generalize_drivers

.buildkite/Manifest.toml

@@ -124,9 +124,9 @@ version = "7.12.0"
 
 [[deps.ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra"]
-git-tree-sha1 = "8556500c18fcad8b4c44058e23fbc4a36143f6be"
+git-tree-sha1 = "ce2ca959f932f5dad70697dd93133d1167cf1e4e"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "1.10.1"
+version = "1.10.2"
 weakdeps = ["SparseArrays"]
 
     [deps.ArrayLayouts.extensions]
@@ -277,9 +277,9 @@ version = "0.10.14"
 
 [[deps.CUDA]]
 deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "Crayons", "DataFrames", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LLVMLoopInfo", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "NVTX", "Preferences", "PrettyTables", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics"]
-git-tree-sha1 = "6e945e876652f2003e6ca74e19a3c45017d3e9f6"
+git-tree-sha1 = "fdd9dfb67dfefd548f51000cc400bb51003de247"
 uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
-version = "5.4.2"
+version = "5.4.3"
 weakdeps = ["ChainRulesCore", "EnzymeCore", "SpecialFunctions"]
 
     [deps.CUDA.extensions]
@@ -625,9 +625,9 @@ version = "0.1.2"
 
 [[deps.DelaunayTriangulation]]
 deps = ["EnumX", "ExactPredicates", "Random"]
-git-tree-sha1 = "b0cb128d2e100646573e1da8565b02491fddb5ef"
+git-tree-sha1 = "078c716cbb032242df18b960e8b1fec6b1b0b9f9"
 uuid = "927a84f5-c5f4-47a5-9785-b46e178433df"
-version = "1.0.4"
+version = "1.0.5"
 
 [[deps.DelimitedFiles]]
 deps = ["Mmap"]
@@ -1066,10 +1066,10 @@ uuid = "46192b85-c4d5-4398-a991-12ede77f4527"
 version = "0.1.6"
 
 [[deps.GPUCompiler]]
-deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"]
-git-tree-sha1 = "518ebd058c9895de468a8c255797b0c53fdb44dd"
+deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"]
+git-tree-sha1 = "ab29216184312f99ff957b32cd63c2fe9c928b91"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "0.26.5"
+version = "0.26.7"
 
 [[deps.GR]]
 deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"]
@@ -1279,9 +1279,9 @@ weakdeps = ["ClimaParams"]
 
 [[deps.IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4"
+git-tree-sha1 = "14eb2b542e748570b56446f4c50fbfb2306ebc45"
 uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
-version = "2024.1.0+0"
+version = "2024.2.0+0"
 
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
@@ -1440,19 +1440,19 @@ version = "3.0.0+1"
 
 [[deps.LLVM]]
 deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"]
-git-tree-sha1 = "389aea28d882a40b5e1747069af71bdbd47a1cae"
+git-tree-sha1 = "020abd49586480c1be84f57da0017b5d3db73f7c"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "7.2.1"
+version = "8.0.0"
 weakdeps = ["BFloat16s"]
 
     [deps.LLVM.extensions]
     BFloat16sExt = "BFloat16s"
 
 [[deps.LLVMExtra_jll]]
 deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc"
+git-tree-sha1 = "c2636c264861edc6d305e6b4d528f09566d24c5e"
 uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab"
-version = "0.0.29+0"
+version = "0.0.30+0"
 
 [[deps.LLVMLoopInfo]]
 git-tree-sha1 = "2e5c102cfc41f48ae4740c7eca7743cc7e7b75ea"
@@ -1700,9 +1700,9 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"]
 
 [[deps.MKL_jll]]
 deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"]
-git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b"
+git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f"
 uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
-version = "2024.1.0+0"
+version = "2024.2.0+0"
 
 [[deps.MLStyle]]
 git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8"
@@ -2332,9 +2332,9 @@ version = "0.6.12"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
-git-tree-sha1 = "76a35763102e16c97d7302f5dc67837d24802035"
+git-tree-sha1 = "b450d967a770fb13d0e26358f58375e20361cf9c"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.25.0"
+version = "3.26.0"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -2477,9 +2477,9 @@ version = "1.2.1"
 
 [[deps.SentinelArrays]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "6bb314cb1aacfa37ef58e5a0ccf4a1ec0311f495"
+git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a"
 uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-version = "1.4.4"
+version = "1.4.5"
 
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

.buildkite/target/pipeline.yml

@@ -13,6 +13,11 @@ steps:
     key: "init_env"
     command:
       - "echo $$JULIA_DEPOT_PATH"
+
+      - echo "--- Instantiate project"
+      - "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
+      - "julia --project -e 'using Pkg; Pkg.status()'"
+
       - echo "--- Instantiate experiments"
       - "julia --project=.buildkite -e 'using Pkg; Pkg.develop(;path=\".\"); Pkg.instantiate(;verbose=true)'"
       - "julia --project=.buildkite -e 'using Pkg; Pkg.status()'"

NEWS.md

@@ -4,6 +4,7 @@ ClimaLand.jl Release Notes
 main
 --------
 - PR[#690] Use the soil parameters in creating the biogeochemistry SoilMet driver for consistency.
+- PR[#692] Generalize our forcing ``drivers" to include prescribed soil organic carbon
 
 v0.13.0
 --------

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);
 
 # 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);

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)
 

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);
 

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);
 

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 =

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);
 

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)
 

experiments/benchmarks/land.jl

@@ -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

experiments/benchmarks/richards.jl

@@ -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)
 

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);
 

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)
 

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(

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(

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()

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(