zero flux if zero lai/sai

.buildkite/pipeline.yml

@@ -43,6 +43,18 @@ steps:
         command: "julia --color=yes --project=.buildkite experiments/standalone/Snow/snow_cdp.jl"
         artifact_paths: "experiments/standalone/Snow/*png"
 
+      - label: "Varying LAI, no stem compartment"
+        command: "julia --color=yes --project=.buildkite experiments/standalone/Vegetation/varying_lai.jl"
+        artifact_paths: "experiments/standalone/Vegetation/varying_lai_no_stem*png"
+
+      - label: "Varying LAI, with stem compartment"
+        command: "julia --color=yes --project=.buildkite experiments/standalone/Vegetation/varying_lai_with_stem.jl"
+        artifact_paths: "experiments/standalone/Vegetation/varying_lai_with_stem*png"
+
+      - label: "zero LAI, zero SAI"
+        command: "julia --color=yes --project=.buildkite experiments/standalone/Vegetation/no_vegetation.jl"
+        artifact_paths: "experiments/standalone/Vegetation/no_veg*png"
+
       - label: "Richards comparison to Bonan"
         command: "julia --color=yes --project=.buildkite experiments/standalone/Soil/richards_comparison.jl"
         artifact_paths: "experiments/standalone/Soil/cpu/comparison*png"

experiments/Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.3"
+julia_version = "1.10.4"
 manifest_format = "2.0"
 project_hash = "973443a0a609649a9289253b6f5bc3de181d9006"
 

