generalize_drivers, organic carbon driver

CliMA · Jul 15, 2024 · 89e068a · 89e068a
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diff --git a/NEWS.md b/NEWS.md
@@ -3,9 +3,13 @@ ClimaLand.jl Release Notes
 
 main
 --------
-- PR[#690] Use the soil parameters in creating the biogeochemistry SoilMet driver for consistency.
+- Use the soil parameters in creating the biogeochemistry SoilMet driver for consistency.
+  PR[#690](https://github.com/CliMA/ClimaLand.jl/pull/690)
+- ![][badge-💥breaking] Generalize our forcing ``drivers" to include prescribed soil organic carbon
+  PR[#692](https://github.com/CliMA/ClimaLand.jl/pull/692)
 - Add a long run with diagnostics
   PR[#688](https://github.com/CliMA/ClimaLand.jl/pull/688)
+
 v0.13.0
 --------
 - NOTE: the breaking PR below was merged by accident in v0.12.5

diff --git a/docs/src/APIs/SoilBiogeochemistry.md b/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

diff --git a/docs/src/APIs/shared_utilities.md b/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

diff --git a/docs/tutorials/integrated/soil_canopy_tutorial.jl b/docs/tutorials/integrated/soil_canopy_tutorial.jl
@@ -177,7 +177,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 soilco2_ps = SoilCO2ModelParameters(FT);
 
 # 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);
@@ -390,7 +390,8 @@ sv = (;
     saveval = Array{NamedTuple}(undef, length(saveat)),
 )
 saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(land)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 updateat = Array(t0:1800:tf)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb);

diff --git a/docs/tutorials/standalone/Bucket/bucket_tutorial.jl b/docs/tutorials/standalone/Bucket/bucket_tutorial.jl
@@ -329,7 +329,8 @@ saved_values = (;
 );
 saving_cb = ClimaLand.NonInterpSavingCallback(saved_values, saveat);
 updateat = copy(saveat)
-updatefunc = ClimaLand.make_update_drivers(bucket_atmos, bucket_rad)
+model_drivers = ClimaLand.get_drivers(model)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb)
 

diff --git a/docs/tutorials/standalone/Canopy/canopy_tutorial.jl b/docs/tutorials/standalone/Canopy/canopy_tutorial.jl
@@ -314,7 +314,8 @@ saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat);
 # Create the callback function which updates the forcing variables,
 # or drivers.
 updateat = Array(t0:1800:tf)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(canopy)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb);
 

diff --git a/docs/tutorials/standalone/Soil/evaporation.jl b/docs/tutorials/standalone/Soil/evaporation.jl
@@ -211,7 +211,8 @@ sv = (;
 )
 saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 updateat = deepcopy(saveat)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(soil)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb);
 

diff --git a/docs/tutorials/standalone/Soil/evaporation_gilat_loess.jl b/docs/tutorials/standalone/Soil/evaporation_gilat_loess.jl
@@ -250,7 +250,8 @@ sv = (;
 )
 saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 updateat = deepcopy(saveat)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(soil)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb)
 sol = SciMLBase.solve(prob, ode_algo; dt = dt, callback = cb, saveat = saveat)
@@ -315,7 +316,8 @@ sv = (;
 )
 saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 updateat = deepcopy(saveat)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(soil)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb)
 sol_no_drainage =

diff --git a/docs/tutorials/standalone/Soil/sublimation.jl b/docs/tutorials/standalone/Soil/sublimation.jl
@@ -197,7 +197,8 @@ sv = (;
 )
 saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 updateat = deepcopy(saveat)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(soil)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb);
 

diff --git a/experiments/benchmarks/bucket.jl b/experiments/benchmarks/bucket.jl
@@ -133,7 +133,8 @@ function setup_prob(t0, tf, Δt; nelements = (100, 10))
         p,
     )
     updateat = collect(t0:(3Δt):tf)
-    updatefunc = ClimaLand.make_update_drivers(bucket_atmos, bucket_rad)
+    drivers = ClimaLand.get_drivers(model)
+    updatefunc = ClimaLand.make_update_drivers(drivers)
     driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
     cb = SciMLBase.CallbackSet(driver_cb)
 

