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Add simple SIF model to photosynthesis #706

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Add simple SIF model to photosynthesis #706

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e86fd4d
add simple SIF model to photosynthesis
AlexisRenchon Jul 24, 2024
4cf8c39
add SIF diurnal to ClimaLandSimulations
AlexisRenchon Jul 30, 2024
8d0ad0a
WIP
AlexisRenchon Jul 30, 2024
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43 changes: 32 additions & 11 deletions ext/CreateParametersExt.jl
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Expand Up @@ -6,7 +6,6 @@ import Insolation.Parameters.InsolationParameters
import SurfaceFluxes.Parameters.SurfaceFluxesParameters
import SurfaceFluxes.UniversalFunctions as UF
import ClimaParams as CP

import ClimaLand
import ClimaLand.Soil
# Parameter structs
Expand All @@ -15,6 +14,7 @@ import ClimaLand.Soil.EnergyHydrologyParameters
import ClimaLand.Canopy.AutotrophicRespirationParameters
import ClimaLand.Canopy.FarquharParameters
import ClimaLand.Canopy.OptimalityFarquharParameters
import ClimaLand.Canopy.SIFParameters
import ClimaLand.Canopy.MedlynConductanceParameters
import ClimaLand.Canopy.BeerLambertParameters
import ClimaLand.Canopy.TwoStreamParameters
Expand Down Expand Up @@ -133,16 +133,24 @@ toml_dict = CP.create_toml_dict(Float32);
ClimaLand.Canopy.FarquharParameters(toml_dict, ClimaLand.Canopy.C3(); Vcmax25 = 99999999, pc = 444444444)
```
"""
FarquharParameters(
function FarquharParameters(
::Type{FT},
mechanism;
kwargs...,
) where {FT <: AbstractFloat} =
FarquharParameters(CP.create_toml_dict(FT), mechanism; kwargs...)
) where {FT <: AbstractFloat}
sif_parameters = SIFParameters{FT}()
FarquharParameters(
CP.create_toml_dict(FT),
mechanism,
sif_parameters;
kwargs...,
)
end

function FarquharParameters(
toml_dict::CP.AbstractTOMLDict,
mechanism;
mechanism,
sif_parameters;
Vcmax25 = 5e-5,
kwargs...,
)
Expand All @@ -167,9 +175,11 @@ function FarquharParameters(
parameters = CP.get_parameter_values(toml_dict, name_map, "Land")
FT = CP.float_type(toml_dict)
MECH = typeof(mechanism)
return FarquharParameters{FT, MECH}(;
SP = typeof(sif_parameters)
return FarquharParameters{FT, MECH, SP}(;
mechanism,
Vcmax25,
sif_parameters,
parameters...,
kwargs...,
)
Expand Down Expand Up @@ -199,13 +209,19 @@ toml_dict = CP.create_toml_dict(Float32);
ClimaLand.Canopy.OptimalityFarquharParameters(toml_dict; pc = 444444444)
```
"""
OptimalityFarquharParameters(
function OptimalityFarquharParameters(
::Type{FT};
kwargs...,
) where {FT <: AbstractFloat} =
OptimalityFarquharParameters(CP.create_toml_dict(FT); kwargs...)
) where {FT <: AbstractFloat}
sif_parameters = SIFParameters{FT}()
OptimalityFarquharParameters(
CP.create_toml_dict(FT),
sif_parameters;
kwargs...,
)
end

function OptimalityFarquharParameters(toml_dict; kwargs...)
function OptimalityFarquharParameters(toml_dict, sif_parameters; kwargs...)
name_map = (;
:Jmax_activation_energy => :ΔHJmax,
:intercellular_O2_concentration => :oi,
Expand All @@ -229,7 +245,12 @@ function OptimalityFarquharParameters(toml_dict; kwargs...)
params = CP.get_parameter_values(toml_dict, name_map, "Land")
FT = CP.float_type(toml_dict)
mechanism = ClimaLand.Canopy.C3()
return OptimalityFarquharParameters{FT}(; params..., kwargs..., mechanism)
return OptimalityFarquharParameters{FT, typeof(sif_parameters)}(;
sif_parameters,
params...,
kwargs...,
mechanism,
)
end


