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Complete the FATES-CLM nitrogen coupling #1472

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2a9e514
prt_carbon_allom_hyp -> fates_c_only & prt_cnp_flex_allom_hyp ->fates_cn
slevis-lmwg Sep 22, 2025
97839f1
Error check recommended in https://github.com/NGEET/fates/issues/1454
slevis-lmwg Oct 18, 2025
b2a1da6
Fix site_npp unit conversion from /s to /yr from code review w Ryan K.
slevis-lmwg Dec 8, 2025
3c82e7b
Remove commented out code that's obsolete
slevis-lmwg Dec 10, 2025
47ef7ed
Move the error check recommended in https://github.com/NGEET/fates/is…
slevis-lmwg Dec 10, 2025
6d79db1
Replace fates_cn with fates_cnp throughout
slevis-lmwg Dec 16, 2025
0d268e0
Remove the new error check and update similar preexisting error check
slevis-lmwg Dec 17, 2025
c7e8537
Merge tag 'sci.1.88.0_api.42.0.0' into fates-cn
slevis-lmwg Dec 17, 2025
7c7f359
Merge tag 'sci.1.89.0_api.43.0.0' into fates-cn
slevis-lmwg Dec 20, 2025
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10 changes: 5 additions & 5 deletions biogeochem/EDCohortDynamicsMod.F90
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Expand Up @@ -68,8 +68,8 @@ Module EDCohortDynamicsMod
use FatesAllometryMod , only : bstore_allom
use FatesAllometryMod , only : ForceDBH
use FatesAllometryMod , only : set_root_fraction
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : fates_c_only
use PRTGenericMod, only : fates_cn
use PRTGenericMod, only : prt_vartypes
use PRTGenericMod, only : carbon12_element
use PRTGenericMod, only : nitrogen_element
Expand Down Expand Up @@ -251,12 +251,12 @@ subroutine InitPRTObject(prt)


select case(hlm_parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)

allocate(c_allom_prt)
prt => c_allom_prt

case (prt_cnp_flex_allom_hyp)
case (fates_cn)

allocate(cnp_allom_prt)
prt => cnp_allom_prt
Expand Down Expand Up @@ -1030,7 +1030,7 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
currentCohort%frmort = (currentCohort%n*currentCohort%frmort + nextc%n*nextc%frmort)/newn

! Nutrients
if(hlm_parteh_mode .eq. prt_cnp_flex_allom_hyp) then
if (hlm_parteh_mode == fates_cn) then

if(nextc%n > currentCohort%n) currentCohort%cnp_limiter = nextc%cnp_limiter

Expand Down
2 changes: 0 additions & 2 deletions biogeochem/EDPatchDynamicsMod.F90
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Expand Up @@ -100,8 +100,6 @@ 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_cnp_flex_allom_hyp
use SFParamsMod, only : SF_VAL_CWD_FRAC
use EDParamsMod, only : logging_event_code
use EDParamsMod, only : logging_export_frac
Expand Down
12 changes: 6 additions & 6 deletions biogeochem/EDPhysiologyMod.F90
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Expand Up @@ -118,8 +118,8 @@ module EDPhysiologyMod
use FatesAllometryMod , only : carea_allom
use FatesAllometryMod , only : CheckIntegratedAllometries
use FatesAllometryMod, only : set_root_fraction
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : fates_c_only
use PRTGenericMod, only : fates_cn
use PRTGenericMod, only : prt_vartypes
use PRTGenericMod, only : leaf_organ
use PRTGenericMod, only : sapw_organ, struct_organ
Expand Down Expand Up @@ -2715,7 +2715,7 @@ subroutine recruitment(currentSite, currentPatch, bc_in)


select case(hlm_parteh_mode)
case (prt_carbon_allom_hyp, prt_cnp_flex_allom_hyp)
case (fates_c_only, fates_cn)

! put all of the leaf mass into the first bin
call SetState(prt, leaf_organ, element_id, m_leaf, 1)
Expand Down Expand Up @@ -3317,7 +3317,7 @@ subroutine UpdateRecruitL2FR(csite)