diff --git a/experiments/benchmarks/land.jl b/experiments/benchmarks/land.jl
@@ -205,7 +205,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     soil_params_mask = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "vGalpha_map_gupta_etal2020_2.5x2.5x4.nc",
+            "vGalpha_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "α",
         subsurface_space;
@@ -219,7 +219,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     vg_α = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "vGalpha_map_gupta_etal2020_2.5x2.5x4.nc",
+            "vGalpha_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "α",
         subsurface_space;
@@ -229,7 +229,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     vg_n = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "vGn_map_gupta_etal2020_2.5x2.5x4.nc",
+            "vGn_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "n",
         subsurface_space;
@@ -251,7 +251,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     θ_r = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "residual_map_gupta_etal2020_2.5x2.5x4.nc",
+            "residual_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "θ_r",
         subsurface_space;
@@ -262,7 +262,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     ν = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "porosity_map_gupta_etal2020_2.5x2.5x4.nc",
+            "porosity_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "ν",
         subsurface_space;
@@ -272,7 +272,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     K_sat = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "ksat_map_gupta_etal2020_2.5x2.5x4.nc",
+            "ksat_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "Ksat",
         subsurface_space;
@@ -409,7 +409,7 @@ 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()
@@ -591,7 +591,8 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     )
 
     updateat = Array(t0:(3600 * 3):tf)
-    updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+    drivers = ClimaLand.get_drivers(land)
+    updatefunc = ClimaLand.make_update_drivers(drivers)
     cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
     return prob, cb
 end

diff --git a/experiments/benchmarks/richards.jl b/experiments/benchmarks/richards.jl
@@ -115,7 +115,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     vg_α = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "vGalpha_map_gupta_etal2020_2.5x2.5x4.nc",
+            "vGalpha_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "α",
         subsurface_space;
@@ -135,7 +135,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     vg_n = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "vGn_map_gupta_etal2020_2.5x2.5x4.nc",
+            "vGn_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "n",
         subsurface_space;
@@ -150,7 +150,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     θ_r = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "residual_map_gupta_etal2020_2.5x2.5x4.nc",
+            "residual_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "θ_r",
         subsurface_space;
@@ -161,7 +161,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     ν = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "porosity_map_gupta_etal2020_2.5x2.5x4.nc",
+            "porosity_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "ν",
         subsurface_space;
@@ -172,7 +172,7 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     K_sat = SpaceVaryingInput(
         joinpath(
             soil_params_artifact_path,
-            "ksat_map_gupta_etal2020_2.5x2.5x4.nc",
+            "ksat_map_gupta_etal2020_1.0x1.0x4.nc",
         ),
         "Ksat",
         subsurface_space;
@@ -277,7 +277,8 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
         p,
     )
     updateat = Array(t0:(2Δt):tf)
-    updatefunc = ClimaLand.make_update_drivers(atmos, nothing)
+    drivers = ClimaLand.get_drivers(model)
+    updatefunc = ClimaLand.make_update_drivers(drivers)
     driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
     cb = SciMLBase.CallbackSet(driver_cb)
 

diff --git a/experiments/integrated/fluxnet/ozark_pft.jl b/experiments/integrated/fluxnet/ozark_pft.jl
@@ -137,8 +137,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 
 soilco2_ps = SoilCO2ModelParameters(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()
@@ -298,7 +297,8 @@ saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 ## How often we want to update the drivers. Note that this uses the defined `t0` and `tf`
 ## defined in the simulatons file
 updateat = Array(t0:DATA_DT:tf)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(land)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb);
 

