem/EDPatchDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,8 @@ module EDPatchDynamicsMod
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_csimpler_allom_hyp
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
Expand Down
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