experiments, docs

docs/tutorials/integrated/soil_canopy_tutorial.jl

@@ -185,18 +185,11 @@ soilco2_sources = (MicrobeProduction{FT}(),);
 
 soilco2_boundary_conditions = (; top = soilco2_top_bc, bottom = soilco2_bot_bc);
 
-soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-    Soil.Biogeochemistry.PrognosticMet{FT}(),
-    Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-    atmos,
-);
-
 soilco2_args = (;
     boundary_conditions = soilco2_boundary_conditions,
     sources = soilco2_sources,
     domain = soil_domain,
     parameters = soilco2_ps,
-    drivers = soilco2_drivers,
 );
 
 # Next we need to set up the [`CanopyModel`](https://clima.github.io/ClimaLand.jl/dev/APIs/canopy/Canopy/#Canopy-Model-Structs).
@@ -306,7 +299,7 @@ canopy_model_args = (; parameters = shared_params, domain = canopy_domain);
 # atmospheric and radiative flux conditions from the observations at the Ozark
 # site as was done in the previous tutorial.
 
-land_input = (atmos = atmos, radiation = radiation)
+land_input = (atmos = atmos, radiation = radiation, soil_organic_carbon = Csom)
 
 land = SoilCanopyModel{FT}(;
     soilco2_type = soilco2_type,

experiments/benchmarks/land.jl

@@ -422,18 +422,11 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     soilco2_boundary_conditions =
         (; top = soilco2_top_bc, bottom = soilco2_bot_bc)
 
-    soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-        Soil.Biogeochemistry.PrognosticMet{FT}(),
-        Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-        atmos,
-    )
-
     soilco2_args = (;
         boundary_conditions = soilco2_boundary_conditions,
         sources = soilco2_sources,
         domain = domain,
         parameters = soilco2_ps,
-        drivers = soilco2_drivers,
     )
 
     # Now we set up the canopy model, which we set up by component:
@@ -538,7 +531,12 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     )
 
     # Integrated plant hydraulics and soil model
-    land_input = (atmos = atmos, radiation = radiation, runoff = runoff_model)
+    land_input = (
+        atmos = atmos,
+        radiation = radiation,
+        runoff = runoff_model,
+        soil_organic_carbon = Csom,
+    )
     land = SoilCanopyModel{FT}(;
         soilco2_type = soilco2_type,
         soilco2_args = soilco2_args,

experiments/integrated/fluxnet/ozark_pft.jl

@@ -150,18 +150,11 @@ soilco2_sources = (MicrobeProduction{FT}(),)
 
 soilco2_boundary_conditions = (; top = soilco2_top_bc, bottom = soilco2_bot_bc)
 
-soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-    Soil.Biogeochemistry.PrognosticMet{FT}(),
-    Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-    atmos,
-)
-
 soilco2_args = (;
     boundary_conditions = soilco2_boundary_conditions,
     sources = soilco2_sources,
     domain = soil_domain,
     parameters = soilco2_ps,
-    drivers = soilco2_drivers,
 )
 
 # Now we set up the canopy model, which we set up by component:
@@ -242,7 +235,7 @@ shared_params = SharedCanopyParameters{FT, typeof(earth_param_set)}(
 canopy_model_args = (; parameters = shared_params, domain = canopy_domain)
 
 # Integrated plant hydraulics and soil model
-land_input = (atmos = atmos, radiation = radiation)
+land_input = (atmos = atmos, radiation = radiation, soil_organic_carbon = Csom)
 land = SoilCanopyModel{FT}(;
     soilco2_type = soilco2_type,
     soilco2_args = soilco2_args,

experiments/integrated/fluxnet/run_fluxnet.jl

@@ -109,18 +109,11 @@ soilco2_sources = (MicrobeProduction{FT}(),)
 
 soilco2_boundary_conditions = (; top = soilco2_top_bc, bottom = soilco2_bot_bc)
 
-soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-    Soil.Biogeochemistry.PrognosticMet{FT}(),
-    Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-    atmos,
-)
-
 soilco2_args = (;
     boundary_conditions = soilco2_boundary_conditions,
     sources = soilco2_sources,
     domain = soil_domain,
     parameters = soilco2_ps,
-    drivers = soilco2_drivers,
 )
 
 # Now we set up the canopy model, which we set up by component:
@@ -199,7 +192,7 @@ shared_params = SharedCanopyParameters{FT, typeof(earth_param_set)}(
 canopy_model_args = (; parameters = shared_params, domain = canopy_domain)
 
 # Integrated plant hydraulics and soil model
-land_input = (atmos = atmos, radiation = radiation)
+land_input = (atmos = atmos, radiation = radiation, soil_organic_carbon = Csom)
 land = SoilCanopyModel{FT}(;
     soilco2_type = soilco2_type,
     soilco2_args = soilco2_args,

experiments/integrated/global/global_soil_canopy.jl

@@ -190,18 +190,11 @@ soilco2_sources = (Soil.Biogeochemistry.MicrobeProduction{FT}(),)
 
 soilco2_boundary_conditions = (; top = soilco2_top_bc, bottom = soilco2_bot_bc)
 
-soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-    Soil.Biogeochemistry.PrognosticMet{FT}(),
-    Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-    atmos,
-)
-
 soilco2_args = (;
     boundary_conditions = soilco2_boundary_conditions,
     sources = soilco2_sources,
     domain = domain,
     parameters = soilco2_ps,
-    drivers = soilco2_drivers,
 )
 
 # Now we set up the canopy model, which we set up by component:
@@ -295,7 +288,12 @@ canopy_model_args = (;
 )
 
 # Integrated plant hydraulics and soil model
-land_input = (atmos = atmos, radiation = radiation, runoff = runoff_model)
+land_input = (
+    atmos = atmos,
+    radiation = radiation,
+    runoff = runoff_model,
+    soil_organic_carbon = Csom,
+)
 land = SoilCanopyModel{FT}(;
     soilco2_type = soilco2_type,
     soilco2_args = soilco2_args,

experiments/integrated/performance/conservation/ozark_conservation_setup.jl

@@ -91,18 +91,11 @@ soilco2_sources = (MicrobeProduction{FT}(),)
 
 soilco2_boundary_conditions = (; top = soilco2_top_bc, bottom = soilco2_bot_bc)
 
-soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-    Soil.Biogeochemistry.PrognosticMet{FT}(),
-    Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-    atmos,
-)
-
 soilco2_args = (;
     boundary_conditions = soilco2_boundary_conditions,
     sources = soilco2_sources,
     domain = soil_domain,
     parameters = soilco2_ps,
-    drivers = soilco2_drivers,
 )
 
 # Now we set up the canopy model, which we set up by component:
@@ -180,7 +173,7 @@ shared_params = SharedCanopyParameters{FT, typeof(earth_param_set)}(
 canopy_model_args = (; parameters = shared_params, domain = canopy_domain)
 
 # Integrated plant hydraulics and soil model
-land_input = (atmos = atmos, radiation = radiation)
+land_input = (atmos = atmos, radiation = radiation, soil_organic_carbon = Csom)
 land = SoilCanopyModel{FT}(;
     soilco2_type = soilco2_type,
     soilco2_args = soilco2_args,

experiments/integrated/performance/profile_allocations.jl

@@ -238,18 +238,11 @@ soilco2_sources = (MicrobeProduction{FT}(),)
 
 soilco2_boundary_conditions = (; top = soilco2_top_bc, bottom = soilco2_bot_bc)
 
-soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-    Soil.Biogeochemistry.PrognosticMet{FT}(),
-    Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-    atmos,
-)
-
 soilco2_args = (;
     boundary_conditions = soilco2_boundary_conditions,
     sources = soilco2_sources,
     domain = soil_domain,
     parameters = soilco2_ps,
-    drivers = soilco2_drivers,
 )
 
 # Now we set up the canopy model, which we set up by component:
@@ -315,7 +308,7 @@ shared_params = SharedCanopyParameters{FT, typeof(earth_param_set)}(
 canopy_model_args = (; parameters = shared_params, domain = canopy_domain)
 
 # Integrated plant hydraulics and soil model
-land_input = (atmos = atmos, radiation = radiation)
+land_input = (atmos = atmos, radiation = radiation, soil_organic_carbon = Csom)
 land = SoilCanopyModel{FT}(;
     soilco2_type = soilco2_type,
     soilco2_args = soilco2_args,

experiments/standalone/Biogeochemistry/experiment.jl

@@ -110,7 +110,7 @@ for (FT, tf) in ((Float32, 2 * dt), (Float64, tf))
     )
 
     # Create integrated model instance
-    land_args = (atmos, Csom)
+    land_args = (atmos = atmos, soil_organic_carbon = Csom)
     model = LandSoilBiogeochemistry{FT}(;
         land_args = land_args,
         soil_args = soil_args,

lib/ClimaLandSimulations/src/Fluxnet/run_fluxnet.jl

@@ -72,18 +72,11 @@ function run_fluxnet(
     soilco2_boundary_conditions =
         (; top = soilco2_top_bc, bottom = CO2 = soilco2_bot_bc)
 
-    soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
-        Soil.Biogeochemistry.PrognosticMet{FT}(),
-        Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
-        drivers.atmos,
-    )
-
     soilco2_args = (;
         boundary_conditions = soilco2_boundary_conditions,
         sources = soilco2_sources,
         domain = soil_domain,
         parameters = soilco2_ps,
-        drivers = soilco2_drivers,
     )
 
     # Now we set up the canopy model, which we set up by component:
@@ -218,7 +211,11 @@ function run_fluxnet(
         (; parameters = shared_params, domain = domain.canopy_domain)
 