diff --git a/experiments/integrated/fluxnet/run_fluxnet.jl b/experiments/integrated/fluxnet/run_fluxnet.jl
@@ -96,8 +96,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 
 soilco2_ps = SoilCO2ModelParameters(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()
@@ -254,7 +253,8 @@ saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 ## How often we want to update the drivers. Note that this uses the defined `t0` and `tf`
 ## defined in the simulatons file
 updateat = Array(t0:DATA_DT:tf)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+model_drivers = ClimaLand.get_drivers(land)
+updatefunc = ClimaLand.make_update_drivers(model_drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb)
 

diff --git a/experiments/integrated/global/global_soil_canopy.jl b/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()
@@ -368,7 +368,8 @@ sv = (;
 )
 saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 updateat = Array(t0:(3600 * 3):tf)
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+drivers = ClimaLand.get_drivers(land)
+updatefunc = ClimaLand.make_update_drivers(drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 cb = SciMLBase.CallbackSet(driver_cb, saving_cb)
 @time sol = SciMLBase.solve(

diff --git a/experiments/integrated/performance/conservation/ozark_conservation.jl b/experiments/integrated/performance/conservation/ozark_conservation.jl
@@ -41,7 +41,8 @@ for float_type in (Float32, Float64)
     saving_cb = ClimaLand.NonInterpSavingCallback(sv, saveat)
 
     updateat = deepcopy(saveat)
-    updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+    drivers = ClimaLand.get_drivers(land)
+    updatefunc = ClimaLand.make_update_drivers(drivers)
     driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
     prob = SciMLBase.ODEProblem(
         CTS.ClimaODEFunction(

diff --git a/experiments/integrated/performance/conservation/ozark_conservation_setup.jl b/experiments/integrated/performance/conservation/ozark_conservation_setup.jl
@@ -82,7 +82,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 soilco2_ps = SoilCO2ModelParameters(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()

diff --git a/experiments/integrated/performance/profile_allocations.jl b/experiments/integrated/performance/profile_allocations.jl
@@ -229,7 +229,7 @@ soilco2_type = Soil.Biogeochemistry.SoilCO2Model{FT}
 soilco2_ps = SoilCO2ModelParameters(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()
@@ -339,7 +339,8 @@ ode_algo = CTS.IMEXAlgorithm(
     ),
 );
 
-updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+drivers = ClimaLand.get_drivers(land)
+updatefunc = ClimaLand.make_update_drivers(drivers)
 driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 # Set initial conditions
 Y, p = set_initial_conditions(land, t0)
@@ -370,7 +371,8 @@ if PROFILING
     # Now that we compiled, solve again but collect profiling information
     Y, p = set_initial_conditions(land, t0)
     updateat = Array(t0:dt:tf)
-    updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+    drivers = ClimaLand.get_drivers(land)
+    updatefunc = ClimaLand.make_update_drivers(drivers)
     driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
     prob = SciMLBase.ODEProblem(
         CTS.ClimaODEFunction(
@@ -394,7 +396,8 @@ if PROFILING
     @info "Save compute flame to flame_file"
     Y, p = set_initial_conditions(land, t0)
     updateat = Array(t0:dt:tf)
-    updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+    drivers = ClimaLand.get_drivers(land)
+    updatefunc = ClimaLand.make_update_drivers(drivers)
     driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
     prob = SciMLBase.ODEProblem(
         CTS.ClimaODEFunction(

diff --git a/experiments/long_runs/land.jl b/experiments/long_runs/land.jl
@@ -408,7 +408,7 @@ function setup_prob(t0, tf, Δt; outdir = outdir, 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()
@@ -590,7 +590,8 @@ function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (101, 15))
     )
 
     updateat = Array(t0:(3600 * 3):tf)
-    updatefunc = ClimaLand.make_update_drivers(atmos, radiation)
+    drivers = ClimaLand.get_drivers(land)
+    updatefunc = ClimaLand.make_update_drivers(drivers)
 
     # ClimaDiagnostics