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Nutrient controls on leaf level photosynthetic processes #768

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c630f8c
Adding in leafn and leafp effect on vcmax25top, vcmax25 parameters, n…
jenniferholm Jul 7, 2021
ccebaa7
Added c-only photosyn. jmax, vcmax in PARTEH case, and option for kp25
jenniferholm Aug 4, 2021
190e449
updated to most recent parameter file; reverted switches back to defa…
jenniferholm Aug 13, 2021
628c598
removed incorrect co2_rcurve_islope25top_ft calculation in photosynth…
jenniferholm Sep 23, 2021
47e8737
removed min/max caps on lnc and lpc and unused vcmaxse equation
jenniferholm Jan 24, 2022
8ccae78
Removed unused testing lines
jenniferholm Mar 30, 2022
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2 changes: 1 addition & 1 deletion biogeochem/FatesSoilBGCFluxMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -1182,7 +1182,7 @@ function ECACScalar(ccohort, element_id) result(c_scalar)
integer, parameter :: downreg_logi = 2
integer, parameter :: downreg_CN_logi = 3

integer, parameter :: downreg_type = downreg_linear
integer, parameter :: downreg_type = downreg_CN_logi


real(r8), parameter :: logi_k = 25.0_r8 ! logistic function k
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160 changes: 132 additions & 28 deletions biogeophys/FatesPlantRespPhotosynthMod.F90
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51 changes: 50 additions & 1 deletion main/EDPftvarcon.F90
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Expand Up @@ -72,7 +72,7 @@ module EDPftvarcon
! decreases light interception
real(r8), allocatable :: c3psn(:) ! index defining the photosynthetic
! pathway C4 = 0, C3 = 1

real(r8), allocatable :: flnr(:) ! fraction of leaf N in Rubisco
real(r8), allocatable :: smpso(:) ! Soil water potential at full stomatal opening
! (non-HYDRO mode only) [mm]
real(r8), allocatable :: smpsc(:) ! Soil water potential at full stomatal closure
Expand All @@ -99,6 +99,10 @@ module EDPftvarcon
real(r8), allocatable :: jmaxhd(:)
real(r8), allocatable :: vcmaxse(:)
real(r8), allocatable :: jmaxse(:)
real(r8), allocatable :: vcmax_np1(:)
real(r8), allocatable :: vcmax_np2(:)
real(r8), allocatable :: vcmax_np3(:)
real(r8), allocatable :: vcmax_np4(:)
real(r8), allocatable :: germination_rate(:) ! Fraction of seed mass germinating per year (yr-1)
real(r8), allocatable :: seed_decay_rate(:) ! Fraction of seed mass (both germinated and
! ungerminated), decaying per year (yr-1)
Expand Down Expand Up @@ -377,6 +381,10 @@ subroutine Register_PFT(this, fates_params)
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_leaf_flnr'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_smpso'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)
Expand Down Expand Up @@ -509,6 +517,22 @@ subroutine Register_PFT(this, fates_params)
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_eca_vcmax_np1'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_eca_vcmax_np2'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_eca_vcmax_np3'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_eca_vcmax_np4'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_seed_germination_rate'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)
Expand Down Expand Up @@ -694,6 +718,10 @@ subroutine Receive_PFT(this, fates_params)
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%clumping_index)

name = 'fates_leaf_flnr'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%flnr)

name = 'fates_leaf_c3psn'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%c3psn)
Expand Down Expand Up @@ -840,6 +868,22 @@ subroutine Receive_PFT(this, fates_params)
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%jmaxse)

name = 'fates_eca_vcmax_np1'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%vcmax_np1)

name = 'fates_eca_vcmax_np2'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%vcmax_np2)

name = 'fates_eca_vcmax_np3'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%vcmax_np3)

name = 'fates_eca_vcmax_np4'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%vcmax_np4)

