Merge branch 'main' into gb/logos

.buildkite/pipeline.yml

@@ -62,6 +62,10 @@ steps:
         command: "julia --color=yes --project=experiments experiments/integrated/fluxnet/run_fluxnet.jl US-Ha1"
         artifact_paths: "experiments/integrated/fluxnet/US-Ha1/out/*png"
 
+      - label: "ozark_pft"
+        command: "julia --color=yes --project=experiments experiments/integrated/fluxnet/ozark_pft.jl"
+        artifact_paths: "experiments/integrated/fluxnet/US-MOz/out/pft/*png"
+
       - label: "ozark_conservation"
         command: "julia --color=yes --project=experiments experiments/integrated/ozark/conservation/ozark_conservation.jl"
         artifact_paths: "experiments/integrated/ozark/conservation/*png"

.gitignore

@@ -3,6 +3,7 @@
 *.txt
 *#
 *~
+*.nc
 *.png
 *.mp4
 *.pdf

Project.toml

@@ -29,16 +29,16 @@ Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd"
 
 [weakdeps]
-CLIMAParameters = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
+ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
 
 [extensions]
-CreateParametersExt = "CLIMAParameters"
+CreateParametersExt = "ClimaParams"
 
 [compat]
 Adapt = "3, 4"
 ArtifactWrappers = "0.2"
 CFTime = "0.1"
-CLIMAParameters = "0.9"
+ClimaParams = "0.10"
 CSV = "0.10"
 CUDA = "5"
 ClimaComms = "0.5.6"
@@ -49,14 +49,14 @@ Dates = "1"
 DocStringExtensions = "0.8, 0.9"
 Flux = "0.14"
 HTTP = "1.10"
-Insolation = "=0.9.1"
+Insolation = "0.9.2"
 IntervalSets = "0.5, 0.6, 0.7"
 LinearAlgebra = "1"
 NCDatasets = "0.11, 0.12, 0.13, 0.14"
 SciMLBase = "1, 2"
 StaticArrays = "1"
 StatsBase = "0.34"
-SurfaceFluxes = "0.9"
-Thermodynamics = "=0.12.3"
+SurfaceFluxes = "0.10"
+Thermodynamics = "0.12"
 cuDNN = "1"
 julia = "1.9"

docs/Manifest.toml

@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.0"
+julia_version = "1.10.1"
 manifest_format = "2.0"
-project_hash = "f930dc7ba66e23f2de897f17dbbdfb065b27141e"
+project_hash = "5f713b750235cf07465e21e92a6bd2f152ad3358"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245"
@@ -192,12 +192,6 @@ git-tree-sha1 = "5afb5c5ba2688ca43a9ad2e5a91cbb93921ccfa1"
 uuid = "179af706-886a-5703-950a-314cd64e0468"
 version = "0.1.3"
 
-[[deps.CLIMAParameters]]
-deps = ["DocStringExtensions", "TOML", "Test"]
-git-tree-sha1 = "9fcb37be791b4762943cbbf15ccf35c99d91460c"
-uuid = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
-version = "0.9.1"
-
 [[deps.CPUSummary]]
 deps = ["CpuId", "IfElse", "PrecompileTools", "Static"]
 git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1"
@@ -294,10 +288,16 @@ deps = ["Adapt", "ArtifactWrappers", "CFTime", "CSV", "CUDA", "ClimaComms", "Cli
 path = ".."
 uuid = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
 version = "0.10.0"
-weakdeps = ["CLIMAParameters"]
+weakdeps = ["ClimaParams"]
 
     [deps.ClimaLand.extensions]
-    CreateParametersExt = "CLIMAParameters"
+    CreateParametersExt = "ClimaParams"
+
+[[deps.ClimaParams]]
+deps = ["DocStringExtensions", "TOML", "Test"]
+git-tree-sha1 = "284afdfa1e8a3d42809ffaab8e411d20d4804560"
+uuid = "5c42b081-d73a-476f-9059-fd94b934656c"
+version = "0.10.1"
 
 [[deps.ClimaTimeSteppers]]
 deps = ["ClimaComms", "Colors", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "KernelAbstractions", "Krylov", "LinearAlgebra", "LinearOperators", "NVTX", "SciMLBase", "StaticArrays"]
@@ -375,7 +375,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.5+1"
+version = "1.1.0+0"
 
 [[deps.CompositionsBase]]
 git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad"
@@ -835,9 +835,9 @@ version = "1.3.1"
 
 [[deps.Git_jll]]
 deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "99f27817475017260f1ff24c771a5efef5765e34"
+git-tree-sha1 = "12945451c5d0e2d0dca0724c3a8d6448b46bbdf9"
 uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb"
-version = "2.44.0+0"
+version = "2.44.0+1"
 
