Extend Vcmax to support SpaceVaryingInput

experiments/benchmarks/land.jl

@@ -369,7 +369,12 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     g1 = FT(141) # Wang et al: 141 sqrt(Pa) for Medlyn model; Natan used 300.
 
     #Photosynthesis model
-    Vcmax25 = FT(9e-5) # from Yujie's paper 4.5e-5 , Natan used 9e-5
+    Vcmax25 = SpaceVaryingInput(
+        "/net/sampo/data1/ClimaArtifacts/artifacts/clm_data/vegetation_properties_map.nc",
+        "vcmx25",
+        surface_space;
+        regridder_type,
+    )
 
     # Plant Hydraulics and general plant parameters
     SAI = FT(0.0) # m2/m2

experiments/long_runs/land.jl

@@ -369,7 +369,13 @@ function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (101, 15))
     g1 = FT(141) # Wang et al: 141 sqrt(Pa) for Medlyn model; Natan used 300.
 
     #Photosynthesis model
-    Vcmax25 = FT(9e-5) # from Yujie's paper 4.5e-5 , Natan used 9e-5
+    Vcmax25 = SpaceVaryingInput(
+        "/net/sampo/data1/ClimaArtifacts/artifacts/clm_data/vegetation_properties_map.nc",
+        "vcmx25",
+        surface_space;
+        regridder_type,
+        file_reader_kwargs = (; preprocess_func = (x) -> x / 1_000_000),
+    )
 
     # Plant Hydraulics and general plant parameters
     SAI = FT(0.0) # m2/m2

ext/CreateParametersExt.jl

@@ -106,19 +106,19 @@ end
 
 """
     function FarquharParameters(
-        FT, 
+        FT,
         mechanism::AbstractPhotosynthesisMechanism;
         Vcmax25 = FT(5e-5),
         kwargs...  # For individual parameter overrides
     )
 
     function FarquharParameters(
-        toml_dict::CP.AbstractTOMLDict, 
+        toml_dict::CP.AbstractTOMLDict,
         mechanism::AbstractPhotosynthesisMechanism;
         Vcmax25 = FT(5e-5),
         kwargs...  # For individual parameter overrides
     )
-    
+
 Constructors for the FarquharParameters struct. Two variants:
 1. Pass in the float-type and retrieve parameter values from the default TOML dict.
 2. Pass in a TOML dictionary to retrieve parameter values.Possible calls:
@@ -166,7 +166,9 @@ 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}(;
+    Vcmax25 = FT.(Vcmax25)
+    VC = typeof(Vcmax25)
+    return FarquharParameters{FT, MECH, VC}(;
         mechanism,
         Vcmax25,
         parameters...,
@@ -181,7 +183,7 @@ end
     )
 
     function OptimalityFarquharParameters(
-        toml_dict::CP.AbstractTOMLDict, 
+        toml_dict::CP.AbstractTOMLDict,
         kwargs...  # For individual parameter overrides
     )
 
@@ -260,7 +262,7 @@ end
 EnergyHydrologyParameters has two constructors: float-type and toml dict based.
 Additional parameters must be added manually: ν, ν_ss_om, ν_ss_quartz, ν_ss_gravel, hydrology_cm, K_sat, S_s, and θ_r
 All parameters can be manually overriden via keyword arguments. Note, however,
-that certain parameters must have the same type (e.g, if a field is 
+that certain parameters must have the same type (e.g, if a field is
 supplied for porosity, it must be supplied for all other parameters
 defined in the interior of the domain). Some parameters are defined only
 on the surface of the domain (e.g albedo), while other are defined everywhere

src/standalone/Vegetation/photosynthesis.jl

@@ -17,17 +17,24 @@ struct C4 <: AbstractPhotosynthesisMechanism end
 
 abstract type AbstractPhotosynthesisModel{FT} <: AbstractCanopyComponent{FT} end
 """
-    FarquharParameters{FT<:AbstractFloat, MECH <: AbstractPhotosynthesisMechanism}
+    FarquharParameters{
+        FT<:AbstractFloat,
+        MECH <: AbstractPhotosynthesisMechanism,
+        VCMAX <: Union{FT, ClimaCore.Fields.Field}
+        }
 
