compute fractional absorbances

CliMA · Nov 13, 2024 · 9b73ade · 9b73ade
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diff --git a/docs/src/APIs/canopy/RadiativeTransfer.md b/docs/src/APIs/canopy/RadiativeTransfer.md
@@ -13,9 +13,9 @@ ClimaLand.Canopy.BeerLambertParameters
 ## Methods
 
 ```@docs
-ClimaLand.Canopy.compute_absorbances!
-ClimaLand.Canopy.plant_absorbed_pfd_beer_lambert
-ClimaLand.Canopy.plant_absorbed_pfd_two_stream
+ClimaLand.Canopy.compute_fractional_absorbances
+ClimaLand.Canopy.canopy_sw_rt_beer_lambert
+ClimaLand.Canopy.canopy_sw_rt_two_stream
 ClimaLand.Canopy.extinction_coeff
 ClimaLand.Canopy.canopy_radiant_energy_fluxes!
 ```
diff --git a/docs/tutorials/standalone/Canopy/canopy_tutorial.jl b/docs/tutorials/standalone/Canopy/canopy_tutorial.jl
@@ -163,7 +163,6 @@ rt_params = TwoStreamParameters(
     τ_NIR_leaf = FT(0.25),
     Ω = FT(0.69),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
 )
 
 rt_model = TwoStreamModel{FT}(rt_params);

diff --git a/experiments/integrated/fluxnet/US-Ha1/US-Ha1_parameters.jl b/experiments/integrated/fluxnet/US-Ha1/US-Ha1_parameters.jl
@@ -39,7 +39,6 @@ ld = FT(0.5)
 G_Function = ConstantGFunction(ld)
 α_PAR_leaf = FT(0.1)
 λ_γ_PAR = FT(5e-7)
-λ_γ_NIR = FT(1.65e-6)
 τ_PAR_leaf = FT(0.05)
 α_NIR_leaf = FT(0.45)
 τ_NIR_leaf = FT(0.25)

diff --git a/experiments/integrated/fluxnet/US-MOz/US-MOz_parameters.jl b/experiments/integrated/fluxnet/US-MOz/US-MOz_parameters.jl
@@ -38,7 +38,6 @@ soil_α_NIR = FT(0.2)
 G_Function = CLMGFunction(χl)
 α_PAR_leaf = FT(0.1)
 λ_γ_PAR = FT(5e-7)
-λ_γ_NIR = FT(1.65e-6)
 τ_PAR_leaf = FT(0.05)
 α_NIR_leaf = FT(0.45)
 τ_NIR_leaf = FT(0.25)

diff --git a/experiments/integrated/fluxnet/US-NR1/US-NR1_parameters.jl b/experiments/integrated/fluxnet/US-NR1/US-NR1_parameters.jl
@@ -42,7 +42,6 @@ ld = FT(0.5)
 G_Function = ConstantGFunction(ld)
 α_PAR_leaf = FT(0.1)
 λ_γ_PAR = FT(5e-7)
-λ_γ_NIR = FT(1.65e-6)
 τ_PAR_leaf = FT(0.05)
 α_NIR_leaf = FT(0.35)
 τ_NIR_leaf = FT(0.25)

diff --git a/experiments/integrated/fluxnet/US-Var/US-Var_parameters.jl b/experiments/integrated/fluxnet/US-Var/US-Var_parameters.jl
@@ -46,7 +46,6 @@ ld = FT(0.5)
 G_Function = ConstantGFunction(ld)
 α_PAR_leaf = FT(0.11)
 λ_γ_PAR = FT(5e-7)
-λ_γ_NIR = FT(1.65e-6)
 τ_PAR_leaf = FT(0.05)
 α_NIR_leaf = FT(0.35)
 τ_NIR_leaf = FT(0.34)

diff --git a/experiments/standalone/Vegetation/no_vegetation.jl b/experiments/standalone/Vegetation/no_vegetation.jl
@@ -74,7 +74,6 @@ rt_params = TwoStreamParameters(
     τ_NIR_leaf = FT(0.25),
     Ω = FT(0.69),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
 )
 
 rt_model = TwoStreamModel{FT}(rt_params);

diff --git a/experiments/standalone/Vegetation/timestep_test.jl b/experiments/standalone/Vegetation/timestep_test.jl
@@ -113,7 +113,6 @@ rt_params = TwoStreamParameters(
     τ_NIR_leaf = FT(0.25),
     Ω = FT(0.69),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
 )
 rt_model = TwoStreamModel{FT}(rt_params);
 