experiments/standalone/Vegetation/no_vegetation.jl

@@ -0,0 +1,270 @@
+import SciMLBase
+using CairoMakie
+using Statistics
+using Dates
+using Insolation
+
+# Load CliMA Packages and ClimaLand Modules:
+
+using ClimaCore
+import ClimaParams as CP
+import ClimaTimeSteppers as CTS
+using StaticArrays
+using ClimaLand
+using ClimaLand.Domains: Point
+using ClimaLand.Canopy
+using ClimaLand.Canopy.PlantHydraulics
+import ClimaLand
+import ClimaLand.Parameters as LP
+const FT = Float32;
+earth_param_set = LP.LandParameters(FT);
+f_root_to_shoot = FT(3.5)
+SAI = FT(0.0)
+plant_ν = FT(2.46e-4) # kg/m^2
+n_stem = Int64(0)
+n_leaf = Int64(1)
+h_leaf = FT(9.5)
+compartment_midpoints = [h_leaf / 2]
+compartment_surfaces = [FT(0), h_leaf]
+land_domain = Point(; z_sfc = FT(0.0))
+include(
+    joinpath(pkgdir(ClimaLand), "experiments/integrated/fluxnet/data_tools.jl"),
+);
+time_offset = 7
+lat = FT(38.7441) # degree
+long = FT(-92.2000) # degree
+atmos_h = FT(32)
+site_ID = "US-MOz"
+data_link = "https://caltech.box.com/shared/static/7r0ci9pacsnwyo0o9c25mhhcjhsu6d72.csv"
+
+include(
+    joinpath(
+        pkgdir(ClimaLand),
+        "experiments/integrated/fluxnet/met_drivers_FLUXNET.jl",
+    ),
+);
+
+z0_m = FT(2)
+z0_b = FT(0.2)
+
+shared_params = SharedCanopyParameters{FT, typeof(earth_param_set)}(
+    z0_m,
+    z0_b,
+    earth_param_set,
+);
+ψ_soil0 = FT(0.0)
+
+soil_driver = PrescribedSoil(
+    FT;
+    root_depths = SVector{10, FT}(-(10:-1:1.0) ./ 10.0 * 2.0 .+ 0.2 / 2.0),
+    ψ = t -> ψ_soil0,
+    α_PAR = FT(0.2),
+    α_NIR = FT(0.4),
+    T = t -> 298.0,
+    ϵ = FT(0.99),
+);
+
+rt_params = TwoStreamParameters(
+    FT;
+    G_Function = ConstantGFunction(FT(0.5)),
+    α_PAR_leaf = FT(0.1),
+    α_NIR_leaf = FT(0.45),
+    τ_PAR_leaf = FT(0.05),
+    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);
+
+cond_params = MedlynConductanceParameters(FT; g1 = FT(141.0))
+
+stomatal_model = MedlynConductanceModel{FT}(cond_params);
+
+
+photo_params = FarquharParameters(FT, Canopy.C3(); Vcmax25 = FT(5e-5))
+
+photosynthesis_model = FarquharModel{FT}(photo_params);
+
+AR_params = AutotrophicRespirationParameters(FT)
+AR_model = AutotrophicRespirationModel{FT}(AR_params);
+
+function fakeLAIfunction(t)
+    if t < 30 * 24 * 3600
+        0.0
+    elseif t < (364 - 30) * 24 * 3600.0
+        max(2.0 * sin(2 * π / (730 * 24 * 3600) * (t - 30 * 24 * 3600)), 0)
+    else
+        0.0
+    end
+end
+
+
+f_root_to_shoot = FT(3.5)
+SAI = FT(0)
+RAI = FT(2 * f_root_to_shoot)
+ai_parameterization =
+    PrescribedSiteAreaIndex{FT}(TimeVaryingInput(fakeLAIfunction), SAI, RAI)
+rooting_depth = FT(1.0);
+
+function root_distribution(z::T; rooting_depth = rooting_depth) where {T}
+    return T(1.0 / rooting_depth) * exp(z / T(rooting_depth))
+end;
+
+K_sat_plant = FT(1.8e-8)
+ψ63 = FT(-4 / 0.0098)
+Weibull_param = FT(4)
+a = FT(0.05 * 0.0098)
+
+conductivity_model =
+    PlantHydraulics.Weibull{FT}(K_sat_plant, ψ63, Weibull_param)
+
+retention_model = PlantHydraulics.LinearRetentionCurve{FT}(a);
+
+ν = FT(0.7)
+S_s = FT(1e-2 * 0.0098)
+
+plant_hydraulics_ps = PlantHydraulics.PlantHydraulicsParameters(;
+    ai_parameterization = ai_parameterization,
+    ν = ν,
+    S_s = S_s,
+    root_distribution = root_distribution,
+    conductivity_model = conductivity_model,
+    retention_model = retention_model,
+);
+
+
+plant_hydraulics = PlantHydraulics.PlantHydraulicsModel{FT}(;
+    parameters = plant_hydraulics_ps,
+    n_stem = n_stem,
+    n_leaf = n_leaf,
+    compartment_surfaces = compartment_surfaces,
+    compartment_midpoints = compartment_midpoints,
+);
+
+energy_model = ClimaLand.Canopy.BigLeafEnergyModel{FT}(
+    BigLeafEnergyParameters{FT}(FT(1e3)),
+)
+
+canopy = ClimaLand.Canopy.CanopyModel{FT}(;
+    parameters = shared_params,
+    domain = land_domain,
+    autotrophic_respiration = AR_model,
+    radiative_transfer = rt_model,