 The required parameters for the Farquhar photosynthesis model.
 $(DocStringExtensions.FIELDS)
 """
 Base.@kwdef struct FarquharParameters{
     FT <: AbstractFloat,
     MECH <: AbstractPhotosynthesisMechanism,
+    VCMAX <: Union{FT, ClimaCore.Fields.Field},
 }
     "Vcmax at 25 °C (mol CO2/m^2/s)"
-    Vcmax25::FT
+    # Vcmax25::Union{FT, ClimaCore.Fields.Field{FT, ClimaCore.Spaces.AbstractSpace}}
+    Vcmax25::VCMAX
+
     "Γstar at 25 °C (mol/mol)"
     Γstar25::FT
     "Michaelis-Menten parameter for CO2 at 25 °C (mol/mol)"
@@ -93,26 +100,24 @@ function photosynthesis_at_a_point_Farquhar(
     c_co2,
     medlyn_factor,
     R,
-    parameters,
+    Vcmax25,
+    Γstar25,
+    ΔHJmax,
+    ΔHVcmax,
+    ΔHΓstar,
+    f,
+    ΔHRd,
+    To,
+    θj,
+    ϕ,
+    mechanism,
+    oi,
+    Kc25,
+    Ko25,
+    ΔHkc,
+    ΔHko,
 )
-    (;
-        Vcmax25,
-        Γstar25,
-        ΔHJmax,
-        ΔHVcmax,
-        ΔHΓstar,
-        f,
-        ΔHRd,
-        To,
-        θj,
-        ϕ,
-        mechanism,
-        oi,
-        Kc25,
-        Ko25,
-        ΔHkc,
-        ΔHko,
-    ) = parameters
+
     Jmax = max_electron_transport(Vcmax25, ΔHJmax, T, To, R)
     J = electron_transport(APAR, Jmax, θj, ϕ)
     Vcmax = compute_Vcmax(Vcmax25, T, To, R, ΔHVcmax)
@@ -123,6 +128,7 @@ function photosynthesis_at_a_point_Farquhar(
     Ko = MM_Ko(Ko25, ΔHko, T, To, R)
     Ac = rubisco_assimilation(mechanism, Vcmax, ci, Γstar, Kc, Ko, oi)
     return net_photosynthesis(Ac, Aj, Rd, β)
+
 end
 
 """
@@ -156,8 +162,27 @@ function update_photosynthesis!(
     c_co2,
     R,
 )
-    (; Vcmax25, f, ΔHRd, To) = model.parameters
-
+    (;
+        Vcmax25,
+        f,
+        ΔHRd,
+        To,
+        Γstar25,
+        ΔHJmax,
+        ΔHVcmax,
+        ΔHΓstar,
+        f,
+        ΔHRd,
+        To,
+        θj,
+        ϕ,
+        mechanism,
+        oi,
+        Kc25,
+        Ko25,
+        ΔHkc,
+        ΔHko,
+    ) = model.parameters
     @. Rd = dark_respiration(Vcmax25, β, f, ΔHRd, T, To, R)
     @. An = photosynthesis_at_a_point_Farquhar(
         T,
@@ -167,7 +192,22 @@ function update_photosynthesis!(
         c_co2,
         medlyn_factor,
         R,
-        model.parameters,
+        Vcmax25,
+        Γstar25,
+        ΔHJmax,
+        ΔHVcmax,
+        ΔHΓstar,
+        f,
+        ΔHRd,
+        To,
+        θj,
+        ϕ,
+        mechanism,
+        oi,
+        Kc25,
+        Ko25,
+        ΔHkc,
+        ΔHko,
     )
     Vcmax25field .= Vcmax25
 end

test/standalone/Vegetation/canopy_model.jl

@@ -22,10 +22,10 @@ import ClimaParams
 @testset "Canopy software pipes" begin
     for FT in (Float32, Float64)
         domain = Point(; z_sfc = FT(0.0))
-
+        Vcmax25 = fill(FT(9e-5), domain.space.surface)
         AR_params = AutotrophicRespirationParameters(FT)
         RTparams = BeerLambertParameters(FT)
-        photosynthesis_params = FarquharParameters(FT, C3())
+        photosynthesis_params = FarquharParameters(FT, C3(); Vcmax25 = Vcmax25)
         stomatal_g_params = MedlynConductanceParameters(FT)
 
         AR_model = AutotrophicRespirationModel{FT}(AR_params)
@@ -515,9 +515,9 @@ end
 @testset "Canopy software pipes with energy model" begin
     for FT in (Float32, Float64)
         domain = Point(; z_sfc = FT(0.0))
-
+        Vcmax25 = fill(FT(9e-5), domain.space.surface)
         RTparams = BeerLambertParameters(FT)
-        photosynthesis_params = FarquharParameters(FT, C3())
+        photosynthesis_params = FarquharParameters(FT, C3(); Vcmax25 = Vcmax25)
         stomatal_g_params = MedlynConductanceParameters(FT)
 
         stomatal_model = MedlynConductanceModel{FT}(stomatal_g_params)
@@ -765,7 +765,7 @@ end
 @testset "Zero LAI;" begin
     for FT in (Float32, Float64)
         domain = Point(; z_sfc = FT(0.0))
-
+        Vcmax25 = fill(FT(9e-5), domain.space.surface)
         BeerLambertparams = BeerLambertParameters(FT)
         # TwoStreamModel parameters
         Ω = FT(0.69)
@@ -787,7 +787,7 @@ end
             τ_NIR_leaf,
             G_Function,
         )
-        photosynthesis_params = FarquharParameters(FT, C3())
+        photosynthesis_params = FarquharParameters(FT, C3(); Vcmax25 = Vcmax25)
         stomatal_g_params = MedlynConductanceParameters(FT)
 
         stomatal_model = MedlynConductanceModel{FT}(stomatal_g_params)