 [[deps.Glib_jll]]
 deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
@@ -926,13 +926,13 @@ version = "1.4.0"
 
 [[deps.Insolation]]
 deps = ["Artifacts", "Dates", "DelimitedFiles", "Interpolations"]
-git-tree-sha1 = "e5bd2e08d94737b3acd1c1c4e6ab737d2494571c"
+git-tree-sha1 = "1a2a8e1f202523619225fb54adf458b9345cee9b"
 uuid = "e98cc03f-d57e-4e3c-b70c-8d51efe9e0d8"
-version = "0.9.1"
-weakdeps = ["CLIMAParameters"]
+version = "0.9.2"
+weakdeps = ["ClimaParams"]
 
     [deps.Insolation.extensions]
-    CreateParametersExt = "CLIMAParameters"
+    CreateParametersExt = "ClimaParams"
 
 [[deps.IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1486,7 +1486,7 @@ version = "0.3.24+0"
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.23+2"
+version = "0.3.23+4"
 
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -2002,13 +2002,13 @@ version = "7.2.1+1"
 
 [[deps.SurfaceFluxes]]
 deps = ["DocStringExtensions", "RootSolvers", "Thermodynamics"]
-git-tree-sha1 = "c2329f2ba04cfd7d93b1fa00d43822b1ccacaa4e"
+git-tree-sha1 = "24086f7e46de40dbd32a49d3fd51a534a5a9bcb0"
 uuid = "49b00bb7-8bd4-4f2b-b78c-51cd0450215f"
-version = "0.9.4"
-weakdeps = ["CLIMAParameters"]
+version = "0.10.0"
+weakdeps = ["ClimaParams"]
 
     [deps.SurfaceFluxes.extensions]
-    CreateParametersExt = "CLIMAParameters"
+    CreateParametersExt = "ClimaParams"
 
 [[deps.SymbolicIndexingInterface]]
 git-tree-sha1 = "251bb311585143931a306175c3b7ced220300578"
@@ -2067,13 +2067,13 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.Thermodynamics]]
 deps = ["DocStringExtensions", "KernelAbstractions", "Random", "RootSolvers"]
-git-tree-sha1 = "9c9ccbdb2ecb490fc69a0392c98766dcc2024eae"
+git-tree-sha1 = "a539e258008ed9275a91e0a374aa1d073e80e2bf"
 uuid = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
-version = "0.12.3"
-weakdeps = ["CLIMAParameters"]
+version = "0.12.4"
+weakdeps = ["ClimaParams"]
 
     [deps.Thermodynamics.extensions]
-    CreateParametersExt = "CLIMAParameters"
+    CreateParametersExt = "ClimaParams"
 
 [[deps.ThreadingUtilities]]
 deps = ["ManualMemory"]

docs/Project.toml

@@ -1,6 +1,6 @@
 [deps]
 ArtifactWrappers = "a14bc488-3040-4b00-9dc1-f6467924858a"
-CLIMAParameters = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
+ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
 ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
@@ -32,8 +32,6 @@ ClimaTimeSteppers = "0.7"
 DataFrames = "1.6"
 Flux = "0.14"
 HTTP = "1.10"
-Insolation = "=0.9.1"
 InteractiveUtils = "1"
 StatsBase = "0.34"
 cuDNN = "1"
-Thermodynamics = "=0.12.3"

docs/make.jl

@@ -19,6 +19,7 @@ tutorials = [
             "standalone/Bucket/coupled_bucket.jl",
         ],
         "Soil modeling" => [
+            "Boundary conditions" => "standalone/Soil/boundary_conditions.jl",
             "Richards Equation" => "standalone/Soil/richards_equation.jl",
             "Energy and Hydrology" => "standalone/Soil/soil_energy_hydrology.jl",
             "Phase Changes" => "standalone/Soil/freezing_front.jl",

docs/src/APIs/Soil.md

@@ -72,16 +72,15 @@ ClimaLand.Soil.soil_surface_infiltration
 ## Soil BC Methods and Types
 
 ```@docs
-ClimaLand.Soil.AbstractSoilBC
 ClimaLand.Soil.MoistureStateBC
-ClimaLand.Soil.FluxBC
+ClimaLand.Soil.HeatFluxBC
+ClimaLand.Soil.WaterFluxBC
 ClimaLand.Soil.TemperatureStateBC
 ClimaLand.Soil.FreeDrainage
 ClimaLand.Soil.RichardsAtmosDrivenFluxBC
 ClimaLand.Soil.AtmosDrivenFluxBC
-ClimaLand.Soil.boundary_vars
-ClimaLand.Soil.boundary_var_domain_names
-ClimaLand.Soil.boundary_var_types
+ClimaLand.Soil.WaterHeatBC
+ClimaLand.Soil.soil_boundary_fluxes!
 ```
 
