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direct usage of parameter datastructure - allometry proof of concept #1528

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275 changes: 120 additions & 155 deletions biogeochem/FatesAllometryMod.F90
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3 changes: 1 addition & 2 deletions biogeophys/LeafBiophysicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -950,7 +950,6 @@ subroutine CiFunc(ci, &
real(r8), intent(out) :: fval ! ci_input - ci_updated (Pa)

!real(r8) :: veg_esat ! Saturation vapor pressure at leaf-surface [Pa]
real(r8) :: veg_qs ! DUMMY, specific humidity at leaf-surface [kg/kg]
real(r8) :: a_gs ! The assimilation (a) for calculating conductance (gs)
! is either = to anet or agross
real(r8) :: ac ! Rubisco-limited gross photosynthesis (umol CO2/m**2/s)
Expand Down Expand Up @@ -1478,7 +1477,7 @@ function LeafHumidityStomaResis(leaf_psi, k_lwp, veg_tempk, can_vpress, can_pres
lwp_star = 1._r8
end if

! call QSat(veg_tempk, can_press, qsat_alt, veg_esat)
call QSat(veg_tempk, can_press, qsat_alt, veg_esat)

qsat_alt = qsat_alt * g_per_kg

Expand Down
11 changes: 8 additions & 3 deletions main/FatesInterfaceMod.F90
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Expand Up @@ -821,11 +821,15 @@ subroutine SetFatesGlobalElements1(use_fates,surf_numpft,surf_numcft,paramfile)
end do
write(fates_log(),*) '============ End FATES Parameter Info ========='
end if

! This assigns named constants to the indices of each
! parameter datastructure, allowing data to be accessed
! directly from the structure
call SetParameterIndices()

! This call transfers parameters from the pstruct data-structure
! into the specific datastructures where parameters have there
! own primitive arrays

call FatesTransferParameters()

fates_numpft = size(prt_params%wood_density,dim=1)
Expand Down Expand Up @@ -2338,8 +2342,9 @@ subroutine UpdateFatesRMeansTStep(sites,bc_in, bc_out)
do while (associated(ccohort))
! call ccohort%tveg_lpa%UpdateRMean(bc_in(s)%t_veg_pa(ifp))
if(.not.ccohort%isnew)then
! [kgC/plant/yr] -> [gC/m2/yr]
site_npp = site_npp + ccohort%npp_acc_hold * ccohort%n*area_inv * g_per_kg
! [kgC/plant/yr] -> [gC/m2/s]
site_npp = site_npp + ccohort%npp_acc_hold * ccohort%n*area_inv * &
g_per_kg * hlm_days_per_year / sec_per_day
end if
ccohort => ccohort%shorter
end do
Expand Down
32 changes: 15 additions & 17 deletions main/FatesParameterDerivedMod.F90
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Expand Up @@ -15,8 +15,9 @@ module FatesParameterDerivedMod
use FatesInterfaceTypesMod, only : nleafage
use FatesInterfaceTypesMod, only : nlevdamage
use FatesGlobals , only : fates_log
use EDParamsMod , only : ED_val_history_damage_bin_edges

use FatesParametersInterface


implicit none
private

Expand Down Expand Up @@ -81,21 +82,21 @@ end subroutine InitAllocateDamageTransitions

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

subroutine Init(this,numpft)
subroutine Init(this)

use EDPftvarcon, only: EDPftvarcon_inst
use SFParamsMod, only: SF_val_CWD_frac
use FatesLitterMod, only : ncwd

class(param_derived_type), intent(inout) :: this
integer, intent(in) :: numpft

! local variables
integer :: ft ! pft index
integer :: iage ! leaf age class index
integer :: numpft

associate( vcmax25top => EDPftvarcon_inst%vcmax25top )

associate( vcmax25top => pstruct%parameters(pid_vcmax25top)%r_data_2d )

numpft = size(vcmax25top,dim=2)

call this%InitAllocate(numpft)
call this%InitDamageTransitions(numpft)