Expand Down
2 changes: 2 additions & 0 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Ha1/US-Ha1_parameters.jl
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Expand Up @@ -158,6 +158,7 @@ function photosynthesis_harvard(;
ΔHΓstar = FT(37830),
ΔHJmax = FT(43540),
ΔHRd = FT(46390),
sif_parameters = SIFParameters{FT}(),
)
return FarquharParameters(
Vcmax25,
Expand All @@ -178,6 +179,7 @@ function photosynthesis_harvard(;
sc,
pc,
mechanism,
sif_parameters,
)
end

Expand Down
2 changes: 2 additions & 0 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-MOz/US-MOz_parameters.jl
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Expand Up @@ -158,6 +158,7 @@ function photosynthesis_ozark(;
ΔHΓstar = FT(37830),
ΔHJmax = FT(43540),
ΔHRd = FT(46390),
sif_parameters = SIFParameters{FT}(),
)
return FarquharParameters(
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do we need to pass sif_parameters here? I thought in our methods in CreateParametersExt we have a default which makes the sif_params and uses them

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We need it here because it calls the struct, not the function.

Note that we plan to refactor ClimaLandSimulations (with the help of Gabriele), to have it better designed in general, with PFT framework, global simulations... and ready for ClimaCalibrate

Vcmax25,
Expand All @@ -178,6 +179,7 @@ function photosynthesis_ozark(;
sc,
pc,
mechanism,
sif_parameters,
)
end

Expand Down
2 changes: 2 additions & 0 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-NR1/US-NR1_parameters.jl
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Expand Up @@ -158,6 +158,7 @@ function photosynthesis_niwotridge(;
ΔHΓstar = FT(37830),
ΔHJmax = FT(43540),
ΔHRd = FT(46390),
sif_parameters = SIFParameters{FT}(),
)
return FarquharParameters(
Vcmax25,
Expand All @@ -178,6 +179,7 @@ function photosynthesis_niwotridge(;
sc,
pc,
mechanism,
sif_parameters,
)
end

Expand Down
2 changes: 2 additions & 0 deletions lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Var/US-Var_parameters.jl
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Expand Up @@ -158,6 +158,7 @@ function photosynthesis_vairaranch(;
ΔHΓstar = FT(37830),
ΔHJmax = FT(43540),
ΔHRd = FT(46390),
sif_parameters = SIFParameters{FT}(),
)
return FarquharParameters(
Vcmax25,
Expand All @@ -178,6 +179,7 @@ function photosynthesis_vairaranch(;
sc,
pc,
mechanism,
sif_parameters,
)
end

Expand Down
2 changes: 2 additions & 0 deletions src/standalone/Vegetation/Canopy.jl
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Expand Up @@ -543,10 +543,12 @@ function ClimaLand.make_update_aux(

# Update Rd, An, Vcmax25 (if applicable to model) in place
Vcmax25 = p.canopy.photosynthesis.Vcmax25
SIF = p.canopy.photosynthesis.SIF
update_photosynthesis!(
Rd,
An,
Vcmax25,
SIF,
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Can we make these two things independent? Why does update_photosynthesis! needs SIF?

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we could, it just currently lives in the photosynthesis name space (stored in canopy.photosynthesis.SIF), we thought it was okay for now with a simple model...

Do you suggest making a new canopy output / model, stored in canopy.SIF, in a Vegetation/SIF.jl file? (similar to what we have, photosynthesis.jl, radiation.jl, stomatalconductance.jl, etc.)

If we do, it will be a bit more involved and a breaking change, but it will allow to have multiple SIF modules

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maybe we could do that for a next PR?

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@kmdeck

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Yes. I think it should be an independent module. If anything it is a radiative variable and it should live in radiation instead of photosynthesis.

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Like SIF would be equivalent to APAR. We measure it with a radiometer.

canopy.photosynthesis,
T_canopy,
p.canopy.radiative_transfer.par.abs,
Expand Down
37 changes: 37 additions & 0 deletions src/standalone/Vegetation/canopy_parameterizations.jl
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Expand Up @@ -1041,3 +1041,40 @@ function plant_respiration_growth(f2::FT, An::FT, Rpm::FT) where {FT}
Rg = f2 * (An - Rpm)
return Rg
end

# 4 Solar Induced Fluorescence (SIF)

# call function below inside photosynthesis.jl p

"""
compute_SIF_at_a_point(Tc::FT,APAR::FT, Vcmax25::FT)