! Difference in dbh (cm) to consider a plant was recruited fairly recently

if(hlm_parteh_mode .ne. prt_cnp_flex_allom_hyp) return
if (hlm_parteh_mode /= fates_cn) return

rec_n(1:numpft,1:nclmax) = 0._r8
rec_l2fr0(1:numpft,1:nclmax) = 0._r8
Expand Down Expand Up @@ -3379,7 +3379,7 @@ subroutine UpdateRecruitStoich(csite)
! Update the total plant stoichiometry of a new recruit, based on the updated
! L2FR values

if(hlm_parteh_mode .ne. prt_cnp_flex_allom_hyp) return
if (hlm_parteh_mode /= fates_cn) return

cpatch => csite%youngest_patch
do while(associated(cpatch))
Expand Down Expand Up @@ -3417,7 +3417,7 @@ subroutine SetRecruitL2FR(csite)
type(fates_cohort_type), pointer :: ccohort
integer :: ft,cl

if(hlm_parteh_mode .ne. prt_cnp_flex_allom_hyp) return
if (hlm_parteh_mode /= fates_cn) return

cpatch => csite%youngest_patch
do while(associated(cpatch))
Expand Down
12 changes: 6 additions & 6 deletions biogeochem/FatesCohortMod.F90
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Expand Up @@ -12,8 +12,8 @@ module FatesCohortMod
use FatesGlobals, only : fates_log
use PRTGenericMod, only : max_nleafage
use PRTGenericMod, only : prt_vartypes
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : fates_c_only
use PRTGenericMod, only : fates_cn
use PRTGenericMod, only : leaf_organ, fnrt_organ, sapw_organ
use PRTGenericMod, only : repro_organ, store_organ, struct_organ
use PRTGenericMod, only : carbon12_element
Expand Down Expand Up @@ -609,7 +609,7 @@ subroutine Create(this, prt, pft, nn, height, coage, dbh, status, &
! initialized with full stores, which match with minimum fineroot biomass
this%l2fr = prt_params%allom_l2fr(pft)

if (hlm_parteh_mode .eq. prt_cnp_flex_allom_hyp) then
if (hlm_parteh_mode == fates_cn) then
this%cx_int = 0._r8 ! Assume balanced N,P/C stores ie log(1) = 0
this%cx0 = 0._r8 ! Assume balanced N,P/C stores ie log(1) = 0
this%ema_dcxdt = 0._r8 ! Assume unchanged dCX/dt
Expand Down Expand Up @@ -727,7 +727,7 @@ subroutine Copy(this, copyCohort)
copyCohort%year_net_uptake = this%year_net_uptake
copyCohort%cnp_limiter = this%cnp_limiter

if (hlm_parteh_mode .eq. prt_cnp_flex_allom_hyp) then
if (hlm_parteh_mode == fates_cn) then
copyCohort%cx_int = this%cx_int
copyCohort%ema_dcxdt = this%ema_dcxdt
copyCohort%cx0 = this%cx0
Expand Down Expand Up @@ -852,7 +852,7 @@ subroutine InitPRTBoundaryConditions(this)
class(fates_cohort_type), intent(inout), target :: this

select case(hlm_parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)

! Register boundary conditions for the Carbon Only Allometric Hypothesis

Expand All @@ -866,7 +866,7 @@ subroutine InitPRTBoundaryConditions(this)
call this%prt%RegisterBCIn(ac_bc_in_id_effnrt, bc_rval = this%effnrt_coh)
call this%prt%RegisterBCIn(ac_bc_in_id_efstem, bc_rval = this%efstem_coh)

case (prt_cnp_flex_allom_hyp)
case (fates_cn)

