Format

Author: Espeer5

ext/CreateParametersExt.jl

@@ -628,7 +628,7 @@ function TwoStreamParameters(
         ρ_leaf = FT.(ρ_leaf)
         τ_leaf = FT.(τ_leaf)
     end
-    
+
     if (isnothing(spectral_discretization))
         spectral_discretization = TwoBandSpectralDiscretization{FT}()
     end

src/standalone/Vegetation/Canopy.jl

@@ -457,7 +457,7 @@ function ClimaLand.make_update_aux(
         p.canopy.radiative_transfer.G .= compute_G(G_Function, θs)
         RT = canopy.radiative_transfer
         banded_sw_d = (sw_d) -> sw_d .* RT.parameters.spectral_discretization.I
-        @. SW_d.= banded_sw_d(p.drivers.SW_d)
+        @. SW_d .= banded_sw_d(p.drivers.SW_d)
         K = p.canopy.radiative_transfer.K
         @. K = extinction_coeff(p.canopy.radiative_transfer.G, θs)
         DOY =
@@ -489,7 +489,10 @@ function ClimaLand.make_update_aux(
         )
 
         # Extract PAR radiation from radiative transfer output
-        get_PAR = (rt) -> sum(map(x -> x.abs, rt) .* spectral_discretization.PAR_proportions)
+        get_PAR =
+            (rt) -> sum(
+                map(x -> x.abs, rt) .* spectral_discretization.PAR_proportions,
+            )
         faPAR = get_PAR.(p.canopy.radiative_transfer.rt)
 
 
@@ -558,7 +561,8 @@ function ClimaLand.make_update_aux(
 
         # Update Rd, An, Vcmax25 (if applicable to model) in place
         Vcmax25 = p.canopy.photosynthesis.Vcmax25
-        get_par_d = (sw_d) -> sum(sw_d .* spectral_discretization.PAR_proportions)
+        get_par_d =
+            (sw_d) -> sum(sw_d .* spectral_discretization.PAR_proportions)
         par_d = get_par_d.(SW_d)
         update_photosynthesis!(
             Rd,

src/standalone/Vegetation/canopy_parameterizations.jl

@@ -99,21 +99,11 @@ function compute_fractional_absorbances!(
 ) where {FT}
     RTP = RT.parameters
     if typeof(RTP.ρ_leaf) <: Tuple
-        @. p.canopy.radiative_transfer.rt = canopy_sw_rt_beer_lambert(
-            RTP.Ω,
-            (RTP.ρ_leaf,),
-            LAI,
-            K,
-            (α_soil,),
-        )
+        @. p.canopy.radiative_transfer.rt =
+            canopy_sw_rt_beer_lambert(RTP.Ω, (RTP.ρ_leaf,), LAI, K, (α_soil,))
     else
-        @. p.canopy.radiative_transfer.rt = canopy_sw_rt_beer_lambert(
-            RTP.Ω,
-            RTP.ρ_leaf,
-            LAI,
-            K,
-            (α_soil,),
-        )
+        @. p.canopy.radiative_transfer.rt =
+            canopy_sw_rt_beer_lambert(RTP.Ω, RTP.ρ_leaf, LAI, K, (α_soil,))
     end
 end
 
@@ -205,7 +195,10 @@ function canopy_sw_rt_beer_lambert(
     AR = (1 .- ρ_leaf) .* (1 - exp(-K * LAI * Ω)) .* (1 .- α_soil)
     TR = exp(-K * LAI * Ω)
     RR = FT(1) .- AR .- TR .* (1 .- α_soil)
-    return ntuple(i -> (; abs = AR[i], refl = RR[i], trans = TR), length(ρ_leaf))
+    return ntuple(
+        i -> (; abs = AR[i], refl = RR[i], trans = TR),
+        length(ρ_leaf),
+    )
 end
 
 """
@@ -269,8 +262,8 @@ function canopy_sw_rt_two_stream(
     c = ω .* β
     d = ω .* β₀ .* μ̄ .* K
     f = ω .* μ̄ .* K .* (1 .- β₀)
-    h = .√(b.^2 .- c.^2) ./ μ̄
-    σ = (μ̄ * K)^2 .+ c.^2 .- b.^2
+    h = .√(b .^ 2 .- c .^ 2) ./ μ̄
+    σ = (μ̄ * K)^2 .+ c .^ 2 .- b .^ 2
 
     u₁ = b .- c ./ α_soil
     u₂ = b .- c .* α_soil
@@ -303,11 +296,15 @@ function canopy_sw_rt_two_stream(
     # h coefficients for direct downward flux
     h₄ = .-f .* p₃ .- c .* d
     h₅ =
-        -1 ./ d₂ .*
-        (h₄ .* (u₂ .+ μ̄ .* h) ./ (σ .* s₁) .+ (u₃ .- h₄ ./ σ .* (u₂ .- μ̄ .* K)) .* s₂)
+        -1 ./ d₂ .* (
+            h₄ .* (u₂ .+ μ̄ .* h) ./ (σ .* s₁) .+
+            (u₃ .- h₄ ./ σ .* (u₂ .- μ̄ .* K)) .* s₂
+        )
     h₆ =
-        1 ./ d₂ .*
-        (h₄ ./ σ .* (u₂ .- μ̄ .* h) .* s₁ .+ (u₃ .- h₄ ./ σ .* (u₂ .- μ̄ .* K)) .* s₂)
+        1 ./ d₂ .* (
+            h₄ ./ σ .* (u₂ .- μ̄ .* h) .* s₁ .+
+            (u₃ .- h₄ ./ σ .* (u₂ .- μ̄ .* K)) .* s₂
+        )
 
