Merge pull request #598 from CliMA/js/atmosv0200

update to atmos v0.20, land v0.7, etc

.gitignore

@@ -32,6 +32,9 @@ docs/src/generated/
 !experiments/ClimaCore/**/Manifest.toml
 !perf/Manifest.toml
 
+# Output
+output/
+
 # Data
 *.vtk
 *.dat

Project.toml

@@ -24,22 +24,22 @@ TempestRemap_jll = "8573a8c5-1df0-515e-a024-abad257ee284"
 Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 
 [compat]
-CLIMAParameters = "0.4, 0.5, 0.6, 0.7"
-ClimaAtmos = "0.19.1"
+CLIMAParameters = "0.8.1"
+ClimaAtmos = "0.20"
 ClimaComms = "0.5.6"
 ClimaCore = "0.11.8"
 ClimaCoreTempestRemap = "0.3"
-ClimaLSM = "0.6"
+ClimaLSM = "0.7"
 Dates = "1"
 DocStringExtensions = "0.8, 0.9"
-Insolation = "0.8"
+Insolation = "0.9"
 JLD2 = "0.4"
-NCDatasets = "0.11, 0.12, 0.13"
+NCDatasets = "0.11, 0.12, 0.13, 0.14"
 Plots = "1.39.0"
 SciMLBase = "1, 2"
 StaticArrays = "1"
 Statistics = "1"
-SurfaceFluxes = "0.8"
+SurfaceFluxes = "0.9"
 TempestRemap_jll = "2"
 Thermodynamics = "0.11"
 julia = "1.8"

config/model_configs/coarse_single_ft64_hourly_checkpoints_co2.yml

@@ -12,7 +12,7 @@ mode_name: "amip"
 moist: "equil"
 mono_surface: false
 precip_model: "0M"
-rad: "allskywithclear"
+rad: "gray"
 run_name: "coarse_single_ft64_hourly_checkpoints_co2"
 t_end: "32days"
 vert_diff: "true"

config/model_configs/target_params_in_slab_test2.yml

@@ -14,7 +14,7 @@ mode_name: "slabplanet"
 moist: "equil"
 mono_surface: true
 precip_model: "0M"
-rad: "allskywithclear"
+rad: "gray"
 rayleigh_sponge: true
 run_name: "target_params_in_slab_test2"
 t_end: "10days"

experiments/AMIP/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.0"
 manifest_format = "2.0"
-project_hash = "e30e3cec173b96ef0f39af976fadb60750b6f220"
+project_hash = "583d53437ea883f44a3bef71d0af7d6b8d674ee0"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245"
@@ -123,9 +123,9 @@ version = "0.4.2"
 
 [[deps.BandedMatrices]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"]
-git-tree-sha1 = "3ac52471386dfcc0f6a3c8aeb37ed37c37701128"
+git-tree-sha1 = "931f3f49902e9b6b527fd7cd02d1cd7b4a84264c"
 uuid = "aae01518-5342-5314-be14-df237901396f"
-version = "1.4.1"
+version = "1.5.0"
 weakdeps = ["SparseArrays"]
 
     [deps.BandedMatrices.extensions]
@@ -176,6 +176,12 @@ git-tree-sha1 = "fc69cbdb4277042f72c6e59cbc7024fbe3034b89"
 uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 version = "0.16.39"
 
+[[deps.Blosc_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "19b98ee7e3db3b4eff74c5c9c72bf32144e24f10"
+uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
+version = "1.21.5+0"
+
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
@@ -195,9 +201,9 @@ version = "0.1.2"
 
 [[deps.CLIMAParameters]]
 deps = ["DocStringExtensions", "TOML", "Test"]
-git-tree-sha1 = "a085251dfe4b0f732fe2b65d5354e6af91a8e931"
+git-tree-sha1 = "ccfac72eed3ccf27ad086564059cab9d64567c7d"
 uuid = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
-version = "0.7.26"
+version = "0.8.5"
 