! Register boundary conditions for the CNP Allometric Hypothesis

Expand Down
10 changes: 5 additions & 5 deletions biogeochem/FatesSoilBGCFluxMod.F90
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Expand Up @@ -15,8 +15,8 @@ module FatesSoilBGCFluxMod
use PRTGenericMod , only : num_elements
use PRTGenericMod , only : element_list
use PRTGenericMod , only : element_pos
use PRTGenericMod , only : prt_carbon_allom_hyp
use PRTGenericMod , only : prt_cnp_flex_allom_hyp
use PRTGenericMod , only : fates_c_only
use PRTGenericMod , only : fates_cn
use PRTGenericMod , only : prt_vartypes
use PRTGenericMod , only : leaf_organ
use PRTGenericMod , only : sapw_organ, struct_organ
Expand Down Expand Up @@ -133,7 +133,7 @@ subroutine UnPackNutrientAquisitionBCs(sites, bc_in)

! We can exit if this is a c-only simulation
select case (hlm_parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)
! These can now be zero'd
do s = 1, nsites
bc_in(s)%plant_nh4_uptake_flux(:,:) = 0._r8
Expand Down Expand Up @@ -269,7 +269,7 @@ subroutine PrepCH4BCs(csite,bc_in,bc_out)


! Exit if we need not communicate with the hlm's ch4 module
! if(.not.(hlm_use_ch4==itrue) .and. .not.(hlm_parteh_mode==prt_cnp_flex_allom_hyp) ) return
! if(.not.(hlm_use_ch4==itrue) .and. .not.(hlm_parteh_mode==fates_cn) ) return

! Initialize to zero
bc_out%annavg_agnpp_pa(:) = 0._r8
Expand All @@ -282,7 +282,7 @@ subroutine PrepCH4BCs(csite,bc_in,bc_out)
bc_out%ema_npp = 0._r8

! Process CH4 variables first
!if(.not.(hlm_use_ch4==itrue) .and. .not.(hlm_parteh_mode==prt_cnp_flex_allom_hyp) )
!if(.not.(hlm_use_ch4==itrue) .and. .not.(hlm_parteh_mode==fates_cn) )

cpatch => csite%oldest_patch
do while (associated(cpatch))
Expand Down
14 changes: 7 additions & 7 deletions biogeophys/FatesPlantRespPhotosynthMod.F90
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Expand Up @@ -44,8 +44,8 @@ module FATESPlantRespPhotosynthMod
use FatesCohortMod, only : fates_cohort_type
use FatesConstantsMod, only : lmrmodel_ryan_1991
use FatesConstantsMod, only : lmrmodel_atkin_etal_2017
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : fates_c_only
use PRTGenericMod, only : fates_cn
use PRTGenericMod, only : carbon12_element
use PRTGenericMod, only : nitrogen_element
use PRTGenericMod, only : leaf_organ
Expand Down Expand Up @@ -497,7 +497,7 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
(hlm_use_planthydro.eq.itrue) .or. &
(hlm_radiation_model .eq. twostr_solver ) .or. &
(nleafage > 1) .or. &
(hlm_parteh_mode .ne. prt_carbon_allom_hyp ) ) then
(hlm_parteh_mode /= fates_c_only) ) then


! These values are incremented, therefore since
Expand Down Expand Up @@ -564,11 +564,11 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
! Then scale this value at the top of the canopy for canopy depth
! Leaf nitrogen concentration at the top of the canopy (g N leaf / m**2 leaf)
select case(hlm_parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)

lnc_top = prt_params%nitr_stoich_p1(ft,prt_params%organ_param_id(leaf_organ))/slatop(ft)

case (prt_cnp_flex_allom_hyp)
case (fates_cn)

leaf_c = currentCohort%prt%GetState(leaf_organ, carbon12_element)
if( (leaf_c*slatop(ft)) > nearzero) then
Expand Down Expand Up @@ -919,15 +919,15 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)


select case(hlm_parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)

live_stem_n = sapw_c_agw * prt_params%nitr_stoich_p1(ft,prt_params%organ_param_id(sapw_organ))

live_croot_n = sapw_c_bgw * prt_params%nitr_stoich_p1(ft,prt_params%organ_param_id(sapw_organ))

fnrt_n = fnrt_c * prt_params%nitr_stoich_p1(ft,prt_params%organ_param_id(fnrt_organ))