Computes observed SIF at 755 nm in W/m^2. Note that Tc is in Kelvin, and photo
synthetic rates are in mol/m^2/s, and APAR is in PPFD.
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"""
function compute_SIF_at_a_point(
APAR::FT,
Tc::FT,
Vcmax25::FT,
R::FT,
photosynthesis_parameters,
) where {FT}

(; ΔHJmax, To, θj, ϕ, sif_parameters) = photosynthesis_parameters
Jmax = max_electron_transport(Vcmax25, ΔHJmax, Tc, To, R)
J = electron_transport(APAR, Jmax, θj, ϕ)
(; kf, kd_p1, kd_p2, min_kd, kn_p1, kn_p2, kp, kappa_p1, kappa_p2) =
sif_parameters
Tf = FT(273.15)
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this is kind of annoying, but we should get T_freeze from the earth_param_set in Canopy.jl update_aux!, and pass as an argument... like we do with R

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@AlexisRenchon AlexisRenchon Jul 30, 2024 •
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Let's do that together!
I am not sure of how to do it correctly, do you mean have Tf as an argument of compute_SIF_at_a_point and get that argument inside Canopy.jl update_aux!?

Is this to reduce allocation? or make sure we use params instead of hard coding?

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+1.

kd = max(kd_p1 * (Tc - Tf) + kd_p2, min_kd)
x = 1 - J / Jmax
kn = (kn_p1 * x - kn_p2) * x
ϕp0 = kp / (kf + kp + kn)
ϕp = J / Jmax * ϕp0
ϕf = kf / (kf + kd + kn) * (1 - ϕp)
κ = kappa_p1 * Vcmax25 * FT(1e6) + kappa_p2 # formula expects Vcmax25 in μmol/m^2/s
F = APAR * ϕf
SIF_755 = F / κ

return SIF_755
end
15 changes: 10 additions & 5 deletions src/standalone/Vegetation/optimality_farquhar.jl
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Expand Up @@ -8,7 +8,7 @@ The required parameters for the optimality Farquhar photosynthesis model.
Currently, only C3 photosynthesis is supported.
$(DocStringExtensions.FIELDS)
"""
Base.@kwdef struct OptimalityFarquharParameters{FT <: AbstractFloat}
Base.@kwdef struct OptimalityFarquharParameters{FT <: AbstractFloat, SP}
"Photosynthesis mechanism: C3 only"
mechanism::C3
"Γstar at 25 °C (mol/mol)"
Expand Down Expand Up @@ -45,6 +45,8 @@ Base.@kwdef struct OptimalityFarquharParameters{FT <: AbstractFloat}
pc::FT
"Constant describing cost of maintaining electron transport (unitless)"
c::FT
"SIF Parameters"
sif_parameters::SP
end

Base.eltype(::OptimalityFarquharParameters{FT}) where {FT} = FT
Expand Down Expand Up @@ -72,14 +74,14 @@ function OptimalityFarquharModel{FT}(
end

ClimaLand.auxiliary_vars(model::OptimalityFarquharModel) =
(:An, :GPP, :Rd, :Vcmax25)
(:An, :GPP, :Rd, :Vcmax25, :SIF)
ClimaLand.auxiliary_types(model::OptimalityFarquharModel{FT}) where {FT} =
(FT, FT, FT, FT)
(FT, FT, FT, FT, FT)
ClimaLand.auxiliary_domain_names(::OptimalityFarquharModel) =
(:surface, :surface, :surface, :surface)
(:surface, :surface, :surface, :surface, :surface)

"""
update_photosynthesis!(Rd, An, Vcmax25,
update_photosynthesis!(Rd, An, Vcmax25,SIF,
model::OptimalityFarquharModel,
T,
APAR,
Expand All @@ -101,6 +103,7 @@ function update_photosynthesis!(
Rd,
An,
Vcmax25,
SIF,
model::OptimalityFarquharModel,
T,
APAR,
Expand Down Expand Up @@ -152,4 +155,6 @@ function update_photosynthesis!(
@. Vcmax25 = Vcmax / arrhenius_function(T, To, R, ΔHVcmax)
@. Rd = dark_respiration(Vcmax25, β, f, ΔHRd, T, To, R)
@. An = net_photosynthesis(Ac, Aj, Rd, β)
@. SIF = compute_SIF_at_a_point(APAR, T, Vcmax25, R, model.parameters)
end
Base.broadcastable(m::OptimalityFarquharParameters) = tuple(m)
50 changes: 43 additions & 7 deletions src/standalone/Vegetation/photosynthesis.jl
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@@ -1,4 +1,33 @@
export FarquharParameters, FarquharModel, C3, C4
export SIFParameters, FarquharParameters, FarquharModel, C3, C4