name = 'fates_seed_germination_rate'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%germination_rate)
Expand Down Expand Up @@ -1309,6 +1353,7 @@ subroutine FatesReportPFTParams(is_master)
write(fates_log(),fmt0) 'xl = ',EDPftvarcon_inst%xl
write(fates_log(),fmt0) 'clumping_index = ',EDPftvarcon_inst%clumping_index
write(fates_log(),fmt0) 'c3psn = ',EDPftvarcon_inst%c3psn
write(fates_log(),fmt0) 'flnr = ',EDPftvarcon_inst%flnr
write(fates_log(),fmt0) 'vcmax25top = ',EDPftvarcon_inst%vcmax25top
write(fates_log(),fmt0) 'smpso = ',EDPftvarcon_inst%smpso
write(fates_log(),fmt0) 'smpsc = ',EDPftvarcon_inst%smpsc
Expand All @@ -1328,6 +1373,10 @@ subroutine FatesReportPFTParams(is_master)
write(fates_log(),fmt0) 'jmaxhd = ',EDPftvarcon_inst%jmaxhd
write(fates_log(),fmt0) 'vcmaxse = ',EDPftvarcon_inst%vcmaxse
write(fates_log(),fmt0) 'jmaxse = ',EDPftvarcon_inst%jmaxse
write(fates_log(),fmt0) 'vcmax_np1 = ',EDPftvarcon_inst%vcmax_np1
write(fates_log(),fmt0) 'vcmax_np1 = ',EDPftvarcon_inst%vcmax_np2
write(fates_log(),fmt0) 'vcmax_np1 = ',EDPftvarcon_inst%vcmax_np3
write(fates_log(),fmt0) 'vcmax_np1 = ',EDPftvarcon_inst%vcmax_np4
write(fates_log(),fmt0) 'germination_timescale = ',EDPftvarcon_inst%germination_rate
write(fates_log(),fmt0) 'seed_decay_turnover = ',EDPftvarcon_inst%seed_decay_rate
write(fates_log(),fmt0) 'trim_limit = ',EDPftvarcon_inst%trim_limit
Expand Down
3 changes: 2 additions & 1 deletion main/FatesInterfaceMod.F90
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Expand Up @@ -238,7 +238,7 @@ subroutine zero_bcs(fates,s)
fates%bc_in(s)%precip24_pa(:) = 0.0_r8
fates%bc_in(s)%relhumid24_pa(:) = 0.0_r8
fates%bc_in(s)%wind24_pa(:) = 0.0_r8

fates%bc_in(s)%t_a10_pa(:) = 0.0_r8
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is this intentional or an overlap with another PR? I can't see where the info is being used here...

fates%bc_in(s)%lightning24(:) = 0.0_r8
fates%bc_in(s)%pop_density(:) = 0.0_r8
fates%bc_in(s)%solad_parb(:,:) = 0.0_r8
Expand Down Expand Up @@ -473,6 +473,7 @@ subroutine allocate_bcin(bc_in, nlevsoil_in, nlevdecomp_in, num_lu_harvest_cats)

! Photosynthesis
allocate(bc_in%filter_photo_pa(maxPatchesPerSite))
allocate(bc_in%t_a10_pa(maxPatchesPerSite))
allocate(bc_in%dayl_factor_pa(maxPatchesPerSite))
allocate(bc_in%esat_tv_pa(maxPatchesPerSite))
allocate(bc_in%eair_pa(maxPatchesPerSite))
Expand Down
5 changes: 4 additions & 1 deletion main/FatesInterfaceTypesMod.F90
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Expand Up @@ -405,7 +405,10 @@ module FatesInterfaceTypesMod

! daylength scaling factor (0-1)
real(r8), allocatable :: dayl_factor_pa(:)


! 10-day running mean of 2m temperature (K)
real(r8), allocatable :: t_a10_pa(:)

! saturation vapor pressure at t_veg (Pa)
real(r8), allocatable :: esat_tv_pa(:)

Expand Down
34 changes: 32 additions & 2 deletions parameter_files/fates_params_default.cdl
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Expand Up @@ -166,6 +166,18 @@ variables:
double fates_eca_vmax_ptase(fates_pft) ;
fates_eca_vmax_ptase:units = "gP/m2/s" ;
fates_eca_vmax_ptase:long_name = "maximum production rate for biochemical P (per m2) (ECA)" ;
double fates_eca_vcmax_np1(fates_pft) ;
fates_eca_vcmax_np1:long_name = "vcmax~np relationship coefficient" ;
fates_eca_vcmax_np1:unit = "" ;
double fates_eca_vcmax_np2(fates_pft) ;
fates_eca_vcmax_np2:long_name = "vcmax~np relationship coefficient" ;
fates_eca_vcmax_np2:unit = "" ;
double fates_eca_vcmax_np3(fates_pft) ;
fates_eca_vcmax_np3:long_name = "vcmax~np relationship coefficient" ;
fates_eca_vcmax_np3:unit = "" ;
double fates_eca_vcmax_np4(fates_pft) ;
fates_eca_vcmax_np4:long_name = "vcmax~np relationship coefficient" ;
fates_eca_vcmax_np4:unit = "" ;
double fates_fire_alpha_SH(fates_pft) ;
fates_fire_alpha_SH:units = "m / (kw/m)**(2/3)" ;
fates_fire_alpha_SH:long_name = "spitfire parameter, alpha scorch height, Equation 16 Thonicke et al 2010" ;
Expand Down Expand Up @@ -247,6 +259,9 @@ variables:
double fates_leaf_c3psn(fates_pft) ;
fates_leaf_c3psn:units = "flag" ;
fates_leaf_c3psn:long_name = "Photosynthetic pathway (1=c3, 0=c4)" ;
double fates_leaf_flnr(fates_pft) ;
fates_leaf_flnr:units = "gN Rubisco / gN leaf" ;
fates_leaf_flnr:long_name = "fraction of leaf N in the Rubisco enzyme" ;
double fates_leaf_clumping_index(fates_pft) ;
fates_leaf_clumping_index:units = "fraction (0-1)" ;
fates_leaf_clumping_index:long_name = "factor describing how much self-occlusion of leaf scattering elements decreases light interception" ;
Expand Down Expand Up @@ -383,10 +398,10 @@ variables:
fates_prescribed_npp_understory:units = "kgC / m^2 / yr" ;
fates_prescribed_npp_understory:long_name = "NPP per unit crown area of understory trees for prescribed physiology mode" ;
double fates_prescribed_nuptake(fates_pft) ;
fates_prescribed_nuptake:units = "fraction" ;
fates_prescribed_nuptake:units = "fraction" ;
fates_prescribed_nuptake:long_name = "Prescribed N uptake flux. 0=fully coupled simulation >0=prescribed (experimental)" ;
double fates_prescribed_puptake(fates_pft) ;
fates_prescribed_puptake:units = "fraction" ;
fates_prescribed_puptake:units = "fraction" ;
fates_prescribed_puptake:long_name = "Prescribed P uptake flux. 0=fully coupled simulation, >0=prescribed (experimental)" ;
double fates_prescribed_recruitment(fates_pft) ;
fates_prescribed_recruitment:units = "n/yr" ;
Expand Down Expand Up @@ -834,6 +849,18 @@ data:
fates_eca_vmax_ptase = 5e-09, 5e-09, 5e-09, 5e-09, 5e-09, 5e-09, 5e-09,
5e-09, 5e-09, 5e-09, 5e-09, 5e-09 ;