     # Integrated plant hydraulics and soil model
-    land_input = (atmos = drivers.atmos, radiation = drivers.radiation)
+    land_input = (
+        atmos = drivers.atmos,
+        radiation = drivers.radiation,
+        soil_organic_carbon = Csom,
+    )
     land = SoilCanopyModel{FT}(;
         soilco2_type = soilco2_type,
         soilco2_args = soilco2_args,

src/integrated/soil_canopy_model.jl

@@ -88,7 +88,7 @@ function SoilCanopyModel{FT}(;
     MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
 }
 
-    (; atmos, radiation) = land_args
+    (; atmos, radiation, soil_organic_carbon) = land_args
     # These should always be set by the constructor.
     sources = (RootExtraction{FT}(), Soil.PhaseChange{FT}())
     if :runoff ∈ propertynames(land_args)
@@ -116,7 +116,7 @@ function SoilCanopyModel{FT}(;
     )
 
     transpiration = Canopy.PlantHydraulics.DiagnosticTranspiration{FT}()
-    soil_driver = PrognosticSoil{typeof(soil.parameters.PAR_albedo)}(
+    canopy_soil_driver = PrognosticSoil{typeof(soil.parameters.PAR_albedo)}(
         soil.parameters.PAR_albedo,
         soil.parameters.NIR_albedo,
     )
@@ -142,7 +142,7 @@ function SoilCanopyModel{FT}(;
             energy = canopy_component_types.energy(
                 canopy_component_args.energy.parameters,
             ),
-            soil_driver = soil_driver,
+            soil_driver = canopy_soil_driver,
             atmos = atmos,
             radiation = radiation,
             canopy_model_args...,
@@ -165,18 +165,20 @@ function SoilCanopyModel{FT}(;
                 transpiration = transpiration,
                 canopy_component_args.hydraulics...,
             ),
-            soil_driver = soil_driver,
+            soil_driver = canopy_soil_driver,
             atmos = atmos,
             radiation = radiation,
             canopy_model_args...,
         )
     end
 
-    soilco2 = Soil.Biogeochemistry.SoilCO2Model{FT}(; soilco2_args...)
-
-    if !(soilco2_args.drivers.met isa PrognosticMet)
-        throw(AssertionError("Must be of type PrognosticMet."))
-    end
+    co2_prognostic_soil = Soil.Biogeochemistry.PrognosticMet(soil.parameters)
+    soil_co2_drivers = Soil.Biogeochemistry.SoilDrivers(
+        co2_prognostic_soil,
+        Soil.Biogeochemistry.PrescribedSOC{FT}(soil_organic_carbon),
+        atmos,
+    )
+    soilco2 = soil_co2_model(; soilco2_args..., drivers = soil_co2_drivers)
 
     return SoilCanopyModel{FT, typeof(soilco2), typeof(soil), typeof(canopy)}(
         soilco2,

src/integrated/soil_energy_hydrology_biogeochemistry.jl

@@ -43,7 +43,7 @@ function LandSoilBiogeochemistry{FT}(;
     soilco2_args::NamedTuple = (;),
 ) where {FT}
 
-    (atmos, Csom) = land_args
+    (; atmos, soil_organic_carbon) = land_args
     soil = Soil.EnergyHydrology{FT}(;
         soil_args..., # soil_args must have sources, boundary_conditions, domain, parameters
     )

src/standalone/Soil/Biogeochemistry/Biogeochemistry.jl

@@ -93,7 +93,7 @@ struct SoilCO2Model{FT, PS, D, BC, S, DT} <:
     "A tuple of sources, each of type AbstractSource"
     sources::S
     "Drivers"
-    driver::DT
+    drivers::DT
 end
 
 
@@ -411,14 +411,14 @@ function ClimaLand.make_update_aux(model::SoilCO2Model)
     function update_aux!(p, Y, t)
         params = model.parameters
         z = model.domain.fields.z
-        T_soil = soil_temperature(model.driver.met, p, Y, t, z)
-        θ_l = soil_moisture(model.driver.met, p, Y, t, z)
-        Csom = soil_SOM_C(model.driver.soc, p, Y, t, z)
+        T_soil = soil_temperature(model.drivers.met, p, Y, t, z)
+        θ_l = soil_moisture(model.drivers.met, p, Y, t, z)
+        Csom = soil_SOM_C(model.drivers.soc, p, Y, t, z)
         P_sfc = p.drivers.P
         θ_w = θ_l
-        ν = model.driver.met.ν
-        θ_a100 = model.driver.met.θ_a100
-        b = model.driver.met.b
+        ν = model.drivers.met.ν
+        θ_a100 = model.drivers.met.θ_a100
+        b = model.drivers.met.b
 
         p.soilco2.D .=
             co2_diffusivity.(T_soil, θ_w, P_sfc, θ_a100, b, ν, params)
@@ -592,7 +592,7 @@ function ClimaLand.boundary_flux(
 end
 
 function ClimaLand.get_drivers(model::SoilCO2Model)
-    return (model.driver.atmos, nothing)
+    return (model.drivers.atmos, nothing)
 end
 
 Base.broadcastable(ps::SoilCO2ModelParameters) = tuple(ps)