case(prt_cnp_flex_allom_hyp)
case(fates_cn)

live_stem_n = prt_params%allom_agb_frac(currentCohort%pft) * &
currentCohort%prt%GetState(sapw_organ, nitrogen_element)
Expand Down
24 changes: 12 additions & 12 deletions functional_unit_testing/parteh/f90src/FatesCohortWrapMod.F90
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Expand Up @@ -35,8 +35,8 @@ module FatesCohortWrapMod
use PRTGenericMod, only : carbon12_element
use PRTGenericMod, only : SetState
use PRTGenericMod, only : prt_global
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : fates_c_only
use PRTGenericMod, only : fates_cn

use PRTAllometricCarbonMod, only : callom_prt_vartypes
use PRTAllometricCarbonMod, only : ac_bc_inout_id_netdc
Expand Down Expand Up @@ -257,12 +257,12 @@ subroutine CohortPySet(ipft,hgt_min,canopy_trim)
! -----------------------------------------------------

select case(ccohort%parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)
prt_global => prt_global_ac
allocate(callom_prt)
ccohort%prt => callom_prt

case(prt_cnp_flex_allom_hyp)
case(fates_cn)
prt_global => prt_global_acnp
allocate(cnpallom_prt)
ccohort%prt => cnpallom_prt
Expand All @@ -276,7 +276,7 @@ subroutine CohortPySet(ipft,hgt_min,canopy_trim)
call ccohort%prt%InitPRTVartype()

select case(ccohort%parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)

call SetState(ccohort%prt,leaf_organ, carbon12_element, leaf_c)
call SetState(ccohort%prt,fnrt_organ, carbon12_element, fnrt_c)
Expand All @@ -291,7 +291,7 @@ subroutine CohortPySet(ipft,hgt_min,canopy_trim)
call ccohort%prt%RegisterBCIn(ac_bc_in_id_pft,bc_ival = ccohort%pft)
call ccohort%prt%RegisterBCIn(ac_bc_in_id_ctrim,bc_rval = ccohort%canopy_trim)

case (prt_cnp_flex_allom_hyp)
case (fates_cn)

! Initializing with the target stoichiometric ratios
! (OR you can initialize with the minimum ratios too.... p2)
Expand Down Expand Up @@ -394,7 +394,7 @@ subroutine WrapDailyPRT(ipft,daily_carbon_gain,canopy_trim,flush_c,drop_frac_c,l
call PRTMaintTurnover(ccohort%prt, ipft, is_drought)

select case(ccohort%parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)
prt_global => prt_global_ac
ccohort%daily_carbon_gain = daily_carbon_gain

Expand All @@ -403,7 +403,7 @@ subroutine WrapDailyPRT(ipft,daily_carbon_gain,canopy_trim,flush_c,drop_frac_c,l
ccohort%daily_r_grow = 0.0_r8
ccohort%carbon_root_efflux = 0.0_r8

case (prt_cnp_flex_allom_hyp)
case (fates_cn)

prt_global => prt_global_acnp
ccohort%daily_carbon_gain = daily_carbon_gain
Expand Down Expand Up @@ -457,9 +457,9 @@ subroutine WrapQueryVars(ipft,crowndamage, leaf_area,crown_area,agb,store_c,targ
canopy_lai(:) = 0._r8

select case(ccohort%parteh_mode)
case (prt_carbon_allom_hyp)
case (fates_c_only)
prt_global => prt_global_ac
case (prt_cnp_flex_allom_hyp)
case (fates_cn)
prt_global => prt_global_acnp
end select

Expand Down Expand Up @@ -547,9 +547,9 @@ subroutine WrapQueryDiagnostics(ipft, dbh, &
ccohort => cohort_array(ipft)

select case(ccohort%parteh_mode)
case (prt_carbon_allom_hyp )
case (fates_c_only )
prt_global => prt_global_ac
case (prt_cnp_flex_allom_hyp)
case (fates_cn)
prt_global => prt_global_acnp
end select