+    photosynthesis = photosynthesis_model,
+    conductance = stomatal_model,
+    energy = energy_model,
+    hydraulics = plant_hydraulics,
+    soil_driver = soil_driver,
+    atmos = atmos,
+    radiation = radiation,
+);
+
+
+Y, p, coords = ClimaLand.initialize(canopy)
+exp_tendency! = make_exp_tendency(canopy);
+
+
+ψ_leaf_0 = FT(-2e5 / 9800)
+
+S_l_ini = inverse_water_retention_curve(retention_model, ψ_leaf_0, ν, S_s)
+
+Y.canopy.hydraulics.ϑ_l.:1 .= augmented_liquid_fraction.(ν, S_l_ini)
+
+
+
+t0 = 0.0
+N_days = 10
+tf = t0 + 3600 * 24 * N_days
+dt = 225.0;
+evaluate!(Y.canopy.energy.T, atmos.T, t0)
+set_initial_cache! = make_set_initial_cache(canopy)
+set_initial_cache!(p, Y, t0);
+
+
+n = 16
+saveat = Array(t0:(n * dt):tf)
+sv = (;
+    t = Array{Float64}(undef, length(saveat)),
+    saveval = Array{NamedTuple}(undef, length(saveat)),
+)
+saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat);
+
+updateat = Array(t0:1800:tf)
+updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
+cb = SciMLBase.CallbackSet(driver_cb, saving_cb);
+
+timestepper = CTS.RK4();
+ode_algo = CTS.ExplicitAlgorithm(timestepper)
+
+prob = SciMLBase.ODEProblem(
+    CTS.ClimaODEFunction(T_exp! = exp_tendency!, dss! = ClimaLand.dss!),
+    Y,
+    (t0, tf),
+    p,
+);
+
+sol = SciMLBase.solve(prob, ode_algo; dt = dt, callback = cb, saveat = saveat);
+
+savedir = joinpath(pkgdir(ClimaLand), "experiments/standalone/Vegetation");
+T = [parent(sol.u[k].canopy.energy.T)[1] for k in 1:length(sol.t)]
+T_atmos = [parent(sv.saveval[k].drivers.T)[1] for k in 1:length(sol.t)]
+ϑ = [parent(sol.u[k].canopy.hydraulics.ϑ_l.:1)[1] for k in 1:length(sol.t)]
+GPP = [
+    parent(sv.saveval[k].canopy.photosynthesis.GPP)[1] * 1e6 for
+    k in 1:length(sol.t)
+]
+resp = [
+    parent(sv.saveval[k].canopy.autotrophic_respiration.Ra)[1] * 1e6 for
+    k in 1:length(sol.t)
+]
+SW_abs = [
+    parent(sv.saveval[k].canopy.radiative_transfer.SW_n)[1] for
+    k in 1:length(sol.t)
+]
+LW_abs = [
+    parent(sv.saveval[k].canopy.radiative_transfer.LW_n)[1] for
+    k in 1:length(sol.t)
+]
+SHF = [parent(sv.saveval[k].canopy.energy.shf)[1] for k in 1:length(sol.t)]
+LHF = [parent(sv.saveval[k].canopy.energy.lhf)[1] for k in 1:length(sol.t)]
+RE = [
+    parent(sv.saveval[k].canopy.energy.fa_energy_roots)[1] for
+    k in 1:length(sol.t)
+]
+R = [
+    parent(sv.saveval[k].canopy.hydraulics.fa_roots)[1] for k in 1:length(sol.t)
+]
+Tr = [parent(sv.saveval[k].canopy.hydraulics.fa.:1)[1] for k in 1:length(sol.t)]
+fig = Figure()
+ax = Axis(fig[1, 1], xlabel = "Time (days)", ylabel = "Temperature (K)")
+lines!(ax, sol.t ./ 24 ./ 3600, T, label = "Canopy")
+lines!(ax, sol.t ./ 24 ./ 3600, T_atmos, label = "Atmos")
+axislegend(ax)
+ax = Axis(fig[2, 1], xlabel = "Time (days)", ylabel = "Volumetric Water")
+lines!(ax, sol.t ./ 24 ./ 3600, ϑ, label = "Canopy")
+axislegend(ax)
+ax = Axis(fig[3, 1], xlabel = "Time (days)", ylabel = "LAI")
+lines!(ax, sol.t ./ 24 ./ 3600, fakeLAIfunction.(sol.t), label = "Canopy")
+axislegend(ax)
+save(joinpath(savedir, "no_veg_state.png"), fig)
+fig2 = Figure()
+ax = Axis(fig2[1, 1], xlabel = "Time (days)", ylabel = "Energy Fluxes")
+lines!(ax, sol.t ./ 24 ./ 3600, SW_abs, label = "SW")
+lines!(ax, sol.t ./ 24 ./ 3600, LW_abs, label = "LW")
+lines!(ax, sol.t ./ 24 ./ 3600, SHF, label = "SHF")
+lines!(ax, sol.t ./ 24 ./ 3600, LHF, label = "LHF")
+lines!(ax, sol.t ./ 24 ./ 3600, RE, label = "RE")
+axislegend(ax)
+ax = Axis(fig2[2, 1], xlabel = "Time (days)", ylabel = "Water Fluxes")
+lines!(ax, sol.t ./ 24 ./ 3600, Tr, label = "Transpiration")
+lines!(ax, sol.t ./ 24 ./ 3600, R, label = "R")
+
+axislegend(ax)
+ax = Axis(fig2[3, 1], xlabel = "Time (days)", ylabel = "Carbon Fluxes")
+lines!(ax, sol.t ./ 24 ./ 3600, GPP, label = "GPP")
+lines!(ax, sol.t ./ 24 ./ 3600, resp, label = "Respiration")
+axislegend(ax)
+save(joinpath(savedir, "no_veg_fluxes.png"), fig2)