 ## Soil Source Types

docs/src/APIs/shared_utilities.md

@@ -54,6 +54,9 @@ ClimaLand.BottomBoundary
 ClimaLand.boundary_flux
 ClimaLand.diffusive_flux
 ClimaLand.get_Δz
+ClimaLand.boundary_vars
+ClimaLand.boundary_var_domain_names
+ClimaLand.boundary_var_types
 ClimaLand.make_tendency_jacobian
 ClimaLand.make_update_jacobian
 ClimaLand.∂tendencyBC∂Y
@@ -64,6 +67,7 @@ ClimaLand.get_drivers
 ## Drivers
 ```@docs
 ClimaLand.PrescribedAtmosphere
+ClimaLand.PrescribedPrecipitation
 ClimaLand.PrescribedRadiativeFluxes
 ClimaLand.CoupledAtmosphere
 ClimaLand.CoupledRadiativeFluxes

docs/tutorials/integrated/soil_canopy_tutorial.jl

@@ -42,7 +42,7 @@ using Insolation
 # Load CliMA Packages and ClimaLand Modules:
 
 using ClimaCore
-import CLIMAParameters as CP
+import ClimaParams as CP
 import ClimaTimeSteppers as CTS
 using ClimaLand
 using ClimaLand.Domains: Column, obtain_surface_domain
@@ -67,7 +67,7 @@ zmax = FT(0)
 f_root_to_shoot = FT(3.5)
 SAI = FT(0.00242)
 maxLAI = FT(4.2)
-capacity = FT(10) # kg/m^2
+plant_ν = FT(2.46e-4)
 n_stem = Int64(1)
 n_leaf = Int64(1)
 h_stem = FT(9)
@@ -209,8 +209,7 @@ soilco2_top_bc = Soil.Biogeochemistry.AtmosCO2StateBC()
 soilco2_bot_bc = Soil.Biogeochemistry.SoilCO2StateBC((p, t) -> 0.0);
 soilco2_sources = (MicrobeProduction{FT}(),);
 
-soilco2_boundary_conditions =
-    (; top = (CO2 = soilco2_top_bc,), bottom = (CO2 = soilco2_bot_bc,));
+soilco2_boundary_conditions = (; top = soilco2_top_bc, bottom = soilco2_bot_bc);
 
 soilco2_drivers = Soil.Biogeochemistry.SoilDrivers(
     Soil.Biogeochemistry.PrognosticMet{FT}(),

docs/tutorials/shared_utilities/driver_tutorial.jl

@@ -45,7 +45,7 @@ using Dates
 using Insolation # for computing zenith angle given lat, lon, time.
 using ClimaLand
 import ClimaLand.Parameters as LP
-import CLIMAParameters
+import ClimaParams
 
 # Assume the local_datetime array is read in from the data file.
 local_datetime = DateTime(2013):Dates.Hour(1):DateTime(2013, 1, 7); # one week, hourly data

docs/tutorials/standalone/Bucket/bucket_tutorial.jl

@@ -130,10 +130,10 @@ import ClimaTimeSteppers as CTS
 # in advance for running distributed simulations.
 using ClimaCore
 
-# We also use CLIMAParameters, which strives to ensure a common set of
+# We also use ClimaParams, which strives to ensure a common set of
 # parameters across all Clima models, and to make parameter estimation
 # more seamless.
-import CLIMAParameters as CP
+import ClimaParams as CP
 
 # We also use Insolation to calculate solar zenith angle and solar insolation.
 
@@ -160,7 +160,7 @@ using Dates
 
 FT = Float32;
 
-# As mentioned we use CLIMAParameters for earth parameters that are
+# As mentioned we use ClimaParams for earth parameters that are
 # required across models (e.g. the density of water and ice, the latent
 # heat of fusion at a reference temperature, etc). The land model requires
 # additional parameters as described in the text above. These two sets

docs/tutorials/standalone/Canopy/canopy_tutorial.jl

@@ -43,7 +43,7 @@ using Insolation
 # Load CliMA Packages and ClimaLand Modules:
 
 using ClimaCore
-import CLIMAParameters as CP
+import ClimaParams as CP
 import ClimaTimeSteppers as CTS
 using StaticArrays
 using ClimaLand
@@ -83,7 +83,7 @@ zmax = FT(0)
 f_root_to_shoot = FT(3.5)
 SAI = FT(0.00242)
 maxLAI = FT(4.2)
-capacity = FT(10) # kg/m^2
+plant_ν = FT(2.46e-4) # kg/m^2
 n_stem = Int64(1)
 n_leaf = Int64(1)
 h_stem = FT(9)

docs/tutorials/standalone/Soil/boundary_conditions.jl

@@ -0,0 +1,31 @@
+# # Boundary conditions for the soil model
+
+# In general, you must supply two boundary conditions for each PDE being
+# solved. These are passed to the model as a NamedTuple
+# of the form `(; top = top_bc, bottom = bottom_bc)`, where both `top_bc`
+# and `bottom_bc` are of type `ClimaLand.AbstractBC`.
+