Expand All @@ -114,14 +115,14 @@ subroutine Init(this,numpft)
! jmax25top(ft) = &
! (2.59_r8 - 0.035_r8*min(max((t10(p)-tfrzc),11._r8),35._r8)) * vcmax25top(ft)

this%jmax25top(ft,iage) = 1.67_r8 * vcmax25top(ft,iage)
this%tpu25top(ft,iage) = 0.167_r8 * vcmax25top(ft,iage)
this%kp25top(ft,iage) = 20000._r8 * vcmax25top(ft,iage)
this%jmax25top(ft,iage) = 1.67_r8 * vcmax25top(iage,ft)
this%tpu25top(ft,iage) = 0.167_r8 * vcmax25top(iage,ft)
this%kp25top(ft,iage) = 20000._r8 * vcmax25top(iage,ft)

end do

! Allocate fraction of aboveground woody biomass in branches
this%branch_frac(ft) = sum(SF_val_CWD_frac(1:3))
this%branch_frac(ft) = sum(pstruct%parameters(pid_cwd_frac)%r_data_1d(1:3),dim=1)

end do !ft

Expand All @@ -133,9 +134,6 @@ end subroutine Init

subroutine InitDamageTransitions(this, numpft)

use EDPftvarcon, only: EDPftvarcon_inst


class(param_derived_type), intent(inout) :: this
integer, intent(in) :: numpft

Expand All @@ -155,7 +153,7 @@ subroutine InitDamageTransitions(this, numpft)
! class widths
! append 100 to ED_val_history_damage_bin_edges
do j = 1,nlevdamage
damage_bin_edges_ex(j) = ED_val_history_damage_bin_edges(j)
damage_bin_edges_ex(j) = pstruct%parameters(pid_damage_bins)%r_data_1d(j) !ED_val_history_damage_bin_edges(j)
end do
damage_bin_edges_ex(j) = 100.0_r8

Expand All @@ -165,7 +163,7 @@ subroutine InitDamageTransitions(this, numpft)

do ft = 1, numpft

damage_frac = EDPftvarcon_inst%damage_frac(ft)
damage_frac = pstruct%parameters(pid_damage_frac)%r_data_1d(ft)

do i = 1, nlevdamage

Expand Down
195 changes: 195 additions & 0 deletions main/FatesParametersInterface.F90
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Expand Up @@ -8,20 +8,215 @@ module FatesParametersInterface
! only uses shr libraries

use JSONParameterUtilsMod, only: params_type
use JSONParameterUtilsMod, only: param_type
use FatesConstantsMod, only : r8 => fates_r8