abstract type AbstractPhotosynthesisModel{FT} <: AbstractCanopyComponent{FT} end

"""
SIFParameters{FT<:AbstractFloat}

The required parameters for the SIF parameterisation [give citation].
$(DocStringExtensions.FIELDS)
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"""
@kwdef struct SIFParameters{FT <: AbstractFloat}
""
kf::FT = FT(0.05)
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""
kd_p1::FT = FT(0.03)
""
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kd_p2::FT = FT(0.0273)
""
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min_kd::FT = FT(0.087)
""
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kn_p1::FT = FT(6.2473)
""
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kn_p2::FT = FT(0.5944)
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""
kp::FT = FT(4.0)
""
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kappa_p1::FT = FT(0.045)
""
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kappa_p2::FT = FT(7.85)
end
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abstract type AbstractPhotosynthesisMechanism end
"""
Expand All @@ -17,14 +46,15 @@ struct C4 <: AbstractPhotosynthesisMechanism end

abstract type AbstractPhotosynthesisModel{FT} <: AbstractCanopyComponent{FT} end
"""
FarquharParameters{FT<:AbstractFloat, MECH <: AbstractPhotosynthesisMechanism}
FarquharParameters{FT<:AbstractFloat, MECH <: AbstractPhotosynthesisMechanism, SP <: SIFParameters}

The required parameters for the Farquhar photosynthesis model.
$(DocStringExtensions.FIELDS)
"""
Base.@kwdef struct FarquharParameters{
FT <: AbstractFloat,
MECH <: AbstractPhotosynthesisMechanism,
SP <: SIFParameters,
}
"Vcmax at 25 °C (mol CO2/m^2/s)"
Vcmax25::FT
Expand Down Expand Up @@ -62,6 +92,8 @@ Base.@kwdef struct FarquharParameters{
pc::FT
"Photosynthesis mechanism: C3 or C4"
mechanism::MECH
""
sif_parameters::SP
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end

Base.eltype(::FarquharParameters{FT}) where {FT} = FT
Expand All @@ -78,12 +110,12 @@ function FarquharModel{FT}(
end

ClimaLand.name(model::AbstractPhotosynthesisModel) = :photosynthesis
ClimaLand.auxiliary_vars(model::FarquharModel) = (:An, :GPP, :Rd, :Vcmax25)
ClimaLand.auxiliary_vars(model::FarquharModel) =
(:An, :GPP, :Rd, :Vcmax25, :SIF)
ClimaLand.auxiliary_types(model::FarquharModel{FT}) where {FT} =
(FT, FT, FT, FT)
(FT, FT, FT, FT, FT)
ClimaLand.auxiliary_domain_names(::FarquharModel) =
(:surface, :surface, :surface, :surface)

(:surface, :surface, :surface, :surface, :surface)

function photosynthesis_at_a_point_Farquhar(
T,
Expand Down Expand Up @@ -126,7 +158,7 @@ function photosynthesis_at_a_point_Farquhar(
end

"""
update_photosynthesis!(Rd, An, Vcmax25,
update_photosynthesis!(Rd, An, Vcmax25, SIF,
model::FarquharModel,
T,
APAR,
Expand All @@ -148,6 +180,7 @@ function update_photosynthesis!(
Rd,
An,
Vcmax25field,
SIF,
model::FarquharModel,
T,
APAR,
Expand All @@ -170,8 +203,11 @@ function update_photosynthesis!(
model.parameters,
)
Vcmax25field .= Vcmax25
@. SIF = compute_SIF_at_a_point(APAR, T, Vcmax25, R, model.parameters)

end
Base.broadcastable(m::AbstractPhotosynthesisMechanism) = tuple(m)
Base.broadcastable(m::FarquharParameters) = tuple(m)
Base.broadcastable(m::SIFParameters) = tuple(m)

include("./optimality_farquhar.jl")
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