diff --git a/experiments/standalone/Vegetation/varying_lai.jl b/experiments/standalone/Vegetation/varying_lai.jl
@@ -74,7 +74,6 @@ rt_params = TwoStreamParameters(
     τ_NIR_leaf = FT(0.25),
     Ω = FT(0.69),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
 )
 
 rt_model = TwoStreamModel{FT}(rt_params);

diff --git a/experiments/standalone/Vegetation/varying_lai_with_stem.jl b/experiments/standalone/Vegetation/varying_lai_with_stem.jl
@@ -74,7 +74,6 @@ rt_params = TwoStreamParameters(
     τ_NIR_leaf = FT(0.25),
     Ω = FT(0.69),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
 )
 
 rt_model = TwoStreamModel{FT}(rt_params);

diff --git a/ext/CreateParametersExt.jl b/ext/CreateParametersExt.jl
@@ -613,7 +613,6 @@ function TwoStreamParameters(
 ) where {F}
     name_map = (;
         :wavelength_per_PAR_photon => :λ_γ_PAR,
-        :wavelength_per_NIR_photon => :λ_γ_NIR,
         :canopy_emissivity => :ϵ_canopy,
     )
 
@@ -670,7 +669,6 @@ function BeerLambertParameters(
 ) where {F}
     name_map = (;
         :wavelength_per_PAR_photon => :λ_γ_PAR,
-        :wavelength_per_NIR_photon => :λ_γ_NIR,
         :canopy_emissivity => :ϵ_canopy,
     )
 

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Ha1/US-Ha1_parameters.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Ha1/US-Ha1_parameters.jl
@@ -105,7 +105,6 @@ function radiative_transfer_harvard(;
     ld = ConstantGFunction(FT(0.5)),
     α_PAR_leaf = FT(0.1),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
     τ_PAR_leaf = FT(0.05),
     α_NIR_leaf = FT(0.45),
     τ_NIR_leaf = FT(0.25),
@@ -121,7 +120,6 @@ function radiative_transfer_harvard(;
         ϵ_canopy = ϵ_canopy,
         Ω = Ω,
         λ_γ_PAR = λ_γ_PAR,
-        λ_γ_NIR = λ_γ_NIR,
         n_layers = n_layers,
     )
 end

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-MOz/US-MOz_parameters.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-MOz/US-MOz_parameters.jl
@@ -105,7 +105,6 @@ function radiative_transfer_ozark(;
     ld = ConstantGFunction(FT(0.5)),
     α_PAR_leaf = FT(0.1),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
     τ_PAR_leaf = FT(0.05),
     α_NIR_leaf = FT(0.45),
     τ_NIR_leaf = FT(0.25),
@@ -121,7 +120,6 @@ function radiative_transfer_ozark(;
         ϵ_canopy = ϵ_canopy,
         Ω = Ω,
         λ_γ_PAR = λ_γ_PAR,
-        λ_γ_NIR = λ_γ_NIR,
         n_layers = n_layers,
     )
 end

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-NR1/US-NR1_parameters.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-NR1/US-NR1_parameters.jl
@@ -105,7 +105,6 @@ function radiative_transfer_niwotridge(;
     ld = ConstantGFunction(FT(0.5)),
     α_PAR_leaf = FT(0.1),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
     τ_PAR_leaf = FT(0.05),
     α_NIR_leaf = FT(0.35),
     τ_NIR_leaf = FT(0.25),
@@ -121,7 +120,6 @@ function radiative_transfer_niwotridge(;
         ϵ_canopy = ϵ_canopy,
         Ω = Ω,
         λ_γ_PAR = λ_γ_PAR,
-        λ_γ_NIR = λ_γ_NIR,
         n_layers = n_layers,
     )
 end

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Var/US-Var_parameters.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Var/US-Var_parameters.jl
@@ -105,7 +105,6 @@ function radiative_transfer_vairaranch(;
     ld = ConstantGFunction(FT(0.5)),
     α_PAR_leaf = FT(0.1),
     λ_γ_PAR = FT(5e-7),
-    λ_γ_NIR = FT(1.65e-6),
     τ_PAR_leaf = FT(0.05),
     α_NIR_leaf = FT(0.45),
     τ_NIR_leaf = FT(0.25),
@@ -121,7 +120,6 @@ function radiative_transfer_vairaranch(;
         ϵ_canopy = ϵ_canopy,
         Ω = Ω,
         λ_γ_PAR = λ_γ_PAR,
-        λ_γ_NIR = λ_γ_NIR,
         n_layers = n_layers,
     )
 end