 [[deps.CPUSummary]]
 deps = ["CpuId", "IfElse", "PrecompileTools", "Static"]
@@ -270,9 +276,9 @@ weakdeps = ["SparseArrays"]
 
 [[deps.ClimaAtmos]]
 deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FastGaussQuadrature", "Insolation", "Interpolations", "IntervalSets", "Krylov", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "Thermodynamics", "YAML"]
-git-tree-sha1 = "03d3c492f00813e5a94de85a22ae2798c812c69d"
+git-tree-sha1 = "10e8fbe55c7a1aae4e28a535b1b4114ad1f2a176"
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
-version = "0.19.2"
+version = "0.20.0"
 
 [[deps.ClimaComms]]
 deps = ["CUDA", "MPI"]
@@ -309,10 +315,10 @@ uuid = "4ade58fe-a8da-486c-bd89-46df092ec0c7"
 version = "0.1.0"
 
 [[deps.ClimaLSM]]
-deps = ["ArtifactWrappers", "CFTime", "CSV", "ClimaComms", "ClimaCore", "ClimaCoreTempestRemap", "DataFrames", "Dates", "DocStringExtensions", "Flux", "HTTP", "IntervalSets", "JLD2", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "StatsBase", "SurfaceFluxes", "Thermodynamics", "cuDNN"]
-git-tree-sha1 = "856e804712907aa32a944ef5c3a028171920fd94"
+deps = ["Adapt", "ArtifactWrappers", "CFTime", "CSV", "CUDA", "ClimaComms", "ClimaCore", "ClimaCoreTempestRemap", "DataFrames", "Dates", "DocStringExtensions", "Flux", "HTTP", "IntervalSets", "JLD2", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "StatsBase", "SurfaceFluxes", "Thermodynamics", "cuDNN"]
+git-tree-sha1 = "63a82b4c5687899b69a362482e5990fd935bc0a5"
 uuid = "7884a58f-fab6-4fd0-82bb-ecfedb2d8430"
-version = "0.6.0"
+version = "0.7.0"
 
 [[deps.ClimaTimeSteppers]]
 deps = ["CUDA", "ClimaComms", "Colors", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "KernelAbstractions", "Krylov", "LinearAlgebra", "LinearOperators", "NVTX", "SciMLBase", "StaticArrays"]
@@ -328,9 +334,9 @@ version = "0.1.12"
 
 [[deps.CloudMicrophysics]]
 deps = ["CLIMAParameters", "DocStringExtensions", "ForwardDiff", "RootSolvers", "SpecialFunctions", "Thermodynamics"]
-git-tree-sha1 = "a6993c57af74e2e0f2191b556178cc8d8c0df9d6"
+git-tree-sha1 = "0c0be34fad945b95fd3c94cca9003bacae990ccf"
 uuid = "6a9e3e04-43cd-43ba-94b9-e8782df3c71b"
-version = "0.15.1"
+version = "0.15.2"
 
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
@@ -367,10 +373,10 @@ uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
 version = "0.12.10"
 
 [[deps.CommonDataModel]]
-deps = ["CFTime", "DataStructures", "Dates", "Preferences", "Printf"]
-git-tree-sha1 = "7f5717cbb2c1ce650cfd454451f282df33103596"
+deps = ["CFTime", "DataStructures", "Dates", "Preferences", "Printf", "Statistics"]
+git-tree-sha1 = "a132d267a055e8173a4a8e83d0d4ddcaeae70f91"
 uuid = "1fbeeb36-5f17-413c-809b-666fb144f157"
-version = "0.2.5"
+version = "0.3.4"
 
 [[deps.CommonSolve]]
 git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c"
@@ -556,10 +562,10 @@ uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
 version = "1.15.1"
 
 [[deps.DiskArrays]]
-deps = ["OffsetArrays"]
-git-tree-sha1 = "1bfa9de80f35ac63c6c381b2d43c590875896a1f"
+deps = ["LRUCache", "OffsetArrays"]
+git-tree-sha1 = "ef25c513cad08d7ebbed158c91768ae32f308336"
 uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
-version = "0.3.22"
+version = "0.3.23"
 