implicit none
private

type(params_type) :: pstruct

! Parameter indexes

integer, public :: pid_vcmax25top
integer, public :: pid_cwd_frac
integer, public :: pid_damage_frac
integer, public :: pid_damage_bins
integer, public :: pid_alloc_organ_id
integer, public :: pid_phen_leaf_habit
integer, public :: pid_phen_stem_drop_frac
integer, public :: pid_phen_fnrt_drop_frac
integer, public :: pid_phen_mindaysoff
integer, public :: pid_phen_drought_thresh
integer, public :: pid_phen_moist_thresh
integer, public :: pid_leaf_slamax
integer, public :: pid_leaf_slatop
integer, public :: pid_allom_sai_scaler
integer, public :: pid_allom_fnrt_prof_a
integer, public :: pid_allom_fnrt_prof_b
integer, public :: pid_allom_fnrt_prof_mode
integer, public :: pid_woody
integer, public :: pid_wood_density
integer, public :: pid_recruit_seed_dbh_thresh
integer, public :: pid_storage_cushion
integer, public :: pid_store_priority_frac
integer, public :: pid_turnover_senleaf_fdrought
integer, public :: pid_turnover_fnrt
integer, public :: pid_leafn_vert_scaler1
integer, public :: pid_leafn_vert_scaler2
integer, public :: pid_recruit_seed_alloc_mature
integer, public :: pid_recruit_seed_alloc
integer, public :: pid_trs_repro_alloc_a
integer, public :: pid_trs_repro_alloc_b
integer, public :: pid_c2b
integer, public :: pid_grperc
integer, public :: pid_allom_dbh_maxh
integer, public :: pid_allom_hmode
integer, public :: pid_allom_lmode
integer, public :: pid_allom_fmode
integer, public :: pid_allom_amode
integer, public :: pid_allom_stmode
integer, public :: pid_allom_cmode
integer, public :: pid_allom_smode
integer, public :: pid_allom_dmode
integer, public :: pid_allom_lapersa_int
integer, public :: pid_allom_lapersa_slp
integer, public :: pid_allom_l2fr
integer, public :: pid_cnp_kp
integer, public :: pid_cnp_ki
integer, public :: pid_cnp_kd
integer, public :: pid_cnp_store_ovrflw_frac
integer, public :: pid_cnp_nfix1
integer, public :: pid_allom_d2h1
integer, public :: pid_allom_d2h2
integer, public :: pid_allom_d2h3
integer, public :: pid_allom_agbfrac
integer, public :: pid_allom_d2l1
integer, public :: pid_allom_d2l2
integer, public :: pid_allom_d2l3
integer, public :: pid_allom_blca_ediff
integer, public :: pid_allom_d2ca_max
integer, public :: pid_allom_d2ca_min
integer, public :: pid_allom_agb1
integer, public :: pid_allom_agb2
integer, public :: pid_allom_agb3
integer, public :: pid_allom_agb4
integer, public :: pid_allom_h2cd1
integer, public :: pid_allom_h2cd2
integer, public :: pid_allom_zroot_maxd
integer, public :: pid_allom_zroot_maxz
integer, public :: pid_allom_zroot_mind
integer, public :: pid_allom_zroot_minz
integer, public :: pid_allom_zroot_k
integer, public :: pid_turnover_branch
integer, public :: pid_cnp_nitr_store_ratio
integer, public :: pid_cnp_phos_store_ratio
integer, public :: pid_turnover_leaf_canopy
integer, public :: pid_turnover_leaf_ustory
integer, public :: pid_stoich_nitr
integer, public :: pid_stoich_phos
integer, public :: pid_alloc_organ_priority
integer, public :: pid_cnp_nitr_retrans
integer, public :: pid_cnp_phos_retrans

public :: pstruct
public :: GetParameterIndices
public :: Transp2dInt
public :: Transp2dReal

contains

subroutine GetParameterIndices()

! Query the parameter data structure for the names
! of known parameters, and identify the data-structure
! index of each, into a named integer constant. These
! integer constants will be used for retrieval.
! This assignment happens once, here.

! Scalar Parameters
pid_damage_bins = pstruct%GetIndexFromName('fates_history_damage_bin_edges')

pid_vcmax25top = pstruct%GetIndexFromName('fates_leaf_vcmax25top')
pid_cwd_frac = pstruct%GetIndexFromName('fates_frag_cwd_frac')
pid_damage_frac = pstruct%GetIndexFromName('fates_damage_frac')