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/run_fluxnet.jl b/lib/ClimaLandSimulations/src/Fluxnet/run_fluxnet.jl
@@ -112,7 +112,6 @@ function run_fluxnet(
             G_Function = params.radiative_transfer.G_Function,
             α_PAR_leaf = params.radiative_transfer.α_PAR_leaf,
             λ_γ_PAR = params.radiative_transfer.λ_γ_PAR,
-            λ_γ_NIR = params.radiative_transfer.λ_γ_NIR,
             τ_PAR_leaf = params.radiative_transfer.τ_PAR_leaf,
             α_NIR_leaf = params.radiative_transfer.α_NIR_leaf,
             τ_NIR_leaf = params.radiative_transfer.τ_NIR_leaf,

diff --git a/src/diagnostics/land_compute_methods.jl b/src/diagnostics/land_compute_methods.jl
@@ -111,38 +111,14 @@ end
 @diagnostic_compute "vcmax25" Union{SoilCanopyModel, LandModel} p.canopy.photosynthesis.Vcmax25
 
 # Canopy - Radiative Transfer
-@diagnostic_compute "near_infrared_radiation_down" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.inc_nir
-@diagnostic_compute "near_infrared_radiation_absorbed" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.nir.abs
-@diagnostic_compute "near_infrared_radiation_reflected" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.nir.refl
-@diagnostic_compute "near_infrared_radiation_transmitted" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.nir.trans
-@diagnostic_compute "photosynthetically_active_radiation_down" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.inc_par
-@diagnostic_compute "photosynthetically_active_radiation_absorbed" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.par.abs
-@diagnostic_compute "photosynthetically_active_radiation_reflected" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.par.refl
-@diagnostic_compute "photosynthetically_active_radiation_transmitted" Union{
-    SoilCanopyModel,
-    LandModel,
-} p.canopy.radiative_transfer.par.trans
+@diagnostic_compute "near_infrared_radiation_down" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.nir_d
+@diagnostic_compute "near_infrared_radiation_absorbed" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.nir.abs
+@diagnostic_compute "near_infrared_radiation_reflected" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.nir.refl
+@diagnostic_compute "near_infrared_radiation_transmitted" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.nir.trans
+@diagnostic_compute "photosynthetically_active_radiation_down" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.par_d
+@diagnostic_compute "photosynthetically_active_radiation_absorbed" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.par.abs
+@diagnostic_compute "photosynthetically_active_radiation_reflected" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.par.refl
+@diagnostic_compute "photosynthetically_active_radiation_transmitted" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.par.trans
 @diagnostic_compute "radiation_longwave_net" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.LW_n
 @diagnostic_compute "radiation_shortwave_net" Union{SoilCanopyModel, LandModel} p.canopy.radiative_transfer.SW_n
 

diff --git a/src/integrated/soil_canopy_model.jl b/src/integrated/soil_canopy_model.jl
@@ -293,12 +293,7 @@ function lsm_radiant_energy_fluxes!(
     _σ = LP.Stefan(earth_param_set)
     LW_d = p.drivers.LW_d
     SW_d = p.drivers.SW_d
-    c = LP.light_speed(earth_param_set)
-    h = LP.planck_constant(earth_param_set)
-    N_a = LP.avogadro_constant(earth_param_set)
-    (; λ_γ_PAR, λ_γ_NIR) = canopy_radiation.parameters
-    energy_per_photon_PAR = h * c / λ_γ_PAR
-    energy_per_photon_NIR = h * c / λ_γ_NIR
+
     T_canopy =
         ClimaLand.Canopy.canopy_temperature(canopy.energy, canopy, Y, p, t)
 
@@ -315,27 +310,25 @@ function lsm_radiant_energy_fluxes!(
     R_net_soil = p.soil.R_n
     LW_u = p.LW_u
     SW_u = p.SW_u
+    par_d = p.canopy.radiative_transfer.par_d
+    nir_d = p.canopy.radiative_transfer.nir_d
+    f_abs_par = p.canopy.radiative_transfer.par.abs
+    f_abs_nir = p.canopy.radiative_transfer.nir.abs
+    f_refl_par = p.canopy.radiative_transfer.par.refl
+    f_refl_nir = p.canopy.radiative_transfer.nir.refl
+    f_trans_par = p.canopy.radiative_transfer.par.trans
+    f_trans_nir = p.canopy.radiative_transfer.nir.trans
     # in total: d - u = CANOPY_ABS + (1-α_soil)*CANOPY_TRANS
     # SW upwelling  = reflected par + reflected nir
-    @. SW_u =
-        energy_per_photon_NIR * N_a * p.canopy.radiative_transfer.nir.refl +
-        energy_per_photon_PAR * N_a * p.canopy.radiative_transfer.par.refl
+    @. SW_u = par_d * f_refl_par + f_refl_nir * nir_d
 