fates_eca_vcmax_np1 = 4.02421875, 3.2345, 4.800, 3.878125, 4.800, 4.7175,
3.9421875, 3.700, 3.7859375, 3.86757, 3.7859375, 4.43859375 ;

fates_eca_vcmax_np2 = 0.7640625, 0.7828125, 0.7453125, 0.9140625, 0.8015625,
0.91875, 1.096875, 0.6, 1.134375, 0.742968, 1.134375, 0.6703125 ;

fates_eca_vcmax_np3 = 0.07125, 0.08375, 0.08625, 0.19125, 0.12125, 0.185,
0.1225, 0.04, 0.1725, 0.126875, 0.1725, 0.14625 ;

fates_eca_vcmax_np4 = 0.282, 0.282, 0.282, 0.282, 0.282, 0.282, 0.282, 0.282,
0.282, 0.282, 0.282, 0.282 ;

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How was variability in these parameters calculated? Also worth noting based on analysis by Luo et al 2021 that the values of Vcmax that we get are v likely to be low-biased based on the parameter values from my 2014 paper.

This will also low-bias Jmax, though if we can get better estimates of Vcmax then I don't think we'll need to edit the Jmax~Vcmax relationship. Am working on getting better estimates of the Vcmax parameters.

fates_fire_alpha_SH = 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
0.2 ;

Expand Down Expand Up @@ -944,6 +971,9 @@ data:
0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75 ;

fates_leaf_c3psn = 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0 ;

fates_leaf_flnr = 0.0461, 0.04875, 0.0546, 0.0515, 0.0716, 0.1007, 0.0517,
0.0943, 0.0943, 0.1365, 0.1365, 0.09 ;

fates_leaf_clumping_index = 0.85, 0.85, 0.8, 0.85, 0.85, 0.9, 0.85, 0.9,
0.9, 0.75, 0.75, 0.75 ;
Expand Down
16 changes: 8 additions & 8 deletions parteh/PRTAllometricCNPMod.F90
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Expand Up @@ -1601,11 +1601,11 @@ subroutine CNPAllocateRemainder(this,c_gain, n_gain, p_gain, &

! If any N or P is still hanging around, put it in storage

state_n(store_id)%ptr = state_n(store_id)%ptr + n_gain
state_p(store_id)%ptr = state_p(store_id)%ptr + p_gain
!state_n(store_id)%ptr = state_n(store_id)%ptr + n_gain
!state_p(store_id)%ptr = state_p(store_id)%ptr + p_gain

n_gain = 0._r8
p_gain = 0._r8
!n_gain = 0._r8
!p_gain = 0._r8


! -----------------------------------------------------------------------------------
Expand Down Expand Up @@ -1638,13 +1638,13 @@ subroutine CNPAllocateRemainder(this,c_gain, n_gain, p_gain, &
! -----------------------------------------------------------------------------------

c_efflux = max(0.0_r8,c_gain)
! n_efflux = max(0.0_r8,n_gain)
! p_efflux = max(0.0_r8,p_gain)
n_efflux = max(0.0_r8,n_gain)
p_efflux = max(0.0_r8,p_gain)


c_gain = 0.0_r8
! n_gain = 0.0_r8
! p_gain = 0.0_r8
n_gain = 0.0_r8
p_gain = 0.0_r8

return
end subroutine CNPAllocateRemainder
Expand Down