remove PrescribedSOC and use new driver

docs/src/APIs/SoilBiogeochemistry.md

@@ -25,7 +25,6 @@ ClimaLand.Soil.Biogeochemistry.AtmosCO2StateBC
 ClimaLand.Soil.Biogeochemistry.AbstractSoilDriver
 ClimaLand.Soil.Biogeochemistry.SoilDrivers
 ClimaLand.Soil.Biogeochemistry.PrescribedMet
-ClimaLand.Soil.Biogeochemistry.PrescribedSOC
 ```
 
 ## Functions of State

docs/src/APIs/shared_utilities.md

@@ -71,6 +71,7 @@ ClimaLand.get_drivers
 ClimaLand.PrescribedAtmosphere
 ClimaLand.PrescribedPrecipitation
 ClimaLand.PrescribedRadiativeFluxes
+ClimaLand.PrescribedSoilOrganicCarbon
 ClimaLand.CoupledAtmosphere
 ClimaLand.CoupledRadiativeFluxes
 ClimaLand.AbstractAtmosphericDrivers

docs/tutorials/integrated/soil_canopy_tutorial.jl

@@ -177,7 +177,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 soilco2_ps = SoilCO2ModelParameters(FT; ν = soil_ν);
 
 # soil microbes args
-Csom = (z, t) -> eltype(z)(5); # kg C m⁻³, this is a guess, not measured at the site
+Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
 soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
 soilco2_bot_bc = Soil.Biogeochemistry.SoilCO2StateBC((p, t) -> 0.0);
@@ -187,7 +187,7 @@ 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),
+    Csom,
     atmos,
 );
 

experiments/benchmarks/land.jl

@@ -412,7 +412,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 
     # soil microbes args
-    Csom = (z, t) -> eltype(z)(5.0)
+    Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
     # Set the soil CO2 BC to being atmospheric CO2
     soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
@@ -424,7 +424,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
 
     soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
         Soil.Biogeochemistry.PrognosticMet{FT}(),
-        Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
+        Csom,
         atmos,
     )
 

experiments/integrated/fluxnet/ozark_pft.jl

@@ -140,8 +140,7 @@ soilco2_ps = SoilCO2ModelParameters(
     ν = soil_ν, # same as soil
 )
 
-# soil microbes args
-Csom = (z, t) -> eltype(z)(5.0)
+Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
 # Set the soil CO2 BC to being atmospheric CO2
 soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
@@ -152,7 +151,7 @@ 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),
+    Csom,
     atmos,
 )
 

experiments/integrated/fluxnet/run_fluxnet.jl

@@ -99,8 +99,7 @@ soilco2_ps = SoilCO2ModelParameters(
     ν = soil_ν, # same as soil
 )
 
-# soil microbes args
-Csom = (z, t) -> eltype(z)(5.0)
+Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
 # Set the soil CO2 BC to being atmospheric CO2
 soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
@@ -111,7 +110,7 @@ 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),
+    Csom,
     atmos,
 )
 

experiments/integrated/global/global_soil_canopy.jl

@@ -181,7 +181,7 @@ soil_model_type = Soil.EnergyHydrology{FT}
 soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 
 # soil microbes args
-Csom = (z, t) -> eltype(z)(5.0)
+Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
 # Set the soil CO2 BC to being atmospheric CO2
 soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
@@ -192,7 +192,7 @@ 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),
+    Csom,
     atmos,
 )
 

experiments/integrated/performance/conservation/ozark_conservation_setup.jl

@@ -82,7 +82,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 soilco2_ps = SoilCO2ModelParameters(FT; ν = soil_ν)
 
 # soil microbes args
-Csom = (z, t) -> eltype(z)(5.0)
+Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
 # Set the soil CO2 BC to being atmospheric CO2
 soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
@@ -93,7 +93,7 @@ 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),
+    Csom,
     atmos,
 )
 

experiments/integrated/performance/profile_allocations.jl

@@ -229,7 +229,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 soilco2_ps = SoilCO2ModelParameters(FT; ν = soil_ν)
 