     # net canopy
-    @. SW_net_canopy =
-        energy_per_photon_NIR * N_a * p.canopy.radiative_transfer.nir.abs +
-        energy_per_photon_PAR * N_a * p.canopy.radiative_transfer.par.abs
+    @. SW_net_canopy = f_abs_par * par_d + f_abs_nir * nir_d
 
     # net soil = (1-α)*trans for par and nir
     @. R_net_soil .=
-        energy_per_photon_NIR *
-        N_a *
-        p.canopy.radiative_transfer.nir.trans *
-        (1 - α_soil_NIR) +
-        energy_per_photon_PAR *
-        N_a *
-        p.canopy.radiative_transfer.par.trans *
-        (1 - α_soil_PAR)
+        f_trans_nir * nir_d * (1 - α_soil_NIR) +
+        f_trans_par * par_d * (1 - α_soil_PAR)
 
     # Working through the math, this satisfies: LW_d - LW_u = LW_c + LW_soil
     ϵ_canopy = p.canopy.radiative_transfer.ϵ # this takes into account LAI/SAI

diff --git a/src/standalone/Vegetation/Canopy.jl b/src/standalone/Vegetation/Canopy.jl
@@ -412,8 +412,8 @@ function ClimaLand.make_update_aux(
         ψ = p.canopy.hydraulics.ψ
         ϑ_l = Y.canopy.hydraulics.ϑ_l
         fa = p.canopy.hydraulics.fa
-        inc_par = p.canopy.radiative_transfer.inc_par
-        inc_nir = p.canopy.radiative_transfer.inc_nir
+        par_d = p.canopy.radiative_transfer.par_d
+        nir_d = p.canopy.radiative_transfer.nir_d
         frac_diff = p.canopy.radiative_transfer.frac_diff
 
         bc = canopy.boundary_conditions
@@ -436,10 +436,8 @@ function ClimaLand.make_update_aux(
         R = FT(LP.gas_constant(earth_param_set))
         T_freeze = FT(LP.T_freeze(earth_param_set))
         thermo_params = earth_param_set.thermo_params
-        (; G_Function, Ω, λ_γ_PAR, λ_γ_NIR) =
-            canopy.radiative_transfer.parameters
-        energy_per_photon_PAR = planck_h * c / λ_γ_PAR
-        energy_per_photon_NIR = planck_h * c / λ_γ_NIR
+        (; G_Function, Ω, λ_γ_PAR) = canopy.radiative_transfer.parameters
+        energy_per_mole_photon_par = planck_h * c / λ_γ_PAR * N_a
         (; g1, g0, Drel) = canopy.conductance.parameters
         area_index = p.canopy.hydraulics.area_index
         LAI = area_index.leaf
@@ -453,8 +451,8 @@ function ClimaLand.make_update_aux(
             (1 - exp(-(LAI + SAI))) #from CLM 5.0, Tech note 4.20
         p.canopy.radiative_transfer.G .= compute_G(G_Function, θs)
         RT = canopy.radiative_transfer
-        compute_PAR!(inc_par, RT, bc.radiation, p, t)
-        compute_NIR!(inc_nir, RT, bc.radiation, p, t)
+        compute_PAR!(par_d, RT, bc.radiation, p, t)
+        compute_NIR!(nir_d, RT, bc.radiation, p, t)
         K = p.canopy.radiative_transfer.K
         @. K = extinction_coeff(p.canopy.radiative_transfer.G, θs)
         DOY =
@@ -469,11 +467,9 @@ function ClimaLand.make_update_aux(
             thermo_params,
         )
 
-        compute_absorbances!(
+        compute_fractional_absorbances!(
             p,
             RT,
-            inc_par,
-            inc_nir,
             LAI,
             K,
             ground_albedo_PAR(
@@ -490,9 +486,6 @@ function ClimaLand.make_update_aux(
                 p,
                 t,
             ),
-            energy_per_photon_PAR,
-            energy_per_photon_NIR,
-            N_a,
             θs,
             frac_diff,
         )
@@ -573,6 +566,8 @@ function ClimaLand.make_update_aux(
             medlyn_factor,
             c_co2_air,
             R,
+            energy_per_mole_photon_par,
+            par_d,
         )
         # update SIF
         SIF = p.canopy.sif.SIF
@@ -585,6 +580,8 @@ function ClimaLand.make_update_aux(
             R,
             T_freeze,
             canopy.photosynthesis.parameters,
+            energy_per_mole_photon_par,
+            par_d,
         )
         @. GPP = compute_GPP(An, K, LAI, Ω)
         @. gs = medlyn_conductance(g0, Drel, medlyn_factor, An, c_co2_air)