 [[deps.Distances]]
 deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
@@ -814,6 +820,11 @@ git-tree-sha1 = "ff38ba61beff76b8f4acad8ab0c97ef73bb670cb"
 uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89"
 version = "3.3.9+0"
 
+[[deps.GMP_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d"
+version = "6.2.1+6"
+
 [[deps.GPUArrays]]
 deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
 git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1"
@@ -872,6 +883,12 @@ git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
 uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
 version = "1.3.1"
 
+[[deps.GnuTLS_jll]]
+deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Nettle_jll", "P11Kit_jll", "Pkg", "Zlib_jll"]
+git-tree-sha1 = "266fe9b2335527cbf569ba4fd0979e3d8c6fd491"
+uuid = "0951126a-58fd-58f1-b5b3-b08c7c4a876d"
+version = "3.7.8+1"
+
 [[deps.Graphite2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011"
@@ -935,9 +952,13 @@ version = "1.4.0"
 
 [[deps.Insolation]]
 deps = ["Artifacts", "Dates", "DelimitedFiles", "Interpolations"]
-git-tree-sha1 = "2679907708edd9bbe2bd98585e575b48f17902c8"
+git-tree-sha1 = "2aaf998568ab59643cefb0fc17eba42f9d5bef37"
 uuid = "e98cc03f-d57e-4e3c-b70c-8d51efe9e0d8"
-version = "0.8.2"
+version = "0.9.0"
+weakdeps = ["CLIMAParameters"]
+
+    [deps.Insolation.extensions]
+    CreateParametersExt = "CLIMAParameters"
 
 [[deps.IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1093,6 +1114,15 @@ git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713"
 uuid = "1d63c593-3942-5779-bab2-d838dc0a180e"
 version = "15.0.7+0"
 
+[[deps.LRUCache]]
+git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59"
+uuid = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637"
+version = "1.6.1"
+weakdeps = ["Serialization"]
+
+    [deps.LRUCache.extensions]
+    SerializationExt = ["Serialization"]
+
 [[deps.LZO_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6"
@@ -1260,6 +1290,12 @@ git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075"
 uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 version = "1.0.3"
 
+[[deps.Lz4_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "6c26c5e8a4203d43b5497be3ec5d4e0c3cde240a"
+uuid = "5ced341a-0733-55b8-9ab6-a4889d929147"
+version = "1.9.4+0"
+
 [[deps.MKL_jll]]
 deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"]
 git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0"
@@ -1372,9 +1408,9 @@ version = "0.2.4"
 
 [[deps.NCDatasets]]
 deps = ["CFTime", "CommonDataModel", "DataStructures", "Dates", "DiskArrays", "NetCDF_jll", "NetworkOptions", "Printf"]
-git-tree-sha1 = "173a378f357e9bb24b22019efb5e4778223ce8cf"
+git-tree-sha1 = "79400cceb1655e7b2fe528a7b114c785bc152e59"
 uuid = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
-version = "0.13.2"
+version = "0.14.1"
 
 [[deps.NLSolversBase]]
 deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
@@ -1431,10 +1467,16 @@ uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391"
 version = "0.1.5"
 
 [[deps.NetCDF_jll]]
-deps = ["Artifacts", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "XML2_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "10c612c81eaffdd6b7c28a45a554cdd9d2f40ff1"
+deps = ["Artifacts", "Blosc_jll", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenMPI_jll", "XML2_jll", "Zlib_jll", "Zstd_jll", "libzip_jll"]
+git-tree-sha1 = "a8af1798e4eb9ff768ce7fdefc0e957097793f15"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.902.208+0"
+version = "400.902.209+0"
+
+[[deps.Nettle_jll]]
+deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "eca63e3847dad608cfa6a3329b95ef674c7160b4"
+uuid = "4c82536e-c426-54e4-b420-14f461c4ed8b"
+version = "3.7.2+0"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@@ -1518,6 +1560,12 @@ git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.6.3"
 