 # soil microbes args
-Csom = (z, t) -> eltype(z)(5.0)
+Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
 # Set the soil CO2 BC to being atmospheric CO2
 soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
@@ -240,7 +240,7 @@ 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),
+    Csom,
     atmos,
 )
 

experiments/standalone/Biogeochemistry/experiment.jl

@@ -69,7 +69,7 @@ for (FT, tf) in ((Float32, 2 * dt), (Float64, tf))
     )
 
     # Make biogeochemistry model args
-    Csom = (z, t) -> eltype(z)(5.0)
+    Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
     co2_parameters = Soil.Biogeochemistry.SoilCO2ModelParameters(FT; ν = 0.556)
     C = FT(100)
@@ -105,7 +105,7 @@ for (FT, tf) in ((Float32, 2 * dt), (Float64, tf))
 
     soil_drivers = Soil.Biogeochemistry.SoilDrivers(
         Soil.Biogeochemistry.PrognosticMet{FT}(),
-        Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
+        Csom,
         atmos,
     )
 

lib/ClimaLandSimulations/src/Fluxnet/run_fluxnet.jl

@@ -63,7 +63,7 @@ function run_fluxnet(
     )
 
     # soil microbes args
-    Csom = (z, t) -> eltype(z)(5.0)
+    Csom = ClimaLand.PrescribedSoilOrganicCarbon{FT}(TimeVaryingInput((t) -> 5))
 
     soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
     soilco2_bot_bc = Soil.Biogeochemistry.SoilCO2FluxBC((p, t) -> 0.0) # no flux
@@ -74,7 +74,7 @@ function run_fluxnet(
 
     soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
         Soil.Biogeochemistry.PrognosticMet{FT}(),
-        Soil.Biogeochemistry.PrescribedSOC{FT}(Csom),
+        Csom,
         drivers.atmos,
     )
 

src/integrated/soil_canopy_model.jl

@@ -590,5 +590,9 @@ end
 
 
 function ClimaLand.get_drivers(model::SoilCanopyModel)
-    return (model.canopy.atmos, model.canopy.radiation)
+    return (
+        model.canopy.atmos,
+        model.canopy.radiation,
+        model.soilco2.driver.soc,
+    )
 end

src/integrated/soil_energy_hydrology_biogeochemistry.jl

@@ -94,8 +94,8 @@ function ClimaLand.get_drivers(model::LandSoilBiogeochemistry)
         <:AbstractRadiativeDrivers,
         <:Soil.AbstractRunoffModel,
     }
-        return (bc.atmos, bc.radiation)
+        return (bc.atmos, bc.radiation, model.soilco2.driver.soc)
     else
-        return (model.soilco2.driver.atmos, nothing)
+        return (model.soilco2.driver.atmos, model.soilco2.driver.soc)
     end
 end

src/shared_utilities/drivers.jl

@@ -11,6 +11,7 @@ export AbstractAtmosphericDrivers,
     AbstractRadiativeDrivers,
     PrescribedAtmosphere,
     PrescribedPrecipitation,
+    PrescribedSoilOrganicCarbon,
     CoupledAtmosphere,
     PrescribedRadiativeFluxes,
     CoupledRadiativeFluxes,
@@ -48,6 +49,21 @@ An abstract type of radiative drivers of land models.
 abstract type AbstractRadiativeDrivers{FT} <: AbstractClimaLandDrivers{FT} end
 
 
+"""
+     PrescribedSoilOrganicCarbon{FT}
+
+A type for prescribing soil organic carbon.
+$(DocStringExtensions.FIELDS)
+"""
+struct PrescribedSoilOrganicCarbon{FT, SOC <: AbstractTimeVaryingInput} <:
+       AbstractClimaLandDrivers{FT}
+    "Soil organic carbon, function of time and space: kg C/m^3"
+    soc::SOC
+end
+
+PrescribedSoilOrganicCarbon{FT}(soc) where {FT} =
+    PrescribedSoilOrganicCarbon{FT, typeof(soc)}(soc)
+
 """
     PrescribedAtmosphere{FT, CA, DT} <: AbstractAtmosphericDrivers{FT}
 
@@ -766,6 +782,28 @@ function initialize_drivers(r::PrescribedRadiativeFluxes{FT}, coords) where {FT}
     return vars.drivers
 end
 
+"""
+    initialize_drivers(r::PrescribedSoilOrganicCarbon{FT}, coords) where {FT}
+
+Creates and returns a NamedTuple for the `PrescribedSoilOrganicCarbon` driver,
+ with variable `soc`.
+"""
+function initialize_drivers(
+    r::PrescribedSoilOrganicCarbon{FT},
+    coords,
+) where {FT}
+    keys = (:soc,)
+    types = (FT,)
+    domain_names = (:subsurface,)
+    model_name = :drivers
+    # intialize_vars packages the variables as a named tuple,
+    # as part of a named tuple with `model_name` as the key.