+# Flux boundary conditions are always passed as the (scalar)
+# z-component of the flux `f`, i.e. F⃗ = f ẑ.
+
+# # Boundary conditions for Richards equation
+# 1. `FreeDrainage <: AbstractWaterBC`: this only can be used at the bottom of the domain.
+
+# 2. `WaterFluxBC <: AbstractWaterBC`: this accepts a prescribed analytic function of the cache `p` and simulation time `t` which returns the flux value. e.g: `WaterFluxBC((p,t) -> 0.0)`.
+
+# 3. `MoistureStateBC <: AbstractWaterBC`: this accepts a prescribed analytic function of the cache `p` and simulation time `t` which returns the value of `ϑ_l` at the boundary . e.g: `MoistureStateBC((p,t) -> 0.2)`.
+
+# 4. `RichardsAtmosDrivenFluxBC <: AbstractWaterBC`: this requires a single argument of abstract type `AbstractTimeVaryingInput`. Under the hood, this specifies the precipitation as a function of space and time (using data read in from a file, or an analytic function) and applies this a flux BC, optionally accounting for surface/subsurface runoff.
+
+# # Boundary conditions for the soil heat equation
+
+# 1. `HeatFluxBC <: AbstractHeatBC`: this accepts a prescribed analytic function of the cache `p` and simulation time `t` which returns the flux value. e.g: `HeatFluxBC((p,t) -> 0.0)`.
+
+# 2. `TemperatureStateBC <: AbstractHeatBC`: this accepts a prescribed analytic function of the cache `p` and simulation time `t` which returns the value of `T` at the boundary . e.g: `TemperatureStateBC((p,t) -> 273.15)`.
+
+# # Boundary conditions for the soil heat + water equations (EnergyHydrology model)
+# The full soil model requires boundary conditions for both Richards equation and the soil heat equation.
+
+# 1. `WaterHeatBC <: AbstractEnergyHydrologyBC`: In many cases, the two boundary conditions can be treated independently. The `WaterHeatBC` requires a boundary condition of abstract type `AbstractWaterBC` and one of type `AbstractHeatBC`, for example, `top = WaterHeatBC(; water = MoistureBC(ϑ_l(p,t)), heat = TemperatureBC(T(p,t)))`.
+
+# 2. `AtmosDrivenFluxBC <: AbstractEnergyHydrologyBC`: This is an example of a set of boundary conditions for the full soil model which cannot be decomposed into two independent boundary conditions for water and heat. In this case, we compute the turbulent surface fluxes with the atmosphere, obtaining a sensible heat, latent heat, and water vapor flux. We also take into account the net radiation at the surface and any precipitation or runoff. This is the BC type used in most land simulations.

docs/tutorials/standalone/Soil/freezing_front.jl

@@ -79,7 +79,7 @@ using DelimitedFiles
 using Plots
 
 using ClimaCore
-import CLIMAParameters as CP
+import ClimaParams as CP
 
 using ClimaLand
 using ClimaLand.Domains: Column
@@ -128,7 +128,7 @@ nelems = 20
 soil_domain = Column(; zlim = (zmin, zmax), nelements = nelems);
 
 # Set the boundary conditions:
-zero_flux_bc = FluxBC((p, t) -> 0.0)
+zero_water_flux_bc = WaterFluxBC((p, t) -> 0.0)
 function top_heat_flux(p, t)
     FT = eltype(p.soil.T)
     p_len = ClimaCore.Spaces.nlevels(axes(p.soil.T))
@@ -140,11 +140,14 @@ function bottom_heat_flux(p, t)
     T_c = ClimaCore.Fields.level(p.soil.T, 1)
     return @. FT(-3 * (T_c - 279.85))
 end
-top_heat_flux_bc = FluxBC(top_heat_flux)
-bottom_heat_flux_bc = FluxBC(bottom_heat_flux)
+top_heat_flux_bc = HeatFluxBC(top_heat_flux)
+bottom_heat_flux_bc = HeatFluxBC(bottom_heat_flux)
 boundary_fluxes = (;
-    top = (water = zero_flux_bc, heat = top_heat_flux_bc),
-    bottom = (water = zero_flux_bc, heat = bottom_heat_flux_bc),
+    top = WaterHeatBC(; water = zero_water_flux_bc, heat = top_heat_flux_bc),
+    bottom = WaterHeatBC(;
+        water = zero_water_flux_bc,
+        heat = bottom_heat_flux_bc,
+    ),
 );
 
 # Create the source term instance. Our phase change model requires