Expand Down
6 changes: 3 additions & 3 deletions main/EDInitMod.F90
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Expand Up @@ -79,8 +79,8 @@ module EDInitMod
use FatesAllometryMod , only : carea_allom
use PRTGenericMod , only : StorageNutrientTarget
use FatesInterfaceTypesMod, only : hlm_parteh_mode
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : fates_c_only
use PRTGenericMod, only : fates_cn
use PRTGenericMod, only : prt_vartypes
use PRTGenericMod, only : leaf_organ
use PRTGenericMod, only : fnrt_organ
Expand Down Expand Up @@ -1310,7 +1310,7 @@ subroutine init_cohorts(site_in, patch_in, bc_in)
end select

select case(hlm_parteh_mode)
case (prt_carbon_allom_hyp, prt_cnp_flex_allom_hyp )
case (fates_c_only, fates_cn )
! Put all of the leaf mass into the first bin
call SetState(prt, leaf_organ, element_id, m_leaf, 1)
do iage = 2,nleafage
Expand Down
6 changes: 3 additions & 3 deletions main/EDMainMod.F90
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Expand Up @@ -27,8 +27,8 @@ module EDMainMod
use FatesInterfaceTypesMod , only : hlm_masterproc
use FatesInterfaceTypesMod , only : numpft
use FatesInterfaceTypesMod , only : hlm_use_nocomp
use PRTGenericMod , only : prt_carbon_allom_hyp
use PRTGenericMod , only : prt_cnp_flex_allom_hyp
use PRTGenericMod , only : fates_c_only
use PRTGenericMod , only : fates_cn
use PRTGenericMod , only : nitrogen_element
use PRTGenericMod , only : phosphorus_element
use EDCohortDynamicsMod , only : terminate_cohorts
Expand Down Expand Up @@ -748,7 +748,7 @@ subroutine ed_integrate_state_variables(currentSite, bc_in, bc_out )
! Update history diagnostics related to Nutrients (if any)
! -----------------------------------------------------------------------------
select case(hlm_parteh_mode)
case (prt_cnp_flex_allom_hyp)
case (fates_cn)
call fates_hist%update_history_nutrflux(currentSite)
end select

Expand Down
6 changes: 3 additions & 3 deletions main/EDPftvarcon.F90
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Expand Up @@ -22,7 +22,7 @@ module EDPftvarcon
use FatesLitterMod, only : ilabile,icellulose,ilignin
use PRTGenericMod, only : leaf_organ, fnrt_organ, store_organ
use PRTGenericMod, only : sapw_organ, struct_organ, repro_organ
use PRTGenericMod, only : prt_cnp_flex_allom_hyp,prt_carbon_allom_hyp
use PRTGenericMod, only : fates_cn, fates_c_only
use FatesInterfaceTypesMod, only : hlm_nitrogen_spec, hlm_phosphorus_spec
use FatesInterfaceTypesMod, only : hlm_parteh_mode
use FatesInterfaceTypesMod, only : hlm_nu_com
Expand Down Expand Up @@ -1714,7 +1714,7 @@ subroutine FatesCheckParams(is_master)
if(.not.is_master) return

select case (hlm_parteh_mode)
case (prt_cnp_flex_allom_hyp)
case (fates_cn)

! Check to see if either RD/ECA/MIC is turned on

Expand Down Expand Up @@ -1792,7 +1792,7 @@ subroutine FatesCheckParams(is_master)
end if
end if

case (prt_carbon_allom_hyp)
case (fates_c_only)
! No additional checks needed for now.
continue

Expand Down
2 changes: 0 additions & 2 deletions main/EDTypesMod.F90
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Expand Up @@ -15,8 +15,6 @@ module EDTypesMod
use PRTGenericMod, only : prt_vartypes
use PRTGenericMod, only : leaf_organ, fnrt_organ, sapw_organ
use PRTGenericMod, only : repro_organ, store_organ, struct_organ
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : num_organ_types
use PRTGenericMod, only : num_elements
use PRTGenericMod, only : element_list
Expand Down
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