     # h coefficients for diffuse upward flux
     h₇ = c .* (u₁ .- μ̄ .* h) ./ (d₁ .* s₁)
@@ -342,12 +339,10 @@ function canopy_sw_rt_two_stream(
 
         # Compute the direct fluxes into/out of the layer
         I_dir_up =
-            h₁ .* exp.(-K * L * Ω) ./ σ .+
-            h₂ .* exp.(.-h .* L .* Ω) .+
+            h₁ .* exp.(-K * L * Ω) ./ σ .+ h₂ .* exp.(.-h .* L .* Ω) .+
             h₃ .* exp.(h .* L .* Ω)
         I_dir_dn =
-            h₄ .* exp.(-K * L * Ω) ./ σ .+
-            h₅ .* exp.(.-h .* L .* Ω) .+
+            h₄ .* exp.(-K * L * Ω) ./ σ .+ h₅ .* exp.(.-h .* L .* Ω) .+
             h₆ .* exp.(h .* L .* Ω)
 
         # Add collimated radiation to downard flux
@@ -372,7 +367,8 @@ function canopy_sw_rt_two_stream(
 
 
         # Add radiation absorbed in the layer to total absorbed radiation
-        F_abs = F_abs .+ (1 - frac_diff) .* I_dir_abs .+ (frac_diff) .* I_dif_abs
+        F_abs =
+            F_abs .+ (1 - frac_diff) .* I_dir_abs .+ (frac_diff) .* I_dif_abs
 
         # Save input/output values to compute energy balance of next layer
         I_dir_up_prev = I_dir_up
@@ -387,7 +383,14 @@ function canopy_sw_rt_two_stream(
     # Convert fractional absorption into absorption and return
     # Ensure floating point precision is correct (it may be different for PAR)
     F_trans = (1 .- F_abs .- F_refl) ./ (1 .- α_soil)
-    return ntuple(i -> (; abs = FT(F_abs[i]), refl = FT(F_refl[i]), trans = FT(F_trans[i])), length(ρ_leaf))
+    return ntuple(
+        i -> (;
+            abs = FT(F_abs[i]),
+            refl = FT(F_refl[i]),
+            trans = FT(F_trans[i]),
+        ),
+        length(ρ_leaf),
+    )
 end
 
 """

src/standalone/Vegetation/ground_drivers.jl

@@ -56,7 +56,9 @@ function PrescribedGroundConditions(
     )),
     ψ::Function = t -> 0.0,
     T::Function = t -> 298.0,
-    spectral_discretization::AbstractSpectralDiscretization = ClimaLand.TwoBandSpectralDiscretization{FT}(),
+    spectral_discretization::AbstractSpectralDiscretization = ClimaLand.TwoBandSpectralDiscretization{
+        FT,
+    }(),
     α_ground::Tuple = FT.((0.2, 0.4)),
     ϵ = FT(0.99),
 )

src/standalone/Vegetation/radiation.jl

@@ -160,10 +160,7 @@ ClimaLand.auxiliary_vars(model::Union{BeerLambertModel, TwoStreamModel}) =
 ClimaLand.auxiliary_types(
     model::Union{BeerLambertModel{FT}, TwoStreamModel{FT}},
 ) where {FT} = (
-    NTuple{
-        length(model.parameters.spectral_discretization.λ) - 1,
-        FT,
-    },
+    NTuple{length(model.parameters.spectral_discretization.λ) - 1, FT},
     NTuple{
         length(model.parameters.spectral_discretization.λ) - 1,
         NamedTuple{(:abs, :refl, :trans), Tuple{FT, FT, FT}},

test/standalone/Vegetation/canopy_model.jl

@@ -578,10 +578,8 @@ end
         mechanism_cases = (FT(1), mechanism_field)
         rooting_cases = (FT(0.5), fill(FT(0.5), domain.space.surface))
         # test default values as field
-        ρ_leaf_cases = (
-            (FT(0.1), FT(0.1)),
-            fill((FT(0.1), FT(0.1)), domain.space.surface),
-        )
+        ρ_leaf_cases =
+            ((FT(0.1), FT(0.1)), fill((FT(0.1), FT(0.1)), domain.space.surface))
         ld_cases = (FT(0.5), fill(FT(0.5), domain.space.surface))
         zipped_params = zip(
             g1_cases,
@@ -1178,10 +1176,8 @@ end
         rooting_cases = (FT(0.5), fill(FT(0.5), domain.space.surface))
         ρ_leaf_cases =
             (FT.((0.1, 0.45)), fill(FT.((0.1, 0.45)), domain.space.surface))
-        τ_leaf_cases = (
-            FT.((0.05, 0.25)),
-            fill(FT.((0.05, 0.25)), domain.space.surface),
-        )
+        τ_leaf_cases =
+            (FT.((0.05, 0.25)), fill(FT.((0.05, 0.25)), domain.space.surface))
         χl_cases = (FT(0.1), fill(FT(0.1), domain.space.surface))
         zipped_params = zip(
             Ω_cases,
@@ -1428,7 +1424,8 @@ end
                 )
                 get_abs = (rt) -> map(x -> x.abs, rt)
                 @test all(
-                    Array(parent(get_abs.(p.canopy.radiative_transfer.rt))) .== FT(0),
+                    Array(parent(get_abs.(p.canopy.radiative_transfer.rt))) .==
+                    FT(0),
                 )
                 @test all(
                     Array(parent(p.canopy.autotrophic_respiration.Ra)) .==