Add AbstractMoistureStressModel with 3 options

This commits adds a portion of Yuchen Li PR #1330,
a new Canopy component type: AbstractMoistureStressModel,
with 3 methods: the existing one (Tuzet) which was previously
in PlantHydraulics, a Piecewise method using dry to wet soil moisture,
and no moisture stress.

Co-authored-by: ychnli <[email protected]>
Co-authored-by: kmdeck <[email protected]>
Co-authored-by: AlexisRenchon <[email protected]>
Co-authored-by: juliasloan25 <[email protected]>

Author: 4 people

NEWS.md

@@ -3,7 +3,7 @@ ClimaLand.jl Release Notes
 
 main
 -------
-
+- Add moisture stress component to the canopy model PR[#1387](https://github.com/CliMA/ClimaLand.jl/pull/1387)
 - Remove `PrognosticSoilConditions` in favor of using `PrognosticGroundConditions` more generally PR[#1411](https://github.com/CliMA/ClimaLand.jl/pull/1411)
 
 v0.20.0

docs/src/APIs/canopy/Photosynthesis.md

@@ -31,7 +31,6 @@ ClimaLand.Canopy.light_assimilation
 ClimaLand.Canopy.max_electron_transport_farquhar
 ClimaLand.Canopy.electron_transport_farquhar
 ClimaLand.Canopy.net_photosynthesis
-ClimaLand.Canopy.moisture_stress
 ClimaLand.Canopy.dark_respiration_farquhar
 ClimaLand.Canopy.MM_Kc
 ClimaLand.Canopy.MM_Ko

docs/src/APIs/canopy/soil_moisture_stress.md

@@ -0,0 +1,26 @@
+# Soil moisture stress
+
+```@meta
+CurrentModule = ClimaLand.Canopy
+```
+
+## Models and Parameters
+
+```@docs
+ClimaLand.Canopy.TuzetMoistureStressParameters
+ClimaLand.Canopy.TuzetMoistureStressModel
+ClimaLand.Canopy.TuzetMoistureStressModel{FT}()
+ClimaLand.Canopy.TuzetMoistureStressModel{FT}(toml_dict::CP.ParamDict)
+ClimaLand.Canopy.PiecewiseMoistureStressParameters
+ClimaLand.Canopy.PiecewiseMoistureStressModel
+ClimaLand.Canopy.PiecewiseMoistureStressModel{FT}()
+Climaland.Canopy.PiecewiseMoistureStressModel{FT}(toml_dict::CP.ParamDict)
+ClimaLand.Canopy.NoMoistureStressModel
+```
+
+## Methods
+
+```@docs
+ClimaLand.Canopy.update_soil_moisture_stress!
+ClimaLand.Canopy.update_piecewise_soil_moisture_stress!
+```

docs/src/tutorials/calibration/obs_site_level_calibration.jl

@@ -238,7 +238,7 @@ function G(Vcmax25, g1)
                 simulation.start_date,
                 simulation.start_date + Day(20),
                 stop_date,
-            )
+            ),
         )
     return observation
 end;

docs/src/tutorials/calibration/perfect_model_site_level_calibration.jl

@@ -206,7 +206,7 @@ function G(Vcmax25)
                 lhf,
                 simulation.start_date,
                 simulation.start_date + Day(20),
-            )
+            ),
         )
     return observation
 end

experiments/integrated/fluxnet/ozark_pmodel.jl

@@ -179,6 +179,16 @@ conductance = PModelConductance{FT}()
 # Set up photosynthesis
 photosynthesis = PModel{FT}()
 
+# Set up soil moisture stress
+soil_moisture_stress_params = PiecewiseMoistureStressParameters(
+    FT;
+    θ_high = soil.parameters.ν,
+    θ_low = soil.parameters.θ_r,
+    c = FT(1.0),
+)
+soil_moisture_stress =
+    PiecewiseMoistureStressModel{FT}(soil_moisture_stress_params)
+
 # Set up plant hydraulics
 # Read in LAI from MODIS data
 surface_space = land_domain.space.surface;
@@ -222,6 +232,7 @@ canopy = Canopy.CanopyModel{FT}(
     radiative_transfer,
     photosynthesis,
     conductance,
+    soil_moisture_stress,
     hydraulics,
     energy,
 )
@@ -265,7 +276,8 @@ simulation = LandSimulation(
     set_ic!,
     updateat,
     diagnostics = diags,
-);
+)
+
 @time solve!(simulation)
 
 comparison_data = FluxnetSimulations.get_comparison_data(site_ID, time_offset)

experiments/integrated/performance/conservation/ozark_conservation.jl

@@ -86,7 +86,7 @@ for float_type in (Float32, Float64)
             [parent(sv.saveval[k].drivers.T)[1] for k in 1:length(sv.t)]
         @assert mean(
             abs.(
-                cos.(radiation.θs.(sv.t, radiation.start_date)) .- cache_cosθs
+                cos.(radiation.θs.(sv.t, radiation.start_date)) .- cache_cosθs,
             ),
         ) < eps(FT)
         T_mutable = Vector{FT}(undef, 1)
@@ -201,7 +201,7 @@ for float_type in (Float32, Float64)
             eps(FT) .+
             abs.(
                 (soil_mass_change_actual - soil_mass_change_exp) ./
-                soil_mass_change_exp
+                soil_mass_change_exp,
             ),
             label = "Soil Water Balance",
         )
@@ -211,7 +211,7 @@ for float_type in (Float32, Float64)
             eps(FT) .+
             abs.(
                 (canopy_mass_change_actual - canopy_mass_change_exp) ./
-                canopy_mass_change_exp
+                canopy_mass_change_exp,
             ),
             label = "Canopy Water Balance",
         )
@@ -272,7 +272,7 @@ for float_type in (Float32, Float64)
             eps(FT) .+
             abs.(
                 (soil_energy_change_actual - soil_energy_change_exp) ./
-                soil_energy_change_exp
+                soil_energy_change_exp,
             ),
             label = "Soil Energy Balance",
         )

ext/land_sim_vis/leaderboard/leaderboard.jl

@@ -205,7 +205,7 @@ function compute_monthly_leaderboard(
         months =
             Dates.month.(
                 Dates.DateTime(sim_var.attributes["start_date"]) .+
-                Dates.Second.(times)
+                Dates.Second.(times),
             )
         months_split, sim_vec_split, rmse_vec_split, bias_vec_split =
             partition_by_val(12, months, sim_vec, rmse_vec, bias_vec)

ext/neural_snow/DataTools.jl

@@ -761,7 +761,7 @@ function serreze_qc(input::DataFrame, id::Int, state::AbstractString)
     data[!, :tmax] = maxmin[!, :tmax]
     flags =
         ismissing.(
-            data[1:(end - 1), [:SWE, :precip, :air_temp_avg, :tmin, :tmax]]
+            data[1:(end - 1), [:SWE, :precip, :air_temp_avg, :tmin, :tmax]],
         )
     flags[!, :date] = data[1:(end - 1), :date]
 

src/ClimaLand.jl

@@ -410,7 +410,8 @@ import .Canopy:
     ground_albedo_PAR,
     ground_albedo_NIR,
     canopy_radiant_energy_fluxes!,
-    root_energy_flux_per_ground_area!
+    root_energy_flux_per_ground_area!,
+    update_piecewise_soil_moisture_stress!
 ### Concrete types of AbstractLandModels
 ### and associated methods
 include("integrated/soil_energy_hydrology_biogeochemistry.jl")