+    # Here we just want the variable named tuple itself
+    vars =
+        ClimaLand.initialize_vars(keys, types, domain_names, coords, model_name)
+    return vars.drivers
+end
+
 """
     initialize_drivers(d::Union{AbstractClimaLandDrivers, Nothing}, coords)
 
@@ -869,3 +907,15 @@ function make_update_drivers(r::PrescribedRadiativeFluxes{FT}) where {FT}
     end
     return update_drivers!
 end
+
+"""
+    make_update_drivers(a::PrescribedSoilOrganicCarbon{FT}) where {FT}
+Creates and returns a function which updates the driver variables
+in the case of a PrescribedSoilOrganicCarbon.
+"""
+function make_update_drivers(a::PrescribedSoilOrganicCarbon{FT}) where {FT}
+    function update_drivers!(p, t)
+        evaluate!(p.drivers.soc, a.soc, t)
+    end
+    return update_drivers!
+end

src/standalone/Soil/Biogeochemistry/Biogeochemistry.jl

@@ -27,7 +27,7 @@ import ClimaLand:
 export SoilCO2ModelParameters,
     SoilCO2Model,
     PrescribedMet,
-    PrescribedSOC,
+    PrescribedSoilOrganicCarbon,
     MicrobeProduction,
     SoilCO2FluxBC,
     AtmosCO2StateBC,
@@ -290,7 +290,7 @@ $(DocStringExtensions.FIELDS)
 struct SoilDrivers{
     FT,
     MET <: AbstractSoilDriver,
-    SOC <: AbstractSoilDriver,
+    SOC <: PrescribedSoilOrganicCarbon{FT},
     ATM <: PrescribedAtmosphere{FT},
 }
     "Soil temperature and moisture drivers - Prescribed or Prognostic"
@@ -334,24 +334,6 @@ function PrescribedMet{FT}(
 end
 
 
-"""
-    PrescribedSOC <: AbstractSoilDriver
-
-A container which holds the prescribed function for soil organic carbon
-
-This is meant for use when running the biogeochemistry model without a soil
-organic carbon model.
-
-$(DocStringExtensions.FIELDS)
-"""
-struct PrescribedSOC{FT, F <: Function} <: AbstractSoilDriver
-    "Carbon content of soil organic matter, of the form f(z::FT, t) where FT <: AbstractFloat"
-    soil_organic_carbon::F
-end
-
-function PrescribedSOC{FT}(Csom) where {FT <: AbstractFloat}
-    return PrescribedSOC{FT, typeof(Csom)}(Csom)
-end
 
 """
     soil_temperature(driver::PrescribedMet, p, Y, t, z)
@@ -373,16 +355,6 @@ function soil_moisture(driver::PrescribedMet, p, Y, t, z)
     return driver.volumetric_liquid_fraction.(z, t)
 end
 
-"""
-    soil_som_C(driver::PrescribedSOC, p, Y, t, z)
-
-Returns the carbon soil organic matter (SOM) at location (z) and time (t) for the prescribed
-soil case.
-"""
-function soil_SOM_C(driver::PrescribedSOC, p, Y, t, z)
-    return driver.soil_organic_carbon.(z, t)
-end
-
 """
     air_pressure(driver::PrescribedAtmosphere, t)
 
@@ -406,7 +378,7 @@ function ClimaLand.make_update_aux(model::SoilCO2Model)
         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)
+        Csom = p.drivers.soc
         P_sfc = air_pressure(model.driver.atmos, p, Y, t)
         θ_w = θ_l
 
@@ -581,7 +553,7 @@ function ClimaLand.boundary_flux(
 end
 
 function ClimaLand.get_drivers(model::SoilCO2Model)
-    return (model.driver.atmos, nothing)
+    return (model.driver.atmos, model.driver.soc)
 end
 
 include("./co2_parameterizations.jl")

src/standalone/Soil/energy_hydrology.jl

@@ -880,6 +880,6 @@ function ClimaLand.get_drivers(model::EnergyHydrology)
     }
         return (bc.atmos, bc.radiation)
     else
-        return (nothing, nothing)
+        return (nothing,)
     end
 end

src/standalone/Soil/rre.jl

@@ -442,8 +442,8 @@ function ClimaLand.get_drivers(model::RichardsModel)
         <:PrescribedPrecipitation,
         <:AbstractRunoffModel,
     }
-        return (bc.precip, nothing)
+        return (bc.precip,)
     else
-        return (nothing, nothing)
+        return (nothing,)
     end
 end