WIP

ext/CreateParametersExt.jl

@@ -14,6 +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
@@ -203,13 +204,15 @@ 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,
@@ -229,11 +232,11 @@ function OptimalityFarquharParameters(toml_dict; kwargs...)
         :CO2_activation_energy => :ΔHkc,
         :moisture_stress_ref_water_pressure => :pc,
     )
-
+    
     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
 
 

src/standalone/Vegetation/Canopy.jl

@@ -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,
             canopy.photosynthesis,
             T_canopy,
             p.canopy.radiative_transfer.par.abs,

src/standalone/Vegetation/canopy_parameterizations.jl

@@ -1057,17 +1057,16 @@ function compute_SIF_at_a_point(
     Tc::FT,
     Vcmax25::FT,
     R::FT,
-    photosynthesis_params,
-    sif_params,
+    photosynthesis_parameters,
 ) where {FT}
 
-    (; ΔHJmax, To, θj, ϕ) = photosynthesis_parameters
-    Jmax = max_electron_transport(Vcmax25, ΔHJmax, T, To, R)
+    (; 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_params
-    Tf = 273.15
-    kd = maximum(kd_p1 * (Tc - Tf) + kd_p2, min_kd)
+        sif_parameters
+    Tf = FT(273.15)
+    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)

src/standalone/Vegetation/optimality_farquhar.jl

@@ -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)"
@@ -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
@@ -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,
@@ -101,6 +103,7 @@ function update_photosynthesis!(
     Rd,
     An,
     Vcmax25,
+    SIF,
     model::OptimalityFarquharModel,
     T,
     APAR,
@@ -152,4 +155,13 @@ 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)
+

src/standalone/Vegetation/photosynthesis.jl

@@ -104,16 +104,13 @@ struct FarquharModel{FT, FP <: FarquharParameters{FT}} <:
 end
 
 function FarquharModel{FT}(
-    parameters::FarquharParameters{FT};
-    sif_parameters = SIFParameters{FT}(),
+    parameters::FarquharParameters{FT}
 ) where {FT <: AbstractFloat}
     return FarquharModel{
         eltype(parameters),
         typeof(parameters),
-        typeof(sif_parameters),
     }(
         parameters,
-        sif_parameters,
     )
 end
 
@@ -166,7 +163,7 @@ function photosynthesis_at_a_point_Farquhar(
 end
 
 """
-    update_photosynthesis!(Rd, An, Vcmax25,
+    update_photosynthesis!(Rd, An, Vcmax25, SIF,
         model::FarquharModel,
         T,
         APAR,
@@ -188,6 +185,7 @@ function update_photosynthesis!(
     Rd,
     An,
     Vcmax25field,
+    SIF,
     model::FarquharModel,
     T,
     APAR,
@@ -216,7 +214,6 @@ function update_photosynthesis!(
         Vcmax25,
         R,
         model.parameters,
-        model.sif_parameters,
     )
 
 end

test/standalone/Vegetation/test_bigleaf_parameterizations.jl

@@ -41,13 +41,14 @@ for FT in (Float32, Float64)
         params = OptimalityFarquharParameters(FT)
         @test params.mechanism == C3()
         model = OptimalityFarquharModel(params)
-        @test ClimaLand.auxiliary_vars(model) == (:An, :GPP, :Rd, :Vcmax25)
-        @test ClimaLand.auxiliary_types(model) == (FT, FT, FT, FT)
+        @test ClimaLand.auxiliary_vars(model) == (:An, :GPP, :Rd, :Vcmax25, :SIF)
+        @test ClimaLand.auxiliary_types(model) == (FT, FT, FT, FT, FT)
         @test ClimaLand.auxiliary_domain_names(model) ==
-              (:surface, :surface, :surface, :surface)
+              (:surface, :surface, :surface, :surface, :surface)
         Rd = zeros(FT, 1)
         An = similar(Rd)
         Vcmax25 = similar(An)
+        SIF = similar(An)
         T = FT(280)
         β = FT(1)
         medlyn_factor = FT(10.0)
@@ -57,6 +58,7 @@ for FT in (Float32, Float64)
             Rd,
             An,
             Vcmax25,
+            SIF,
             model,
             T,
             APAR,
@@ -68,6 +70,7 @@ for FT in (Float32, Float64)
         @test Rd[1] != 0.0
         @test Vcmax25[1] != 0.0
         @test An[1] != 0.0
+        @test SIF[1] !=0.0
     end
 
     @testset "Big Leaf Parameterizations, FT = $FT" begin