pid_alloc_organ_id = pstruct%GetIndexFromName('fates_alloc_organ_id')
pid_phen_leaf_habit = pstruct%GetIndexFromName('fates_phen_leaf_habit')
pid_phen_stem_drop_frac = pstruct%GetIndexFromName('fates_phen_stem_drop_fraction')
pid_phen_fnrt_drop_frac = pstruct%GetIndexFromName('fates_phen_fnrt_drop_fraction')
pid_phen_mindaysoff = pstruct%GetIndexFromName('fates_phen_mindaysoff')
pid_phen_drought_thresh = pstruct%GetIndexFromName('fates_phen_drought_threshold')
pid_phen_moist_thresh = pstruct%GetIndexFromName('fates_phen_moist_threshold')
pid_leaf_slamax = pstruct%GetIndexFromName('fates_leaf_slamax')
pid_leaf_slatop = pstruct%GetIndexFromName('fates_leaf_slatop')
pid_allom_sai_scaler = pstruct%GetIndexFromName('fates_allom_sai_scaler')
pid_allom_fnrt_prof_a = pstruct%GetIndexFromName('fates_allom_fnrt_prof_a')
pid_allom_fnrt_prof_b = pstruct%GetIndexFromName('fates_allom_fnrt_prof_b')
pid_allom_fnrt_prof_mode = pstruct%GetIndexFromName('fates_allom_fnrt_prof_mode')
pid_woody = pstruct%GetIndexFromName('fates_woody')
pid_wood_density = pstruct%GetIndexFromName('fates_wood_density')
pid_recruit_seed_dbh_thresh = pstruct%GetIndexFromName('fates_recruit_seed_dbh_repro_threshold')
pid_storage_cushion = pstruct%GetIndexFromName('fates_alloc_storage_cushion')
pid_store_priority_frac = pstruct%GetIndexFromName('fates_alloc_store_priority_frac')
pid_turnover_senleaf_fdrought = pstruct%GetIndexFromName('fates_turnover_senleaf_fdrought')
pid_turnover_fnrt = pstruct%GetIndexFromName('fates_turnover_fnrt')
pid_leafn_vert_scaler1 = pstruct%GetIndexFromName('fates_leafn_vert_scaler_coeff1')
pid_leafn_vert_scaler2 = pstruct%GetIndexFromName('fates_leafn_vert_scaler_coeff2')
pid_recruit_seed_alloc_mature = pstruct%GetIndexFromName('fates_recruit_seed_alloc_mature')
pid_recruit_seed_alloc = pstruct%GetIndexFromName('fates_recruit_seed_alloc')
pid_trs_repro_alloc_a = pstruct%GetIndexFromName('fates_trs_repro_alloc_a')
pid_trs_repro_alloc_b = pstruct%GetIndexFromName('fates_trs_repro_alloc_b')
pid_c2b = pstruct%GetIndexFromName('fates_c2b')
pid_grperc = pstruct%GetIndexFromName('fates_grperc')
pid_allom_dbh_maxh = pstruct%GetIndexFromName('fates_allom_dbh_maxheight')
pid_allom_hmode = pstruct%GetIndexFromName('fates_allom_hmode')
pid_allom_lmode = pstruct%GetIndexFromName('fates_allom_lmode')
pid_allom_fmode = pstruct%GetIndexFromName('fates_allom_fmode')
pid_allom_amode = pstruct%GetIndexFromName('fates_allom_amode')
pid_allom_stmode = pstruct%GetIndexFromName('fates_allom_stmode')
pid_allom_cmode = pstruct%GetIndexFromName('fates_allom_cmode')
pid_allom_smode = pstruct%GetIndexFromName('fates_allom_smode')
pid_allom_dmode = pstruct%GetIndexFromName('fates_allom_dmode')
pid_allom_lapersa_int = pstruct%GetIndexFromName('fates_allom_la_per_sa_int')
pid_allom_lapersa_slp = pstruct%GetIndexFromName('fates_allom_la_per_sa_slp')
pid_allom_l2fr = pstruct%GetIndexFromName('fates_allom_l2fr')
pid_cnp_kp = pstruct%GetIndexFromName('fates_cnp_pid_kp')
pid_cnp_ki = pstruct%GetIndexFromName('fates_cnp_pid_ki')