+[[deps.P11Kit_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "2cd396108e178f3ae8dedbd8e938a18726ab2fbf"
+uuid = "c2071276-7c44-58a7-b746-946036e04d0a"
+version = "0.24.1+0"
+
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15"
@@ -1571,9 +1619,9 @@ version = "1.4.0"
 
 [[deps.Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"]
-git-tree-sha1 = "38a748946dca52a622e79eea6ed35c6737499109"
+git-tree-sha1 = "c4fa93d7d66acad8f6f4ff439576da9d2e890ee0"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.40.0"
+version = "1.40.1"
 
     [deps.Plots.extensions]
     FileIOExt = "FileIO"
@@ -1669,10 +1717,14 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[deps.RRTMGP]]
-deps = ["Adapt", "CUDA", "ClimaComms", "DocStringExtensions", "GaussQuadrature", "Random", "StaticArrays"]
-git-tree-sha1 = "40ea97b2334725cef9b7f9e2fc2f76b35596807d"
+deps = ["Adapt", "Artifacts", "CUDA", "ClimaComms", "DocStringExtensions", "GaussQuadrature", "Random", "StaticArrays"]
+git-tree-sha1 = "3493869e9bbe529dfd8dada02b455847bdb46f27"
 uuid = "a01a1ee8-cea4-48fc-987c-fc7878d79da1"
-version = "0.10.0"
+version = "0.11.0"
+weakdeps = ["CLIMAParameters"]
+
+    [deps.RRTMGP.extensions]
+    CreateParametersExt = "CLIMAParameters"
 
 [[deps.Random]]
 deps = ["SHA"]
@@ -1782,9 +1834,9 @@ version = "0.1.0"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"]
-git-tree-sha1 = "535bb76be2c1090a09767b18b160f5729ad12aff"
+git-tree-sha1 = "75bae786dc8b07ec3c2159d578886691823bcb42"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.23.0"
+version = "2.23.1"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -1976,10 +2028,14 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
 version = "7.2.1+1"
 
 [[deps.SurfaceFluxes]]
-deps = ["CLIMAParameters", "DocStringExtensions", "RootSolvers", "Thermodynamics"]
-git-tree-sha1 = "a167924897731ee57ef0197bb19357bfc2d007bc"
+deps = ["DocStringExtensions", "RootSolvers", "Thermodynamics"]
+git-tree-sha1 = "6431256ee7c06ed2900fd46688f355e5a43e90eb"
 uuid = "49b00bb7-8bd4-4f2b-b78c-51cd0450215f"
-version = "0.8.1"
+version = "0.9.1"
+weakdeps = ["CLIMAParameters"]
+
+    [deps.SurfaceFluxes.extensions]
+    CreateParametersExt = "CLIMAParameters"
 
 [[deps.SymbolicIndexingInterface]]
 git-tree-sha1 = "b3103f4f50a3843e66297a2456921377c78f5e31"
@@ -2049,9 +2105,13 @@ version = "1.0.1"
 
 [[deps.Thermodynamics]]
 deps = ["DocStringExtensions", "KernelAbstractions", "Random", "RootSolvers"]
-git-tree-sha1 = "2de4b5ccc71baf3578959928c295a2fa13105db7"
+git-tree-sha1 = "d3b8b0346aa5f101135fbe3cd62acaeb2074a50a"
 uuid = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
-version = "0.11.2"
+version = "0.11.6"
+weakdeps = ["CLIMAParameters"]
+
+    [deps.Thermodynamics.extensions]
+    CreateParametersExt = "CLIMAParameters"
 
 [[deps.ThreadingUtilities]]
 deps = ["ManualMemory"]
@@ -2488,6 +2548,12 @@ git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c"
 uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
 version = "1.3.7+1"
 
+[[deps.libzip_jll]]
+deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "9a6ac803f3c17fe7cf66430a8bfc7186800f08a4"
+uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1"
+version = "1.9.2+0"
+
 [[deps.mtdev_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11"