pid_cnp_kd = pstruct%GetIndexFromName('fates_cnp_pid_kd')
pid_cnp_store_ovrflw_frac = pstruct%GetIndexFromName('fates_cnp_store_ovrflw_frac')
pid_cnp_nfix1 = pstruct%GetIndexFromName('fates_cnp_nfix1')
pid_allom_agbfrac = pstruct%GetIndexFromName('fates_allom_agb_frac')
pid_allom_d2h1 = pstruct%GetIndexFromName('fates_allom_d2h1')
pid_allom_d2h2 = pstruct%GetIndexFromName('fates_allom_d2h2')
pid_allom_d2h3 = pstruct%GetIndexFromName('fates_allom_d2h3')
pid_allom_d2l1 = pstruct%GetIndexFromName('fates_allom_d2bl1')
pid_allom_d2l2 = pstruct%GetIndexFromName('fates_allom_d2bl2')
pid_allom_d2l3 = pstruct%GetIndexFromName('fates_allom_d2bl3')
pid_allom_blca_ediff = pstruct%GetIndexFromName('fates_allom_blca_expnt_diff')
pid_allom_d2ca_max = pstruct%GetIndexFromName('fates_allom_d2ca_coefficient_max')
pid_allom_d2ca_min = pstruct%GetIndexFromName('fates_allom_d2ca_coefficient_min')
pid_allom_agb1 = pstruct%GetIndexFromName('fates_allom_agb1')
pid_allom_agb2 = pstruct%GetIndexFromName('fates_allom_agb2')
pid_allom_agb3 = pstruct%GetIndexFromName('fates_allom_agb3')
pid_allom_agb4 = pstruct%GetIndexFromName('fates_allom_agb4')
pid_allom_h2cd1 = pstruct%GetIndexFromName('fates_allom_h2cd1')
pid_allom_h2cd2 = pstruct%GetIndexFromName('fates_allom_h2cd2')
pid_allom_zroot_maxd = pstruct%GetIndexFromName('fates_allom_zroot_max_dbh')
pid_allom_zroot_maxz = pstruct%GetIndexFromName('fates_allom_zroot_max_z')
pid_allom_zroot_mind = pstruct%GetIndexFromName('fates_allom_zroot_min_dbh')
pid_allom_zroot_minz = pstruct%GetIndexFromName('fates_allom_zroot_min_z')
pid_allom_zroot_k = pstruct%GetIndexFromName('fates_allom_zroot_k')
pid_turnover_branch = pstruct%GetIndexFromName('fates_turnover_branch')
pid_cnp_nitr_store_ratio = pstruct%GetIndexFromName('fates_cnp_nitr_store_ratio')
pid_cnp_phos_store_ratio = pstruct%GetIndexFromName('fates_cnp_phos_store_ratio')
pid_turnover_leaf_canopy = pstruct%GetIndexFromName('fates_turnover_leaf_canopy')
pid_turnover_leaf_ustory = pstruct%GetIndexFromName('fates_turnover_leaf_ustory')
pid_stoich_nitr = pstruct%GetIndexFromName('fates_stoich_nitr')
pid_stoich_phos = pstruct%GetIndexFromName('fates_stoich_phos')
pid_alloc_organ_priority = pstruct%GetIndexFromName('fates_alloc_organ_priority')
pid_cnp_nitr_retrans = pstruct%GetIndexFromName('fates_cnp_turnover_nitr_retrans')
pid_cnp_phos_retrans = pstruct%GetIndexFromName('fates_cnp_turnover_phos_retrans')

end subroutine GetParameterIndices

subroutine CheckParameters

type(param_type), pointer :: param(:)
integer :: corr_id
real(r8) :: correction

param => pstruct%parameters

! Apply correction to cwd fractions
correction = 1._r8 - sum(param(pid_cwd_frac)%r_data_1d(:),dim=1)
corr_id = maxloc(param(pid_cwd_frac)%r_data_1d(:),dim=1)
param(pid_cwd_frac)%r_data_1d(corr_id) = param(pid_cwd_frac)%r_data_1d(corr_id) + correction


end subroutine CheckParameters


subroutine Transp2dInt(i_2d_in,i_2d_out)

! The FATES JSON parameter files have a legacy from the netcdf
Expand Down
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